Index
All Classes and Interfaces|All Packages|Constant Field Values|Serialized Form
A
- a - Variable in class loci.formats.in.VentanaReader.Overlap
- about() - Static method in class loci.plugins.About
- About - Class in loci.plugins
-
Displays a small information dialog about the Bio-Formats Plugins package.
- About() - Constructor for class loci.plugins.About
- abs() - Method in class loci.plugins.util.RecordedImageProcessor
- absoluteTime - Variable in class loci.formats.in.OperettaReader.Plane
- absoluteTime - Variable in class loci.formats.in.PrairieMetadata.Frame
-
absoluteTimeattribute of this<Frame>. - ABSORB_FILENAME - Enum constant in enum class loci.formats.in.SPEReader.SpeHeaderEntry
- ABSORB_LIVE - Enum constant in enum class loci.formats.in.SPEReader.SpeHeaderEntry
- ABSORB_MODE - Enum constant in enum class loci.formats.in.SPEReader.SpeHeaderEntry
- ABSORB_STRIP_NUM - Enum constant in enum class loci.formats.in.SPEReader.SpeHeaderEntry
- AbstractOMEXMLMetadata - Class in loci.formats.ome
- AbstractOMEXMLMetadata() - Constructor for class loci.formats.ome.AbstractOMEXMLMetadata
- ac - Variable in class loci.formats.in.FakeReader
-
Channel of last opened image plane.
- accept(File) - Method in class loci.formats.gui.ComboFileFilter
-
Accepts files with the proper filename prefix.
- accept(File) - Method in class loci.formats.gui.ExtensionFileFilter
-
Accepts files with the proper extensions.
- accept(File) - Method in class loci.formats.gui.FormatFileFilter
-
Accepts files in accordance with the file format reader.
- accept(File) - Method in class loci.formats.gui.NoExtensionFileFilter
-
Accepts files with no extension.
- accept(File) - Method in class loci.formats.NumberFilter
-
Tests if a specified file should be included in a file list.
- accept(String) - Method in class loci.formats.NumberFilter
-
Tests if a specified file should be included in a file list.
- ACCESSION_NUMBER - Enum constant in enum class loci.formats.dicom.DicomAttribute
- accumulate - Variable in class loci.formats.in.SDTInfo
- ACCUMULATION - Static variable in class loci.formats.in.CellSensReader
- ACCUMULATION_MODE - Static variable in class loci.formats.in.CellSensReader
- ACCUMULATIONS - Enum constant in enum class loci.formats.in.SPEReader.SpeHeaderEntry
- acqType - Variable in class loci.formats.in.OperettaReader.Channel
- acqType - Variable in class loci.formats.in.OperettaReader.Plane
- acquire - Variable in class loci.formats.in.ZeissLSMReader.SubBlock
- acquiredDate - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataTempBuffer
- acquiredDate - Variable in class loci.formats.in.LIFReader
- acquiredDate - Variable in class loci.formats.in.ZeissCZIReader
- acquiredDate - Variable in class loci.formats.in.ZeissLSMReader
- acquiredWells - Variable in class loci.formats.in.CV7000Reader
- ACQUISITION_CONTEXT_SEQUENCE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- ACQUISITION_CONTRAST - Enum constant in enum class loci.formats.dicom.DicomAttribute
- ACQUISITION_CYCLE_TIME - Static variable in class loci.formats.in.FluoviewReader
- ACQUISITION_DATE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- ACQUISITION_DEVICE_PROCESSING_CODE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- ACQUISITION_DEVICE_PROCESSING_DESCRIPTION - Enum constant in enum class loci.formats.dicom.DicomAttribute
- ACQUISITION_DURATION - Enum constant in enum class loci.formats.dicom.DicomAttribute
- ACQUISITION_FILE - Static variable in class loci.formats.in.ScanrReader
- ACQUISITION_MATRIX - Enum constant in enum class loci.formats.dicom.DicomAttribute
- ACQUISITION_NUMBER - Enum constant in enum class loci.formats.dicom.DicomAttribute
- ACQUISITION_PROPERTIES - Static variable in class loci.formats.in.CellSensReader
- ACQUISITION_START_CONDITION - Enum constant in enum class loci.formats.dicom.DicomAttribute
- ACQUISITION_START_CONDITION_DATA - Enum constant in enum class loci.formats.dicom.DicomAttribute
- ACQUISITION_TERMINATION_CONDITION - Enum constant in enum class loci.formats.dicom.DicomAttribute
- ACQUISITION_TERMINATION_CONDITION_DATA - Enum constant in enum class loci.formats.dicom.DicomAttribute
- ACQUISITION_TIME - Enum constant in enum class loci.formats.dicom.DicomAttribute
- ACQUISITION_TIME_SYNCHRONIZED - Enum constant in enum class loci.formats.dicom.DicomAttribute
- ACQUISITION_TIME_TAG - Static variable in class loci.formats.in.FlowSightReader
- ACQUISITION_TIMESTAMP - Enum constant in enum class loci.formats.dicom.DicomAttribute
- acquisitionDate - Variable in class loci.formats.in.BaseZeissReader
- acquisitionDate - Variable in class loci.formats.in.BioRadSCNReader
- acquisitionDate - Variable in class loci.formats.in.ColumbusReader
- acquisitionDate - Variable in class loci.formats.in.OIRReader
- acquisitionDate - Variable in class loci.formats.in.SISReader
- acquisitionDates - Variable in class loci.formats.in.FlexReader
- acquisitionMode - Variable in class loci.formats.in.ZeissCZIReader.Channel
- acquisitions - Variable in class loci.formats.in.ZeissCZIReader
- ACQUISITIONS_IN_SERIES - Enum constant in enum class loci.formats.dicom.DicomAttribute
- acquisitionTime - Variable in class loci.formats.in.CellSensReader.Pyramid
- act - Variable in class loci.formats.in.GIFReader
-
Active color table.
- actionIndex - Variable in class loci.formats.in.CV7000Reader.Channel
- actionIndex - Variable in class loci.formats.in.CV7000Reader.MeasurementSettingsHandler
- actionIndex - Variable in class loci.formats.in.CV7000Reader.Plane
- actionPerformed(ActionEvent) - Method in class loci.formats.gui.CacheComponent
-
Handles combo box changes.
- actionPerformed(ActionEvent) - Method in class loci.formats.gui.DataConverter
- actionPerformed(ActionEvent) - Method in class loci.formats.gui.ImageViewer
-
Handles menu commands.
- actionPerformed(ActionEvent) - Method in class loci.formats.tools.EditTiffG
- actionPerformed(ActionEvent) - Method in class loci.plugins.config.ConfigWindow
- actionPerformed(ActionEvent) - Method in class loci.plugins.in.SeriesDialog
- actionPerformed(ActionEvent) - Method in class loci.plugins.shortcut.ShortcutPanel
-
Handles button presses.
- actionPerformed(ActionEvent) - Method in class loci.plugins.util.DataBrowser
- actionPerformed(ActionEvent) - Method in class loci.plugins.util.SearchableWindow
- actionPerformed(ActionEvent) - Method in class loci.plugins.util.SearchableWindow.SearchBox
- active - Variable in class loci.formats.in.FV1000Reader.ChannelData
- active - Variable in class loci.formats.in.LeicaHandler.Detector
- active - Variable in class loci.formats.in.LeicaReader.Detector
- ACTIVE_CHANNEL - Static variable in class loci.formats.in.CellSensReader
- ACTIVE_LAYER_INDEX_VECTOR - Static variable in class loci.formats.in.CellSensReader
- ACTIVE_LAYER_VECTOR - Static variable in class loci.formats.in.CellSensReader
- ACTIVE_STACK_DIMENSION - Static variable in class loci.formats.in.CellSensReader
- activeChannel - Variable in class loci.formats.in.OperettaReader.OperettaHandler
- activeChannelIndices - Variable in class loci.formats.in.LeicaReader
- activeChannels - Variable in class loci.formats.in.PrairieMetadata
-
Set of active channel indices.
- activeDetector - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataTempBuffer
- activeDetector - Variable in class loci.formats.in.LIFReader
- activePlane - Variable in class loci.formats.in.OperettaReader.OperettaHandler
- ACTUAL_FRAME_DURATION - Enum constant in enum class loci.formats.dicom.DicomAttribute
- ACTUAL_TEMPERATURE - Static variable in class loci.formats.in.FluoviewReader
- ADC_BIT_ADJUST - Enum constant in enum class loci.formats.in.SPEReader.SpeHeaderEntry
- ADC_OFFSET - Enum constant in enum class loci.formats.in.SPEReader.SpeHeaderEntry
- ADC_RATE - Enum constant in enum class loci.formats.in.SPEReader.SpeHeaderEntry
- ADC_RESOLUTION - Enum constant in enum class loci.formats.in.SPEReader.SpeHeaderEntry
- ADC_TYPE - Enum constant in enum class loci.formats.in.SPEReader.SpeHeaderEntry
- adcDE - Variable in class loci.formats.in.SDTInfo
-
ADC sample delay (SPC-930).
- adcRE - Variable in class loci.formats.in.SDTInfo
- adcResShift - Variable in class loci.formats.in.SPCReader
- adcZoom - Variable in class loci.formats.in.SDTInfo
- add() - Method in class loci.formats.MetadataList
-
Add a empty primary array element.
- add(byte) - Method in class loci.formats.codec.ByteVector
- add(byte[]) - Method in class loci.formats.codec.ByteVector
- add(byte[], int, int) - Method in class loci.formats.codec.ByteVector
- add(double) - Method in class loci.plugins.util.RecordedImageProcessor
- add(int) - Method in class loci.formats.MetadataList
-
Add a empty primary array element.
- add(int) - Method in class loci.plugins.util.RecordedImageProcessor
- add(int, CoreMetadata) - Method in class loci.formats.CoreMetadataList
-
Add a secondary array element to the specified primary array
- add(int, T) - Method in class loci.formats.MetadataList
-
Add a secondary array element to the specified primary array
- add(List<T>) - Method in class loci.formats.MetadataList
-
Add a new primary element containing the specified values.
- add(T) - Method in class loci.formats.MetadataList
-
Add a new primary element containing a single specified value.
- addAnnotation(MetadataStore, SlideBook7Reader.CAnnotation70, int, int, int) - Method in class loci.formats.in.SlideBook7Reader
- addCacheListener(CacheListener) - Method in class loci.formats.cache.Cache
- addCacheListener(CacheListener) - Method in interface loci.formats.cache.CacheReporter
-
Adds a listener for status update events.
- addCacheListener(CacheListener) - Method in class loci.formats.cache.CacheStrategy
- addChannelDimension(int) - Method in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataTempBuffer
-
Adds channel dimension
- addCheckbox(GenericDialog, String) - Method in class loci.plugins.prefs.OptionsDialog
-
Adds a checkbox to the given dialog object corresponding to the boolean option identified by the specified key.
- addChoice(GenericDialog, String) - Method in class loci.plugins.prefs.OptionsDialog
-
Adds a choice to the given dialog object corresponding to the string option identified by the specified key.
- addClass(int, Class<? extends T>) - Method in class loci.formats.ClassList
-
Adds the given class, which must be assignable to the base class, to the list.
- addClass(Class<? extends T>) - Method in class loci.formats.ClassList
-
Adds the given class, which must be assignable to the base class, to the list.
- addDimension(int, Dimension) - Method in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataTempBuffer
-
Inserts dimension to buffer and optionally adapts other dimension-dependent values
- addDirectory(String, int) - Method in class loci.formats.in.L2DReader
-
Recursively add all of the files in the given directory to the used file list.
- addEntry(Comparable<Object>, DefaultListModel) - Static method in class loci.plugins.config.ConfigWindow
- addFile(String) - Method in class loci.formats.internal.WellContainer
- addFile(String, int, int) - Method in class loci.formats.in.JDCEReader.JDCEWell
-
Add file for the given field and plane indexes.
- addFileToList(String) - Method in class loci.formats.in.DCIMGReader
- addFileToList(String, boolean) - Method in class loci.formats.in.DicomReader
-
Determine if the given file belongs in the same dataset as this file.
- addGlobalMeta(String, boolean) - Method in class loci.formats.FormatReader
-
Adds an entry to the global metadata table.
- addGlobalMeta(String, byte) - Method in class loci.formats.FormatReader
-
Adds an entry to the global metadata table.
- addGlobalMeta(String, char) - Method in class loci.formats.FormatReader
-
Adds an entry to the global metadata table.
- addGlobalMeta(String, double) - Method in class loci.formats.FormatReader
-
Adds an entry to the global metadata table.
- addGlobalMeta(String, float) - Method in class loci.formats.FormatReader
-
Adds an entry to the global metadata table.
- addGlobalMeta(String, int) - Method in class loci.formats.FormatReader
-
Adds an entry to the global metadata table.
- addGlobalMeta(String, long) - Method in class loci.formats.FormatReader
-
Adds an entry to the global metadata table.
- addGlobalMeta(String, short) - Method in class loci.formats.FormatReader
-
Adds an entry to the global metadata table.
- addGlobalMeta(String, Object) - Method in class loci.formats.FormatReader
-
Adds an entry to the global metadata table.
- addGlobalMetaList(String, Object) - Method in class loci.formats.FormatReader
-
Add the given key/value pair to the global metadata hashtable.
- addInfo(DicomTag) - Method in class loci.formats.in.DicomReader
- ADDITIONAL_DRUG_SEQUENCE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- ADDITIONAL_PATIENT_HISTORY - Enum constant in enum class loci.formats.dicom.DicomAttribute
- addMeta(String, Object, Hashtable<String, Object>) - Method in class loci.formats.FormatReader
-
Adds an entry to the specified Hashtable.
- addMetadataList(double[], String) - Method in class loci.formats.in.ZeissXRMReader
-
Add each double value in an array to the original metadata table, using the given key.
- addMetadataList(double[], String, boolean) - Method in class loci.formats.in.ZeissXRMReader
-
Add each double value in an array to the original metadata table, using the given key.
- addMetadataOnly(OMEXMLMetadata, int) - Method in interface loci.formats.services.OMEXMLService
-
Insert a MetadataOnly element under the Image specified by 'index' in the given OME-XML metadata object.
- addMetadataOnly(OMEXMLMetadata, int) - Method in class loci.formats.services.OMEXMLServiceImpl
- addMetadataOnly(OMEXMLMetadata, int, boolean) - Method in interface loci.formats.services.OMEXMLService
-
Insert a MetadataOnly element under the Image specified by 'index' in the given OME-XML metadata object.
- addMetadataOnly(OMEXMLMetadata, int, boolean) - Method in class loci.formats.services.OMEXMLServiceImpl
- addMetaList(String, Object, Hashtable<String, Object>) - Method in class loci.formats.FormatReader
-
Add the given key/value pair to the given hashtable.
- addMissingDimensions(int) - Method in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataTempBuffer
-
Adds Z, T and S dimension if they haven't been added already
- addModuloAlong(OMEXMLMetadata, CoreMetadata, int) - Method in interface loci.formats.services.OMEXMLService
-
Adds ModuloAlong* annotations to the given OME-XML metadata object, using the given CoreMetadata object to determine modulo dimensions.
- addModuloAlong(OMEXMLMetadata, CoreMetadata, int) - Method in class loci.formats.services.OMEXMLServiceImpl
- addOption(String, String) - Method in class loci.formats.ClassList
-
Add a key/value pair to the list of options.
- addOriginalMetadata(String, DicomTag) - Method in class loci.formats.in.DicomReader
-
Store the given tag's value (if present) in the original metadata hashtable using the provided key.
- addPlaneMetadata(JDCEReader.PlaneMetadata, int[]) - Method in class loci.formats.in.JDCEReader.JDCEWell
- addPossible(String) - Method in class loci.plugins.prefs.StringOption
-
Adds a possible value to the list.
- addProp(HashMap<String, String>, String, String, HashMap<String, String>) - Method in class loci.plugins.config.ConfigWindow
- addPtyFiles() - Method in class loci.formats.in.FV1000Reader
- addScrollBars(Container) - Static method in class loci.plugins.util.WindowTools
-
Adds AWT scroll bars to the given container.
- addSeriesMeta(String, boolean) - Method in class loci.formats.FormatReader
-
Adds an entry to the metadata table for the current series.
- addSeriesMeta(String, byte) - Method in class loci.formats.FormatReader
-
Adds an entry to the metadata table for the current series.
- addSeriesMeta(String, char) - Method in class loci.formats.FormatReader
-
Adds an entry to the metadata table for the current series.
- addSeriesMeta(String, double) - Method in class loci.formats.FormatReader
-
Adds an entry to the metadata table for the current series.
- addSeriesMeta(String, float) - Method in class loci.formats.FormatReader
-
Adds an entry to the metadata table for the current series.
- addSeriesMeta(String, int) - Method in class loci.formats.FormatReader
-
Adds an entry to the metadata table for the current series.
- addSeriesMeta(String, long) - Method in class loci.formats.FormatReader
-
Adds an entry to the metadata table for the current series.
- addSeriesMeta(String, short) - Method in class loci.formats.FormatReader
-
Adds an entry to the metadata table for the current series.
- addSeriesMeta(String, Object) - Method in class loci.formats.FormatReader
-
Adds an entry to the metadata table for the current series.
- addSeriesMeta(String, Object) - Method in class loci.formats.in.LeicaMicrosystemsMetadata.LMSFileReader
- addSeriesMetaList(String, Object) - Method in class loci.formats.FormatReader
-
Add the given key/value pair to the current series metadata hashtable.
- addSeriesMetaList(String, Object) - Method in class loci.formats.in.LeicaMicrosystemsMetadata.LMSFileReader
- addStatusListener(StatusListener) - Method in class loci.plugins.in.ImagePlusReader
- addStatusListener(StatusListener) - Method in class loci.plugins.in.ImportProcess
- addSubResolutions() - Method in class loci.formats.in.OMETiffReader
- addToHashtable() - Method in class loci.formats.in.ZeissLSMReader.SubBlock
- addUsedFile(String, String) - Method in class loci.formats.in.PerkinElmerReader
-
Add the given file to the used files list.
- addUserCommentMeta(Element, int) - Method in class loci.formats.in.LeicaMicrosystemsMetadata.LMSMetadataExtractor
-
Extracts user comments and adds them to the reader's
CoreMetadata - addUserCommentMeta(Element, int) - Method in class loci.formats.in.LIFReader
- addValue(List, Object, int) - Method in class loci.formats.in.ImarisHDFReader
- addZOffset(int, Double) - Method in class loci.formats.in.DicomReader
- adjust - Variable in class loci.formats.in.SlidebookReader
- adjustEndianness - Variable in class loci.formats.in.GatanReader
- adjustForWhiteBalance(short, int) - Method in class loci.formats.in.DNGReader
- adjustForWhiteBalance(short, int) - Method in class loci.formats.in.NikonReader
- adjustmentValueChanged(AdjustmentEvent) - Method in class loci.plugins.util.DataBrowser
- adjustWellDimensions() - Method in class loci.formats.in.ScanrReader
- ADMITTING_DIAGNOSES_CODE_SEQUENCE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- ADMITTING_DIAGNOSES_DESCRIPTION - Enum constant in enum class loci.formats.dicom.DicomAttribute
- advanceBlock() - Method in class loci.formats.in.APNGReader.PNGInputStream
- AE - Enum constant in enum class loci.formats.dicom.DicomVR
- AFIHandler() - Constructor for class loci.formats.in.AFIReader.AFIHandler
- AFIReader - Class in loci.formats.in
-
AFIReader is the file format reader for Aperio AFI files.
- AFIReader() - Constructor for class loci.formats.in.AFIReader
-
Constructs a new AFI reader.
- AFIReader.AFIHandler - Class in loci.formats.in
- ag - Variable in class loci.formats.FileStitcher.ExternalSeries
- AIMReader - Class in loci.formats.in
-
AIMReader is the file format reader for .aim files.
- AIMReader() - Constructor for class loci.formats.in.AIMReader
-
Constructs a new AIM reader.
- airPressure - Variable in class loci.formats.in.ZeissCZIReader
- AISF - Static variable in class loci.formats.in.VolocityClippingReader
- AL3D_MAGIC_STRING - Static variable in class loci.formats.in.AliconaReader
- AliconaReader - Class in loci.formats.in
-
AliconaReader is the file format reader for Alicona AL3D files.
- AliconaReader() - Constructor for class loci.formats.in.AliconaReader
-
Constructs a new Alicona reader.
- ALIGNED_RECTANGLE - Enum constant in enum class loci.formats.in.BaseZeissReader.FeatureType
- ALIGNMENT - Static variable in class loci.formats.in.ZeissCZIReader
- ALL - Enum constant in enum class loci.formats.in.MetadataLevel
- ALL_DOMAINS - Static variable in class loci.formats.FormatTools
-
List of all supported domains.
- ALL_TYPES - Static variable in class loci.formats.gui.GUITools
-
String to use for "all types" combination filter.
- allBlockLengths - Variable in class loci.formats.in.SDTInfo
- allBlockOffsets - Variable in class loci.formats.in.SDTInfo
- allFiles - Variable in class loci.formats.in.BrukerReader
- allFiles - Variable in class loci.formats.in.CV7000Reader
- allFiles - Variable in class loci.formats.in.PerkinElmerReader
-
List of all files to open
- allFiles - Variable in class loci.formats.in.SPCReader
-
List of all files to open
- allFiles - Variable in class loci.formats.in.VectraReader
- allocatedSize - Variable in class loci.formats.in.ZeissCZIReader.Segment
- ALLOW_AUTOSTITCHING_DEFAULT - Static variable in class loci.formats.in.ZeissCZIReader
- ALLOW_AUTOSTITCHING_KEY - Static variable in class loci.formats.in.ZeissCZIReader
- allowAutostitching() - Method in class loci.formats.in.ZeissCZIReader
- allowCZIAutostitch() - Static method in class loci.plugins.util.LociPrefs
- allowOpen - Variable in class loci.formats.gui.FormatFileFilter
-
Whether it is ok to open a file to determine its type.
- allowOpen - Variable in class loci.formats.ImageReader
- allowShow - Variable in class loci.plugins.util.DataBrowser
- allPixelsFiles - Variable in class loci.formats.in.OlympusTileReader
- ALPHABET_LENGTH - Static variable in class loci.formats.ResourceNamer
- alphabeticIndexCount(String) - Static method in class loci.formats.ResourceNamer
- alphaShort - Variable in class loci.formats.gui.Index16ColorModel
-
Lookup tables.
- alreadyChecked() - Method in class loci.formats.UpgradeChecker
-
Return true if an upgrade check has already been performed in this JVM session.
- ALT_JPEG - Enum constant in enum class loci.formats.tiff.TiffCompression
- ALT_JPEG2000 - Enum constant in enum class loci.formats.tiff.TiffCompression
- altCodec - Variable in class loci.formats.in.QTReader
-
Some movies use two video codecs -- this is the second codec.
- ALTERNATE_REPRESENTATION_SEQUENCE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- alternateCenter - Variable in class loci.formats.in.LeicaHandler
- alternateCenter - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataTempBuffer
- alternateCenter - Variable in class loci.formats.in.LIFReader
- altPlanes - Variable in class loci.formats.in.QTReader
-
Number of frames that use the alternate codec.
- AmiraParameters - Class in loci.formats.tools
-
AmiraParameters handles parsing and writing of AmiraMesh headers.
- AmiraParameters(String) - Constructor for class loci.formats.tools.AmiraParameters
- AmiraParameters(RandomAccessInputStream) - Constructor for class loci.formats.tools.AmiraParameters
- AmiraReader - Class in loci.formats.in
-
This is a file format reader for AmiraMesh data.
- AmiraReader() - Constructor for class loci.formats.in.AmiraReader
- AmiraReader.ASCII - Class in loci.formats.in
-
This class provides a not-quite-efficient, but simple reader for planes stored in ASCII-encoded numbers.
- AmiraReader.HxRLE - Class in loci.formats.in
-
This is the reader for RLE-compressed AmiraMeshes.
- AmiraReader.HxZip - Class in loci.formats.in
-
This is the reader for GZip-compressed AmiraMeshes.
- AmiraReader.PlaneReader - Interface in loci.formats.in
-
This is the common interface for all formats, compressed or not.
- AMP_MODE - Enum constant in enum class loci.formats.in.SPEReader.SpeHeaderEntry
- amplificationGain - Variable in class loci.formats.in.ZeissLSMReader.DetectionChannel
- ANALOG_GAIN - Enum constant in enum class loci.formats.in.SPEReader.SpeHeaderEntry
- AnalysisFile() - Constructor for class loci.formats.in.MIASReader.AnalysisFile
- analysisFiles - Variable in class loci.formats.in.MIASReader
- AnalyzeReader - Class in loci.formats.in
-
AnalyzeReader is the file format reader for Analyze 7.5 files.
- AnalyzeReader() - Constructor for class loci.formats.in.AnalyzeReader
-
Constructs a new Analyze reader.
- ANATOMIC_REGION_MODIFIER_SEQUENCE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- ANATOMIC_REGION_SEQUENCE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- ANATOMIC_STRUCTURE_SEQUENCE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- and(int) - Method in class loci.plugins.util.RecordedImageProcessor
- ANDOR_MAGIC_STRING - Static variable in class loci.formats.in.FluoviewReader
- ANDOR_SHIFT_SPEED - Static variable in class loci.formats.in.CellSensReader
- ANGIO_FLAG - Enum constant in enum class loci.formats.dicom.DicomAttribute
- angle - Variable in class loci.formats.in.ZeissTIFFHandler.Scaling.Dimension
- ANGLE - Static variable in class loci.formats.in.ZeissLSMReader
- ANGLE3 - Enum constant in enum class loci.formats.in.BaseZeissReader.FeatureType
- ANGLE4 - Enum constant in enum class loci.formats.in.BaseZeissReader.FeatureType
- angles - Variable in class loci.formats.in.ZeissCZIReader
- ANGULAR_POSITION - Enum constant in enum class loci.formats.dicom.DicomAttribute
- ANGULAR_STEP - Enum constant in enum class loci.formats.dicom.DicomAttribute
- anim - Variable in class loci.formats.gui.ImageViewer
- anim - Variable in class loci.plugins.util.DataBrowser
- animate - Variable in class loci.plugins.util.DataBrowser
- ANIMATION - Enum constant in enum class loci.formats.codec.CompressionType
- ANIMATION_KEY - Static variable in class loci.formats.gui.ImageViewer
- ANN_BOOLEAN_VALUE - Static variable in class loci.formats.in.FakeReader
- ANN_COMMENT_VALUE - Static variable in class loci.formats.in.FakeReader
- ANN_DOUBLE_VALUE - Static variable in class loci.formats.in.FakeReader
- ANN_LONG_VALUE - Static variable in class loci.formats.in.FakeReader
- ANN_TAG_VALUE - Static variable in class loci.formats.in.FakeReader
- ANN_TERM_VALUE - Static variable in class loci.formats.in.FakeReader
- ANN_TIME_VALUE - Static variable in class loci.formats.in.FakeReader
- ANN_XML_VALUE_END - Static variable in class loci.formats.in.FakeReader
- ANN_XML_VALUE_START - Static variable in class loci.formats.in.FakeReader
- annBool - Variable in class loci.formats.in.FakeReader
- annComment - Variable in class loci.formats.in.FakeReader
- annDouble - Variable in class loci.formats.in.FakeReader
- annLong - Variable in class loci.formats.in.FakeReader
- annMap - Variable in class loci.formats.in.FakeReader
- ANNOTATION_NAMESPACE - Static variable in class loci.formats.in.FakeReader
- ANNOTATION_PREFIX - Static variable in class loci.formats.in.FakeReader
- ANNOTATION_SUFFIX - Static variable in class loci.formats.in.VectraReader
- annotationBoolCount - Variable in class loci.formats.in.FakeReader
- annotationCommentCount - Variable in class loci.formats.in.FakeReader
- annotationCount - Variable in class loci.formats.in.FakeReader
- annotationDoubleCount - Variable in class loci.formats.in.FakeReader
- annotationLongCount - Variable in class loci.formats.in.FakeReader
- annotationMapCount - Variable in class loci.formats.in.FakeReader
- annotationTagCount - Variable in class loci.formats.in.FakeReader
- annotationTermCount - Variable in class loci.formats.in.FakeReader
- annotationTimeCount - Variable in class loci.formats.in.FakeReader
- annotationXmlCount - Variable in class loci.formats.in.FakeReader
- annTag - Variable in class loci.formats.in.FakeReader
- annTerm - Variable in class loci.formats.in.FakeReader
- annTime - Variable in class loci.formats.in.FakeReader
- annXml - Variable in class loci.formats.in.FakeReader
- ANO_SUFFIX - Static variable in class loci.formats.in.PerkinElmerReader
- ANODE_TARGET_MATERIAL - Enum constant in enum class loci.formats.dicom.DicomAttribute
- ANSI - Enum constant in enum class loci.formats.in.BaseZeissReader.Charset
- APERIO_IMAGE_DESCRIPTION_PREFIX - Static variable in class loci.formats.in.SVSReader
-
TIFF image description prefix for Aperio SVS files.
- APERTURE_VALUE - Static variable in class loci.formats.tiff.IFD
- APLReader - Class in loci.formats.in
-
APLReader is the file format reader for Olympus APL files.
- APLReader() - Constructor for class loci.formats.in.APLReader
-
Constructs a new APL reader.
- APNGReader - Class in loci.formats.in
-
APNGReader is the file format reader for Animated Portable Network Graphics (APNG) images.
- APNGReader() - Constructor for class loci.formats.in.APNGReader
-
Constructs a new APNGReader.
- APNGReader.PNGBlock - Class in loci.formats.in
- APNGReader.PNGInputStream - Class in loci.formats.in
-
InputStream implementation that stitches together IDAT blocks into a seamless zlib stream.
- APNGWriter - Class in loci.formats.out
-
APNGWriter is the file format writer for PNG and APNG files.
- APNGWriter() - Constructor for class loci.formats.out.APNGWriter
- append(ILoggingEvent) - Method in class loci.plugins.util.IJStatusEchoer
- append(List<Class<? extends T>>) - Method in class loci.formats.ClassList
-
Appends a list of classes which must be assignable to the base class
- append(ClassList<T>) - Method in class loci.formats.ClassList
-
Appends a class list which must be assignable to the base class
- APPEND - Enum constant in enum class loci.formats.dicom.ResolutionStrategy
- appendHexValue(StringBuilder, String, int) - Method in class loci.formats.in.BaseZeissReader.Shape
- appendServerMap(String, String) - Static method in class loci.formats.in.FlexReader
-
Add the path 'realName' to the mapping for the server named 'alias'.
- appendValue(StringBuilder, String, Object) - Method in class loci.formats.in.BaseZeissReader.Shape
- APPLICABLE_FRAME_RANGE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- applyCalibration(ImagePlus) - Method in class loci.plugins.in.Calibrator
-
Applies spatial calibrations to an image stack.
- applyColors(List<ImagePlus>) - Method in class loci.plugins.in.Colorizer
- applyColors(List<ImagePlus>) - Method in class loci.plugins.in.ImagePlusReader
- applyDisplayRanges(ImagePlus, int) - Method in class loci.plugins.in.Colorizer
- applyMatrix() - Method in class loci.formats.in.OperettaReader.Plane
-
Applies the orientationMatrix to positionX, positionY, and positionZ.
- applyMethodStack(List<RecordedImageProcessor.MethodEntry>) - Method in class loci.plugins.util.RecordedImageProcessor
- applyTable(int[]) - Method in class loci.plugins.util.RecordedImageProcessor
- applyTransformation(byte[], int, int, int, int, int, int) - Method in class loci.formats.in.TissueFAXSReader
-
Extension point for doing something to an FOV immediately after decompression, before any stitching or cropping.
- ARABIC_CHARSET - Enum constant in enum class loci.formats.in.BaseZeissReader.Charset
- ARCHIVE - Static variable in class loci.formats.in.FlexReader
- AreaInfo() - Constructor for class loci.formats.in.CellVoyagerReader.AreaInfo
- AreaOfInterest() - Constructor for class loci.formats.in.VentanaReader.AreaOfInterest
- areas - Variable in class loci.formats.in.CellVoyagerReader.WellInfo
- areas - Variable in class loci.formats.in.VentanaReader
- ARFReader - Class in loci.formats.in
-
ARFReader is the file format reader for Axon Raw Format (ARF) files, produced by INDEC BioSystems's Imaging Workbench software.
- ARFReader() - Constructor for class loci.formats.in.ARFReader
-
Constructs a new ARF reader.
- arg - Variable in class loci.plugins.LociExporter
-
Argument passed to setup method.
- arg - Variable in class loci.plugins.Slicer
-
Plugin options.
- args - Static variable in class loci.plugins.shortcut.ShortcutPanel
-
Details for installed plugins.
- args - Variable in class loci.plugins.util.RecordedImageProcessor.MethodEntry
- ARRAY - Static variable in class loci.formats.in.GatanReader
-
Data types.
- ArrayListOfArrayLists(int, Class<T>) - Method in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataTempBuffer
- ArrayListOfHashMaps(int, Class<T>, Class<S>) - Method in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataTempBuffer
- arrayToString(Array) - Method in class loci.formats.services.NetCDFServiceImpl
- ARROW - Enum constant in enum class loci.formats.in.BaseZeissReader.PointStyle
- ARROW - Static variable in class loci.formats.in.FV1000Reader
- ARROW - Static variable in class loci.formats.in.LeicaHandler.ROI
- ARROW - Static variable in class loci.formats.in.LeicaMicrosystemsMetadata.ROI
- ARROW - Static variable in class loci.formats.in.LIFReader.ROI
- ARROWS - Enum constant in enum class loci.formats.in.BaseZeissReader.LineEndStyle
- ARTIST - Static variable in class loci.formats.tiff.IFD
- AS - Enum constant in enum class loci.formats.dicom.DicomVR
- ascii - Variable in class loci.formats.in.AmiraReader
- ascii - Variable in class loci.formats.tools.AmiraParameters
- ASCII - Enum constant in enum class loci.formats.tiff.IFDType
- ASCII(int, int) - Constructor for class loci.formats.in.AmiraReader.ASCII
- AsciiImage - Class in loci.formats.tools
-
A utility class for outputting a BufferedImage as ASCII text.
- AsciiImage(BufferedImage) - Constructor for class loci.formats.tools.AsciiImage
- asMap() - Method in class loci.formats.in.DeltavisionReader.DVExtHdrFields
- asRetrieve(MetadataStore) - Method in interface loci.formats.services.OMEXMLService
-
Gets the given
MetadataStoreobject as aMetadataRetrieve. - asRetrieve(MetadataStore) - Method in class loci.formats.services.OMEXMLServiceImpl
- assertId(String, boolean, int) - Static method in class loci.formats.FormatTools
-
Asserts that the current file is either null, or not, according to the given flag.
- assertStep(ImportStep) - Method in class loci.plugins.in.ImportProcess
- assignPlaneIndices() - Method in class loci.formats.in.ZeissCZIReader
- assignValues(double[]) - Method in class loci.formats.in.TextReader
-
Assigns values from the given row into the data array.
- associatedXmlDoc - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.LMSFileReader
- ASSOCIATION - Enum constant in enum class loci.formats.codec.JPEG2000BoxType
- asStore(MetadataRetrieve) - Method in interface loci.formats.services.OMEXMLService
-
Gets the given
MetadataRetrieveobject as aMetadataStore. - asStore(MetadataRetrieve) - Method in class loci.formats.services.OMEXMLServiceImpl
- ASTERISK - Enum constant in enum class loci.formats.in.BaseZeissReader.PointStyle
- ASTRONOMY_DOMAIN - Static variable in class loci.formats.FormatTools
-
Identifies the astronomy domain.
- ASYNCH - Enum constant in enum class loci.formats.in.SPEReader.SpeHeaderEntry
- AT - Enum constant in enum class loci.formats.dicom.DicomVR
- attachCompanionFiles() - Method in class loci.formats.in.DicomReader
-
DICOM datasets produced by: http://www.ct-imaging.de/index.php/en/ct-systeme-e/mikro-ct-e.html contain a bunch of extra metadata and log files.
- attachListeners(List<TextField>, List<Panel>) - Method in class loci.plugins.in.ColorDialog
- attachment - Variable in class loci.formats.in.ZeissCZIReader.Attachment
- attachment - Variable in class loci.formats.in.ZeissCZIReader.Metadata
- Attachment(String, long) - Constructor for class loci.formats.in.ZeissCZIReader.Attachment
- attachmentData - Variable in class loci.formats.in.ZeissCZIReader.Attachment
- AttachmentDirectory() - Constructor for class loci.formats.in.ZeissCZIReader.AttachmentDirectory
- attachmentDirectoryPosition - Variable in class loci.formats.in.ZeissCZIReader.FileHeader
- AttachmentEntry(RandomAccessInputStream) - Constructor for class loci.formats.in.ZeissCZIReader.AttachmentEntry
- attachmentSize - Variable in class loci.formats.in.ZeissCZIReader.SubBlock
- attenuation - Variable in class loci.formats.in.ZeissLSMReader.IlluminationChannel
- attr(Element, String) - Method in class loci.formats.in.PrairieMetadata
-
Gets the attribute value with the given name, or null if not defined.
- ATTR_NAME_STYLE_END - Static variable in class loci.formats.gui.XMLCellRenderer
- ATTR_NAME_STYLE_START - Static variable in class loci.formats.gui.XMLCellRenderer
- ATTR_VALUE_STYLE_END - Static variable in class loci.formats.gui.XMLCellRenderer
- ATTR_VALUE_STYLE_START - Static variable in class loci.formats.gui.XMLCellRenderer
- attribute - Variable in class loci.formats.dicom.DicomTag
- attributeList - Variable in class loci.formats.services.NetCDFServiceImpl
- AUTO_CLEAN - Enum constant in enum class loci.formats.in.SPEReader.SpeHeaderEntry
- AUTO_SPECTRO - Enum constant in enum class loci.formats.in.SPEReader.SpeHeaderEntry
- AUTOEXPOSURE - Static variable in class loci.formats.in.CellSensReader
- AUTORECON_PATH - Static variable in class loci.formats.in.ZeissXRMReader
- autoscale(byte[], int, int, int, boolean) - Static method in class loci.formats.ImageTools
-
Perform autoscaling on the given byte array; map min to 0 and max to 255.
- autoscale(BufferedImage) - Static method in class loci.formats.gui.AWTImageTools
-
Perform autoscaling on the given BufferedImage.
- autoscale(BufferedImage, int, int) - Static method in class loci.formats.gui.AWTImageTools
-
Perform autoscaling on the given BufferedImage; map min to 0 and max to 255.
- autoscaleBox - Variable in class loci.plugins.in.MainDialog
- autoThreshold() - Method in class loci.plugins.util.RecordedImageProcessor
- autoUpdate - Variable in class loci.formats.cache.Cache
-
Whether the cache should automatically update when a parameter changes.
- AV_GAIN - Enum constant in enum class loci.formats.in.SPEReader.SpeHeaderEntry
- AV_GAIN_USED - Enum constant in enum class loci.formats.in.SPEReader.SpeHeaderEntry
- available() - Method in class loci.formats.in.APNGReader.PNGInputStream
- availMem - Variable in class loci.plugins.in.MemoryDialog
-
Remaining memory for the JVM.
- AVERAGE - Static variable in class loci.formats.in.APNGReader
- AVERAGE_PULSE_WIDTH - Enum constant in enum class loci.formats.dicom.DicomAttribute
- AVERAGING - Static variable in class loci.formats.in.CellSensReader
- AVI_MAGIC_STRING - Static variable in class loci.formats.in.AVIReader
- AVIReader - Class in loci.formats.in
-
AVIReader is the file format reader for AVI files.
- AVIReader() - Constructor for class loci.formats.in.AVIReader
-
Constructs a new AVI reader.
- AVIWriter - Class in loci.formats.out
-
AVIWriter is the file format writer for AVI files.
- AVIWriter() - Constructor for class loci.formats.out.AVIWriter
- AWTImageTools - Class in loci.formats.gui
-
A utility class with convenience methods for manipulating images in
BufferedImageform. - AWTImageTools() - Constructor for class loci.formats.gui.AWTImageTools
- axis - Variable in class loci.formats.gui.CacheIndicator
- AxisGuesser - Class in loci.formats
-
AxisGuesser guesses which blocks in a file pattern correspond to which dimensional axes (Z, T, C or S), potentially recommending an adjustment in dimension order within the files, depending on the confidence of each guess.
- AxisGuesser(FilePattern, String, int, int, int, boolean) - Constructor for class loci.formats.AxisGuesser
-
Guesses dimensional axis assignments corresponding to the given file pattern, using the specified dimensional information from within each file as a guide.
- axisTypes - Variable in class loci.formats.AxisGuesser
-
Guessed axis types.
B
- b - Variable in class loci.formats.in.VentanaReader.Overlap
- b(String) - Method in class loci.formats.in.PrairieMetadata
-
Converts the given string to a
boolean. - BACKGROUND_FILE - Enum constant in enum class loci.formats.in.SPEReader.SpeHeaderEntry
- BACKGROUND_TABLE - Static variable in class loci.formats.in.LiFlimReader
- backgroundC - Variable in class loci.formats.in.LiFlimReader
- backgroundColor - Variable in class loci.formats.in.CellSensReader
- backgroundDatatype - Variable in class loci.formats.in.LiFlimReader
- backgroundF - Variable in class loci.formats.in.LiFlimReader
- backgroundP - Variable in class loci.formats.in.LiFlimReader
- backgroundT - Variable in class loci.formats.in.LiFlimReader
- backgroundX - Variable in class loci.formats.in.LiFlimReader
- backgroundY - Variable in class loci.formats.in.LiFlimReader
- backgroundZ - Variable in class loci.formats.in.LiFlimReader
- backupHandler - Variable in class loci.formats.in.ND2Reader
- BACKWARD_ORDER - Static variable in interface loci.formats.cache.ICacheStrategy
- backwardsStageX - Variable in class loci.formats.in.DeltavisionReader
-
Whether or not the stage moved backwards.
- backwardsStageY - Variable in class loci.formats.in.DeltavisionReader
- BALTIC_CHARSET - Enum constant in enum class loci.formats.in.BaseZeissReader.Charset
- bandUsed - Variable in class loci.formats.in.NDPISReader
- bankData - Variable in class loci.formats.gui.SignedByteBuffer
- bankData - Variable in class loci.formats.gui.UnsignedIntBuffer
- BAR - Enum constant in enum class loci.formats.in.BaseZeissReader.PointStyle
- barcode - Variable in class loci.formats.in.LeicaSCNReader.ImageCollection
- BARCODE_VALUE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- barrierFilter - Variable in class loci.formats.in.FV1000Reader.ChannelData
- base - Variable in class loci.formats.ClassList
-
Base class to which all classes are assignable.
- BASE_OFFSET - Static variable in class loci.formats.in.BioRadGelReader
- Base64Codec - Class in loci.formats.codec
-
Implements encoding (compress) and decoding (decompress) methods for Base64.
- Base64Codec() - Constructor for class loci.formats.codec.Base64Codec
- BaseCodec - Class in loci.formats.codec
-
BaseCodec contains default implementation and testing for classes implementing the Codec interface, and acts as a base class for any of the compression classes.
- BaseCodec() - Constructor for class loci.formats.codec.BaseCodec
- basedir - Variable in class loci.formats.in.ZeissTIFFReader.TIFFInfo
- BASELINE_CLAMP - Static variable in class loci.formats.in.FluoviewReader
- BASELINE_OFFSET - Static variable in class loci.formats.in.FluoviewReader
- BASELINE_OFFSET_CLAMP - Static variable in class loci.formats.in.CellSensReader
- BaseMetadata - Interface in loci.formats.meta
- basename - Variable in class loci.formats.in.ZeissTIFFHandler.Plane
- baseName - Variable in class loci.formats.in.OIRReader
- baseReader - Variable in class loci.plugins.in.ImportProcess
- baseTiff - Variable in class loci.formats.in.MicromanagerReader.Position
- BaseTiffReader - Class in loci.formats.in
-
BaseTiffReader is the superclass for file format readers compatible with or derived from the TIFF 6.0 file format.
- BaseTiffReader(String, String) - Constructor for class loci.formats.in.BaseTiffReader
-
Constructs a new BaseTiffReader.
- BaseTiffReader(String, String[]) - Constructor for class loci.formats.in.BaseTiffReader
-
Constructs a new BaseTiffReader.
- baseTileHeight - Variable in class loci.formats.out.DicomWriter
- baseTileWidth - Variable in class loci.formats.out.DicomWriter
- baseX - Variable in class loci.formats.in.VentanaReader.TIFFTile
- baseY - Variable in class loci.formats.in.VentanaReader.TIFFTile
- BaseZeissReader - Class in loci.formats.in
-
BaseZeissReader contains common functionality required by readers for Zeiss AxioVision formats.
- BaseZeissReader(String, String) - Constructor for class loci.formats.in.BaseZeissReader
-
Constructs a new ZeissZVI reader.
- BaseZeissReader(String, String[]) - Constructor for class loci.formats.in.BaseZeissReader
-
Constructs a new ZeissZVI reader.
- BaseZeissReader.Charset - Enum Class in loci.formats.in
- BaseZeissReader.Context - Enum Class in loci.formats.in
- BaseZeissReader.DrawStyle - Enum Class in loci.formats.in
-
Line drawing styles.
- BaseZeissReader.FeatureType - Enum Class in loci.formats.in
-
Feature types.
- BaseZeissReader.FillStyle - Enum Class in loci.formats.in
-
Fill styles.
- BaseZeissReader.Layer - Class in loci.formats.in
-
Layer class representing an AxioVision layer; used to contain a collection of shapes.
- BaseZeissReader.LineEndPositions - Enum Class in loci.formats.in
- BaseZeissReader.LineEndStyle - Enum Class in loci.formats.in
-
Line ending styles.
- BaseZeissReader.PointStyle - Enum Class in loci.formats.in
-
Point styles.
- BaseZeissReader.Shape - Class in loci.formats.in
-
Shape class representing the metadata within an AxioVision Shape ROI
- BaseZeissReader.Tag - Class in loci.formats.in
-
Content of a single tag from a Tags block.
- BaseZeissReader.TextAlignment - Enum Class in loci.formats.in
- bayerPattern - Variable in class loci.formats.in.MRWReader
- bbox - Variable in class loci.formats.in.BDVReader
- BBOX - Static variable in class loci.formats.in.BDVReader.H5Constants
- BBOX - Static variable in class loci.formats.in.CellH5Reader.CellH5Constants
- BCKGRND_SUB - Enum constant in enum class loci.formats.in.SPEReader.SpeHeaderEntry
- BDReader - Class in loci.formats.in
-
BDReader is the file format reader for BD Pathway datasets.
- BDReader() - Constructor for class loci.formats.in.BDReader
-
Constructs a new ScanR reader.
- BDV_MAGIC_STRING - Static variable in class loci.formats.in.BDVReader
- BDVReader - Class in loci.formats.in
-
Reader for BDV files.
- BDVReader() - Constructor for class loci.formats.in.BDVReader
-
Constructs a new BDV reader.
- BDVReader.BDVXMLHandler - Class in loci.formats.in
- BDVReader.H5Constants - Class in loci.formats.in
- BDVReader.H5Coordinate - Class in loci.formats.in
- bdvxml - Variable in class loci.formats.in.BDVReader
- BDVXMLHandler() - Constructor for class loci.formats.in.BDVReader.BDVXMLHandler
- BEAM_SPLITTER_FILTER - Static variable in class loci.formats.in.ZeissLSMReader
- BEAM_SPLITTER_FILTER_SET - Static variable in class loci.formats.in.ZeissLSMReader
- BeamSplitter() - Constructor for class loci.formats.in.ZeissLSMReader.BeamSplitter
- BEAT_REJECTION_FLAG - Enum constant in enum class loci.formats.dicom.DicomAttribute
- begin - Variable in class loci.formats.FilePatternBlock
- BEZIER_WITH_ARROW - Static variable in class loci.formats.in.ZeissLSMReader
- BF - Class in loci.plugins
-
Miscellaneous plugins utility methods.
- BF() - Constructor for class loci.plugins.BF
- BFVirtualStack - Class in loci.plugins.util
-
Subclass of VirtualStack that uses Bio-Formats to read planes on demand.
- BFVirtualStack(String, IFormatReader, boolean, boolean, boolean) - Constructor for class loci.plugins.util.BFVirtualStack
- bgr - Variable in class loci.formats.in.CellSensReader
- BGR - Static variable in class loci.formats.in.CellSensReader
- BGR_24 - Static variable in class loci.formats.in.ZeissCZIReader
- BGR_24 - Static variable in class loci.formats.services.JPEGXRServiceImpl
- BGR_32 - Static variable in class loci.formats.services.JPEGXRServiceImpl
- BGR_48 - Static variable in class loci.formats.in.ZeissCZIReader
- BGR_FLOAT - Static variable in class loci.formats.in.ZeissCZIReader
- BGRA_32 - Static variable in class loci.formats.services.JPEGXRServiceImpl
- BGRA_8 - Static variable in class loci.formats.in.ZeissCZIReader
- bgrToRgb(byte[], boolean, int, int) - Static method in class loci.formats.ImageTools
- BH_HEADER_CHKSUM - Static variable in class loci.formats.in.SDTInfo
- BH_HEADER_NOT_VALID - Static variable in class loci.formats.in.SDTInfo
- BH_HEADER_VALID - Static variable in class loci.formats.in.SDTInfo
- BIFormatReader - Class in loci.formats.in
-
BIFormatReader is the superclass for file format readers that use java.awt.image.BufferedImage as the native data type.
- BIFormatReader(String, String) - Constructor for class loci.formats.in.BIFormatReader
-
Constructs a new BIFormatReader.
- BIFormatReader(String, String[]) - Constructor for class loci.formats.in.BIFormatReader
-
Constructs a new BIFormatReader.
- BIG - Static variable in class loci.formats.tiff.TiffConstants
- BIG_TIFF - Static variable in class loci.formats.tiff.IFD
- BIG_TIFF_BYTES_PER_ENTRY - Static variable in class loci.formats.tiff.TiffConstants
-
The number of bytes in each IFD entry of a BigTIFF file.
- BIG_TIFF_CUTOFF - Static variable in class loci.formats.tiff.TiffConstants
-
Number of bytes at which to automatically switch to BigTIFF This is approximately 3.9 GB instead of 4 GB, to allow space for the IFDs.
- BIG_TIFF_MAGIC_NUMBER - Static variable in class loci.formats.tiff.TiffConstants
- BIG_TIFF_SUFFIXES - Static variable in class loci.formats.out.TiffWriter
- bigEndianTransferSyntax - Variable in class loci.formats.dicom.DicomTag
- bigTiff - Variable in class loci.formats.out.DicomWriter
- bigTiff - Variable in class loci.formats.tiff.TiffParser
-
Whether or not the TIFF file contains BigTIFF data.
- bigTiff - Variable in class loci.formats.tiff.TiffSaver
-
Whether or not to write BigTIFF data.
- bin - Variable in class loci.formats.in.InCellReader
- binary - Variable in class loci.formats.in.EPSReader
-
Flag indicating binary data.
- BINARY_SETUP - Static variable in class loci.formats.in.SDTInfo
- binData - Variable in class loci.formats.in.OMEXMLReader
- BinData(int, int) - Constructor for class loci.formats.in.OMEXMLReader.BinData
- binDataOffsets - Variable in class loci.formats.in.OMEXMLReader
- binning - Variable in class loci.formats.in.BDReader
- binning - Variable in class loci.formats.in.BioRadSCNReader
- binning - Variable in class loci.formats.in.CV7000Reader.Channel
- binning - Variable in class loci.formats.in.MetamorphHandler
- binning - Variable in class loci.formats.in.MetamorphReader
- binning - Variable in class loci.formats.in.MicromanagerReader.Position
- binning - Variable in class loci.formats.in.ND2Handler
- binning - Variable in class loci.formats.in.PCIReader
- binning - Variable in class loci.formats.in.SimplePCITiffReader
- binning - Variable in class loci.formats.in.ZeissLSMReader
- binning - Variable in class loci.formats.in.ZeissLSMReader.Recording
- binnings - Variable in class loci.formats.in.FlexReader
- binnings - Variable in class loci.formats.in.ZeissCZIReader
- binningX - Variable in class loci.formats.in.CellSensReader.Pyramid
- binningY - Variable in class loci.formats.in.CellSensReader.Pyramid
- binSize - Variable in class loci.formats.in.SPCReader
- binX - Variable in class loci.formats.in.FlexReader
-
Camera binning values.
- binX - Variable in class loci.formats.in.IvisionReader
- binY - Variable in class loci.formats.in.FlexReader
-
Camera binning values.
- binY - Variable in class loci.formats.in.IvisionReader
- BIO_FORMATS - Enum constant in enum class loci.plugins.util.LibraryChecker.Library
- BioFormatsExtensionPrinter - Class in loci.formats.tools
-
This class is used to generate a text file containing all of the image file extensions supported by Bio-Formats.
- BioFormatsExtensionPrinter() - Constructor for class loci.formats.tools.BioFormatsExtensionPrinter
- BioRadGelReader - Class in loci.formats.in
-
BioRadGelReader is the file format reader for Bio-Rad gel files.
- BioRadGelReader() - Constructor for class loci.formats.in.BioRadGelReader
-
Constructs a new Bio-Rad gel reader.
- BioRadHandler() - Constructor for class loci.formats.in.BioRadReader.BioRadHandler
- BioRadReader - Class in loci.formats.in
-
BioRadReader is the file format reader for Bio-Rad PIC files.
- BioRadReader() - Constructor for class loci.formats.in.BioRadReader
-
Constructs a new BioRadReader.
- BioRadReader.BioRadHandler - Class in loci.formats.in
-
SAX handler for parsing XML.
- BioRadReader.Note - Class in loci.formats.in
- BioRadSCNReader - Class in loci.formats.in
-
BioRadSCNReader is the reader for Bio-Rad .scn files
- BioRadSCNReader() - Constructor for class loci.formats.in.BioRadSCNReader
-
Constructs a new Bio-Rad .scn reader.
- BioRadSCNReader.SCNHandler - Class in loci.formats.in
- BIPLANE_ACQUISITION_SEQUENCE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- biReader - Variable in class loci.formats.gui.DataConverter
- BIT - Static variable in class loci.formats.FormatTools
-
Identifies the BIT data type used to store pixel values.
- BIT_DEPTH - Static variable in class loci.formats.in.CellSensReader
- BitBuffer - Class in loci.formats.codec
-
Deprecated.Use loci.common.RandomAccessInputStream instead
- BitBuffer(byte[]) - Constructor for class loci.formats.codec.BitBuffer
-
Deprecated.Default constructor.
- bitDepth - Variable in class loci.formats.in.CellSensReader.Pyramid
- bitInc - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.Channel
- BITMASK_COMPRESSION - Static variable in class loci.formats.in.FlowSightReader
- bits - Variable in class loci.formats.in.BrukerReader
- bits - Variable in class loci.formats.in.TargaReader
- BITS_ALLOCATED - Enum constant in enum class loci.formats.dicom.DicomAttribute
- BITS_PER_COMPONENT - Enum constant in enum class loci.formats.codec.JPEG2000BoxType
- BITS_PER_SAMPLE - Static variable in class loci.formats.tiff.IFD
- BITS_STORED - Enum constant in enum class loci.formats.dicom.DicomAttribute
- bitsPerPixel - Variable in class loci.formats.CoreMetadata
-
Number of valid bits per pixel.
- bitsPerPixel - Variable in class loci.formats.in.QTReader
-
Pixel depth.
- bitsPerSample - Variable in class loci.formats.codec.CodecOptions
-
Number of bits per channel.
- BitWriter - Class in loci.formats.codec
-
Deprecated.Use loci.common.RandomAccessOutputStream instead
- BitWriter() - Constructor for class loci.formats.codec.BitWriter
-
Deprecated.Constructs a new bit writer.
- BitWriter(int) - Constructor for class loci.formats.codec.BitWriter
-
Deprecated.Constructs a new bit writer with the given initial buffer size.
- biWriter - Variable in class loci.formats.gui.DataConverter
- bizarreMultichannelAcquisition - Variable in class loci.formats.in.MetamorphReader
- BLACK_IS_ZERO - Enum constant in enum class loci.formats.tiff.PhotoInterp
- blank(byte[]) - Method in class loci.formats.in.PrairieReader
-
Blanks out and returns the given buffer.
- blankImage(int, int, int, int) - Static method in class loci.formats.gui.AWTImageTools
-
Creates a blank image with the given dimensions and transfer type.
- blankThumbBytes - Variable in class loci.formats.FileStitcher.ExternalSeries
- BLEMISH_APPLIED - Enum constant in enum class loci.formats.in.SPEReader.SpeHeaderEntry
- BLEMISH_FILE - Enum constant in enum class loci.formats.in.SPEReader.SpeHeaderEntry
- block - Variable in class loci.formats.FilePatternBlock
-
String representation of this block.
- BLOCK_END - Static variable in class loci.formats.FilePatternBlock
-
Identifies the end of a block.
- BLOCK_START - Static variable in class loci.formats.FilePatternBlock
-
Identifies the start of a block.
- blockData - Variable in class loci.formats.in.ZeissLSMReader.SubBlock
- blockLength - Variable in class loci.formats.in.APNGReader.PNGInputStream
- blockLength - Variable in class loci.formats.in.PQBinReader
-
No of timeBins pre-loaded as a block
- blockLength - Variable in class loci.formats.in.SDTInfo
-
reserved2 now contains block (set) length.
- blockLength - Variable in class loci.formats.in.SDTReader
-
No of timeBins pre-loaded as a block
- blockNo - Variable in class loci.formats.in.SDTInfo
-
Number of the block in the file.
- blockOffsets - Variable in class loci.formats.in.KLBReader
- blockPointer - Variable in class loci.formats.in.APNGReader.PNGInputStream
- blocks - Variable in class loci.formats.FilePattern
-
List of pattern blocks for this file pattern.
- blocks - Variable in class loci.formats.in.APNGReader
- blockSize - Variable in class loci.formats.in.GIFReader
-
Block size.
- blockSize - Variable in class loci.formats.in.VolocityReader.Stack
- blockSizeZPerResolution - Variable in class loci.formats.in.ImarisHDFReader
- blocksPerPlane - Variable in class loci.formats.in.KLBReader
- blocksPerPlane - Variable in class loci.formats.in.OIRReader
- blockType - Variable in class loci.formats.in.APNGReader.PNGInputStream
- blockType - Variable in class loci.formats.in.SDTInfo
-
See blockType defines below.
- BLUE - Enum constant in enum class loci.formats.in.LeicaMicrosystemsMetadata.Channel.ChannelType
- BLUE_GAIN - Static variable in class loci.formats.in.CellSensReader
- BLUE_LUT_DATA - Enum constant in enum class loci.formats.dicom.DicomAttribute
- BLUE_LUT_DESCRIPTOR - Enum constant in enum class loci.formats.dicom.DicomAttribute
- BLUE_MIN - Static variable in class loci.plugins.in.Colorizer
- BLUE_MULTIPLIER - Static variable in class loci.formats.in.NDPIReader
- BLUE_OFFSET - Static variable in class loci.formats.in.CellSensReader
- BLUE_TO_GREEN_MIN - Static variable in class loci.plugins.in.Colorizer
- blueGain - Variable in class loci.formats.in.CellSensReader.Pyramid
- blueOffset - Variable in class loci.formats.in.CellSensReader.Pyramid
- blueOffset - Static variable in class org.libjpegturbo.turbojpeg.TJ
- blueShort - Variable in class loci.formats.gui.Index16ColorModel
-
Lookup tables.
- BMP - Enum constant in enum class loci.formats.in.LeicaMicrosystemsMetadata.LMSFileReader.ImageFormat
- BMP - Static variable in class loci.formats.in.CellSensReader
- BMP_MAGIC_STRING - Static variable in class loci.formats.in.BMPReader
- bmpBitsPerPixel - Variable in class loci.formats.in.AVIReader
- bmpColorsUsed - Variable in class loci.formats.in.AVIReader
- bmpCompression - Variable in class loci.formats.in.AVIReader
- BMPReader - Class in loci.formats.in
-
BMPReader is the file format reader for Microsoft Bitmap (BMP) files.
- BMPReader() - Constructor for class loci.formats.in.BMPReader
-
Constructs a new BMP reader.
- bmpScanLineSize - Variable in class loci.formats.in.AVIReader
- bmpWidth - Variable in class loci.formats.in.AVIReader
- BODY_PART_EXAMINED - Enum constant in enum class loci.formats.dicom.DicomAttribute
- BODY_PART_THICKNESS - Enum constant in enum class loci.formats.dicom.DicomAttribute
- bold - Variable in class loci.formats.in.BaseZeissReader.Shape
- BONE_THERMAL_INDEX - Enum constant in enum class loci.formats.dicom.DicomAttribute
- BOOLEAN - Static variable in class loci.formats.in.CellSensReader
- BooleanIM3Record(String, int, long, int) - Constructor for class loci.formats.in.IM3Reader.BooleanIM3Record
- BooleanOption - Class in loci.plugins.prefs
-
A boolean option for one of the plugins.
- BooleanOption(String, boolean, String, String, boolean) - Constructor for class loci.plugins.prefs.BooleanOption
-
Constructs a boolean option with the given parameters.
- BooleanOption(HashMap<String, String>) - Constructor for class loci.plugins.prefs.BooleanOption
-
Constructs a boolean option with the parameters from the given map.
- BORDER - Static variable in class loci.plugins.shortcut.ShortcutPanel
-
Number of pixels for window border.
- BORDER_DENSITY - Enum constant in enum class loci.formats.dicom.DicomAttribute
- bordL - Variable in class loci.formats.in.SDTInfo
- bordU - Variable in class loci.formats.in.SDTInfo
- BOTH - Enum constant in enum class loci.formats.in.BaseZeissReader.LineEndPositions
- boundingBox - Variable in class loci.formats.in.VentanaReader.AreaOfInterest
- boundValues - Variable in class loci.formats.services.MDBServiceImpl
- BOX_SIZE - Static variable in class loci.formats.in.FakeReader
- boxes - Variable in class loci.plugins.in.SeriesDialog
- bpp - Variable in class loci.formats.in.BaseZeissReader
-
Number of bytes per pixel.
- bpp - Variable in class loci.formats.in.BMPReader
-
Number of bits per pixel.
- bpp - Variable in class loci.formats.in.MIASReader
- bpp - Variable in class loci.formats.in.SPCReader
- bpp - Variable in class loci.formats.out.CellH5Writer
- BRANCH_OF_SERVICE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- BRIGHTNESS - Static variable in class loci.formats.in.CellSensReader
- BRIGHTNESS_VALUE - Static variable in class loci.formats.tiff.IFD
- brokenNotes - Variable in class loci.formats.in.BioRadReader
- BrowserOptionsWindow - Class in loci.plugins.util
-
Extension of JFrame that allows the user to adjust caching settings.
- BrowserOptionsWindow(String, Cache, String[]) - Constructor for class loci.plugins.util.BrowserOptionsWindow
- BrukerReader - Class in loci.formats.in
-
BrukerReader is the file format reader for Bruker MRI files.
- BrukerReader() - Constructor for class loci.formats.in.BrukerReader
-
Constructs a new Bruker reader.
- btsType - Variable in class loci.formats.in.CV7000Reader.MeasurementDataHandler
- buffer - Variable in class loci.formats.codec.BitBuffer
-
Deprecated.
- buffer - Variable in class loci.formats.in.ImarisHDFReader
- BUFFER_SIZE - Static variable in class loci.formats.in.ND2Reader
- BUFFER_SIZE - Static variable in class loci.formats.in.OIRReader
- BUFFER_SIZE - Static variable in class loci.formats.in.ZeissCZIReader
- BufferedImageReader - Class in loci.formats.gui
-
A reader wrapper for reading image planes as BufferedImage objects.
- BufferedImageReader() - Constructor for class loci.formats.gui.BufferedImageReader
-
Constructs a BufferedImageReader around a new image reader.
- BufferedImageReader(IFormatReader) - Constructor for class loci.formats.gui.BufferedImageReader
-
Constructs a BufferedImageReader with the given reader.
- BufferedImageSource - Class in loci.formats.gui
-
Retrieves BufferedImages from a data source using Bio-Formats.
- BufferedImageSource(IFormatReader) - Constructor for class loci.formats.gui.BufferedImageSource
- BufferedImageWriter - Class in loci.formats.gui
-
A writer wrapper for writing image planes from BufferedImage objects.
- BufferedImageWriter() - Constructor for class loci.formats.gui.BufferedImageWriter
-
Constructs a BufferedImageWriter around a new image writer.
- BufferedImageWriter(IFormatWriter) - Constructor for class loci.formats.gui.BufferedImageWriter
-
Constructs a BufferedImageWriter with the given writer.
- bufLength - Variable in class loci.formats.in.SPCReader
- bufSize(int, int, int) - Static method in class org.libjpegturbo.turbojpeg.TJ
-
Returns the maximum size of the buffer (in bytes) required to hold a JPEG image with the given width and height, and level of chrominance subsampling.
- bufSizeYUV(int, int, int) - Static method in class org.libjpegturbo.turbojpeg.TJ
-
Returns the size of the buffer (in bytes) required to hold a YUV planar image with the given width, height, and level of chrominance subsampling.
- BUILDER - Static variable in class loci.formats.meta.OriginalMetadataAnnotation
- buildExtensions() - Method in class loci.plugins.macro.MacroFunctions
-
Builds the list of extensions, using reflection, from public methods of this class.
- buildFileChooser(FileFilter[]) - Static method in class loci.formats.gui.GUITools
-
Builds a file chooser with the given file filters, as well as an "All supported file types" combo filter.
- buildFileChooser(FileFilter[], boolean) - Static method in class loci.formats.gui.GUITools
-
Builds a file chooser with the given file filters, as well as an "All supported file types" combo filter, if one is not already specified.
- buildFileChooser(IFormatHandler) - Static method in class loci.formats.gui.GUITools
-
Constructs a file chooser for the given file format handler.
- buildFileChooser(IFormatHandler, boolean) - Static method in class loci.formats.gui.GUITools
-
Constructs a file chooser for the given file format handler.
- buildFileFilters(IFormatHandler) - Static method in class loci.formats.gui.GUITools
-
Constructs a list of file filters for the given file format handler.
- buildFiles(String, int, List<String>) - Method in class loci.formats.FilePattern
- buildTIFFList(int) - Method in class loci.formats.in.MicromanagerReader
- buildTIFFList(int, String) - Method in class loci.formats.in.MicromanagerReader
-
Populate the list of TIFF files using the given file name as a pattern.
- BurleighReader - Class in loci.formats.in
-
BurleighReader is the file format reader for Burleigh .img files.
- BurleighReader() - Constructor for class loci.formats.in.BurleighReader
-
Constructs a new Burleigh reader.
- BURNED_IN_ANNOTATION - Enum constant in enum class loci.formats.dicom.DicomAttribute
- BYTE - Enum constant in enum class loci.formats.in.SPEReader.SpeHeaderType
- BYTE - Enum constant in enum class loci.formats.tiff.IFDType
- BYTE - Static variable in class loci.formats.in.GatanReader
- BYTE_COUNT_HIGH_BYTES - Static variable in class loci.formats.in.NDPIReader
- BYTE_COUNT_OFFSET - Static variable in class loci.formats.out.QTWriter
-
Seek to this offset to update the total number of pixel bytes.
- ByteArraySource - Class in loci.formats.cache
-
Retrieves byte arrays from a data source (e.g., a file) using Bio-Formats.
- ByteArraySource(String) - Constructor for class loci.formats.cache.ByteArraySource
-
Constructs a byte array source that draws from the given file.
- ByteArraySource(IFormatReader) - Constructor for class loci.formats.cache.ByteArraySource
-
Constructs a byte array source from the given Bio-Formats reader.
- ByteArrayToInt(byte[], int) - Method in class loci.formats.in.SlideBook7Reader.CNpyHeader
- ByteArrayToShort(byte[], int) - Method in class loci.formats.in.SlideBook7Reader.CNpyHeader
- ByteArrayToShort(byte[], int) - Method in class loci.formats.in.SlideBook7Reader.DataLoader
- byteOrder - Variable in class org.libjpegturbo.turbojpeg.TJCompressor
- byteOrder - Variable in class org.libjpegturbo.turbojpeg.TJDecompressor
- bytes - Variable in class loci.formats.tiff.TiffSaver
-
Output bytes.
- BYTES_PER_ENTRY - Static variable in class loci.formats.tiff.TiffConstants
-
The number of bytes in each IFD entry.
- bytesFromReader(IFormatReader) - Method in class loci.formats.Memoizer.RandomAccessDeser
- bytesInc - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.Channel
- bytesInc - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.Dimension
- bytesPerAxis - Variable in class loci.formats.in.LeicaHandler
- bytesPerElement - Variable in enum class loci.formats.tiff.IFDType
-
Number of bytes per element of this type.
- bytesPerImage - Variable in class loci.formats.in.DCIMGReader
- bytesPerLine - Variable in class loci.formats.in.PCXReader
-
Number of bytes per scan line - may be different than image width.
- bytesPerPixel - Variable in class loci.formats.in.AmiraReader.ASCII
- bytesPerPixel - Variable in class loci.formats.in.OpenlabRawReader
-
Number of bytes per pixel.
- bytesPerPixel - Variable in class loci.formats.out.AVIWriter
- bytesPerPlane - Variable in class loci.formats.in.AVIReader
- bytesPerRow - Variable in class loci.formats.in.DCIMGReader
- bytesPerSample - Variable in class loci.formats.in.OBFReader.Stack
- byteValue() - Method in class loci.formats.tiff.TiffRational
-
Returns the value of the specified number as a byte.
- ByteVector - Class in loci.formats.codec
-
A growable array of bytes.
- ByteVector() - Constructor for class loci.formats.codec.ByteVector
- ByteVector(byte[]) - Constructor for class loci.formats.codec.ByteVector
- ByteVector(int) - Constructor for class loci.formats.codec.ByteVector
C
- c - Variable in class loci.formats.in.LeicaSCNReader.Dimension
- c - Variable in class loci.formats.in.MicromanagerReader.Index
- c - Variable in class loci.formats.in.OIRReader.CZTKey
- c - Variable in class loci.formats.in.OperettaReader.Plane
- c - Variable in class loci.formats.tools.AmiraParameters
- C - Enum constant in enum class loci.formats.in.LeicaMicrosystemsMetadata.Dimension.DimensionKey
- C - Static variable in class loci.formats.in.CellSensReader
- C_AXIS - Static variable in class loci.formats.AxisGuesser
-
Axis type for channels.
- C_KEY - Static variable in class loci.formats.in.LiFlimReader
- C_PREFIXES - Static variable in class loci.formats.AxisGuesser
-
Prefixes indicating channel dimension.
- C_STRING - Static variable in class loci.formats.in.SDTInfo
- C01_MAGIC_BYTES - Static variable in class loci.formats.in.CellomicsReader
- cache - Variable in class loci.formats.cache.Cache
-
Master array containing cached objects.
- cache - Variable in class loci.formats.cache.CacheUpdater
- cache - Variable in class loci.formats.gui.CacheComponent
-
The cache that this component controls.
- cache - Variable in class loci.formats.gui.CacheIndicator
- cache - Variable in class loci.plugins.util.BFVirtualStack
- Cache - Class in loci.formats.cache
-
Cache provides a means of managing subsets of large collections of image planes in memory.
- Cache(ICacheStrategy, ICacheSource, boolean) - Constructor for class loci.formats.cache.Cache
-
Constructs an object cache with the given cache strategy and source.
- CacheComponent - Class in loci.formats.gui
-
GUI component for managing a cache.
- CacheComponent(Cache, String[]) - Constructor for class loci.formats.gui.CacheComponent
-
Creates a cache GUI component.
- CacheComponent(Cache, String[], String) - Constructor for class loci.formats.gui.CacheComponent
-
Creates a cache GUI component with the ability to change between the various source types (mainly for debugging purposes).
- CacheConsole - Class in loci.formats.tools
-
CacheConsole provides an interactive interpreter for testing the Bio-Formats caching implementation.
- CacheConsole() - Constructor for class loci.formats.tools.CacheConsole
- cachedTileBuffer - Variable in class loci.formats.in.MIASReader
-
Cached tile buffer to avoid re-allocations when reading tiles.
- cachedTileBuffer - Variable in class loci.formats.tiff.TiffParser
-
Cached tile buffer to avoid re-allocations when reading tiles.
- CacheEvent - Class in loci.formats.cache
-
A event indicating a cache update.
- CacheEvent(Object, int) - Constructor for class loci.formats.cache.CacheEvent
-
Constructs a cache event.
- CacheEvent(Object, int, int) - Constructor for class loci.formats.cache.CacheEvent
-
Constructs a cache event.
- CacheException - Exception Class in loci.formats.cache
-
CacheException is the exception thrown when something goes wrong performing a cache operation.
- CacheException() - Constructor for exception class loci.formats.cache.CacheException
- CacheException(String) - Constructor for exception class loci.formats.cache.CacheException
- CacheException(String, Throwable) - Constructor for exception class loci.formats.cache.CacheException
- CacheException(Throwable) - Constructor for exception class loci.formats.cache.CacheException
- CacheIndicator - Class in loci.formats.gui
-
Indicator GUI component showing which planes are currently in the cache for a given dimensional axis at a particular dimensional position.
- CacheIndicator(Cache, int) - Constructor for class loci.formats.gui.CacheIndicator
-
Creates a new cache indicator for the given cache.
- CacheIndicator(Cache, int, Component, int, int) - Constructor for class loci.formats.gui.CacheIndicator
-
Creates a new cache indicator.
- CacheListener - Interface in loci.formats.cache
-
A listener for cache updates.
- CacheReporter - Interface in loci.formats.cache
-
Interface for components capable of reporting cache updates.
- CacheSource - Class in loci.formats.cache
-
Superclass of cache sources that retrieve image planes from a data source (e.g., a file) using Bio-Formats.
- CacheSource(String) - Constructor for class loci.formats.cache.CacheSource
-
Constructs a cache source that draws from the given file.
- CacheSource(IFormatReader) - Constructor for class loci.formats.cache.CacheSource
-
Constructs a cache source from the given Bio-Formats reader.
- CacheStrategy - Class in loci.formats.cache
-
Superclass of cache strategies.
- CacheStrategy(int[]) - Constructor for class loci.formats.cache.CacheStrategy
-
Constructs a cache strategy.
- cacheUpdated(CacheEvent) - Method in interface loci.formats.cache.CacheListener
-
Called when cache is updated.
- cacheUpdated(CacheEvent) - Method in class loci.formats.gui.CacheComponent
-
Updates GUI to match latest cache state.
- cacheUpdated(CacheEvent) - Method in class loci.formats.gui.CacheIndicator
- CacheUpdater - Class in loci.formats.cache
-
Thread responsible for updating the cache (loading and dropping planes) in the background.
- CacheUpdater(Cache) - Constructor for class loci.formats.cache.CacheUpdater
- calcPhotons - Variable in class loci.formats.in.SDTInfo
-
No of photons.
- calculateDimensions() - Method in class loci.formats.in.ZeissCZIReader
- calculateDimensions(int, boolean) - Method in class loci.formats.in.ZeissCZIReader
- calculatePixelsOffsets(long) - Method in class loci.formats.in.DicomReader
-
Calculate offsets to all pixel data (tiles or planes) in the file, starting from the given offset.
- calculateTilePlaneIndexes() - Method in class loci.formats.in.DicomReader
- CALIBRATION - Static variable in class loci.formats.in.CellSensReader
- CALIBRATION - Static variable in class loci.formats.in.OpenlabReader
- calibrationTable - Variable in class loci.plugins.util.BFVirtualStack
- calibrationUnit - Variable in class loci.formats.in.TiffReader
- Calibrator - Class in loci.plugins.in
-
Logic for calibrating images.
- Calibrator(ImportProcess) - Constructor for class loci.plugins.in.Calibrator
- CAlignManipRecord70() - Constructor for class loci.formats.in.SlideBook7Reader.CAlignManipRecord70
- CALIPER - Enum constant in enum class loci.formats.in.BaseZeissReader.FeatureType
- callDeferredSetters(ReaderWrapper) - Method in class loci.formats.WrappedReader
-
A helper may not exist before initFile() is called.
- callLegacyReader() - Method in class loci.formats.DelegateReader
- CAMERA_GAIN - Static variable in class loci.formats.in.CellSensReader
- CAMERA_GAMMA - Static variable in class loci.formats.in.CellSensReader
- CAMERA_OFFSET - Static variable in class loci.formats.in.CellSensReader
- CAMERA_SERIAL_SETTING - Static variable in class loci.formats.in.FluoviewReader
- cameraIDs - Variable in class loci.formats.in.FlexReader
- cameraMode - Variable in class loci.formats.in.MicromanagerReader.Position
- cameraModel - Variable in class loci.formats.in.ND2Handler
- cameraName - Variable in class loci.formats.in.SimplePCITiffReader
- cameraName - Variable in class loci.formats.in.SISReader
- cameraNumber - Variable in class loci.formats.in.CV7000Reader.Channel
- cameraRef - Variable in class loci.formats.in.MicromanagerReader.Position
- cameraRefs - Variable in class loci.formats.in.FlexReader
- cameraType - Variable in class loci.formats.in.SimplePCITiffReader
- CAN_GROUP - Static variable in class loci.formats.FormatTools
- CAN_GROUP - Static variable in interface loci.formats.IFormatReader
- CAN_VRTL_CHIP - Enum constant in enum class loci.formats.in.SPEReader.SpeHeaderEntry
- canAdjustDimensions - Variable in class loci.formats.in.ND2Handler
- cancel - Variable in class loci.plugins.in.ImportProcess
-
Whether the process has been canceled.
- cancel() - Method in class loci.plugins.in.ImportProcess
-
Cancels the import process.
- canceled - Variable in class loci.plugins.LociImporter
-
Flag indicating whether last operation was canceled.
- canceled - Variable in class loci.plugins.Slicer
-
Flag indicating whether last operation was canceled.
- canceled - Variable in class loci.plugins.Updater
-
Flag indicating whether last operation was canceled.
- canChangePattern() - Method in class loci.formats.FileStitcher
- canClose - Variable in class loci.formats.tiff.TiffParser
- canCloseReader - Variable in class loci.formats.gui.ImageViewer
- canDetectBigTiff - Variable in class loci.formats.out.TiffWriter
-
Whether or not BigTIFF can be used automatically.
- canDoStacks() - Method in class loci.formats.FormatWriter
- canDoStacks() - Method in interface loci.formats.IFormatWriter
-
Reports whether the writer can save multiple images to a single file.
- canDoStacks() - Method in class loci.formats.ImageWriter
- canDoStacks() - Method in class loci.formats.out.APNGWriter
- canDoStacks() - Method in class loci.formats.out.AVIWriter
- canDoStacks() - Method in class loci.formats.out.CellH5Writer
- canDoStacks() - Method in class loci.formats.out.DicomWriter
- canDoStacks() - Method in class loci.formats.out.ICSWriter
- canDoStacks() - Method in class loci.formats.out.JavaWriter
- canDoStacks() - Method in class loci.formats.out.JPEG2000Writer
-
Overridden to indicate that stacks are not supported.
- canDoStacks() - Method in class loci.formats.out.OMEXMLWriter
- canDoStacks() - Method in class loci.formats.out.QTWriter
- canDoStacks() - Method in class loci.formats.out.TiffWriter
- canDoStacks() - Method in class loci.formats.out.V3DrawWriter
- canDoStacks() - Method in class loci.formats.WriterWrapper
- canDoUpgradeCheck() - Method in class loci.formats.UpgradeChecker
-
Return whether or not we are ever allowed to perform an upgrade check.
- canImport(JComponent, DataFlavor[]) - Method in class loci.plugins.shortcut.ShortcutTransferHandler
- canLookForND - Variable in class loci.formats.in.MetamorphReader
- canMerge() - Method in class loci.formats.ChannelMerger
-
Determines whether the channels in the file can be merged.
- CANNOT_GROUP - Static variable in class loci.formats.FormatTools
- CANNOT_GROUP - Static variable in interface loci.formats.IFormatReader
- CAnnotation70() - Constructor for class loci.formats.in.SlideBook7Reader.CAnnotation70
- CAnnotations() - Constructor for class loci.formats.in.SlideBook7Reader.CImageGroup.CAnnotations
- CANON_TAG - Static variable in class loci.formats.in.DNGReader
- CanonRawReader - Class in loci.formats.in
-
CanonRawReader is the file format reader for Canon RAW files.
- CanonRawReader() - Constructor for class loci.formats.in.CanonRawReader
-
Constructs a new Canon RAW reader.
- canParse - Variable in class loci.formats.in.LeicaHandler
- canReadAttachments() - Method in class loci.formats.in.ZeissCZIReader
- canSeparateSeries - Variable in class loci.formats.in.MinimalTiffReader
-
Whether or not IFDs with different dimensions can be split into separate series.
- canUseBankDataDirectly(WritableRaster, int, Class<? extends DataBuffer>) - Static method in class loci.formats.gui.AWTImageTools
-
Whether we can return the data buffer's bank data without performing any copy or conversion operations.
- canUsePrecompressedTiles(IFormatReader, IFormatWriter, int, int) - Static method in class loci.formats.FormatTools
-
Compare the given reader and writer at the specified series and resolution to see if pre-compressed tiles can be transferred directly from the reader to the writer.
- canUsePrevious - Variable in class loci.formats.in.QTReader
-
Flag indicating whether we can safely use prevPixels.
- CANVAS_COLOR_1 - Static variable in class loci.formats.in.CellSensReader
- CANVAS_COLOR_2 - Static variable in class loci.formats.in.CellSensReader
- CAPTURE_EDITOR_DATA - Static variable in class loci.formats.in.NikonReader
- CAPTURE_MODE - Static variable in class loci.formats.in.NDPIReader
- CAPTURE_RESOLUTION - Enum constant in enum class loci.formats.codec.JPEG2000BoxType
- CARDIAC_NUMBER_OF_IMAGES - Enum constant in enum class loci.formats.dicom.DicomAttribute
- CASSETTE_ORIENTATION - Enum constant in enum class loci.formats.dicom.DicomAttribute
- CASSETTE_SIZE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- cast(Class<?>) - Method in class loci.formats.ClassList
-
Cast the given class to something that extends the base class.
- category - Variable in class loci.formats.in.BaseZeissReader.Tag
- category - Variable in class loci.formats.in.ZeissTIFFHandler.Scaling
- category - Variable in class loci.formats.in.ZeissTIFFHandler.Tag
- CAuxDoubleData() - Constructor for class loci.formats.in.SlideBook7Reader.CImageGroup.CAuxDoubleData
- CAuxFloatData() - Constructor for class loci.formats.in.SlideBook7Reader.CImageGroup.CAuxFloatData
- CAuxSInt32Data() - Constructor for class loci.formats.in.SlideBook7Reader.CImageGroup.CAuxSInt32Data
- CAuxSInt64Data() - Constructor for class loci.formats.in.SlideBook7Reader.CImageGroup.CAuxSInt64Data
- CAuxXmlData() - Constructor for class loci.formats.in.SlideBook7Reader.CImageGroup.CAuxXmlData
- cBegin - Variable in class loci.plugins.in.ImporterOptions
- CCD_SENSITIVITY - Static variable in class loci.formats.in.CellSensReader
- CChannelDef70() - Constructor for class loci.formats.in.SlideBook7Reader.CChannelDef70
- CChannelRecord70() - Constructor for class loci.formats.in.SlideBook7Reader.CChannelRecord70
- cChoice - Variable in class loci.formats.gui.DataConverter
- cChoice - Variable in class loci.plugins.in.SwapDialog
- CCITT_1D - Enum constant in enum class loci.formats.tiff.TiffCompression
- CCompressionBase() - Constructor for class loci.formats.in.SlideBook7Reader.CCompressionBase
- CCube() - Constructor for class loci.formats.in.SlideBook7Reader.CCube
- CCubeAnnotation70() - Constructor for class loci.formats.in.SlideBook7Reader.CCubeAnnotation70
- cdata - Variable in class loci.formats.in.LeicaSCNReader.LeicaSCNHandler
- cdata - Variable in class loci.formats.in.ZeissTIFFHandler
- CDataTableHeaderRecord70() - Constructor for class loci.formats.in.SlideBook7Reader.CDataTableHeaderRecord70
- CELL_LENGTH - Static variable in class loci.formats.tiff.IFD
- CELL_WIDTH - Static variable in class loci.formats.tiff.IFD
- CellH5Constants() - Constructor for class loci.formats.in.CellH5Reader.CellH5Constants
- CellH5Coordinate(String, String, String) - Constructor for class loci.formats.in.CellH5Reader.CellH5Coordinate
- CellH5PathsToImageData - Variable in class loci.formats.in.CellH5Reader
- CellH5PositionList - Variable in class loci.formats.in.CellH5Reader
- CellH5Reader - Class in loci.formats.in
-
Reader for CellH5 (HDF) files.
- CellH5Reader() - Constructor for class loci.formats.in.CellH5Reader
-
Constructs a new CellH5 HDF reader.
- CellH5Reader.CellH5Constants - Class in loci.formats.in
- CellH5Reader.CellH5Coordinate - Class in loci.formats.in
- CellH5Writer - Class in loci.formats.out
-
CellH5Writer is the file format writer for CellH5 format.
- CellH5Writer() - Constructor for class loci.formats.out.CellH5Writer
- CellH5Writer(String, String[]) - Constructor for class loci.formats.out.CellH5Writer
- cellObjectNames - Variable in class loci.formats.in.BDVReader
- cellObjectNames - Variable in class loci.formats.in.CellH5Reader
- cellomicsPattern - Variable in class loci.formats.in.CellomicsReader
- CellomicsReader - Class in loci.formats.in
-
Reader for Cellomics C01 files.
- CellomicsReader() - Constructor for class loci.formats.in.CellomicsReader
-
Constructs a new Cellomics reader.
- CellomicsReader.ChannelFile - Class in loci.formats.in
- CellSensReader - Class in loci.formats.in
-
CellSensReader is the file format reader for cellSens .vsi files.
- CellSensReader() - Constructor for class loci.formats.in.CellSensReader
-
Constructs a new cellSens reader.
- CellSensReader.Pyramid - Class in loci.formats.in
- CellSensReader.TileCoordinate - Class in loci.formats.in
- CellSensWidgets - Class in loci.plugins.config
-
Custom widgets for configuring Bio-Formats CellSens .vsi support.
- CellSensWidgets() - Constructor for class loci.plugins.config.CellSensWidgets
- CellVoyagerReader - Class in loci.formats.in
-
A bioformat reader for the Yokagawa Cellvoyager CV1000 automated microscope ( http://www.yokogawa.com/scanner/products/cv1000e.htm).
- CellVoyagerReader() - Constructor for class loci.formats.in.CellVoyagerReader
- CellVoyagerReader.AreaInfo - Class in loci.formats.in
- CellVoyagerReader.ChannelInfo - Class in loci.formats.in
- CellVoyagerReader.FieldInfo - Class in loci.formats.in
- CellVoyagerReader.WellInfo - Class in loci.formats.in
- CellWorxReader - Class in loci.formats.in
-
CellWorxReader is the file format reader for CellWorx .pnl files.
- CellWorxReader() - Constructor for class loci.formats.in.CellWorxReader
-
Constructs a new CellWorx reader.
- CellWorxReader(String, String[]) - Constructor for class loci.formats.in.CellWorxReader
- cEnd - Variable in class loci.plugins.in.ImporterOptions
- CENTER - Enum constant in enum class loci.formats.in.BaseZeissReader.TextAlignment
- CENTER_OF_CIRCULAR_COLLIMATOR - Enum constant in enum class loci.formats.dicom.DicomAttribute
- CENTER_OF_CIRCULAR_SHUTTER - Enum constant in enum class loci.formats.dicom.DicomAttribute
- CENTER_OF_ROTATION_OFFSET - Enum constant in enum class loci.formats.dicom.DicomAttribute
- CENTERED_ORDER - Static variable in interface loci.formats.cache.ICacheStrategy
- centerPixelValue - Variable in class loci.formats.in.DicomReader
- centerX - Variable in class loci.formats.in.CellVoyagerReader.WellInfo
- centerY - Variable in class loci.formats.in.CellVoyagerReader.WellInfo
- certain - Variable in class loci.formats.AxisGuesser
-
Whether the guesser is confident that all axis types are correct.
- certain - Variable in class loci.formats.in.OMETiffReader.OMETiffPlane
-
Certainty flag, for dealing with unspecified NumPlanes.
- CExposureRecord70() - Constructor for class loci.formats.in.SlideBook7Reader.CExposureRecord70
- cf - Variable in class org.libjpegturbo.turbojpeg.TJTransform
-
Custom filter instance
- CFA_ARRAY - Enum constant in enum class loci.formats.tiff.PhotoInterp
- CFA_PATTERN - Static variable in class loci.formats.tiff.IFD
- cfaPattern - Variable in class loci.formats.in.DNGReader
- cfaPattern - Variable in class loci.formats.in.NikonReader
- cfdHF - Variable in class loci.formats.in.SDTInfo
- cfdLH - Variable in class loci.formats.in.SDTInfo
- cfdLL - Variable in class loci.formats.in.SDTInfo
- cfdZC - Variable in class loci.formats.in.SDTInfo
- CFG_SUFFIX - Static variable in class loci.formats.in.PerkinElmerReader
- CFG_SUFFIX - Static variable in class loci.formats.in.PrairieReader
- cfgFile - Variable in class loci.formats.in.PrairieReader
-
The associated XML files.
- CFluorDef70() - Constructor for class loci.formats.in.SlideBook7Reader.CFluorDef70
- CFRAPRegionAnnotation70() - Constructor for class loci.formats.in.SlideBook7Reader.CFRAPRegionAnnotation70
- CFRETManipRecord70() - Constructor for class loci.formats.in.SlideBook7Reader.CFRETManipRecord70
- CHAINED_LAYERS - Static variable in class loci.formats.in.CellSensReader
- chan - Variable in class loci.formats.in.SDTInfo
-
Routing channel number.
- CHANDESC - Static variable in class loci.formats.in.LeicaReader
- changeOutputFile(String) - Method in class loci.formats.FormatWriter
- changeOutputFile(String) - Method in interface loci.formats.IFormatWriter
-
Switch the output file for the current dataset.
- changeOutputFile(String) - Method in class loci.formats.ImageWriter
- changeOutputFile(String) - Method in class loci.formats.WriterWrapper
- chanMax - Variable in class loci.formats.MinMaxCalculator
-
Max values for each channel.
- chanMin - Variable in class loci.formats.MinMaxCalculator
-
Min values for each channel.
- channel - Variable in class loci.formats.dicom.DicomTile
- channel - Variable in class loci.formats.in.CellomicsReader.ChannelFile
- channel - Variable in class loci.formats.in.ColumbusReader.Plane
- channel - Variable in class loci.formats.in.CV7000Reader.Plane
- channel - Variable in class loci.formats.in.LeicaHandler.Detector
- channel - Variable in class loci.formats.in.LeicaHandler.MultiBand
- channel - Variable in class loci.formats.in.PrairieMetadata.PFile
-
channelof this<File>. - channel - Variable in class loci.formats.in.SPCReader
- Channel - Class in loci.formats.in.LeicaMicrosystemsMetadata
-
This class represents image channels extracted from LMS image xmls.
- Channel() - Constructor for class loci.formats.in.CV7000Reader.Channel
- Channel() - Constructor for class loci.formats.in.LeicaHandler.Channel
- Channel() - Constructor for class loci.formats.in.OIRReader.Channel
- Channel() - Constructor for class loci.formats.in.OperettaReader.Channel
- Channel() - Constructor for class loci.formats.in.TissueFAXSReader.Channel
- Channel() - Constructor for class loci.formats.in.ZeissCZIReader.Channel
- Channel(int, int, double, double, String, String, long) - Constructor for class loci.formats.in.LeicaMicrosystemsMetadata.Channel
- Channel(String) - Constructor for class loci.formats.in.TecanReader.Channel
- Channel(CV7000Reader.Channel) - Constructor for class loci.formats.in.CV7000Reader.Channel
- Channel(OIRReader.Channel) - Constructor for class loci.formats.in.OIRReader.Channel
- CHANNEL - Static variable in class loci.formats.FormatTools
-
Identifies the Channel dimensional type, representing a generic channel dimension.
- CHANNEL_ACQUIRE - Static variable in class loci.formats.in.ZeissLSMReader
- CHANNEL_AMPLIFIER_GAIN - Static variable in class loci.formats.in.ZeissLSMReader
- CHANNEL_CONTRAST_BRIGHTNESS - Static variable in class loci.formats.in.CellSensReader
- CHANNEL_COUNT_TAG - Static variable in class loci.formats.in.FlowSightReader
- CHANNEL_DEFINITION - Enum constant in enum class loci.formats.codec.JPEG2000BoxType
- CHANNEL_DESCRIPTION_CODE_SEQUENCE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- CHANNEL_DESCS_TAG - Static variable in class loci.formats.in.FlowSightReader
- CHANNEL_DETECTOR_GAIN - Static variable in class loci.formats.in.ZeissLSMReader
- CHANNEL_DIM - Static variable in class loci.formats.in.CellSensReader
- CHANNEL_FILTER - Static variable in class loci.formats.in.ZeissLSMReader
- CHANNEL_FILTER_SET - Static variable in class loci.formats.in.ZeissLSMReader
- CHANNEL_GAMMA_CORRECTION - Static variable in class loci.formats.in.CellSensReader
- CHANNEL_INFO_PROPERTIES - Static variable in class loci.formats.in.CellSensReader
- CHANNEL_NAME - Static variable in class loci.formats.FormatTools
- CHANNEL_NAME - Static variable in class loci.formats.in.CellSensReader
- CHANNEL_NAME - Static variable in class loci.formats.in.ZeissLSMReader
- CHANNEL_NAMES_TAG - Static variable in class loci.formats.in.FlowSightReader
- CHANNEL_NUM - Static variable in class loci.formats.FormatTools
- CHANNEL_OVERFLOW - Static variable in class loci.formats.in.CellSensReader
- CHANNEL_PINHOLE_DIAMETER - Static variable in class loci.formats.in.ZeissLSMReader
- CHANNEL_PREFIX - Static variable in class loci.formats.in.KLBReader
-
Prefixes indicating dimensions and projections
- CHANNEL_PRIORITIES - Static variable in class loci.formats.in.LIFReader
- CHANNEL_PROPERTIES - Static variable in class loci.formats.in.CellSensReader
- CHANNEL_TAG - Static variable in class loci.formats.in.SlidebookTiffReader
- CHANNEL_TRANSPARENCY_VALUE - Static variable in class loci.formats.in.CellSensReader
- CHANNEL_VISIBLE - Static variable in class loci.formats.in.CellSensReader
- Channel.ChannelType - Enum Class in loci.formats.in.LeicaMicrosystemsMetadata
- channelBytesIncs - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.LMSMetadataExtractor
- channelColor - Variable in class loci.formats.in.ColumbusReader.Plane
- channelColor - Variable in class loci.formats.in.LeicaReader
- channelColor - Variable in class loci.formats.in.ZeissLSMReader
- channelColors - Variable in class loci.formats.in.BaseZeissReader
- channelColors - Variable in class loci.formats.in.ImprovisionTiffReader
- channelColors - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataTempBuffer
- channelColors - Variable in class loci.formats.in.MicromanagerReader.Position
- channelColors - Variable in class loci.formats.in.ND2Reader
- channelCount - Variable in class loci.formats.in.CellSensReader
- ChannelData() - Constructor for class loci.formats.in.FV1000Reader.ChannelData
- channelDescs - Variable in class loci.formats.in.FlowSightReader
- ChannelFile(String, int, int, int, int) - Constructor for class loci.formats.in.CellomicsReader.ChannelFile
- channelFiller - Variable in class loci.plugins.in.ImportProcess
- ChannelFiller - Class in loci.formats
-
For indexed color data representing true color, factors out the indices, replacing them with the color table values directly.
- ChannelFiller() - Constructor for class loci.formats.ChannelFiller
-
Constructs a ChannelFiller around a new image reader.
- ChannelFiller(IFormatReader) - Constructor for class loci.formats.ChannelFiller
-
Constructs a ChannelFiller with a given reader.
- channelId - Variable in class loci.formats.in.OIRReader.Detector
- channelID - Variable in class loci.formats.in.OperettaReader.Channel
- channelIDs - Variable in class loci.formats.in.IonpathMIBITiffReader
- channelIndex - Variable in class loci.formats.in.CV7000Reader.Plane
- channelIndexes - Variable in class loci.formats.in.BDVReader
- channelIndices - Variable in class loci.formats.in.BaseZeissReader
- ChannelInfo() - Constructor for class loci.formats.in.CellVoyagerReader.ChannelInfo
- channelInfos - Variable in class loci.formats.in.CellVoyagerReader
- channelLengths - Variable in class loci.formats.in.ICSReader
-
The length of each channel axis.
- channelMax - Variable in class loci.formats.in.ImarisHDFReader
- ChannelMerger - Class in loci.formats
-
Logic to automatically merge channels in a file.
- ChannelMerger() - Constructor for class loci.formats.ChannelMerger
-
Constructs a ChannelMerger around a new image reader.
- ChannelMerger(IFormatReader) - Constructor for class loci.formats.ChannelMerger
-
Constructs a ChannelMerger with the given reader.
- channelMin - Variable in class loci.formats.in.ImarisHDFReader
- channelName - Variable in class loci.formats.in.BaseZeissReader
- channelName - Variable in class loci.formats.in.ColumbusReader.Plane
- channelName - Variable in class loci.formats.in.ImarisHDFReader
- channelName - Variable in class loci.formats.in.MetamorphHandler
- channelName - Variable in class loci.formats.in.OpenlabReader.PlaneInfo
- channelName - Variable in class loci.formats.in.OperettaReader.Channel
- channelName - Variable in class loci.formats.in.OperettaReader.Plane
- channelName - Variable in class loci.formats.in.PrairieMetadata.PFile
-
channelNameattribute of this<File>. - channelName - Variable in class loci.formats.in.SISReader
- channelName - Variable in class loci.formats.in.TecanReader.Image
- channelName - Variable in class loci.formats.in.ZeissLSMReader.DetectionChannel
- channelNames - Variable in class loci.formats.dicom.DicomFileInfo
- channelNames - Variable in class loci.formats.in.BDReader
- channelNames - Variable in class loci.formats.in.CellSensReader.Pyramid
- channelNames - Variable in class loci.formats.in.DicomReader
- channelNames - Variable in class loci.formats.in.FlexReader
- channelNames - Variable in class loci.formats.in.FlowSightReader
- channelNames - Variable in class loci.formats.in.FluoviewReader
- channelNames - Variable in class loci.formats.in.InCellReader
- channelNames - Variable in class loci.formats.in.IonpathMIBITiffReader
- channelNames - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataTempBuffer
- channelNames - Variable in class loci.formats.in.LeicaReader
- channelNames - Variable in class loci.formats.in.LIFReader
- channelNames - Variable in class loci.formats.in.MetamorphHandler
- channelNames - Variable in class loci.formats.in.ND2Handler
- channelNames - Variable in class loci.formats.in.ScanrReader
- channelNames - Variable in class loci.formats.in.SlidebookTiffReader
- channelNames - Variable in class loci.formats.in.VolocityReader.Stack
- channelNames - Variable in class loci.formats.in.ZeissLSMReader
- channelNumber - Variable in class loci.formats.in.CellVoyagerReader.ChannelInfo
- channelNumber - Variable in class loci.plugins.util.RecordedImageProcessor
- channelOrder - Variable in class loci.formats.in.PhotoshopTiffReader
- channelPrios - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataTempBuffer
- channels - Variable in class loci.formats.codec.CodecOptions
-
Number of channels.
- channels - Variable in class loci.formats.in.CV7000Reader
- channels - Variable in class loci.formats.in.FV1000Reader
- channels - Variable in class loci.formats.in.KLBReader
- channels - Variable in class loci.formats.in.LeicaHandler
- channels - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataTempBuffer
- channels - Variable in class loci.formats.in.LiFlimReader
- channels - Variable in class loci.formats.in.MicromanagerReader.Position
- channels - Variable in class loci.formats.in.OIRReader
- channels - Variable in class loci.formats.in.OperettaReader.OperettaHandler
- channels - Variable in class loci.formats.in.PrairieReader
-
List of active channels.
- channels - Variable in class loci.formats.in.SDTInfo
- channels - Variable in class loci.formats.in.SDTReader
-
Number of spectral channels.
- channels - Variable in class loci.formats.in.TecanReader
- channels - Variable in class loci.formats.in.TextReader
-
List of channel labels.
- channels - Variable in class loci.formats.in.TissueFAXSReader.ScanRegion
- channels - Variable in class loci.formats.in.ZeissCZIReader
- channelSeparator - Variable in class loci.plugins.in.ImportProcess
- ChannelSeparator - Class in loci.formats
-
Logic to automatically separate the channels in a file.
- ChannelSeparator() - Constructor for class loci.formats.ChannelSeparator
-
Constructs a ChannelSeparator around a new image reader.
- ChannelSeparator(IFormatReader) - Constructor for class loci.formats.ChannelSeparator
-
Constructs a ChannelSeparator with the given reader.
- channelsPerTimepoint - Variable in class loci.formats.in.InCellReader
- channelTag - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.Channel
- channelType - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.Channel
- channelType - Variable in class loci.formats.in.OperettaReader.Channel
- channelType - Variable in class loci.formats.in.OperettaReader.Plane
- ChannelType() - Constructor for enum class loci.formats.in.LeicaMicrosystemsMetadata.Channel.ChannelType
- channelTypes - Variable in class loci.formats.in.ICSReader
-
The type of each channel axis.
- channelWavelengths - Variable in class loci.formats.in.CellSensReader.Pyramid
- CHAR - Static variable in class loci.formats.in.CellSensReader
- CHAR - Static variable in class loci.formats.in.GatanReader
- characters(char[], int, int) - Method in class loci.formats.in.AFIReader.AFIHandler
- characters(char[], int, int) - Method in class loci.formats.in.BDVReader.BDVXMLHandler
- characters(char[], int, int) - Method in class loci.formats.in.BioRadSCNReader.SCNHandler
- characters(char[], int, int) - Method in class loci.formats.in.ColumbusReader.MeasurementHandler
- characters(char[], int, int) - Method in class loci.formats.in.CV7000Reader.MeasurementDataHandler
- characters(char[], int, int) - Method in class loci.formats.in.CV7000Reader.MeasurementSettingsHandler
- characters(char[], int, int) - Method in class loci.formats.in.FEITiffReader.FEIHandler
- characters(char[], int, int) - Method in class loci.formats.in.FlexReader.FlexHandler
- characters(char[], int, int) - Method in class loci.formats.in.ImaconReader.ImaconHandler
- characters(char[], int, int) - Method in class loci.formats.in.InCellReader.InCellHandler
- characters(char[], int, int) - Method in class loci.formats.in.IvisionReader.IvisionHandler
- characters(char[], int, int) - Method in class loci.formats.in.LeicaSCNReader.LeicaSCNHandler
- characters(char[], int, int) - Method in class loci.formats.in.OMEXMLReader.OMEXMLHandler
- characters(char[], int, int) - Method in class loci.formats.in.OperettaReader.OperettaHandler
- characters(char[], int, int) - Method in class loci.formats.in.ScanrReader.ScanrHandler
- characters(char[], int, int) - Method in class loci.formats.in.ZeissTIFFHandler
- characters(char[], int, int) - Method in class loci.formats.out.OMEXMLWriter.OMEHandler
- charData - Variable in class loci.formats.in.FlexReader.FlexHandler
- CHARS - Static variable in class loci.formats.tools.AsciiImage
- charset - Variable in class loci.formats.in.BaseZeissReader.Shape
- Charset(int, String) - Constructor for enum class loci.formats.in.BaseZeissReader.Charset
- CHARSET_OF_FILE_SET_DESCRIPTOR_FILE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- CHECK - Static variable in class loci.formats.in.ZeissLMSReader
- checkBufferSize(IFormatReader, int) - Static method in class loci.formats.FormatTools
- checkBufferSize(IFormatReader, int, int, int) - Static method in class loci.formats.FormatTools
-
Checks that the given buffer size is large enough to hold a w * h image as returned by the given reader.
- checkClass(String) - Static method in class loci.plugins.util.LibraryChecker
-
Checks whether the given class is available.
- checkCommentImageJ(String) - Method in class loci.formats.in.TiffReader
- checkCommentMetamorph(String) - Method in class loci.formats.in.TiffReader
- checkElement(Element, String) - Method in class loci.formats.in.PrairieMetadata
-
Checks that the given element has the specified name.
- checkFlip(boolean, Length) - Method in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataStoreInitializer
- checkFlip(boolean, Length) - Method in class loci.formats.in.LIFReader
- checkForLofLayout(RandomAccessInputStream, String) - Method in class loci.formats.in.LOFReader
-
Checks if file layout meets lof file specifications
- checkHeader() - Method in class loci.formats.tiff.TiffParser
-
Checks the TIFF header.
- checkImageFormat() - Method in class loci.formats.in.LeicaMicrosystemsMetadata.XlifDocument
- checkImageIndex(int) - Method in class loci.formats.ome.OMEPyramidStore
-
Verify that the given index is non-negative and less than the Image count.
- checkImageJ() - Static method in class loci.plugins.util.LibraryChecker
-
Checks whether ImageJ is new enough for the Bio-Formats plugins.
- checkImageJ(String, String) - Static method in class loci.plugins.util.LibraryChecker
-
Returns true the current ImageJ version is greater than or equal to the specified version.
- checkImageJ(String, String, String) - Static method in class loci.plugins.util.LibraryChecker
-
Returns true the current ImageJ version is greater than or equal to the specified version.
- checkJava() - Static method in class loci.plugins.util.LibraryChecker
-
Checks for a new enough version of the Java Runtime Environment.
- checkKey(String, String) - Method in class loci.formats.in.MetamorphHandler
-
Check if the value needs to be saved.
- checkKey(String, String) - Method in class loci.plugins.in.ImporterOptions
-
Tests whether the given boolean key is set in the specified options.
- checkLatest(String, String) - Static method in class loci.plugins.config.InstallWizard
- checkLibrary(String, String, HashSet<String>) - Static method in class loci.plugins.util.LibraryChecker
-
Checks whether the given class is available; if not, adds the specified JAR file name to the hash set (presumably to report it missing to the user).
- checkLibrary(LibraryChecker.Library, HashSet<String>) - Static method in class loci.plugins.util.LibraryChecker
-
Checks for a required library.
- checkMissing(HashSet<String>) - Static method in class loci.plugins.util.LibraryChecker
-
Reports missing libraries in the given hash set to the user.
- checkObsoleteOptions() - Method in class loci.plugins.in.ImporterOptions
-
Handles obsolete macro keys, for backward compatibility.
- checkPALM(String) - Method in class loci.formats.in.ZeissCZIReader
- checkParams - Variable in class loci.formats.out.TiffWriter
-
Whether or not to check the parameters passed to saveBytes.
- checkParams(int, byte[], int, int, int, int) - Method in class loci.formats.FormatWriter
-
Ensure that the arguments that are being passed to saveBytes(...) are valid.
- checkPerformed - Static variable in class loci.plugins.in.UpgradeDialog
-
Whether an upgrade check has already been performed this session.
- checkPixelCount(boolean) - Method in class loci.formats.out.DicomWriter
- checkPlaneNumber(IFormatReader, int) - Static method in class loci.formats.FormatTools
-
Checks that the given plane number is valid for the given reader.
- checkPlaneParameters(IFormatReader, int, int, int, int, int, int) - Static method in class loci.formats.FormatTools
-
Convenience method for checking that the plane number, tile size and buffer sizes are all valid for the given reader.
- checkPoints(int) - Method in enum class loci.formats.in.BaseZeissReader.FeatureType
- checkPrecompressedSupport() - Method in class loci.formats.out.DicomWriter
-
Check if pre-compressed tiles are supported with the current options.
- checkResolutionIndex(int, int) - Method in class loci.formats.ome.OMEPyramidStore
-
Verify that the given image and resolution indices are valid.
- checkSuffix(String, String) - Static method in class loci.formats.FormatHandler
-
Performs suffix matching for the given filename.
- checkSuffix(String, String[]) - Static method in class loci.formats.FormatHandler
-
Performs suffix matching for the given filename.
- checkTileSize(IFormatReader, int, int, int, int) - Static method in class loci.formats.FormatTools
-
Checks that the given tile size is valid for the given reader.
- checkTime(long, int, long, long) - Method in class loci.formats.in.TextReader
- checkUnit(String, String...) - Method in class loci.formats.in.ICSReader
-
Verifies that a unit matches the expected value.
- children - Variable in class loci.formats.dicom.DicomTag
- children - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.LMSCollectionXmlDocument
- CHINESEBIG5_CHARSET - Enum constant in enum class loci.formats.in.BaseZeissReader.Charset
- CHIP_FLAG - Enum constant in enum class loci.formats.in.SPEReader.SpeHeaderEntry
- CHIP_SIZE_X - Static variable in class loci.formats.in.FluoviewReader
- CHIP_SIZE_Y - Static variable in class loci.formats.in.FluoviewReader
- CHistogramRecord70() - Constructor for class loci.formats.in.SlideBook7Reader.CHistogramRecord70
- chksum - Variable in class loci.formats.in.SDTInfo
- CHUNK_SIZE - Static variable in class loci.formats.UpgradeChecker
-
Number of bytes to read from the CI server at a time.
- chunkFilePositions - Variable in class loci.formats.in.OBFReader.Stack
- chunkFileStart - Variable in class loci.formats.in.OBFReader.State
- chunkLogicalPositions - Variable in class loci.formats.in.OBFReader.Stack
- chunkLogicalStart - Variable in class loci.formats.in.OBFReader.State
- ChunkMapEntry() - Constructor for class loci.formats.in.ND2Reader.ChunkMapEntry
- chunkSize - Variable in class loci.formats.in.OBFReader.State
- chunkSizes - Variable in class loci.formats.in.QTReader
-
Number of bytes in each plane.
- CI_SERVER - Static variable in class loci.formats.UpgradeChecker
-
Location of the OME continuous integration server.
- CIE_LAB - Enum constant in enum class loci.formats.tiff.PhotoInterp
- CImageData() - Constructor for class loci.formats.in.SlideBook7Reader.CImageData
- CImageGroup(SlideBook7Reader.CSBFile70, String) - Constructor for class loci.formats.in.SlideBook7Reader.CImageGroup
- CImageRecord70() - Constructor for class loci.formats.in.SlideBook7Reader.CImageRecord70
- cIndex - Variable in class loci.formats.in.BaseZeissReader
- cIndex - Variable in class loci.plugins.util.DataBrowser
- CINE_RATE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- CINEPAK - Enum constant in enum class loci.formats.codec.CompressionType
- CIRCLE - Enum constant in enum class loci.formats.in.BaseZeissReader.FeatureType
- CIRCLE - Static variable in class loci.formats.in.FV1000Reader
- CIRCLE - Static variable in class loci.formats.in.ZeissLSMReader
- CIRCLE_3POINT - Static variable in class loci.formats.in.ZeissLSMReader
- cLabel - Variable in class loci.formats.gui.DataConverter
- CLASS_IMAGE_5D - Static variable in class loci.plugins.in.ImporterOptions
- CLASS_LABELS - Static variable in class loci.formats.in.BDVReader.H5Constants
- CLASS_LABELS - Static variable in class loci.formats.in.CellH5Reader.CellH5Constants
- CLASS_VIEW_5D - Static variable in class loci.plugins.in.ImporterOptions
- ClassDecoder() - Constructor for class loci.formats.in.SlideBook7Reader.ClassDecoder
- classes - Variable in class loci.formats.ClassList
-
List of classes.
- classes - Variable in class loci.formats.in.BDVReader
- classes - Variable in class loci.formats.in.CellH5Reader
- CLASSES_IN_STUDY - Enum constant in enum class loci.formats.dicom.DicomAttribute
- classList - Variable in class loci.formats.FileStitcher
- ClassList<T> - Class in loci.formats
-
ClassList is a list of classes for use with
ImageReaderorImageWriter, parsed from a configuration file such as readers.txt or writers.txt. - ClassList(Class<T>) - Constructor for class loci.formats.ClassList
-
Constructs a list of classes, initially empty.
- ClassList(String, Class<T>) - Constructor for class loci.formats.ClassList
-
Constructs a list of classes from the given configuration file.
- ClassList(String, Class<T>, Class<?>) - Constructor for class loci.formats.ClassList
-
Constructs a list of classes from the given configuration file.
- CLEANS - Enum constant in enum class loci.formats.in.SPEReader.SpeHeaderEntry
- cleanup() - Method in class loci.formats.Memoizer
- clear() - Method in class loci.formats.codec.ByteVector
- clear() - Method in class loci.formats.MetadataList
-
Clear the array.
- clear(int) - Method in class loci.formats.MetadataList
-
Clear the specified primary array element.
- clearSeries() - Method in class loci.plugins.in.ImporterOptions
- clearXML() - Method in class loci.formats.in.ZeissCZIReader.Metadata
- cLengths - Variable in class loci.plugins.util.DataBrowser
- CLensDef70() - Constructor for class loci.formats.in.SlideBook7Reader.CLensDef70
- CLINICAL_TRIAL_COORDINATING_CENTER - Enum constant in enum class loci.formats.dicom.DicomAttribute
- CLINICAL_TRIAL_PROTOCOL_ID - Enum constant in enum class loci.formats.dicom.DicomAttribute
- CLINICAL_TRIAL_PROTOCOL_NAME - Enum constant in enum class loci.formats.dicom.DicomAttribute
- CLINICAL_TRIAL_SITE_ID - Enum constant in enum class loci.formats.dicom.DicomAttribute
- CLINICAL_TRIAL_SITE_NAME - Enum constant in enum class loci.formats.dicom.DicomAttribute
- CLINICAL_TRIAL_SPONSOR_NAME - Enum constant in enum class loci.formats.dicom.DicomAttribute
- CLINICAL_TRIAL_SUBJECT_ID - Enum constant in enum class loci.formats.dicom.DicomAttribute
- CLINICAL_TRIAL_SUBJECT_READING_ID - Enum constant in enum class loci.formats.dicom.DicomAttribute
- CLINICAL_TRIAL_TIME_POINT_DESCRIPTION - Enum constant in enum class loci.formats.dicom.DicomAttribute
- CLINICAL_TRIAL_TIME_POINT_ID - Enum constant in enum class loci.formats.dicom.DicomAttribute
- CLIPPING - Static variable in class loci.formats.in.CellSensReader
- CLIPPING_MAGIC_STRING - Static variable in class loci.formats.in.VolocityClippingReader
- CLIPPING_STATE - Static variable in class loci.formats.in.CellSensReader
- clippingData - Variable in class loci.formats.in.VolocityReader.Stack
- CLOCK_SPEED - Enum constant in enum class loci.formats.in.SPEReader.SpeHeaderEntry
- CLOCKWISE - Static variable in class loci.formats.in.FluoviewReader
- clone() - Method in class loci.formats.CoreMetadata
- clone() - Method in class loci.formats.SwappableMetadata
- clone(IFormatReader, int) - Method in class loci.formats.CoreMetadata
- clone(IFormatReader, int) - Method in class loci.formats.SwappableMetadata
- close() - Method in class loci.formats.codec.JPEGTileDecoder
- close() - Method in class loci.formats.FileStitcher
- close() - Method in class loci.formats.FileStitcher.ExternalSeries
- close() - Method in class loci.formats.FormatReader
- close() - Method in class loci.formats.FormatWriter
- close() - Method in class loci.formats.gui.PreviewPane
-
Closes the underlying image reader.
- close() - Method in class loci.formats.ImageReader
- close() - Method in class loci.formats.ImageWriter
- close() - Method in class loci.formats.in.ZeissCZIReader.Segment
- close() - Method in class loci.formats.Memoizer
- close() - Method in interface loci.formats.Memoizer.Deser
- close() - Method in class loci.formats.Memoizer.KryoDeser
- close() - Method in class loci.formats.out.APNGWriter
- close() - Method in class loci.formats.out.AVIWriter
- close() - Method in class loci.formats.out.CellH5Writer
- close() - Method in class loci.formats.out.DicomWriter
- close() - Method in class loci.formats.out.ICSWriter
- close() - Method in class loci.formats.out.JavaWriter
- close() - Method in class loci.formats.out.OMETiffWriter
- close() - Method in class loci.formats.out.OMEXMLWriter
- close() - Method in class loci.formats.out.PyramidOMETiffWriter
- close() - Method in class loci.formats.out.QTWriter
- close() - Method in class loci.formats.out.TiffWriter
- close() - Method in class loci.formats.out.V3DrawWriter
- close() - Method in class loci.formats.ReaderWrapper
- close() - Method in interface loci.formats.services.EXIFService
- close() - Method in class loci.formats.services.EXIFServiceImpl
- close() - Method in interface loci.formats.services.JHDFService
-
Closes and resets the service.
- close() - Method in class loci.formats.services.JHDFServiceImpl
- close() - Method in interface loci.formats.services.JPEGTurboService
-
Free resources associated with the initialized stream.
- close() - Method in class loci.formats.services.JPEGTurboServiceImpl
- close() - Method in interface loci.formats.services.MDBService
-
Close the currently initialized file.
- close() - Method in class loci.formats.services.MDBServiceImpl
- close() - Method in interface loci.formats.services.MetakitService
- close() - Method in class loci.formats.services.MetakitServiceImpl
- close() - Method in interface loci.formats.services.NetCDFService
-
Closes and resets the service.
- close() - Method in class loci.formats.services.NetCDFServiceImpl
- close() - Method in interface loci.formats.services.POIService
-
Close the current POI file system.
- close() - Method in class loci.formats.services.POIServiceImpl
- close() - Method in class loci.formats.tiff.OnDemandLongArray
- close() - Method in class loci.formats.tiff.TiffParser
-
Close the underlying stream, if this TiffParser was constructed with a file path.
- close() - Method in class loci.formats.tiff.TiffSaver
-
Closes the output stream if not null.
- close() - Method in class loci.formats.WrappedReader
- close() - Method in class loci.formats.WriterWrapper
- close() - Method in class loci.plugins.config.TextAreaWriter
-
Closing a TextAreaWriter does nothing.
- close() - Method in class loci.plugins.macro.LociFunctions
- close() - Method in class loci.plugins.util.VirtualImagePlus
- close() - Method in class loci.plugins.util.VirtualReader
- close() - Method in class org.libjpegturbo.turbojpeg.TJCompressor
-
Free the native structures associated with this compressor instance.
- close() - Method in class org.libjpegturbo.turbojpeg.TJDecompressor
-
Free the native structures associated with this decompressor instance.
- close(boolean) - Method in class loci.formats.ChannelSeparator
- close(boolean) - Method in class loci.formats.DelegateReader
- close(boolean) - Method in class loci.formats.FileStitcher
- close(boolean) - Method in class loci.formats.FileStitcher.ExternalSeries
- close(boolean) - Method in class loci.formats.FormatReader
- close(boolean) - Method in interface loci.formats.IFormatReader
-
Closes the currently open file.
- close(boolean) - Method in class loci.formats.ImageReader
- close(boolean) - Method in class loci.formats.in.AFIReader
- close(boolean) - Method in class loci.formats.in.AIMReader
- close(boolean) - Method in class loci.formats.in.AliconaReader
- close(boolean) - Method in class loci.formats.in.AmiraReader
- close(boolean) - Method in class loci.formats.in.AnalyzeReader
- close(boolean) - Method in class loci.formats.in.APLReader
- close(boolean) - Method in class loci.formats.in.APNGReader
- close(boolean) - Method in class loci.formats.in.AVIReader
- close(boolean) - Method in class loci.formats.in.BaseZeissReader
- close(boolean) - Method in class loci.formats.in.BDReader
- close(boolean) - Method in class loci.formats.in.BDVReader
- close(boolean) - Method in class loci.formats.in.BioRadReader
- close(boolean) - Method in class loci.formats.in.BioRadSCNReader
- close(boolean) - Method in class loci.formats.in.BMPReader
- close(boolean) - Method in class loci.formats.in.BrukerReader
- close(boolean) - Method in class loci.formats.in.BurleighReader
- close(boolean) - Method in class loci.formats.in.CanonRawReader
- close(boolean) - Method in class loci.formats.in.CellH5Reader
- close(boolean) - Method in class loci.formats.in.CellomicsReader
- close(boolean) - Method in class loci.formats.in.CellSensReader
- close(boolean) - Method in class loci.formats.in.CellWorxReader
- close(boolean) - Method in class loci.formats.in.ColumbusReader
- close(boolean) - Method in class loci.formats.in.CV7000Reader
- close(boolean) - Method in class loci.formats.in.DCIMGReader
- close(boolean) - Method in class loci.formats.in.DeltavisionReader
- close(boolean) - Method in class loci.formats.in.DicomReader
- close(boolean) - Method in class loci.formats.in.DNGReader
- close(boolean) - Method in class loci.formats.in.EPSReader
- close(boolean) - Method in class loci.formats.in.FakeReader
- close(boolean) - Method in class loci.formats.in.FEIReader
- close(boolean) - Method in class loci.formats.in.FEITiffReader
- close(boolean) - Method in class loci.formats.in.FitsReader
- close(boolean) - Method in class loci.formats.in.FlexReader
- close(boolean) - Method in class loci.formats.in.FlowSightReader
- close(boolean) - Method in class loci.formats.in.FluoviewReader
- close(boolean) - Method in class loci.formats.in.FujiReader
- close(boolean) - Method in class loci.formats.in.FV1000Reader
- close(boolean) - Method in class loci.formats.in.GatanDM2Reader
- close(boolean) - Method in class loci.formats.in.GatanReader
- close(boolean) - Method in class loci.formats.in.GIFReader
- close(boolean) - Method in class loci.formats.in.HamamatsuVMSReader
- close(boolean) - Method in class loci.formats.in.HitachiReader
- close(boolean) - Method in class loci.formats.in.HRDGDFReader
- close(boolean) - Method in class loci.formats.in.ICSReader
- close(boolean) - Method in class loci.formats.in.IM3Reader
- close(boolean) - Method in class loci.formats.in.ImaconReader
- close(boolean) - Method in class loci.formats.in.ImageIOReader
- close(boolean) - Method in class loci.formats.in.ImagicReader
- close(boolean) - Method in class loci.formats.in.ImarisHDFReader
- close(boolean) - Method in class loci.formats.in.ImarisReader
- close(boolean) - Method in class loci.formats.in.IMODReader
- close(boolean) - Method in class loci.formats.in.ImprovisionTiffReader
- close(boolean) - Method in class loci.formats.in.ImspectorReader
- close(boolean) - Method in class loci.formats.in.InCell3000Reader
- close(boolean) - Method in class loci.formats.in.InCellReader
- close(boolean) - Method in class loci.formats.in.InveonReader
- close(boolean) - Method in class loci.formats.in.IonpathMIBITiffReader
- close(boolean) - Method in class loci.formats.in.IPLabReader
- close(boolean) - Method in class loci.formats.in.IPWReader
- close(boolean) - Method in class loci.formats.in.IvisionReader
- close(boolean) - Method in class loci.formats.in.JDCEReader
- close(boolean) - Method in class loci.formats.in.JEOLReader
- close(boolean) - Method in class loci.formats.in.JPEG2000Reader
- close(boolean) - Method in class loci.formats.in.JPEGReader
- close(boolean) - Method in class loci.formats.in.JPXReader
- close(boolean) - Method in class loci.formats.in.KhorosReader
- close(boolean) - Method in class loci.formats.in.KLBReader
- close(boolean) - Method in class loci.formats.in.KodakReader
- close(boolean) - Method in class loci.formats.in.L2DReader
- close(boolean) - Method in class loci.formats.in.LeicaMicrosystemsMetadata.LMSFileReader
- close(boolean) - Method in class loci.formats.in.LeicaMicrosystemsMetadata.MultipleImagesReader
- close(boolean) - Method in class loci.formats.in.LeicaReader
- close(boolean) - Method in class loci.formats.in.LeicaSCNReader
- close(boolean) - Method in class loci.formats.in.LiFlimReader
- close(boolean) - Method in class loci.formats.in.LIFReader
- close(boolean) - Method in class loci.formats.in.LIMReader
- close(boolean) - Method in class loci.formats.in.LOFReader
- close(boolean) - Method in class loci.formats.in.MetamorphReader
- close(boolean) - Method in class loci.formats.in.MetamorphTiffReader
- close(boolean) - Method in class loci.formats.in.MIASReader
- close(boolean) - Method in class loci.formats.in.MicroCTReader
- close(boolean) - Method in class loci.formats.in.MicromanagerReader
- close(boolean) - Method in class loci.formats.in.MINCReader
- close(boolean) - Method in class loci.formats.in.MinimalTiffReader
- close(boolean) - Method in class loci.formats.in.MNGReader
- close(boolean) - Method in class loci.formats.in.MolecularImagingReader
- close(boolean) - Method in class loci.formats.in.MRCReader
- close(boolean) - Method in class loci.formats.in.MRWReader
- close(boolean) - Method in class loci.formats.in.NAFReader
- close(boolean) - Method in class loci.formats.in.ND2Reader
- close(boolean) - Method in class loci.formats.in.NDPIReader
- close(boolean) - Method in class loci.formats.in.NDPISReader
- close(boolean) - Method in class loci.formats.in.NiftiReader
- close(boolean) - Method in class loci.formats.in.NikonElementsTiffReader
- close(boolean) - Method in class loci.formats.in.NikonReader
- close(boolean) - Method in class loci.formats.in.NikonTiffReader
- close(boolean) - Method in class loci.formats.in.NRRDReader
- close(boolean) - Method in class loci.formats.in.OBFReader
- close(boolean) - Method in class loci.formats.in.OIRReader
- close(boolean) - Method in class loci.formats.in.OlympusTileReader
- close(boolean) - Method in class loci.formats.in.OMETiffReader
- close(boolean) - Method in class loci.formats.in.OMEXMLReader
- close(boolean) - Method in class loci.formats.in.OpenlabRawReader
- close(boolean) - Method in class loci.formats.in.OpenlabReader
- close(boolean) - Method in class loci.formats.in.OperettaReader
- close(boolean) - Method in class loci.formats.in.PCIReader
- close(boolean) - Method in class loci.formats.in.PCORAWReader
- close(boolean) - Method in class loci.formats.in.PCXReader
- close(boolean) - Method in class loci.formats.in.PDSReader
- close(boolean) - Method in class loci.formats.in.PerkinElmerReader
- close(boolean) - Method in class loci.formats.in.PGMReader
- close(boolean) - Method in class loci.formats.in.PhotoshopTiffReader
- close(boolean) - Method in class loci.formats.in.PictReader
- close(boolean) - Method in class loci.formats.in.PQBinReader
- close(boolean) - Method in class loci.formats.in.PrairieReader
- close(boolean) - Method in class loci.formats.in.PSDReader
- close(boolean) - Method in class loci.formats.in.QTReader
- close(boolean) - Method in class loci.formats.in.QuesantReader
- close(boolean) - Method in class loci.formats.in.RHKReader
- close(boolean) - Method in class loci.formats.in.SBIGReader
- close(boolean) - Method in class loci.formats.in.ScanrReader
- close(boolean) - Method in class loci.formats.in.SDTReader
- close(boolean) - Method in class loci.formats.in.SEQReader
- close(boolean) - Method in class loci.formats.in.SIFReader
- close(boolean) - Method in class loci.formats.in.SimplePCITiffReader
- close(boolean) - Method in class loci.formats.in.SISReader
- close(boolean) - Method in class loci.formats.in.SlideBook7Reader
- close(boolean) - Method in class loci.formats.in.SlidebookReader
- close(boolean) - Method in class loci.formats.in.SlidebookTiffReader
- close(boolean) - Method in class loci.formats.in.SPCReader
- close(boolean) - Method in class loci.formats.in.SPEReader
- close(boolean) - Method in class loci.formats.in.SpiderReader
- close(boolean) - Method in class loci.formats.in.SVSReader
- close(boolean) - Method in class loci.formats.in.TargaReader
- close(boolean) - Method in class loci.formats.in.TCSReader
- close(boolean) - Method in class loci.formats.in.TecanReader
- close(boolean) - Method in class loci.formats.in.TextReader
- close(boolean) - Method in class loci.formats.in.TiffReader
- close(boolean) - Method in class loci.formats.in.TileJPEGReader
- close(boolean) - Method in class loci.formats.in.TillVisionReader
- close(boolean) - Method in class loci.formats.in.TissueFAXSReader
- close(boolean) - Method in class loci.formats.in.TopometrixReader
- close(boolean) - Method in class loci.formats.in.TrestleReader
- close(boolean) - Method in class loci.formats.in.UBMReader
- close(boolean) - Method in class loci.formats.in.UnisokuReader
- close(boolean) - Method in class loci.formats.in.VarianFDFReader
- close(boolean) - Method in class loci.formats.in.VectraReader
- close(boolean) - Method in class loci.formats.in.VeecoReader
- close(boolean) - Method in class loci.formats.in.VentanaReader
- close(boolean) - Method in class loci.formats.in.VisitechReader
- close(boolean) - Method in class loci.formats.in.VolocityClippingReader
- close(boolean) - Method in class loci.formats.in.VolocityReader
- close(boolean) - Method in class loci.formats.in.XLEFReader
- close(boolean) - Method in class loci.formats.in.ZeissCZIReader
- close(boolean) - Method in class loci.formats.in.ZeissLMSReader
- close(boolean) - Method in class loci.formats.in.ZeissLSMReader
- close(boolean) - Method in class loci.formats.in.ZeissTIFFReader
- close(boolean) - Method in class loci.formats.in.ZeissXRMReader
- close(boolean) - Method in class loci.formats.in.ZeissZVIReader
- close(boolean) - Method in class loci.formats.in.ZipReader
- close(boolean) - Method in class loci.formats.Memoizer
- close(boolean) - Method in class loci.formats.MinMaxCalculator
- close(boolean) - Method in class loci.formats.ReaderWrapper
- close(boolean) - Method in class loci.formats.SubResolutionFormatReader
- close(boolean) - Method in class loci.formats.WrappedReader
- CLOSED_ARROW - Static variable in class loci.formats.in.ZeissLSMReader
- CLOSED_BEZIER - Static variable in class loci.formats.in.ZeissLSMReader
- CLOSED_POLYLINE - Static variable in class loci.formats.in.ZeissLSMReader
- CloseFile() - Method in class loci.formats.in.SlideBook7Reader.DataLoader
- closeFileOnly() - Method in class loci.plugins.macro.LociFunctions
- cm - Variable in class loci.formats.FormatWriter
-
Default color model.
- CMainViewRecord70() - Constructor for class loci.formats.in.SlideBook7Reader.CMainViewRecord70
- CMaskPositions() - Constructor for class loci.formats.in.SlideBook7Reader.CImageGroup.CMaskPositions
- CMaskRecord70() - Constructor for class loci.formats.in.SlideBook7Reader.CMaskRecord70
- CMYK - Enum constant in enum class loci.formats.tiff.PhotoInterp
- cNames - Variable in class loci.formats.in.ImprovisionTiffReader
- CNpyHeader() - Constructor for class loci.formats.in.SlideBook7Reader.CNpyHeader
- co2Percent - Variable in class loci.formats.in.ZeissCZIReader
- COARSE_FRAME_IFD - Static variable in class loci.formats.in.CellSensReader
- COARSE_PYRAMID_LEVEL - Static variable in class loci.formats.in.CellSensReader
- COC - Enum constant in enum class loci.formats.codec.JPEG2000SegmentMarker
- COD - Enum constant in enum class loci.formats.codec.JPEG2000SegmentMarker
- code - Variable in enum class loci.formats.codec.CompressionType
-
Code for the compression.
- code - Variable in enum class loci.formats.codec.JPEG2000BoxType
-
Code for the box type.
- code - Variable in enum class loci.formats.codec.JPEG2000SegmentMarker
-
Code for the segment marker.
- code - Variable in enum class loci.formats.dicom.DicomVR
- code - Variable in class loci.formats.in.FV1000Reader
- code - Variable in enum class loci.formats.tiff.IFDType
-
Code for the IFD type in the actual TIFF file.
- code - Variable in enum class loci.formats.tiff.PhotoInterp
-
Code for the IFD type in the actual TIFF file.
- code - Variable in enum class loci.formats.tiff.TiffCompression
-
Code for the TIFF compression in the actual TIFF file.
- CODE_MEANING - Enum constant in enum class loci.formats.dicom.DicomAttribute
- CODE_VALUE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- codeBlockSize - Variable in class loci.formats.codec.JPEG2000CodecOptions
-
The maximum code-block size to use per tile-component as it would be provided to:
J2KImageWriteParam.setCodeBlockSize(int[])(WRITE). - codec - Variable in class loci.formats.codec.WrappedCodec
- codec - Variable in class loci.formats.gui.DataConverter
- codec - Variable in class loci.formats.in.ND2Reader
-
Codec to use when decompressing pixel data.
- codec - Variable in class loci.formats.in.QTReader
-
Video codec used by this movie.
- codec - Variable in class loci.formats.out.QTWriter
-
The codec to use.
- codec - Variable in enum class loci.formats.tiff.TiffCompression
-
TIFF compression codec.
- Codec - Interface in loci.formats.codec
-
This class is an interface for any kind of compression or decompression.
- CODEC_ANIMATION - Static variable in class loci.formats.out.QTWriter
-
Value indicating Animation codec.
- CODEC_CINEPAK - Static variable in class loci.formats.out.QTWriter
-
Value indicating Cinepak codec.
- CODEC_H_263 - Static variable in class loci.formats.out.QTWriter
-
Value indicating H.263 codec.
- CODEC_MOTION_JPEG_B - Static variable in class loci.formats.out.QTWriter
-
Value indicating Motion JPEG-B codec.
- CODEC_MPEG_4 - Static variable in class loci.formats.out.QTWriter
-
Value indicating MPEG-4 codec.
- CODEC_RAW - Static variable in class loci.formats.out.QTWriter
-
Value indicating Raw codec.
- CODEC_SORENSON - Static variable in class loci.formats.out.QTWriter
-
Value indicating Sorenson codec.
- CODEC_SORENSON_3 - Static variable in class loci.formats.out.QTWriter
-
Value indicating Sorenson 3 codec.
- codecName - Variable in enum class loci.formats.tiff.TiffCompression
-
Name of the TIFF compression codec.
- codecOptions - Variable in class loci.formats.tiff.TiffParser
-
Codec options to be used when decoding compressed pixel data.
- CodecOptions - Class in loci.formats.codec
-
Options for compressing and decompressing data.
- CodecOptions() - Constructor for class loci.formats.codec.CodecOptions
-
Construct a new CodecOptions.
- CodecOptions(CodecOptions) - Constructor for class loci.formats.codec.CodecOptions
-
Construct a new CodecOptions using the given CodecOptions.
- codestreamOffset - Variable in class loci.formats.in.JPEG2000MetadataParser
-
Offset to first contiguous codestream.
- codestreamPixelType - Variable in class loci.formats.in.JPEG2000MetadataParser
-
Pixel type as specified in the JPEG 2000 codestream..
- codestreamSizeC - Variable in class loci.formats.in.JPEG2000MetadataParser
-
Number of channels the image as specified in the JPEG 2000 codestream.
- codestreamSizeX - Variable in class loci.formats.in.JPEG2000MetadataParser
-
Width of the image as specified in the JPEG 2000 codestream.
- codestreamSizeY - Variable in class loci.formats.in.JPEG2000MetadataParser
-
Height of the image as specified in the JPEG 2000 codestream.
- CODING_SCHEME_DESIGNATOR - Enum constant in enum class loci.formats.dicom.DicomAttribute
- CODING_SCHEME_EXTERNAL_ID - Enum constant in enum class loci.formats.dicom.DicomAttribute
- CODING_SCHEME_ID - Enum constant in enum class loci.formats.dicom.DicomAttribute
- CODING_SCHEME_NAME - Enum constant in enum class loci.formats.dicom.DicomAttribute
- CODING_SCHEME_REGISTRY - Enum constant in enum class loci.formats.dicom.DicomAttribute
- CODING_SCHEME_UID - Enum constant in enum class loci.formats.dicom.DicomAttribute
- CODING_SCHEME_VERSION - Enum constant in enum class loci.formats.dicom.DicomAttribute
- cOffset - Variable in class loci.formats.out.DicomWriter.PlaneOffset
- col - Variable in class loci.formats.in.CellomicsReader.ChannelFile
- col - Variable in class loci.formats.in.CellVoyagerReader.WellInfo
- col - Variable in class loci.formats.in.ColumbusReader.Plane
- col - Variable in class loci.formats.in.OperettaReader.Plane
- col - Variable in class loci.formats.in.ZeissCZIReader.SubBlock
- colCount - Variable in class loci.formats.in.BaseZeissReader
- collection - Variable in class loci.formats.in.LeicaHandler
- collection - Variable in class loci.formats.in.LeicaSCNReader.LeicaSCNHandler
- COLLECTION_VOLUME - Static variable in class loci.formats.in.CellSensReader
- COLLIMATOR_GRID_NAME - Enum constant in enum class loci.formats.dicom.DicomAttribute
- COLLIMATOR_LEFT_VERTICAL_EDGE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- COLLIMATOR_LOWER_HORIZONTAL_EDGE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- COLLIMATOR_RIGHT_VERTICAL_EDGE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- COLLIMATOR_SHAPE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- COLLIMATOR_TYPE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- COLLIMATOR_UPPER_HORIZONTAL_EDGE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- colName - Variable in class loci.formats.in.InCellReader
- color - Variable in class loci.formats.in.CellVoyagerReader.ChannelInfo
- color - Variable in class loci.formats.in.CV7000Reader.Channel
- color - Variable in class loci.formats.in.LeicaHandler.ROI
- color - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.ROI
- color - Variable in class loci.formats.in.LIFReader.ROI
- color - Variable in class loci.formats.in.OIRReader.Channel
- color - Variable in class loci.formats.in.TissueFAXSReader.Channel
- color - Variable in class loci.formats.in.ZeissCZIReader.Channel
- COLOR_BAR - Static variable in class loci.formats.in.FV1000Reader
- COLOR_MAP - Static variable in class loci.formats.in.CanonRawReader
- COLOR_MAP - Static variable in class loci.formats.in.DNGReader
- COLOR_MAP - Static variable in class loci.formats.in.NikonReader
- COLOR_MAP - Static variable in class loci.formats.tiff.IFD
- COLOR_MAP_1 - Static variable in class loci.formats.in.MRWReader
- COLOR_MAP_2 - Static variable in class loci.formats.in.MRWReader
- COLOR_MODE - Static variable in class loci.formats.in.NikonReader
- COLOR_MODE_COLORIZED - Static variable in class loci.plugins.in.ImporterOptions
- COLOR_MODE_COMPOSITE - Static variable in class loci.plugins.in.ImporterOptions
- COLOR_MODE_CUSTOM - Static variable in class loci.plugins.in.ImporterOptions
- COLOR_MODE_DEFAULT - Static variable in class loci.plugins.in.ImporterOptions
- COLOR_MODE_GRAYSCALE - Static variable in class loci.plugins.in.ImporterOptions
- COLOR_SPACE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- COLOR_SPACE - Static variable in class loci.formats.in.CellSensReader
- COLOR_SPACE - Static variable in class loci.formats.tiff.IFD
- color16 - Variable in class loci.formats.in.IvisionReader
- ColorDialog - Class in loci.plugins.in
-
Bio-Formats Importer custom color chooser dialog box.
- ColorDialog(ImportProcess) - Constructor for class loci.plugins.in.ColorDialog
- colorize - Variable in class loci.plugins.util.BFVirtualStack
- Colorizer - Class in loci.plugins.in
-
Logic for colorizing images.
- Colorizer(ImportProcess) - Constructor for class loci.plugins.in.Colorizer
- colorMap - Variable in class loci.formats.in.TargaReader
- colorModeChoice - Variable in class loci.plugins.in.MainDialog
- colorModel - Variable in class loci.formats.codec.CodecOptions
-
Color model to use when constructing an image (WRITE).
- colors - Variable in class loci.formats.in.ImarisHDFReader
- colors - Variable in class loci.formats.in.IMODReader
- colors - Variable in class loci.formats.in.ND2Handler
- colors - Variable in class loci.formats.in.ND2Reader
- COLORS - Enum constant in enum class loci.plugins.in.ImportStep
- COLORS - Variable in class loci.formats.in.BDVReader
- COLORS - Variable in class loci.formats.in.CellH5Reader
- COLORSPACE - Static variable in class loci.formats.in.CellSensReader
- colorTables - Variable in class loci.formats.in.GIFReader
- COLOUR_SPECIFICATION - Enum constant in enum class loci.formats.codec.JPEG2000BoxType
- cols - Variable in class loci.formats.in.CellSensReader
- colT - Variable in class loci.formats.in.SDTInfo
- ColumbusReader - Class in loci.formats.in
-
ColumbusReader is the file format reader for screens exported from PerkinElmer Columbus.
- ColumbusReader() - Constructor for class loci.formats.in.ColumbusReader
-
Constructs a new Columbus reader.
- ColumbusReader.MeasurementHandler - Class in loci.formats.in
- ColumbusReader.Plane - Class in loci.formats.in
- column - Variable in class loci.formats.in.CV7000Reader.Field
- column - Variable in class loci.formats.in.FlexReader.FlexFile
- column - Variable in class loci.formats.in.OMEXMLReader.BinData
- column - Variable in class loci.formats.tools.AmiraParameters
- COLUMN_ANGULATION - Enum constant in enum class loci.formats.dicom.DicomAttribute
- COLUMN_POSITION_IN_MATRIX - Enum constant in enum class loci.formats.dicom.DicomAttribute
- columnIndex - Variable in class loci.formats.internal.WellContainer
- COLUMNS - Enum constant in enum class loci.formats.dicom.DicomAttribute
- COLUMNS - Static variable in class loci.formats.gui.DataConverter
- COM - Enum constant in enum class loci.formats.codec.JPEG2000SegmentMarker
- ComboFileFilter - Class in loci.formats.gui
-
A file filter that recognizes files from a union of other filters.
- ComboFileFilter(FileFilter[], String) - Constructor for class loci.formats.gui.ComboFileFilter
-
Constructs a new filter from a list of other filters.
- comment - Variable in class loci.formats.in.FluoviewReader
- comment - Variable in class loci.formats.in.MicromanagerReader.Position
- comment - Variable in class loci.formats.in.QuesantReader
- comment - Variable in class loci.formats.in.SVSCoreMetadata
- COMMENT_STYLE_END - Static variable in class loci.formats.gui.XMLCellRenderer
- COMMENT_STYLE_START - Static variable in class loci.formats.gui.XMLCellRenderer
- comments - Variable in class loci.formats.in.JPEG2000MetadataParser
-
List of comments stored in the file.
- comments - Variable in class loci.formats.in.SVSReader
- COMMENTS - Enum constant in enum class loci.formats.in.SPEReader.SpeHeaderEntry
- comp - Variable in class loci.formats.gui.CacheIndicator
- COMPANION_KEY - Static variable in class loci.formats.out.OMETiffWriter
- COMPANION_SUFFIXES - Static variable in class loci.formats.in.TiffReader
- companionFile - Variable in class loci.formats.in.TiffReader
- companionFiles - Variable in class loci.formats.in.DCIMGReader
- companionFiles - Variable in class loci.formats.in.DicomReader
- comparator - Static variable in class loci.formats.CoreMetadataList
- compare(File, File) - Method in class loci.formats.in.XLEFReader.PathComparator
- compare(Object, Object) - Method in class loci.formats.cache.CacheStrategy
-
Default comparator orders dimensional positions based on distance from the current position, taking into account axis priorities and planar ordering.
- compare(String, String) - Method in class loci.formats.in.MetamorphTiffReader.NumericComparator
- compareTo(Object) - Method in class loci.formats.gui.ComboFileFilter
-
Compares two FileFilter objects alphanumerically.
- compareTo(Object) - Method in class loci.formats.gui.ExtensionFileFilter
-
Compares two FileFilter objects alphanumerically.
- compareTo(Object) - Method in class loci.formats.gui.FormatFileFilter
-
Compares two FileFilter objects alphanumerically.
- compareTo(Object) - Method in class loci.formats.gui.NoExtensionFileFilter
-
Compares two FileFilter objects alphanumerically.
- compareTo(Object) - Method in class loci.formats.tiff.TiffIFDEntry
- compareTo(Object) - Method in class loci.plugins.config.FormatEntry
- compareTo(Object) - Method in class loci.plugins.config.LibraryEntry
- compareTo(DicomFileInfo) - Method in class loci.formats.dicom.DicomFileInfo
- compareTo(DicomTag) - Method in class loci.formats.dicom.DicomTag
- compareTo(OlympusTileReader.Tile) - Method in class loci.formats.in.OlympusTileReader.Tile
- compareTo(VentanaReader.Overlap) - Method in class loci.formats.in.VentanaReader.Overlap
- compareTo(WellContainer) - Method in class loci.formats.internal.WellContainer
- compareTo(TiffRational) - Method in class loci.formats.tiff.TiffRational
-
Compares this object with the specified object for order.
- compareTo(ThumbLoader.SeriesInfo) - Method in class loci.plugins.in.ThumbLoader.SeriesInfo
- compareTokens(String[], int, String[], int) - Method in class loci.formats.in.ICSReader
- COMPLETE - Enum constant in enum class loci.plugins.in.ImportStep
- COMPLEX - Static variable in class loci.formats.in.CellSensReader
- COMPLEX - Static variable in class loci.formats.in.ZeissCZIReader
- COMPLEX_FLOAT - Static variable in class loci.formats.in.ZeissCZIReader
- COMPLEX_IMAGE_COMPONENT - Enum constant in enum class loci.formats.dicom.DicomAttribute
- COMPONENT_HEIGHT - Static variable in class loci.formats.gui.CacheIndicator
- COMPONENT_MAPPING - Enum constant in enum class loci.formats.codec.JPEG2000BoxType
- COMPONENT_WIDTH - Static variable in class loci.formats.gui.CacheIndicator
- COMPONENTS_CONFIGURATION - Static variable in class loci.formats.tiff.IFD
- compress(byte[]) - Method in class loci.formats.out.OMEXMLWriter
-
Compress the given byte array using the current codec.
- compress(byte[][], CodecOptions) - Method in class loci.formats.codec.BaseCodec
-
2D data block encoding default implementation.
- compress(byte[][], CodecOptions) - Method in interface loci.formats.codec.Codec
-
Compresses a block of data.
- compress(byte[][], CodecOptions) - Method in class loci.formats.codec.WrappedCodec
- compress(byte[], int) - Method in class org.libjpegturbo.turbojpeg.TJCompressor
-
Compress the uncompressed source image associated with this compressor instance and output a JPEG image to the given destination buffer.
- compress(byte[], int, int, int, int, byte[], int, int, int) - Method in class org.libjpegturbo.turbojpeg.TJCompressor
- compress(byte[], CodecOptions) - Method in interface loci.formats.codec.Codec
-
Compresses a block of data.
- compress(byte[], CodecOptions) - Method in class loci.formats.codec.JPEGXRCodec
- compress(byte[], CodecOptions) - Method in class loci.formats.codec.NikonCodec
- compress(byte[], CodecOptions) - Method in class loci.formats.codec.TargaRLECodec
- compress(byte[], CodecOptions) - Method in class loci.formats.codec.WrappedCodec
- compress(byte[], CodecOptions) - Method in enum class loci.formats.tiff.TiffCompression
-
Encodes a strip of data.
- compress(int) - Method in class org.libjpegturbo.turbojpeg.TJCompressor
-
Compress the uncompressed source image associated with this compressor instance and return a buffer containing a JPEG image.
- compress(int[], int, int, int, int, byte[], int, int, int) - Method in class org.libjpegturbo.turbojpeg.TJCompressor
- compress(BufferedImage, byte[], int) - Method in class org.libjpegturbo.turbojpeg.TJCompressor
-
Compress the uncompressed source image stored in
srcImageand output a JPEG image to the given destination buffer. - compress(BufferedImage, int) - Method in class org.libjpegturbo.turbojpeg.TJCompressor
-
Compress the uncompressed source image stored in
srcImageand return a buffer containing a JPEG image. - compressBuffer(int, byte[], int, int, int, int) - Method in class loci.formats.out.JPEG2000Writer
-
Compresses the buffer.
- compressed - Variable in class loci.formats.in.NAFReader
- compressed - Variable in class loci.formats.in.OpenlabReader.PlaneInfo
- compressed - Variable in class loci.formats.in.PSDReader
- compressed - Variable in class loci.formats.in.SBIGReader
- compressed - Variable in class loci.formats.in.TargaReader
- COMPRESSED_BITS_PER_PIXEL - Static variable in class loci.formats.tiff.IFD
- compressedSize - Variable in class loci.formats.in.AmiraReader.HxRLE
- compressedSize - Variable in class loci.formats.in.AmiraReader.HxZip
- compressedSize - Variable in class org.libjpegturbo.turbojpeg.TJCompressor
- compression - Variable in enum class loci.formats.codec.CompressionType
-
The compression used.
- compression - Variable in class loci.formats.FormatWriter
-
Current compression type.
- compression - Variable in class loci.formats.in.AmiraReader
- compression - Variable in class loci.formats.in.APNGReader
- compression - Variable in class loci.formats.in.BMPReader
-
Compression type
- compression - Variable in class loci.formats.in.LiFlimReader
- compression - Variable in class loci.formats.in.OBFReader.Stack
- compression - Variable in class loci.formats.in.OMEXMLReader
- compression - Variable in class loci.formats.in.PhotoshopTiffReader
- compression - Variable in class loci.formats.in.ZeissCZIReader.DirectoryEntry
- COMPRESSION - Static variable in class loci.formats.tiff.IFD
- COMPRESSION_BZIP2 - Static variable in class loci.formats.in.KLBReader
- COMPRESSION_FORCE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- COMPRESSION_GZIP - Static variable in class loci.formats.in.LiFlimReader
- COMPRESSION_J2K - Static variable in class loci.formats.out.TiffWriter
- COMPRESSION_J2K_LOSSY - Static variable in class loci.formats.out.TiffWriter
- COMPRESSION_JPEG - Static variable in class loci.formats.out.TiffWriter
- COMPRESSION_KEY - Static variable in class loci.formats.in.LiFlimReader
- COMPRESSION_LZW - Static variable in class loci.formats.out.TiffWriter
- COMPRESSION_NONE - Static variable in class loci.formats.in.KLBReader
- COMPRESSION_NONE - Static variable in class loci.formats.in.LiFlimReader
- COMPRESSION_SUFFIXES - Static variable in class loci.formats.FormatHandler
-
Suffixes for supported compression types.
- COMPRESSION_UNCOMPRESSED - Static variable in class loci.formats.out.TiffWriter
- COMPRESSION_ZLIB - Static variable in class loci.formats.in.KLBReader
- COMPRESSION_ZLIB - Static variable in class loci.formats.out.TiffWriter
- compressionMethodPointer - Variable in class loci.formats.out.DicomWriter
- compressionType - Variable in class loci.formats.in.CellSensReader
- compressionType - Variable in class loci.formats.in.KLBReader
- CompressionType - Enum Class in loci.formats.codec
-
An enumeration of compression types.
- CompressionType(int, String) - Constructor for enum class loci.formats.codec.CompressionType
-
Default constructor.
- compressionTypes - Variable in class loci.formats.FormatWriter
-
Available compression types.
- computeAxisLengths() - Method in class loci.formats.FileStitcher
-
Computes axis length arrays, and total axis lengths.
- computeIndices(int) - Method in class loci.formats.FileStitcher
-
Gets the file index, and image index into that file, corresponding to the given global image index.
- computeNameAndLocation() - Method in class loci.plugins.in.ImportProcess
-
Initializes the idName and idLoc derived values.
- computePhysicalSize(int, String, String) - Method in class loci.formats.in.VarianFDFReader
-
Return the physical size of a pixel, in microns, along an arbitrary axis based on the supplied physical and pixel lengths of the axis.
- computeSeriesLabels(IFormatReader) - Method in class loci.plugins.in.ImportProcess
- computeSizeT(int) - Method in class loci.formats.in.PrairieReader
-
Scans the parsed metadata to determine the number of actual time points versus the number of actual stage positions.
- computeVariableTimeInterval(IMetadata, int) - Method in class loci.plugins.in.Calibrator
- concatenate(List<ImagePlus>) - Method in class loci.plugins.in.Concatenator
-
Concatenates the list of images as appropriate.
- concatenate(List<ImagePlus>) - Method in class loci.plugins.in.ImagePlusReader
- concatenateBox - Variable in class loci.plugins.in.MainDialog
- concatenateTokens(String[], int, int) - Method in class loci.formats.in.ICSReader
- CONCATENATION_FRAME_OFFSET_NUMBER - Enum constant in enum class loci.formats.dicom.DicomAttribute
- concatenationIndex - Variable in class loci.formats.dicom.DicomFileInfo
- concatenationNumber - Variable in class loci.formats.in.DicomReader
- Concatenator - Class in loci.plugins.in
-
Logic for concatenating multiple images together.
- Concatenator() - Constructor for class loci.plugins.in.Concatenator
- CONDENSER_LENS_POWER - Enum constant in enum class loci.formats.dicom.DicomAttribute
- confidence - Variable in class loci.formats.in.VentanaReader.Overlap
- config - Variable in class loci.formats.in.PrairieMetadata
-
Key/value pairs from CFG and/or ENV files.
- ConfigWindow - Class in loci.plugins.config
-
A window for managing configuration of the Bio-Formats plugins.
- ConfigWindow() - Constructor for class loci.plugins.config.ConfigWindow
- constructDialog() - Method in class loci.plugins.in.ColorDialog
- constructDialog() - Method in class loci.plugins.in.CropDialog
- constructDialog() - Method in class loci.plugins.in.FilePatternDialog
- constructDialog() - Method in class loci.plugins.in.IdDialog
- constructDialog() - Method in class loci.plugins.in.ImporterDialog
- constructDialog() - Method in class loci.plugins.in.LocationDialog
- constructDialog() - Method in class loci.plugins.in.MainDialog
- constructDialog() - Method in class loci.plugins.in.MemoryDialog
- constructDialog() - Method in class loci.plugins.in.RangeDialog
- constructDialog() - Method in class loci.plugins.in.SeriesDialog
- constructDialog() - Method in class loci.plugins.in.SwapDialog
- constructDialog() - Method in class loci.plugins.in.UpgradeDialog
- constructImage(int, int, int, int, boolean, boolean, DataBuffer) - Static method in class loci.formats.gui.AWTImageTools
-
Creates an image with the given DataBuffer.
- constructImage(int, int, int, int, boolean, boolean, DataBuffer, ColorModel) - Static method in class loci.formats.gui.AWTImageTools
-
Creates an image with the given DataBuffer.
- constructImageTitle(IFormatReader, String, String, boolean) - Method in class loci.plugins.in.ImagePlusReader
- constructSliceLabel(int, IFormatReader, IMetadata, int, int, int, int) - Method in class loci.plugins.in.ImagePlusReader
- CONT_CLEAN - Enum constant in enum class loci.formats.in.SPEReader.SpeHeaderEntry
- CONTAINER_ID - Enum constant in enum class loci.formats.dicom.DicomAttribute
- CONTAINER_ID_ISSUER_SEQUENCE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- CONTAINER_TYPE_CODE_SEQUENCE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- CONTAINER_TYPES - Static variable in class loci.formats.in.QTReader
-
List of identifiers for each container atom.
- ContainerRecord(String, int, long, int) - Constructor for class loci.formats.in.IM3Reader.ContainerRecord
- CONTENT_DATE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- CONTENT_TIME - Enum constant in enum class loci.formats.dicom.DicomAttribute
- contentFileType - Variable in class loci.formats.in.ZeissCZIReader.AttachmentEntry
- contentGUID - Variable in class loci.formats.in.ZeissCZIReader.AttachmentEntry
- context - Variable in class loci.formats.in.BaseZeissReader.Tag
- Context() - Constructor for enum class loci.formats.in.BaseZeissReader.Context
- CONTEXT_GROUP_EXTENSION_CREATOR - Enum constant in enum class loci.formats.dicom.DicomAttribute
- CONTEXT_GROUP_EXTENSION_FLAG - Enum constant in enum class loci.formats.dicom.DicomAttribute
- CONTEXT_GROUP_LOCAL_VERSION - Enum constant in enum class loci.formats.dicom.DicomAttribute
- CONTEXT_GROUP_VERSION - Enum constant in enum class loci.formats.dicom.DicomAttribute
- CONTEXT_ID - Enum constant in enum class loci.formats.dicom.DicomAttribute
- CONTIGUOUS_CODESTREAM - Enum constant in enum class loci.formats.codec.JPEG2000BoxType
- CONTRAST - Static variable in class loci.formats.in.CellSensReader
- CONTRAST - Static variable in class loci.formats.tiff.IFD
- CONTRAST_ALLERGIES - Enum constant in enum class loci.formats.dicom.DicomAttribute
- CONTRAST_BOLUS_ADMIN_ROUTE_SEQUENCE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- CONTRAST_BOLUS_AGENT - Enum constant in enum class loci.formats.dicom.DicomAttribute
- CONTRAST_BOLUS_AGENT_SEQUENCE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- CONTRAST_BOLUS_INGREDIENT - Enum constant in enum class loci.formats.dicom.DicomAttribute
- CONTRAST_BOLUS_ROUTE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- CONTRAST_BOLUS_START_TIME - Enum constant in enum class loci.formats.dicom.DicomAttribute
- CONTRAST_BOLUS_STOP_TIME - Enum constant in enum class loci.formats.dicom.DicomAttribute
- CONTRAST_BOLUS_TOTAL_DOSE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- CONTRAST_BOLUS_VOLUME - Enum constant in enum class loci.formats.dicom.DicomAttribute
- CONTRAST_BRIGHTNESS - Static variable in class loci.formats.in.CellSensReader
- CONTRAST_FLOW_DURATION - Enum constant in enum class loci.formats.dicom.DicomAttribute
- CONTRAST_FLOW_RATE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- CONTRAST_FRAME_AVERAGING - Enum constant in enum class loci.formats.dicom.DicomAttribute
- CONTRAST_INGREDIENT_CONCENTRATION - Enum constant in enum class loci.formats.dicom.DicomAttribute
- CONTRAST_TARGET - Static variable in class loci.formats.in.CellSensReader
- CONTROLLER_NUM - Enum constant in enum class loci.formats.in.SPEReader.SpeHeaderEntry
- CONTROLLER_VER - Enum constant in enum class loci.formats.in.SPEReader.SpeHeaderEntry
- CONVERSION_TYPE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- convert - Variable in class loci.formats.gui.DataConverter
- convert(String, String) - Static method in class loci.formats.FormatTools
-
Convenience method for converting the specified input file to the specified output file.
- convert(IFormatReader, IFormatWriter, String) - Static method in class loci.formats.FormatTools
-
Convenience method for writing all of the images and metadata obtained from the specified IFormatReader into the specified IFormatWriter.
- convert12to16LSB(byte[]) - Static method in class loci.formats.in.LiFlimReader
- convert12to16MSB(byte[]) - Static method in class loci.formats.in.LiFlimReader
- convertMetadata(String, MetadataStore) - Method in interface loci.formats.services.OMEXMLService
-
Converts information from an OME-XML string (source) into a metadata store (destination).
- convertMetadata(String, MetadataStore) - Method in class loci.formats.services.OMEXMLServiceImpl
- convertMetadata(MetadataRetrieve, MetadataStore) - Method in interface loci.formats.services.OMEXMLService
-
Copies information from a metadata retrieval object (source) into a metadata store (destination).
- convertMetadata(MetadataRetrieve, MetadataStore) - Method in class loci.formats.services.OMEXMLServiceImpl
- convertMetadata(OMEXMLMetadata, MetadataStore) - Method in class loci.formats.in.OMETiffReader
-
Convert metadata contained within an OMEXMLMetadata object to a separate MetadataStore.
- convertMetadata(MetadataRetrieve, MetadataStore) - Static method in class loci.formats.meta.MetadataConverter
-
Deprecated.Copies information from a metadata retrieval object (source) into a metadata store (destination).
- convertPixelType(int) - Method in class loci.formats.in.CellSensReader
- convertPixelType(int) - Method in class loci.formats.in.JPEG2000MetadataParser
- convertPixelType(int) - Method in class loci.formats.in.TillVisionReader
- convertPixelType(int) - Method in class loci.formats.in.ZeissCZIReader
- convertPixelType(CoreMetadata, int) - Method in class loci.formats.in.KLBReader
- convertPixelType(CoreMetadata, int) - Method in class loci.formats.in.ZeissCZIReader
- convertRenderedImage(RenderedImage) - Static method in class loci.formats.gui.AWTImageTools
-
Converts a java.awt.image.RenderedImage into a java.awt.image.BufferedImage.
- convertTo8Bit(short[][]) - Method in class loci.plugins.util.ImageProcessorReader
- convertToByte(boolean) - Method in class loci.plugins.util.RecordedImageProcessor
- convertToFloat() - Method in class loci.plugins.util.RecordedImageProcessor
- convertToLong(byte[], int) - Method in class loci.formats.in.SlideBook7Reader.CCompressionBase
- convertToRGB() - Method in class loci.plugins.util.RecordedImageProcessor
- convertToShort(boolean) - Method in class loci.plugins.util.RecordedImageProcessor
- convertUnits(int) - Method in class loci.formats.in.IMODReader
- convertUnits(String) - Method in class loci.formats.in.GatanReader
- CONVOLUTION_KERNEL - Enum constant in enum class loci.formats.dicom.DicomAttribute
- convolve(float[], int, int) - Method in class loci.plugins.util.RecordedImageProcessor
- convolve3x3(int[]) - Method in class loci.plugins.util.RecordedImageProcessor
- COOKIE - Static variable in class loci.formats.in.IM3Reader
-
First 4 bytes of file is "1985"
- COOLING_ON - Static variable in class loci.formats.in.CellSensReader
- coordinate - Variable in class loci.formats.in.CellSensReader.TileCoordinate
- Coordinate(int, int, int) - Constructor for class loci.formats.in.ZeissCZIReader.Coordinate
- coordinates - Variable in class loci.formats.in.BaseZeissReader
- COptovarDef70() - Constructor for class loci.formats.in.SlideBook7Reader.COptovarDef70
- copy(OperettaReader.Plane) - Method in class loci.formats.in.OperettaReader.Channel
-
Copy data from this Channel to the given Plane.
- copyBits(ImageProcessor, int, int, int) - Method in class loci.plugins.util.RecordedImageProcessor
- copyCorrectionImageToBuffer(TissueFAXSReader.ScanRegion, Region, int[], byte[]) - Method in class loci.formats.in.TissueFAXSReader
- copyOptions(CodecOptions, CodecOptions) - Static method in class loci.formats.codec.WrappedCodec
- copyPixelBlock(OIRReader.PixelBlock, byte[], int, int, int, int, int) - Method in class loci.formats.in.OIRReader
- copyPixels(int, int, int, int, int, int, byte[], byte[], boolean) - Method in class loci.formats.in.ND2Reader
- copyRegion(Region, byte[], Region, byte[], int) - Method in class loci.formats.in.TissueFAXSReader
- copyRegionToBuffer(TissueFAXSReader.ScanRegion, int, Region, int[], byte[]) - Method in class loci.formats.in.TissueFAXSReader
- COPYRIGHT - Static variable in class loci.formats.tiff.IFD
- copyScaled(BufferedImage, BufferedImage, Object) - Static method in class loci.formats.gui.AWTImageTools
-
Copies the source image into the target, applying scaling.
- copyTile(IFD, byte[], int, int) - Method in class loci.formats.in.MinimalTiffReader
- core - Variable in class loci.formats.DimensionSwapper
-
Core metadata associated with this dimension swapper.
- core - Variable in class loci.formats.FileStitcher
-
Core metadata.
- core - Variable in class loci.formats.FormatReader
-
Core metadata values.
- core - Variable in class loci.formats.in.LeicaHandler
- core - Variable in class loci.formats.in.ND2Handler
- core - Variable in class loci.formats.in.VolocityReader.Stack
- core - Variable in class loci.formats.SubResolutionFormatReader
-
List of
CoreMetadataobjects for each series and resolution. - coreIndex - Variable in class loci.formats.FileStitcher
-
The number of the current series.
- coreIndex - Variable in class loci.formats.FormatReader
-
The number of the current series.
- coreIndex - Variable in class loci.formats.in.ZeissCZIReader.SubBlock
- coreIndexToSeries(int) - Method in class loci.formats.FileStitcher
- coreIndexToSeries(int) - Method in class loci.formats.FormatReader
- coreIndexToSeries(int) - Method in interface loci.formats.IFormatReader
-
Deprecated.This method is no longer required for sub-resolution support.
- coreIndexToSeries(int) - Method in class loci.formats.ImageReader
- coreIndexToSeries(int) - Method in class loci.formats.ReaderWrapper
- coreIndexToSeries(int) - Method in class loci.formats.SubResolutionFormatReader
- coreIndexToSeries(int) - Method in class loci.formats.WrappedReader
- coreMetadata - Variable in class loci.formats.dicom.DicomFileInfo
- coreMetaData - Static variable in class loci.formats.in.SPEReader
- CoreMetadata - Class in loci.formats
-
Encompasses core metadata values.
- CoreMetadata() - Constructor for class loci.formats.CoreMetadata
- CoreMetadata(CoreMetadata) - Constructor for class loci.formats.CoreMetadata
- CoreMetadata(IFormatReader, int) - Constructor for class loci.formats.CoreMetadata
- CoreMetadataList - Class in loci.formats
- CoreMetadataList() - Constructor for class loci.formats.CoreMetadataList
- CoreMetadataList(int) - Constructor for class loci.formats.CoreMetadataList
-
Construct a list containing a specified number of primary elements.
- CoreMetadataList(int[]) - Constructor for class loci.formats.CoreMetadataList
-
Construct a list containing a specified number of primary and secondary elements.
- CoreMetadataList(int, int) - Constructor for class loci.formats.CoreMetadataList
-
Construct a list containing a specified number of primary elements and a fixed number of secondary elements.
- CoreMetadataList(List<CoreMetadata>) - Constructor for class loci.formats.CoreMetadataList
- CoreMetadataList(CoreMetadataList) - Constructor for class loci.formats.CoreMetadataList
- CORRECTED_IMAGE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- correction - Variable in class loci.formats.in.ND2Handler
- correction - Variable in class loci.formats.in.NikonTiffReader
- correction - Variable in class loci.formats.in.ZeissLSMReader.Recording
- correctionCollar - Variable in class loci.formats.in.ZeissCZIReader
- correctionFile - Variable in class loci.formats.in.CV7000Reader.Channel
- correctionImageCoreIndex - Variable in class loci.formats.in.TissueFAXSReader.ScanRegion
- correctionImageIDs - Variable in class loci.formats.in.TissueFAXSReader.ScanRegion
- corrections - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataTempBuffer
- corrections - Variable in class loci.formats.in.LIFReader
- correctUnits(Double, String) - Method in class loci.formats.in.ColumbusReader
-
Calculate value in micrometers based on input value and units.
- cortime - Variable in class loci.formats.in.SDTInfo
-
Correlation time [ms].
- COSMIC_APPLIED - Enum constant in enum class loci.formats.in.SPEReader.SpeHeaderEntry
- COSMIC_THRESHOLD - Enum constant in enum class loci.formats.in.SPEReader.SpeHeaderEntry
- COSMIC_TYPE - Enum constant in enum class loci.formats.in.SPEReader.SpeHeaderEntry
- count - Variable in class loci.formats.in.LeicaHandler
- count - Variable in class loci.formats.in.ZeissTIFFHandler.TagSet
- count() - Method in class loci.formats.in.LeicaSCNReader.LeicaSCNHandler
- COUNT_RATE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- COUNTER_CLOCKWISE - Static variable in class loci.formats.in.FluoviewReader
- CountImageDataFiles() - Method in class loci.formats.in.SlideBook7Reader.CImageGroup
- countImages() - Method in class loci.formats.in.BaseZeissReader
- countImages() - Method in class loci.formats.in.ZeissTIFFReader
- countImages() - Method in class loci.formats.in.ZeissZVIReader
- COUNTRY_OF_RESIDENCE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- COUNTS_ACCUMULATED - Enum constant in enum class loci.formats.dicom.DicomAttribute
- CRANIAL_THERMAL_INDEX - Enum constant in enum class loci.formats.dicom.DicomAttribute
- CRatioManipRecord70() - Constructor for class loci.formats.in.SlideBook7Reader.CRatioManipRecord70
- crc(byte[]) - Method in class loci.formats.out.APNGWriter
- crc(byte[], int, int) - Method in class loci.formats.out.APNGWriter
- create(Map<String, Object>) - Method in class loci.formats.filter.LZ4Filter.LZ4FilterProvider
- createAngle(Double, Unit<Angle>) - Static method in class loci.formats.FormatTools
- createAngle(Integer, Unit<Angle>) - Static method in class loci.formats.FormatTools
- createAngle(T, Unit<Angle>) - Static method in class loci.formats.FormatTools
- createBaseReader() - Method in class loci.plugins.in.ImportProcess
-
Initializes an
IFormatReaderaccording to the current configuration. - createChannelDimension(int, long) - Static method in class loci.formats.in.LeicaMicrosystemsMetadata.Dimension
- createChannelPriorities() - Static method in class loci.formats.in.LIFReader
- createCodec(boolean) - Method in class loci.formats.in.ND2Reader
- createColorModel() - Method in class loci.plugins.util.ImageProcessorReader
- createCompatibleWritableRaster(int, int) - Method in class loci.formats.gui.Index16ColorModel
- createCompatibleWritableRaster(int, int) - Method in class loci.formats.gui.SignedColorModel
- createCompatibleWritableRaster(int, int) - Method in class loci.formats.gui.UnsignedIntColorModel
- created - Variable in class loci.formats.out.QTWriter
-
Time the file was created.
- createElectricPotential(Double, Unit<ElectricPotential>) - Static method in class loci.formats.FormatTools
- createElectricPotential(Integer, Unit<ElectricPotential>) - Static method in class loci.formats.FormatTools
- createElectricPotential(T, Unit<ElectricPotential>) - Static method in class loci.formats.FormatTools
- createFileInfo() - Method in class loci.plugins.in.ImagePlusReader
- createFileInfo(String) - Method in class loci.formats.in.DicomReader
-
Construct a DicomFileInfo for the given file.
- createFrequency(Double, Unit<Frequency>) - Static method in class loci.formats.FormatTools
- createFrequency(Integer, Unit<Frequency>) - Static method in class loci.formats.FormatTools
- createFrequency(T, Unit<Frequency>) - Static method in class loci.formats.FormatTools
- createGroup(String) - Method in interface loci.formats.services.JHDFService
-
Writes an array as sub-slice into an existing HDF5 dataset
- createGroup(String) - Method in class loci.formats.services.JHDFServiceImpl
- createImage() - Method in class loci.plugins.util.RecordedImageProcessor
- createImage(String, ImageStack, List<LUT>) - Static method in class loci.plugins.in.ImagePlusReader
-
Creates an
ImagePlusfrom the given image stack. - createImage(String, List<ImageProcessor>) - Static method in class loci.plugins.in.ImagePlusReader
-
Creates an
ImagePlusfrom the given image processors. - createIndexMap(int) - Method in class loci.formats.in.FakeReader
-
Creates a mapping between indices and color values.
- createInputStream() - Method in class loci.formats.out.TiffWriter
- createKeys() - Static method in class loci.formats.in.ZeissLSMReader
- createLength(Double, Unit<Length>) - Static method in class loci.formats.FormatTools
- createLength(Integer, Unit<Length>) - Static method in class loci.formats.FormatTools
- createLength(T, Unit<Length>) - Static method in class loci.formats.FormatTools
- createLSID(String, int...) - Static method in class loci.formats.MetadataTools
-
Constructs an LSID, given the object type and indices.
- createMetadata(String, CoreMetadata) - Method in class loci.formats.tools.MakeTestOmeTiff
- createModulo(OMEXMLMetadata, Modulo, StructuredAnnotations, Image, int, int, int) - Method in class loci.formats.services.OMEXMLServiceImpl
-
Create a ModuloAlong* annotation corresponding to the given
Modulo. - createOMEXMLMetadata() - Static method in class loci.formats.MetadataTools
-
Creates an OME-XML metadata object using reflection, to avoid direct dependencies on the optional
loci.formats.omepackage. - createOMEXMLMetadata() - Method in interface loci.formats.services.OMEXMLService
-
Creates an OME-XML metadata object using reflection, to avoid direct dependencies on the optional
loci.formats.omepackage. - createOMEXMLMetadata() - Method in class loci.formats.services.OMEXMLServiceImpl
- createOMEXMLMetadata(String) - Method in interface loci.formats.services.OMEXMLService
-
Creates an OME-XML metadata object using reflection, to avoid direct dependencies on the optional
loci.formats.omepackage, wrapping a DOM representation of the given OME-XML string. - createOMEXMLMetadata(String) - Method in class loci.formats.services.OMEXMLServiceImpl
- createOMEXMLMetadata(String, String) - Method in interface loci.formats.services.OMEXMLService
-
Creates an OME-XML metadata object using reflection, to avoid direct dependencies on the optional
loci.formats.omepackage, wrapping a DOM representation of the given OME-XML string. - createOMEXMLMetadata(String, String) - Method in class loci.formats.services.OMEXMLServiceImpl
- createOMEXMLRoot(String) - Method in interface loci.formats.services.OMEXMLService
-
Constructs an OME root node.
- createOMEXMLRoot(String) - Method in class loci.formats.services.OMEXMLServiceImpl
- createOutputStream() - Method in class loci.formats.FormatWriter
-
Create an output stream for the current file path.
- createPlane(String, CoreMetadata, int) - Method in class loci.formats.tools.MakeTestOmeTiff
- createPower(Double, Unit<Power>) - Static method in class loci.formats.FormatTools
- createPower(Integer, Unit<Power>) - Static method in class loci.formats.FormatTools
- createPower(T, Unit<Power>) - Static method in class loci.formats.FormatTools
- createPressure(Double, Unit<Pressure>) - Static method in class loci.formats.FormatTools
- createPressure(Integer, Unit<Pressure>) - Static method in class loci.formats.FormatTools
- createPressure(T, Unit<Pressure>) - Static method in class loci.formats.FormatTools
- createProcessor(int, int) - Method in class loci.plugins.util.RecordedImageProcessor
- createROI(MetadataStore, int) - Method in class loci.formats.in.GatanReader
-
Create an empty ROI and link it to the Image.
- createRoot(String) - Method in class loci.formats.services.OMEXMLServiceImpl
-
Constructs an OME root node.
- createStack(List<ImageProcessor>, List<String>, List<LUT>) - Static method in class loci.plugins.in.ImagePlusReader
-
Creates an image stack from the given image processors.
- createSwatch(Color) - Method in class loci.plugins.in.ColorDialog
- createTemperature(Double, Unit<Temperature>) - Static method in class loci.formats.FormatTools
- createTemperature(Integer, Unit<Temperature>) - Static method in class loci.formats.FormatTools
- createTemperature(T, Unit<Temperature>) - Static method in class loci.formats.FormatTools
- createTiffSaver() - Method in class loci.formats.out.TiffWriter
- createTime(Double, Unit<Time>) - Static method in class loci.formats.FormatTools
- createTime(Integer, Unit<Time>) - Static method in class loci.formats.FormatTools
- createTime(T, Unit<Time>) - Static method in class loci.formats.FormatTools
- createVirtualStack(ImportProcess, int, List<LUT>) - Method in class loci.plugins.in.ImagePlusReader
- createWriter(String, CoreMetadata, String) - Method in class loci.formats.tools.MakeTestOmeTiff
- CREATION_DATE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- CREATION_TIME - Enum constant in enum class loci.formats.dicom.DicomAttribute
- CREATION_TIME - Static variable in class loci.formats.in.CellSensReader
- creationDate - Variable in class loci.formats.in.FV1000Reader
- creationDate - Variable in class loci.formats.in.ImaconReader
- creationDate - Variable in class loci.formats.in.InCellReader
- creationDate - Variable in class loci.formats.in.IvisionReader
- creationDate - Variable in class loci.formats.in.LeicaSCNReader.Image
- creationDate - Variable in class loci.formats.in.PCIReader
- CREATOR - Static variable in class loci.formats.FormatTools
-
Value to use when setting creator/software fields in exported files.
- CREATOR_KEY - Static variable in class loci.formats.out.OMETiffWriter
- CREATOR_KEY - Static variable in class loci.formats.out.OMEXMLWriter
- CREATOR_TAG - Static variable in class loci.formats.in.ImaconReader
- CREATOR_VERSION_UID - Enum constant in enum class loci.formats.dicom.DicomAttribute
- CRemapChannelLUT70() - Constructor for class loci.formats.in.SlideBook7Reader.CRemapChannelLUT70
- CRemapManipRecord70() - Constructor for class loci.formats.in.SlideBook7Reader.CRemapManipRecord70
- CRemapPoint() - Constructor for class loci.formats.in.SlideBook7Reader.CRemapPoint
- CRG - Enum constant in enum class loci.formats.codec.JPEG2000SegmentMarker
- crop() - Method in class loci.plugins.util.RecordedImageProcessor
- CROP - Enum constant in enum class loci.plugins.in.ImportStep
- cropBox - Variable in class loci.plugins.in.MainDialog
- CropDialog - Class in loci.plugins.in
-
Bio-Formats Importer crop options dialog box.
- CropDialog(ImportProcess) - Constructor for class loci.plugins.in.CropDialog
-
Creates a crop options dialog for the Bio-Formats Importer.
- cropRegion - Variable in class loci.plugins.in.ImporterOptions
- CROSS - Enum constant in enum class loci.formats.in.BaseZeissReader.FillStyle
- CROSS - Enum constant in enum class loci.formats.in.BaseZeissReader.PointStyle
- crossChan - Variable in class loci.formats.in.SDTInfo
-
Cross FCS routing channel number when chan = crossChan and mod == crossMod - Auto FCS otherwise - Cross FCS.
- CROSSHAIR - Enum constant in enum class loci.formats.in.BaseZeissReader.PointStyle
- CrosshairStrategy - Class in loci.formats.cache
-
A crosshair strategy caches planes extending from the the current dimensional position along each individual axis, but not combinations of axes.
- CrosshairStrategy(int[]) - Constructor for class loci.formats.cache.CrosshairStrategy
-
Constructs a crosshair strategy.
- crossMod - Variable in class loci.formats.in.SDTInfo
-
Cross FCS module number.
- crossMtResol - Variable in class loci.formats.in.SDTInfo
-
Macro time clock of cross FCS module in 0.1 ns units.
- CS - Enum constant in enum class loci.formats.dicom.DicomVR
- CS_2C - Static variable in class loci.formats.gui.TwoChannelColorSpace
- CSBFile70(String) - Constructor for class loci.formats.in.SlideBook7Reader.CSBFile70
- CSBPoint() - Constructor for class loci.formats.in.SlideBook7Reader.CSBPoint
- cScroll - Variable in class loci.plugins.util.DataBrowser
- cSlider - Variable in class loci.formats.gui.ImageViewer
- CSlideRecord70() - Constructor for class loci.formats.in.SlideBook7Reader.CSlideRecord70
- cSliders - Variable in class loci.plugins.util.DataBrowser
- cStep - Variable in class loci.plugins.in.ImporterOptions
- CSV_SUFFIX - Static variable in class loci.formats.in.PerkinElmerReader
- CUnknownAnnotation70() - Constructor for class loci.formats.in.SlideBook7Reader.CUnknownAnnotation70
- curCycle - Variable in class loci.formats.in.SDTInfo
-
Current cycle (accumulation cycle in FLOW mode) - (if multi-cycle measurement).
- curPage - Variable in class loci.formats.in.SDTInfo
-
Current measured page.
- current - Variable in class loci.formats.ImageReader
-
Current form index.
- current - Variable in class loci.formats.ImageWriter
-
Current form index.
- current - Variable in class loci.formats.in.ZeissXRMReader
- current_layer - Variable in class loci.formats.in.ZeissTIFFHandler
- current_scaling - Variable in class loci.formats.in.ZeissTIFFHandler
- current_shape - Variable in class loci.formats.in.ZeissTIFFHandler
- current_tag - Variable in class loci.formats.in.ZeissTIFFHandler
- current_tagset - Variable in class loci.formats.in.ZeissTIFFHandler
- currentBlock - Variable in class loci.formats.in.APNGReader.PNGInputStream
- currentBlock - Variable in class loci.formats.in.PQBinReader
-
Block of time bins currently stored for faster loading.
- currentBlock - Variable in class loci.formats.in.SDTReader
-
Block of time bins currently stored for faster loading.
- currentChannel - Variable in class loci.formats.in.CV7000Reader.MeasurementSettingsHandler
- currentChunk - Variable in class loci.formats.in.OBFReader.State
- currentCol - Variable in class loci.formats.in.InCellReader.InCellHandler
- currentElement - Variable in class loci.formats.in.AFIReader.AFIHandler
- currentElement - Variable in class loci.formats.in.IvisionReader.IvisionHandler
- currentField - Variable in class loci.formats.in.CV7000Reader.MeasurementDataHandler
- currentField - Variable in class loci.formats.in.InCellReader.InCellHandler
- currentFile - Variable in class loci.formats.services.JHDFServiceImpl
- currentFile - Variable in class loci.formats.services.NetCDFServiceImpl
- currentFragment - Variable in class loci.formats.out.OMEXMLWriter
- currentFrame - Variable in class loci.formats.in.SPCReader
- currentIcsId - Variable in class loci.formats.in.ICSReader
-
Current filename.
- currentId - Variable in class loci.formats.FormatHandler
-
Name of current file.
- currentId - Variable in class loci.formats.ImageReader
-
Name of current file.
- currentId - Variable in class loci.formats.ImageWriter
-
Name of current file.
- currentIdsId - Variable in class loci.formats.in.ICSReader
- currentImage - Variable in class loci.formats.in.InCellReader.InCellHandler
- currentImage - Variable in class loci.formats.in.LeicaSCNReader.LeicaSCNHandler
- currentImageFile - Variable in class loci.formats.in.InCellReader.MinimalInCellHandler
- currentLine - Variable in class loci.formats.in.SPCReader
- currentName - Variable in class loci.formats.in.ColumbusReader.MeasurementHandler
- currentName - Variable in class loci.formats.in.OperettaReader.OperettaHandler
- currentNo - Variable in class loci.formats.in.AmiraReader.HxRLE
- currentNo - Variable in class loci.formats.in.AmiraReader.HxZip
- currentPixel - Variable in class loci.formats.in.SPCReader
- currentPlane - Variable in class loci.formats.in.InCellReader.InCellHandler
- currentPlane - Variable in class loci.formats.in.ZeissZVIReader
- currentPlane - Variable in class loci.formats.out.DicomWriter
- currentPlaneIndex - Variable in class loci.formats.in.ZeissZVIReader
- currentPos - Variable in class loci.formats.cache.Cache
-
Current dimensional position.
- currentProcessor - Variable in class loci.plugins.util.BFVirtualStack
- currentQName - Variable in class loci.formats.in.BDVReader.BDVXMLHandler
- currentQName - Variable in class loci.formats.in.InCellReader.InCellHandler
- currentQName - Variable in class loci.formats.in.OMEXMLReader.OMEXMLHandler
- currentRow - Variable in class loci.formats.in.InCellReader.InCellHandler
- currentSetupIndex - Variable in class loci.formats.in.BDVReader.BDVXMLHandler
- currentSlice - Variable in class loci.plugins.util.BFVirtualStack
- currentStreamPosition - Variable in class loci.formats.in.DCIMGReader
- currentThumbnail - Variable in class loci.formats.in.InCellReader.MinimalInCellHandler
- currentTileFile - Variable in class loci.formats.in.DicomReader
- currentTileStream - Variable in class loci.formats.in.DicomReader
- currentValue - Variable in class loci.formats.in.ColumbusReader.MeasurementHandler
- currentValue - Variable in class loci.formats.in.CV7000Reader.MeasurementDataHandler
- currentValue - Variable in class loci.formats.in.CV7000Reader.MeasurementSettingsHandler
- currentValue - Variable in class loci.formats.in.OperettaReader.OperettaHandler
- currentValue - Variable in class loci.formats.in.ScanrReader.ScanrHandler
- curStep - Variable in class loci.formats.in.SDTInfo
-
Current step (if multi-step measurement).
- curve - Variable in class loci.formats.codec.NikonCodecOptions
- curve - Variable in class loci.formats.in.NikonReader
- CURVE - Static variable in class loci.formats.in.NikonReader
- CURVE_DATE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- CURVE_TIME - Enum constant in enum class loci.formats.dicom.DicomAttribute
- CUS_TIMING_FLAG - Enum constant in enum class loci.formats.in.SPEReader.SpeHeaderEntry
- CUSTOM_BITS - Static variable in class loci.formats.in.SimplePCITiffReader
- CUSTOM_GRAYSCALE - Static variable in class loci.formats.in.CellSensReader
- CUSTOM_RENDERED - Static variable in class loci.formats.tiff.IFD
- customColors - Variable in class loci.plugins.in.ImporterOptions
- customFilter(ShortBuffer, Rectangle, Rectangle, int, int, TJTransform) - Method in interface org.libjpegturbo.turbojpeg.TJCustomFilter
-
A callback function that can be used to modify the DCT coefficients after they are losslessly transformed but before they are transcoded to a new JPEG file.
- cutIn - Variable in class loci.formats.in.LeicaHandler.MultiBand
- cutInPopulated - Variable in class loci.formats.in.LeicaReader
- cutIns - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataTempBuffer
- cutIns - Variable in class loci.formats.in.LIFReader
- cutOut - Variable in class loci.formats.in.LeicaHandler.MultiBand
- cutOutPopulated - Variable in class loci.formats.in.LeicaReader
- cutOuts - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataTempBuffer
- cutOuts - Variable in class loci.formats.in.LIFReader
- CV7000Reader - Class in loci.formats.in
- CV7000Reader() - Constructor for class loci.formats.in.CV7000Reader
-
Constructs a new Yokogawa CV7000 reader.
- CV7000Reader.Channel - Class in loci.formats.in
- CV7000Reader.Field - Class in loci.formats.in
- CV7000Reader.LightSource - Class in loci.formats.in
- CV7000Reader.MeasurementDataHandler - Class in loci.formats.in
- CV7000Reader.MeasurementDetailHandler - Class in loci.formats.in
- CV7000Reader.MeasurementSettingsHandler - Class in loci.formats.in
- CV7000Reader.MinMax - Class in loci.formats.in
- CV7000Reader.Plane - Class in loci.formats.in
- CV7000Reader.WPIHandler - Class in loci.formats.in
- cycle - Variable in class loci.formats.in.PrairieMetadata.Sequence
-
cycleof this<Sequence>. - cycle - Variable in class loci.formats.in.TecanReader.Image
- cycleMax - Variable in class loci.formats.in.PrairieMetadata
-
Maximum cycle value.
- cycleMin - Variable in class loci.formats.in.PrairieMetadata
-
Minimum cycle value.
- cycles - Variable in class loci.formats.in.SDTInfo
-
Cycles (accumulation cycles in FLOW mode).
- CYTELL_MAGIC_STRING - Static variable in class loci.formats.in.InCellReader
- CZI_MAGIC_STRING - Static variable in class loci.formats.in.ZeissCZIReader
- CZTKey(int, int, int) - Constructor for class loci.formats.in.OIRReader.CZTKey
- cztToPixelBlocks - Variable in class loci.formats.in.OIRReader
D
- d(String) - Method in class loci.formats.in.PrairieMetadata
-
Converts the given string to a
Double, ornullif incompatible. - DA - Enum constant in enum class loci.formats.dicom.DicomVR
- DAILY - Static variable in class loci.plugins.Updater
- DAILY_BUILD - Static variable in class loci.formats.UpgradeChecker
-
Location of the JAR artifacts for Bio-Formats' daily build.
- DarkImage - Variable in class loci.formats.in.LiFlimReader
- DarkImage_KEY - Static variable in class loci.formats.in.LiFlimReader
- DASH - Enum constant in enum class loci.formats.in.BaseZeissReader.DrawStyle
- DASH_DOT - Enum constant in enum class loci.formats.in.BaseZeissReader.DrawStyle
- DASH_DOT_DOT - Enum constant in enum class loci.formats.in.BaseZeissReader.DrawStyle
- data - Variable in class loci.formats.in.ICSReader
-
Image data.
- data - Variable in class loci.formats.in.IM3Reader
- data - Variable in class loci.formats.in.TextReader
-
Because we have no way of indexing into the text file efficiently in general, we cheat and store the entire file's data in a giant array.
- data - Variable in class loci.formats.MetadataList
- DATA_CHANNEL_ACQUIRE - Static variable in class loci.formats.in.ZeissLSMReader
- DATA_CHANNEL_NAME - Static variable in class loci.formats.in.ZeissLSMReader
- DATA_COLLECTION_DIAMETER - Enum constant in enum class loci.formats.dicom.DicomAttribute
- DATA_DIR - Static variable in class loci.formats.in.VolocityReader
- DATA_IDENTIFIER - Static variable in class loci.formats.in.SDTInfo
-
For normal .sdt files (setup + data).
- DATA_LABEL - Enum constant in enum class loci.formats.in.SPEReader.SpeHeaderEntry
- DATA_POINT_COLUMNS - Enum constant in enum class loci.formats.dicom.DicomAttribute
- DATA_POINT_ROWS - Enum constant in enum class loci.formats.dicom.DicomAttribute
- DATA_REPRESENTATION - Enum constant in enum class loci.formats.dicom.DicomAttribute
- DATA_SIGNATURE - Static variable in class loci.formats.out.AVIWriter
- dataBlockLength - Variable in class loci.formats.in.SDTInfo
- dataBlockOffs - Variable in class loci.formats.in.SDTInfo
-
Offset of the first data block.
- DataBrowser - Class in loci.plugins.util
-
Extension of StackWindow with additional UI trimmings for animation, virtual stack caching options, metadata, and general beautification.
- DataBrowser(ImagePlus) - Constructor for class loci.plugins.util.DataBrowser
- DataBrowser(ImagePlus, ImageCanvas, String[], int[]) - Constructor for class loci.plugins.util.DataBrowser
- DataBrowser(ImagePlus, ImageCanvas, String[], int[], XMLWindow) - Constructor for class loci.plugins.util.DataBrowser
- DataChannel() - Constructor for class loci.formats.in.ZeissLSMReader.DataChannel
- DataConverter - Class in loci.formats.gui
-
A utility for reorganizing and converting QuickTime movies, TIFF series and other 4D datasets.
- DataConverter() - Constructor for class loci.formats.gui.DataConverter
- DataConverter.RowPanel - Class in loci.formats.gui
- dataFile - Variable in class loci.formats.in.NRRDReader
-
Name of data file, if the current extension is 'nhdr'.
- dataId - Variable in class loci.formats.in.OIRReader.Laser
- DataLoader(String) - Constructor for class loci.formats.in.SlideBook7Reader.DataLoader
- dataOffs - Variable in class loci.formats.in.SDTInfo
-
Offset of the data block from the beginning of the file.
- dataOffset - Variable in class loci.formats.in.DCIMGReader
- dataOffset - Variable in class loci.formats.in.LiFlimReader
-
Offset to start of pixel data.
- dataOffset - Variable in class loci.formats.in.ZeissCZIReader.Attachment
- dataOffset - Variable in class loci.formats.in.ZeissCZIReader.SubBlock
- dataPointers - Variable in class loci.formats.in.InveonReader
- DATASET - Static variable in class loci.formats.in.ZeissXRMReader
- DATASET_SUBTYPE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- datasetDescription - Variable in class loci.formats.FormatReader
-
Short description of the structure of the dataset.
- dataSets - Variable in class loci.formats.in.IM3Reader
- dataSize - Variable in class loci.formats.in.MRWReader
- dataSize - Variable in class loci.formats.in.ZeissCZIReader.Attachment
- dataSize - Variable in class loci.formats.in.ZeissCZIReader.SubBlock
- dataStore - Variable in class loci.formats.in.PQBinReader
- dataStore - Variable in class loci.formats.in.SDTReader
- datatype - Variable in class loci.formats.in.LiFlimReader
- dataType - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.Channel
- DATATYPE - Enum constant in enum class loci.formats.in.SPEReader.SpeHeaderEntry
- DATATYPE_INT16 - Static variable in class loci.formats.in.LiFlimReader
- DATATYPE_INT32 - Static variable in class loci.formats.in.LiFlimReader
- DATATYPE_INT8 - Static variable in class loci.formats.in.LiFlimReader
- DATATYPE_KEY - Static variable in class loci.formats.in.LiFlimReader
- DATATYPE_REAL32 - Static variable in class loci.formats.in.LiFlimReader
- DATATYPE_REAL64 - Static variable in class loci.formats.in.LiFlimReader
- DATATYPE_UINT12 - Static variable in class loci.formats.in.LiFlimReader
- DATATYPE_UINT16 - Static variable in class loci.formats.in.LiFlimReader
- DATATYPE_UINT32 - Static variable in class loci.formats.in.LiFlimReader
- DATATYPE_UINT8 - Static variable in class loci.formats.in.LiFlimReader
- date - Variable in class loci.formats.in.DicomReader
- date - Variable in class loci.formats.in.FEITiffReader
- date - Variable in class loci.formats.in.FluoviewReader
- date - Variable in class loci.formats.in.LEOReader
- date - Variable in class loci.formats.in.MetamorphHandler
- date - Variable in class loci.formats.in.MicroCTReader
- date - Variable in class loci.formats.in.ND2Handler
- date - Variable in class loci.formats.in.PrairieMetadata
-
The date of the acquisition.
- date - Variable in class loci.formats.in.QuesantReader
- date - Variable in class loci.formats.in.SDTInfo
-
Date of creation.
- date - Variable in class loci.formats.in.SimplePCITiffReader
- date - Variable in class loci.formats.in.SVSReader
- DATE - Enum constant in enum class loci.formats.in.SPEReader.SpeHeaderEntry
- DATE - Static variable in class loci.formats.FormatTools
-
Date on which this release was built.
- DATE - Static variable in class loci.formats.in.CellSensReader
- DATE_FORMAT - Static variable in class loci.formats.in.BrukerReader
- DATE_FORMAT - Static variable in class loci.formats.in.CellWorxReader
- DATE_FORMAT - Static variable in class loci.formats.in.DeltavisionReader
-
Deprecated.Use
DeltavisionReader.DATE_FORMATSinstead - DATE_FORMAT - Static variable in class loci.formats.in.FEITiffReader
- DATE_FORMAT - Static variable in class loci.formats.in.FluoviewReader
-
Date format
- DATE_FORMAT - Static variable in class loci.formats.in.FujiReader
- DATE_FORMAT - Static variable in class loci.formats.in.FV1000Reader
- DATE_FORMAT - Static variable in class loci.formats.in.GelReader
- DATE_FORMAT - Static variable in class loci.formats.in.HitachiReader
- DATE_FORMAT - Static variable in class loci.formats.in.IvisionReader
- DATE_FORMAT - Static variable in class loci.formats.in.KodakReader
- DATE_FORMAT - Static variable in class loci.formats.in.L2DReader
- DATE_FORMAT - Static variable in class loci.formats.in.LeicaReader
-
Format for dates.
- DATE_FORMAT - Static variable in class loci.formats.in.MetamorphTiffReader
- DATE_FORMAT - Static variable in class loci.formats.in.MicroCTReader
- DATE_FORMAT - Static variable in class loci.formats.in.MicromanagerReader
- DATE_FORMAT - Static variable in class loci.formats.in.MolecularImagingReader
- DATE_FORMAT - Static variable in class loci.formats.in.ND2Handler
- DATE_FORMAT - Static variable in class loci.formats.in.PDSReader
- DATE_FORMAT - Static variable in class loci.formats.in.PerkinElmerReader
- DATE_FORMAT - Static variable in class loci.formats.in.PrairieReader
- DATE_FORMAT - Static variable in class loci.formats.in.SBIGReader
- DATE_FORMAT - Static variable in class loci.formats.in.SimplePCITiffReader
- DATE_FORMAT - Static variable in class loci.formats.in.SpiderReader
- DATE_FORMAT - Static variable in class loci.formats.in.SVSReader
- DATE_FORMAT - Static variable in class loci.formats.in.TCSReader
- DATE_FORMATS - Static variable in class loci.formats.in.BaseTiffReader
- DATE_FORMATS - Static variable in class loci.formats.in.DeltavisionReader
- DATE_FORMATS - Static variable in class loci.formats.in.ICSReader
- DATE_FORMATS - Static variable in class loci.formats.in.LEOReader
- DATE_FORMATS - Static variable in class loci.formats.in.TillVisionReader
- DATE_OF_LAST_CALIBRATION - Enum constant in enum class loci.formats.dicom.DicomAttribute
- DATE_OF_LAST_DETECTOR_CALIBRATION - Enum constant in enum class loci.formats.dicom.DicomAttribute
- DATE_OF_SECONDARY_CAPTURE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- DATE_TIME - Static variable in class loci.formats.tiff.IFD
- DATE_TIME_DIGITIZED - Static variable in class loci.formats.tiff.IFD
- DATE_TIME_FORMAT - Static variable in class loci.formats.in.GelReader
- DATE_TIME_ORIGINAL - Static variable in class loci.formats.tiff.IFD
- dates - Variable in class loci.formats.in.TillVisionReader
- datestamp - Variable in class loci.formats.in.TCSReader
- DATESTAMP - Static variable in class loci.formats.in.ZeissXRMReader
- datestamps - Variable in class loci.formats.in.ZeissXRMReader
- datFile - Variable in class loci.formats.in.InveonReader
- datFile - Variable in class loci.formats.in.UnisokuReader
- DB_DT - Enum constant in enum class loci.formats.dicom.DicomAttribute
- dBlock - Variable in class loci.formats.in.GIFReader
-
Current data block.
- DCIMG_PIXELTYPE_MONO16 - Static variable in class loci.formats.in.DCIMGReader
- DCIMG_PIXELTYPE_MONO8 - Static variable in class loci.formats.in.DCIMGReader
- DCIMG_VERSION_0 - Static variable in class loci.formats.in.DCIMGReader
- DCIMG_VERSION_1 - Static variable in class loci.formats.in.DCIMGReader
- DCIMGReader - Class in loci.formats.in
-
DCIMGReader reads Hamamatsu DCIMG files.
- DCIMGReader() - Constructor for class loci.formats.in.DCIMGReader
- deadTimeComp - Variable in class loci.formats.in.SDTInfo
- debug(String) - Static method in class loci.plugins.BF
- decode(byte[]) - Method in class loci.formats.filter.LZ4Filter
- decode(APNGReader.PNGInputStream) - Method in class loci.formats.in.APNGReader
- decode(APNGReader.PNGInputStream, int, int) - Method in class loci.formats.in.APNGReader
- Decode(MappingNode) - Method in class loci.formats.in.SlideBook7Reader.CImageRecord70
- Decode(MappingNode) - Method in class loci.formats.in.SlideBook7Reader.ClassDecoder
- Decode(MappingNode, int) - Method in class loci.formats.in.SlideBook7Reader.CChannelDef70
- Decode(MappingNode, int) - Method in class loci.formats.in.SlideBook7Reader.CChannelRecord70
- Decode(MappingNode, int) - Method in class loci.formats.in.SlideBook7Reader.CCubeAnnotation70
- Decode(MappingNode, int) - Method in class loci.formats.in.SlideBook7Reader.CFRAPRegionAnnotation70
- Decode(MappingNode, int) - Method in class loci.formats.in.SlideBook7Reader.ClassDecoder
- Decode(MappingNode, int) - Method in class loci.formats.in.SlideBook7Reader.CUnknownAnnotation70
- decode12BitCamera(byte[], int) - Method in class loci.formats.in.ZeissCZIReader
- decodeDate(int) - Static method in class loci.formats.in.MetamorphReader
-
Converts a Julian date value into a human-readable string.
- decodeImageData() - Method in class loci.formats.in.GIFReader
-
Decodes LZW image data into a pixel array.
- decoder - Variable in class loci.formats.codec.JPEGTileDecoder
- decodeTile(int, int, int) - Method in class loci.formats.in.CellSensReader
- decodeTime(int) - Static method in class loci.formats.in.MetamorphReader
-
Converts a time value in milliseconds into a human-readable string.
- DecodeUnknownString(String, Node) - Method in class loci.formats.in.SlideBook7Reader.CAnnotation70
- DecodeUnknownString(String, Node) - Method in class loci.formats.in.SlideBook7Reader.ClassDecoder
- decompress(byte[]) - Method in class loci.formats.codec.BaseCodec
- decompress(byte[]) - Method in interface loci.formats.codec.Codec
-
Decompresses a block of data.
- decompress(byte[]) - Method in class loci.formats.codec.WrappedCodec
- decompress(byte[]) - Method in interface loci.formats.services.JPEGXRService
-
Decompress the given JPEG-XR compressed byte array and return as a byte array.
- decompress(byte[]) - Method in class loci.formats.services.JPEGXRServiceImpl
- decompress(byte[][]) - Method in class loci.formats.codec.BaseCodec
- decompress(byte[][]) - Method in interface loci.formats.codec.Codec
-
Decompresses a block of data.
- decompress(byte[][]) - Method in class loci.formats.codec.WrappedCodec
- decompress(byte[][], CodecOptions) - Method in class loci.formats.codec.BaseCodec
-
2D data block decoding default implementation.
- decompress(byte[][], CodecOptions) - Method in interface loci.formats.codec.Codec
-
Decompresses a block of data.
- decompress(byte[][], CodecOptions) - Method in class loci.formats.codec.WrappedCodec
- decompress(byte[], int, byte[], int, int, int, int, int) - Method in class org.libjpegturbo.turbojpeg.TJDecompressor
- decompress(byte[], int, int) - Method in class loci.formats.codec.ZstdCodec
- decompress(byte[], int, int[], int, int, int, int, int) - Method in class org.libjpegturbo.turbojpeg.TJDecompressor
- decompress(byte[], int, int, int, int, int) - Method in class org.libjpegturbo.turbojpeg.TJDecompressor
-
Decompress the JPEG source image associated with this decompressor instance and output a decompressed image to the given destination buffer.
- decompress(byte[], CodecOptions) - Method in class loci.formats.codec.BaseCodec
- decompress(byte[], CodecOptions) - Method in interface loci.formats.codec.Codec
-
Decompresses a block of data.
- decompress(byte[], CodecOptions) - Method in class loci.formats.codec.JPEGXRCodec
-
The CodecOptions parameter should have the following fields set:
maxBytesinterleavedbitsPerSamplelittleEndianwidthheight - decompress(byte[], CodecOptions) - Method in class loci.formats.codec.WrappedCodec
- decompress(byte[], CodecOptions) - Method in enum class loci.formats.tiff.TiffCompression
-
Decodes a strip of data.
- decompress(int, int, int, int) - Method in class org.libjpegturbo.turbojpeg.TJDecompressor
-
Decompress the JPEG source image associated with this decompressor instance and return a
BufferedImageinstance containing the decompressed image. - decompress(int, int, int, int, int) - Method in class org.libjpegturbo.turbojpeg.TJDecompressor
-
Decompress the JPEG source image associated with this decompressor instance and return a buffer containing the decompressed image.
- decompress(BufferedImage, int) - Method in class org.libjpegturbo.turbojpeg.TJDecompressor
-
Decompress the JPEG source image associated with this decompressor instance and output a decompressed image to the given
BufferedImageinstance. - decompress(RandomAccessInputStream, CodecOptions) - Method in class loci.formats.codec.BaseCodec
- decompress(RandomAccessInputStream, CodecOptions) - Method in interface loci.formats.codec.Codec
-
Decompresses data from the given RandomAccessInputStream.
- decompress(RandomAccessInputStream, CodecOptions) - Method in class loci.formats.codec.JPEGXRCodec
- decompress(RandomAccessInputStream, CodecOptions) - Method in class loci.formats.codec.NikonCodec
-
The CodecOptions parameter must be an instance of
NikonCodecOptions, and should have the following fields set:losslessvPredictorcurvesplitbitsPerSamplemaxByteswidthheight - decompress(RandomAccessInputStream, CodecOptions) - Method in class loci.formats.codec.TargaRLECodec
-
The CodecOptions parameter should have the following fields set:
maxBytesCodecOptions.bitsPerSample - decompress(RandomAccessInputStream, CodecOptions) - Method in class loci.formats.codec.WrappedCodec
- DecompressBuffer(byte[]) - Method in class loci.formats.in.SlideBook7Reader.CCompressionBase
- decompressHeader(byte[], int) - Method in class org.libjpegturbo.turbojpeg.TJDecompressor
- decompressor - Variable in class loci.formats.filter.LZ4Filter
- decompressor - Variable in class loci.formats.in.AmiraReader.HxZip
- decompressToYUV(byte[], int) - Method in class org.libjpegturbo.turbojpeg.TJDecompressor
-
Decompress the JPEG source image associated with this decompressor instance and output a YUV planar image to the given destination buffer.
- decompressToYUV(byte[], int, byte[], int) - Method in class org.libjpegturbo.turbojpeg.TJDecompressor
- decompressToYUV(int) - Method in class org.libjpegturbo.turbojpeg.TJDecompressor
-
Decompress the JPEG source image associated with this decompressor instance and return a buffer containing a YUV planar image.
- deconvolutionLogFile - Variable in class loci.formats.in.DeltavisionReader
- DEEP_GREY_10 - Static variable in class loci.formats.in.OpenlabReader
- DEEP_GREY_11 - Static variable in class loci.formats.in.OpenlabReader
- DEEP_GREY_12 - Static variable in class loci.formats.in.OpenlabReader
- DEEP_GREY_13 - Static variable in class loci.formats.in.OpenlabReader
- DEEP_GREY_14 - Static variable in class loci.formats.in.OpenlabReader
- DEEP_GREY_15 - Static variable in class loci.formats.in.OpenlabReader
- DEEP_GREY_16 - Static variable in class loci.formats.in.OpenlabReader
- DEEP_GREY_9 - Static variable in class loci.formats.in.OpenlabReader
- DEFAULT_BACKGROUND_COLOR - Static variable in class loci.formats.in.CellSensReader
- DEFAULT_CALLER - Static variable in class loci.formats.UpgradeChecker
-
Value of "bioformats.caller" for Bio-Formats utilities.
- DEFAULT_COLORS - Static variable in class loci.plugins.in.ImporterOptions
-
Default custom colors for each channel.
- DEFAULT_DIMENSION_ORDER - Static variable in class loci.formats.in.FakeReader
- DEFAULT_DISPLAY_RESOLUTION - Enum constant in enum class loci.formats.codec.JPEG2000BoxType
- DEFAULT_GAMMA - Static variable in class loci.formats.in.NDPIReader
- DEFAULT_IMAGE - Static variable in class loci.formats.in.CellSensReader
- DEFAULT_LINEARIZATION_TABLE - Static variable in class loci.formats.codec.NikonCodec
- DEFAULT_MINIMUM_ELAPSED - Static variable in class loci.formats.Memoizer
-
Default value for
Memoizer.minimumElapsedif none is provided in the constructor. - DEFAULT_PIXEL_TYPE - Static variable in class loci.formats.in.FakeReader
- DEFAULT_RANGE - Static variable in class loci.formats.cache.CacheStrategy
-
Default cache range.
- DEFAULT_RESOLUTION_SCALE - Static variable in class loci.formats.in.FakeReader
- DEFAULT_RGB_CHANNEL_COUNT - Static variable in class loci.formats.in.FakeReader
- DEFAULT_RGB_DIMENSION_ORDER - Static variable in class loci.formats.in.FakeReader
- DEFAULT_SAMPLE_IFD - Static variable in class loci.formats.in.CellSensReader
- DEFAULT_SERIES - Static variable in class loci.formats.in.KLBReader
- DEFAULT_SIZE_C - Static variable in class loci.formats.in.FakeReader
- DEFAULT_SIZE_T - Static variable in class loci.formats.in.FakeReader
- DEFAULT_SIZE_X - Static variable in class loci.formats.in.FakeReader
- DEFAULT_SIZE_Y - Static variable in class loci.formats.in.FakeReader
- DEFAULT_SIZE_Z - Static variable in class loci.formats.in.FakeReader
- DEFAULT_UNCOMPRESSED - Enum constant in enum class loci.formats.tiff.TiffCompression
- defaultClasses - Static variable in class loci.formats.ImageReader
-
Default list of reader classes, for use with noargs constructor.
- defaultClasses - Static variable in class loci.formats.ImageWriter
-
Default list of writer classes, for use with noargs constructor.
- defaultDateEnabled - Static variable in class loci.formats.MetadataTools
- defaultExposureTime - Variable in class loci.formats.in.CellSensReader.Pyramid
- DefaultJPEGReader() - Constructor for class loci.formats.in.JPEGReader.DefaultJPEGReader
- DefaultMetadataOptions - Class in loci.formats.in
-
Default implementation of
MetadataOptions. - DefaultMetadataOptions() - Constructor for class loci.formats.in.DefaultMetadataOptions
-
Construct a new
DefaultMetadataOptions. - DefaultMetadataOptions(MetadataLevel) - Constructor for class loci.formats.in.DefaultMetadataOptions
-
Construct a new
DefaultMetadataOptions. - defaultMinMax(int) - Static method in class loci.formats.FormatTools
-
Get the default range for the specified pixel type.
- defaultValue - Variable in class loci.plugins.prefs.BooleanOption
-
The option's default value.
- defaultValue - Variable in class loci.plugins.prefs.DoubleOption
-
The option's default value.
- defaultValue - Variable in class loci.plugins.prefs.StringOption
-
The option's default value.
- defaultVR - Variable in enum class loci.formats.dicom.DicomAttribute
- defaultXMLSkip - Variable in class loci.formats.in.OIRReader
- DEFINITION - Static variable in class loci.formats.in.BDVReader.H5Constants
- DEFINITION - Static variable in class loci.formats.in.CellH5Reader.CellH5Constants
- DEFLATE - Enum constant in enum class loci.formats.tiff.TiffCompression
- DELAY_TIME - Enum constant in enum class loci.formats.in.SPEReader.SpeHeaderEntry
- delegate - Variable in class loci.formats.in.SimplePCITiffReader
- DelegateReader - Class in loci.formats
-
DelegateReader is a file format reader that selects which reader to use for a format if there are two readers which handle the same format.
- DelegateReader(String, String) - Constructor for class loci.formats.DelegateReader
-
Constructs a new delegate reader.
- DelegateReader(String, String[]) - Constructor for class loci.formats.DelegateReader
-
Constructs a new delegate reader.
- deleteMemo() - Method in class loci.formats.Memoizer
-
Force the current memo file to be deleted, if it exists.
- deleteQuietly(File) - Method in class loci.formats.Memoizer
-
Attempts to delete an existing file, logging at warn if the deletion returns false or at error if an exception is thrown.
- deleteSlice(int) - Method in class loci.plugins.util.BFVirtualStack
- DELIMITERS - Static variable in class loci.formats.in.ImarisHDFReader
- deltaT - Variable in class loci.formats.in.ColumbusReader.Plane
- deltaT - Variable in class loci.formats.in.FV1000Reader.PlaneData
- deltaT - Variable in class loci.formats.in.InCellReader.Image
- deltaT - Variable in class loci.formats.in.IvisionReader
- deltaT - Variable in class loci.formats.in.LeicaHandler
- deltaT - Variable in class loci.formats.in.NiftiReader
- deltaT - Variable in class loci.formats.in.OperettaReader.Plane
- deltaT - Variable in class loci.formats.in.ScanrReader
- DeltavisionReader - Class in loci.formats.in
-
DeltavisionReader is the file format reader for Deltavision files.
- DeltavisionReader() - Constructor for class loci.formats.in.DeltavisionReader
-
Constructs a new Deltavision reader.
- DeltavisionReader.DVExtHdrFields - Class in loci.formats.in
-
This private class structure holds the details for the extended header.
- denom - Variable in class loci.formats.tiff.TiffRational
-
Components of the rational's fractional representation.
- denom - Variable in class org.libjpegturbo.turbojpeg.TJScalingFactor
-
Denominator
- depth - Variable in class loci.formats.tools.AmiraParameters
- DEPTH_OF_SCAN_FIELD - Enum constant in enum class loci.formats.dicom.DicomAttribute
- DERIVATION_CODE_SEQUENCE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- DERIVATION_DESCRIPTION - Enum constant in enum class loci.formats.dicom.DicomAttribute
- DERIVATION_IMAGE_SEQUENCE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- desc - Variable in class loci.formats.gui.ComboFileFilter
-
Description.
- desc - Variable in class loci.formats.gui.ExtensionFileFilter
-
Description.
- desc - Variable in class loci.formats.gui.FormatFileFilter
-
Description.
- description - Variable in enum class loci.formats.dicom.DicomAttribute
- description - Variable in class loci.formats.in.CV7000Reader.WPIHandler
- description - Variable in class loci.formats.in.NiftiReader
- description - Variable in class loci.formats.in.PrairieMetadata.ValueItem
- description - Variable in class loci.formats.in.TiffReader
- description - Variable in class loci.formats.in.VolocityReader.Stack
- description - Variable in class loci.formats.in.ZeissCZIReader
- description - Variable in class loci.formats.in.ZeissLSMReader.Recording
- description() - Method in interface loci.formats.in.PrairieMetadata.Value
- description() - Method in class loci.formats.in.PrairieMetadata.ValueItem
- description() - Method in class loci.formats.in.PrairieMetadata.ValueTable
- DESCRIPTION_MARKER - Static variable in class loci.formats.in.TillVisionReader
- descriptions - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataTempBuffer
- descriptions - Variable in class loci.formats.in.LIFReader
- destroy() - Method in class org.libjpegturbo.turbojpeg.TJCompressor
- destroy() - Method in class org.libjpegturbo.turbojpeg.TJDecompressor
- detailPath - Variable in class loci.formats.in.CV7000Reader
- details - Variable in class loci.formats.in.PerkinElmerReader
- DetectionChannel() - Constructor for class loci.formats.in.ZeissLSMReader.DetectionChannel
- detector - Variable in class loci.formats.in.LeicaHandler.Channel
- detector - Variable in class loci.formats.in.VolocityReader.Stack
- Detector() - Constructor for class loci.formats.in.LeicaHandler.Detector
- Detector() - Constructor for class loci.formats.in.LeicaReader.Detector
- Detector() - Constructor for class loci.formats.in.OIRReader.Detector
- DETECTOR_ACTIVATION_OFFSET - Enum constant in enum class loci.formats.dicom.DicomAttribute
- DETECTOR_ACTIVE_DIMENSIONS - Enum constant in enum class loci.formats.dicom.DicomAttribute
- DETECTOR_ACTIVE_ORIGIN - Enum constant in enum class loci.formats.dicom.DicomAttribute
- DETECTOR_ACTIVE_SHAPE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- DETECTOR_ACTIVE_TIME - Enum constant in enum class loci.formats.dicom.DicomAttribute
- DETECTOR_BINNING - Enum constant in enum class loci.formats.dicom.DicomAttribute
- DETECTOR_CONDITIONS_NOMINAL_FLAG - Enum constant in enum class loci.formats.dicom.DicomAttribute
- DETECTOR_CONFIGURATION - Enum constant in enum class loci.formats.dicom.DicomAttribute
- DETECTOR_DESCRIPTION - Enum constant in enum class loci.formats.dicom.DicomAttribute
- DETECTOR_ELEMENT_PHYSICAL_SIZE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- DETECTOR_ELEMENT_SPACING - Enum constant in enum class loci.formats.dicom.DicomAttribute
- DETECTOR_ID - Enum constant in enum class loci.formats.dicom.DicomAttribute
- DETECTOR_MANUFACTURER_NAME - Enum constant in enum class loci.formats.dicom.DicomAttribute
- DETECTOR_MODE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- DETECTOR_MODEL_NAME - Enum constant in enum class loci.formats.dicom.DicomAttribute
- DETECTOR_PRIMARY_ANGLE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- DETECTOR_SECONDARY_ANGLE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- DETECTOR_TEMP - Enum constant in enum class loci.formats.in.SPEReader.SpeHeaderEntry
- DETECTOR_TEMPERATURE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- DETECTOR_TIME_SINCE_LAST_EXPOSURE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- DETECTOR_TYPE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- DETECTOR_TYPE - Enum constant in enum class loci.formats.in.SPEReader.SpeHeaderEntry
- detectorChannel - Variable in class loci.formats.in.LeicaHandler
- detectorGain - Variable in class loci.formats.in.BaseZeissReader
- detectorID - Variable in class loci.formats.in.MicromanagerReader.Position
- detectorIDs - Variable in class loci.formats.in.ZeissCZIReader
- detectorIndexes - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataTempBuffer
- detectorIndexes - Variable in class loci.formats.in.LIFReader
- detectorManufacturer - Variable in class loci.formats.in.FluoviewReader
- detectorManufacturer - Variable in class loci.formats.in.MicromanagerReader.Position
- detectorModel - Variable in class loci.formats.in.MicromanagerReader.Position
- detectorModels - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataTempBuffer
- detectorModels - Variable in class loci.formats.in.LIFReader
- detectorOffset - Variable in class loci.formats.in.BaseZeissReader
- detectorOffset - Variable in class loci.formats.in.OpenlabReader
- detectorOffsets - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataTempBuffer
- detectorOffsets - Variable in class loci.formats.in.LIFReader
- detectorRefs - Variable in class loci.formats.in.ZeissCZIReader
- detectors - Variable in class loci.formats.in.FEITiffReader
- detectors - Variable in class loci.formats.in.LeicaHandler
- detectors - Variable in class loci.formats.in.LeicaReader
- detectors - Variable in class loci.formats.in.OIRReader
- detType - Variable in class loci.formats.in.SDTInfo
-
Detector type (SPC-930 in camera mode).
- DEVICE_ID - Static variable in class loci.formats.in.CellSensReader
- DEVICE_MANUFACTURER - Static variable in class loci.formats.in.CellSensReader
- DEVICE_NAME - Static variable in class loci.formats.in.CellSensReader
- DEVICE_SERIAL_NUMBER - Enum constant in enum class loci.formats.dicom.DicomAttribute
- DEVICE_SUBTYPE - Static variable in class loci.formats.in.CellSensReader
- deviceIDs - Variable in class loci.formats.in.CellSensReader.Pyramid
- deviceManufacturers - Variable in class loci.formats.in.CellSensReader.Pyramid
- deviceNames - Variable in class loci.formats.in.CellSensReader.Pyramid
- deviceTypes - Variable in class loci.formats.in.CellSensReader.Pyramid
- devModel - Variable in class loci.formats.in.LeicaSCNReader.Image
- devVersion - Variable in class loci.formats.in.LeicaSCNReader.Image
- DIAGONAL_CROSS - Enum constant in enum class loci.formats.in.BaseZeissReader.FillStyle
- dialog - Variable in class loci.plugins.in.ThumbLoader
- DIAMOND - Enum constant in enum class loci.formats.in.BaseZeissReader.PointStyle
- dichroic - Variable in class loci.formats.in.FlexReader.FilterGroup
- dichroicMap - Variable in class loci.formats.in.FlexReader
- dichroicModels - Variable in class loci.formats.in.NikonTiffReader
- DICOM_MAGIC_STRING - Static variable in class loci.formats.in.DicomReader
- DICOM_SUFFIXES - Static variable in class loci.formats.in.DicomReader
- DicomAttribute - Enum Class in loci.formats.dicom
-
Describes a DICOM attribute (integer tag, associated description, and expected VR).
- DicomAttribute(int) - Constructor for enum class loci.formats.dicom.DicomAttribute
- DicomFileInfo - Class in loci.formats.dicom
-
Structure containing metadata for one DICOM file (instance).
- DicomFileInfo() - Constructor for class loci.formats.dicom.DicomFileInfo
-
Construct an empty object to be populated later.
- DicomFileInfo(String) - Constructor for class loci.formats.dicom.DicomFileInfo
-
Construct an object from the given file.
- DicomJSONProvider - Class in loci.formats.dicom
-
Provide DICOM tags from a file containing JSON.
- DicomJSONProvider() - Constructor for class loci.formats.dicom.DicomJSONProvider
- DicomReader - Class in loci.formats.in
-
DicomReader is the file format reader for DICOM files.
- DicomReader() - Constructor for class loci.formats.in.DicomReader
-
Constructs a new DICOM reader.
- DicomTag - Class in loci.formats.dicom
-
Represents a complete DICOM tag, including the dictionary attribute, actual VR, value, and any "child" tags (in the case of a sequence).
- DicomTag(int, DicomVR) - Constructor for class loci.formats.dicom.DicomTag
- DicomTag(RandomAccessInputStream, boolean, long, boolean) - Constructor for class loci.formats.dicom.DicomTag
-
Read a complete tag and value from the given input stream.
- DicomTag(RandomAccessInputStream, boolean, long, boolean, boolean) - Constructor for class loci.formats.dicom.DicomTag
-
Read a complete tag and optionally a value from the given input stream.
- DicomTag(DicomAttribute) - Constructor for class loci.formats.dicom.DicomTag
- DicomTag(DicomAttribute, DicomVR) - Constructor for class loci.formats.dicom.DicomTag
- DicomTile - Class in loci.formats.dicom
-
Represents a tile stored in a DICOM file.
- DicomTile() - Constructor for class loci.formats.dicom.DicomTile
- DicomVR - Enum Class in loci.formats.dicom
-
Enumeration of valid DICOM value representations (VRs).
- DicomVR(int, int) - Constructor for enum class loci.formats.dicom.DicomVR
- DicomWriter - Class in loci.formats.out
-
DicomWriter is the file format writer for DICOM files.
- DicomWriter() - Constructor for class loci.formats.out.DicomWriter
- DicomWriter.PlaneOffset - Class in loci.formats.out
- DicomWriter.UIDCreator - Class in loci.formats.out
-
Helper class for creating UIDs.
- dict - Static variable in enum class loci.formats.dicom.DicomAttribute
- diff - Variable in class loci.formats.in.BioRadGelReader
- difference(byte[], IFD) - Static method in enum class loci.formats.tiff.TiffCompression
-
Performs in-place differencing according to the given predictor value.
- DIGITAL_IMAGE_FORMAT_ACQUIRED - Enum constant in enum class loci.formats.dicom.DicomAttribute
- DIGITAL_ZOOM_RATIO - Static variable in class loci.formats.tiff.IFD
- DIGITIZING_DEVICE_TRANSPORT_DIRECTION - Enum constant in enum class loci.formats.dicom.DicomAttribute
- digits(int) - Static method in class loci.plugins.in.ImporterMetadata
-
Computes the given value's number of digits.
- dilate() - Method in class loci.plugins.util.RecordedImageProcessor
- DIM_INDEX_1 - Static variable in class loci.formats.in.CellSensReader
- DIM_INDEX_2 - Static variable in class loci.formats.in.CellSensReader
- DIM_ORDER - Enum constant in enum class loci.plugins.in.ImportStep
- DIMDESCR - Static variable in class loci.formats.in.LeicaReader
- dimension - Variable in class loci.formats.in.ZeissCZIReader.DimensionEntry
- dimension - Variable in class loci.formats.in.ZeissTIFFHandler.Scaling.Dimension
- Dimension - Class in loci.formats.in.LeicaMicrosystemsMetadata
-
This class represents image dimensions extracted from LMS image xmls.
- Dimension() - Constructor for class loci.formats.in.LeicaMicrosystemsMetadata.Dimension
- Dimension(Integer) - Constructor for class loci.formats.in.ZeissTIFFHandler.Scaling.Dimension
-
Constructor.
- Dimension(Dimension.DimensionKey, int, long, String, Double, boolean) - Constructor for class loci.formats.in.LeicaMicrosystemsMetadata.Dimension
- Dimension(Attributes) - Constructor for class loci.formats.in.LeicaSCNReader.Dimension
- DIMENSION_DESCRIPTION_LABEL - Enum constant in enum class loci.formats.dicom.DicomAttribute
- DIMENSION_DESCRIPTION_VOLUME - Static variable in class loci.formats.in.CellSensReader
- DIMENSION_INCREMENT_ID - Static variable in class loci.formats.in.CellSensReader
- DIMENSION_INDEX_POINTER - Enum constant in enum class loci.formats.dicom.DicomAttribute
- DIMENSION_INDEX_PRIVATE_CREATOR - Enum constant in enum class loci.formats.dicom.DicomAttribute
- DIMENSION_INDEX_SEQUENCE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- DIMENSION_INDEX_VALUES - Enum constant in enum class loci.formats.dicom.DicomAttribute
- DIMENSION_MEANING - Static variable in class loci.formats.in.CellSensReader
- DIMENSION_NAME - Static variable in class loci.formats.in.CellSensReader
- DIMENSION_NAMES - Static variable in class loci.formats.in.LeicaReader
- DIMENSION_ORGANIZATION_SEQUENCE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- DIMENSION_ORGANIZATION_TYPE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- DIMENSION_ORGANIZATION_UID - Enum constant in enum class loci.formats.dicom.DicomAttribute
- DIMENSION_SIZE - Static variable in class loci.formats.in.CellSensReader
- DIMENSION_START_ID - Static variable in class loci.formats.in.CellSensReader
- DIMENSION_VALUE_ID - Static variable in class loci.formats.in.CellSensReader
- Dimension.DimensionKey - Enum Class in loci.formats.in.LeicaMicrosystemsMetadata
- dimensionCount - Variable in class loci.formats.in.ZeissCZIReader.DirectoryEntry
- dimensionEntries - Variable in class loci.formats.in.ZeissCZIReader.DirectoryEntry
- DimensionEntry(RandomAccessInputStream) - Constructor for class loci.formats.in.ZeissCZIReader.DimensionEntry
- dimensionIndex - Variable in class loci.formats.out.DicomWriter.PlaneOffset
- DimensionKey(int, char) - Constructor for enum class loci.formats.in.LeicaMicrosystemsMetadata.Dimension.DimensionKey
- dimensionLength - Variable in class loci.formats.out.ICSWriter
- dimensionM - Variable in class loci.formats.in.ZeissLSMReader
- dimensionOffset - Variable in class loci.formats.out.ICSWriter
- dimensionOrder - Variable in class loci.formats.CoreMetadata
-
Order in which dimensions are stored.
- dimensionOrder - Variable in class loci.formats.in.FluoviewReader
- dimensionOrdering - Variable in class loci.formats.in.CellSensReader.Pyramid
- dimensionP - Variable in class loci.formats.in.ZeissLSMReader
- dimensions - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataTempBuffer
- DIMENSIONS_STRING - Static variable in class loci.formats.in.KodakReader
- dimensionsSwapped - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.MultipleImagesReader
- dimensionSwapper - Variable in class loci.plugins.in.ImportProcess
- DimensionSwapper - Class in loci.formats
-
Handles swapping the dimension order of an image series.
- DimensionSwapper() - Constructor for class loci.formats.DimensionSwapper
-
Constructs a DimensionSwapper around a new image reader.
- DimensionSwapper(IFormatReader) - Constructor for class loci.formats.DimensionSwapper
-
Constructs a DimensionSwapper with the given reader.
- dimensionTag - Variable in class loci.formats.in.CellSensReader
- dimOrder - Variable in class loci.formats.AxisGuesser
-
Original ordering of internal dimensional axes.
- dims - Variable in class loci.formats.in.LeicaSCNReader.Pixels
- dims - Variable in class loci.formats.in.ZeissTIFFHandler.Scaling
- dims_blockSize - Variable in class loci.formats.in.KLBReader
- dims_xyzct - Variable in class loci.formats.in.KLBReader
- dir - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.LMSXmlDocument
- dir - Variable in class loci.formats.in.VolocityReader
- direction - Variable in class loci.formats.in.VentanaReader.Overlap
- directory - Variable in class loci.formats.Memoizer
-
Directory where all memo files should be created.
- directory - Variable in class loci.formats.services.EXIFServiceImpl
- Directory() - Constructor for class loci.formats.in.ZeissCZIReader.Directory
- DIRECTORY_RECORD_SEQUENCE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- DIRECTORY_RECORD_TYPE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- directoryCache - Variable in class loci.formats.in.ZeissTIFFReader
- directoryEntry - Variable in class loci.formats.in.ZeissCZIReader.SubBlock
- DirectoryEntry(RandomAccessInputStream) - Constructor for class loci.formats.in.ZeissCZIReader.DirectoryEntry
- directoryList - Variable in class loci.formats.in.CellWorxReader
- directoryPosition - Variable in class loci.formats.in.ZeissCZIReader.FileHeader
- directoryRoot - Variable in class loci.formats.tools.FakeImage
- dirty - Variable in class loci.formats.cache.CacheStrategy
-
Whether load order array needs to be recomputed before building the next load list.
- disableChromaSubsampling - Variable in class loci.formats.codec.CodecOptions
-
Whether or not to use chroma subsampling.
- DISPLAY_COLOR - Static variable in class loci.formats.in.CellSensReader
- DISPLAY_CONTRAST_BRIGHTNESS - Static variable in class loci.formats.in.CellSensReader
- DISPLAY_GAMMA_CORRECTION - Static variable in class loci.formats.in.CellSensReader
- DISPLAY_LIMITS - Static variable in class loci.formats.in.CellSensReader
- DISPLAY_LUT - Static variable in class loci.formats.in.CellSensReader
- DISPLAY_MAPPING_VOLUME - Static variable in class loci.formats.in.CellSensReader
- DISPLAY_PROCESSOR_TYPE - Static variable in class loci.formats.in.CellSensReader
- DISPLAY_STACK_ID - Static variable in class loci.formats.in.CellSensReader
- DISPLAY_STACK_INDEX - Static variable in class loci.formats.in.CellSensReader
- DISPLAY_VISIBLE - Static variable in class loci.formats.in.CellSensReader
- DISPLAY_WINDOW_LABEL_VECTOR - Enum constant in enum class loci.formats.dicom.DicomAttribute
- displayColor - Variable in class loci.formats.in.SVSReader
- displayDataBrowser(ImagePlus) - Method in class loci.plugins.in.DisplayHandler
- displayDialog(GenericDialog) - Method in class loci.plugins.in.IdDialog
-
Asks user whether Bio-Formats should automatically check for upgrades, and if so, checks for an upgrade and prompts user to install it.
- displayDialog(GenericDialog) - Method in class loci.plugins.in.ImporterDialog
-
Displays the dialog, or grabs values from macro options.
- displayDialog(GenericDialog) - Method in class loci.plugins.in.SeriesDialog
- displayDialog(GenericDialog) - Method in class loci.plugins.in.UpgradeDialog
-
Asks user whether Bio-Formats should automatically check for upgrades, and if so, checks for an upgrade and prompts user to install it.
- DISPLAYED_LUT_ID - Static variable in class loci.formats.in.CellSensReader
- DisplayHandler - Class in loci.plugins.in
-
Logic for displaying images and metadata onscreen using ImageJ.
- DisplayHandler(ImportProcess) - Constructor for class loci.plugins.in.DisplayHandler
- displayImage(ImagePlus) - Method in class loci.plugins.in.DisplayHandler
-
Displays the given image according to the configured options.
- displayImage5D(ImagePlus) - Method in class loci.plugins.in.DisplayHandler
- displayImages(ImagePlus[]) - Method in class loci.plugins.in.DisplayHandler
-
Displays the given images according to the configured options.
- displayName - Variable in class loci.formats.in.OperettaReader.OperettaHandler
- displayNormal(ImagePlus) - Method in class loci.plugins.in.DisplayHandler
-
Displays in a normal ImageJ window.
- displayOMEXML() - Method in class loci.plugins.in.DisplayHandler
-
Displays OME-XML metadata in a tree in its own window.
- displayOriginalMetadata() - Method in class loci.plugins.in.DisplayHandler
-
Displays standard metadata in a table in its own window.
- displayROIs(ImagePlus[]) - Method in class loci.plugins.in.DisplayHandler
- displayTag - Variable in class loci.formats.in.BaseZeissReader.Shape
- displayUsage() - Method in class loci.formats.tools.MakeTestOmeTiff
- displayView5D(ImagePlus) - Method in class loci.plugins.in.DisplayHandler
- dispose - Variable in class loci.formats.in.GIFReader
- dispose() - Method in class loci.formats.gui.CacheComponent
- distance(int, int) - Method in class loci.formats.cache.CacheStrategy
-
Computes the distance from the given axis value to the axis center, taking into account the axis ordering scheme.
- DISTANCE - Enum constant in enum class loci.formats.in.BaseZeissReader.FeatureType
- DISTANCE_BETWEEN_FOCAL_PLANES - Enum constant in enum class loci.formats.dicom.DicomAttribute
- DISTANCE_SOURCE_TO_DETECTOR - Enum constant in enum class loci.formats.dicom.DicomAttribute
- DISTANCE_SOURCE_TO_PATIENT - Enum constant in enum class loci.formats.dicom.DicomAttribute
- dither - Variable in class loci.formats.in.SDTInfo
- DLL_DATA_IDENTIFIER - Static variable in class loci.formats.in.SDTInfo
-
For .sdt files created using DLL function SPC_save_data_to_sdtfile (no setup, only data).
- DM2_MAGIC_BYTES - Static variable in class loci.formats.in.GatanDM2Reader
- DM3_MAGIC_BYTES - Static variable in class loci.formats.in.GatanReader
- DM4_MAGIC_BYTES - Static variable in class loci.formats.in.GatanReader
- DNGReader - Class in loci.formats.in
-
DNGReader is the file format reader for Canon DNG (TIFF) files.
- DNGReader() - Constructor for class loci.formats.in.DNGReader
-
Constructs a new DNG reader.
- doc - Variable in class loci.formats.gui.XMLWindow
- doc - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.LMSXmlDocument
- doCaching - Variable in class loci.formats.tiff.TiffParser
- doChannels - Variable in class loci.formats.in.CellWorxReader
- doCrop() - Method in class loci.plugins.in.ImporterOptions
- DOCUMENT_AUTHOR - Static variable in class loci.formats.in.CellSensReader
- DOCUMENT_COMPANY - Static variable in class loci.formats.in.CellSensReader
- DOCUMENT_CREATOR_BUILD_NUMBER - Static variable in class loci.formats.in.CellSensReader
- DOCUMENT_CREATOR_MAJOR_VERSION - Static variable in class loci.formats.in.CellSensReader
- DOCUMENT_CREATOR_MINOR_VERSION - Static variable in class loci.formats.in.CellSensReader
- DOCUMENT_CREATOR_NAME - Static variable in class loci.formats.in.CellSensReader
- DOCUMENT_CREATOR_PACKAGE - Static variable in class loci.formats.in.CellSensReader
- DOCUMENT_CREATOR_SUB_VERSION - Static variable in class loci.formats.in.CellSensReader
- DOCUMENT_KEYS - Static variable in class loci.formats.in.ICSReader
- DOCUMENT_NAME - Static variable in class loci.formats.in.CellSensReader
- DOCUMENT_NAME - Static variable in class loci.formats.tiff.IFD
- DOCUMENT_NOTE - Static variable in class loci.formats.in.CellSensReader
- DOCUMENT_PRODUCT - Static variable in class loci.formats.in.CellSensReader
- DOCUMENT_PRODUCT_NAME - Static variable in class loci.formats.in.CellSensReader
- DOCUMENT_PRODUCT_VERSION - Static variable in class loci.formats.in.CellSensReader
- DOCUMENT_PROPERTIES - Static variable in class loci.formats.in.CellSensReader
- DOCUMENT_THUMB - Static variable in class loci.formats.in.CellSensReader
- DOCUMENT_TIME - Static variable in class loci.formats.in.CellSensReader
- DOCUMENT_TYPE_HINT - Static variable in class loci.formats.in.CellSensReader
- doFormatLayout(FormatEntry) - Method in class loci.plugins.config.ConfigWindow
- doInPlaceCaching - Variable in class loci.formats.Memoizer
-
If
true, then all memo files will be created in the same directory as the original file. - domains - Variable in class loci.formats.FormatReader
-
List of domains in which this format is used.
- doMustGroup() - Method in class loci.plugins.in.ImporterOptions
- doNotChangePattern - Variable in class loci.formats.FileStitcher
- DOPPLER_CORRECTION_ANGLE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- DOPPLER_SAMPLE_VOLUME_X_POSITION - Enum constant in enum class loci.formats.dicom.DicomAttribute
- DOPPLER_SAMPLE_VOLUME_Y_POSITION - Enum constant in enum class loci.formats.dicom.DicomAttribute
- doRecording - Variable in class loci.plugins.util.RecordedImageProcessor
- doStitchTiles() - Method in class loci.plugins.in.ImporterOptions
- doT - Variable in class loci.formats.in.InCellReader.MinimalInCellHandler
- DOT - Enum constant in enum class loci.formats.in.BaseZeissReader.DrawStyle
- DOT - Static variable in class loci.formats.ResourceNamer
- DOT_RANGE - Static variable in class loci.formats.tiff.IFD
- DOUBLE - Enum constant in enum class loci.formats.tiff.IFDType
- DOUBLE - Static variable in class loci.formats.FormatTools
-
Identifies the DOUBLE data type used to store pixel values.
- DOUBLE - Static variable in class loci.formats.in.CellSensReader
- DOUBLE - Static variable in class loci.formats.in.GatanReader
- DOUBLE_2 - Static variable in class loci.formats.in.CellSensReader
- DOUBLE_2_2 - Static variable in class loci.formats.in.CellSensReader
- DOUBLE_3 - Static variable in class loci.formats.in.CellSensReader
- DOUBLE_3_3 - Static variable in class loci.formats.in.CellSensReader
- DOUBLE_4 - Static variable in class loci.formats.in.CellSensReader
- DOUBLE_4_4 - Static variable in class loci.formats.in.CellSensReader
- DOUBLE_ARRAY_2 - Static variable in class loci.formats.in.CellSensReader
- DOUBLE_ARRAY_3 - Static variable in class loci.formats.in.CellSensReader
- DOUBLE_FLOAT_PIXEL_DATA - Enum constant in enum class loci.formats.dicom.DicomAttribute
- DOUBLE_INTERVAL - Static variable in class loci.formats.in.CellSensReader
- DOUBLE_RECT - Static variable in class loci.formats.in.CellSensReader
- doubleCapacity() - Method in class loci.formats.codec.ByteVector
- DoubleOption - Class in loci.plugins.prefs
-
A double option for one of the plugins.
- DoubleOption(String, boolean, String, String, double) - Constructor for class loci.plugins.prefs.DoubleOption
-
Constructs a double option with the given parameters.
- DoubleOption(HashMap<String, String>) - Constructor for class loci.plugins.prefs.DoubleOption
-
Constructs a double option with the parameters from the given map.
- doubleValue() - Method in class loci.formats.tiff.TiffRational
-
Returns the value of the specified number as a double.
- doUpgradeCheck() - Method in class loci.plugins.in.ImporterOptions
- download(URLConnection) - Static method in class loci.plugins.config.InstallWizard
- download(URLConnection, File) - Static method in class loci.plugins.config.InstallWizard
- DOWNWARDS_DIAGONAL - Enum constant in enum class loci.formats.in.BaseZeissReader.FillStyle
- doZ - Variable in class loci.formats.in.InCellReader.MinimalInCellHandler
- DP80_FRAME_CENTERING - Static variable in class loci.formats.in.CellSensReader
- drawColour - Variable in class loci.formats.in.BaseZeissReader.Shape
- drawDot(int, int) - Method in class loci.plugins.util.RecordedImageProcessor
- drawLine(int, int, int, int) - Method in class loci.plugins.util.RecordedImageProcessor
- drawOval(int, int, int, int) - Method in class loci.plugins.util.RecordedImageProcessor
- drawPixel(int, int) - Method in class loci.plugins.util.RecordedImageProcessor
- drawPolygon(Polygon) - Method in class loci.plugins.util.RecordedImageProcessor
- drawRect(int, int, int, int) - Method in class loci.plugins.util.RecordedImageProcessor
- drawString(String) - Method in class loci.plugins.util.RecordedImageProcessor
- drawString(String, int, int) - Method in class loci.plugins.util.RecordedImageProcessor
- drawStyle - Variable in class loci.formats.in.BaseZeissReader.Shape
- DrawStyle(int) - Constructor for enum class loci.formats.in.BaseZeissReader.DrawStyle
- DRI - Static variable in class loci.formats.services.JPEGTurboServiceImpl
- drivePictDecoder(int) - Method in class loci.formats.in.PictReader
-
Handles the opcodes in the PICT file.
- DS - Enum constant in enum class loci.formats.dicom.DicomVR
- DT - Enum constant in enum class loci.formats.dicom.DicomVR
- dualCamera - Variable in class loci.formats.in.MetamorphHandler
- dualCamera - Variable in class loci.formats.in.MetamorphTiffReader
- DUMMY_PIXEL - Static variable in class loci.formats.out.EPSWriter
- DummyMetadata - Class in loci.formats.meta
- DummyMetadata() - Constructor for class loci.formats.meta.DummyMetadata
- dumpXML() - Method in class loci.formats.ome.OMEPyramidStore
- duplicate() - Method in class loci.plugins.util.RecordedImageProcessor
- duplicate(Class<? extends IFormatReader>) - Method in class loci.formats.ReaderWrapper
-
Performs a deep copy of the reader, including nested wrapped readers.
- duplicate(Class<? extends IFormatWriter>) - Method in class loci.formats.WriterWrapper
-
Performs a deep copy of the writer, including nested wrapped writers.
- DUPLICATE_PLANES_DEFAULT - Static variable in class loci.formats.in.CV7000Reader
- DUPLICATE_PLANES_DEFAULT - Static variable in class loci.formats.in.InCellReader
- DUPLICATE_PLANES_KEY - Static variable in class loci.formats.in.CV7000Reader
- DUPLICATE_PLANES_KEY - Static variable in class loci.formats.in.InCellReader
- duplicatePlanes() - Method in class loci.formats.in.CV7000Reader
- duplicatePlanes() - Method in class loci.formats.in.InCellReader
- duplicateRecurse(Class<? extends IFormatReader>) - Method in class loci.formats.ReaderWrapper
- duplicateRecurse(Class<? extends IFormatWriter>) - Method in class loci.formats.WriterWrapper
- DV_MAGIC_BYTES_1 - Static variable in class loci.formats.in.DeltavisionReader
- DV_MAGIC_BYTES_2 - Static variable in class loci.formats.in.DeltavisionReader
- DVExtHdrFields(RandomAccessInputStream) - Constructor for class loci.formats.in.DeltavisionReader.DVExtHdrFields
- DWORD - Static variable in class loci.formats.in.CellSensReader
- dyeName - Variable in class loci.formats.in.FV1000Reader.ChannelData
- dyeName - Variable in class loci.formats.in.LeicaHandler.MultiBand
- dyeNames - Variable in class loci.formats.in.SVSReader
- dyes - Variable in class loci.formats.in.ND2Handler
- DYNAMIC_PROPERTIES - Static variable in class loci.formats.in.CellSensReader
- DynamicMetadataOptions - Class in loci.formats.in
-
Configuration object for readers and writers.
- DynamicMetadataOptions() - Constructor for class loci.formats.in.DynamicMetadataOptions
-
Creates an options object with metadata level set to
DynamicMetadataOptions.METADATA_LEVEL_DEFAULTand file validation set toDynamicMetadataOptions.READER_VALIDATE_DEFAULT. - DynamicMetadataOptions(MetadataLevel) - Constructor for class loci.formats.in.DynamicMetadataOptions
-
Creates an options object with metadata level set to the specified value and file validation set to
DynamicMetadataOptions.READER_VALIDATE_DEFAULT
E
- ealDE - Variable in class loci.formats.in.SDTInfo
- eArrow - Enum constant in enum class loci.formats.in.SlideBook7Reader.EGraphicType
- EASTEUROPE_CHARSET - Enum constant in enum class loci.formats.in.BaseZeissReader.Charset
- ECAT7_MAGIC - Static variable in class loci.formats.in.Ecat7Reader
- ECAT7_MAGIC_REGEX - Static variable in class loci.formats.in.Ecat7Reader
- Ecat7Reader - Class in loci.formats.in
-
Ecat7Reader is the file format reader for ECAT 7 files.
- Ecat7Reader() - Constructor for class loci.formats.in.Ecat7Reader
-
Constructs a new ECAT7 reader.
- ECHO_NUMBER - Enum constant in enum class loci.formats.dicom.DicomAttribute
- ECHO_TIME - Enum constant in enum class loci.formats.dicom.DicomAttribute
- ECHO_TRAIN_LENGTH - Enum constant in enum class loci.formats.dicom.DicomAttribute
- eCompressionJetRaw - Static variable in class loci.formats.in.SlideBook7Reader.CCompressionBase
- eCompressionLz4 - Static variable in class loci.formats.in.SlideBook7Reader.CCompressionBase
- eCompressionNone - Static variable in class loci.formats.in.SlideBook7Reader.CCompressionBase
- eCompressionRLE - Static variable in class loci.formats.in.SlideBook7Reader.CCompressionBase
- eCompressionZlib - Static variable in class loci.formats.in.SlideBook7Reader.CCompressionBase
- eCompressionZstd - Static variable in class loci.formats.in.SlideBook7Reader.CCompressionBase
- edf - Variable in class loci.formats.dicom.DicomFileInfo
- edf - Variable in class loci.formats.in.DicomReader
- EditTiffG - Class in loci.formats.tools
-
Provides a GUI for editing TIFF file comments.
- EditTiffG() - Constructor for class loci.formats.tools.EditTiffG
- eEllipse - Enum constant in enum class loci.formats.in.SlideBook7Reader.EGraphicType
- EFFECTIVE_DURATION - Enum constant in enum class loci.formats.dicom.DicomAttribute
- effectiveFieldCount - Variable in class loci.formats.in.FlexReader
- EFI_HEIGHT_MAP - Static variable in class loci.formats.in.CellSensReader
- EFI_SHARPNESS_MAP - Static variable in class loci.formats.in.CellSensReader
- EFI_STACK - Static variable in class loci.formats.in.CellSensReader
- EFI_TEXTURE_MAP - Static variable in class loci.formats.in.CellSensReader
- EGraphicType() - Constructor for enum class loci.formats.in.SlideBook7Reader.EGraphicType
- el(NodeList, int) - Method in class loci.formats.in.PrairieMetadata
-
Gets the
indexth element from the given list of nodes. - ELEMENT_STYLE_END - Static variable in class loci.formats.gui.XMLCellRenderer
- ELEMENT_STYLE_START - Static variable in class loci.formats.gui.XMLCellRenderer
- elementLength - Variable in class loci.formats.dicom.DicomTag
- elementName - Variable in class loci.formats.in.LeicaHandler
- elements - Variable in class loci.formats.FilePatternBlock
-
Elements within this block, e.g.
- eLine - Enum constant in enum class loci.formats.in.SlideBook7Reader.EGraphicType
- ELLIPSE - Enum constant in enum class loci.formats.in.BaseZeissReader.FeatureType
- ELLIPSE - Static variable in class loci.formats.in.FV1000Reader
- ELLIPSE - Static variable in class loci.formats.in.GatanReader
- ELLIPSE - Static variable in class loci.formats.in.ZeissLSMReader
- ellipses - Variable in class loci.formats.in.FakeReader
- EM_DAC - Static variable in class loci.formats.in.FluoviewReader
- EM_DOMAIN - Static variable in class loci.formats.FormatTools
-
Identifies the electron microscopy domain.
- EM_GAIN - Static variable in class loci.formats.in.CellSensReader
- EMBEDDED_STREAM - Static variable in class loci.formats.in.VolocityReader
- embeddedImages - Variable in class loci.formats.in.TillVisionReader
- embeddedOffset - Variable in class loci.formats.in.TillVisionReader
- emFilters - Variable in class loci.formats.in.InCellReader
- emission - Variable in class loci.formats.in.FlexReader.FilterGroup
- emission - Variable in class loci.formats.in.OIRReader.Channel
- emission - Variable in class loci.formats.in.ZeissCZIReader.Channel
- emissionFilter - Variable in class loci.formats.in.FV1000Reader.ChannelData
- emissionWavelength - Variable in class loci.formats.in.SVSReader
- emissionWavelengths - Variable in class loci.formats.in.FakeReader
- EMPTY_STRING - Static variable in class loci.formats.in.IM3Reader
- emWave - Variable in class loci.formats.in.BDReader
- emWave - Variable in class loci.formats.in.FV1000Reader.ChannelData
- emWave - Variable in class loci.formats.in.ImarisHDFReader
- emWave - Variable in class loci.formats.in.ND2Handler
- emWave - Variable in class loci.formats.in.NikonTiffReader
- emWave - Variable in class loci.formats.in.TissueFAXSReader.Channel
- emWavelen - Variable in class loci.formats.in.DeltavisionReader.DVExtHdrFields
-
Emission filter wavelength.
- emWavelength - Variable in class loci.formats.in.BaseZeissReader
- emWavelength - Variable in class loci.formats.in.ColumbusReader.Plane
- emWavelength - Variable in class loci.formats.in.MetamorphReader
-
The TIFF's emWavelength
- emWavelength - Variable in class loci.formats.in.OperettaReader.Channel
- emWavelength - Variable in class loci.formats.in.OperettaReader.Plane
- emWaves - Variable in class loci.formats.in.InCellReader
- emWaves - Variable in class loci.formats.in.LeicaReader
- enabledBox - Variable in class loci.plugins.config.ConfigWindow
- encloses(Region, Region) - Method in class loci.formats.in.DicomReader
- encode(byte[]) - Method in class loci.formats.filter.LZ4Filter
- encodeYUV(byte[], int) - Method in class org.libjpegturbo.turbojpeg.TJCompressor
-
Encode the uncompressed source image associated with this compressor instance and output a YUV planar image to the given destination buffer.
- encodeYUV(byte[], int, int, int, int, byte[], int, int) - Method in class org.libjpegturbo.turbojpeg.TJCompressor
- encodeYUV(int) - Method in class org.libjpegturbo.turbojpeg.TJCompressor
-
Encode the uncompressed source image associated with this compressor instance and return a buffer containing a YUV planar image.
- encodeYUV(int[], int, int, int, int, byte[], int, int) - Method in class org.libjpegturbo.turbojpeg.TJCompressor
- encodeYUV(BufferedImage, byte[], int) - Method in class org.libjpegturbo.turbojpeg.TJCompressor
-
Encode the uncompressed source image stored in
srcImageand output a YUV planar image to the given destination buffer. - encodeYUV(BufferedImage, int) - Method in class org.libjpegturbo.turbojpeg.TJCompressor
-
Encode the uncompressed source image stored in
srcImageand return a buffer containing a YUV planar image. - encoding - Variable in class loci.formats.in.NRRDReader
-
Data encoding.
- ENCODING - Static variable in class loci.formats.in.LIFReader
-
The encoding used in this file.
- ENCODING - Static variable in class loci.formats.in.LOFReader
-
The encoding used in this file.
- end - Variable in class loci.formats.FilePatternBlock
- end - Variable in class loci.formats.Modulo
- END - Static variable in class loci.formats.in.GIFReader
- END_TICKS - Enum constant in enum class loci.formats.in.BaseZeissReader.LineEndStyle
- endDocument() - Method in class loci.formats.in.BDVReader.BDVXMLHandler
- endDocument() - Method in class loci.formats.in.ND2Handler
- endDocument() - Method in class loci.formats.in.OMEXMLReader.OMEXMLHandler
- endElement(String, String, String) - Method in class loci.formats.in.BDVReader.BDVXMLHandler
- endElement(String, String, String) - Method in class loci.formats.in.BioRadSCNReader.SCNHandler
- endElement(String, String, String) - Method in class loci.formats.in.ColumbusReader.MeasurementHandler
- endElement(String, String, String) - Method in class loci.formats.in.CV7000Reader.MeasurementDataHandler
- endElement(String, String, String) - Method in class loci.formats.in.CV7000Reader.MeasurementSettingsHandler
- endElement(String, String, String) - Method in class loci.formats.in.FEITiffReader.FEIHandler
- endElement(String, String, String) - Method in class loci.formats.in.FlexReader.FlexHandler
- endElement(String, String, String) - Method in class loci.formats.in.InCellReader.InCellHandler
- endElement(String, String, String) - Method in class loci.formats.in.InCellReader.MinimalInCellHandler
- endElement(String, String, String) - Method in class loci.formats.in.IvisionReader.IvisionHandler
- endElement(String, String, String) - Method in class loci.formats.in.LeicaHandler
- endElement(String, String, String) - Method in class loci.formats.in.LeicaSCNReader.LeicaSCNHandler
- endElement(String, String, String) - Method in class loci.formats.in.OMEXMLReader.OMEXMLHandler
- endElement(String, String, String) - Method in class loci.formats.in.OperettaReader.OperettaHandler
- endElement(String, String, String) - Method in class loci.formats.in.ScanrReader.ScanrHandler
- endElement(String, String, String) - Method in class loci.formats.in.ZeissTIFFHandler
- endElement(String, String, String) - Method in class loci.formats.out.OMEXMLWriter.OMEHandler
- endElement(String, String, String, Attributes) - Method in class loci.formats.in.ND2Handler
- ENDIANNESS_OFFSET - Static variable in class loci.formats.in.MRCReader
- endIndex - Variable in class loci.formats.FilePattern
-
Indices into the pattern indicating the end of a numerical block.
- endOfFrameFlag - Variable in class loci.formats.in.SPCReader
- endOfFrameList - Variable in class loci.formats.in.SPCReader
- endOffset - Variable in class loci.formats.dicom.DicomTile
- endPointer - Variable in class loci.formats.in.LIFReader
- endPointer - Variable in class loci.formats.in.LOFReader
- endPos - Variable in class loci.formats.out.AVIWriter
- endTime - Variable in class loci.formats.in.CV7000Reader
- endTime - Variable in class loci.formats.in.SDTInfo
-
Macro time of the last photon.
- endX - Variable in class loci.formats.in.SPEReader.SpeROI
- endY - Variable in class loci.formats.in.SPEReader.SpeROI
- energyConvFactor - Variable in class loci.formats.in.DeltavisionReader.DVExtHdrFields
-
Energy conversion factor.
- ENHANCED_DYNAMIC_RANGE - Static variable in class loci.formats.in.CellSensReader
- ensureNonExisting(String) - Method in class loci.formats.tools.MakeTestOmeTiff
- entries - Variable in class loci.formats.in.ZeissCZIReader.AttachmentDirectory
- entries - Variable in class loci.formats.in.ZeissCZIReader.Directory
- entryName - Variable in class loci.formats.in.ZipReader
- entryToString(Object, String) - Static method in class loci.formats.tools.AmiraParameters
- ENV_SUFFIX - Static variable in class loci.formats.in.PrairieReader
- envFile - Variable in class loci.formats.in.PrairieReader
-
The associated XML files.
- eObjectPath - Enum constant in enum class loci.formats.in.SlideBook7Reader.EGraphicType
- EOC - Enum constant in enum class loci.formats.codec.JPEG2000SegmentMarker
- EOI - Static variable in class loci.formats.services.JPEGTurboServiceImpl
- EPH - Enum constant in enum class loci.formats.codec.JPEG2000SegmentMarker
- ePoint - Enum constant in enum class loci.formats.in.SlideBook7Reader.EGraphicType
- ePolygon - Enum constant in enum class loci.formats.in.SlideBook7Reader.EGraphicType
- EPSReader - Class in loci.formats.in
-
Reader is the file format reader for Encapsulated PostScript (EPS) files.
- EPSReader() - Constructor for class loci.formats.in.EPSReader
-
Constructs a new EPS reader.
- EPSWriter - Class in loci.formats.out
-
EPSWriter is the file format writer for Encapsulated PostScript (EPS) files.
- EPSWriter() - Constructor for class loci.formats.out.EPSWriter
- epxDiv - Variable in class loci.formats.in.SDTInfo
- equal(Length, Length) - Static method in class loci.formats.in.PrairieReader
-
Determines whether the two
Lengthvalues are equal. - equalReaders(IFormatReader, IFormatReader) - Static method in class loci.formats.FormatTools
-
Check if the two given readers are equal.
- equals(Object) - Method in class loci.formats.in.CellSensReader.TileCoordinate
- equals(Object) - Method in class loci.formats.in.CV7000Reader.Field
- equals(Object) - Method in class loci.formats.in.MetamorphTiffReader.Well
- equals(Object) - Method in class loci.formats.in.OIRReader.CZTKey
- equals(Object) - Method in class loci.formats.in.ZeissCZIReader.Coordinate
- equals(Object) - Method in class loci.formats.tiff.TiffRational
-
Indicates whether some other object is "equal to" this one.
- equals(Object) - Method in class loci.formats.TileStitcher.TileCoordinate
- equals(Object) - Method in class loci.plugins.config.FormatEntry
- equals(Object) - Method in class loci.plugins.prefs.OptionsList
- equals(TJScalingFactor) - Method in class org.libjpegturbo.turbojpeg.TJScalingFactor
-
Returns true or false, depending on whether this instance and
otherhave the same numerator and denominator. - equals(Node, Node) - Method in class loci.formats.services.OMEXMLServiceImpl
-
Compares two Elements for equality.
- equalStrips - Variable in class loci.formats.in.MinimalTiffReader
- equalStrips - Variable in class loci.formats.tiff.TiffParser
- eRectangle - Enum constant in enum class loci.formats.in.SlideBook7Reader.EGraphicType
- erode() - Method in class loci.plugins.util.RecordedImageProcessor
- eShape - Enum constant in enum class loci.formats.in.SlideBook7Reader.EGraphicType
- ESTIMATED_RADIOGRAPHIC_MAG_FACTOR - Enum constant in enum class loci.formats.dicom.DicomAttribute
- ETHNIC_GROUP - Enum constant in enum class loci.formats.dicom.DicomAttribute
- evalFile(String) - Method in class loci.formats.in.ZeissTIFFReader
-
Evaluate the metadata of a TIFF/XML file collection, and return this to the user.
- EVENT_ELAPSED_TIME - Enum constant in enum class loci.formats.dicom.DicomAttribute
- EVENT_TIMER_NAME - Enum constant in enum class loci.formats.dicom.DicomAttribute
- eVolume - Enum constant in enum class loci.formats.in.SlideBook7Reader.EGraphicType
- excitation - Variable in class loci.formats.in.CV7000Reader.Channel
- excitation - Variable in class loci.formats.in.FlexReader.FilterGroup
- excitation - Variable in class loci.formats.in.OIRReader.Channel
- excitation - Variable in class loci.formats.in.ZeissCZIReader.Channel
- excitationFilter - Variable in class loci.formats.in.FV1000Reader.ChannelData
- excitationWavelength - Variable in class loci.formats.in.SVSReader
- excitationWavelengths - Variable in class loci.formats.in.FakeReader
- exclude - Variable in class loci.formats.in.InCellReader
- execute() - Method in class loci.plugins.in.ImportProcess
-
Performs the import preparation process, notifying status listeners at each step.
- exFilters - Variable in class loci.formats.in.InCellReader
- EXIF - Static variable in class loci.formats.tiff.IFD
- EXIF_VERSION - Static variable in class loci.formats.tiff.IFD
- EXIFService - Interface in loci.formats.services
- EXIFServiceImpl - Class in loci.formats.services
- EXIFServiceImpl() - Constructor for class loci.formats.services.EXIFServiceImpl
- exists - Variable in class loci.formats.in.OMETiffReader.OMETiffPlane
-
Whether or not the file meant to contain this plane exists.
- exists(String) - Method in interface loci.formats.services.JHDFService
-
Checks if path in HDF5 file exists.
- exists(String) - Method in class loci.formats.services.JHDFServiceImpl
- exit() - Method in class loci.formats.tools.EditTiffG
- exp() - Method in class loci.plugins.util.RecordedImageProcessor
- EXP_ACCUMS - Enum constant in enum class loci.formats.in.SPEReader.SpeHeaderEntry
- EXP_REPEATS - Enum constant in enum class loci.formats.in.SPEReader.SpeHeaderEntry
- EXP_TIME_LOCAL - Enum constant in enum class loci.formats.in.SPEReader.SpeHeaderEntry
- EXP_TIME_UTC - Enum constant in enum class loci.formats.in.SPEReader.SpeHeaderEntry
- expandPixels(int, byte[], byte[], int) - Method in class loci.formats.in.PictReader
-
Expand an array of bytes.
- EXPANSION_TABLE - Static variable in class loci.formats.in.PictReader
-
Table used in expanding pixels that use less than 8 bits.
- expectETS - Variable in class loci.formats.in.CellSensReader
- EXPERIMENT - Static variable in class loci.formats.in.LeicaReader
- EXPERIMENT_FILE - Static variable in class loci.formats.in.BDReader
- EXPERIMENT_FILE - Static variable in class loci.formats.in.ScanrReader
- experimenterName - Variable in class loci.formats.in.ImaconReader
- explode() - Method in class loci.formats.FilePatternBlock
- exporter - Variable in class loci.plugins.LociExporter
- Exporter - Class in loci.plugins.out
-
Core logic for the Bio-Formats Exporter ImageJ plugin.
- Exporter(LociExporter, ImagePlus) - Constructor for class loci.plugins.out.Exporter
- exposure - Variable in class loci.formats.in.BDReader
- exposure - Variable in class loci.formats.in.InCellReader.Image
- exposure - Variable in class loci.formats.in.InCellReader.InCellHandler
- exposure - Variable in class loci.formats.in.ZeissCZIReader.Channel
- EXPOSURE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- EXPOSURE - Enum constant in enum class loci.formats.in.SPEReader.SpeHeaderEntry
- EXPOSURE_BIAS_VALUE - Static variable in class loci.formats.tiff.IFD
- EXPOSURE_CONTROL_MODE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- EXPOSURE_IN_UAS - Enum constant in enum class loci.formats.dicom.DicomAttribute
- EXPOSURE_INDEX - Static variable in class loci.formats.tiff.IFD
- EXPOSURE_METERING_MODE - Static variable in class loci.formats.in.CellSensReader
- EXPOSURE_MODE - Static variable in class loci.formats.tiff.IFD
- EXPOSURE_PROGRAM - Static variable in class loci.formats.tiff.IFD
- EXPOSURE_RATIO - Static variable in class loci.formats.in.NDPIReader
- EXPOSURE_TIME - Enum constant in enum class loci.formats.dicom.DicomAttribute
- EXPOSURE_TIME - Static variable in class loci.formats.in.CellSensReader
- EXPOSURE_TIME - Static variable in class loci.formats.in.FluoviewReader
- EXPOSURE_TIME - Static variable in class loci.formats.in.NDPIReader
- EXPOSURE_TIME - Static variable in class loci.formats.tiff.IFD
-
EXIF tags.
- EXPOSURE_UNITS - Enum constant in enum class loci.formats.in.SPEReader.SpeHeaderEntry
- exposures - Variable in class loci.formats.in.MetamorphHandler
- exposures - Variable in class loci.formats.in.ScanrReader
- EXPOSURES_ON_PLATE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- exposureScale - Variable in class loci.formats.in.SVSReader
- exposureTime - Variable in class loci.formats.in.BaseZeissReader
- exposureTime - Variable in class loci.formats.in.BioRadSCNReader
- exposureTime - Variable in class loci.formats.in.CV7000Reader.Channel
- exposureTime - Variable in class loci.formats.in.FakeReader
-
exposure time per plane info
- exposureTime - Variable in class loci.formats.in.FluoviewReader
- exposureTime - Variable in class loci.formats.in.IvisionReader
- exposureTime - Variable in class loci.formats.in.JDCEReader.PlaneMetadata
- exposureTime - Variable in class loci.formats.in.LeicaReader
- exposureTime - Variable in class loci.formats.in.LiFlimReader
- exposureTime - Variable in class loci.formats.in.MetamorphReader
- exposureTime - Variable in class loci.formats.in.MicroCTReader
- exposureTime - Variable in class loci.formats.in.MicromanagerReader.Position
- exposureTime - Variable in class loci.formats.in.ND2Handler
- exposureTime - Variable in class loci.formats.in.ND2Reader
- exposureTime - Variable in class loci.formats.in.OperettaReader.Channel
- exposureTime - Variable in class loci.formats.in.OperettaReader.Plane
- exposureTime - Variable in class loci.formats.in.SVSReader
- exposureTime - Variable in class loci.formats.in.TecanReader.Channel
- exposureTime - Variable in class loci.formats.in.TecanReader.Image
- exposureTime - Variable in class loci.formats.in.ZeissCZIReader.SubBlock
- exposureTimes - Variable in class loci.formats.in.CellSensReader.Pyramid
- exposureTimes - Variable in class loci.formats.in.LeicaHandler
- exposureTimes - Variable in class loci.formats.in.SimplePCITiffReader
- exposureTimes - Variable in class loci.formats.in.TillVisionReader
- exposureTimes - Variable in class loci.formats.in.ZeissXRMReader
- exposureTimeUnit - Variable in class loci.formats.in.LiFlimReader
- expTime - Variable in class loci.formats.in.DeltavisionReader.DVExtHdrFields
-
Exposure time in seconds.
- expTimes - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataTempBuffer
- expTimes - Variable in class loci.formats.in.LIFReader
- EXT_TRIGGER - Enum constant in enum class loci.formats.in.SPEReader.SpeHeaderEntry
- extCount - Variable in class loci.formats.in.PerkinElmerReader
- EXTENDED_DEPTH_OF_FIELD - Enum constant in enum class loci.formats.dicom.DicomAttribute
- EXTENDED_OFFSET_TABLE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- EXTENDED_OFFSET_TABLE_LENGTHS - Enum constant in enum class loci.formats.dicom.DicomAttribute
- EXTENSION - Static variable in class loci.formats.in.GIFReader
- ExtensionFileFilter - Class in loci.formats.gui
-
A file filter based on file extensions, for use with a JFileChooser.
- ExtensionFileFilter(String[], String) - Constructor for class loci.formats.gui.ExtensionFileFilter
-
Constructs a new filter that accepts the given extensions.
- ExtensionFileFilter(String, String) - Constructor for class loci.formats.gui.ExtensionFileFilter
-
Constructs a new filter that accepts the given extension.
- extensions - Variable in class loci.plugins.config.ConfigWindow
- extensions - Variable in class loci.plugins.macro.MacroFunctions
- EXTERNAL_DATA_VOLUME - Static variable in class loci.formats.in.CellSensReader
- EXTERNAL_FILE_PROPERTIES - Static variable in class loci.formats.in.CellSensReader
- externals - Variable in class loci.formats.FileStitcher
- ExternalSeries(FilePattern) - Constructor for class loci.formats.FileStitcher.ExternalSeries
- extHdrFields - Variable in class loci.formats.in.DeltavisionReader
-
Initialize an array of Extended Header Field structures.
- extHeaderSize - Variable in class loci.formats.in.MRCReader
-
Size of extended header
- extIndex - Variable in class loci.formats.in.PerkinElmerReader.PixelsFile
- EXTRA_FILES - Static variable in class loci.formats.in.VectraReader
- EXTRA_IMAGES - Static variable in class loci.formats.in.AFIReader
- EXTRA_SAMPLES - Static variable in class loci.formats.in.CellSensReader
- EXTRA_SAMPLES - Static variable in class loci.formats.tiff.IFD
- EXTRA_SAMPLES_PROPERTIES - Static variable in class loci.formats.in.CellSensReader
- EXTRA_TAG_1 - Static variable in class loci.formats.in.VentanaReader
- EXTRA_TAG_2 - Static variable in class loci.formats.in.VentanaReader
- extractCoreMetaData() - Method in class loci.formats.tools.AmiraParameters
- extractTokensFromFakeSeries(String) - Method in class loci.formats.in.FakeReader
- extraFiles - Variable in class loci.formats.in.CellSensReader
- extraFiles - Variable in class loci.formats.in.CV7000Reader
- extraFiles - Variable in class loci.formats.in.OlympusTileReader
- extraFiles - Variable in class loci.formats.in.TecanReader
- extraFiles - Variable in class loci.formats.in.VolocityReader
- extraImages - Variable in class loci.formats.in.SVSReader
- extraImages - Variable in class loci.formats.in.ZeissCZIReader
- extras - Variable in class loci.formats.in.LeicaHandler
- extras - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.LMSMetadataExtractor
- exts - Variable in class loci.formats.gui.ExtensionFileFilter
-
List of valid extensions.
- extSize - Variable in class loci.formats.in.DeltavisionReader
-
Size of extended header.
- exWave - Variable in class loci.formats.in.BDReader
- exWave - Variable in class loci.formats.in.FV1000Reader.ChannelData
- exWave - Variable in class loci.formats.in.ImarisHDFReader
- exWave - Variable in class loci.formats.in.LeicaHandler.Channel
- exWave - Variable in class loci.formats.in.ND2Handler
- exWave - Variable in class loci.formats.in.NikonTiffReader
- exWave - Variable in class loci.formats.in.TissueFAXSReader.Channel
- exWavelen - Variable in class loci.formats.in.DeltavisionReader.DVExtHdrFields
-
Excitation filter wavelength.
- exWavelength - Variable in class loci.formats.in.BaseZeissReader
- exWavelength - Variable in class loci.formats.in.ColumbusReader.Plane
- exWavelength - Variable in class loci.formats.in.OperettaReader.Channel
- exWavelength - Variable in class loci.formats.in.OperettaReader.Plane
- exWaves - Variable in class loci.formats.in.InCellReader
- exWaves - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataTempBuffer
- exWaves - Variable in class loci.formats.in.LeicaReader
- exWaves - Variable in class loci.formats.in.LIFReader
F
- F_KEY - Static variable in class loci.formats.in.LiFlimReader
- F_NUMBER - Static variable in class loci.formats.tiff.IFD
- factor - Variable in class loci.formats.in.ZeissTIFFHandler.Scaling.Dimension
- factors - Variable in class loci.formats.in.FlexReader.FlexFile
- factors - Variable in class loci.formats.in.FlexReader.FlexHandler
- factory - Variable in class loci.formats.FormatReader
- FAIL_ON_MISSING_DEFAULT - Static variable in class loci.formats.in.CellSensReader
- FAIL_ON_MISSING_DEFAULT - Static variable in class loci.formats.in.OMETiffReader
- FAIL_ON_MISSING_KEY - Static variable in class loci.formats.in.CellSensReader
- FAIL_ON_MISSING_KEY - Static variable in class loci.formats.in.OMETiffReader
- FAILED_SOP_SEQUENCE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- FAILED_SOP_UID_LIST - Enum constant in enum class loci.formats.dicom.DicomAttribute
- failOnMissingETS() - Method in class loci.formats.in.CellSensReader
- failOnMissingTIFF() - Method in class loci.formats.in.OMETiffReader
- FAILURE_REASON - Enum constant in enum class loci.formats.dicom.DicomAttribute
- FAKE_EXT - Static variable in class loci.formats.ResourceNamer
- fakeBigTiff - Variable in class loci.formats.tiff.TiffParser
-
Whether or not 64-bit offsets are used for non-BigTIFF files.
- FakeImage - Class in loci.formats.tools
-
Generates fake image structures.
- FakeImage(Location) - Constructor for class loci.formats.tools.FakeImage
- FakeReader - Class in loci.formats.in
-
FakeReader is the file format reader for faking input data.
- FakeReader() - Constructor for class loci.formats.in.FakeReader
-
Constructs a new fake reader.
- FakeReader.TextLine - Class in loci.formats.in
- fakeSeries - Variable in class loci.formats.in.FakeReader
-
List of used files if the fake is a SPW structure
- falseColor - Variable in class loci.formats.CoreMetadata
-
Indicates whether or not we can ignore the color map (if present).
- FAN_SPEED - Static variable in class loci.formats.in.CellSensReader
- fb - Variable in class loci.formats.in.BaseZeissReader.Shape
- fcc - Variable in class loci.formats.in.AVIReader
- FCS_DATA_IDENTIFIER - Static variable in class loci.formats.in.SDTInfo
-
For .sdt files created in FIFO mode (setup, data blocks = Decay, FCS, FIDA, FILDA & MCS curves for each used routing channel).
- fcsDecayCalc - Variable in class loci.formats.in.SDTInfo
-
Bit 0 = 1 - decay curve calculated.
- fcsPoints - Variable in class loci.formats.in.SDTInfo
-
No of FCS values.
- fcsType - Variable in class loci.formats.in.SDTInfo
-
0 - linear FCS with log binning (100 bins/log) when bit 15 = 1 (0x8000) - Multi-Tau FCS where bits 14-0 = ktau parameter.
- fctlCount - Variable in class loci.formats.in.APNGReader.PNGInputStream
- FD - Enum constant in enum class loci.formats.dicom.DicomVR
- fdatValid - Variable in class loci.formats.in.APNGReader.PNGInputStream
- FEATURE - Static variable in class loci.formats.in.BDVReader.H5Constants
- FEATURE - Static variable in class loci.formats.in.CellH5Reader.CellH5Constants
- FeatureType(int, int) - Constructor for enum class loci.formats.in.BaseZeissReader.FeatureType
- FEI_MAGIC_STRING - Static variable in class loci.formats.in.FEIReader
- FEIHandler() - Constructor for class loci.formats.in.FEITiffReader.FEIHandler
- FEIReader - Class in loci.formats.in
-
FEIReader is the file format reader for FEI and Philips .img files.
- FEIReader() - Constructor for class loci.formats.in.FEIReader
-
Constructs a new FEI reader.
- FEITiffReader - Class in loci.formats.in
-
FEITiffReader is the file format reader for TIFF files produced by various FEI software.
- FEITiffReader() - Constructor for class loci.formats.in.FEITiffReader
- FEITiffReader.FEIHandler - Class in loci.formats.in
- fetchRow(MdbTableDef) - Method in class loci.formats.services.MDBServiceImpl
-
Fetches the next row from the table, ignoring potential parsing exceptions.
- fetchXMLId() - Method in class loci.formats.in.BDVReader
- fidaPoints - Variable in class loci.formats.in.SDTInfo
-
No of FIDA values.
- fidaTime - Variable in class loci.formats.in.SDTInfo
-
Interval time [ms] for FIDA histogram.
- field - Variable in class loci.formats.in.CellomicsReader.ChannelFile
- field - Variable in class loci.formats.in.ColumbusReader.Plane
- field - Variable in class loci.formats.in.CV7000Reader.Field
- field - Variable in class loci.formats.in.CV7000Reader.Plane
- field - Variable in class loci.formats.in.FlexReader.FlexFile
- field - Variable in class loci.formats.in.OperettaReader.Plane
- field - Variable in class loci.formats.in.TecanReader.Image
- Field() - Constructor for class loci.formats.in.CV7000Reader.Field
- FIELD - Static variable in class loci.formats.ResourceNamer
- FIELD_AUX_FLAGS - Static variable in class loci.formats.in.IM3Reader
- FIELD_BAND_INDEX - Static variable in class loci.formats.in.IM3Reader
- FIELD_BANDS - Static variable in class loci.formats.in.IM3Reader
- FIELD_CLASS_ID - Static variable in class loci.formats.in.IM3Reader
- FIELD_DATA - Static variable in class loci.formats.in.IM3Reader
- FIELD_DATA_SET - Static variable in class loci.formats.in.IM3Reader
- FIELD_EXPOSURE - Static variable in class loci.formats.in.IM3Reader
- FIELD_FILE_VERSION - Static variable in class loci.formats.in.IM3Reader
- FIELD_FILTER_PAIR - Static variable in class loci.formats.in.IM3Reader
- FIELD_FIXED_FILTER - Static variable in class loci.formats.in.IM3Reader
- FIELD_HOMOGENEOUS - Static variable in class loci.formats.in.IM3Reader
- FIELD_INDEX - Static variable in class loci.formats.in.ND2Handler
- FIELD_MAGNITUDES - Static variable in class loci.formats.in.IM3Reader
- FIELD_MANUFACTURER - Static variable in class loci.formats.in.IM3Reader
- FIELD_MILLIMETERS_PER_PIXEL - Static variable in class loci.formats.in.IM3Reader
- FIELD_NAME - Static variable in class loci.formats.in.IM3Reader
- FIELD_NUANCE_FLAGS - Static variable in class loci.formats.in.IM3Reader
- FIELD_OBJECTIVE - Static variable in class loci.formats.in.IM3Reader
- FIELD_PART_NUMBER - Static variable in class loci.formats.in.IM3Reader
- FIELD_PROTOCOL - Static variable in class loci.formats.in.IM3Reader
- FIELD_PROXY_PARENT_FILE_NAME - Static variable in class loci.formats.in.IM3Reader
- FIELD_SAMPLE_ID - Static variable in class loci.formats.in.IM3Reader
- FIELD_SHAPE - Static variable in class loci.formats.in.IM3Reader
- FIELD_SOURCE_FILE_NAME - Static variable in class loci.formats.in.IM3Reader
- FIELD_SPECTRA - Static variable in class loci.formats.in.IM3Reader
- FIELD_SPECTRAL_BASIS_INFO - Static variable in class loci.formats.in.IM3Reader
- FIELD_SPECTRAL_LIBRARY - Static variable in class loci.formats.in.IM3Reader
- FIELD_SPECTRUM - Static variable in class loci.formats.in.IM3Reader
- FIELD_THUMBNAIL - Static variable in class loci.formats.in.IM3Reader
- FIELD_TIMESTAMP - Static variable in class loci.formats.in.IM3Reader
- FIELD_TYPE - Static variable in class loci.formats.in.CellSensReader
- FIELD_TYPE_ID - Static variable in class loci.formats.in.IM3Reader
- FIELD_USER_COMMENTS - Static variable in class loci.formats.in.IM3Reader
- FIELD_VALUES - Static variable in class loci.formats.in.IM3Reader
- FIELD_WAVELENGTH - Static variable in class loci.formats.in.IM3Reader
- FIELD_WAVELENGTHS - Static variable in class loci.formats.in.IM3Reader
- fieldCol - Variable in class loci.formats.in.MetamorphTiffReader.Well
- fieldCols - Variable in class loci.formats.in.BDReader
- fieldColumnCount - Variable in class loci.formats.in.MetamorphTiffReader
- fieldColumns - Variable in class loci.formats.in.ScanrReader
- fieldCount - Variable in class loci.formats.in.CellWorxReader
- fieldCount - Variable in class loci.formats.in.FlexReader
- fieldCount - Variable in class loci.formats.in.InCellReader
- fieldCount - Variable in class loci.formats.internal.WellContainer
- fieldIndex - Variable in class loci.formats.in.FluoviewReader
- fieldIndex - Variable in class loci.formats.in.ND2Reader
- FieldInfo() - Constructor for class loci.formats.in.CellVoyagerReader.FieldInfo
- fieldMap - Variable in class loci.formats.in.CellWorxReader
- fieldNames - Variable in class loci.formats.in.ZeissCZIReader
- fieldOffsets - Variable in class loci.formats.in.FluoviewReader
- fieldPositionX - Variable in class loci.formats.in.ScanrReader
- fieldPositionY - Variable in class loci.formats.in.ScanrReader
- fieldPosX - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataTempBuffer
- fieldPosX - Variable in class loci.formats.in.LIFReader
- fieldPosY - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataTempBuffer
- fieldPosY - Variable in class loci.formats.in.LIFReader
- fieldRow - Variable in class loci.formats.in.MetamorphTiffReader.Well
- fieldRowCount - Variable in class loci.formats.in.MetamorphTiffReader
- fieldRows - Variable in class loci.formats.in.BDReader
- fieldRows - Variable in class loci.formats.in.ScanrReader
- fields - Variable in class loci.formats.in.CellVoyagerReader.AreaInfo
- fields - Variable in class loci.formats.in.CV7000Reader
- fields - Variable in class loci.formats.in.FakeReader
- fifoTyp - Variable in class loci.formats.in.SDTInfo
- fildaPoints - Variable in class loci.formats.in.SDTInfo
-
No of FILDA values.
- fildaTime - Variable in class loci.formats.in.SDTInfo
-
Interval time [ms] for FILDA histogram.
- file - Variable in class loci.formats.dicom.DicomFileInfo
- file - Variable in class loci.formats.dicom.DicomTile
- file - Variable in class loci.formats.in.ColumbusReader.Plane
- file - Variable in class loci.formats.in.CV7000Reader.Plane
- file - Variable in class loci.formats.in.FlexReader.FlexFile
- file - Variable in class loci.formats.in.OIRReader.PixelBlock
- file - Variable in class loci.formats.in.OlympusTileReader.Tile
- file - Variable in class loci.formats.in.TecanReader.Image
- file - Variable in class loci.formats.in.TissueFAXSReader.ScanRegion
- file - Variable in class loci.formats.tools.EditTiffG
- FILE - Enum constant in enum class loci.formats.codec.JPEG2000BoxType
- FILE - Enum constant in enum class loci.plugins.in.ImportStep
- FILE_LENGTH - Static variable in class loci.formats.in.CanonRawReader
- FILE_MAGIC_STRING - Static variable in class loci.formats.in.OBFReader
- FILE_META_INFO_GROUP_LENGTH - Enum constant in enum class loci.formats.dicom.DicomAttribute
- FILE_META_INFO_VERSION - Enum constant in enum class loci.formats.dicom.DicomAttribute
- FILE_SET_CONSISTENCY_FLAG - Enum constant in enum class loci.formats.dicom.DicomAttribute
- FILE_SET_DESCRIPTOR_FILE_ID - Enum constant in enum class loci.formats.dicom.DicomAttribute
- FILE_SET_ID - Enum constant in enum class loci.formats.dicom.DicomAttribute
- FILE_SOURCE - Static variable in class loci.formats.tiff.IFD
- file_version - Variable in class loci.formats.in.OBFReader
- fileBox - Variable in class loci.formats.tools.EditTiffG
- fileExists(String) - Static method in class loci.formats.in.LeicaMicrosystemsMetadata.LMSFileReader
-
Checks if file at path exists
- fileExists(String) - Static method in class loci.formats.in.LeicaMicrosystemsMetadata.LMSXmlDocument
-
Checks if file at path exists and corrects paths to be case sensitive
- fileGroupOption(String) - Method in class loci.formats.FormatReader
- fileGroupOption(String) - Method in interface loci.formats.IFormatReader
-
Returns an indication of whether the files in a multi-file dataset can be handled individually.
- fileGroupOption(String) - Method in class loci.formats.ImageReader
- fileGroupOption(String) - Method in class loci.formats.in.AFIReader
- fileGroupOption(String) - Method in class loci.formats.in.AnalyzeReader
- fileGroupOption(String) - Method in class loci.formats.in.APLReader
- fileGroupOption(String) - Method in class loci.formats.in.BDReader
- fileGroupOption(String) - Method in class loci.formats.in.BioRadReader
- fileGroupOption(String) - Method in class loci.formats.in.BrukerReader
- fileGroupOption(String) - Method in class loci.formats.in.CellomicsReader
- fileGroupOption(String) - Method in class loci.formats.in.CellSensReader
- fileGroupOption(String) - Method in class loci.formats.in.CellVoyagerReader
- fileGroupOption(String) - Method in class loci.formats.in.CellWorxReader
- fileGroupOption(String) - Method in class loci.formats.in.ColumbusReader
- fileGroupOption(String) - Method in class loci.formats.in.CV7000Reader
- fileGroupOption(String) - Method in class loci.formats.in.DCIMGReader
- fileGroupOption(String) - Method in class loci.formats.in.DicomReader
- fileGroupOption(String) - Method in class loci.formats.in.FlexReader
- fileGroupOption(String) - Method in class loci.formats.in.FujiReader
- fileGroupOption(String) - Method in class loci.formats.in.FV1000Reader
- fileGroupOption(String) - Method in class loci.formats.in.HitachiReader
- fileGroupOption(String) - Method in class loci.formats.in.ICSReader
- fileGroupOption(String) - Method in class loci.formats.in.ImagicReader
- fileGroupOption(String) - Method in class loci.formats.in.InCellReader
- fileGroupOption(String) - Method in class loci.formats.in.JDCEReader
- fileGroupOption(String) - Method in class loci.formats.in.KLBReader
- fileGroupOption(String) - Method in class loci.formats.in.L2DReader
- fileGroupOption(String) - Method in class loci.formats.in.LeicaReader
- fileGroupOption(String) - Method in class loci.formats.in.MetamorphReader
- fileGroupOption(String) - Method in class loci.formats.in.MIASReader
- fileGroupOption(String) - Method in class loci.formats.in.MicroCTReader
- fileGroupOption(String) - Method in class loci.formats.in.MicromanagerReader
- fileGroupOption(String) - Method in class loci.formats.in.NDPIReader
- fileGroupOption(String) - Method in class loci.formats.in.NDPISReader
- fileGroupOption(String) - Method in class loci.formats.in.NiftiReader
- fileGroupOption(String) - Method in class loci.formats.in.NRRDReader
- fileGroupOption(String) - Method in class loci.formats.in.OIRReader
- fileGroupOption(String) - Method in class loci.formats.in.OlympusTileReader
- fileGroupOption(String) - Method in class loci.formats.in.OMETiffReader
- fileGroupOption(String) - Method in class loci.formats.in.OperettaReader
- fileGroupOption(String) - Method in class loci.formats.in.PerkinElmerReader
- fileGroupOption(String) - Method in class loci.formats.in.PrairieReader
- fileGroupOption(String) - Method in class loci.formats.in.ScanrReader
- fileGroupOption(String) - Method in class loci.formats.in.SPCReader
- fileGroupOption(String) - Method in class loci.formats.in.SVSReader
- fileGroupOption(String) - Method in class loci.formats.in.TCSReader
- fileGroupOption(String) - Method in class loci.formats.in.TecanReader
- fileGroupOption(String) - Method in class loci.formats.in.TillVisionReader
- fileGroupOption(String) - Method in class loci.formats.in.TrestleReader
- fileGroupOption(String) - Method in class loci.formats.in.VentanaReader
- fileGroupOption(String) - Method in class loci.formats.in.VisitechReader
- fileGroupOption(String) - Method in class loci.formats.in.XLEFReader
- fileGroupOption(String) - Method in class loci.formats.in.ZeissLSMReader
- fileGroupOption(String) - Method in class loci.formats.in.ZeissTIFFReader
- fileGroupOption(String) - Method in class loci.formats.ReaderWrapper
- fileGroupOption(String, String[]) - Method in class loci.plugins.macro.LociFunctions
- fileGUID - Variable in class loci.formats.in.ZeissCZIReader.FileHeader
- FileHeader() - Constructor for class loci.formats.in.ZeissCZIReader.FileHeader
- fileIndex - Variable in class loci.formats.dicom.DicomTile
- fileIndex - Variable in class loci.formats.in.ColumbusReader.Plane
- FileInfo - Class in loci.formats
-
Encompasses basic metadata about a file.
- FileInfo() - Constructor for class loci.formats.FileInfo
- FILEINFO_STRING - Static variable in class loci.formats.in.KodakReader
- fileLength - Variable in class loci.formats.in.LeicaReader
-
Length of each file name.
- filelist - Variable in class loci.formats.in.KLBReader
- fileList - Variable in class loci.formats.in.DicomReader
- fileMap - Variable in class loci.formats.in.CellSensReader
- fileMetaLengthPointer - Variable in class loci.formats.out.DicomWriter
- filename - Variable in class loci.formats.FileInfo
-
Absolute path to this file.
- filename - Variable in class loci.formats.gui.ImageViewer
- filename - Variable in class loci.formats.in.CellomicsReader.ChannelFile
- filename - Variable in class loci.formats.in.InCellReader.Image
- filename - Variable in class loci.formats.in.MIASReader.AnalysisFile
- filename - Variable in class loci.formats.in.OperettaReader.Plane
- filename - Variable in class loci.formats.in.PrairieMetadata.PFile
-
filenameattribute of this<File>. - filename - Variable in class loci.formats.in.ZeissCZIReader.Segment
- filename - Variable in class loci.formats.in.ZeissTIFFReader.Plane
- filename - Variable in class loci.formats.tiff.TiffSaver
-
Output filename.
- fileNameMap - Variable in class loci.formats.in.MicromanagerReader.Position
- filenames - Variable in class loci.formats.in.FV1000Reader
- fileOffset - Variable in class loci.formats.dicom.DicomTile
- fileOffset - Variable in class loci.formats.in.LIFReader.MemoryBlock
- filePart - Variable in class loci.formats.in.ZeissCZIReader.AttachmentEntry
- filePart - Variable in class loci.formats.in.ZeissCZIReader.DirectoryEntry
- filePart - Variable in class loci.formats.in.ZeissCZIReader.FileHeader
- filepath - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.LMSXmlDocument
- filePath - Variable in class loci.formats.services.POIServiceImpl
- FILEPATH - Enum constant in enum class loci.formats.in.LeicaMicrosystemsMetadata.LMSXmlDocument.InitFrom
- FilePattern - Class in loci.formats
-
Represents a collection of files meant to be part of the same data series.
- FilePattern(String) - Constructor for class loci.formats.FilePattern
-
Creates a pattern object for files with the given pattern string.
- FilePattern(String, String) - Constructor for class loci.formats.FilePattern
-
Creates a pattern object using the given filename and directory path as a template.
- FilePattern(Location) - Constructor for class loci.formats.FilePattern
-
Creates a pattern object using the given file as a template.
- FilePatternBlock - Class in loci.formats
-
FilePatternBlock represents a single block in a
FilePattern. - FilePatternBlock(String) - Constructor for class loci.formats.FilePatternBlock
-
Builds a FilePatternBlock from a block string.
- FilePatternDialog - Class in loci.plugins.in
-
Bio-Formats Importer file pattern dialog box.
- FilePatternDialog(ImportProcess) - Constructor for class loci.plugins.in.FilePatternDialog
-
Creates a file pattern dialog for the Bio-Formats Importer.
- FilePatternReader - Class in loci.formats.in
- FilePatternReader() - Constructor for class loci.formats.in.FilePatternReader
-
Constructs a new pattern reader.
- filePosition - Variable in class loci.formats.in.ZeissCZIReader.AttachmentEntry
- filePosition - Variable in class loci.formats.in.ZeissCZIReader.DirectoryEntry
- fileReader - Variable in class loci.formats.gui.ImageViewer
-
Reader for files on disk.
- files - Variable in class loci.formats.FilePattern
-
File listing for this file pattern.
- files - Variable in class loci.formats.FileStitcher.ExternalSeries
- files - Variable in class loci.formats.in.CellomicsReader
- files - Variable in class loci.formats.in.HamamatsuVMSReader
- files - Variable in class loci.formats.in.ImprovisionTiffReader
- files - Variable in class loci.formats.in.LeicaReader
-
Array of image file names.
- files - Variable in class loci.formats.in.MetamorphTiffReader
- files - Variable in class loci.formats.in.OlympusTileReader.Tile
- files - Variable in class loci.formats.in.PerkinElmerReader
-
List of files to open.
- files - Variable in class loci.formats.in.PrairieMetadata.Frame
-
<File>elements beneath this<Frame>, keyed on each file'schannel. - files - Variable in class loci.formats.in.SEQReader
- files - Variable in class loci.formats.in.SlidebookTiffReader
- files - Variable in class loci.formats.in.TrestleReader
- files - Variable in class loci.formats.in.VarianFDFReader
- files - Variable in class loci.formats.in.VisitechReader
-
Files in this dataset.
- files - Variable in class loci.formats.in.ZeissZVIReader
- files - Variable in class loci.formats.internal.WellContainer
- files - Variable in class loci.formats.services.POIServiceImpl
- fileSave - Variable in class loci.formats.gui.ImageViewer
- fileSizes - Variable in class loci.formats.services.POIServiceImpl
- fileStitcher - Variable in class loci.plugins.in.ImportProcess
- FileStitcher - Class in loci.formats
-
Logic to stitch together files with similar names.
- FileStitcher() - Constructor for class loci.formats.FileStitcher
-
Constructs a FileStitcher around a new image reader.
- FileStitcher(boolean) - Constructor for class loci.formats.FileStitcher
-
Constructs a FileStitcher around a new image reader.
- FileStitcher(IFormatReader) - Constructor for class loci.formats.FileStitcher
-
Constructs a FileStitcher with the given reader.
- FileStitcher(IFormatReader, boolean) - Constructor for class loci.formats.FileStitcher
-
Constructs a FileStitcher with the given reader.
- FileStitcher.ExternalSeries - Class in loci.formats
- fileSystem - Variable in class loci.formats.services.POIServiceImpl
- fileView - Variable in class loci.formats.gui.ImageViewer
- fileWriter - Variable in class loci.formats.gui.ImageViewer
-
Writer for files on disk.
- fill() - Method in class loci.plugins.util.RecordedImageProcessor
- fill(ImageProcessor) - Method in class loci.plugins.util.RecordedImageProcessor
- FILL_ORDER - Static variable in class loci.formats.tiff.IFD
- fillAcquisitionDate(MetadataStore, String, int) - Method in class loci.formats.in.FakeReader
- fillAnnotations(MetadataStore, int) - Method in class loci.formats.in.FakeReader
- fillChannelWavelengths(MetadataStore) - Method in class loci.formats.in.FakeReader
- fillColor - Variable in class loci.formats.FormatReader
-
Fill value for undefined pixels.
- fillColor - Variable in class loci.formats.in.CellSensReader.Pyramid
- fillColour - Variable in class loci.formats.in.BaseZeissReader.Shape
- filled - Variable in class loci.formats.ChannelFiller
-
Whether to fill in the indices.
- FILLED_ARROW - Enum constant in enum class loci.formats.in.BaseZeissReader.PointStyle
- FILLED_ARROWS - Enum constant in enum class loci.formats.in.BaseZeissReader.LineEndStyle
- fillExposureTime(MetadataStore) - Method in class loci.formats.in.FakeReader
- fillInData() - Method in class loci.formats.in.ZeissCZIReader.Attachment
- fillInData() - Method in class loci.formats.in.ZeissCZIReader.AttachmentDirectory
- fillInData() - Method in class loci.formats.in.ZeissCZIReader.Directory
- fillInData() - Method in class loci.formats.in.ZeissCZIReader.FileHeader
- fillInData() - Method in class loci.formats.in.ZeissCZIReader.Metadata
- fillInData() - Method in class loci.formats.in.ZeissCZIReader.Segment
- fillInData() - Method in class loci.formats.in.ZeissCZIReader.SubBlock
- fillInIFD(IFD) - Method in class loci.formats.tiff.TiffParser
-
Fill in IFD entries that are stored at an arbitrary offset.
- fillInstrumentRefs(MetadataStore) - Method in class loci.formats.in.FakeReader
- fillMetadataPass1(MetadataStore) - Method in class loci.formats.in.BaseZeissReader
-
Read and store basic dimensions in model
- fillMetadataPass1(MetadataStore) - Method in class loci.formats.in.ZeissTIFFReader
- fillMetadataPass1(MetadataStore) - Method in class loci.formats.in.ZeissZVIReader
- fillMetadataPass2(MetadataStore) - Method in class loci.formats.in.BaseZeissReader
-
Read and store basic dimensions in model
- fillMetadataPass2(MetadataStore) - Method in class loci.formats.in.ZeissTIFFReader
- fillMetadataPass3(MetadataStore) - Method in class loci.formats.in.BaseZeissReader
-
Read and store basic dimensions in model
- fillMetadataPass3(MetadataStore) - Method in class loci.formats.in.ZeissZVIReader
- fillMetadataPass4(MetadataStore) - Method in class loci.formats.in.BaseZeissReader
-
Read and store basic dimensions in model
- fillMetadataPass5(MetadataStore) - Method in class loci.formats.in.BaseZeissReader
-
Read and store basic dimensions in model
- fillMetadataPass5(MetadataStore) - Method in class loci.formats.in.ZeissTIFFReader
- fillMetadataPass5(MetadataStore) - Method in class loci.formats.in.ZeissZVIReader
- fillMetadataPass6(MetadataStore) - Method in class loci.formats.in.BaseZeissReader
-
Read and store basic dimensions in model
- fillMetadataPass7(MetadataStore) - Method in class loci.formats.in.BaseZeissReader
-
Store basic dimensions in model
- fillMetadataStore(MetadataStore, int, int, int, int) - Method in class loci.formats.internal.WellContainer
- fillMetadataStore(MetadataStore, int, int, int, int, int) - Method in class loci.formats.internal.WellContainer
- fillOval(int, int, int, int) - Method in class loci.plugins.util.RecordedImageProcessor
- fillPhysicalSizes(MetadataStore) - Method in class loci.formats.in.FakeReader
- fillPolygon(Polygon) - Method in class loci.plugins.util.RecordedImageProcessor
- fillRegions(MetadataStore, int) - Method in class loci.formats.in.FakeReader
- fillStyle - Variable in class loci.formats.in.BaseZeissReader.Shape
- FillStyle(int) - Constructor for enum class loci.formats.in.BaseZeissReader.FillStyle
- filter - Variable in class loci.formats.in.ZeissLSMReader.BeamSplitter
- filter - Variable in class loci.formats.in.ZeissLSMReader.DetectionChannel
- filter(int) - Method in class loci.plugins.util.RecordedImageProcessor
- FILTER_MATERIAL - Enum constant in enum class loci.formats.dicom.DicomAttribute
- FILTER_SET_NAME - Static variable in class loci.formats.in.NDPIReader
- FILTER_THICKNESS_MAX - Enum constant in enum class loci.formats.dicom.DicomAttribute
- FILTER_THICKNESS_MIN - Enum constant in enum class loci.formats.dicom.DicomAttribute
- FILTER_TYPE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- FilterGroup() - Constructor for class loci.formats.in.FlexReader.FilterGroup
- filterMap - Variable in class loci.formats.in.FlexReader
- filterMetadata - Variable in class loci.formats.FormatReader
-
Whether or not to filter out invalid metadata.
- FilterMetadata - Class in loci.formats.meta
- FilterMetadata(MetadataStore, boolean) - Constructor for class loci.formats.meta.FilterMetadata
- filterModels - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataTempBuffer
- filterModels - Variable in class loci.formats.in.LIFReader
- filterModels - Variable in class loci.formats.in.NikonTiffReader
- filterRefPopulated - Variable in class loci.formats.in.LeicaReader
- filterSet - Variable in class loci.formats.in.FlexReader.FlexHandler
- filterSet - Variable in class loci.formats.in.ZeissLSMReader.BeamSplitter
- filterSet - Variable in class loci.formats.in.ZeissLSMReader.DetectionChannel
- FILTERSET - Static variable in class loci.formats.in.LeicaReader
- filterSetMap - Variable in class loci.formats.in.FlexReader
- filterSetRef - Variable in class loci.formats.in.ZeissCZIReader.Channel
- filterSets - Variable in class loci.formats.in.FlexReader
- filts - Variable in class loci.formats.gui.ComboFileFilter
-
List of filters to be combined.
- finalize() - Method in class org.libjpegturbo.turbojpeg.TJCompressor
- finalize() - Method in class org.libjpegturbo.turbojpeg.TJDecompressor
- find(String[]) - Method in class loci.formats.in.PrairieReader
-
Finds the first file with one of the given suffixes.
- find(String, String) - Static method in class loci.plugins.Updater
- findAllFiles(Location, ArrayList<String>) - Method in class loci.formats.in.TecanReader
- findAllFiles(Location, ArrayList<String>, boolean) - Method in class loci.formats.in.SlideBook7Reader
- findChildWithID(Node, String, String) - Method in class loci.formats.services.OMEXMLServiceImpl
-
Return the child node with specified value for the "ID" attribute.
- findDBFiles() - Method in class loci.formats.in.TissueFAXSReader
-
If a .tfcyto file was provided, then that is the only file that should be read.
- findEdges() - Method in class loci.plugins.util.RecordedImageProcessor
- findExtraMetadata() - Method in class loci.formats.in.TecanReader
- findFiles(Location) - Method in class loci.formats.in.FlexReader
-
Search for files that correspond to the given file.
- findFiles(Location, String[]) - Method in class loci.formats.in.FlexReader
- findImages(Connection, HashMap<Integer, String>) - Method in class loci.formats.in.TecanReader
- findImages(RandomAccessInputStream) - Method in class loci.formats.in.TillVisionReader
- findKeyValue(String[], String[][]) - Method in class loci.formats.in.ICSReader
- findKeyValueForCategory(String[], String[][]) - Method in class loci.formats.in.ICSReader
- findKeyValueOther(String[], String[][]) - Method in class loci.formats.in.ICSReader
- findLEIFile(String) - Method in class loci.formats.in.LeicaReader
-
Find the .lei file that belongs to the same dataset as the given file.
- findLogFiles() - Method in class loci.formats.in.DeltavisionReader
-
Find the log files.
- findLogFiles() - Method in class loci.formats.in.FakeReader
- findMetadataFiles() - Method in class loci.formats.in.PrairieReader
- findNextBlock() - Method in class loci.formats.in.OpenlabReader
- FindNextClass(MappingNode, int) - Method in class loci.formats.in.SlideBook7Reader.ClassDecoder
- findNextOffset(RandomAccessInputStream) - Method in class loci.formats.in.TillVisionReader
- findNextOffset(RandomAccessInputStream, byte[]) - Method in class loci.formats.in.TillVisionReader
- findNextXMLBlock(RandomAccessInputStream) - Method in class loci.formats.in.OIRReader
- findOffset() - Method in class loci.formats.in.ImspectorReader
-
Find the offset to the next block of pixel data.
- findOffset(boolean) - Method in class loci.formats.in.ImspectorReader
- findOIFFile(String) - Method in class loci.formats.in.FV1000Reader
- findPattern(File) - Static method in class loci.formats.FilePattern
-
Identifies the group pattern from a given file within that group.
- findPattern(String) - Static method in class loci.formats.FilePattern
-
Identifies the group pattern from a given file within that group.
- findPattern(String) - Method in class loci.formats.FileStitcher
- findPattern(String[]) - Static method in class loci.formats.FilePattern
-
Generate a pattern from a list of file names.
- findPattern(String, String) - Static method in class loci.formats.FilePattern
-
Identifies the group pattern from a given filename and directory.
- findPattern(String, String[], int, int, String) - Static method in class loci.formats.FilePattern
- findPattern(String, String, String[]) - Static method in class loci.formats.FilePattern
-
Identifies the group pattern from a given filename, directory and list of candidate filenames.
- findPattern(String, String, String[], int[]) - Static method in class loci.formats.FilePattern
-
Identifies the group pattern from a given filename, directory and list of candidate filenames.
- findPattern(Location) - Static method in class loci.formats.FilePattern
-
Identifies the group pattern from a given file within that group.
- findPatterns(String) - Method in class loci.formats.FileStitcher
-
Finds the file pattern for the given ID, based on the state of the file stitcher.
- findPixelOffsets() - Method in class loci.formats.in.JPXReader
- findPixelsFiles() - Method in class loci.formats.in.CellWorxReader
- findPixelsFiles() - Method in class loci.formats.in.MetaxpressTiffReader
- findPixelsOffset(int) - Method in class loci.formats.in.VisitechReader
- findPlateDimensions(Connection) - Method in class loci.formats.in.TecanReader
- findRootNode(Node) - Method in class loci.formats.services.OMEXMLServiceImpl
-
Return the absolute root node for the specified child node.
- findSeriesPatterns(String) - Static method in class loci.formats.FilePattern
-
Works like
FilePattern.findSeriesPatterns(String, String, String[]), but dir and nameList are inferred from the given file's absolute path. - findSeriesPatterns(String, String, String[]) - Static method in class loci.formats.FilePattern
-
Similar to
FilePattern.findPattern(String, String, String[]), but this does not merge series indices into a pattern block. - findString(String) - Method in class loci.formats.in.KodakReader
- findTIFFs() - Method in class loci.formats.in.MetamorphTiffReader
- findXML(String) - Static method in class loci.formats.in.ColumbusReader
- findZipEntries() - Method in class loci.formats.in.ZipReader
- finish(ImportProcess) - Method in class loci.plugins.in.Importer
- finishTime - Variable in class loci.formats.in.PerkinElmerReader
- finishTiming() - Method in class loci.plugins.in.ImagePlusReader
- FIRMWARE_VERSION - Static variable in class loci.formats.in.NDPIReader
- FIRMWARE_VERSION - Static variable in class loci.formats.in.NikonReader
- firstAvailable(int...) - Method in class loci.plugins.in.SwapDialog
- firstDataStream - Variable in class loci.formats.tools.AmiraParameters
- firstFile - Variable in class loci.formats.in.PrairieMetadata.Frame
-
The first actual
<File>element for this<Frame>. - firstFrame - Variable in class loci.formats.in.PrairieMetadata.Sequence
-
The first actual
<Frame>element for this<Sequence>. - firstIFD - Variable in class loci.formats.tiff.TiffParser
-
Cached first IFD in the current file.
- firstIndex - Variable in class loci.formats.in.PerkinElmerReader.PixelsFile
- firstSequence - Variable in class loci.formats.in.PrairieMetadata
-
The first actual
<Sequence>element. - firstSeriesChannels - Variable in class loci.formats.in.MetamorphReader
- firstStamp - Variable in class loci.formats.in.LeicaHandler
- firstTimeLoop - Variable in class loci.formats.in.ND2Handler
- firstTimepoint - Variable in class loci.formats.in.BDVReader
- firstWellPlanes() - Method in class loci.formats.in.FlexReader
-
Returns the number of planes in the first well that has data.
- fis - Variable in class loci.formats.Memoizer.KryoDeser
- FitsReader - Class in loci.formats.in
-
FitsReader is the file format reader for Flexible Image Transport System (FITS) images.
- FitsReader() - Constructor for class loci.formats.in.FitsReader
-
Constructs a new FitsReader.
- fixed - Variable in class loci.formats.FilePatternBlock
-
Whether or not this is a fixed-width block.
- fixUnits(Length) - Method in class loci.formats.out.DicomWriter
-
Check if the unit for the given Length is "pixel" or "referenceframe".
- FL - Enum constant in enum class loci.formats.dicom.DicomVR
- FLAG_ACCURATEDCT - Static variable in class org.libjpegturbo.turbojpeg.TJ
-
Use the most accurate DCT/IDCT algorithm available in the underlying codec.
- FLAG_BOTTOMUP - Static variable in class org.libjpegturbo.turbojpeg.TJ
-
The uncompressed source/destination image is stored in bottom-up (Windows, OpenGL) order, not top-down (X11) order.
- FLAG_FASTDCT - Static variable in class org.libjpegturbo.turbojpeg.TJ
-
Use the fastest DCT/IDCT algorithm available in the underlying codec.
- FLAG_FASTUPSAMPLE - Static variable in class org.libjpegturbo.turbojpeg.TJ
-
When decompressing, use the fastest chrominance upsampling algorithm available in the underlying codec.
- FLAG_FORCEMMX - Static variable in class org.libjpegturbo.turbojpeg.TJ
-
Turn off CPU auto-detection and force TurboJPEG to use MMX code (if the underlying codec supports it.)
- FLAG_FORCESSE - Static variable in class org.libjpegturbo.turbojpeg.TJ
-
Turn off CPU auto-detection and force TurboJPEG to use SSE code (if the underlying codec supports it.)
- FLAG_FORCESSE2 - Static variable in class org.libjpegturbo.turbojpeg.TJ
-
Turn off CPU auto-detection and force TurboJPEG to use SSE2 code (if the underlying codec supports it.)
- FLAG_FORCESSE3 - Static variable in class org.libjpegturbo.turbojpeg.TJ
-
Turn off CPU auto-detection and force TurboJPEG to use SSE3 code (if the underlying codec supports it.)
- flags - Variable in class loci.formats.in.BaseZeissReader.Layer
- flags - Variable in class loci.formats.in.SDTInfo
-
Scan clocks bits 2-0 (frame, line, pixel), rates_read - bit 15.
- FLASH - Static variable in class loci.formats.tiff.IFD
- FLASH_COMPENSATION - Static variable in class loci.formats.in.NikonReader
- FLASH_ENERGY - Static variable in class loci.formats.tiff.IFD
- FLASH_MODE - Static variable in class loci.formats.in.NikonReader
- FLASH_PIX_VERSION - Static variable in class loci.formats.tiff.IFD
- FLASH_SETTING - Static variable in class loci.formats.in.NikonReader
- FLASH_USED - Static variable in class loci.formats.in.NikonReader
- FLAT_FIELD - Enum constant in enum class loci.formats.in.SPEReader.SpeHeaderEntry
- FLAT_FIELD_FILE - Enum constant in enum class loci.formats.in.SPEReader.SpeHeaderEntry
- flattenedIndex(int, int) - Method in class loci.formats.CoreMetadataList
- flattenedIndexes(int) - Method in class loci.formats.CoreMetadataList
- flattenedResolutions - Variable in class loci.formats.FormatReader
-
Whether or not resolutions are flattened.
- flattenedSize() - Method in class loci.formats.CoreMetadataList
-
Get flattened size (all resolutions in all series)
- flattenHashtables() - Method in class loci.formats.FormatReader
-
Call
FormatReader.updateMetadataLists(Hashtable)on all metadata hashtables. - flattenHashtables() - Method in class loci.formats.SubResolutionFormatReader
-
Call
FormatReader.updateMetadataLists(Hashtable)on all metadata hashtables. - flbckX - Variable in class loci.formats.in.SDTInfo
- flbckY - Variable in class loci.formats.in.SDTInfo
- flex - Variable in class loci.formats.in.FlexReader.MeaHandler
- FLEX - Static variable in class loci.formats.in.FlexReader
-
Custom IFD entry for Flex XML.
- FLEX_SUFFIX - Static variable in class loci.formats.in.FlexReader
- FlexFile() - Constructor for class loci.formats.in.FlexReader.FlexFile
- flexFiles - Variable in class loci.formats.in.FlexReader
- FlexHandler(List<String>, List<String>, MetadataStore, boolean, int, int) - Constructor for class loci.formats.in.FlexReader.FlexHandler
- FlexReader - Class in loci.formats.in
-
FlexReader is a file format reader for Evotec Flex files.
- FlexReader() - Constructor for class loci.formats.in.FlexReader
-
Constructs a new Flex reader.
- FlexReader.FilterGroup - Class in loci.formats.in
-
Stores a grouping of filters.
- FlexReader.FlexFile - Class in loci.formats.in
- FlexReader.FlexHandler - Class in loci.formats.in
-
SAX handler for parsing XML.
- FlexReader.MeaHandler - Class in loci.formats.in
-
SAX handler for parsing XML from .mea files.
- FlexReader.ResHandler - Class in loci.formats.in
-
SAX handler for parsing XML from .res files.
- FLIM_DOMAIN - Static variable in class loci.formats.FormatTools
-
Identifies the fluorescence-lifetime domain.
- flip - Variable in class loci.formats.in.QTReader
- FLIP_ANGLE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- flipHorizontal() - Method in class loci.plugins.util.RecordedImageProcessor
- flipVertical() - Method in class loci.plugins.util.RecordedImageProcessor
- flipX - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataTempBuffer
- flipX - Variable in class loci.formats.in.LIFReader
- flipY - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataTempBuffer
- flipY - Variable in class loci.formats.in.LIFReader
- FLOAT - Enum constant in enum class loci.formats.in.SPEReader.SpeHeaderType
- FLOAT - Enum constant in enum class loci.formats.tiff.IFDType
- FLOAT - Static variable in class loci.formats.FormatTools
-
Identifies the FLOAT data type used to store pixel values.
- FLOAT - Static variable in class loci.formats.in.CellSensReader
- FLOAT - Static variable in class loci.formats.in.GatanReader
- FLOAT - Static variable in class loci.formats.in.SPEReader
- FLOAT_PIXEL_DATA - Enum constant in enum class loci.formats.dicom.DicomAttribute
- FLOAT32_TYPE - Static variable in class loci.formats.in.KLBReader
- FLOAT64_TYPE - Static variable in class loci.formats.in.KLBReader
- FloatIM3Record(String, int, long, int) - Constructor for class loci.formats.in.IM3Reader.FloatIM3Record
- floatValue() - Method in class loci.formats.tiff.TiffRational
-
Returns the value of the specified number as a float.
- FLOW_DATA_IDENTIFIER - Static variable in class loci.formats.in.SDTInfo
-
For .sdt files created automatically in Continuous Flow mode measurement (no setup, only data).
- FlowSightReader - Class in loci.formats.in
- FlowSightReader() - Constructor for class loci.formats.in.FlowSightReader
- fluor - Variable in class loci.formats.in.CV7000Reader.Channel
- fluor - Variable in class loci.formats.in.ZeissCZIReader.Channel
- FLUOVIEW_MAGIC_STRING - Static variable in class loci.formats.in.FluoviewReader
-
String identifying a Fluoview file.
- FluoviewReader - Class in loci.formats.in
-
FluoviewReader is the file format reader for Olympus Fluoview TIFF files AND Andor Bio-imaging Division (ABD) TIFF files.
- FluoviewReader() - Constructor for class loci.formats.in.FluoviewReader
-
Constructs a new Fluoview TIFF reader.
- flush() - Method in class loci.plugins.config.TextAreaWriter
-
Flushing a TextAreaWriter does nothing .
- flushBlockSize - Variable in class loci.formats.in.OBFReader.Stack
- flushPoints - Variable in class loci.formats.in.OBFReader.Stack
- fmt - Variable in class loci.formats.in.GelReader
- fmt - Variable in class loci.formats.in.OpenlabReader
- FOCAL_DISTANCE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- FOCAL_LENGTH - Static variable in class loci.formats.tiff.IFD
- FOCAL_LENGTH_35MM_FILM - Static variable in class loci.formats.tiff.IFD
- FOCAL_PLANE_RESOLUTION_UNIT - Static variable in class loci.formats.tiff.IFD
- FOCAL_PLANE_X_RESOLUTION - Static variable in class loci.formats.tiff.IFD
- FOCAL_PLANE_Y_RESOLUTION - Static variable in class loci.formats.tiff.IFD
- FOCAL_SPOTS - Enum constant in enum class loci.formats.dicom.DicomAttribute
- FOCUS_DEPTH - Enum constant in enum class loci.formats.dicom.DicomAttribute
- FOCUS_IMAGE - Static variable in class loci.formats.in.CellSensReader
- FOCUS_METHOD - Enum constant in enum class loci.formats.dicom.DicomAttribute
- FOCUS_MODE - Static variable in class loci.formats.in.NikonReader
- FOCUS_OFFSET - Static variable in class loci.formats.in.NDPIReader
- FOCUS_POINT_REGIONS - Static variable in class loci.formats.in.NDPIReader
- FOCUS_TIME - Static variable in class loci.formats.in.NDPIReader
- focusGained(FocusEvent) - Method in class loci.plugins.in.MainDialog
-
Handles information pane updates when component focus changes.
- focusLost(FocusEvent) - Method in class loci.plugins.in.MainDialog
- focusOffset - Variable in class loci.formats.in.TecanReader.Channel
- font - Variable in class loci.formats.in.FakeReader.TextLine
- font - Variable in class loci.formats.tools.MakeTestOmeTiff.TextLine
- fontName - Variable in class loci.formats.in.BaseZeissReader.Shape
- fontName - Variable in class loci.formats.in.LeicaHandler.ROI
- fontName - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.ROI
- fontName - Variable in class loci.formats.in.LIFReader.ROI
- fontSize - Variable in class loci.formats.in.BaseZeissReader.Shape
- fontSize - Variable in class loci.formats.in.GatanReader.ROIShape
- fontSize - Variable in class loci.formats.in.LeicaHandler.ROI
- fontSize - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.ROI
- fontSize - Variable in class loci.formats.in.LIFReader.ROI
- fontWeight - Variable in class loci.formats.in.BaseZeissReader.Shape
- FOOTER_SIZE - Static variable in class loci.formats.in.SIFReader
- footerPointer - Variable in class loci.formats.out.APNGWriter
- force - Variable in class loci.formats.gui.DataConverter
- forceType - Variable in class loci.formats.gui.DataConverter
- forkFile - Variable in class loci.formats.in.QTReader
- format - Variable in class loci.formats.FormatHandler
-
Name of this file format.
- formatCompression(IFD) - Method in class loci.formats.out.TiffWriter
-
Sets the compression code for the specified IFD.
- formatDouble(double) - Method in class loci.formats.in.ZeissXRMReader
-
Format double value to 2 decimal places, rounding to nearest.
- FormatEntry - Class in loci.plugins.config
-
A list entry for the configuration window's Formats tab.
- FormatEntry(PrintWriter, Object) - Constructor for class loci.plugins.config.FormatEntry
- FormatException - Exception Class in loci.formats
-
FormatException is the exception thrown when something goes wrong performing a file format operation.
- FormatException() - Constructor for exception class loci.formats.FormatException
- FormatException(String) - Constructor for exception class loci.formats.FormatException
- FormatException(String, Throwable) - Constructor for exception class loci.formats.FormatException
- FormatException(Throwable) - Constructor for exception class loci.formats.FormatException
- FormatFileFilter - Class in loci.formats.gui
-
A file filter for a biological file format, for use with a JFileChooser.
- FormatFileFilter(IFormatReader) - Constructor for class loci.formats.gui.FormatFileFilter
-
Constructs a new filter that accepts files of the given reader's type.
- FormatFileFilter(IFormatReader, boolean) - Constructor for class loci.formats.gui.FormatFileFilter
-
Constructs a new filter that accepts files of the given reader's type, allowing the reader to open files only if the allowOpen flag is set.
- formatFixedWidth(double, int) - Static method in class loci.formats.out.DicomWriter
-
Format the given double as a string with no more than
widthcharacters. - FormatHandler - Class in loci.formats
-
Abstract superclass of all biological file format readers and writers.
- FormatHandler(String, String) - Constructor for class loci.formats.FormatHandler
-
Constructs a format handler with the given name and default suffix.
- FormatHandler(String, String[]) - Constructor for class loci.formats.FormatHandler
-
Constructs a format handler with the given name and default suffixes.
- formatHex(int) - Method in class loci.formats.in.BaseZeissReader.Shape
- formatInfo - Variable in class loci.plugins.config.ConfigWindow
- formatLabel - Variable in class loci.formats.gui.PreviewPane
-
Labels containing thumbnail and dimensional information.
- formatMetadata(String, String) - Static method in class loci.formats.in.IonpathMIBITiffReader
- formatName - Variable in class loci.plugins.config.FormatEntry
- FormatReader - Class in loci.formats
-
Abstract superclass of all biological file format readers.
- FormatReader(String, String) - Constructor for class loci.formats.FormatReader
-
Constructs a format reader with the given name and default suffix.
- FormatReader(String, String[]) - Constructor for class loci.formats.FormatReader
-
Constructs a format reader with the given name and default suffixes.
- FORMATS - Static variable in class loci.formats.in.GelReader
- formatsList - Variable in class loci.plugins.config.ConfigWindow
- formatsListModel - Variable in class loci.plugins.config.ConfigWindow
- formatTag(int) - Static method in enum class loci.formats.dicom.DicomAttribute
-
Format the given tag as a pair of comma-separated hex strings.
- formatText - Variable in class loci.formats.gui.PreviewPane
- formatTip - Variable in class loci.formats.gui.PreviewPane
- FormatTools - Class in loci.formats
-
A utility class for format reader and writer implementations.
- FormatTools() - Constructor for class loci.formats.FormatTools
- FormatWriter - Class in loci.formats
-
Abstract superclass of all biological file format writers.
- FormatWriter(String, String) - Constructor for class loci.formats.FormatWriter
-
Constructs a format writer with the given name and default suffix.
- FormatWriter(String, String[]) - Constructor for class loci.formats.FormatWriter
-
Constructs a format writer with the given name and default suffixes.
- FORMS - Enum constant in enum class loci.plugins.util.LibraryChecker.Library
- FORWARD_ORDER - Static variable in interface loci.formats.cache.ICacheStrategy
- fos - Variable in class loci.formats.Memoizer.KryoDeser
- found - Variable in class loci.formats.in.ZeissTIFFHandler.TagSet
- foundChannelTag - Variable in class loci.formats.in.CellSensReader
- foundHTDFile(String) - Method in class loci.formats.in.CellWorxReader
- foundMontage - Variable in class loci.formats.in.GatanReader
- foundPlateLayout - Variable in class loci.formats.in.ScanrReader.ScanrHandler
- foundPositions - Variable in class loci.formats.in.ScanrReader
- fourPixelCorrectionInFooter - Variable in class loci.formats.in.DCIMGReader
- fourPixelCorrectionLine - Variable in class loci.formats.in.DCIMGReader
- fourPixelCorrectionOffset - Variable in class loci.formats.in.DCIMGReader
- fourPixelOffsetInFrame - Variable in class loci.formats.in.DCIMGReader
- FOV_DIMENSIONS - Enum constant in enum class loci.formats.dicom.DicomAttribute
- FOV_HORIZONTAL_FLIP - Enum constant in enum class loci.formats.dicom.DicomAttribute
- FOV_ORIGIN - Enum constant in enum class loci.formats.dicom.DicomAttribute
- FOV_ROTATION - Enum constant in enum class loci.formats.dicom.DicomAttribute
- FOV_SHAPE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- fovs - Variable in class loci.formats.in.TissueFAXSReader.ScanRegion
- fp - Variable in class loci.formats.AxisGuesser
-
File pattern identifying dimensional axis blocks.
- fp - Variable in class loci.plugins.in.FilePatternDialog
- fps - Variable in class loci.formats.FormatWriter
-
Frame rate to use when writing in frames per second, if applicable.
- fps - Variable in class loci.formats.gui.DataConverter
- fps - Variable in class loci.formats.gui.ImageViewer
- fpsSpin - Variable in class loci.plugins.util.DataBrowser
- frame - Variable in class loci.formats.in.PrairieMetadata.PFile
-
The
<Frame>containing this<File>. - Frame(PrairieMetadata.Sequence, Element) - Constructor for class loci.formats.in.PrairieMetadata.Frame
-
Creates a new frame by parsing the given
<Frame>element. - FRAME_ACQUISITION_DATETIME - Enum constant in enum class loci.formats.dicom.DicomAttribute
- FRAME_ACQUISITION_DURATION - Enum constant in enum class loci.formats.dicom.DicomAttribute
- FRAME_CONTENT_SEQUENCE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- FRAME_DELAY - Enum constant in enum class loci.formats.dicom.DicomAttribute
- FRAME_DIMENSION_POINTER - Enum constant in enum class loci.formats.dicom.DicomAttribute
- FRAME_INCREMENT_POINTER - Enum constant in enum class loci.formats.dicom.DicomAttribute
- FRAME_LABEL_VECTOR - Enum constant in enum class loci.formats.dicom.DicomAttribute
- FRAME_NUMBERS_OF_INTEREST - Enum constant in enum class loci.formats.dicom.DicomAttribute
- FRAME_OF_INTEREST_DESCRIPTION - Enum constant in enum class loci.formats.dicom.DicomAttribute
- FRAME_OF_INTEREST_TYPE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- FRAME_OF_REFERENCE_UID - Enum constant in enum class loci.formats.dicom.DicomAttribute
- FRAME_OFFSET - Static variable in class loci.formats.out.AVIWriter
- FRAME_OFFSET_2 - Static variable in class loci.formats.out.AVIWriter
- FRAME_ORIGIN - Static variable in class loci.formats.in.CellSensReader
- FRAME_PRIMARY_ANGLE_VECTOR - Enum constant in enum class loci.formats.dicom.DicomAttribute
- FRAME_PROPERTIES - Static variable in class loci.formats.in.CellSensReader
- FRAME_REFERENCE_DATETIME - Enum constant in enum class loci.formats.dicom.DicomAttribute
- FRAME_SCALE - Static variable in class loci.formats.in.CellSensReader
- FRAME_SECONDARY_ANGLE_VECTOR - Enum constant in enum class loci.formats.dicom.DicomAttribute
- FRAME_SIZE - Static variable in class loci.formats.in.CellSensReader
- FRAME_TIME - Enum constant in enum class loci.formats.dicom.DicomAttribute
- FRAME_TIME_VECTOR - Enum constant in enum class loci.formats.dicom.DicomAttribute
- FRAME_TRANSFER - Static variable in class loci.formats.in.CellSensReader
- FRAME_TYPE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- FRAME_TYPE - Static variable in class loci.formats.in.CellSensReader
- FRAME_VOI_LUT_SEQUENCE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- frameClockList - Variable in class loci.formats.in.SPCReader
- frameCoordinates - Variable in class loci.formats.in.APNGReader
- frameFooterSize - Variable in class loci.formats.in.DCIMGReader
- frameIndex - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.Dimension
- frameIndex(PrairieMetadata.Sequence, int, int, int) - Method in class loci.formats.in.PrairieReader
-
Gets the frame index associated with the given (Z, T) position of the specified series.
- frames - Variable in class loci.formats.in.PrairieMetadata.Sequence
-
<Frame>elements beneath this<Sequence>, keyed on each frame'sindex. - framesAreTime - Variable in class loci.formats.in.PrairieReader
-
Whether a series uses
Frames as time points rather than focal planes (i.e., sizeZ and sizeT values inverted). - frameValues - Variable in class loci.formats.in.PrairieMetadata.Frame
-
Table of key/value pairs for this
<Frame>. - FRAMING_TYPE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- FREE_BYTE_COUNTS - Static variable in class loci.formats.tiff.IFD
- FREE_LINE - Static variable in class loci.formats.in.FV1000Reader
- FREE_OFFSETS - Static variable in class loci.formats.tiff.IFD
- FREE_SHAPE - Static variable in class loci.formats.in.FV1000Reader
- frequencies - Variable in class loci.formats.in.LiFlimReader
- FREQUENCY - Static variable in class loci.formats.FormatTools
-
Identifies the Frequency dimensional type, representing a dimension consisting of frequencies.
- fromCIEXYZ(float[]) - Method in class loci.formats.gui.TwoChannelColorSpace
- fromRGB(float[]) - Method in class loci.formats.gui.TwoChannelColorSpace
- FujiReader - Class in loci.formats.in
-
FujiReader is the file format reader for Fuji LAS 3000 datasets.
- FujiReader() - Constructor for class loci.formats.in.FujiReader
-
Constructs a new Fuji reader.
- fullImage - Variable in class loci.formats.in.MRWReader
- fullResolutionCoreIndex - Variable in class loci.formats.in.TissueFAXSReader.ScanRegion
- FULLY_AUTO_FOCUS - Static variable in class loci.formats.in.NDPIReader
- FUNCTIONAL_GROUP_POINTER - Enum constant in enum class loci.formats.dicom.DicomAttribute
- FUNCTIONAL_GROUP_PRIVATE_CREATOR - Enum constant in enum class loci.formats.dicom.DicomAttribute
- FV1000_MAGIC_STRING_1 - Static variable in class loci.formats.in.FV1000Reader
- FV1000_MAGIC_STRING_2 - Static variable in class loci.formats.in.FV1000Reader
- FV1000_SUFFIXES - Static variable in class loci.formats.in.FV1000Reader
- FV1000Reader - Class in loci.formats.in
-
FV1000Reader is the file format reader for Fluoview FV 1000 OIB and Fluoview FV 1000 OIF files.
- FV1000Reader() - Constructor for class loci.formats.in.FV1000Reader
-
Constructs a new FV1000 reader.
- FV1000Reader.ChannelData - Class in loci.formats.in
- FV1000Reader.PlaneData - Class in loci.formats.in
G
- gain - Variable in class loci.formats.in.BDReader
- gain - Variable in class loci.formats.in.BioRadReader
- gain - Variable in class loci.formats.in.BioRadSCNReader
- gain - Variable in class loci.formats.in.CellSensReader.Pyramid
- gain - Variable in class loci.formats.in.FV1000Reader.ChannelData
- gain - Variable in class loci.formats.in.ImarisHDFReader
- gain - Variable in class loci.formats.in.InCellReader
- gain - Variable in class loci.formats.in.IvisionReader
- gain - Variable in class loci.formats.in.LeicaHandler.Channel
- gain - Variable in class loci.formats.in.MetamorphHandler
- gain - Variable in class loci.formats.in.MetamorphReader
- gain - Variable in class loci.formats.in.MicromanagerReader.Position
- gain - Variable in class loci.formats.in.ND2Handler
- gain - Variable in class loci.formats.in.NikonTiffReader
- gain - Variable in class loci.formats.in.OIRReader.Detector
- gain - Variable in class loci.formats.in.OpenlabReader
- gain - Variable in class loci.formats.in.ZeissCZIReader.Channel
- gain - Variable in class loci.formats.in.ZeissCZIReader
- gain - Variable in class loci.formats.in.ZeissLSMReader.DetectionChannel
- GAIN - Enum constant in enum class loci.formats.in.SPEReader.SpeHeaderEntry
- GAIN_CONTROL - Static variable in class loci.formats.tiff.IFD
- GAIN_UNIT - Static variable in class loci.formats.in.CellSensReader
- gains - Variable in class loci.formats.in.FluoviewReader
- gains - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataTempBuffer
- gains - Variable in class loci.formats.in.LIFReader
- gains - Variable in class loci.formats.in.ZeissCZIReader
- gamma - Variable in class loci.formats.in.GatanReader
- gamma(double) - Method in class loci.plugins.util.RecordedImageProcessor
- GAMMA_CORRECTION - Static variable in class loci.formats.in.CellSensReader
- GANTRY_DETECTOR_SKEW - Enum constant in enum class loci.formats.dicom.DicomAttribute
- GANTRY_DETECTOR_TILT - Enum constant in enum class loci.formats.dicom.DicomAttribute
- GatanDM2Reader - Class in loci.formats.in
-
GatanDM2Reader is the file format reader for Gatan .dm2 files.
- GatanDM2Reader() - Constructor for class loci.formats.in.GatanDM2Reader
-
Constructs a new Gatan .dm2 reader.
- GatanReader - Class in loci.formats.in
-
GatanReader is the file format reader for Gatan files.
- GatanReader() - Constructor for class loci.formats.in.GatanReader
-
Constructs a new Gatan reader.
- GatanReader.ROIShape - Class in loci.formats.in
- GB2313_CHARSET - Enum constant in enum class loci.formats.in.BaseZeissReader.Charset
- gct - Variable in class loci.formats.in.GIFReader
-
Global color table.
- GEL_DOMAIN - Static variable in class loci.formats.FormatTools
-
Identifies the gel and blot imaging domain.
- GelReader - Class in loci.formats.in
-
GelReader is the file format reader for Molecular Dynamics GEL TIFF files.
- GelReader() - Constructor for class loci.formats.in.GelReader
-
Constructs a new GEL reader.
- GENERAL_PARAMS - Static variable in class loci.formats.in.ZeissXRMReader
- generateMemo(String) - Method in class loci.formats.Memoizer
-
Convenience method to generate (or regenerate) the memo file for a given file.
- generateScreen(int, int, int, int, int) - Method in class loci.formats.tools.FakeImage
-
Creates a fake SPW file/directory structure.
- GENERATOR_POWER - Enum constant in enum class loci.formats.dicom.DicomAttribute
- GEOMETRIC - Enum constant in enum class loci.formats.in.SPEReader.SpeHeaderEntry
- get(int) - Method in class loci.formats.codec.ByteVector
- get(int) - Static method in enum class loci.formats.codec.CompressionType
-
Retrieves the compression by reverse lookup of its "code".
- get(int) - Static method in enum class loci.formats.codec.JPEG2000BoxType
-
Retrieves the box type by reverse lookup of its "code".
- get(int) - Static method in enum class loci.formats.codec.JPEG2000SegmentMarker
-
Retrieves the segment marker by reverse lookup of its "code".
- get(int) - Static method in enum class loci.formats.dicom.DicomAttribute
-
Lookup the attribute for the given tag.
- get(int) - Static method in enum class loci.formats.dicom.DicomVR
- get(int) - Static method in enum class loci.formats.in.BaseZeissReader.Charset
- get(int) - Static method in enum class loci.formats.in.BaseZeissReader.DrawStyle
- get(int) - Static method in enum class loci.formats.in.BaseZeissReader.FeatureType
- get(int) - Static method in enum class loci.formats.in.BaseZeissReader.FillStyle
- get(int) - Static method in enum class loci.formats.in.BaseZeissReader.LineEndPositions
- get(int) - Static method in enum class loci.formats.in.BaseZeissReader.LineEndStyle
- get(int) - Static method in enum class loci.formats.in.BaseZeissReader.PointStyle
- get(int) - Static method in enum class loci.formats.in.BaseZeissReader.TextAlignment
- get(int) - Method in interface loci.formats.in.PrairieMetadata.Value
- get(int) - Method in class loci.formats.in.PrairieMetadata.ValueItem
- get(int) - Method in class loci.formats.in.PrairieMetadata.ValueTable
- get(int) - Static method in enum class loci.formats.tiff.IFDType
-
Retrieves a IFD type by reverse lookup of its "code".
- get(int) - Method in class loci.formats.tiff.OnDemandLongArray
- get(int) - Static method in enum class loci.formats.tiff.PhotoInterp
-
Retrieves a photometric interpretation by reverse lookup of its "code".
- get(int) - Static method in enum class loci.formats.tiff.TiffCompression
-
Retrieves a TIFF compression instance by code.
- get(int) - Method in class loci.plugins.util.RecordedImageProcessor
- get(int, int) - Method in class loci.formats.MetadataList
-
Get the array element for the specified indexes.
- get(int, int) - Method in class loci.plugins.util.RecordedImageProcessor
- get(Object) - Method in interface loci.formats.in.PrairieMetadata.Value
- get(Object) - Method in class loci.formats.in.PrairieMetadata.ValueItem
- get(String) - Method in class loci.formats.in.DynamicMetadataOptions
-
Get the value of property
name. - get(String, String) - Method in class loci.formats.in.DynamicMetadataOptions
-
Get the value of property
name. - get(List<T>, int, T) - Method in class loci.plugins.in.ImporterOptions
- get(Codec) - Static method in enum class loci.formats.codec.CompressionType
-
Look up the compression type by Codec instance.
- get16BitLookupTable() - Method in class loci.formats.ChannelFiller
- get16BitLookupTable() - Method in class loci.formats.DelegateReader
- get16BitLookupTable() - Method in class loci.formats.FileStitcher
- get16BitLookupTable() - Method in class loci.formats.FormatReader
- get16BitLookupTable() - Method in interface loci.formats.IFormatReader
-
Gets the 16-bit color lookup table associated with the most recently opened image.
- get16BitLookupTable() - Method in class loci.formats.ImageReader
- get16BitLookupTable() - Method in class loci.formats.in.BaseZeissReader
- get16BitLookupTable() - Method in class loci.formats.in.DicomReader
- get16BitLookupTable() - Method in class loci.formats.in.FakeReader
- get16BitLookupTable() - Method in class loci.formats.in.FilePatternReader
- get16BitLookupTable() - Method in class loci.formats.in.FV1000Reader
- get16BitLookupTable() - Method in class loci.formats.in.ImarisHDFReader
- get16BitLookupTable() - Method in class loci.formats.in.ImprovisionTiffReader
- get16BitLookupTable() - Method in class loci.formats.in.InCellReader
- get16BitLookupTable() - Method in class loci.formats.in.JPEG2000Reader
- get16BitLookupTable() - Method in class loci.formats.in.JPXReader
- get16BitLookupTable() - Method in class loci.formats.in.LeicaReader
- get16BitLookupTable() - Method in class loci.formats.in.LIFReader
- get16BitLookupTable() - Method in class loci.formats.in.LOFReader
- get16BitLookupTable() - Method in class loci.formats.in.MIASReader
- get16BitLookupTable() - Method in class loci.formats.in.MinimalTiffReader
- get16BitLookupTable() - Method in class loci.formats.in.ND2Reader
- get16BitLookupTable() - Method in class loci.formats.in.OIRReader
- get16BitLookupTable() - Method in class loci.formats.in.OMETiffReader
- get16BitLookupTable() - Method in class loci.formats.in.PDSReader
- get16BitLookupTable() - Method in class loci.formats.in.PerkinElmerReader
- get16BitLookupTable() - Method in class loci.formats.in.SlidebookTiffReader
- get16BitLookupTable() - Method in class loci.formats.in.TCSReader
- get16BitLookupTable() - Method in class loci.formats.in.VentanaReader
- get16BitLookupTable() - Method in class loci.formats.in.ZeissCZIReader
- get16BitLookupTable() - Method in class loci.formats.in.ZeissLSMReader
- get16BitLookupTable() - Method in class loci.formats.in.ZipReader
- get16BitLookupTable() - Method in class loci.formats.ReaderWrapper
- get16BitLookupTable() - Method in class loci.formats.WrappedReader
- get8BitLookupTable() - Method in class loci.formats.ChannelFiller
- get8BitLookupTable() - Method in class loci.formats.DelegateReader
- get8BitLookupTable() - Method in class loci.formats.FileStitcher
- get8BitLookupTable() - Method in class loci.formats.FormatReader
- get8BitLookupTable() - Method in interface loci.formats.IFormatReader
-
Gets the 8-bit color lookup table associated with the most recently opened image.
- get8BitLookupTable() - Method in class loci.formats.ImageReader
- get8BitLookupTable() - Method in class loci.formats.in.AmiraReader
- get8BitLookupTable() - Method in class loci.formats.in.APNGReader
- get8BitLookupTable() - Method in class loci.formats.in.AVIReader
- get8BitLookupTable() - Method in class loci.formats.in.BaseZeissReader
- get8BitLookupTable() - Method in class loci.formats.in.BDVReader
- get8BitLookupTable() - Method in class loci.formats.in.BioRadReader
- get8BitLookupTable() - Method in class loci.formats.in.BMPReader
- get8BitLookupTable() - Method in class loci.formats.in.CellH5Reader
- get8BitLookupTable() - Method in class loci.formats.in.DicomReader
- get8BitLookupTable() - Method in class loci.formats.in.FakeReader
- get8BitLookupTable() - Method in class loci.formats.in.FilePatternReader
- get8BitLookupTable() - Method in class loci.formats.in.GIFReader
- get8BitLookupTable() - Method in class loci.formats.in.ImarisHDFReader
- get8BitLookupTable() - Method in class loci.formats.in.ImprovisionTiffReader
- get8BitLookupTable() - Method in class loci.formats.in.InCellReader
- get8BitLookupTable() - Method in class loci.formats.in.IPWReader
- get8BitLookupTable() - Method in class loci.formats.in.JPEG2000Reader
- get8BitLookupTable() - Method in class loci.formats.in.JPXReader
- get8BitLookupTable() - Method in class loci.formats.in.KhorosReader
- get8BitLookupTable() - Method in class loci.formats.in.LeicaReader
- get8BitLookupTable() - Method in class loci.formats.in.LIFReader
- get8BitLookupTable() - Method in class loci.formats.in.LOFReader
- get8BitLookupTable() - Method in class loci.formats.in.MIASReader
- get8BitLookupTable() - Method in class loci.formats.in.MinimalTiffReader
- get8BitLookupTable() - Method in class loci.formats.in.ND2Reader
- get8BitLookupTable() - Method in class loci.formats.in.OIRReader
- get8BitLookupTable() - Method in class loci.formats.in.OMETiffReader
- get8BitLookupTable() - Method in class loci.formats.in.OpenlabReader
- get8BitLookupTable() - Method in class loci.formats.in.PCXReader
- get8BitLookupTable() - Method in class loci.formats.in.PerkinElmerReader
- get8BitLookupTable() - Method in class loci.formats.in.PictReader
- get8BitLookupTable() - Method in class loci.formats.in.PSDReader
- get8BitLookupTable() - Method in class loci.formats.in.SlidebookTiffReader
- get8BitLookupTable() - Method in class loci.formats.in.TargaReader
- get8BitLookupTable() - Method in class loci.formats.in.TCSReader
- get8BitLookupTable() - Method in class loci.formats.in.VentanaReader
- get8BitLookupTable() - Method in class loci.formats.in.ZeissCZIReader
- get8BitLookupTable() - Method in class loci.formats.in.ZeissLMSReader
- get8BitLookupTable() - Method in class loci.formats.in.ZeissLSMReader
- get8BitLookupTable() - Method in class loci.formats.in.ZipReader
- get8BitLookupTable() - Method in class loci.formats.ReaderWrapper
- get8BitLookupTable() - Method in class loci.formats.WrappedReader
- get8BitLookupTable(ColorModel) - Static method in class loci.formats.gui.AWTImageTools
-
Converts an IndexColorModel to a 2D byte array.
- getAbsoluteTime() - Method in class loci.formats.in.PrairieMetadata.Frame
-
Gets the
absoluteTimeassociated with thisFrame. - getAcquisitionMode(String) - Method in class loci.formats.FormatReader
-
Deprecated.
- getAcquisitionMode(String) - Method in class loci.formats.in.OperettaReader
-
Deprecated.
- getAcquisitionMode(String) - Static method in class loci.formats.MetadataTools
-
Retrieves an
AcquisitionModeenumeration value for the given String. - getActiveChannels() - Method in class loci.formats.in.PrairieMetadata
-
Gets the list of active channel indices, in sorted order.
- getAdjustedIndex(int) - Method in class loci.formats.FileStitcher
-
Gets the local reader index for use with the given image plane.
- getAdjustedOrder() - Method in class loci.formats.AxisGuesser
-
Gets the adjusted dimension order.
- getAdvancedSeriesUsedFiles(boolean) - Method in class loci.formats.FileStitcher
- getAdvancedSeriesUsedFiles(boolean) - Method in class loci.formats.FormatReader
- getAdvancedSeriesUsedFiles(boolean) - Method in interface loci.formats.IFormatReader
-
Returns an array of FileInfo objects representing the files needed to open the current series.
- getAdvancedSeriesUsedFiles(boolean) - Method in class loci.formats.ImageReader
- getAdvancedSeriesUsedFiles(boolean) - Method in class loci.formats.ReaderWrapper
- getAdvancedUsedFiles(boolean) - Method in class loci.formats.FileStitcher
- getAdvancedUsedFiles(boolean) - Method in class loci.formats.FormatReader
- getAdvancedUsedFiles(boolean) - Method in interface loci.formats.IFormatReader
-
Returns an array of FileInfo objects representing the files needed to open this dataset.
- getAdvancedUsedFiles(boolean) - Method in class loci.formats.ImageReader
- getAdvancedUsedFiles(boolean) - Method in class loci.formats.ReaderWrapper
- getAllChildren(Integer) - Method in class loci.formats.in.VolocityReader
- getAllFiles() - Method in class loci.formats.internal.WellContainer
- getAllFiles(String) - Method in class loci.formats.FilePattern
- getAllRegions(int) - Method in class loci.formats.in.TissueFAXSReader
- getAlpha(int) - Method in class loci.formats.gui.Index16ColorModel
- getAlpha(int) - Method in class loci.formats.gui.SignedColorModel
- getAlpha(int) - Method in class loci.formats.gui.UnsignedIntColorModel
- getAlpha(Object) - Method in class loci.formats.gui.SignedColorModel
- getAlpha(Object) - Method in class loci.formats.gui.UnsignedIntColorModel
- getAlphas() - Method in class loci.formats.gui.Index16ColorModel
-
Return the array of alpha color components.
- getArcType(String) - Method in class loci.formats.FormatReader
-
Deprecated.
- getArcType(String) - Static method in class loci.formats.MetadataTools
-
Retrieves an
ArcTypeenumeration value for the given String. - getArray(String, int[], int[]) - Method in interface loci.formats.services.NetCDFService
-
Retrieves an HDF path's values.
- getArray(String, int[], int[]) - Method in class loci.formats.services.NetCDFServiceImpl
- getAttr(Node, String) - Method in class loci.formats.in.LeicaMicrosystemsMetadata.LMSXmlDocument
-
Returns the value of an attribute of a node, if existing
- getAttributeList() - Method in interface loci.formats.services.NetCDFService
-
Retrieves an exhaustive list of the HDF paths for all attributes in the HDF document.
- getAttributeList() - Method in class loci.formats.services.NetCDFServiceImpl
- getAttributeValue(String) - Method in interface loci.formats.services.NetCDFService
-
Retrieves an attribute's value.
- getAttributeValue(String) - Method in class loci.formats.services.NetCDFServiceImpl
- getAutoscaleInfo() - Method in class loci.plugins.in.ImporterOptions
- getAutoThreshold() - Method in class loci.plugins.util.RecordedImageProcessor
- getAutoThreshold(int[]) - Method in class loci.plugins.util.RecordedImageProcessor
- getAvailableMemory() - Method in class loci.plugins.in.MemoryDialog
- getAvailableOptions() - Method in class loci.formats.FormatReader
-
Returns the list of available metadata options.
- getAvailableOptions() - Method in class loci.formats.in.CellSensReader
- getAvailableOptions() - Method in class loci.formats.in.CV7000Reader
- getAvailableOptions() - Method in class loci.formats.in.GatanReader
- getAvailableOptions() - Method in class loci.formats.in.InCellReader
- getAvailableOptions() - Method in class loci.formats.in.LIFReader
- getAvailableOptions() - Method in class loci.formats.in.ND2Reader
- getAvailableOptions() - Method in class loci.formats.in.OMETiffReader
- getAvailableOptions() - Method in class loci.formats.in.ScanrReader
- getAvailableOptions() - Method in class loci.formats.in.SVSReader
- getAvailableOptions() - Method in class loci.formats.in.VentanaReader
- getAvailableOptions() - Method in class loci.formats.in.ZeissCZIReader
- getAxisCount(int) - Method in class loci.formats.AxisGuesser
-
Gets the number of axes in the pattern of the given type.
- getAxisCountC() - Method in class loci.formats.AxisGuesser
-
Gets the number of C axes in the pattern.
- getAxisCountS() - Method in class loci.formats.AxisGuesser
-
Gets the number of S axes in the pattern.
- getAxisCountT() - Method in class loci.formats.AxisGuesser
-
Gets the number of T axes in the pattern.
- getAxisCountZ() - Method in class loci.formats.AxisGuesser
-
Gets the number of Z axes in the pattern.
- getAxisGuesser() - Method in class loci.formats.FileStitcher.ExternalSeries
- getAxisGuesser() - Method in class loci.formats.FileStitcher
-
Gets the axis guesser object used to guess which dimensional axes are which.
- getAxisType(String) - Static method in class loci.formats.AxisGuesser
-
Convert the given label to an axis type.
- getAxisTypes() - Method in class loci.formats.AxisGuesser
-
Gets the guessed axis type for each dimensional block.
- getAxisTypes() - Method in class loci.formats.FileStitcher
-
Gets the axis type for each dimensional block.
- getBackgroundValue() - Method in class loci.plugins.util.RecordedImageProcessor
- getBaseReader() - Method in class loci.plugins.in.ImportProcess
-
Valid only after
ImportStep.READER. - getBestIndex(Color) - Method in class loci.plugins.util.RecordedImageProcessor
- getBGRComponents(short[]) - Method in class loci.formats.services.JPEGXRServiceImpl
- getBinaryOnlyOMEXML(String, String, String) - Method in class loci.formats.out.OMETiffWriter
- getBinning() - Method in class loci.formats.in.MetamorphHandler
- getBinning(String) - Method in class loci.formats.FormatReader
-
Deprecated.
- getBinning(String) - Static method in class loci.formats.MetadataTools
-
Retrieves an
Binningenumeration value for the given String. - getBinnings() - Method in class loci.formats.in.ND2Handler
- getBitDepth() - Method in class loci.formats.in.PrairieMetadata
-
Gets the
bitDepthrecorded in the configuration. - getBits(int) - Method in class loci.formats.codec.BitBuffer
-
Deprecated.Returns an int value representing the value of the bits read from the byte array, from the current position.
- getBitsPerPixel() - Method in class loci.formats.ChannelFiller
- getBitsPerPixel() - Method in class loci.formats.FileStitcher
- getBitsPerPixel() - Method in class loci.formats.FormatReader
- getBitsPerPixel() - Method in interface loci.formats.IFormatReader
-
Gets the number of valid bits per pixel.
- getBitsPerPixel() - Method in class loci.formats.ImageReader
- getBitsPerPixel() - Method in class loci.formats.in.LeicaMicrosystemsMetadata.MultipleImagesReader
- getBitsPerPixel() - Method in class loci.formats.ReaderWrapper
- getBitsPerPixel() - Method in class loci.formats.WrappedReader
- getBitsPerPixel(int) - Method in class loci.formats.in.OBFReader
- getBitsPerSample() - Method in class loci.formats.tiff.IFD
-
Retrieves the image's bits per sample (TIFF tag BitsPerSample) from a given TIFF IFD.
- getBitsPerSample(int) - Method in class loci.formats.in.NDPIReader
-
Get the number of bits per sample associated with the given capture mode.
- getBlankThumbBytes() - Method in class loci.formats.FileStitcher.ExternalSeries
- getBlock() - Method in class loci.formats.FilePatternBlock
-
Gets the block string.
- getBlock(int) - Method in class loci.formats.FilePattern
-
Gets the specified file pattern block (e.g., <0-9>).
- getBlock(int, String) - Method in class loci.formats.in.ScanrReader
- getBlock(String) - Method in class loci.formats.in.OIRReader
- getBlocks() - Method in class loci.formats.FilePattern
-
Gets all file pattern blocks.
- getBlue(int) - Method in class loci.formats.gui.Index16ColorModel
- getBlue(int) - Method in class loci.formats.gui.SignedColorModel
- getBlue(int) - Method in class loci.formats.gui.UnsignedIntColorModel
- getBlue(Object) - Method in class loci.formats.gui.SignedColorModel
- getBlue(Object) - Method in class loci.formats.gui.UnsignedIntColorModel
- getBlueOffset(int) - Static method in class org.libjpegturbo.turbojpeg.TJ
-
For the given pixel format, returns the number of bytes that the blue component is offset from the start of the pixel.
- getBlues() - Method in class loci.formats.gui.Index16ColorModel
-
Return the array of blue color components.
- getBoolean(String) - Method in class loci.formats.in.DynamicMetadataOptions
-
Get the value of property
nameas a Boolean. - getBoolean(String, Boolean) - Method in class loci.formats.in.DynamicMetadataOptions
-
Get the value of property
nameas a Boolean. - getBooleanOption(String) - Method in class loci.plugins.prefs.OptionsList
-
Gets the boolean option with the given key.
- getBooleanValue(String) - Method in class loci.plugins.Slicer
-
Gets the value of the given macro key as a boolean.
- getBounds(BigInteger[], boolean) - Static method in class loci.formats.FilePattern
-
Gets a string containing start, end and step values for a sorted list of numbers.
- getBufferedImage() - Method in class loci.plugins.util.RecordedImageProcessor
- getBuildDate(String[]) - Method in class loci.plugins.macro.LociFunctions
- getByte(int) - Method in class loci.formats.in.SPEReader.SpeHeader
-
Private method used to retrieve a Byte value from the SPE header
- getByte(SPEReader.SpeHeaderEntry) - Method in class loci.formats.in.SPEReader.SpeHeader
-
Method used to retrieve data values for Byte entries into the SPE header table
- getByteBuffer() - Method in class loci.formats.codec.BitBuffer
-
Deprecated.Return the backing byte array.
- getByteCount(boolean) - Method in class loci.formats.tiff.IFD
-
Get the maximum number of bytes needed to represent this IFD.
- getBytes(BufferedImage) - Static method in class loci.formats.gui.AWTImageTools
-
Extracts pixel data as arrays of unsigned bytes, one per channel.
- getBytes(BufferedImage, boolean) - Static method in class loci.formats.gui.AWTImageTools
-
Get the bytes from an image, merging the channels as necessary.
- getBytes(WritableRaster) - Static method in class loci.formats.gui.AWTImageTools
-
Extracts pixel data as arrays of unsigned bytes, one per channel.
- getBytes(WritableRaster, int, int, int, int) - Static method in class loci.formats.gui.AWTImageTools
-
Extracts pixel data as arrays of unsigned bytes, one per channel.
- getBytesPerElement() - Method in enum class loci.formats.tiff.IFDType
-
Retrieves the number of bytes per element.
- getBytesPerPixel(int) - Static method in class loci.formats.FormatTools
-
Retrieves how many bytes per pixel the current plane or section has.
- getBytesPerPixel(String) - Static method in class loci.formats.FormatTools
-
Retrieves the number of bytes per pixel in the current plane.
- GetBytesPerPixel() - Method in class loci.formats.in.SlideBook7Reader.CImageGroup
- getBytesPerSample() - Method in class loci.formats.tiff.IFD
-
Retrieves the image's bytes per sample (derived from tag BitsPerSample) from this IFD.
- getC() - Method in class loci.formats.gui.ImageViewer
-
Gets the C value of the currently displayed image.
- getC(String) - Method in class loci.formats.in.OIRReader
- getCache() - Method in class loci.formats.gui.CacheComponent
- getCache() - Method in class loci.plugins.util.BFVirtualStack
- getCacheListeners() - Method in class loci.formats.cache.Cache
- getCacheListeners() - Method in interface loci.formats.cache.CacheReporter
-
Gets a list of all registered status update listeners.
- getCacheListeners() - Method in class loci.formats.cache.CacheStrategy
- getCalibrationTable() - Method in class loci.plugins.util.RecordedImageProcessor
- getCameraModel() - Method in class loci.formats.in.ND2Handler
- getCaptureMode(int) - Method in class loci.formats.in.NDPIReader
-
Get the description of the given capture mode.
- getCategory() - Method in class loci.formats.in.BaseZeissReader.Tag
- getCBegin(int) - Method in class loci.plugins.in.ImporterOptions
- getCBegin(int) - Method in class loci.plugins.in.ImportProcess
- getCCount(int) - Method in class loci.plugins.in.ImportProcess
-
Valid only after
ImportStep.SERIES. - getCEnd(int) - Method in class loci.plugins.in.ImporterOptions
- getCEnd(int) - Method in class loci.plugins.in.ImportProcess
-
Valid only after
ImportStep.STACK. - getChannel() - Method in class loci.formats.in.PrairieMetadata.PFile
-
Gets the
channelassociated with thisFile. - getChannel(String) - Method in class loci.formats.in.CellomicsReader
- getChannelColor(int) - Method in class loci.formats.in.LIFReader
- getChannelColorFromFile(String) - Method in class loci.formats.in.MIASReader
-
Get the color associated with the given file's channel.
- getChannelColors() - Method in class loci.formats.in.ND2Handler
- getChannelCount() - Method in class loci.formats.in.SDTReader
-
Gets the number of spectral channels.
- getChannelDescriptionNodes(Element) - Method in class loci.formats.in.LeicaMicrosystemsMetadata.LMSMetadataExtractor
- getChannelDescriptionNodes(Element) - Method in class loci.formats.in.LIFReader
- getChannelDimCount(Double[]) - Method in class loci.plugins.macro.LociFunctions
- getChannelDimensionBytesInc(int) - Method in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataTempBuffer
- getChannelDimLength(Double, Double[]) - Method in class loci.plugins.macro.LociFunctions
- getChannelDimType(Double, String[]) - Method in class loci.plugins.macro.LociFunctions
- getChannelFiller() - Method in class loci.plugins.in.ImportProcess
-
Valid only after
ImportStep.STACK. - getChannelGlobalMaximum(int) - Method in class loci.formats.MinMaxCalculator
-
Retrieves a specified channel's global maximum.
- getChannelGlobalMinimum(int) - Method in class loci.formats.MinMaxCalculator
-
Retrieves a specified channel's global minimum.
- getChannelIndex(CV7000Reader.Plane) - Method in class loci.formats.in.CV7000Reader
- getChannelIndex(Element) - Static method in class loci.formats.in.LeicaMicrosystemsMetadata.LMSMetadataExtractor
- getChannelIndex(Element) - Method in class loci.formats.in.LIFReader
- getChannelIndexOfCellObjectName(String) - Method in class loci.formats.in.BDVReader
- getChannelIndexOfCellObjectName(String) - Method in class loci.formats.in.CellH5Reader
- GetChannelIndexOfPath(String) - Method in class loci.formats.in.SlideBook7Reader.CSBFile70
- getChannelKnownMaximum(int) - Method in class loci.formats.MinMaxCalculator
-
Retrieves the specified channel's maximum based on the images that have been read.
- getChannelKnownMinimum(int) - Method in class loci.formats.MinMaxCalculator
-
Retrieves the specified channel's minimum based on the images that have been read.
- getChannelLabel(int) - Method in class loci.formats.in.TextReader
-
Gets the label for the given channel.
- getChannelName() - Method in class loci.formats.in.MetamorphHandler
- getChannelName() - Method in class loci.formats.in.PrairieMetadata.PFile
-
Gets the
channelNameassociated with thisFile. - GetChannelName(int) - Method in class loci.formats.in.SlideBook7Reader.CImageGroup
- getChannelNames() - Method in class loci.formats.in.DicomReader
- getChannelNames() - Method in class loci.formats.in.MetamorphHandler
- getChannelNames() - Method in class loci.formats.in.ND2Handler
- getChannelPriority(String) - Method in class loci.formats.in.LeicaMicrosystemsMetadata.LMSMetadataExtractor
- getChannelSeparator() - Method in class loci.plugins.in.ImportProcess
-
Valid only after
ImportStep.STACK. - getChar(int) - Method in class loci.formats.tools.AsciiImage
- getCheckboxes(GenericDialog) - Static method in class loci.plugins.util.WindowTools
- getChild() - Method in class loci.plugins.util.RecordedImageProcessor
- getChild(Element, String) - Static method in class loci.formats.in.CellVoyagerReader
- getChild(Element, String[]) - Static method in class loci.formats.in.CellVoyagerReader
- getChildIndex(Integer, String) - Method in class loci.formats.in.VolocityReader
- getChildNode(Element, String) - Method in class loci.formats.in.OlympusTileReader
- getChildNodes(Element) - Method in class loci.formats.in.OBFReader
- getChildren(Element, String) - Static method in class loci.formats.in.CellVoyagerReader
- getChildrenFiles(boolean) - Method in class loci.formats.in.LeicaMicrosystemsMetadata.LMSCollectionXmlDocument
-
Returns filepaths of all files which are referenced by this document.
- getChildText(Element, String) - Static method in class loci.formats.in.CellVoyagerReader
- getChildText(Element, String[]) - Static method in class loci.formats.in.CellVoyagerReader
- getChildValue(Element, String) - Method in class loci.formats.in.OlympusTileReader
- GetChildWithName(Node, String) - Method in class loci.formats.in.LeicaMicrosystemsMetadata.LMSXmlDocument
- getChoices(GenericDialog) - Static method in class loci.plugins.util.WindowTools
- getClass(String) - Method in class loci.formats.in.DynamicMetadataOptions
-
Get the value of property
nameas a class. - getClass(String, Class<?>) - Method in class loci.formats.in.DynamicMetadataOptions
-
Get the value of property
nameas a class. - getClasses() - Method in class loci.formats.ClassList
-
Gets the list of classes as an array.
- getCode() - Method in enum class loci.formats.codec.CompressionType
-
Implemented as specified by the
CodedEnumI/F. - getCode() - Method in enum class loci.formats.codec.JPEG2000BoxType
-
Implemented as specified by the
CodedEnumI/F. - getCode() - Method in enum class loci.formats.codec.JPEG2000SegmentMarker
-
Implemented as specified by the
CodedEnumI/F. - getCode() - Method in enum class loci.formats.dicom.DicomVR
- getCode() - Method in enum class loci.formats.tiff.IFDType
- getCode() - Method in enum class loci.formats.tiff.PhotoInterp
- getCode() - Method in enum class loci.formats.tiff.TiffCompression
- getCodec() - Method in interface loci.formats.ICompressedTileWriter
- getCodec() - Method in class loci.formats.ImageWriter
- getCodec() - Method in class loci.formats.out.DicomWriter
- getCodec() - Method in class loci.formats.out.TiffWriter
- getCodec() - Method in enum class loci.formats.tiff.TiffCompression
- getCodec() - Method in class loci.formats.WriterWrapper
- getCodec(int) - Method in class loci.formats.in.TissueFAXSReader
- getCodecName() - Method in enum class loci.formats.tiff.TiffCompression
-
Retrieves the name of the TIFF compression codec.
- getCodecName(int) - Method in class loci.formats.in.AVIReader
- getCodecOptions() - Method in class loci.formats.FormatWriter
- getCodecOptions() - Method in interface loci.formats.ICompressedTileWriter
- getCodecOptions() - Method in class loci.formats.ImageWriter
- getCodecOptions() - Method in class loci.formats.tiff.TiffParser
-
Retrieves the current set of codec options being used to decompress pixel data.
- getCodecOptions() - Method in class loci.formats.WriterWrapper
- getCodecOptions(TissueFAXSReader.ScanRegion) - Method in class loci.formats.in.TissueFAXSReader
- getCodestreamOffset() - Method in class loci.formats.in.JPEG2000MetadataParser
-
Retrieves the offset to the first contiguous codestream.
- getCodestreamPixelType() - Method in class loci.formats.in.JPEG2000MetadataParser
-
Returns the pixel type as specified in the header.
- getCodestreamSizeC() - Method in class loci.formats.in.JPEG2000MetadataParser
-
Returns the number of channels the image has as specified in the header.
- getCodestreamSizeX() - Method in class loci.formats.in.JPEG2000MetadataParser
-
Returns the width of the image as specified in the header.
- getCodestreamSizeY() - Method in class loci.formats.in.JPEG2000MetadataParser
-
Returns the height of the image as specified in the header.
- getColor() - Method in class loci.formats.in.TissueFAXSReader.Channel
-
Color returned by DB is ARGB, OME model is RGBA.
- getColor(Double) - Method in class loci.formats.in.OperettaReader
-
Translate emission wavelength to color, based upon: https://www.perkinelmer.com/CMSResources/Images/44-6551APP_PhotocellApplicationNotes.pdf
- getColorMap(IFD) - Method in class loci.formats.tiff.TiffParser
-
Retrieve the color map associated with the given IFD.
- getColorMode() - Method in class loci.plugins.in.ImporterOptions
- getColorModeInfo() - Method in class loci.plugins.in.ImporterOptions
- getColorModel() - Method in class loci.formats.FormatWriter
- getColorModel() - Method in interface loci.formats.IFormatWriter
-
Gets the color model.
- getColorModel() - Method in class loci.formats.ImageWriter
- getColorModel() - Method in class loci.formats.WriterWrapper
- getColorModel() - Method in class loci.plugins.util.RecordedImageProcessor
- getColorModes() - Method in class loci.plugins.in.ImporterOptions
- getColorValue(TextField) - Method in class loci.plugins.in.ColorDialog
- getColumn() - Method in class loci.formats.in.OMEXMLReader.BinData
- getColumn(int, int, int[], int) - Method in class loci.plugins.util.RecordedImageProcessor
- getColumNames(int) - Method in interface loci.formats.services.MetakitService
- getColumNames(int) - Method in class loci.formats.services.MetakitServiceImpl
- getColumnIndex() - Method in class loci.formats.internal.WellContainer
- getColumnNames(String) - Method in interface loci.formats.services.MetakitService
- getColumnNames(String) - Method in class loci.formats.services.MetakitServiceImpl
- getColumnTypes(int) - Method in interface loci.formats.services.MetakitService
- getColumnTypes(int) - Method in class loci.formats.services.MetakitServiceImpl
- getColumnTypes(String) - Method in interface loci.formats.services.MetakitService
- getColumnTypes(String) - Method in class loci.formats.services.MetakitServiceImpl
- getComment() - Method in class loci.formats.tiff.IFD
-
Convenience method for obtaining the ImageDescription from this IFD.
- getComment() - Method in class loci.formats.tiff.TiffParser
-
Convenience method for obtaining a stream's first ImageDescription.
- getComment(int, int) - Method in class loci.formats.in.MetamorphReader
- getComments() - Method in class loci.formats.in.JPEG2000MetadataParser
-
Retrieves the list of comments stored in the file.
- getCompanion() - Method in class loci.formats.out.OMETiffWriter
-
Get the value of the
OMETiffWriter.COMPANION_KEYoption. - getComponent(int, int) - Method in class loci.formats.gui.UnsignedIntColorModel
- getCompressedByteCount(IFD, int, int) - Method in class loci.formats.in.MinimalTiffReader
- getCompressedSize() - Method in class org.libjpegturbo.turbojpeg.TJCompressor
-
Returns the size of the image (in bytes) generated by the most recent compress/encode operation.
- getCompressedTile(byte[], int, int) - Method in interface loci.formats.services.JPEGTurboService
-
Similar to getTile(int, int), but returns the JPEG-compressed bytes.
- getCompressedTile(byte[], int, int) - Method in class loci.formats.services.JPEGTurboServiceImpl
- getCompressedTile(int, int) - Method in interface loci.formats.services.JPEGTurboService
-
Similar to getTile(int, int), but returns the JPEG-compressed bytes.
- getCompressedTile(int, int) - Method in class loci.formats.services.JPEGTurboServiceImpl
- getCompression() - Method in enum class loci.formats.codec.CompressionType
-
Returns the compression.
- getCompression() - Method in class loci.formats.FormatWriter
- getCompression() - Method in interface loci.formats.IFormatWriter
-
Gets the current compression type.
- getCompression() - Method in class loci.formats.ImageWriter
- getCompression() - Method in class loci.formats.tiff.IFD
-
Retrieves the image's compression type (TIFF tag Compression) from this IFD.
- getCompression() - Method in class loci.formats.WriterWrapper
- getCompression(int) - Method in class loci.formats.in.OBFReader
- getCompression(String) - Method in class loci.formats.FormatReader
-
Deprecated.
- getCompression(String) - Static method in class loci.formats.MetadataTools
-
Retrieves an
Compressionenumeration value for the given String. - getCompressionCodecOptions(IFD) - Method in enum class loci.formats.tiff.TiffCompression
-
Creates a set of codec options for compression.
- getCompressionCodecOptions(IFD, CodecOptions) - Method in enum class loci.formats.tiff.TiffCompression
-
Creates a set of codec options for compression.
- getCompressionMap() - Static method in enum class loci.formats.tiff.TiffCompression
- getCompressionMethod() - Method in class loci.formats.out.DicomWriter
- getCompressionTypes() - Method in class loci.formats.FormatWriter
- getCompressionTypes() - Method in interface loci.formats.IFormatWriter
-
Gets the available compression types.
- getCompressionTypes() - Method in class loci.formats.ImageWriter
- getCompressionTypes() - Method in class loci.formats.WriterWrapper
- getConcatenateInfo() - Method in class loci.plugins.in.ImporterOptions
- getConcatenationIndex() - Method in class loci.formats.in.DicomReader
- getConfig() - Method in class loci.formats.in.PrairieMetadata
-
Gets the map of configuration key/value pairs.
- getConfig(String) - Method in class loci.formats.in.PrairieMetadata
-
Gets the
valueof the given configurationkey. - getConstraintsForCell(int, int, Container, int) - Static method in class loci.plugins.config.SpringUtilities
- getContrastMethod(String) - Method in class loci.formats.FormatReader
-
Deprecated.
- getContrastMethod(String) - Static method in class loci.formats.MetadataTools
-
Retrieves an
ContrastMethodenumeration value for the given String. - getCore() - Method in class loci.formats.in.LeicaMicrosystemsMetadata.LMSFileReader
- getCoreIndex() - Method in class loci.formats.FileStitcher
- getCoreIndex() - Method in class loci.formats.FormatReader
- getCoreIndex() - Method in interface loci.formats.IFormatReader
-
Deprecated.This method is no longer required for sub-resolution support.
- getCoreIndex() - Method in class loci.formats.ImageReader
- getCoreIndex() - Method in class loci.formats.ReaderWrapper
- getCoreIndex() - Method in class loci.formats.SubResolutionFormatReader
- getCoreIndex() - Method in class loci.formats.WrappedReader
- getCoreMetadataList() - Method in class loci.formats.DimensionSwapper
- getCoreMetadataList() - Method in class loci.formats.FileStitcher
- getCoreMetadataList() - Method in class loci.formats.FormatReader
- getCoreMetadataList() - Method in interface loci.formats.IFormatReader
-
Deprecated.Reader internals should not be accessed by reader users
- getCoreMetadataList() - Method in class loci.formats.ImageReader
- getCoreMetadataList() - Method in class loci.formats.in.FilePatternReader
- getCoreMetadataList() - Method in class loci.formats.in.LeicaHandler
- getCoreMetadataList() - Method in class loci.formats.in.ND2Handler
- getCoreMetadataList() - Method in class loci.formats.ReaderWrapper
- getCoreMetadataList() - Method in class loci.formats.SubResolutionFormatReader
- getCoreMetadataList() - Method in class loci.formats.WrappedReader
- getCorrection() - Method in class loci.formats.in.ND2Handler
- getCorrection(String) - Method in class loci.formats.FormatReader
-
Deprecated.
- getCorrection(String) - Static method in class loci.formats.MetadataTools
-
Retrieves an
Correctionenumeration value for the given String. - getCount() - Method in class loci.formats.FilePattern
-
Gets the number of elements for each pattern block.
- getCreationDate() - Method in interface loci.formats.services.EXIFService
- getCreationDate() - Method in class loci.formats.services.EXIFServiceImpl
- getCropInfo() - Method in class loci.plugins.in.ImporterOptions
- getCropRegion(int) - Method in class loci.plugins.in.ImporterOptions
- getCropRegion(int) - Method in class loci.plugins.in.ImportProcess
-
Valid only after
ImportStep.STACK. - getCStep(int) - Method in class loci.plugins.in.ImporterOptions
- getCStep(int) - Method in class loci.plugins.in.ImportProcess
- getCurrentColorModel() - Method in class loci.plugins.util.RecordedImageProcessor
- getCurrentCore() - Method in class loci.formats.FormatReader
-
Get the CoreMetadata corresponding to the current series and resolution
- getCurrentCore() - Method in class loci.formats.SubResolutionFormatReader
-
Get the CoreMetadata corresponding to the current series and resolution
- getCurrentFile() - Method in class loci.formats.FormatReader
- getCurrentFile() - Method in interface loci.formats.IFormatReader
-
Returns the current file.
- getCurrentFile() - Method in class loci.formats.ImageReader
- getCurrentFile() - Method in class loci.formats.ReaderWrapper
- getCurrentFile() - Method in class loci.plugins.in.ImportProcess
-
Valid only after
ImportStep.STACK. - getCurrentFile(String[]) - Method in class loci.plugins.macro.LociFunctions
- getCurrentPos() - Method in class loci.formats.cache.Cache
-
Gets the current dimensional position.
- getCurrentPyramid() - Method in class loci.formats.in.CellSensReader
-
Get an object representing the pyramid which contains the current series/resolution.
- getCurrentPyramidIndex() - Method in class loci.formats.in.CellSensReader
-
Get an index to the pyramid which contains the current series/resolution.
- getCustomColor(int, int) - Method in class loci.plugins.in.ImporterOptions
- getCustomColorKey(int, int) - Method in class loci.plugins.in.ImporterOptions
- getCutIn(Double) - Static method in class loci.formats.FormatTools
- getCutOut(Double) - Static method in class loci.formats.FormatTools
- getCycle() - Method in class loci.formats.in.PrairieMetadata.Sequence
-
Gets the
cycleassociated with thisSequence. - getCycleCount() - Method in class loci.formats.in.PrairieMetadata
-
Gets the number of recorded cycles.
- getCycleMax() - Method in class loci.formats.in.PrairieMetadata
-
Gets the maximum cycle value.
- getCycleMin() - Method in class loci.formats.in.PrairieMetadata
-
Gets the minimum cycle value.
- getCZTag(IFD) - Method in class loci.formats.in.ZeissLSMReader
- getData() - Method in class loci.formats.gui.SignedByteBuffer
- getData() - Method in class loci.formats.gui.SignedShortBuffer
- getData() - Method in class loci.formats.gui.UnsignedIntBuffer
- getData(int) - Method in class loci.formats.gui.SignedByteBuffer
- getData(int) - Method in class loci.formats.gui.SignedShortBuffer
- getData(int) - Method in class loci.formats.gui.UnsignedIntBuffer
- getDataElements(int, Object) - Method in class loci.formats.gui.Index16ColorModel
- getDataElements(int, Object) - Method in class loci.formats.gui.SignedColorModel
- getDataElements(int, Object) - Method in class loci.formats.gui.UnsignedIntColorModel
- GetDataOffsetForBlock(int) - Method in class loci.formats.in.SlideBook7Reader.CCompressionBase
- getDatasetStructureDescription() - Method in class loci.formats.FormatReader
- getDatasetStructureDescription() - Method in interface loci.formats.IFormatReader
-
Returns a short description of the dataset structure.
- getDatasetStructureDescription() - Method in class loci.formats.ImageReader
- getDatasetStructureDescription() - Method in class loci.formats.ReaderWrapper
- getDatasetStructureDescription() - Method in class loci.formats.WrappedReader
- GetDataSizeForBlock(int) - Method in class loci.formats.in.SlideBook7Reader.CCompressionBase
- getDate() - Method in class loci.formats.in.MetamorphHandler
- getDate() - Method in class loci.formats.in.ND2Handler
- getDate() - Method in class loci.formats.in.PrairieMetadata
-
Gets the date of the acquisition.
- getDatestamp() - Method in class loci.formats.in.SVSReader
- getDecompressedStream(String) - Method in class loci.formats.in.CellomicsReader
- getDefault() - Method in class loci.plugins.prefs.BooleanOption
-
Gets the default value of the option.
- getDefault() - Method in class loci.plugins.prefs.DoubleOption
-
Gets the default value of the option.
- getDefault() - Method in class loci.plugins.prefs.StringOption
-
Gets the default value of the option.
- getDefaultColorModel() - Method in class loci.plugins.util.RecordedImageProcessor
- getDefaultConfiguration() - Static method in class loci.formats.gui.AWTImageTools
-
Gets the default graphics configuration for the environment.
- getDefaultCustomColor(int) - Method in class loci.plugins.in.ImporterOptions
- getDefaultOptions() - Static method in class loci.formats.codec.CodecOptions
-
Return CodecOptions with reasonable default values.
- getDefaultOptions() - Static method in class loci.formats.codec.JPEG2000CodecOptions
-
Return JPEG2000CodecOptions with reasonable default values.
- getDefaultOptions(CodecOptions) - Static method in class loci.formats.codec.JPEG2000CodecOptions
-
Return JPEG2000CodecOptions using the given CodecOptions as the default.
- getDefaultReaderClasses() - Static method in class loci.formats.ImageReader
- getDefaultValue(String) - Method in class loci.plugins.prefs.OptionsList
-
Gets the default value of the string option with the given key.
- getDefaultVR() - Method in enum class loci.formats.dicom.DicomAttribute
-
Get the known default VR for this attribute, or IMPLICIT if our dictionary does not include a default VR.
- getDefaultVR(int) - Static method in enum class loci.formats.dicom.DicomAttribute
- getDefaultWriterClasses() - Static method in class loci.formats.ImageWriter
- getDeltaT() - Method in class loci.formats.in.LeicaHandler
- getDenom() - Method in class org.libjpegturbo.turbojpeg.TJScalingFactor
-
Returns denominator
- getDenominator() - Method in class loci.formats.tiff.TiffRational
-
Gets this number's denominator.
- getDescription() - Method in enum class loci.formats.dicom.DicomAttribute
-
Get the human-readable description associated with this attribute.
- getDescription() - Method in class loci.formats.gui.ComboFileFilter
-
Returns the filter's description.
- getDescription() - Method in class loci.formats.gui.ExtensionFileFilter
-
Gets the filter's description.
- getDescription() - Method in class loci.formats.gui.FormatFileFilter
-
Gets the filter's description.
- getDescription() - Method in class loci.formats.gui.NoExtensionFileFilter
-
Gets the filter's description.
- getDescription(int) - Static method in enum class loci.formats.dicom.DicomAttribute
- getDeser() - Method in class loci.formats.Memoizer
-
Returns a configured
Kryoinstance. - getDetectorType(String) - Method in class loci.formats.FormatReader
-
Deprecated.
- getDetectorType(String) - Static method in class loci.formats.MetadataTools
-
Retrieves an
DetectorTypeenumeration value for the given String. - getDeviceSubtype(String) - Method in class loci.formats.in.CellSensReader
- getDimension(int, Dimension.DimensionKey) - Method in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataTempBuffer
- getDimension(String) - Method in class loci.formats.in.ZeissTIFFHandler.Scaling
-
Get a dimension by its index.
- getDimension(String) - Method in interface loci.formats.services.NetCDFService
-
Retrieves the length of a dimension.
- getDimension(String) - Method in class loci.formats.services.NetCDFServiceImpl
- getDimension(RandomAccessInputStream) - Method in class loci.formats.in.I2IReader
- getDimensionDescriptionNodes(Element) - Method in class loci.formats.in.LeicaMicrosystemsMetadata.LMSMetadataExtractor
- getDimensionDescriptionNodes(Element) - Method in class loci.formats.in.LIFReader
- getDimensionEntry(String) - Method in class loci.formats.in.ZeissCZIReader.DirectoryEntry
- getDimensionOrder() - Method in class loci.formats.ChannelMerger
- getDimensionOrder() - Method in class loci.formats.ChannelSeparator
- getDimensionOrder() - Method in class loci.formats.DimensionSwapper
- getDimensionOrder() - Method in class loci.formats.FileStitcher
- getDimensionOrder() - Method in class loci.formats.FormatReader
- getDimensionOrder() - Method in interface loci.formats.IFormatReader
-
Gets a five-character string representing the dimension order in which planes will be returned.
- getDimensionOrder() - Method in class loci.formats.ImageReader
- getDimensionOrder() - Method in class loci.formats.ReaderWrapper
- getDimensionOrder() - Method in class loci.formats.WrappedReader
- getDimensionOrder(int) - Method in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataTempBuffer
-
Returns the dimension order as a string
- getDimensionOrder(String) - Method in class loci.formats.FormatReader
-
Deprecated.
- getDimensionOrder(String) - Static method in class loci.formats.MetadataTools
-
Retrieves an
DimensionOrderenumeration value for the given String. - getDimensionOrder(String[]) - Method in class loci.plugins.macro.LociFunctions
- getDimensions(int) - Method in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataTempBuffer
- getDimensionSwapper() - Method in class loci.plugins.in.ImportProcess
-
Valid only after
ImportStep.STACK. - getDirectory(String) - Method in class loci.formats.services.NetCDFServiceImpl
- getDisplayColor() - Method in class loci.formats.in.SVSReader
- getDoc() - Method in class loci.formats.in.LeicaMicrosystemsMetadata.LMSXmlDocument
- getDocument() - Method in class loci.formats.gui.XMLWindow
-
Gets the XML document currently being displayed within the window.
- getDocumentBytes(String) - Method in interface loci.formats.services.POIService
-
Retrieve all of the raw bytes that correspond to the given file name.
- getDocumentBytes(String) - Method in class loci.formats.services.POIServiceImpl
- getDocumentBytes(String, int) - Method in interface loci.formats.services.POIService
-
Retrieve at most 'length' bytes that correspond to the given file name.
- getDocumentBytes(String, int) - Method in class loci.formats.services.POIServiceImpl
- getDocumentList() - Method in interface loci.formats.services.POIService
-
Retrieve a list of all files in the current POI file system.
- getDocumentList() - Method in class loci.formats.services.POIServiceImpl
- getDocumentStream(String) - Method in interface loci.formats.services.POIService
-
Retrieve a RandomAccessInputStream corresponding to the given file name.
- getDocumentStream(String) - Method in class loci.formats.services.POIServiceImpl
- getDomains() - Method in class loci.formats.FormatReader
- getDomains() - Method in interface loci.formats.IFormatReader
-
Returns the list of domains represented by the current file.
- getDomains() - Method in class loci.formats.ImageReader
- getDomains() - Method in class loci.formats.in.CellomicsReader
- getDomains() - Method in class loci.formats.in.ICSReader
- getDomains() - Method in class loci.formats.in.MetamorphReader
- getDomains() - Method in class loci.formats.in.MetamorphTiffReader
- getDomains() - Method in class loci.formats.in.NiftiReader
- getDomains() - Method in class loci.formats.in.OMETiffReader
- getDomains() - Method in class loci.formats.in.OMEXMLReader
- getDomains() - Method in class loci.formats.ReaderWrapper
- getDomains() - Method in class loci.formats.WrappedReader
- getDouble(String) - Method in class loci.formats.in.DynamicMetadataOptions
-
Get the value of property
nameas a Double. - getDouble(String, Double) - Method in class loci.formats.in.DynamicMetadataOptions
-
Get the value of property
nameas a Double. - GetDoubleArray(Node, String, Boolean) - Method in class loci.formats.in.SlideBook7Reader.ClassDecoder
- getDoubles(BufferedImage) - Static method in class loci.formats.gui.AWTImageTools
-
Extracts pixel data as arrays of doubles, one per channel.
- getDoubles(WritableRaster) - Static method in class loci.formats.gui.AWTImageTools
-
Extracts pixel data as arrays of doubles, one per channel.
- getDoubles(WritableRaster, int, int, int, int) - Static method in class loci.formats.gui.AWTImageTools
-
Extracts pixel data as arrays of doubles, one per channel.
- getDoubleValue(int) - Method in class loci.formats.in.ZeissLSMReader.SubBlock
- getDyeNames() - Method in class loci.formats.in.SVSReader
- getEffectiveSeries(int) - Method in class loci.formats.in.ZeissLSMReader
- getEffectiveSizeC() - Method in class loci.formats.FormatReader
- getEffectiveSizeC() - Method in interface loci.formats.IFormatReader
-
Gets the effective size of the C dimension, guaranteeing that getEffectiveSizeC() * getSizeZ() * getSizeT() == getImageCount() regardless of the result of isRGB().
- getEffectiveSizeC() - Method in class loci.formats.ImageReader
- getEffectiveSizeC() - Method in class loci.formats.ReaderWrapper
- getEffectiveSizeC() - Method in class loci.formats.WrappedReader
- getEffectiveSizeC(Double[]) - Method in class loci.plugins.macro.LociFunctions
- GetElapsedTime(int) - Method in class loci.formats.in.SlideBook7Reader.CImageGroup
- getElem(int) - Method in class loci.formats.gui.SignedByteBuffer
- getElem(int) - Method in class loci.formats.gui.UnsignedIntBuffer
- getElem(int, int) - Method in class loci.formats.gui.SignedByteBuffer
- getElem(int, int) - Method in class loci.formats.gui.SignedShortBuffer
- getElem(int, int) - Method in class loci.formats.gui.UnsignedIntBuffer
- getElemDouble(int) - Method in class loci.formats.gui.UnsignedIntBuffer
- getElemDouble(int, int) - Method in class loci.formats.gui.UnsignedIntBuffer
- getElementNode() - Method in class loci.formats.in.LeicaMicrosystemsMetadata.XlifDocument
- getElements() - Method in class loci.formats.FilePattern
-
Gets individual elements for each pattern block.
- getElements() - Method in class loci.formats.FilePatternBlock
-
Gets all block elements.
- getElementSize(String) - Method in interface loci.formats.services.JHDFService
-
Retrieves the Element Size of a dataset in Byte.
- getElementSize(String) - Method in class loci.formats.services.JHDFServiceImpl
- getElemFloat(int) - Method in class loci.formats.gui.UnsignedIntBuffer
- getElemFloat(int, int) - Method in class loci.formats.gui.UnsignedIntBuffer
- getEmission() - Method in class loci.formats.in.SVSReader
- getEmissionWavelength(Double) - Static method in class loci.formats.FormatTools
- getEmissionWavelengths() - Method in class loci.formats.in.ND2Handler
- getEndPointer() - Method in class loci.formats.dicom.DicomTag
-
Get the file pointer at which the value ends (useful for sequences and byte streams).
- getEndX() - Method in class loci.formats.in.SPEReader.SpeROI
- getEndY() - Method in class loci.formats.in.SPEReader.SpeROI
- getEntries(IRandomAccess) - Method in class loci.formats.in.IM3Reader.FloatIM3Record
-
Return all entries as an array
- getEntry(IRandomAccess, int) - Method in class loci.formats.in.IM3Reader.BooleanIM3Record
-
Get the boolean value at the given index
- getEntry(IRandomAccess, int) - Method in class loci.formats.in.IM3Reader.FloatIM3Record
-
Get the floating-point value at the given index
- getEntry(IRandomAccess, int) - Method in class loci.formats.in.IM3Reader.IntIM3Record
-
Get the integer value at the given index
- getEnum(String, T) - Method in class loci.formats.in.DynamicMetadataOptions
-
Get the value of property
nameas an enumerated type. - getErrorMessage() - Method in class loci.formats.FilePattern
-
Gets the file pattern error message, if any.
- getExcitation() - Method in class loci.formats.in.SVSReader
- getExcitationWavelength(Double) - Static method in class loci.formats.FormatTools
- getExcitationWavelengths() - Method in class loci.formats.in.ND2Handler
- getExifIFDs() - Method in class loci.formats.tiff.TiffParser
-
Returns EXIF IFDs.
- getExifTagName(int) - Static method in class loci.formats.in.BaseTiffReader
- getExperimenterName() - Method in class loci.formats.in.OperettaReader.OperettaHandler
- getExperimentType(String) - Method in class loci.formats.FormatReader
-
Deprecated.
- getExperimentType(String) - Static method in class loci.formats.MetadataTools
-
Retrieves an
ExperimentTypeenumeration value for the given String. - getExposures() - Method in class loci.formats.in.MetamorphHandler
- getExposureTime() - Method in class loci.formats.in.SVSReader
- GetExposureTime(int) - Method in class loci.formats.in.SlideBook7Reader.CImageGroup
- getExposureTimes() - Method in class loci.formats.in.LeicaHandler
- getExposureTimes() - Method in class loci.formats.in.ND2Handler
- getExtension() - Method in class loci.formats.gui.ExtensionFileFilter
-
Gets the filter's first valid extension.
- getExtensionFunctions() - Method in class loci.plugins.macro.MacroFunctions
- getExtensions() - Method in class loci.formats.gui.ExtensionFileFilter
-
Gets the filter's valid extensions.
- getExternalSeries() - Method in class loci.formats.FileStitcher
- getExternalSeries(int) - Method in class loci.formats.FileStitcher
- getExtraSeries(String) - Method in class loci.formats.in.ZeissLSMReader
- getf(int) - Method in class loci.plugins.util.RecordedImageProcessor
- getf(int, int) - Method in class loci.plugins.util.RecordedImageProcessor
- getField(int) - Method in class loci.formats.in.FluoviewReader
- getField(String) - Method in class loci.formats.in.CellomicsReader
- getField(String) - Method in class loci.formats.in.FlexReader
- getField(String) - Method in class loci.formats.in.MetamorphTiffReader
- getFieldCount() - Method in class loci.formats.internal.WellContainer
- getFieldFromSeries(int) - Method in class loci.formats.in.InCellReader
- getFieldIndex() - Method in class loci.formats.in.ND2Handler
- getFieldName(int) - Static method in class loci.formats.tiff.IFD
-
This method uses reflection to scan the values of this class's static fields, returning the first matching field's name.
- getFilamentType(String) - Method in class loci.formats.FormatReader
-
Deprecated.
- getFilamentType(String) - Static method in class loci.formats.MetadataTools
-
Retrieves an
FilamentTypeenumeration value for the given String. - getFile() - Method in interface loci.formats.services.JHDFService
-
Retrieves the current initialized file path.
- getFile() - Method in class loci.formats.services.JHDFServiceImpl
- getFile() - Method in interface loci.formats.services.NetCDFService
-
Retrieves the current initialized file path.
- getFile() - Method in class loci.formats.services.NetCDFServiceImpl
- getFile(int) - Method in class loci.formats.in.JDCEReader
- getFile(int) - Method in class loci.formats.in.MicromanagerReader.Position
- getFile(int) - Method in class loci.formats.in.PerkinElmerReader
- getFile(int) - Method in class loci.formats.in.PrairieMetadata.Frame
-
Gets the
Filewith the givenchannel. - getFile(int, int) - Method in class loci.formats.in.CellWorxReader
-
Retrieve the .pnl file corresponding to the given series.
- getFile(int, int) - Method in class loci.formats.in.PrairieMetadata.Sequence
-
Gets the
Frameat the given (cycle,index,channel). - getFile(int, int) - Method in class loci.formats.internal.WellContainer
- getFile(int, int, int) - Method in class loci.formats.in.PrairieMetadata
-
Gets the
Frameat the given (cycle,index,channel). - getFile(Integer, String) - Method in class loci.formats.in.VolocityReader
- getFile(String) - Method in class loci.formats.in.DynamicMetadataOptions
-
Get the value of property
nameas a file object. - getFile(String) - Method in class loci.formats.in.FV1000Reader
- getFile(String, int, int, int, int, int) - Method in class loci.formats.in.MicromanagerReader.Position
- getFile(String, File) - Method in class loci.formats.in.DynamicMetadataOptions
-
Get the value of property
nameas a file object. - getFileHandle(String) - Method in class loci.formats.in.FlexReader
- getFileIndex(int) - Method in class loci.formats.in.PerkinElmerReader
- getFilename() - Method in class loci.formats.in.PrairieMetadata.PFile
-
Gets the
filenameassociated with thisFile. - getFilename(int, int) - Method in class loci.formats.in.BDReader
- getFilename(int, int) - Method in class loci.formats.out.DicomWriter
- getFilename(int, int, IFormatReader, String) - Static method in class loci.formats.FormatTools
- getFilename(int, int, IFormatReader, String, boolean) - Static method in class loci.formats.FormatTools
- getFilename(int, int, MetadataRetrieve, String, boolean) - Static method in class loci.formats.FormatTools
- getFilenames(String, IFormatReader) - Static method in class loci.formats.FormatTools
- getFilepath() - Method in class loci.formats.in.LeicaMicrosystemsMetadata.LMSXmlDocument
- getFilePattern() - Method in class loci.formats.AxisGuesser
-
Gets the file pattern.
- getFilePattern() - Method in class loci.formats.FileStitcher.ExternalSeries
- getFilePattern() - Method in class loci.formats.FileStitcher
-
Gets the file pattern object used to build the list of files.
- getFiles() - Method in class loci.formats.FilePattern
-
Gets a listing of all files matching this file pattern.
- getFiles() - Method in class loci.formats.FileStitcher.ExternalSeries
- getFiles(int) - Method in class loci.formats.in.JDCEReader.JDCEWell
- getFiles(int) - Method in class loci.formats.internal.WellContainer
- getFileSize(String) - Method in interface loci.formats.services.POIService
-
Retrieve the total number of bytes in the given file.
- getFileSize(String) - Method in class loci.formats.services.POIServiceImpl
- getFileStitcher() - Method in class loci.plugins.in.ImportProcess
-
Valid only after
ImportStep.STACK. - getFileVersion(RandomAccessInputStream) - Method in class loci.formats.in.OBFReader
- getFillColor() - Method in class loci.formats.FormatReader
- getFillColor() - Method in interface loci.formats.IFormatReader
-
Return the fill value for undefined pixels.
- getFillColor() - Method in class loci.formats.ImageReader
- getFillColor() - Method in class loci.formats.in.ZeissCZIReader
- getFillColor() - Method in class loci.formats.ReaderWrapper
- getFillRule(String) - Method in class loci.formats.FormatReader
-
Deprecated.
- getFillRule(String) - Static method in class loci.formats.MetadataTools
-
Retrieves an
FillRuleenumeration value for the given String. - getFilter(String) - Method in class loci.formats.in.FV1000Reader.ChannelData
- getFilters() - Method in class loci.formats.gui.ComboFileFilter
-
Gets the list of file filters forming this filter combination.
- getFilterType(String) - Method in class loci.formats.FormatReader
-
Deprecated.
- getFilterType(String) - Static method in class loci.formats.MetadataTools
-
Retrieves an
FilterTypeenumeration value for the given String. - getFirst() - Method in class loci.formats.FilePattern
-
Gets the START element for all blocks.
- getFirst() - Method in class loci.formats.FilePatternBlock
-
Gets the first element in a range block.
- getFirstChannel(String) - Method in class loci.formats.in.SlidebookTiffReader
- getFirstChild(Element, String) - Method in class loci.formats.in.OIRReader
- getFirstChild(Element, String) - Method in class loci.formats.in.PrairieMetadata
-
Gets the first child element with the given name.
- getFirstComment(int) - Method in class loci.formats.in.MetamorphReader
-
Returns the TIFF comment from the first IFD of the first STK file in the given series.
- getFirstFile() - Method in class loci.formats.in.PrairieMetadata.Frame
-
Gets the first
Fileof theSequence. - getFirstFrame() - Method in class loci.formats.in.PrairieMetadata.Sequence
-
Gets the first
Frameof theSequence. - getFirstIFD() - Method in class loci.formats.tiff.TiffParser
-
Gets the first IFD within the TIFF file, or null if the input source is not a valid TIFF file.
- getFirstIFD(String) - Static method in class loci.formats.in.OMETiffReader
- getFirstIFDEntry(int) - Method in class loci.formats.tiff.TiffParser
-
Retrieve a given entry from the first IFD in the stream.
- getFirstNode(Element, String) - Method in class loci.formats.in.ZeissCZIReader
- getFirstNodeValue(Element, String) - Method in class loci.formats.in.ZeissCZIReader
- getFirstOffset() - Method in class loci.formats.tiff.TiffParser
-
Gets offset to the first IFD, or -1 if stream is not TIFF.
- getFirstSequence() - Method in class loci.formats.in.PrairieMetadata
-
Gets the first
Sequence. - getFirstTimeInfo() - Method in class loci.plugins.in.ImporterOptions
- getFixedHeader() - Method in class loci.formats.services.JPEGTurboServiceImpl
- getFlattenedList() - Method in class loci.formats.CoreMetadataList
- getFlexFiles() - Method in class loci.formats.in.FlexReader.MeaHandler
- getFloat(String) - Method in class loci.formats.in.DynamicMetadataOptions
-
Get the value of property
nameas a Float. - getFloat(String, Float) - Method in class loci.formats.in.DynamicMetadataOptions
-
Get the value of property
nameas a Float. - getFloatArray() - Method in class loci.plugins.util.RecordedImageProcessor
- GetFloatArray(Node, String, Boolean) - Method in class loci.formats.in.SlideBook7Reader.ClassDecoder
- getFloats(BufferedImage) - Static method in class loci.formats.gui.AWTImageTools
-
Extracts pixel data as arrays of floats, one per channel.
- getFloats(WritableRaster) - Static method in class loci.formats.gui.AWTImageTools
-
Extracts pixel data as arrays of floats, one per channel.
- getFloats(WritableRaster, int, int, int, int) - Static method in class loci.formats.gui.AWTImageTools
-
Extracts pixel data as arrays of floats, one per channel.
- getFloatValue(int) - Method in class loci.formats.in.ZeissLSMReader.SubBlock
- getFontFamily(String) - Method in class loci.formats.FormatReader
-
Deprecated.
- getFontFamily(String) - Static method in class loci.formats.MetadataTools
-
Retrieves an
FontFamilyenumeration value for the given String. - getFontMetrics() - Method in class loci.plugins.util.RecordedImageProcessor
- getFontSize(Integer) - Static method in class loci.formats.FormatTools
- getFontStyle(String) - Method in class loci.formats.FormatReader
-
Deprecated.
- getFontStyle(String) - Static method in class loci.formats.MetadataTools
-
Retrieves an
FontStyleenumeration value for the given String. - getForceThumbnailsInfo() - Method in class loci.plugins.in.ImporterOptions
- getForegroundValue() - Method in class loci.plugins.util.RecordedImageProcessor
- getFormat() - Method in class loci.formats.FormatHandler
- getFormat() - Method in interface loci.formats.IFormatHandler
-
Gets the name of this file format.
- getFormat() - Method in class loci.formats.ImageReader
- getFormat() - Method in class loci.formats.ImageWriter
- getFormat() - Method in class loci.formats.ReaderWrapper
- getFormat() - Method in class loci.formats.WriterWrapper
- getFormat(String) - Method in class loci.formats.ImageReader
-
Gets a string describing the file format for the given file.
- getFormat(String) - Method in class loci.formats.ImageWriter
-
Gets a string describing the file format for the given file.
- getFormat(String, String[]) - Method in class loci.plugins.macro.LociFunctions
- getFourPixelCorrectionLine() - Method in class loci.formats.in.DCIMGReader
- getFourPixelCorrectionOffset() - Method in class loci.formats.in.DCIMGReader
- getFrame() - Method in class loci.formats.in.PrairieMetadata.PFile
-
Gets the
<Frame>containing this<File>. - getFrame(int) - Method in class loci.formats.in.PrairieMetadata.Sequence
-
Gets the
Framewith the givenindex. - getFrame(int, int) - Method in class loci.formats.in.PrairieMetadata
-
Gets the
Frameat the given (cycleandindex). - getFramesPerSecond() - Method in class loci.formats.FormatWriter
- getFramesPerSecond() - Method in interface loci.formats.IFormatWriter
-
Gets the frames per second to use when writing.
- getFramesPerSecond() - Method in class loci.formats.ImageWriter
- getFramesPerSecond() - Method in class loci.formats.WriterWrapper
- getGain() - Method in class loci.formats.in.MetamorphHandler
- getGain(int) - Method in class loci.formats.in.PrairieMetadata.Frame
-
Gets the
cth gain for thisFrame. - getGains() - Method in class loci.formats.in.ND2Handler
- getGlobalMeta(String) - Method in class loci.formats.FormatReader
-
Gets a value from the global metadata table.
- getGlobalMetadata() - Method in class loci.formats.FormatReader
- getGlobalMetadata() - Method in interface loci.formats.IFormatReader
-
Obtains the hashtable containing the metadata field/value pairs from the current file.
- getGlobalMetadata() - Method in class loci.formats.ImageReader
- getGlobalMetadata() - Method in class loci.formats.in.LeicaHandler
- getGlobalMetadata() - Method in class loci.formats.ReaderWrapper
- getGlobalMetadata() - Method in class loci.formats.WrappedReader
- getGrandchildren(Element, String) - Method in class loci.formats.in.ZeissCZIReader
- getGrandchildren(Element, String, String) - Method in class loci.formats.in.ZeissCZIReader
- getGreen(int) - Method in class loci.formats.gui.Index16ColorModel
- getGreen(int) - Method in class loci.formats.gui.SignedColorModel
- getGreen(int) - Method in class loci.formats.gui.UnsignedIntColorModel
- getGreen(Object) - Method in class loci.formats.gui.SignedColorModel
- getGreen(Object) - Method in class loci.formats.gui.UnsignedIntColorModel
- getGreenOffset(int) - Static method in class org.libjpegturbo.turbojpeg.TJ
-
For the given pixel format, returns the number of bytes that the green component is offset from the start of the pixel.
- getGreens() - Method in class loci.formats.gui.Index16ColorModel
-
Return the array of green color components.
- getGroup(String) - Method in class loci.formats.services.NetCDFServiceImpl
-
Retrieves a group based on its fully qualified path.
- getGroupFilesInfo() - Method in class loci.plugins.in.ImporterOptions
- getGroupX() - Method in class loci.formats.in.SPEReader.SpeROI
- getGroupY() - Method in class loci.formats.in.SPEReader.SpeROI
- getHeader() - Method in class loci.formats.in.SPEReader.SpeHeader
- getHeaderPixelType() - Method in class loci.formats.in.JPEG2000MetadataParser
-
Returns the pixel type as specified in the header.
- getHeaderSize() - Method in class loci.formats.in.SPEReader.SpeHeader
- getHeaderSizeC() - Method in class loci.formats.in.JPEG2000MetadataParser
-
Returns the number of channels the image has as specified in the header.
- getHeaderSizeX() - Method in class loci.formats.in.JPEG2000MetadataParser
-
Returns the width of the image as specified in the header.
- getHeaderSizeY() - Method in class loci.formats.in.JPEG2000MetadataParser
-
Returns the height of the image as specified in the header.
- getHeight() - Method in class loci.formats.codec.JPEGTileDecoder
- getHeight() - Method in class loci.plugins.util.BFVirtualStack
- getHeight() - Method in class loci.plugins.util.RecordedImageProcessor
- getHeight() - Method in class org.libjpegturbo.turbojpeg.TJDecompressor
-
Returns the height of the JPEG image associated with this decompressor instance.
- getHeight(IFormatReader, String, int) - Static method in class loci.plugins.util.BFVirtualStack
- getHelper() - Method in class loci.formats.in.FilePatternReader
- getHelper() - Method in class loci.formats.WrappedReader
-
Get the helper class that reads images
- getHistogram() - Method in class loci.plugins.util.RecordedImageProcessor
- GetHistogramDataFile(String, Integer, Integer) - Method in class loci.formats.in.SlideBook7Reader.CSBFile70
- getHistogramMax() - Method in class loci.plugins.util.RecordedImageProcessor
- getHistogramMin() - Method in class loci.plugins.util.RecordedImageProcessor
- getHistogramSize() - Method in class loci.plugins.util.RecordedImageProcessor
- getId() - Method in class loci.formats.filter.LZ4Filter
- getId() - Method in class loci.formats.filter.LZ4Filter.LZ4FilterProvider
- getId() - Method in class loci.plugins.in.ImporterOptions
- getId(String) - Method in class loci.formats.tools.MakeTestOmeTiff
- getIdInfo() - Method in class loci.plugins.in.ImporterOptions
- getIdLocation() - Method in class loci.plugins.in.ImportProcess
-
Valid only after
ImportStep.READER. - getIdName() - Method in class loci.plugins.in.ImportProcess
-
Valid only after
ImportStep.READER. - getIFD(int) - Method in class loci.formats.in.SVSReader
-
Get the IFD corresponding to the given plane in the current series.
- getIFD(long) - Method in class loci.formats.tiff.TiffParser
-
Gets the IFD stored at the given offset.
- getIFDComment(int) - Method in class loci.formats.in.VectraReader
- getIFDIndex() - Method in class loci.formats.in.CellSensReader
- getIFDIndex(int) - Method in class loci.formats.in.VentanaReader
-
Note that all planes for a particular resolution or extra image are packed into a single IFD, so the IFD index does not depend upon the plane (e.g.
- getIFDIndex(int, int) - Method in class loci.formats.in.NDPIReader
- getIFDIndex(int, int) - Method in class loci.formats.in.SVSReader
- getIFDIndex(int, int) - Method in class loci.formats.in.VectraReader
-
Returns the index of the IFD to be used for the given core index and image number.
- getIFDIntArray(int) - Method in class loci.formats.tiff.IFD
-
Gets the given directory entry values in int format from this IFD, performing some error checking.
- getIFDIntValue(int) - Method in class loci.formats.tiff.IFD
-
Gets the given directory entry value in int format from this IFD, or -1 if the given directory does not exist.
- getIFDIntValue(int, int) - Method in class loci.formats.tiff.IFD
-
Gets the given directory entry value in int format from this IFD, performing some error checking.
- getIFDLongArray(int) - Method in class loci.formats.tiff.IFD
-
Gets the given directory entry values in long format from this IFD, performing some error checking.
- getIFDLongValue(int, long) - Method in class loci.formats.tiff.IFD
-
Gets the given directory entry value in long format from this IFD, performing some error checking.
- getIFDOffsets() - Method in class loci.formats.tiff.TiffParser
-
Gets the offsets to every IFD in the file.
- getIFDRationalValue(int) - Method in class loci.formats.tiff.IFD
-
Gets the given directory entry value in rational format from this IFD, performing some error checking.
- getIFDs() - Method in class loci.formats.in.MinimalTiffReader
-
Gets the list of IFDs associated with the current TIFF's image planes.
- getIFDs() - Method in class loci.formats.tiff.TiffParser
-
Deprecated.Use
TiffParser.getMainIFDs()andTiffParser.getSubIFDs(IFD)instead. - getIFDShortArray(int) - Method in class loci.formats.tiff.IFD
-
Gets the given directory entry values in short format from this IFD, performing some error checking.
- getIFDStringValue(int) - Method in class loci.formats.tiff.IFD
-
Gets the given directory entry value as a string from this IFD, performing some error checking.
- getIFDTagName(int) - Static method in class loci.formats.tiff.IFD
-
Gets the name of the IFD tag encoded by the given number.
- getIFDTextValue(int) - Method in class loci.formats.tiff.IFD
-
Gets the given directory entry value as a string (regardless of type).
- getIFDValue(int) - Method in class loci.formats.tiff.IFD
-
Gets the given directory entry value from this IFD.
- getIFDValue(int, Class) - Method in class loci.formats.tiff.IFD
-
Gets the given directory entry value from this IFD, performing some error checking.
- getIFDValue(TiffIFDEntry) - Method in class loci.formats.tiff.TiffParser
-
Retrieve the value corresponding to the given TiffIFDEntry.
- getIlluminationType(String) - Method in class loci.formats.FormatReader
-
Deprecated.
- getIlluminationType(String) - Static method in class loci.formats.MetadataTools
-
Retrieves an
IlluminationTypeenumeration value for the given String. - getImage() - Method in class loci.formats.gui.ImageViewer
-
Gets the currently displayed image.
- getImageCount() - Method in class loci.formats.ChannelMerger
- getImageCount() - Method in class loci.formats.ChannelSeparator
- getImageCount() - Method in class loci.formats.FileStitcher
- getImageCount() - Method in class loci.formats.FormatReader
- getImageCount() - Method in interface loci.formats.IFormatReader
-
Determines the number of image planes in the current file.
- getImageCount() - Method in class loci.formats.ImageReader
- getImageCount() - Method in class loci.formats.in.LeicaMicrosystemsMetadata.XlefDocument
-
Returns number of images which are referenced by xlifs
- getImageCount() - Method in class loci.formats.ReaderWrapper
- getImageCount() - Method in class loci.formats.WrappedReader
- getImageCount(Double[]) - Method in class loci.plugins.macro.LociFunctions
- getImageCreationDate() - Method in class loci.formats.in.BaseTiffReader
-
Retrieves the image creation date.
- getImageCreationDate(String[]) - Method in class loci.plugins.macro.LociFunctions
- getImageData(int, int, int) - Method in class loci.formats.in.CellH5Reader
- getImageData(int, int, int, int, int) - Method in class loci.formats.in.BDVReader
- getImageData(int, int, int, int, int) - Method in class loci.formats.in.ImarisHDFReader
-
Retrieve an array corresponding to the specified image tile.
- GetImageDataFile(String, Integer, Integer) - Method in class loci.formats.in.SlideBook7Reader.CSBFile70
- getImageDescription(Element) - Method in class loci.formats.in.LeicaMicrosystemsMetadata.LMSMetadataExtractor
- getImageDescription(Element) - Method in class loci.formats.in.LIFReader
- getImageFile(String) - Method in class loci.formats.in.TecanReader
-
Turn a relative image file path into an absolute path.
- getImageFormat() - Method in class loci.formats.in.LeicaMicrosystemsMetadata.LMSFileReader
-
Returns the file format in which actual image bytes are stored
- getImageFormat() - Method in class loci.formats.in.LeicaMicrosystemsMetadata.MultipleImagesReader
- getImageFormat() - Method in class loci.formats.in.LeicaMicrosystemsMetadata.XlifDocument
- getImageFormat() - Method in class loci.formats.in.LOFReader
- getImageFormat() - Method in class loci.formats.in.XLEFReader
- GetImageGroup(int) - Method in class loci.formats.in.SlideBook7Reader.DataLoader
- GetImageGroupDirectory(String) - Method in class loci.formats.in.SlideBook7Reader.CSBFile70
- getImageIndex() - Method in class loci.formats.gui.ImageViewer
-
Gets the index of the currently displayed image.
- getImageIndex(int) - Method in class loci.formats.in.FluoviewReader
- getImageIndex(String) - Method in class loci.formats.in.PCIReader
-
Get the image index from the image file name.
- getImageLength() - Method in class loci.formats.tiff.IFD
-
Retrieves the image's length (TIFF tag ImageLength) from a given TIFF IFD.
- getImageName() - Method in class loci.formats.in.LeicaMicrosystemsMetadata.LMSImageXmlDocument
-
Returns the name of the image (it might be contained in the XML or otherwise e.g.
- getImageName() - Method in class loci.formats.in.LeicaMicrosystemsMetadata.LofXmlDocument
- getImageName() - Method in class loci.formats.in.LeicaMicrosystemsMetadata.XlifDocument
- getImageName() - Method in class loci.formats.in.MetamorphHandler
- getImageName(int) - Method in class loci.formats.in.VectraReader
- getImageNode() - Method in class loci.formats.in.LeicaMicrosystemsMetadata.LMSImageXmlDocument
-
Returns the image node of the xml document which contains image metadata
- getImageNode() - Method in class loci.formats.in.LeicaMicrosystemsMetadata.LofXmlDocument
- getImageNode() - Method in class loci.formats.in.LeicaMicrosystemsMetadata.XlifDocument
- getImageNumber(String, int) - Method in class loci.formats.in.ZeissZVIReader
- getImagePaths() - Method in class loci.formats.in.LeicaMicrosystemsMetadata.XlifDocument
- getImageReader() - Method in class loci.plugins.in.ImportProcess
-
Valid only after
ImportStep.READER. - getImageSequence(int) - Method in class loci.formats.in.DeltavisionReader
-
Get the image sequence string.
- getImagesPerFile() - Method in class loci.formats.FileStitcher.ExternalSeries
- getImagesPerFile(String, IFormatReader) - Static method in class loci.formats.FormatTools
- getImageType() - Method in class loci.formats.in.DicomReader
- getImageType(int) - Method in class loci.formats.in.VectraReader
- getImageType(String, int, boolean, int) - Method in class loci.formats.out.DicomWriter
- getImageWidth() - Method in class loci.formats.tiff.IFD
-
Retrieves the image's width (TIFF tag ImageWidth) from a given TIFF IFD.
- getImagingDevice() - Method in class loci.formats.in.PrairieMetadata.Frame
-
Gets the imaging device associated with this
Frame. - getImmersion() - Method in class loci.formats.in.ND2Handler
- getImmersion() - Method in class loci.formats.in.PrairieMetadata.Frame
-
Extracts the immersion from the objective lens string.
- getImmersion(String) - Method in class loci.formats.FormatReader
-
Deprecated.
- getImmersion(String) - Static method in class loci.formats.MetadataTools
-
Retrieves an
Immersionenumeration value for the given String. - getIndex() - Method in class loci.formats.cache.CacheEvent
-
Gets the index relevant to the cache update, if any.
- getIndex() - Method in class loci.formats.in.BaseZeissReader.Tag
- getIndex() - Method in class loci.formats.in.PrairieMetadata.Frame
-
Gets the
indexassociated with thisFrame. - getIndex(int, int) - Method in class loci.formats.out.DicomWriter
- getIndex(int, int, int) - Method in class loci.formats.ChannelMerger
- getIndex(int, int, int) - Method in class loci.formats.ChannelSeparator
- getIndex(int, int, int) - Method in class loci.formats.DimensionSwapper
- getIndex(int, int, int) - Method in class loci.formats.FileStitcher
- getIndex(int, int, int) - Method in class loci.formats.FormatReader
- getIndex(int, int, int) - Method in interface loci.formats.IFormatReader
-
Gets the rasterized index corresponding to the given Z, C and T coordinates (real sizes).
- getIndex(int, int, int) - Method in class loci.formats.ImageReader
- getIndex(int, int, int) - Method in class loci.formats.ReaderWrapper
- getIndex(int, int, int) - Method in class loci.formats.WrappedReader
- getIndex(int, int, int, int, int, int) - Method in class loci.formats.ChannelMerger
- getIndex(int, int, int, int, int, int) - Method in class loci.formats.ChannelSeparator
- getIndex(int, int, int, int, int, int) - Method in class loci.formats.DimensionSwapper
- getIndex(int, int, int, int, int, int) - Method in class loci.formats.FileStitcher
- getIndex(int, int, int, int, int, int) - Method in class loci.formats.FormatReader
- getIndex(int, int, int, int, int, int) - Method in interface loci.formats.IFormatReader
-
Gets the rasterized index corresponding to the given Z, C, T, moduloZ, moduloC and moduloT coordinates (effective sizes).
- getIndex(int, int, int, int, int, int) - Method in class loci.formats.ImageReader
- getIndex(int, int, int, int, int, int) - Method in class loci.formats.ReaderWrapper
- getIndex(Double, Double, Double, Double[]) - Method in class loci.plugins.macro.LociFunctions
- getIndex(String) - Method in class loci.formats.in.JDCEReader.JDCEWell
- getIndex(String, int, int, int, int, int, int, int) - Static method in class loci.formats.FormatTools
-
Gets the rasterized index corresponding to the given Z, C and T coordinates (real sizes).
- getIndex(String, int, int, int, int, int, int, int, int, int, int, int, int, int) - Static method in class loci.formats.FormatTools
-
Gets the rasterized index corresponding to the given Z, C, T, ModuloZ, ModuloC, ModuloT coordinates (effective sizes).
- getIndex(IFormatReader, int, int, int) - Static method in class loci.formats.FormatTools
-
Gets the rasterized index corresponding to the given Z, C and T coordinates (real sizes).
- getIndex(IFormatReader, int, int, int, int, int, int) - Static method in class loci.formats.FormatTools
-
Gets the rasterized index corresponding to the given Z, C, T, ModuloZ, ModuloC and ModuloT coordinates (effective sizes).
- getIndexCount() - Method in class loci.formats.in.PrairieMetadata.Sequence
-
Gets the number of recorded indices at this
Sequence. - getIndexMax() - Method in class loci.formats.in.PrairieMetadata.Sequence
-
Gets the maximum index value.
- getIndexMin() - Method in class loci.formats.in.PrairieMetadata.Sequence
-
Gets the minimum index value.
- getInfo() - Method in class loci.formats.in.SDTReader
-
Gets object containing SDT header information.
- getInfo() - Method in class loci.plugins.prefs.Option
-
Gets documentation about the option.
- getInfo(String) - Method in class loci.plugins.prefs.OptionsList
-
Gets the documentation for the option with the given key.
- GetInfo() - Method in class loci.formats.in.SlideBook7Reader.CImageGroup
- getIniFile(String) - Method in class loci.formats.in.FV1000Reader
- getInputOrder() - Method in class loci.formats.DimensionSwapper
- getInputOrder(int) - Method in class loci.plugins.in.ImporterOptions
- getInputStream(String) - Method in interface loci.formats.services.POIService
-
Retrieve an InputStream corresponding to the given file name.
- getInputStream(String) - Method in class loci.formats.services.POIServiceImpl
- getInstance(int) - Static method in class loci.formats.gui.TwoChannelColorSpace
- getInstrumentType() - Method in class loci.formats.in.OperettaReader.OperettaHandler
- getInt(int) - Method in class loci.formats.in.SPEReader.SpeHeader
-
Private method used to retrieve an Integer value from the SPE header
- getInt(SPEReader.SpeHeaderEntry) - Method in class loci.formats.in.SPEReader.SpeHeader
-
Method used to retrieve data values for Integer entries into the SPE header table
- getIntArray() - Method in class loci.plugins.util.RecordedImageProcessor
- getIntArray(SPEReader.SpeHeaderEntry) - Method in class loci.formats.in.SPEReader.SpeHeader
-
Method used to retrieve data values for Integer Array entries into the SPE header table
- getInteger(String) - Method in class loci.formats.in.DynamicMetadataOptions
-
Get the value of property
nameas an Integer. - getInteger(String, Integer) - Method in class loci.formats.in.DynamicMetadataOptions
-
Get the value of property
nameas an Integer. - GetIntegerArray(Node, String, Boolean) - Method in class loci.formats.in.SlideBook7Reader.ClassDecoder
- GetIntegerValue(MappingNode, int, String) - Method in class loci.formats.in.SlideBook7Reader.ClassDecoder
- GetInterplaneSpacing() - Method in class loci.formats.in.SlideBook7Reader.CImageGroup
- getInterpolate() - Method in class loci.plugins.util.RecordedImageProcessor
- getInterpolatedPixel(double, double) - Method in class loci.plugins.util.RecordedImageProcessor
- getInts(BufferedImage) - Static method in class loci.formats.gui.AWTImageTools
-
Extracts pixel data as arrays of signed integers, one per channel.
- getInts(WritableRaster) - Static method in class loci.formats.gui.AWTImageTools
-
Extracts pixel data as arrays of signed integers, one per channel.
- getInts(WritableRaster, int, int, int, int) - Static method in class loci.formats.gui.AWTImageTools
-
Extracts pixel data as arrays of signed integers, one per channel.
- getIntValue(int) - Method in class loci.formats.in.ZeissLSMReader.SubBlock
- getJPEGBuf() - Method in class org.libjpegturbo.turbojpeg.TJDecompressor
-
Returns the JPEG image buffer associated with this decompressor instance.
- getJPEGSize() - Method in class org.libjpegturbo.turbojpeg.TJDecompressor
-
Returns the size of the JPEG image (in bytes) associated with this decompressor instance.
- getKey() - Method in class loci.formats.in.BaseZeissReader.Tag
- getKey() - Method in class loci.formats.meta.OriginalMetadataAnnotation
- getKey() - Method in class loci.plugins.prefs.Option
-
Gets the option's key name.
- getKey(int) - Method in class loci.formats.in.BaseZeissReader.Tag
-
Return the string corresponding to the given ID.
- getKey(int) - Method in class loci.formats.in.MetamorphReader
- getKeyID() - Method in class loci.formats.in.BaseZeissReader.Tag
- getL(String) - Method in class loci.formats.in.OIRReader
- getLabel() - Method in class loci.plugins.prefs.Option
-
Gets label describing the option.
- getLabel(String) - Method in class loci.plugins.prefs.OptionsList
-
Gets the label for the option with the given key.
- getLabels() - Method in class loci.plugins.config.CellSensWidgets
- getLabels() - Method in interface loci.plugins.config.IFormatWidgets
- getLabels() - Method in class loci.plugins.config.LIFWidgets
- getLabels() - Method in class loci.plugins.config.ND2Widgets
- getLabels() - Method in class loci.plugins.config.SDTWidgets
- getLabels() - Method in class loci.plugins.config.TiffDelegateWidgets
- getLabels() - Method in class loci.plugins.config.ZeissCZIWidgets
- getLaserMedium(String) - Method in class loci.formats.FormatReader
-
Deprecated.
- getLaserMedium(String) - Static method in class loci.formats.MetadataTools
-
Retrieves an
LaserMediumenumeration value for the given String. - getLaserPower() - Method in class loci.formats.in.PrairieMetadata
-
Gets the first
laserPowerrecorded in the configuration. - getLaserType(String) - Method in class loci.formats.FormatReader
-
Deprecated.
- getLaserType(String) - Static method in class loci.formats.MetadataTools
-
Retrieves an
LaserTypeenumeration value for the given String. - getLast() - Method in class loci.formats.FilePattern
-
Gets the STOP element for all blocks.
- getLast() - Method in class loci.formats.FilePatternBlock
-
Gets the last element in a range block.
- getLatestVersion() - Method in interface loci.formats.services.OMEXMLService
-
Retrieves the latest supported version of the OME-XML schema.
- getLatestVersion() - Method in class loci.formats.services.OMEXMLServiceImpl
- getLength() - Method in class loci.formats.in.LeicaMicrosystemsMetadata.Dimension
- getLength(long) - Method in class loci.formats.in.OBFReader
- getLength(RandomAccessInputStream) - Method in class loci.formats.dicom.DicomTag
-
Get the length of the next value in the given input stream.
- getLengths() - Method in class loci.formats.cache.CacheStrategy
- getLengths() - Method in interface loci.formats.cache.ICacheStrategy
-
Gets the lengths of all the axes.
- getLengths(IFormatReader) - Static method in class loci.formats.tools.CacheConsole
-
Helper utility for constructing lengths array, used by main.
- getLensNA() - Method in class loci.formats.in.MetamorphHandler
- GetLensName() - Method in class loci.formats.in.SlideBook7Reader.CImageGroup
- getLensRI() - Method in class loci.formats.in.MetamorphHandler
- getLetter() - Method in class loci.formats.ResourceNamer
-
Returns a
Stringrepresenting a single letter (in the case where the class instance has been initialized with a resource count lower than 26) or a concatenation of two letters (if resource count is higher than 26). - getLevel() - Method in class loci.formats.in.TissueFAXSReader
- getLine(double, double, double, double) - Method in class loci.plugins.util.RecordedImageProcessor
- getLinesPerFrame() - Method in class loci.formats.in.PrairieMetadata.Frame
-
Gets the lines per frame for this
Frame. - GetListOfHistogramDataFiles(String) - Method in class loci.formats.in.SlideBook7Reader.CSBFile70
- GetListOfHistogramSummaryFiles(String) - Method in class loci.formats.in.SlideBook7Reader.CSBFile70
- GetListOfImageDataFiles(String) - Method in class loci.formats.in.SlideBook7Reader.CSBFile70
- GetListOfImageGroupTitles() - Method in class loci.formats.in.SlideBook7Reader.CSBFile70
- GetListOfMaskDataFiles(String) - Method in class loci.formats.in.SlideBook7Reader.CSBFile70
- getListOfNpyDataFiles(String, String) - Method in class loci.formats.in.SlideBook7Reader.CSBFile70
- getLoadList(int[]) - Method in class loci.formats.cache.CacheStrategy
- getLoadList(int[]) - Method in interface loci.formats.cache.ICacheStrategy
-
Gets the indices of the objects to cache, surrounding the object at the given position.
- getLocation() - Method in class loci.plugins.in.ImporterOptions
- getLocationFromResourceName(Location, String, int, String) - Method in class loci.formats.ResourceNamer
-
Creates a new
Locationinstance using the provided parent path and child node name. - getLocationInfo() - Method in class loci.plugins.in.ImporterOptions
- getLocations() - Method in class loci.plugins.in.ImporterOptions
- getLong(int) - Method in class loci.formats.in.SPEReader.SpeHeader
-
Private method used to retrieve a Long value from the SPE header
- getLong(String) - Method in class loci.formats.in.DynamicMetadataOptions
-
Get the value of property
nameas a Long. - getLong(String, Long) - Method in class loci.formats.in.DynamicMetadataOptions
-
Get the value of property
nameas a Long. - getLong(SPEReader.SpeHeaderEntry) - Method in class loci.formats.in.SPEReader.SpeHeader
-
Method used to retrieve data values for Long enteries into the SPE header table
- getLongArray(SPEReader.SpeHeaderEntry) - Method in class loci.formats.in.SPEReader.SpeHeader
-
Method used to retrieve data values for Long Array entries into the SPE header table
- GetLongArray(Node, String, Boolean) - Method in class loci.formats.in.SlideBook7Reader.ClassDecoder
- getLookupTable() - Method in class loci.formats.in.JPEG2000MetadataParser
-
Returns the color lookup table stored in the file, or null if a lookup table is not present.
- getLookupTable(ColorModel) - Static method in class loci.formats.gui.AWTImageTools
-
Convers an Index16ColorModel to a 2D short array.
- getLookupTable(Map) - Method in class loci.formats.in.AmiraReader
- getLookupTableComponentCount() - Method in class loci.formats.ChannelFiller
-
Gets the number of color components in the lookup table.
- getLSMFileFromSeries(int) - Method in class loci.formats.in.ZeissLSMReader
- getLutNames() - Method in class loci.formats.in.LeicaHandler
- getLutUpdateMode() - Method in class loci.plugins.util.RecordedImageProcessor
- getMagnification() - Method in class loci.formats.in.ND2Handler
- getMagnification() - Method in class loci.formats.in.PrairieMetadata.Frame
-
Extracts the magnification from the objective lens string.
- getMagnification() - Method in class loci.formats.in.SVSReader
- GetMagnification() - Method in class loci.formats.in.SlideBook7Reader.CImageGroup
- getMagnitudes() - Method in class loci.formats.in.IM3Reader.Spectrum
- getMainIFDs() - Method in class loci.formats.tiff.TiffParser
-
Returns the main list of IFDs in the file.
- getMap() - Method in class loci.formats.tools.AmiraParameters
- getMarker(String) - Method in class loci.formats.FormatReader
-
Deprecated.
- getMarker(String) - Static method in class loci.formats.MetadataTools
-
Retrieves an
Markerenumeration value for the given String. - getMarkers(IFD) - Method in class loci.formats.in.NDPIReader
-
Get the array of restart markers (offsets) for the given IFD.
- getMask() - Method in class loci.plugins.util.RecordedImageProcessor
- getMaskArray() - Method in class loci.plugins.util.RecordedImageProcessor
- GetMaskDataFile(String, Integer) - Method in class loci.formats.in.SlideBook7Reader.CSBFile70
- getMax() - Method in class loci.plugins.util.RecordedImageProcessor
- getMaxFieldCount(Integer) - Static method in class loci.formats.FormatTools
- getMaximumSize() - Method in class loci.formats.gui.CacheIndicator
- getMaximumSize() - Method in class loci.formats.gui.DataConverter.RowPanel
- getMaxThreshold() - Method in class loci.plugins.util.RecordedImageProcessor
- getMCUHeight(int) - Static method in class org.libjpegturbo.turbojpeg.TJ
-
Returns the MCU block height for the given level of chrominance subsampling.
- getMCUWidth(int) - Static method in class org.libjpegturbo.turbojpeg.TJ
-
Returns the MCU block width for the given level of chrominance subsampling.
- getMDBFile(String) - Method in class loci.formats.in.ZeissLSMReader
- getMeasurementID() - Method in class loci.formats.in.ColumbusReader.MeasurementHandler
- getMeasurementID() - Method in class loci.formats.in.OperettaReader.OperettaHandler
- getMeasurementName() - Method in class loci.formats.in.ColumbusReader.MeasurementHandler
- getMeasurementTime() - Method in class loci.formats.in.OperettaReader.OperettaHandler
- getMedium(String) - Method in class loci.formats.FormatReader
-
Deprecated.
- getMedium(String) - Static method in class loci.formats.MetadataTools
-
Retrieves an
Mediumenumeration value for the given String. - getMember(String) - Method in interface loci.formats.services.JHDFService
-
Retrieves the all members of a group.
- getMember(String) - Method in class loci.formats.services.JHDFServiceImpl
- getMemoFile() - Method in class loci.formats.Memoizer
- getMemoFile(String) - Method in class loci.formats.Memoizer
-
Constructs a
Fileobject fromidstring. - getMemoryUsage() - Method in class loci.plugins.in.ImportProcess
-
Gets a projection of required memory in bytes.
- getMessage() - Method in enum class loci.plugins.in.ImportStep
- getMetadata() - Method in class loci.formats.in.ND2Handler
- getMetadataLevel() - Method in class loci.formats.in.DefaultMetadataOptions
- getMetadataLevel() - Method in class loci.formats.in.DynamicMetadataOptions
- getMetadataLevel() - Method in interface loci.formats.in.MetadataOptions
-
Get the configured metadata level.
- getMetadataOptions() - Method in class loci.formats.DelegateReader
- getMetadataOptions() - Method in class loci.formats.FormatHandler
- getMetadataOptions() - Method in class loci.formats.ImageReader
- getMetadataOptions() - Method in class loci.formats.ImageWriter
- getMetadataOptions() - Method in interface loci.formats.IMetadataConfigurable
- getMetadataOptions() - Method in class loci.formats.ReaderWrapper
- getMetadataOptions() - Method in class loci.formats.WriterWrapper
- getMetadataOptionsFile(String) - Static method in class loci.formats.in.DynamicMetadataOptions
- getMetadataPixelType(int) - Method in class loci.formats.in.ZeissXRMReader
- getMetadataRetrieve() - Method in class loci.formats.FormatWriter
- getMetadataRetrieve() - Method in interface loci.formats.IFormatWriter
-
Retrieves the current metadata retrieval object for this writer.
- getMetadataRetrieve() - Method in class loci.formats.ImageWriter
- getMetadataRetrieve() - Method in class loci.formats.WriterWrapper
- getMetadataRoot(String) - Method in class loci.formats.in.LIFReader
- getMetadataRoot(String) - Method in class loci.formats.in.OlympusTileReader
- getMetadataStore() - Method in class loci.formats.FileStitcher
- getMetadataStore() - Method in class loci.formats.FormatReader
- getMetadataStore() - Method in interface loci.formats.IFormatReader
-
Retrieves the current metadata store for this reader.
- getMetadataStore() - Method in class loci.formats.ImageReader
- getMetadataStore() - Method in class loci.formats.in.FilePatternReader
- getMetadataStore() - Method in class loci.formats.Memoizer
- getMetadataStore() - Method in class loci.formats.ReaderWrapper
- getMetadataStoreForConversion() - Method in class loci.formats.in.OMETiffReader
-
Deprecated.Use the general
FormatReader.getMetadataStore()method. - getMetadataStoreForDisplay() - Method in class loci.formats.in.OMETiffReader
-
Deprecated.Use the general
FormatReader.getMetadataStore()method. - getMetadataStoreRoot() - Method in class loci.formats.FileStitcher
- getMetadataStoreRoot() - Method in class loci.formats.FormatReader
- getMetadataStoreRoot() - Method in interface loci.formats.IFormatReader
-
Retrieves the current metadata store's root object.
- getMetadataStoreRoot() - Method in class loci.formats.ImageReader
- getMetadataStoreRoot() - Method in class loci.formats.ReaderWrapper
- getMetadataStoreRoot() - Method in class loci.formats.WrappedReader
- getMetadataString(String) - Method in class loci.plugins.in.ImporterMetadata
-
Returns a string with each key/value pair on its own line.
- getMetadataType() - Method in enum class loci.formats.tiff.PhotoInterp
-
Retrieves the metadata type of the photometric interpretation.
- getMetadataValue(String) - Method in class loci.formats.FormatReader
- getMetadataValue(String) - Method in interface loci.formats.IFormatReader
-
Obtains the specified metadata field's value for the current file.
- getMetadataValue(String) - Method in class loci.formats.ImageReader
- getMetadataValue(String) - Method in class loci.formats.ReaderWrapper
- getMetadataValue(String) - Method in class loci.formats.WrappedReader
- getMetadataValue(String, String[]) - Method in class loci.plugins.macro.LociFunctions
- getMethodStack() - Method in class loci.plugins.util.BFVirtualStack
- getMethodStack() - Method in class loci.plugins.util.RecordedImageProcessor
- getMicrobeamManipulationType(String) - Method in class loci.formats.FormatReader
-
Deprecated.
- getMicrobeamManipulationType(String) - Static method in class loci.formats.MetadataTools
-
Retrieves an
MicrobeamManipulationTypeenumeration value for the given String. - getMicronsPerPixelX() - Method in class loci.formats.in.PrairieMetadata.Frame
-
Gets the microns per pixel along X for this
Frame. - getMicronsPerPixelY() - Method in class loci.formats.in.PrairieMetadata.Frame
-
Gets the microns per pixel along Y for this
Frame. - getMicroscopeType(String) - Method in class loci.formats.FormatReader
-
Deprecated.
- getMicroscopeType(String) - Static method in class loci.formats.MetadataTools
-
Retrieves an
MicroscopeTypeenumeration value for the given String. - getMin() - Method in class loci.plugins.util.RecordedImageProcessor
- getMinimumSize() - Method in class loci.formats.gui.CacheIndicator
- getMinMaxCalculator() - Method in class loci.plugins.in.ImportProcess
-
Valid only after
ImportStep.STACK. - getMinMaxStore() - Method in class loci.formats.MinMaxCalculator
-
Retrieves the current active min-max store for the calculator.
- getMinThreshold() - Method in class loci.plugins.util.RecordedImageProcessor
- getModalities() - Method in class loci.formats.in.ND2Handler
- getModuloAlong(OMEXMLMetadata, String, int) - Method in class loci.formats.services.OMEXMLServiceImpl
-
Create a
Modulocorresponding to the given ModuloAlong* tag. - getModuloAlongC(OMEXMLMetadata, int) - Method in interface loci.formats.services.OMEXMLService
-
Retrieve the ModuloAlongC annotation in the given Image in the given OME-XML metadata object.
- getModuloAlongC(OMEXMLMetadata, int) - Method in class loci.formats.services.OMEXMLServiceImpl
- getModuloAlongT(OMEXMLMetadata, int) - Method in interface loci.formats.services.OMEXMLService
-
Retrieve the ModuloAlongT annotation in the given Image in the given OME-XML metadata object.
- getModuloAlongT(OMEXMLMetadata, int) - Method in class loci.formats.services.OMEXMLServiceImpl
- getModuloAlongZ(OMEXMLMetadata, int) - Method in interface loci.formats.services.OMEXMLService
-
Retrieve the ModuloAlongZ annotation in the given Image in the given OME-XML metadata object.
- getModuloAlongZ(OMEXMLMetadata, int) - Method in class loci.formats.services.OMEXMLServiceImpl
- getModuloC() - Method in class loci.formats.FormatReader
- getModuloC() - Method in interface loci.formats.IFormatReader
- getModuloC() - Method in class loci.formats.ImageReader
- getModuloC() - Method in class loci.formats.ReaderWrapper
- getModuloC() - Method in class loci.formats.WrappedReader
- getModuloT() - Method in class loci.formats.FormatReader
- getModuloT() - Method in interface loci.formats.IFormatReader
- getModuloT() - Method in class loci.formats.ImageReader
- getModuloT() - Method in class loci.formats.ReaderWrapper
- getModuloT() - Method in class loci.formats.WrappedReader
- getModuloZ() - Method in class loci.formats.FormatReader
- getModuloZ() - Method in interface loci.formats.IFormatReader
- getModuloZ() - Method in class loci.formats.ImageReader
- getModuloZ() - Method in class loci.formats.ReaderWrapper
- getModuloZ() - Method in class loci.formats.WrappedReader
- getMontage(int) - Method in class loci.formats.in.FluoviewReader
- getMustGroupInfo() - Method in class loci.plugins.in.ImporterOptions
- getName() - Method in enum class loci.formats.codec.JPEG2000BoxType
-
Returns the name of the box type.
- getName() - Method in enum class loci.formats.codec.JPEG2000SegmentMarker
-
Returns the name of the segment marker.
- getName() - Method in class loci.formats.filter.LZ4Filter
- getName() - Method in class loci.formats.filter.LZ4Filter.LZ4FilterProvider
- getName() - Method in enum class loci.formats.in.BaseZeissReader.Charset
- getName() - Method in class loci.formats.in.IM3Reader.Spectrum
- getName() - Method in class loci.formats.in.LeicaMicrosystemsMetadata.XlifDocument
- getName() - Method in enum class loci.formats.tiff.PhotoInterp
-
Retrieves the given name of the photometric interpretation.
- getName(int) - Method in class loci.formats.gui.TwoChannelColorSpace
- getName(String) - Method in class loci.formats.services.NetCDFServiceImpl
- getName(Node) - Method in class loci.formats.in.OlympusTileReader
- GetName() - Method in class loci.formats.in.SlideBook7Reader.CImageGroup
- getNamingConvention(String) - Method in class loci.formats.FormatReader
-
Deprecated.
- getNamingConvention(String) - Static method in class loci.formats.MetadataTools
-
Retrieves an
NamingConventionenumeration value for the given String. - getNativeDataType() - Method in class loci.formats.ChannelFiller
- getNativeDataType() - Method in class loci.formats.ChannelMerger
- getNativeDataType() - Method in class loci.formats.ChannelSeparator
- getNativeDataType() - Method in class loci.formats.FormatHandler
- getNativeDataType() - Method in interface loci.formats.IFormatHandler
-
Returns the native data type of image planes for this reader, as returned by
IFormatReader.openPlane(int, int, int, int, int)orIFormatWriter.savePlane(int, java.lang.Object). - getNativeDataType() - Method in class loci.formats.ImageReader
- getNativeDataType() - Method in class loci.formats.ImageWriter
- getNativeDataType() - Method in class loci.formats.in.BIFormatReader
- getNativeDataType() - Method in class loci.formats.in.TextReader
- getNativeDataType() - Method in class loci.formats.MinMaxCalculator
- getNativeDataType() - Method in class loci.formats.out.ImageIOWriter
- getNativeDataType() - Method in class loci.formats.ReaderWrapper
- getNativeDataType() - Method in class loci.formats.TileStitcher
- getNativeDataType() - Method in class loci.formats.WrappedReader
- getNativeDataType() - Method in class loci.formats.WriterWrapper
- getNativeDataType() - Method in class loci.plugins.util.ImageProcessorReader
- getNChannels() - Method in class loci.plugins.util.RecordedImageProcessor
- getNDVersionSuffix(Location) - Method in class loci.formats.in.MetamorphReader
-
Parses the given ND file to determined the version and return the expected file suffix
- getNextLine(byte[]) - Method in class loci.formats.in.MicromanagerReader
- getNextLine(List<String>) - Method in class loci.formats.in.TextReader
- getNextOffset(long) - Method in class loci.formats.tiff.TiffParser
-
Read a file offset.
- getNextTag(RandomAccessInputStream) - Method in class loci.formats.dicom.DicomTag
-
Get the next 4 byte DICOM tag from the given input stream.
- getNextTag(RandomAccessInputStream) - Method in class loci.formats.in.ZeissZVIReader
- getNodes(Element, String) - Method in class loci.formats.in.LeicaMicrosystemsMetadata.LMSMetadataExtractor
-
Returns all (grand*n)children nodes with given node name
- getNodes(Element, String) - Method in class loci.formats.in.LIFReader
- getNonThumbnailIFDs() - Method in class loci.formats.tiff.TiffParser
-
Returns non-thumbnail IFDs.
- getNormalizedName() - Method in class loci.formats.in.ZeissCZIReader.AttachmentEntry
- getNum() - Method in class org.libjpegturbo.turbojpeg.TJScalingFactor
-
Returns numerator
- getNumber(String) - Method in class loci.formats.NumberFilter
-
Gets numbers filling the asterisk positions.
- getNumberValue() - Method in class loci.formats.dicom.DicomTag
-
Get a number representation of the current value, or null if not a number.
- getNumBytes(int) - Method in class loci.formats.in.GatanReader
- GetNumCaptures() - Method in class loci.formats.in.SlideBook7Reader.DataLoader
- GetNumChannels() - Method in class loci.formats.in.SlideBook7Reader.CImageGroup
- GetNumColumns() - Method in class loci.formats.in.SlideBook7Reader.CImageGroup
- getNumComponents() - Method in class loci.formats.gui.TwoChannelColorSpace
- getNumEntries(IRandomAccess) - Method in class loci.formats.in.IM3Reader.BooleanIM3Record
-
Get the # of boolean values in this record
- getNumEntries(IRandomAccess) - Method in class loci.formats.in.IM3Reader.FloatIM3Record
-
Get the # of floating-point values in this record
- getNumEntries(IRandomAccess) - Method in class loci.formats.in.IM3Reader.IntIM3Record
-
Get the # of integer values in this record
- getNumerator() - Method in class loci.formats.tiff.TiffRational
-
Gets this number's numerator.
- getNumericalAperture() - Method in class loci.formats.in.ND2Handler
- getNumericFields(GenericDialog) - Method in class loci.plugins.in.ColorDialog
- getNumericFields(GenericDialog) - Static method in class loci.plugins.util.WindowTools
- GetNumPlanes() - Method in class loci.formats.in.SlideBook7Reader.CImageGroup
- GetNumPositions() - Method in class loci.formats.in.SlideBook7Reader.CImageGroup
- GetNumRows() - Method in class loci.formats.in.SlideBook7Reader.CImageGroup
- GetNumTimepoints() - Method in class loci.formats.in.SlideBook7Reader.CImageGroup
- getObject(int) - Method in class loci.formats.cache.ByteArraySource
- getObject(int) - Method in class loci.formats.cache.CacheSource
- getObject(int) - Method in interface loci.formats.cache.ICacheSource
-
Get the object corresponding to the given index.
- getObject(int) - Method in class loci.formats.gui.BufferedImageSource
- getObject(int) - Method in class loci.plugins.util.ImageProcessorSource
- getObject(int[]) - Method in class loci.formats.cache.Cache
-
Gets the cached object at the given dimensional position.
- getObjectCount() - Method in class loci.formats.cache.CacheSource
- getObjectCount() - Method in interface loci.formats.cache.ICacheSource
-
Get the total number of objects that this source can retrieve.
- getObjectCount() - Method in class loci.formats.gui.BufferedImageSource
- getObjectCount() - Method in class loci.plugins.util.ImageProcessorSource
- getObjectiveLens() - Method in class loci.formats.in.PrairieMetadata.Frame
-
Gets the objective lens string for this
Frame. - getObjectiveLensNA() - Method in class loci.formats.in.PrairieMetadata.Frame
-
Gets the numerical aperture of the lens for this
Frame. - getObjectiveManufacturer() - Method in class loci.formats.in.PrairieMetadata.Frame
-
Extracts the objective manufacturer from the objective lens string.
- getObjectiveModel() - Method in class loci.formats.in.ND2Handler
- getOffset(int) - Method in class loci.formats.in.PrairieMetadata.Frame
-
Gets the
cth offset for thisFrame. - getOffsets() - Method in class loci.formats.in.ND2Reader
- getOMEMetadata() - Method in class loci.plugins.in.ImportProcess
-
Valid only after
ImportStep.READER. - getOMEMetadata(MetadataRetrieve) - Method in interface loci.formats.services.OMEXMLService
-
Returns a
OMEXMLMetadataobject with the same contents as the given MetadataRetrieve, converting it if necessary. - getOMEMetadata(MetadataRetrieve) - Method in class loci.formats.services.OMEXMLServiceImpl
- getOMEXML() - Method in class loci.plugins.in.ImportProcess
-
Valid only after
ImportStep.READER. - getOMEXML(String) - Method in class loci.formats.out.OMETiffWriter
- getOMEXML(MetadataRetrieve) - Method in interface loci.formats.services.OMEXMLService
-
Extracts an OME-XML metadata string from the given metadata object, by converting to an OME-XML metadata object if necessary.
- getOMEXML(MetadataRetrieve) - Method in class loci.formats.services.OMEXMLServiceImpl
- getOmeXmlMetadata() - Method in class loci.formats.in.FakeReader
- getOmeXmlService() - Method in class loci.formats.in.FakeReader
- getOMEXMLVersion(Object) - Method in interface loci.formats.services.OMEXMLService
-
Gets the schema version for the given OME-XML metadata or root object (e.g., "2007-06" or "2003-FC").
- getOMEXMLVersion(Object) - Method in class loci.formats.services.OMEXMLServiceImpl
- getOnDemandStripOffsets() - Method in class loci.formats.tiff.IFD
- getOpenAllSeriesInfo() - Method in class loci.plugins.in.ImporterOptions
- getOpticalZoom() - Method in class loci.formats.in.PrairieMetadata.Frame
-
Gets the optical zoom associated with this
Frame. - getOptimalTileHeight() - Method in class loci.formats.DelegateReader
- getOptimalTileHeight() - Method in class loci.formats.FormatReader
- getOptimalTileHeight() - Method in interface loci.formats.IFormatReader
-
Returns the optimal sub-image height for use with openBytes.
- getOptimalTileHeight() - Method in class loci.formats.ImageReader
- getOptimalTileHeight() - Method in class loci.formats.in.AFIReader
- getOptimalTileHeight() - Method in class loci.formats.in.AmiraReader
- getOptimalTileHeight() - Method in class loci.formats.in.APLReader
- getOptimalTileHeight() - Method in class loci.formats.in.BaseZeissReader
- getOptimalTileHeight() - Method in class loci.formats.in.BDReader
- getOptimalTileHeight() - Method in class loci.formats.in.BioRadReader
- getOptimalTileHeight() - Method in class loci.formats.in.CellH5Reader
- getOptimalTileHeight() - Method in class loci.formats.in.CellSensReader
- getOptimalTileHeight() - Method in class loci.formats.in.DicomReader
- getOptimalTileHeight() - Method in class loci.formats.in.EPSReader
- getOptimalTileHeight() - Method in class loci.formats.in.FlexReader
- getOptimalTileHeight() - Method in class loci.formats.in.FV1000Reader
- getOptimalTileHeight() - Method in class loci.formats.in.HamamatsuVMSReader
- getOptimalTileHeight() - Method in class loci.formats.in.ImageIOReader
- getOptimalTileHeight() - Method in class loci.formats.in.ImarisHDFReader
- getOptimalTileHeight() - Method in class loci.formats.in.InCellReader
- getOptimalTileHeight() - Method in class loci.formats.in.IPWReader
- getOptimalTileHeight() - Method in class loci.formats.in.JDCEReader
- getOptimalTileHeight() - Method in class loci.formats.in.L2DReader
- getOptimalTileHeight() - Method in class loci.formats.in.LeicaReader
- getOptimalTileHeight() - Method in class loci.formats.in.LeicaSCNReader
- getOptimalTileHeight() - Method in class loci.formats.in.LIFReader
- getOptimalTileHeight() - Method in class loci.formats.in.LOFReader
- getOptimalTileHeight() - Method in class loci.formats.in.MIASReader
- getOptimalTileHeight() - Method in class loci.formats.in.MicromanagerReader
- getOptimalTileHeight() - Method in class loci.formats.in.MinimalTiffReader
- getOptimalTileHeight() - Method in class loci.formats.in.NDPIReader
- getOptimalTileHeight() - Method in class loci.formats.in.NDPISReader
- getOptimalTileHeight() - Method in class loci.formats.in.NRRDReader
- getOptimalTileHeight() - Method in class loci.formats.in.OIRReader
- getOptimalTileHeight() - Method in class loci.formats.in.OlympusTileReader
- getOptimalTileHeight() - Method in class loci.formats.in.OMETiffReader
- getOptimalTileHeight() - Method in class loci.formats.in.OpenlabReader
- getOptimalTileHeight() - Method in class loci.formats.in.PCIReader
- getOptimalTileHeight() - Method in class loci.formats.in.PerkinElmerReader
- getOptimalTileHeight() - Method in class loci.formats.in.PrairieReader
- getOptimalTileHeight() - Method in class loci.formats.in.PyramidTiffReader
- getOptimalTileHeight() - Method in class loci.formats.in.ScanrReader
- getOptimalTileHeight() - Method in class loci.formats.in.SVSReader
- getOptimalTileHeight() - Method in class loci.formats.in.TissueFAXSReader
- getOptimalTileHeight() - Method in class loci.formats.in.TrestleReader
- getOptimalTileHeight() - Method in class loci.formats.in.VectraReader
- getOptimalTileHeight() - Method in class loci.formats.in.VentanaReader
- getOptimalTileHeight() - Method in class loci.formats.in.VisitechReader
- getOptimalTileHeight() - Method in class loci.formats.in.ZeissCZIReader
- getOptimalTileHeight() - Method in class loci.formats.in.ZeissLSMReader
- getOptimalTileHeight() - Method in class loci.formats.ReaderWrapper
- getOptimalTileHeight() - Method in class loci.formats.WrappedReader
- getOptimalTileWidth() - Method in class loci.formats.DelegateReader
- getOptimalTileWidth() - Method in class loci.formats.FormatReader
- getOptimalTileWidth() - Method in interface loci.formats.IFormatReader
-
Returns the optimal sub-image width for use with openBytes.
- getOptimalTileWidth() - Method in class loci.formats.ImageReader
- getOptimalTileWidth() - Method in class loci.formats.in.AFIReader
- getOptimalTileWidth() - Method in class loci.formats.in.APLReader
- getOptimalTileWidth() - Method in class loci.formats.in.BDReader
- getOptimalTileWidth() - Method in class loci.formats.in.CellSensReader
- getOptimalTileWidth() - Method in class loci.formats.in.DicomReader
- getOptimalTileWidth() - Method in class loci.formats.in.EPSReader
- getOptimalTileWidth() - Method in class loci.formats.in.FlexReader
- getOptimalTileWidth() - Method in class loci.formats.in.FV1000Reader
- getOptimalTileWidth() - Method in class loci.formats.in.HamamatsuVMSReader
- getOptimalTileWidth() - Method in class loci.formats.in.ImarisHDFReader
- getOptimalTileWidth() - Method in class loci.formats.in.InCellReader
- getOptimalTileWidth() - Method in class loci.formats.in.IPWReader
- getOptimalTileWidth() - Method in class loci.formats.in.JDCEReader
- getOptimalTileWidth() - Method in class loci.formats.in.L2DReader
- getOptimalTileWidth() - Method in class loci.formats.in.LeicaReader
- getOptimalTileWidth() - Method in class loci.formats.in.LeicaSCNReader
- getOptimalTileWidth() - Method in class loci.formats.in.MIASReader
- getOptimalTileWidth() - Method in class loci.formats.in.MicromanagerReader
- getOptimalTileWidth() - Method in class loci.formats.in.MinimalTiffReader
- getOptimalTileWidth() - Method in class loci.formats.in.NDPIReader
- getOptimalTileWidth() - Method in class loci.formats.in.NDPISReader
- getOptimalTileWidth() - Method in class loci.formats.in.OIRReader
- getOptimalTileWidth() - Method in class loci.formats.in.OlympusTileReader
- getOptimalTileWidth() - Method in class loci.formats.in.OMETiffReader
- getOptimalTileWidth() - Method in class loci.formats.in.PCIReader
- getOptimalTileWidth() - Method in class loci.formats.in.PerkinElmerReader
- getOptimalTileWidth() - Method in class loci.formats.in.PrairieReader
- getOptimalTileWidth() - Method in class loci.formats.in.PyramidTiffReader
- getOptimalTileWidth() - Method in class loci.formats.in.ScanrReader
- getOptimalTileWidth() - Method in class loci.formats.in.SVSReader
- getOptimalTileWidth() - Method in class loci.formats.in.TissueFAXSReader
- getOptimalTileWidth() - Method in class loci.formats.in.TrestleReader
- getOptimalTileWidth() - Method in class loci.formats.in.VectraReader
- getOptimalTileWidth() - Method in class loci.formats.in.VentanaReader
- getOptimalTileWidth() - Method in class loci.formats.in.ZeissCZIReader
- getOptimalTileWidth() - Method in class loci.formats.ReaderWrapper
- getOptimalTileWidth() - Method in class loci.formats.WrappedReader
- getOptimalWidth() - Method in class loci.formats.in.ZeissLSMReader
- getOption(String) - Method in class loci.plugins.prefs.OptionsList
-
Gets the option with the given key.
- getOptions() - Method in class loci.formats.ClassList
-
Gets the list of options as a map.
- getOptions() - Method in class loci.plugins.in.ImportProcess
- getOptions(CodecOptions) - Static method in class loci.formats.codec.WrappedCodec
- getOrder() - Method in class loci.formats.cache.CacheStrategy
- getOrder() - Method in interface loci.formats.cache.ICacheStrategy
-
Retrieves the order in which objects should be loaded along each axis.
- getOriginalIndex(int) - Method in class loci.formats.ChannelMerger
-
Returns the image number in the original dataset that corresponds to the given image number.
- getOriginalIndex(int) - Method in class loci.formats.ChannelSeparator
-
Returns the image number in the original dataset that corresponds to the given image number.
- getOriginalMetadata() - Method in class loci.plugins.in.ImportProcess
-
Valid only after
ImportStep.METADATA. - getOriginalMetadata(OMEXMLMetadata) - Method in interface loci.formats.services.OMEXMLService
-
Parse any OriginalMetadata annotations from the given OME-XML metadata object and store them in a Hashtable.
- getOriginalMetadata(OMEXMLMetadata) - Method in class loci.formats.services.OMEXMLServiceImpl
- getOriginalOrder() - Method in class loci.formats.AxisGuesser
-
Gets the original dimension order.
- getOriginalOrder() - Method in class loci.formats.FileStitcher.ExternalSeries
- getPacking(String) - Static method in class loci.formats.in.LIPixelFormat
- getPage() - Method in class loci.formats.in.PrairieMetadata.PFile
-
Gets the
pageassociated with thisFile. - getParent(int) - Method in class loci.formats.in.LeicaSCNReader
- getParentFiles() - Method in class loci.formats.in.LeicaMicrosystemsMetadata.LMSXmlDocument
-
Returns all files which directly or indirectly reference this LMS xml file.
- getParentName(Integer) - Method in class loci.formats.in.VolocityReader
- getPath() - Method in class loci.plugins.util.BFVirtualStack
- getPath(String) - Method in class loci.formats.in.ImarisHDFReader
- getPath(PrairieMetadata.PFile) - Method in class loci.formats.in.PrairieReader
-
Gets the absolute path to the filename of the given
PrairieMetadata.PFile. - getPathToImageData() - Method in class loci.formats.in.CellH5Reader.CellH5Coordinate
- getPathToSegmentationData() - Method in class loci.formats.in.CellH5Reader.CellH5Coordinate
- getPattern() - Method in class loci.formats.FilePattern
-
Gets the file pattern string.
- getPhotometricInterpretation() - Method in class loci.formats.tiff.IFD
-
Retrieves the image's photometric interpretation (TIFF tag PhotometricInterpretation) from this IFD.
- getPhysicalHeight() - Method in class loci.formats.in.ZeissCZIReader.SubBlock
- getPhysicalSize(Double, String) - Static method in class loci.formats.FormatTools
- getPhysicalSize(Length) - Method in class loci.formats.out.DicomWriter
- getPhysicalSizes() - Method in class loci.formats.in.SVSReader
- getPhysicalSizeX(Double) - Static method in class loci.formats.FormatTools
-
Formats the input value for the physical size in X into a length in microns
- getPhysicalSizeX(Double, String) - Static method in class loci.formats.FormatTools
-
Formats the input value for the physical size in X into a length of the given unit.
- getPhysicalSizeX(Double, Unit<Length>) - Static method in class loci.formats.FormatTools
-
Formats the input value for the physical size in X into a length of the given unit.
- getPhysicalSizeY(Double) - Static method in class loci.formats.FormatTools
-
Formats the input value for the physical size in Y into a length in microns
- getPhysicalSizeY(Double, String) - Static method in class loci.formats.FormatTools
-
Formats the input value for the physical size in Y into a length of the given unit.
- getPhysicalSizeY(Double, Unit<Length>) - Static method in class loci.formats.FormatTools
-
Formats the input value for the physical size in Y into a length of the given unit.
- getPhysicalSizeZ(Double) - Static method in class loci.formats.FormatTools
-
Formats the input value for the physical size in Z into a length in microns.
- getPhysicalSizeZ(Double, String) - Static method in class loci.formats.FormatTools
-
Formats the input value for the physical size in Z into a length of the given unit.
- getPhysicalSizeZ(Double, Unit<Length>) - Static method in class loci.formats.FormatTools
-
Formats the input value for the physical size in Z into a length of the given unit.
- getPhysicalWidth() - Method in class loci.formats.in.ZeissCZIReader.SubBlock
- getPinholeSize() - Method in class loci.formats.in.ND2Handler
- getPixel(int, int) - Method in class loci.plugins.util.RecordedImageProcessor
- getPixel(int, int, int[]) - Method in class loci.plugins.util.RecordedImageProcessor
- getPixelBytes(BufferedImage, boolean) - Static method in class loci.formats.gui.AWTImageTools
-
Return a 2D array of bytes representing the image.
- getPixelBytes(BufferedImage, boolean, int, int, int, int) - Static method in class loci.formats.gui.AWTImageTools
-
Return a 2D array of bytes representing the image.
- getPixelBytes(WritableRaster, boolean) - Static method in class loci.formats.gui.AWTImageTools
-
Return a 2D array of bytes representing the image.
- getPixelBytes(WritableRaster, boolean, int, int, int, int) - Static method in class loci.formats.gui.AWTImageTools
-
Return a 2D array of bytes representing the image.
- getPixelCount() - Method in class loci.plugins.util.RecordedImageProcessor
- getPixelFormat(byte[]) - Method in class loci.formats.services.JPEGXRServiceImpl
- getPixelInterpolated(double, double) - Method in class loci.plugins.util.RecordedImageProcessor
- getPixels() - Method in class loci.plugins.util.RecordedImageProcessor
- getPixels(BufferedImage) - Static method in class loci.formats.gui.AWTImageTools
-
Gets the image's pixel data as arrays of primitives, one per channel.
- getPixels(BufferedImage, int, int, int, int) - Static method in class loci.formats.gui.AWTImageTools
-
Gets the image's pixel data as arrays of primitives, one per channel.
- getPixels(WritableRaster) - Static method in class loci.formats.gui.AWTImageTools
-
Gets the raster's pixel data as arrays of primitives, one per channel.
- getPixels(WritableRaster, int, int, int, int) - Static method in class loci.formats.gui.AWTImageTools
-
Gets the raster's pixel data as arrays of primitives, one per channel.
- getPixelsCopy() - Method in class loci.plugins.util.RecordedImageProcessor
- getPixelSize(int) - Static method in class org.libjpegturbo.turbojpeg.TJ
-
Returns the pixel size (in bytes) of the given pixel format.
- getPixelSizeX() - Method in class loci.formats.in.DicomReader
- getPixelSizeX() - Method in class loci.formats.in.MetamorphHandler
- getPixelSizeX() - Method in class loci.formats.in.ND2Handler
- getPixelSizeY() - Method in class loci.formats.in.DicomReader
- getPixelSizeY() - Method in class loci.formats.in.MetamorphHandler
- getPixelSizeY() - Method in class loci.formats.in.ND2Handler
- getPixelSizeZ() - Method in class loci.formats.in.DicomReader
- getPixelSizeZ() - Method in class loci.formats.in.ND2Handler
- getPixelsPerLine() - Method in class loci.formats.in.PrairieMetadata.Frame
-
Gets the pixels per line for this
Frame. - getPixelsPhysicalSizeX(Double[]) - Method in class loci.plugins.macro.LociFunctions
- getPixelsPhysicalSizeY(Double[]) - Method in class loci.plugins.macro.LociFunctions
- getPixelsPhysicalSizeZ(Double[]) - Method in class loci.plugins.macro.LociFunctions
- getPixelsTimeIncrement(Double[]) - Method in class loci.plugins.macro.LociFunctions
- getPixelString(int) - Method in class loci.formats.in.DeltavisionReader
-
Get a descriptive string representing the pixel type.
- getPixelType() - Method in class loci.formats.FileStitcher
- getPixelType() - Method in class loci.formats.FormatReader
- getPixelType() - Method in interface loci.formats.IFormatReader
-
Gets the pixel type.
- getPixelType() - Method in class loci.formats.ImageReader
- getPixelType() - Method in class loci.formats.in.LeicaMicrosystemsMetadata.MultipleImagesReader
- getPixelType() - Method in class loci.formats.ReaderWrapper
- getPixelType() - Method in class loci.formats.tiff.IFD
-
Retrieves the image's pixel type based on the BitsPerSample tag.
- getPixelType() - Method in class loci.formats.WrappedReader
- getPixelType(int) - Method in class loci.formats.in.DeltavisionReader
-
Get the OME pixel type from the pixel type stored in the file.
- getPixelType(int) - Method in class loci.formats.in.OBFReader
- getPixelType(int) - Method in class loci.formats.in.ZeissXRMReader
-
Convert an XRM data type to a Bio-Formats pixel type.
- getPixelType(BufferedImage) - Static method in class loci.formats.gui.AWTImageTools
-
Gets the pixel type of the given image.
- getPixelType(String) - Method in class loci.formats.FormatReader
-
Deprecated.
- getPixelType(String) - Static method in class loci.formats.MetadataTools
-
Retrieves an
PixelTypeenumeration value for the given String. - getPixelType(String[]) - Method in class loci.plugins.macro.LociFunctions
- getPixelTypeFromString(String) - Method in class loci.formats.in.LiFlimReader
- getPixelTypes() - Method in class loci.formats.FormatWriter
- getPixelTypes() - Method in interface loci.formats.IFormatWriter
-
Gets the supported pixel types.
- getPixelTypes() - Method in class loci.formats.ImageWriter
- getPixelTypes() - Method in class loci.formats.WriterWrapper
- getPixelTypes(String) - Method in class loci.formats.FormatWriter
- getPixelTypes(String) - Method in interface loci.formats.IFormatWriter
-
Gets the supported pixel types for the given codec.
- getPixelTypes(String) - Method in class loci.formats.ImageWriter
- getPixelTypes(String) - Method in class loci.formats.out.APNGWriter
- getPixelTypes(String) - Method in class loci.formats.out.AVIWriter
- getPixelTypes(String) - Method in class loci.formats.out.CellH5Writer
- getPixelTypes(String) - Method in class loci.formats.out.DicomWriter
- getPixelTypes(String) - Method in class loci.formats.out.EPSWriter
- getPixelTypes(String) - Method in class loci.formats.out.ICSWriter
- getPixelTypes(String) - Method in class loci.formats.out.ImageIOWriter
- getPixelTypes(String) - Method in class loci.formats.out.JavaWriter
- getPixelTypes(String) - Method in class loci.formats.out.JPEG2000Writer
-
Overridden to return the formats supported by the writer.
- getPixelTypes(String) - Method in class loci.formats.out.JPEGWriter
- getPixelTypes(String) - Method in class loci.formats.out.OMEXMLWriter
- getPixelTypes(String) - Method in class loci.formats.out.QTWriter
- getPixelTypes(String) - Method in class loci.formats.out.TiffWriter
- getPixelTypes(String) - Method in class loci.formats.out.V3DrawWriter
- getPixelTypes(String) - Method in class loci.formats.WriterWrapper
- getPixelTypeString(int) - Static method in class loci.formats.FormatTools
-
Takes a pixel type value and gets a corresponding string representation.
- getPixelValue(int, int) - Method in class loci.plugins.util.RecordedImageProcessor
- getPlanarConfiguration() - Method in class loci.formats.tiff.IFD
-
Retrieves the image's planar configuration (TIFF tag PlanarConfiguration) from this IFD.
- getPlane(int[]) - Method in class loci.formats.in.OpenlabReader
- getPlane(int, int) - Method in class loci.formats.in.FV1000Reader
- getPlaneByteOffset(int, int, int) - Method in class loci.formats.in.DeltavisionReader
-
Given any specific Z, W, and T of a plane, determine the absolute byte offset of the plane in the file.
- getPlaneCount() - Method in class loci.formats.FormatWriter
-
Retrieve the total number of planes in the current series.
- getPlaneCount() - Method in class loci.formats.out.CellH5Writer
- getPlaneCount() - Method in class loci.formats.out.TiffWriter
- getPlaneCount(int) - Method in class loci.formats.FormatWriter
-
Retrieve the total number of planes in given series.
- getPlaneDataPath(int, int, int) - Method in class loci.formats.in.ImarisHDFReader
- getPlaneIndex(int, int) - Method in class loci.formats.in.DeltavisionReader
- getPlaneIndex(IFormatReader, int) - Static method in class loci.plugins.macro.LociFunctions
-
Finds the Plane index corresponding to the given image plane number.
- getPlaneMaximum(int) - Method in class loci.formats.MinMaxCalculator
-
Retrieves the maximum pixel value for the specified plane.
- getPlaneMetadata(int, int[]) - Method in class loci.formats.in.JDCEReader.JDCEWell
- getPlaneMinimum(int) - Method in class loci.formats.MinMaxCalculator
-
Retrieves the minimum pixel value for the specified plane.
- getPlanePath(int, int, int) - Method in class loci.formats.in.ImarisHDFReader
- getPlanePositionX(Double[], Double) - Method in class loci.plugins.macro.LociFunctions
- getPlanePositionY(Double[], Double) - Method in class loci.plugins.macro.LociFunctions
- getPlanePositionZ(Double[], Double) - Method in class loci.plugins.macro.LociFunctions
- getPlanes() - Method in class loci.formats.in.CV7000Reader.MeasurementDataHandler
- getPlanes() - Method in class loci.formats.in.OperettaReader.OperettaHandler
- getPlaneSize(IFormatReader) - Static method in class loci.formats.FormatTools
-
Returns the size in bytes of a single plane.
- getPlaneSize(IFormatReader, int, int) - Static method in class loci.formats.FormatTools
-
Returns the size in bytes of a w * h tile.
- getPlanesToLoad(int) - Method in class loci.plugins.in.ImagePlusReader
- getPlaneTimingDeltaT(Double[], Double) - Method in class loci.plugins.macro.LociFunctions
- getPlaneTimingExposureTime(Double[], Double) - Method in class loci.plugins.macro.LociFunctions
- getPlateAcquisition() - Method in class loci.formats.internal.WellContainer
- getPlateColumns() - Method in class loci.formats.in.ColumbusReader.MeasurementHandler
- getPlateColumns() - Method in class loci.formats.in.CV7000Reader.WPIHandler
- getPlateColumns() - Method in class loci.formats.in.OperettaReader.OperettaHandler
- getPlateDescription() - Method in class loci.formats.in.CV7000Reader.WPIHandler
- getPlateDescription() - Method in class loci.formats.in.OperettaReader.OperettaHandler
- getPlateID() - Method in class loci.formats.in.CV7000Reader.WPIHandler
- getPlateIdentifier() - Method in class loci.formats.in.OperettaReader.OperettaHandler
- getPlateName() - Method in class loci.formats.in.ColumbusReader.MeasurementHandler
- getPlateName() - Method in class loci.formats.in.CV7000Reader.WPIHandler
- getPlateName() - Method in class loci.formats.in.OperettaReader.OperettaHandler
- getPlateName(String) - Method in class loci.formats.in.CellomicsReader
- getPlateName(String) - Method in class loci.formats.in.CellWorxReader
- getPlateRows() - Method in class loci.formats.in.ColumbusReader.MeasurementHandler
- getPlateRows() - Method in class loci.formats.in.CV7000Reader.WPIHandler
- getPlateRows() - Method in class loci.formats.in.OperettaReader.OperettaHandler
- getPlateType() - Method in class loci.formats.in.ColumbusReader.MeasurementHandler
- getPoints() - Method in enum class loci.formats.in.BaseZeissReader.FeatureType
- getPoints(int) - Method in class loci.formats.in.FakeReader
- getPos(int) - Method in class loci.formats.in.FluoviewReader
- getPosition(int) - Method in class loci.formats.in.ZeissLSMReader
- getPositionFromFile(String) - Method in class loci.formats.in.MIASReader
-
Returns an array of length 5 that contains the well, time point, Z and channel indices corresponding to the given analysis file.
- getPositionNames() - Method in class loci.formats.in.ND2Handler
- getPositionX() - Method in class loci.formats.in.DicomReader
- getPositionX() - Method in class loci.formats.in.PrairieMetadata.Frame
-
Gets the X stage position associated with this
Frame. - getPositionY() - Method in class loci.formats.in.DicomReader
- getPositionY() - Method in class loci.formats.in.PrairieMetadata.Frame
-
Gets the Y stage position associated with this
Frame. - getPositionZ() - Method in class loci.formats.in.DicomReader
- getPositionZ() - Method in class loci.formats.in.PrairieMetadata.Frame
-
Gets the Z stage position associated with this
Frame. - getPossible() - Method in class loci.plugins.prefs.StringOption
-
Gets the list of possible values.
- getPossible(String) - Method in class loci.plugins.prefs.OptionsList
-
Gets the possible values for the string option with the given key.
- getPossibleDomains(String) - Method in class loci.formats.FormatReader
- getPossibleDomains(String) - Method in interface loci.formats.IFormatReader
-
Returns a list of scientific domains in which this format is used.
- getPossibleDomains(String) - Method in class loci.formats.ImageReader
- getPossibleDomains(String) - Method in class loci.formats.ReaderWrapper
- getPossibleDomains(String) - Method in class loci.formats.WrappedReader
- getPossiblePositions() - Method in class loci.formats.cache.CacheStrategy
-
Gets positions to consider for possible inclusion in the cache, assuming a current position at the origin (0).
- getPossiblePositions() - Method in class loci.formats.cache.CrosshairStrategy
- getPossiblePositions() - Method in class loci.formats.cache.RectangleStrategy
- getPowers() - Method in class loci.formats.in.ND2Handler
- getPref(String, Class<? extends IFormatReader>, boolean) - Static method in class loci.plugins.util.LociPrefs
- getPreferredSize() - Method in class loci.formats.gui.CacheIndicator
- getPreferredSize() - Method in class loci.formats.gui.PreviewPane
- getPrefix() - Method in class loci.formats.FilePattern
-
Gets the pattern's substring that comes before any block sections.
- getPrefix(int) - Method in class loci.formats.FilePattern
-
Gets the pattern's substring between block i-1 (or the beginning of the pattern, if i is 0) and block i.
- getPrefix(String) - Method in class loci.formats.in.ZeissTIFFReader
- getPrefixes() - Method in class loci.formats.FilePattern
-
Gets all block prefixes.
- getPrefixMetadataName(String) - Method in class loci.formats.in.MicromanagerReader
- getPreviewNameIndex(String) - Method in class loci.formats.in.FV1000Reader
- getPriorities() - Method in class loci.formats.cache.CacheStrategy
- getPriorities() - Method in interface loci.formats.cache.ICacheStrategy
-
Retrieves the priority for caching each axis.
- getProcessor(int) - Method in class loci.plugins.util.BFVirtualStack
- getPulse(String) - Method in class loci.formats.FormatReader
-
Deprecated.
- getPulse(String) - Static method in class loci.formats.MetadataTools
-
Retrieves an
Pulseenumeration value for the given String. - getPyramidHeight() - Method in class loci.formats.in.NDPIReader
- getQuietInfo() - Method in class loci.plugins.in.ImporterOptions
- getRange() - Method in class loci.formats.cache.CacheStrategy
- getRange() - Method in interface loci.formats.cache.ICacheStrategy
-
Retrieves the number of objects to cache along each axis.
- getRasterLength(int[]) - Static method in class loci.formats.FormatTools
-
Computes the number of raster values for a positional array with the given lengths.
- getReader() - Method in class loci.formats.FileStitcher
-
Gets the wrapped reader prototype.
- getReader() - Method in class loci.formats.gui.FormatFileFilter
-
Returns the filter's reader.
- getReader() - Method in class loci.formats.ImageReader
-
Gets the reader used to open the current file.
- getReader() - Method in class loci.formats.ReaderWrapper
-
Gets the wrapped reader.
- getReader() - Method in class loci.formats.services.JAIIIOServiceImpl
-
Set up the JPEG-2000 image reader.
- getReader() - Method in class loci.plugins.in.ImportProcess
-
Valid only after
ImportStep.STACK. - getReader() - Method in class loci.plugins.util.BFVirtualStack
- getReader(int) - Method in class loci.formats.FileStitcher.ExternalSeries
- getReader(int) - Method in class loci.formats.FileStitcher
-
Gets the reader appropriate for use with the given image plane.
- getReader(int, int) - Method in class loci.formats.FileStitcher
-
Gets the reader that should be used with the given series and image plane.
- getReader(Class<? extends IFormatReader>) - Method in class loci.formats.ImageReader
-
Gets the file format reader instance matching the given class.
- getReader(String) - Method in class loci.formats.ImageReader
-
Gets the reader used to open the given file.
- getReader(String, boolean) - Method in class loci.formats.in.CellWorxReader
- getReader(String, boolean) - Method in class loci.formats.in.MetaxpressTiffReader
- getReader(IFormatReader, Class<? extends IFormatReader>) - Static method in class loci.formats.FormatTools
-
Recursively look for the first underlying reader that is an instance of the given class.
- getReaderIndex(int) - Method in class loci.formats.in.XLEFReader
-
Returns the index of the correct reader for the series index.
- getReaders() - Method in class loci.formats.FileStitcher.ExternalSeries
- getReaders() - Method in class loci.formats.ImageReader
-
Gets all constituent file format readers.
- getReadOutRate() - Method in class loci.formats.in.MetamorphHandler
- getRealSTKFile(Location) - Method in class loci.formats.in.MetamorphReader
-
Check that the given STK file exists.
- getRecordedProcessor() - Method in class loci.plugins.util.BFVirtualStack
- getRed(int) - Method in class loci.formats.gui.Index16ColorModel
- getRed(int) - Method in class loci.formats.gui.SignedColorModel
- getRed(int) - Method in class loci.formats.gui.UnsignedIntColorModel
- getRed(Object) - Method in class loci.formats.gui.SignedColorModel
- getRed(Object) - Method in class loci.formats.gui.UnsignedIntColorModel
- getRedOffset(int) - Static method in class org.libjpegturbo.turbojpeg.TJ
-
For the given pixel format, returns the number of bytes that the red component is offset from the start of the pixel.
- getReds() - Method in class loci.formats.gui.Index16ColorModel
-
Return the array of red color components.
- getRefractiveIndex() - Method in class loci.formats.in.ND2Handler
- getRegion() - Method in class loci.formats.in.TissueFAXSReader
- getRegion(int) - Method in class loci.formats.in.TissueFAXSReader
- getRelativeTime() - Method in class loci.formats.in.PrairieMetadata.Frame
-
Gets the
relativeTimeassociated with thisFrame. - getReorderedIndex(String, String, int, int, int, int, int) - Static method in class loci.formats.FormatTools
-
Converts index from one dimension order to another.
- getReorderedIndex(IFormatReader, String, int) - Static method in class loci.formats.FormatTools
-
Converts index from the given dimension order to the reader's native one.
- getRequiredDirectories(String[]) - Method in class loci.formats.FileStitcher
- getRequiredDirectories(String[]) - Method in class loci.formats.FormatReader
- getRequiredDirectories(String[]) - Static method in class loci.formats.FormatTools
-
Returns the maximum number of directories below the common parent of a list of file paths
- getRequiredDirectories(String[]) - Method in interface loci.formats.IFormatReader
-
Returns the number of parent directories that are important when processing the given list of files.
- getRequiredDirectories(String[]) - Method in class loci.formats.ImageReader
- getRequiredDirectories(String[]) - Method in class loci.formats.in.BrukerReader
- getRequiredDirectories(String[]) - Method in class loci.formats.in.CellVoyagerReader
- getRequiredDirectories(String[]) - Method in class loci.formats.in.ColumbusReader
- getRequiredDirectories(String[]) - Method in class loci.formats.in.CV7000Reader
- getRequiredDirectories(String[]) - Method in class loci.formats.in.DicomReader
- getRequiredDirectories(String[]) - Method in class loci.formats.in.MIASReader
- getRequiredDirectories(String[]) - Method in class loci.formats.in.MicroCTReader
- getRequiredDirectories(String[]) - Method in class loci.formats.in.OMETiffReader
- getRequiredDirectories(String[]) - Method in class loci.formats.in.OperettaReader
- getRequiredDirectories(String[]) - Method in class loci.formats.in.TecanReader
- getRequiredDirectories(String[]) - Method in class loci.formats.ReaderWrapper
- getResolution() - Method in class loci.formats.FileStitcher
- getResolution() - Method in class loci.formats.FormatReader
- getResolution() - Method in class loci.formats.FormatWriter
- getResolution() - Method in class loci.formats.ImageReader
- getResolution() - Method in class loci.formats.ImageWriter
- getResolution() - Method in interface loci.formats.IPyramidHandler
-
Get the current resolution level.
- getResolution() - Method in class loci.formats.ReaderWrapper
- getResolution() - Method in class loci.formats.SubResolutionFormatReader
- getResolution() - Method in class loci.formats.WrappedReader
- getResolution() - Method in class loci.formats.WriterWrapper
- getResolutionCount() - Method in class loci.formats.FormatReader
- getResolutionCount() - Method in class loci.formats.FormatWriter
- getResolutionCount() - Method in class loci.formats.ImageReader
- getResolutionCount() - Method in class loci.formats.ImageWriter
- getResolutionCount() - Method in interface loci.formats.IPyramidHandler
-
Return the number of resolutions for the current series.
- getResolutionCount() - Method in class loci.formats.ReaderWrapper
- getResolutionCount() - Method in class loci.formats.SubResolutionFormatReader
- getResolutionCount() - Method in class loci.formats.WrappedReader
- getResolutionCount() - Method in class loci.formats.WriterWrapper
- getResolutionCount(int) - Method in interface loci.formats.meta.IPyramidStore
-
Retrieve the number of pyramid resolutions defined for the given Image.
- getResolutionCount(int) - Method in class loci.formats.ome.OMEPyramidStore
- getResolutionIndex() - Method in class loci.formats.in.CellSensReader
-
Get the current pyramid resolution, accounting for flattened resolutions as needed.
- getResolutionLevels() - Method in class loci.formats.in.JPEG2000MetadataParser
-
Returns the number of resolution levels the file JPEG 2000 data has.
- getResolutionMultiplier() - Method in class loci.formats.tiff.IFD
-
Retrieve the value by which to multiply the X and Y resolution so that the resolutions are in microns per pixel.
- getResolutions() - Method in class loci.formats.FormatWriter
- getResolutions() - Method in interface loci.formats.IFormatWriter
-
Get a list of resolution objects for the current series.
- getResolutions() - Method in class loci.formats.ImageWriter
- getResolutions() - Method in class loci.formats.WriterWrapper
- getResolutionSizeX(int, int) - Method in interface loci.formats.meta.IPyramidStore
-
Retrieve the image width in pixels of the given pyramid resolution.
- getResolutionSizeX(int, int) - Method in class loci.formats.ome.OMEPyramidStore
- getResolutionSizeY(int, int) - Method in interface loci.formats.meta.IPyramidStore
-
Retrieve the image height in pixels of the given pyramid resolution.
- getResolutionSizeY(int, int) - Method in class loci.formats.ome.OMEPyramidStore
- getResolutionUnitFromComment(IFD) - Method in class loci.formats.in.BaseTiffReader
-
Extracts the resolution unit symbol from the comment field
- getRestartMarkers() - Method in interface loci.formats.services.JPEGTurboService
- getRestartMarkers() - Method in class loci.formats.services.JPEGTurboServiceImpl
- getRevision(String[]) - Method in class loci.plugins.macro.LociFunctions
- getRgbChannel(int, byte[]) - Method in class loci.formats.in.XLEFReader
-
Returns single channel data for an rgb plane
- getRGBChannelCount() - Method in class loci.formats.FormatReader
- getRGBChannelCount() - Method in interface loci.formats.IFormatReader
-
Gets the number of channels returned with each call to openBytes.
- getRGBChannelCount() - Method in class loci.formats.ImageReader
- getRGBChannelCount() - Method in class loci.formats.in.LeicaMicrosystemsMetadata.MultipleImagesReader
- getRGBChannelCount() - Method in class loci.formats.ReaderWrapper
- getRGBChannelCount() - Method in class loci.formats.WrappedReader
- getRGBChannelCount(Double[]) - Method in class loci.plugins.macro.LociFunctions
- getRoi() - Method in class loci.plugins.util.RecordedImageProcessor
- getROIs() - Method in class loci.formats.in.ND2Handler
- getROIs() - Method in class loci.formats.in.SPEReader.SpeHeader
-
Method used to read and return meta data for upto 10 rectangular ROI's stored in the SPE header table
- getROIsMode() - Method in class loci.plugins.in.ImporterOptions
- getROIsModeInfo() - Method in class loci.plugins.in.ImporterOptions
- getROIsModes() - Method in class loci.plugins.in.ImporterOptions
- GetRootDirectory() - Method in class loci.formats.in.SlideBook7Reader.DataLoader
- getRotationTransform(double) - Method in class loci.formats.FormatReader
-
Construct an
AffineTransformcorresponding to the given angle. - getRow() - Method in class loci.formats.in.OMEXMLReader.BinData
- getRow(int, int, int[], int) - Method in class loci.plugins.util.RecordedImageProcessor
- getRowCount(int) - Method in interface loci.formats.services.MetakitService
- getRowCount(int) - Method in class loci.formats.services.MetakitServiceImpl
- getRowCount(String) - Method in interface loci.formats.services.MetakitService
- getRowCount(String) - Method in class loci.formats.services.MetakitServiceImpl
- getRowData(int, int) - Method in interface loci.formats.services.MetakitService
- getRowData(int, int) - Method in class loci.formats.services.MetakitServiceImpl
- getRowData(int, String) - Method in interface loci.formats.services.MetakitService
- getRowData(int, String) - Method in class loci.formats.services.MetakitServiceImpl
- getRowData(String[], double[]) - Method in class loci.formats.in.TextReader
-
Parses numerical row data from the given tokens.
- getRowIndex() - Method in class loci.formats.internal.WellContainer
- getRowsPerStrip() - Method in class loci.formats.tiff.IFD
-
Retrieves the number of rows per strip for image (TIFF tag RowsPerStrip) from this IFD.
- getSample(RandomAccessInputStream, CodecOptions) - Method in class loci.formats.codec.HuffmanCodec
- getSample(BitBuffer, CodecOptions) - Method in class loci.formats.codec.HuffmanCodec
-
Deprecated.
- getSampleData() - Method in class loci.formats.in.ImarisHDFReader
- getSamples(IFD, byte[]) - Method in class loci.formats.tiff.TiffParser
- getSamples(IFD, byte[], int, int, long, long) - Method in class loci.formats.tiff.TiffParser
- getSamples(IFD, byte[], int, int, long, long, int, int) - Method in class loci.formats.tiff.TiffParser
- getSamplesPerPixel() - Method in class loci.formats.FormatWriter
-
Retrieve the number of samples per pixel for the current series.
- getSamplesPerPixel() - Method in class loci.formats.tiff.IFD
-
Retrieves the number of samples per pixel for the image (TIFF tag SamplesPerPixel) from this IFD.
- getSamplesPerPixel(int) - Method in class loci.formats.FormatWriter
-
Retrieve the number of samples per pixel for given series.
- GetSBClassName() - Method in class loci.formats.in.SlideBook7Reader.ClassDecoder
- getScale(int) - Method in class loci.formats.in.VentanaReader
- getScaled(int) - Method in class org.libjpegturbo.turbojpeg.TJScalingFactor
-
Returns the scaled value of
dimension. - getScaledHeight(int, int) - Method in class org.libjpegturbo.turbojpeg.TJDecompressor
-
Returns the height of the largest scaled down image that the TurboJPEG decompressor can generate without exceeding the desired image width and height.
- getScaledWidth(int, int) - Method in class org.libjpegturbo.turbojpeg.TJDecompressor
-
Returns the width of the largest scaled down image that the TurboJPEG decompressor can generate without exceeding the desired image width and height.
- getScalingFactors() - Static method in class org.libjpegturbo.turbojpeg.TJ
-
Returns a list of fractional scaling factors that the JPEG decompressor in this implementation of TurboJPEG supports.
- getScanline(int) - Method in class loci.formats.codec.JPEGTileDecoder
- getScanlinePad() - Method in class loci.formats.in.ND2Reader
- getScanNames() - Method in class loci.formats.in.L2DReader
-
Return a list of scan names.
- getScanProfileXML() - Method in class loci.formats.in.VectraReader
-
Returns an XML string corresponding to the ScanProfile node.
- getScientificNotationPattern(int, int, int) - Static method in class loci.formats.out.DicomWriter
- getScreenName() - Method in class loci.formats.in.ColumbusReader.MeasurementHandler
- getSequence() - Method in class loci.formats.in.PrairieMetadata.Frame
-
Gets the
<Sequence>containing this<Frame>. - getSequence(int) - Method in class loci.formats.in.PrairieMetadata
-
Gets the
Sequenceat the givencycle. - getSequences() - Method in class loci.formats.in.PrairieMetadata
-
Gets all
Sequences, ordered bycycle. - getSeries() - Method in class loci.formats.FileStitcher
- getSeries() - Method in class loci.formats.FormatReader
- getSeries() - Method in class loci.formats.FormatWriter
- getSeries() - Method in interface loci.formats.IFormatReader
-
Gets the currently active series.
- getSeries() - Method in interface loci.formats.IFormatWriter
-
Returns the current series.
- getSeries() - Method in class loci.formats.ImageReader
- getSeries() - Method in class loci.formats.ImageWriter
- getSeries() - Method in class loci.formats.ReaderWrapper
- getSeries() - Method in class loci.formats.SubResolutionFormatReader
- getSeries() - Method in class loci.formats.WrappedReader
- getSeries() - Method in class loci.formats.WriterWrapper
- getSeries(Double[]) - Method in class loci.plugins.macro.LociFunctions
- getSeriesCount() - Method in class loci.formats.FileStitcher
- getSeriesCount() - Method in class loci.formats.FormatReader
- getSeriesCount() - Method in interface loci.formats.IFormatReader
-
Gets the number of series in this file.
- getSeriesCount() - Method in class loci.formats.ImageReader
- getSeriesCount() - Method in class loci.formats.in.ND2Handler
- getSeriesCount() - Method in class loci.formats.ReaderWrapper
- getSeriesCount() - Method in class loci.formats.SubResolutionFormatReader
- getSeriesCount() - Method in class loci.formats.TileStitcher
- getSeriesCount() - Method in class loci.formats.WrappedReader
- getSeriesCount() - Method in class loci.plugins.in.ImportProcess
-
Valid only after
ImportStep.STACK. - getSeriesCount(Double[]) - Method in class loci.plugins.macro.LociFunctions
- getSeriesHashtable(int) - Method in class loci.formats.in.LeicaHandler
- getSeriesIndex(int, int, int) - Method in class loci.formats.in.MetamorphTiffReader
- getSeriesLabel(int) - Method in class loci.plugins.in.ImportProcess
-
Valid only after
ImportStep.STACK. - getSeriesList() - Method in class loci.formats.CoreMetadataList
- getSeriesMeta(String) - Method in class loci.formats.FormatReader
-
Gets an entry from the metadata table for the current series.
- getSeriesMetadata() - Method in class loci.formats.FileStitcher
- getSeriesMetadata() - Method in class loci.formats.FormatReader
- getSeriesMetadata() - Method in interface loci.formats.IFormatReader
-
Obtains the hashtable containing metadata field/value pairs from the current series in the current file.
- getSeriesMetadata() - Method in class loci.formats.ImageReader
- getSeriesMetadata() - Method in class loci.formats.ReaderWrapper
- getSeriesMetadata() - Method in class loci.formats.WrappedReader
- getSeriesMetadataValue(String) - Method in class loci.formats.FormatReader
- getSeriesMetadataValue(String) - Method in interface loci.formats.IFormatReader
-
Obtains the specified metadata field's value for the current series in the current file.
- getSeriesMetadataValue(String) - Method in class loci.formats.ImageReader
- getSeriesMetadataValue(String) - Method in class loci.formats.ReaderWrapper
- getSeriesMetadataValue(String) - Method in class loci.formats.WrappedReader
- getSeriesMetadataValue(String, String[]) - Method in class loci.plugins.macro.LociFunctions
- getSeriesName(String[]) - Method in class loci.plugins.macro.LociFunctions
- getSeriesPerReaderIndex(int) - Method in class loci.formats.in.XLEFReader
-
Returns the index of the series (tile) in the corresponding reader
- getSeriesUsedFiles() - Method in class loci.formats.FileStitcher
- getSeriesUsedFiles() - Method in class loci.formats.FormatReader
- getSeriesUsedFiles() - Method in interface loci.formats.IFormatReader
-
Returns an array of filenames needed to open the current series.
- getSeriesUsedFiles() - Method in class loci.formats.ImageReader
- getSeriesUsedFiles() - Method in class loci.formats.ReaderWrapper
- getSeriesUsedFiles(boolean) - Method in class loci.formats.DelegateReader
- getSeriesUsedFiles(boolean) - Method in class loci.formats.FileStitcher
- getSeriesUsedFiles(boolean) - Method in class loci.formats.FormatReader
- getSeriesUsedFiles(boolean) - Method in interface loci.formats.IFormatReader
-
Returns an array of filenames needed to open the current series.
- getSeriesUsedFiles(boolean) - Method in class loci.formats.ImageReader
- getSeriesUsedFiles(boolean) - Method in class loci.formats.in.AFIReader
- getSeriesUsedFiles(boolean) - Method in class loci.formats.in.AnalyzeReader
- getSeriesUsedFiles(boolean) - Method in class loci.formats.in.APLReader
- getSeriesUsedFiles(boolean) - Method in class loci.formats.in.BDReader
- getSeriesUsedFiles(boolean) - Method in class loci.formats.in.BioRadReader
- getSeriesUsedFiles(boolean) - Method in class loci.formats.in.BrukerReader
- getSeriesUsedFiles(boolean) - Method in class loci.formats.in.CellomicsReader
- getSeriesUsedFiles(boolean) - Method in class loci.formats.in.CellSensReader
- getSeriesUsedFiles(boolean) - Method in class loci.formats.in.CellVoyagerReader
- getSeriesUsedFiles(boolean) - Method in class loci.formats.in.CellWorxReader
- getSeriesUsedFiles(boolean) - Method in class loci.formats.in.ColumbusReader
- getSeriesUsedFiles(boolean) - Method in class loci.formats.in.CV7000Reader
- getSeriesUsedFiles(boolean) - Method in class loci.formats.in.DCIMGReader
- getSeriesUsedFiles(boolean) - Method in class loci.formats.in.DeltavisionReader
- getSeriesUsedFiles(boolean) - Method in class loci.formats.in.DicomReader
- getSeriesUsedFiles(boolean) - Method in class loci.formats.in.FakeReader
- getSeriesUsedFiles(boolean) - Method in class loci.formats.in.FilePatternReader
- getSeriesUsedFiles(boolean) - Method in class loci.formats.in.FlexReader
- getSeriesUsedFiles(boolean) - Method in class loci.formats.in.FujiReader
- getSeriesUsedFiles(boolean) - Method in class loci.formats.in.FV1000Reader
- getSeriesUsedFiles(boolean) - Method in class loci.formats.in.HamamatsuVMSReader
- getSeriesUsedFiles(boolean) - Method in class loci.formats.in.HitachiReader
- getSeriesUsedFiles(boolean) - Method in class loci.formats.in.ICSReader
- getSeriesUsedFiles(boolean) - Method in class loci.formats.in.ImagicReader
- getSeriesUsedFiles(boolean) - Method in class loci.formats.in.ImprovisionTiffReader
- getSeriesUsedFiles(boolean) - Method in class loci.formats.in.InCellReader
- getSeriesUsedFiles(boolean) - Method in class loci.formats.in.JDCEReader
- getSeriesUsedFiles(boolean) - Method in class loci.formats.in.JEOLReader
- getSeriesUsedFiles(boolean) - Method in class loci.formats.in.JPEGReader
- getSeriesUsedFiles(boolean) - Method in class loci.formats.in.L2DReader
- getSeriesUsedFiles(boolean) - Method in class loci.formats.in.LeicaReader
- getSeriesUsedFiles(boolean) - Method in class loci.formats.in.LIFReader
- getSeriesUsedFiles(boolean) - Method in class loci.formats.in.LOFReader
- getSeriesUsedFiles(boolean) - Method in class loci.formats.in.MetamorphReader
- getSeriesUsedFiles(boolean) - Method in class loci.formats.in.MetaxpressTiffReader
- getSeriesUsedFiles(boolean) - Method in class loci.formats.in.MIASReader
- getSeriesUsedFiles(boolean) - Method in class loci.formats.in.MicroCTReader
- getSeriesUsedFiles(boolean) - Method in class loci.formats.in.MicromanagerReader
- getSeriesUsedFiles(boolean) - Method in class loci.formats.in.NDPISReader
- getSeriesUsedFiles(boolean) - Method in class loci.formats.in.NiftiReader
- getSeriesUsedFiles(boolean) - Method in class loci.formats.in.NRRDReader
- getSeriesUsedFiles(boolean) - Method in class loci.formats.in.OIRReader
- getSeriesUsedFiles(boolean) - Method in class loci.formats.in.OlympusTileReader
- getSeriesUsedFiles(boolean) - Method in class loci.formats.in.OMETiffReader
- getSeriesUsedFiles(boolean) - Method in class loci.formats.in.OperettaReader
- getSeriesUsedFiles(boolean) - Method in class loci.formats.in.PCORAWReader
- getSeriesUsedFiles(boolean) - Method in class loci.formats.in.PDSReader
- getSeriesUsedFiles(boolean) - Method in class loci.formats.in.PerkinElmerReader
- getSeriesUsedFiles(boolean) - Method in class loci.formats.in.PrairieReader
- getSeriesUsedFiles(boolean) - Method in class loci.formats.in.QTReader
- getSeriesUsedFiles(boolean) - Method in class loci.formats.in.ScanrReader
- getSeriesUsedFiles(boolean) - Method in class loci.formats.in.SEQReader
- getSeriesUsedFiles(boolean) - Method in class loci.formats.in.SlidebookTiffReader
- getSeriesUsedFiles(boolean) - Method in class loci.formats.in.SPCReader
- getSeriesUsedFiles(boolean) - Method in class loci.formats.in.TCSReader
- getSeriesUsedFiles(boolean) - Method in class loci.formats.in.TecanReader
- getSeriesUsedFiles(boolean) - Method in class loci.formats.in.TiffReader
- getSeriesUsedFiles(boolean) - Method in class loci.formats.in.TillVisionReader
- getSeriesUsedFiles(boolean) - Method in class loci.formats.in.TissueFAXSReader
- getSeriesUsedFiles(boolean) - Method in class loci.formats.in.TrestleReader
- getSeriesUsedFiles(boolean) - Method in class loci.formats.in.VarianFDFReader
- getSeriesUsedFiles(boolean) - Method in class loci.formats.in.VectraReader
- getSeriesUsedFiles(boolean) - Method in class loci.formats.in.VisitechReader
- getSeriesUsedFiles(boolean) - Method in class loci.formats.in.VolocityReader
- getSeriesUsedFiles(boolean) - Method in class loci.formats.in.XLEFReader
- getSeriesUsedFiles(boolean) - Method in class loci.formats.in.ZeissCZIReader
- getSeriesUsedFiles(boolean) - Method in class loci.formats.in.ZeissLSMReader
- getSeriesUsedFiles(boolean) - Method in class loci.formats.in.ZeissTIFFReader
- getSeriesUsedFiles(boolean) - Method in class loci.formats.ReaderWrapper
- getSeriesUsedFiles(boolean) - Method in class loci.formats.WrappedReader
- getService() - Method in class loci.formats.Memoizer
- getShape(String) - Method in interface loci.formats.services.JHDFService
-
Retrieves the shape of a dataset.
- getShape(String) - Method in class loci.formats.services.JHDFServiceImpl
- getShort(int) - Method in class loci.formats.in.SPEReader.SpeHeader
-
Private method used to retrieve a Short value from the SPE header
- getShort(SPEReader.SpeHeaderEntry) - Method in class loci.formats.in.SPEReader.SpeHeader
-
Method used to retrieve data values for Short entries into the SPE header table
- getShortArray(SPEReader.SpeHeaderEntry) - Method in class loci.formats.in.SPEReader.SpeHeader
-
Method used to retrieve data values for Short Array entries into the SPE header table
- getShorts(BufferedImage) - Static method in class loci.formats.gui.AWTImageTools
-
Extracts pixel data as arrays of unsigned shorts, one per channel.
- getShorts(WritableRaster) - Static method in class loci.formats.gui.AWTImageTools
-
Extracts pixel data as arrays of unsigned shorts, one per channel.
- getShorts(WritableRaster, int, int, int, int) - Static method in class loci.formats.gui.AWTImageTools
-
Extracts pixel data as arrays of unsigned shorts, one per channel.
- getShowMetadataInfo() - Method in class loci.plugins.in.ImporterOptions
- getShowOMEXMLInfo() - Method in class loci.plugins.in.ImporterOptions
- getShowROIsInfo() - Method in class loci.plugins.in.ImporterOptions
- GetSingleTimepointFile() - Method in class loci.formats.in.SlideBook7Reader.CImageGroup
- getSize() - Method in class loci.plugins.util.BFVirtualStack
- getSize(Image) - Static method in class loci.formats.gui.AWTImageTools
-
Gets the width and height of the given AWT image, waiting for it to finish loading if necessary.
- getSizeC() - Method in class loci.formats.ChannelFiller
- getSizeC() - Method in class loci.formats.DimensionSwapper
- getSizeC() - Method in class loci.formats.FileStitcher
- getSizeC() - Method in class loci.formats.FormatReader
- getSizeC() - Method in interface loci.formats.IFormatReader
-
Gets the size of the C dimension.
- getSizeC() - Method in class loci.formats.ImageReader
- getSizeC() - Method in class loci.formats.in.LeicaMicrosystemsMetadata.MultipleImagesReader
- getSizeC() - Method in class loci.formats.ReaderWrapper
- getSizeC() - Method in class loci.formats.WrappedReader
- getSizeC(Double[]) - Method in class loci.plugins.macro.LociFunctions
- getSizeT() - Method in class loci.formats.DimensionSwapper
- getSizeT() - Method in class loci.formats.FileStitcher
- getSizeT() - Method in class loci.formats.FormatReader
- getSizeT() - Method in interface loci.formats.IFormatReader
-
Gets the size of the T dimension.
- getSizeT() - Method in class loci.formats.ImageReader
- getSizeT() - Method in class loci.formats.ReaderWrapper
- getSizeT() - Method in class loci.formats.WrappedReader
- getSizeT(Double[]) - Method in class loci.plugins.macro.LociFunctions
- getSizeX() - Method in class loci.formats.DimensionSwapper
- getSizeX() - Method in class loci.formats.FileStitcher
- getSizeX() - Method in class loci.formats.FormatReader
- getSizeX() - Method in class loci.formats.FormatWriter
- getSizeX() - Method in interface loci.formats.IFormatReader
-
Gets the size of the X dimension.
- getSizeX() - Method in class loci.formats.ImageReader
- getSizeX() - Method in class loci.formats.ReaderWrapper
- getSizeX() - Method in class loci.formats.TileStitcher
- getSizeX() - Method in class loci.formats.WrappedReader
- getSizeX(Double[]) - Method in class loci.plugins.macro.LociFunctions
- getSizeY() - Method in class loci.formats.DimensionSwapper
- getSizeY() - Method in class loci.formats.FileStitcher
- getSizeY() - Method in class loci.formats.FormatReader
- getSizeY() - Method in class loci.formats.FormatWriter
- getSizeY() - Method in interface loci.formats.IFormatReader
-
Gets the size of the Y dimension.
- getSizeY() - Method in class loci.formats.ImageReader
- getSizeY() - Method in class loci.formats.ReaderWrapper
- getSizeY() - Method in class loci.formats.TileStitcher
- getSizeY() - Method in class loci.formats.WrappedReader
- getSizeY(Double[]) - Method in class loci.plugins.macro.LociFunctions
- getSizeZ() - Method in class loci.formats.DimensionSwapper
- getSizeZ() - Method in class loci.formats.FileStitcher
- getSizeZ() - Method in class loci.formats.FormatReader
- getSizeZ() - Method in interface loci.formats.IFormatReader
-
Gets the size of the Z dimension.
- getSizeZ() - Method in class loci.formats.ImageReader
- getSizeZ() - Method in class loci.formats.ReaderWrapper
- getSizeZ() - Method in class loci.formats.WrappedReader
- getSizeZ(Double[]) - Method in class loci.plugins.macro.LociFunctions
- getSliceLabelBaseIndex() - Static method in class loci.plugins.util.LociPrefs
- getSliceLabelPattern() - Static method in class loci.plugins.util.LociPrefs
- GetSlideRootDirectory() - Method in class loci.formats.in.SlideBook7Reader.CSBFile70
- getSnapshotPixels() - Method in class loci.plugins.util.RecordedImageProcessor
- getSource() - Method in class loci.formats.cache.Cache
-
Gets the cache's caching source.
- getSource() - Method in class loci.formats.cache.CacheEvent
-
Gets the source of the cache update.
- getSpecifyRangesInfo() - Method in class loci.plugins.in.ImporterOptions
- getSpectra() - Method in class loci.formats.in.IM3Reader
-
If a Nuance file is a spectral library set (.csl) file, there is a spectral library inside that contains a profile of spectral bin magnitudes for each of several measured fluorophores (or auto fluorescence).
- getSpeeds() - Method in class loci.formats.in.ND2Handler
- getSplitChannelsInfo() - Method in class loci.plugins.in.ImporterOptions
- getSplitFocalPlanesInfo() - Method in class loci.plugins.in.ImporterOptions
- getSplitTimepointsInfo() - Method in class loci.plugins.in.ImporterOptions
- getStackFormat() - Method in class loci.plugins.in.ImporterOptions
- getStackFormatInfo() - Method in class loci.plugins.in.ImporterOptions
- getStackFormats() - Method in class loci.plugins.in.ImporterOptions
- getStackOrder() - Method in class loci.plugins.in.ImporterOptions
- getStackOrder() - Method in class loci.plugins.in.ImportProcess
-
Valid only after
ImportStep.STACK. - getStackOrderInfo() - Method in class loci.plugins.in.ImporterOptions
- getStackOrders() - Method in class loci.plugins.in.ImporterOptions
- getStackSize() - Method in class loci.formats.in.SPEReader.SpeHeader
-
Method used to determined the stack size of the SPE file.
- getStackType(String) - Method in class loci.formats.in.CellSensReader
- getStageLabel() - Method in class loci.formats.in.MetamorphHandler
- getStagePosition(Double, String) - Static method in class loci.formats.FormatTools
-
Formats the input value for the stage position into a length of the given unit.
- getStagePosition(Double, Unit<Length>) - Static method in class loci.formats.FormatTools
-
Formats the input value for the stage position into a length of the given unit.
- getStagePositionX() - Method in class loci.formats.in.MetamorphHandler
- getStagePositionY() - Method in class loci.formats.in.MetamorphHandler
- getStageX() - Method in class loci.formats.in.MetamorphReader
- getStageY() - Method in class loci.formats.in.MetamorphReader
- getStart(Hashtable<String, Object>) - Method in class loci.formats.in.MINCReader
- getStartX() - Method in class loci.formats.in.SPEReader.SpeROI
- getStartY() - Method in class loci.formats.in.SPEReader.SpeROI
- getStatistics(int, int, double, double) - Method in class loci.plugins.util.VirtualImagePlus
- getStep() - Method in class loci.formats.FilePattern
-
Gets the STEP element for all blocks.
- getStep() - Method in class loci.formats.FilePatternBlock
-
Gets the difference between consecutive elements in a range block.
- getStep() - Method in enum class loci.plugins.in.ImportStep
- getStep(int) - Static method in enum class loci.plugins.in.ImportStep
- getStepSize(Hashtable<String, Object>) - Method in class loci.formats.in.MINCReader
- getStitchTilesInfo() - Method in class loci.plugins.in.ImporterOptions
- getStoredLength(DicomTag) - Method in class loci.formats.out.DicomWriter
- getStrategy() - Method in class loci.formats.cache.Cache
-
Gets the cache's caching strategy.
- getStream() - Method in class loci.formats.in.ZeissCZIReader.Segment
- getStream() - Method in class loci.formats.tiff.OnDemandLongArray
- getStream() - Method in class loci.formats.tiff.TiffParser
-
Gets the stream from which TIFF data is being parsed.
- getStream() - Method in class loci.formats.tiff.TiffSaver
-
Gets the stream from which TIFF data is being saved.
- getStream(int) - Method in class loci.formats.in.VolocityReader
- getStream(String) - Method in class loci.formats.in.DicomReader
- getStreams() - Method in class loci.formats.tools.AmiraParameters
- getString(boolean) - Method in class loci.formats.in.LeicaReader
- getString(int) - Method in class loci.formats.in.LeicaReader
- getString(int, int) - Method in class loci.formats.in.SPEReader.SpeHeader
-
Private method used to retrieve a String value from the SPE header
- getString(Integer) - Method in class loci.formats.in.VolocityReader
- getString(SPEReader.SpeHeaderEntry) - Method in class loci.formats.in.SPEReader.SpeHeader
-
Method used to retrieve data values for String entries into the SPE header table
- GetStringArray(Node, String, Boolean, Boolean) - Method in class loci.formats.in.SlideBook7Reader.ClassDecoder
- getStringOption(String) - Method in class loci.plugins.prefs.OptionsList
-
Gets the string option with the given key.
- getStringValue() - Method in class loci.formats.dicom.DicomTag
-
Get a string representation of the current value.
- getStringValue(int) - Method in class loci.formats.in.ZeissLSMReader.SubBlock
- GetStringValue(MappingNode, int, String, Boolean) - Method in class loci.formats.in.SlideBook7Reader.ClassDecoder
- getStringWidth(String) - Method in class loci.plugins.util.RecordedImageProcessor
- getStripByteCounts() - Method in class loci.formats.tiff.IFD
-
Retrieves strip byte counts for the image (TIFF tag StripByteCounts) from this IFD.
- getStripOffsets() - Method in class loci.formats.tiff.IFD
-
Retrieves the strip offsets for the image (TIFF tag StripOffsets) from this IFD.
- getSubC(Modulo, int) - Static method in class loci.plugins.in.ImagePlusReader
- getSubCTypes(Modulo) - Static method in class loci.plugins.in.ImagePlusReader
- getSubIFDs(IFD) - Method in class loci.formats.tiff.TiffParser
-
Returns the SUBIFDS belonging to a given IFD.
- getSubimage(byte[], byte[], int, int, int, int, int, int, int, int, boolean) - Static method in class loci.formats.ImageTools
- getSubimage(BufferedImage, boolean, int, int, int, int) - Static method in class loci.formats.gui.AWTImageTools
-
Returns a subimage of the specified image.
- getSubsamp() - Method in class org.libjpegturbo.turbojpeg.TJDecompressor
-
Returns the level of chrominance subsampling used in the JPEG image associated with this decompressor instance.
- getSuffix() - Method in class loci.formats.FilePattern
-
Gets the pattern's substring that comes after all block sections.
- getSuffixes() - Method in class loci.formats.FormatHandler
- getSuffixes() - Method in interface loci.formats.IFormatHandler
-
Gets the default file suffixes for this file format.
- getSuffixes() - Method in class loci.formats.ImageReader
- getSuffixes() - Method in class loci.formats.ImageWriter
- getSuffixes() - Method in class loci.formats.ReaderWrapper
- getSuffixes() - Method in class loci.formats.WriterWrapper
- getSupportedMetadataLevels() - Method in class loci.formats.DelegateReader
- getSupportedMetadataLevels() - Method in class loci.formats.FormatHandler
- getSupportedMetadataLevels() - Method in class loci.formats.ImageReader
- getSupportedMetadataLevels() - Method in class loci.formats.ImageWriter
- getSupportedMetadataLevels() - Method in interface loci.formats.IMetadataConfigurable
- getSupportedMetadataLevels() - Method in class loci.formats.ReaderWrapper
- getSupportedMetadataLevels() - Method in class loci.formats.WriterWrapper
- getSwapDimensionsInfo() - Method in class loci.plugins.in.ImporterOptions
- getT() - Method in class loci.formats.gui.ImageViewer
-
Gets the T value of the currently displayed image.
- getT(String) - Method in class loci.formats.in.OIRReader
- getTableCount() - Method in interface loci.formats.services.MetakitService
- getTableCount() - Method in class loci.formats.services.MetakitServiceImpl
- getTableData(int) - Method in interface loci.formats.services.MetakitService
- getTableData(int) - Method in class loci.formats.services.MetakitServiceImpl
- getTableData(String) - Method in interface loci.formats.services.MetakitService
- getTableData(String) - Method in class loci.formats.services.MetakitServiceImpl
- getTableNames() - Method in interface loci.formats.services.MetakitService
- getTableNames() - Method in class loci.formats.services.MetakitServiceImpl
- getTag() - Method in enum class loci.formats.dicom.DicomAttribute
-
Get the 4 byte integer tag.
- getTag() - Method in class loci.formats.tiff.TiffIFDEntry
-
Retrieves the entry's Tag value.
- getTag(String) - Static method in enum class loci.formats.dicom.DicomAttribute
- getTagName(int) - Method in class loci.formats.in.CellSensReader
- getTags() - Method in class loci.formats.dicom.DicomJSONProvider
- getTags() - Method in interface loci.formats.dicom.ITagProvider
-
Retrieve the tags defined by this provider.
- getTags() - Method in class loci.formats.in.DicomReader
-
Provide the complete hierarchy of DICOM tags.
- getTags() - Method in interface loci.formats.services.EXIFService
- getTags() - Method in class loci.formats.services.EXIFServiceImpl
- getTBegin(int) - Method in class loci.plugins.in.ImporterOptions
- getTBegin(int) - Method in class loci.plugins.in.ImportProcess
- getTCount(int) - Method in class loci.plugins.in.ImportProcess
-
Valid only after
ImportStep.SERIES. - getTemperature() - Method in class loci.formats.in.MetamorphHandler
- getTemperatures() - Method in class loci.formats.in.ND2Handler
- getTEnd(int) - Method in class loci.plugins.in.ImporterOptions
- getTEnd(int) - Method in class loci.plugins.in.ImportProcess
-
Valid only after
ImportStep.STACK. - getThumbnailIFDs() - Method in class loci.formats.in.MinimalTiffReader
-
Gets the list of IFDs associated with the current TIFF's thumbnails.
- getThumbnailIFDs() - Method in class loci.formats.tiff.TiffParser
-
Returns thumbnail IFDs.
- getThumbSizeX() - Method in class loci.formats.FileStitcher
- getThumbSizeX() - Method in class loci.formats.FormatReader
- getThumbSizeX() - Method in interface loci.formats.IFormatReader
-
Get the size of the X dimension for the thumbnail.
- getThumbSizeX() - Method in class loci.formats.ImageReader
- getThumbSizeX() - Method in class loci.formats.in.LeicaSCNReader
- getThumbSizeX() - Method in class loci.formats.in.MinimalTiffReader
- getThumbSizeX() - Method in class loci.formats.in.VentanaReader
- getThumbSizeX() - Method in class loci.formats.ReaderWrapper
- getThumbSizeX() - Method in class loci.formats.WrappedReader
- getThumbSizeY() - Method in class loci.formats.FileStitcher
- getThumbSizeY() - Method in class loci.formats.FormatReader
- getThumbSizeY() - Method in interface loci.formats.IFormatReader
-
Get the size of the Y dimension for the thumbnail.
- getThumbSizeY() - Method in class loci.formats.ImageReader
- getThumbSizeY() - Method in class loci.formats.in.LeicaSCNReader
- getThumbSizeY() - Method in class loci.formats.in.MinimalTiffReader
- getThumbSizeY() - Method in class loci.formats.in.VentanaReader
- getThumbSizeY() - Method in class loci.formats.ReaderWrapper
- getThumbSizeY() - Method in class loci.formats.WrappedReader
- getTIFFCompression() - Method in class loci.formats.out.DicomWriter
- getTIFFCompression() - Method in class loci.formats.out.TiffWriter
-
Get the TIFF compression enum value that corresponds to the current compression type.
- getTiffFiles(String, char, int, int, int, int) - Method in class loci.formats.in.MetaxpressTiffReader
- getTIFFList() - Method in class loci.formats.in.LeicaReader
- getTiffs() - Method in class loci.formats.in.BDReader
- getTile(byte[], int, int, int, int) - Method in interface loci.formats.services.JPEGTurboService
-
Get the uncompressed bytes representing the given bounding box.
- getTile(byte[], int, int, int, int) - Method in class loci.formats.services.JPEGTurboServiceImpl
- getTile(byte[], Region, Region) - Method in class loci.formats.out.TiffWriter
- getTile(int, int) - Method in interface loci.formats.services.JPEGTurboService
-
Get the uncompressed bytes representing the given tile index.
- getTile(int, int) - Method in class loci.formats.services.JPEGTurboServiceImpl
- getTile(int, int, int, int, Region) - Method in class loci.formats.in.MIASReader
- getTile(DicomTile, byte[], int, int, int, int) - Method in class loci.formats.in.DicomReader
-
Decompress pixel data associated with the given DicomTile.
- getTile(IFD, byte[], int, int) - Method in class loci.formats.tiff.TiffParser
- getTileCodec(int) - Method in class loci.formats.ChannelFiller
- getTileCodec(int) - Method in class loci.formats.ChannelMerger
- getTileCodec(int) - Method in class loci.formats.ChannelSeparator
- getTileCodec(int) - Method in class loci.formats.DimensionSwapper
- getTileCodec(int) - Method in class loci.formats.FileStitcher
- getTileCodec(int) - Method in interface loci.formats.ICompressedTileReader
-
Retrieve a codec that can be used to decompress compressed tiles.
- getTileCodec(int) - Method in class loci.formats.ImageReader
- getTileCodec(int) - Method in class loci.formats.in.DicomReader
- getTileCodec(int) - Method in class loci.formats.in.NDPIReader
- getTileCodec(int) - Method in class loci.formats.in.SVSReader
- getTileCodec(int) - Method in class loci.formats.ReaderWrapper
- getTileCodec(int) - Method in class loci.formats.TileStitcher
- getTileCodec(DicomTile) - Method in class loci.formats.in.DicomReader
-
Get a Codec that can be used to decompress the given tile.
- getTileCodecOptions(int, int, int) - Method in class loci.formats.ChannelFiller
- getTileCodecOptions(int, int, int) - Method in class loci.formats.ChannelMerger
- getTileCodecOptions(int, int, int) - Method in class loci.formats.ChannelSeparator
- getTileCodecOptions(int, int, int) - Method in class loci.formats.DimensionSwapper
- getTileCodecOptions(int, int, int) - Method in class loci.formats.FileStitcher
- getTileCodecOptions(int, int, int) - Method in interface loci.formats.ICompressedTileReader
-
Retrieve codec options that can be used to decompressed the specified tile.
- getTileCodecOptions(int, int, int) - Method in class loci.formats.ImageReader
- getTileCodecOptions(int, int, int) - Method in class loci.formats.in.DicomReader
- getTileCodecOptions(int, int, int) - Method in class loci.formats.in.NDPIReader
- getTileCodecOptions(int, int, int) - Method in class loci.formats.in.SVSReader
- getTileCodecOptions(int, int, int) - Method in class loci.formats.ReaderWrapper
- getTileCodecOptions(int, int, int) - Method in class loci.formats.TileStitcher
- getTileCodecOptions(DicomTile) - Method in class loci.formats.in.DicomReader
-
Get a CodecOptions that can be used to decompress the given tile.
- getTileColumn(int, int, int) - Method in class loci.formats.in.VentanaReader
- getTileColumns() - Method in interface loci.formats.services.JPEGTurboService
- getTileColumns() - Method in class loci.formats.services.JPEGTurboServiceImpl
- getTileColumns(int) - Method in class loci.formats.FormatReader
- getTileColumns(int) - Method in interface loci.formats.ICompressedTileReader
-
Get the number of columns of tiles in the specified plane in the current series.
- getTileColumns(int) - Method in class loci.formats.ImageReader
- getTileColumns(int) - Method in class loci.formats.in.DicomReader
- getTileColumns(int) - Method in class loci.formats.in.NDPIReader
- getTileColumns(int) - Method in class loci.formats.in.SVSReader
- getTileColumns(int) - Method in class loci.formats.ReaderWrapper
- getTileColumns(int) - Method in class loci.formats.TileStitcher
- getTileCount() - Method in class loci.formats.in.LeicaMicrosystemsMetadata.XlifDocument
-
Returns the number of tiles referenced by this xlif
- getTileFilename(int, int, int, String) - Static method in class loci.formats.FormatTools
- getTileHeight() - Method in interface loci.formats.services.JPEGTurboService
- getTileHeight() - Method in class loci.formats.services.JPEGTurboServiceImpl
- getTileIndex(int) - Method in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataStoreInitializer
- getTileIndex(int) - Method in class loci.formats.in.LIFReader
- getTileIndex(int) - Method in class loci.formats.in.LOFReader
- getTileIndex(IFD, int, int) - Method in class loci.formats.in.MinimalTiffReader
-
Get the index of the tile corresponding to given IFD (plane) and tile XY indexes.
- getTileLength() - Method in class loci.formats.tiff.IFD
-
Returns the length of an image tile.
- getTileList(int, Region, boolean) - Method in class loci.formats.in.DicomReader
-
Get a list of tiles corresponding to the given plane.
- getTileRows() - Method in interface loci.formats.services.JPEGTurboService
- getTileRows() - Method in class loci.formats.services.JPEGTurboServiceImpl
- getTileRows(int) - Method in class loci.formats.FormatReader
- getTileRows(int) - Method in interface loci.formats.ICompressedTileReader
-
Get the number of rows of tiles in the specified plane in the current series.
- getTileRows(int) - Method in class loci.formats.ImageReader
- getTileRows(int) - Method in class loci.formats.in.DicomReader
- getTileRows(int) - Method in class loci.formats.in.NDPIReader
- getTileRows(int) - Method in class loci.formats.in.SVSReader
- getTileRows(int) - Method in class loci.formats.ReaderWrapper
- getTileRows(int) - Method in class loci.formats.TileStitcher
- getTiles() - Method in class loci.formats.in.DicomReader
- getTiles(int) - Method in class loci.formats.in.DicomReader
- getTileSize() - Method in class loci.formats.in.CellSensReader
-
Get the expected decompressed size of a single tile, in bytes.
- getTileSizeX() - Method in class loci.formats.FormatWriter
- getTileSizeX() - Method in interface loci.formats.IFormatWriter
-
Retrieves the current tile width Defaults to 0 if not supported
- getTileSizeX() - Method in class loci.formats.ImageWriter
- getTileSizeX() - Method in class loci.formats.out.DicomWriter
- getTileSizeX() - Method in class loci.formats.out.TiffWriter
- getTileSizeX() - Method in class loci.formats.WriterWrapper
- getTileSizeY() - Method in class loci.formats.FormatWriter
- getTileSizeY() - Method in interface loci.formats.IFormatWriter
-
Retrieves the current tile height Defaults to 0 if not supported
- getTileSizeY() - Method in class loci.formats.ImageWriter
- getTileSizeY() - Method in class loci.formats.out.DicomWriter
- getTileSizeY() - Method in class loci.formats.out.TiffWriter
- getTileSizeY() - Method in class loci.formats.WriterWrapper
- getTilesPerColumn() - Method in class loci.formats.tiff.IFD
-
Returns the number of image tiles per column.
- getTilesPerRow() - Method in class loci.formats.tiff.IFD
-
Returns the number of image tiles per row.
- getTileWidth() - Method in interface loci.formats.services.JPEGTurboService
- getTileWidth() - Method in class loci.formats.services.JPEGTurboServiceImpl
- getTileWidth() - Method in class loci.formats.tiff.IFD
-
Returns the width of an image tile.
- getTime(Double, String) - Static method in class loci.formats.FormatTools
-
Formats the input value for the time into a length of the given unit.
- getTimeBinCount() - Method in class loci.formats.in.SDTReader
-
Gets the number of bins in the lifetime histogram.
- GetTimepointOfPath(String) - Method in class loci.formats.in.SlideBook7Reader.CSBFile70
- getTimepoints() - Method in class loci.formats.in.ND2Handler
- getTimestamp() - Method in class loci.formats.in.DicomReader
- getTimestamp(String) - Method in class loci.formats.in.BDReader
- getTimestamp(String) - Method in class loci.formats.in.SlidebookTiffReader
- getTimestampIndex(String) - Method in class loci.formats.in.PCIReader
- getTimestampMicroseconds(String) - Method in class loci.formats.in.DicomReader
-
Convert the timestamp from a TM value to microseconds.
- getTimestamps() - Method in class loci.formats.in.MetamorphHandler
- getTotalPlaneHeaderSize() - Method in class loci.formats.in.DeltavisionReader
- getTransferSyntax() - Method in class loci.formats.out.DicomWriter
- getTransformedSizes() - Method in class org.libjpegturbo.turbojpeg.TJTransformer
-
Returns an array containing the sizes of the transformed JPEG images from the most recent call to
transform(). - getTreeCellRendererComponent(JTree, Object, boolean, boolean, boolean, int, boolean) - Method in class loci.formats.gui.XMLCellRenderer
- getTStep(int) - Method in class loci.plugins.in.ImporterOptions
- getTStep(int) - Method in class loci.plugins.in.ImportProcess
- getType() - Method in class loci.formats.cache.CacheEvent
-
Gets the type of cache update.
- getType() - Method in class loci.formats.gui.TwoChannelColorSpace
- getType() - Method in class loci.formats.in.PrairieMetadata.Sequence
-
Gets the
typeassociated with thisSequence. - getType() - Method in class loci.formats.tiff.TiffIFDEntry
-
Retrieves the entry's Type value.
- getType(Object, boolean) - Static method in enum class loci.formats.tiff.IFDType
-
Get the type corresponding to the given value.
- getUID() - Method in class loci.formats.out.DicomWriter.UIDCreator
- getUIDRoot() - Method in class loci.formats.out.DicomWriter
- getUnderlyingReaders() - Method in class loci.formats.FileStitcher
- getUnderlyingReaders() - Method in class loci.formats.FormatReader
- getUnderlyingReaders() - Method in interface loci.formats.IFormatReader
-
Retrieves all underlying readers.
- getUnderlyingReaders() - Method in class loci.formats.ImageReader
- getUnderlyingReaders() - Method in class loci.formats.ReaderWrapper
- getUnderlyingReaders() - Method in class loci.formats.WrappedReader
- getUngroupFilesInfo() - Method in class loci.plugins.in.ImporterOptions
- getUpgradeCheckInfo() - Method in class loci.plugins.in.ImporterOptions
- getUsedFile(Double, String[]) - Method in class loci.plugins.macro.LociFunctions
- getUsedFileCount(Double[]) - Method in class loci.plugins.macro.LociFunctions
- getUsedFiles() - Method in class loci.formats.FileStitcher
- getUsedFiles() - Method in class loci.formats.FormatReader
- getUsedFiles() - Method in interface loci.formats.IFormatReader
-
Returns an array of filenames needed to open this dataset.
- getUsedFiles() - Method in class loci.formats.ImageReader
- getUsedFiles() - Method in class loci.formats.ReaderWrapper
- getUsedFiles(boolean) - Method in class loci.formats.FileStitcher
- getUsedFiles(boolean) - Method in class loci.formats.FormatReader
- getUsedFiles(boolean) - Method in interface loci.formats.IFormatReader
-
Returns an array of filenames needed to open this dataset.
- getUsedFiles(boolean) - Method in class loci.formats.ImageReader
- getUsedFiles(boolean) - Method in class loci.formats.in.BDVReader
- getUsedFiles(boolean) - Method in class loci.formats.in.CellomicsReader
- getUsedFiles(boolean) - Method in class loci.formats.in.CV7000Reader
- getUsedFiles(boolean) - Method in class loci.formats.in.FilePatternReader
- getUsedFiles(boolean) - Method in class loci.formats.in.InveonReader
- getUsedFiles(boolean) - Method in class loci.formats.in.KLBReader
- getUsedFiles(boolean) - Method in class loci.formats.in.MetamorphTiffReader
- getUsedFiles(boolean) - Method in class loci.formats.in.MetaxpressTiffReader
- getUsedFiles(boolean) - Method in class loci.formats.in.OperettaReader
- getUsedFiles(boolean) - Method in class loci.formats.in.SlideBook7Reader
- getUsedFiles(boolean) - Method in class loci.formats.in.TecanReader
- getUsedFiles(boolean) - Method in class loci.formats.in.UnisokuReader
- getUsedFiles(boolean) - Method in class loci.formats.in.XLEFReader
- getUsedFiles(boolean) - Method in class loci.formats.ReaderWrapper
- getUsedFiles(boolean) - Method in class loci.formats.WrappedReader
- getUUID(String) - Method in class loci.formats.in.ImprovisionTiffReader
- getUUID(String) - Method in class loci.formats.out.OMETiffWriter
-
Gets the UUID corresponding to the given filename.
- getValue() - Method in enum class loci.formats.in.BaseZeissReader.Charset
- getValue() - Method in enum class loci.formats.in.BaseZeissReader.DrawStyle
- getValue() - Method in enum class loci.formats.in.BaseZeissReader.FeatureType
- getValue() - Method in enum class loci.formats.in.BaseZeissReader.FillStyle
- getValue() - Method in enum class loci.formats.in.BaseZeissReader.LineEndPositions
- getValue() - Method in enum class loci.formats.in.BaseZeissReader.LineEndStyle
- getValue() - Method in enum class loci.formats.in.BaseZeissReader.PointStyle
- getValue() - Method in class loci.formats.in.BaseZeissReader.Tag
- getValue() - Method in enum class loci.formats.in.BaseZeissReader.TextAlignment
- getValue() - Method in class loci.plugins.prefs.BooleanOption
-
Gets the current value of the option.
- getValue() - Method in class loci.plugins.prefs.DoubleOption
-
Gets the current value of the option.
- getValue() - Method in class loci.plugins.prefs.StringOption
-
Gets the current value of the option.
- getValue(String) - Method in class loci.formats.in.PrairieMetadata.Frame
-
Gets the
valueof the givenkey, beneath thisFrame, inferring the value from the parent<Sequence>or grandparent<PVScan>section as needed. - getValue(String) - Method in class loci.formats.in.PrairieMetadata
-
Gets the
valueof the givenkey, at the top-level<PVScan>element. - getValue(String) - Method in class loci.formats.in.PrairieMetadata.Sequence
-
Gets the
valueof the givenkey, beneath thisSequence, inferring the value from the parent<PVScan>section as needed. - getValue(String) - Method in class loci.plugins.prefs.OptionsList
-
Gets the value of the string option with the given key.
- getValue(IRandomAccess) - Method in class loci.formats.in.IM3Reader.StringIM3Record
-
Return the string value for this record
- getValueCount() - Method in class loci.formats.tiff.TiffIFDEntry
-
Retrieves the entry's ValueCount value.
- getValueForKey() - Method in class loci.formats.meta.OriginalMetadataAnnotation
-
Return just the value (i.e.
- getValueOffset() - Method in class loci.formats.tiff.TiffIFDEntry
-
Retrieves the entry's ValueOffset value.
- getValues() - Method in class loci.formats.in.PrairieMetadata.Frame
-
Gets the table of
Framekey/value pairs. - getValues() - Method in class loci.formats.in.PrairieMetadata
-
Gets the table of
PVScankey/value pairs. - getValues() - Method in class loci.formats.in.PrairieMetadata.Sequence
-
Gets the table of
Framekey/value pairs. - getValueStartPointer() - Method in class loci.formats.dicom.DicomTag
-
Get the file pointer at which the value starts (useful for sequences and byte streams).
- getVariableAttributes(String) - Method in interface loci.formats.services.NetCDFService
-
Retrieves all of a variable's attributes.
- getVariableAttributes(String) - Method in class loci.formats.services.NetCDFServiceImpl
- getVariableList() - Method in interface loci.formats.services.NetCDFService
-
Retrieves an exhaustive list of the HDF paths for all variables in the HDF document.
- getVariableList() - Method in class loci.formats.services.NetCDFServiceImpl
- getVariableValue(String) - Method in interface loci.formats.services.NetCDFService
-
Retrieves a variable's value.
- getVariableValue(String) - Method in class loci.formats.services.NetCDFServiceImpl
- getVersion() - Method in class loci.formats.in.LiFlimReader
- getVersionNumber(String[]) - Method in class loci.plugins.macro.LociFunctions
- getVirtualInfo() - Method in class loci.plugins.in.ImporterOptions
- getVirtualReader() - Method in class loci.plugins.in.ImportProcess
-
Valid only after
ImportStep.STACK. - getVoltage() - Method in class loci.formats.in.ND2Handler
- getVolumeName(int) - Method in class loci.formats.in.CellSensReader
- GetVoxelSize() - Method in class loci.formats.in.SlideBook7Reader.CImageGroup
- getWaitTime() - Method in class loci.formats.in.PrairieMetadata
-
Gets the
waitTimerecorded in the configuration. - getWavelength(Double) - Static method in class loci.formats.FormatTools
- getWavelength(Double, String) - Static method in class loci.formats.FormatTools
-
Formats the input value for the wavelength into a length of the given unit.
- getWavelengthMax() - Method in class loci.formats.in.PrairieMetadata.PFile
-
Gets the
wavelengthMaxassociated with thisFile. - getWavelengthMin() - Method in class loci.formats.in.PrairieMetadata.PFile
-
Gets the
wavelengthMinassociated with thisFile. - getWavelengths() - Method in class loci.formats.in.IM3Reader.Spectrum
- getWavelengths() - Method in class loci.formats.in.MetamorphHandler
- getWell(int) - Method in class loci.formats.in.CellWorxReader
-
Retrieve the well index corresponding to the given series.
- getWell(int) - Method in class loci.formats.in.MetamorphTiffReader
- getWell(String) - Method in class loci.formats.in.FlexReader
-
Returns a two-element array containing the well row and well column corresponding to the given file.
- getWellColumn(int) - Method in class loci.formats.in.CellWorxReader
-
Retrieve the well column corresponding to the given series.
- getWellColumn(String) - Method in class loci.formats.in.CellomicsReader
- getWellColumn(String) - Method in class loci.formats.in.MetamorphTiffReader
- getWellCoords(String) - Method in class loci.formats.in.MetamorphReader
- getWellFromSeries(int) - Method in class loci.formats.in.InCellReader
- getWellIndex() - Method in class loci.formats.internal.WellContainer
- getWellLabels(Connection) - Method in class loci.formats.in.TecanReader
- getWellLink(PreparedStatement, String) - Method in class loci.formats.in.TecanReader
-
Get the well identifier and field indexfor the given Id in the ImagingResult table.
- getWellName(int, int) - Static method in class loci.formats.FormatTools
-
Create a simple name for the well at the given row and column.
- getWellName(String) - Method in class loci.formats.in.CellomicsReader
- getWellRow(int) - Method in class loci.formats.in.CellWorxReader
-
Retrieve the well row corresponding to the given series.
- getWellRow(String) - Method in class loci.formats.in.CellomicsReader
- getWellRow(String) - Method in class loci.formats.in.MetamorphTiffReader
- getWellRowName(int) - Static method in class loci.formats.FormatTools
-
Create a simple name for the given row of wells.
- getWidgets() - Method in class loci.plugins.config.CellSensWidgets
- getWidgets() - Method in interface loci.plugins.config.IFormatWidgets
- getWidgets() - Method in class loci.plugins.config.LIFWidgets
- getWidgets() - Method in class loci.plugins.config.ND2Widgets
- getWidgets() - Method in class loci.plugins.config.SDTWidgets
- getWidgets() - Method in class loci.plugins.config.TiffDelegateWidgets
- getWidgets() - Method in class loci.plugins.config.ZeissCZIWidgets
- getWidth() - Method in class loci.formats.codec.JPEGTileDecoder
- getWidth() - Method in enum class loci.formats.dicom.DicomVR
- getWidth() - Method in class loci.plugins.util.BFVirtualStack
- getWidth() - Method in class loci.plugins.util.RecordedImageProcessor
- getWidth() - Method in class org.libjpegturbo.turbojpeg.TJDecompressor
-
Returns the width of the JPEG image associated with this decompressor instance.
- getWidth(IFormatReader, String, int) - Static method in class loci.plugins.util.BFVirtualStack
- getWindowlessInfo() - Method in class loci.plugins.in.ImporterOptions
- getWrapped() - Method in class loci.formats.codec.BitBuffer
-
Deprecated.
- getWrapped() - Method in class loci.formats.codec.BitWriter
-
Deprecated.
- getWrapped() - Method in class loci.formats.codec.ByteVector
- getWrapped() - Method in class loci.formats.codec.JPEGTileDecoder
- getWriter() - Method in class loci.formats.ImageWriter
-
Gets the writer used to save the current file.
- getWriter() - Method in class loci.formats.WriterWrapper
-
Gets the wrapped writer.
- getWriter(Class<? extends IFormatWriter>) - Method in class loci.formats.ImageWriter
-
Gets the file format writer instance matching the given class.
- getWriter(String) - Method in class loci.formats.ImageWriter
-
Gets the writer used to save the given file.
- getWriters() - Method in class loci.formats.ImageWriter
-
Gets all constituent file format writers.
- getX(double[]) - Method in class loci.formats.in.TextReader
- getX(int) - Method in class loci.formats.in.FakeReader
- getXFields() - Method in class loci.formats.in.ND2Handler
- getXlifs() - Method in class loci.formats.in.LeicaMicrosystemsMetadata.LMSCollectionXmlDocument
-
Returns all XlifDocuments referenced by this and by all referenced XlcfDocuments
- getXML() - Method in class loci.formats.tools.EditTiffG
- GetXPosition(int) - Method in class loci.formats.in.SlideBook7Reader.CImageGroup
- getXPositions() - Method in class loci.formats.in.ND2Handler
- getXResolution() - Method in class loci.formats.tiff.IFD
-
Retrieve the X resolution (TIFF tag XResolution) from this IFD.
- getY(double[]) - Method in class loci.formats.in.TextReader
- getY(int) - Method in class loci.formats.in.FakeReader
- getYesNo(RandomAccessInputStream) - Method in class loci.formats.in.ZeissXRMReader
- GetYPosition(int) - Method in class loci.formats.in.SlideBook7Reader.CImageGroup
- getYPositions() - Method in class loci.formats.in.ND2Handler
- getYResolution() - Method in class loci.formats.tiff.IFD
-
Retrieve the Y resolution (TIFF tag YResolution) from this IFD.
- getZ() - Method in class loci.formats.gui.ImageViewer
-
Gets the Z value of the currently displayed image.
- getZ(String) - Method in class loci.formats.in.OIRReader
- getZBegin(int) - Method in class loci.plugins.in.ImporterOptions
- getZBegin(int) - Method in class loci.plugins.in.ImportProcess
- getZCount(int) - Method in class loci.plugins.in.ImportProcess
-
Valid only after
ImportStep.SERIES. - getZCTCoords(int) - Method in class loci.formats.ChannelMerger
- getZCTCoords(int) - Method in class loci.formats.ChannelSeparator
- getZCTCoords(int) - Method in class loci.formats.DimensionSwapper
- getZCTCoords(int) - Method in class loci.formats.FileStitcher
- getZCTCoords(int) - Method in class loci.formats.FormatReader
- getZCTCoords(int) - Method in interface loci.formats.IFormatReader
-
Gets the Z, C and T coordinates (real sizes) corresponding to the given rasterized index value.
- getZCTCoords(int) - Method in class loci.formats.ImageReader
- getZCTCoords(int) - Method in class loci.formats.out.DicomWriter
- getZCTCoords(int) - Method in class loci.formats.ReaderWrapper
- getZCTCoords(int) - Method in class loci.formats.WrappedReader
- getZCTCoords(Double, Double[], Double[], Double[]) - Method in class loci.plugins.macro.LociFunctions
- getZCTCoords(String, int, int, int, int, int) - Static method in class loci.formats.FormatTools
-
Gets the Z, C and T coordinates corresponding to the given rasterized index value (real sizes).
- getZCTCoords(String, int, int, int, int, int, int, int, int) - Static method in class loci.formats.FormatTools
-
Gets the Z, C and T coordinates corresponding to the given rasterized index value.
- getZCTCoords(IFormatReader, int) - Static method in class loci.formats.FormatTools
-
Gets the Z, C and T coordinates corresponding to the given rasterized index value (real sizes).
- getZCTModuloCoords(int) - Method in class loci.formats.ChannelMerger
- getZCTModuloCoords(int) - Method in class loci.formats.ChannelSeparator
- getZCTModuloCoords(int) - Method in class loci.formats.DimensionSwapper
- getZCTModuloCoords(int) - Method in class loci.formats.FileStitcher
- getZCTModuloCoords(int) - Method in class loci.formats.FormatReader
- getZCTModuloCoords(int) - Method in interface loci.formats.IFormatReader
-
Gets the Z, C, T, moduloZ, moduloC and moduloT coordinates (effective sizes) corresponding to the given rasterized index value.
- getZCTModuloCoords(int) - Method in class loci.formats.ImageReader
- getZCTModuloCoords(int) - Method in class loci.formats.ReaderWrapper
- getZCTModuloCoords(IFormatReader, int) - Static method in class loci.formats.FormatTools
-
Gets the Z, C, T, ModuloZ, ModuloC and ModuloZ coordinates corresponding to the given rasterized index value (effective sizes).
- getZEnd(int) - Method in class loci.plugins.in.ImporterOptions
- getZEnd(int) - Method in class loci.plugins.in.ImportProcess
-
Valid only after
ImportStep.STACK. - getZeroOffset(ImagePlus) - Static method in class loci.plugins.in.Colorizer
- getZOffsets() - Method in class loci.formats.in.DicomReader
- getZOffsets(int) - Method in class loci.formats.in.DicomReader
- getZoom() - Method in class loci.formats.in.MetamorphHandler
- GetZPosition(int, int) - Method in class loci.formats.in.SlideBook7Reader.CImageGroup
- getZPositions() - Method in class loci.formats.in.MetamorphHandler
- getZPositions() - Method in class loci.formats.in.ND2Handler
- getZSections() - Method in class loci.formats.in.ND2Handler
- getZStep(int) - Method in class loci.plugins.in.ImporterOptions
- getZStep(int) - Method in class loci.plugins.in.ImportProcess
- GIF_MAGIC_STRING - Static variable in class loci.formats.in.GIFReader
- GIFReader - Class in loci.formats.in
-
GIFReader is the file format reader for Graphics Interchange Format (GIF) files.
- GIFReader() - Constructor for class loci.formats.in.GIFReader
-
Constructs a new GIF reader.
- global - Variable in class loci.formats.in.BMPReader
-
Offset to image data.
- globalMetadata - Variable in class loci.formats.in.LeicaHandler
- gradient(int, int, int) - Method in class loci.formats.tools.MakeTestOmeTiff
- GRADIENT_LUT - Static variable in class loci.formats.in.CellSensReader
- GRAPHICS - Static variable in class loci.formats.in.GIFReader
- GRAPHICS_DOMAIN - Static variable in class loci.formats.FormatTools
-
Identifies the graphics domain.
- GRAY_ALPHA - Static variable in class loci.formats.in.APNGReader
- GRAY_DOUBLE - Static variable in class loci.formats.in.ZeissCZIReader
- GRAY_FLOAT - Static variable in class loci.formats.in.ZeissCZIReader
- GRAY_RESPONSE_CURVE - Static variable in class loci.formats.tiff.IFD
- GRAY_RESPONSE_UNIT - Static variable in class loci.formats.tiff.IFD
- GRAY16 - Static variable in class loci.formats.in.ZeissCZIReader
- GRAY32 - Static variable in class loci.formats.in.ZeissCZIReader
- GRAY8 - Static variable in class loci.formats.in.ZeissCZIReader
-
Pixel type constants.
- GRAYSCALE - Static variable in class loci.formats.in.APNGReader
-
Color types.
- GREEK_CHARSET - Enum constant in enum class loci.formats.in.BaseZeissReader.Charset
- GREEN - Enum constant in enum class loci.formats.in.LeicaMicrosystemsMetadata.Channel.ChannelType
- GREEN_GAIN - Static variable in class loci.formats.in.CellSensReader
- GREEN_LUT_DATA - Enum constant in enum class loci.formats.dicom.DicomAttribute
- GREEN_LUT_DESCRIPTOR - Enum constant in enum class loci.formats.dicom.DicomAttribute
- GREEN_MULTIPLIER - Static variable in class loci.formats.in.NDPIReader
- GREEN_OFFSET - Static variable in class loci.formats.in.CellSensReader
- GREEN_TO_RED_MIN - Static variable in class loci.plugins.in.Colorizer
- greenGain - Variable in class loci.formats.in.CellSensReader.Pyramid
- greenOffset - Variable in class loci.formats.in.CellSensReader.Pyramid
- greenOffset - Static variable in class org.libjpegturbo.turbojpeg.TJ
- greenShort - Variable in class loci.formats.gui.Index16ColorModel
-
Lookup tables.
- GREYSCALE_COMPRESSION - Static variable in class loci.formats.in.FlowSightReader
- GRID - Enum constant in enum class loci.formats.dicom.DicomAttribute
- GRID - Static variable in class loci.formats.in.FV1000Reader
- GRID_ABSORBING_MATERIAL - Enum constant in enum class loci.formats.dicom.DicomAttribute
- GRID_ASPECT_RATIO - Enum constant in enum class loci.formats.dicom.DicomAttribute
- GRID_FOCAL_DISTANCE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- GRID_PERIOD - Enum constant in enum class loci.formats.dicom.DicomAttribute
- GRID_PITCH - Enum constant in enum class loci.formats.dicom.DicomAttribute
- GRID_SPACING_MATERIAL - Enum constant in enum class loci.formats.dicom.DicomAttribute
- GRID_THICKNESS - Enum constant in enum class loci.formats.dicom.DicomAttribute
- GRIDSIZE_OFFSET - Static variable in class loci.formats.in.MRCReader
- group - Variable in class loci.formats.FileStitcher
- group - Variable in class loci.formats.FormatReader
-
Whether or not to group multi-file formats.
- GROUP - Static variable in class loci.formats.in.GatanReader
-
Tag types.
- GROUP_3_FAX - Enum constant in enum class loci.formats.tiff.TiffCompression
- GROUP_4_FAX - Enum constant in enum class loci.formats.tiff.TiffCompression
- groupFiles() - Method in class loci.formats.in.TCSReader
- groupFiles(String[], MetadataStore) - Method in class loci.formats.in.FlexReader
- groupFilesBox - Variable in class loci.plugins.in.MainDialog
- groupX - Variable in class loci.formats.in.SPEReader.SpeROI
- groupY - Variable in class loci.formats.in.SPEReader.SpeROI
- GUITools - Class in loci.formats.gui
-
A utility class for working with graphical user interfaces.
- GUITools() - Constructor for class loci.formats.gui.GUITools
- gz - Variable in class loci.formats.in.LiFlimReader
-
Stream to use for reading gzip-compressed pixel data.
- gzip - Variable in class loci.formats.in.ICSReader
-
Whether or not the pixels are GZIP-compressed.
- gzip - Variable in class loci.formats.in.LiFlimReader
-
True if gzip compression was used to deflate the pixels.
- gzip - Variable in class loci.formats.in.NRRDReader
- gzipStream - Variable in class loci.formats.in.ICSReader
- gzPos - Variable in class loci.formats.in.LiFlimReader
-
Image number indicating position in gzip stream.
- gzSeries - Variable in class loci.formats.in.LiFlimReader
-
Series number indicating position in gzip stream.
H
- H_263 - Enum constant in enum class loci.formats.codec.CompressionType
- H5Constants() - Constructor for class loci.formats.in.BDVReader.H5Constants
- H5Coordinate(String, String, String) - Constructor for class loci.formats.in.BDVReader.H5Coordinate
- h5Id - Variable in class loci.formats.in.BDVReader
- H5PathsToImageData - Variable in class loci.formats.in.BDVReader
- H5PositionList - Variable in class loci.formats.in.BDVReader
- HALFTONE_HINTS - Static variable in class loci.formats.tiff.IFD
- HamamatsuVMSReader - Class in loci.formats.in
-
HamamatsuVMSReader is the file format reader for Hamamatsu VMS datasets.
- HamamatsuVMSReader() - Constructor for class loci.formats.in.HamamatsuVMSReader
-
Constructs a new Hamamatsu VMS reader.
- handle - Variable in class org.libjpegturbo.turbojpeg.TJCompressor
- handle - Variable in class org.libjpegturbo.turbojpeg.TJDecompressor
- handleBitmap(int) - Method in class loci.formats.in.PictReader
-
Extract the image data in a PICT bitmap structure.
- handleExtension(String, Object[]) - Method in class loci.plugins.macro.MacroFunctions
- handleFilter(Element, int) - Method in class loci.formats.in.VectraReader
- handleKeyValue(String, String) - Method in class loci.formats.in.MicromanagerReader
-
Process a piece of metadata represented by a key/value pair.
- handleMetadataStore(IFormatReader) - Method in class loci.formats.Memoizer
-
Return the
IFormatReaderinstance that is passed in or null if it has been invalidated, which will include the instance being closed. - handlePixmap(int) - Method in class loci.formats.in.PictReader
-
Extracts the image data in a PICT pixmap structure.
- handlePixmap(int, int) - Method in class loci.formats.in.PictReader
-
Handles the unpacking of the image data.
- handler - Variable in class loci.formats.in.LeicaSCNReader
- handler - Variable in class loci.formats.in.NikonElementsTiffReader
- handler - Variable in class loci.formats.in.ZeissTIFFReader.TIFFInfo
- handleReferencedFile(DicomTag, String) - Method in class loci.formats.in.DicomReader
- handleSize - Variable in class loci.formats.in.BaseZeissReader.Shape
- handleTXMMetadata(String, RandomAccessInputStream) - Method in class loci.formats.in.ZeissXRMReader
-
Parse metadata fields specific to .txm files.
- handleTXRMMetadata(String, RandomAccessInputStream) - Method in class loci.formats.in.ZeissXRMReader
-
Parse metadata fields specific to .txrm files.
- HANGUL_CHARSET - Enum constant in enum class loci.formats.in.BaseZeissReader.Charset
- HARDCOPY_CREATION_DEVICE_ID - Enum constant in enum class loci.formats.dicom.DicomAttribute
- HARDCOPY_DEVICE_MANUFACTURER - Enum constant in enum class loci.formats.dicom.DicomAttribute
- HARDCOPY_DEVICE_MODEL_NAME - Enum constant in enum class loci.formats.dicom.DicomAttribute
- HARDCOPY_DEVICE_SOFTWARE_VERSION - Enum constant in enum class loci.formats.dicom.DicomAttribute
- HARMONY_MAGIC - Static variable in class loci.formats.in.OperettaReader
- harvestResults(GenericDialog) - Method in class loci.plugins.in.ColorDialog
- harvestResults(GenericDialog) - Method in class loci.plugins.in.CropDialog
- harvestResults(GenericDialog) - Method in class loci.plugins.in.FilePatternDialog
- harvestResults(GenericDialog) - Method in class loci.plugins.in.IdDialog
- harvestResults(GenericDialog) - Method in class loci.plugins.in.ImporterDialog
- harvestResults(GenericDialog) - Method in class loci.plugins.in.LocationDialog
- harvestResults(GenericDialog) - Method in class loci.plugins.in.MainDialog
- harvestResults(GenericDialog) - Method in class loci.plugins.in.MemoryDialog
- harvestResults(GenericDialog) - Method in class loci.plugins.in.RangeDialog
- harvestResults(GenericDialog) - Method in class loci.plugins.in.SeriesDialog
- harvestResults(GenericDialog) - Method in class loci.plugins.in.SwapDialog
- harvestResults(GenericDialog) - Method in class loci.plugins.in.UpgradeDialog
- HAS_EXTERNAL_FILE - Static variable in class loci.formats.in.CellSensReader
- hasAbsoluteZ - Variable in class loci.formats.in.MetamorphReader
- hasAbsoluteZValid - Variable in class loci.formats.in.MetamorphReader
- HasAssociatedEtsFile - Variable in class loci.formats.in.CellSensReader.Pyramid
- hasChipOffsets - Variable in class loci.formats.in.MetamorphReader
- hasCompanionFiles - Variable in class loci.formats.FormatReader
-
Whether this format supports multi-file datasets.
- hasCompanionFiles() - Method in class loci.formats.FormatReader
- hasCompanionFiles() - Method in interface loci.formats.IFormatReader
-
Returns true if this format supports multi-file datasets.
- hasCompanionFiles() - Method in class loci.formats.ImageReader
- hasCompanionFiles() - Method in class loci.formats.in.FilePatternReader
- hasCompanionFiles() - Method in class loci.formats.ReaderWrapper
- hasCompanionFiles() - Method in class loci.formats.WrappedReader
- hasDetectorSettings - Variable in class loci.formats.in.ZeissCZIReader
- hasDualCamera() - Method in class loci.formats.in.MetamorphHandler
- hasExtendedMeasureInfo - Variable in class loci.formats.in.SDTInfo
- hasFlattenedResolutions() - Method in class loci.formats.FormatReader
- hasFlattenedResolutions() - Method in interface loci.formats.IFormatReader
-
Return whether or not resolution flattening is enabled.
- hasFlattenedResolutions() - Method in class loci.formats.ImageReader
- hasFlattenedResolutions() - Method in class loci.formats.in.FilePatternReader
- hasFlattenedResolutions() - Method in class loci.formats.ReaderWrapper
- hashCode - Variable in class loci.formats.in.OIRReader.CZTKey
- hashCode() - Method in class loci.formats.in.CV7000Reader.Field
- hashCode() - Method in class loci.formats.in.MetamorphTiffReader.Well
- hashCode() - Method in class loci.formats.in.OIRReader.CZTKey
- hashCode() - Method in class loci.formats.in.ZeissCZIReader.Coordinate
- hashCode() - Method in class loci.formats.tiff.TiffRational
-
Reasonable hash value for use with hashtables.
- hashCode() - Method in class loci.plugins.config.FormatEntry
- hashCode() - Method in class loci.plugins.prefs.OptionsList
- hasInstrumentData - Variable in class loci.formats.in.ICSReader
- hasMeasFCSInfo - Variable in class loci.formats.in.SDTInfo
- hasMeasHISTInfo - Variable in class loci.formats.in.SDTInfo
- hasMeasStopInfo - Variable in class loci.formats.in.SDTInfo
- hasMeasureInfo - Variable in class loci.formats.in.SDTInfo
- hasPaddingByte - Variable in class loci.formats.in.IvisionReader
- hasPlaneReader - Variable in class loci.formats.in.AmiraReader
- hasResolutions() - Method in class loci.formats.FormatWriter
- hasSPW - Variable in class loci.formats.in.OMETiffReader
- hasSPW - Variable in class loci.formats.in.OMEXMLReader
- hasStagePositions - Variable in class loci.formats.in.MetamorphReader
- HCS_DOMAIN - Static variable in class loci.formats.FormatTools
-
Identifies the high content screening domain.
- HDF_MAGIC_STRING - Static variable in class loci.formats.in.BDVReader
- HDF_MAGIC_STRING - Static variable in class loci.formats.in.CellH5Reader
- HDF_MAGIC_STRING - Static variable in class loci.formats.in.ImarisHDFReader
- hdfReader - Variable in class loci.formats.services.JHDFServiceImpl
-
Root of the HDF5 file.
- hdfWriter - Variable in class loci.formats.services.JHDFServiceImpl
-
Root of the HDF5 file.
- HDRI_EXPOSURE_RANGE - Static variable in class loci.formats.in.CellSensReader
- HDRI_FRAMES - Static variable in class loci.formats.in.CellSensReader
- HDRI_MAP_MODE - Static variable in class loci.formats.in.CellSensReader
- HDRI_ON - Static variable in class loci.formats.in.CellSensReader
- header - Variable in class loci.formats.in.SPEReader
- header - Variable in class loci.formats.in.SPEReader.SpeHeader
- header - Variable in class loci.formats.services.JPEGTurboServiceImpl
- HEADER - Enum constant in enum class loci.formats.codec.JPEG2000BoxType
- HEADER - Static variable in class loci.formats.in.InveonReader
- HEADER_LENGTH - Static variable in class loci.formats.in.DeltavisionReader
- HEADER_LENGTH - Static variable in class loci.formats.in.DicomReader
- HEADER_MARKER - Static variable in class loci.formats.in.VisitechReader
- HEADER_SIZE - Static variable in class loci.formats.in.Ecat7Reader
- HEADER_SIZE - Static variable in class loci.formats.in.GatanDM2Reader
- HEADER_SIZE - Static variable in class loci.formats.in.I2IReader
- HEADER_SIZE - Static variable in class loci.formats.in.INRReader
- HEADER_SIZE - Static variable in class loci.formats.in.MRCReader
- HEADER_SIZE - Static variable in class loci.formats.in.OpenlabRawReader
- HEADER_SIZE - Static variable in class loci.formats.in.PovrayReader
- HEADER_SIZE - Static variable in class loci.formats.in.PQBinReader
- HEADER_SIZE - Static variable in class loci.formats.in.RHKReader
- HEADER_SIZE - Static variable in class loci.formats.in.SBIGReader
- HEADER_SIZE - Static variable in class loci.formats.in.SeikoReader
- HEADER_SIZE - Static variable in class loci.formats.in.SMCameraReader
- HEADER_SIZE - Static variable in class loci.formats.in.UBMReader
- HEADER_SIZE - Static variable in class loci.formats.in.WATOPReader
- HEADER_SIZE - Static variable in class loci.formats.in.ZeissCZIReader
- HEADER_VER - Enum constant in enum class loci.formats.in.SPEReader.SpeHeaderEntry
- headerIFDs - Variable in class loci.formats.in.LeicaReader
-
Array of IFD-like structures containing metadata.
- headerPixelType - Variable in class loci.formats.in.JPEG2000MetadataParser
-
Pixel type as specified in the header.
- headerSize - Variable in class loci.formats.in.DCIMGReader
- headerSize - Variable in class loci.formats.in.FEIReader
- headerSize - Variable in class loci.formats.in.KLBReader
- headerSize - Variable in class loci.formats.in.MicroCTReader
- headerSize - Variable in class loci.formats.in.OxfordInstrumentsReader
- headerSize - Static variable in class loci.formats.in.SPEReader.SpeHeader
- headerSize - Variable in class loci.formats.in.SpiderReader
- headerSizeC - Variable in class loci.formats.in.JPEG2000MetadataParser
-
Number of channels the image has as specified in the header.
- headerSizeX - Variable in class loci.formats.in.JPEG2000MetadataParser
-
Width of the image as specified in the header.
- headerSizeY - Variable in class loci.formats.in.JPEG2000MetadataParser
-
Height of the image as specified in the header.
- headerValid - Variable in class loci.formats.in.SDTInfo
- headerVersion - Variable in class loci.formats.in.KLBReader
- HEART_RATE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- HEBREW_CHARSET - Enum constant in enum class loci.formats.in.BaseZeissReader.Charset
- height - Variable in class loci.formats.codec.CodecOptions
-
Height, in pixels, of the image.
- height - Variable in class loci.formats.in.BaseZeissReader.Shape
- height - Variable in class loci.formats.in.CellSensReader.Pyramid
- height - Variable in class loci.formats.in.CellVoyagerReader.AreaInfo
- height - Variable in class loci.formats.in.CellVoyagerReader.ChannelInfo
- height - Variable in class loci.formats.in.OpenlabReader.PlaneInfo
- height - Variable in class loci.formats.in.SDTInfo
- height - Variable in class loci.formats.tools.AmiraParameters
- HEIGHT - Enum constant in enum class loci.formats.in.SPEReader.SpeHeaderEntry
- HELIOS_TAG - Static variable in class loci.formats.in.FEITiffReader
- HELP_MENU - Static variable in class loci.plugins.shortcut.ShortcutPanel
-
Name of the 'About Plugins' submenu.
- helper - Variable in class loci.formats.gui.SignedColorModel
- helper - Variable in class loci.formats.gui.SignedShortBuffer
- helper - Variable in class loci.formats.gui.UnsignedIntColorModel
- helper - Variable in class loci.formats.in.FilePatternReader
- helper - Variable in class loci.formats.in.JDCEReader
- helper - Variable in class loci.formats.in.NRRDReader
-
Helper reader.
- helperReader - Variable in class loci.formats.in.HitachiReader
- helperReader - Variable in class loci.formats.in.OlympusTileReader
- helperReader - Variable in class loci.formats.in.TecanReader
- hex2Rgb(String) - Static method in class loci.formats.in.BDVReader
- hex2Rgb(String) - Static method in class loci.formats.in.CellH5Reader
- HIDDEN_LAYER - Static variable in class loci.formats.in.CellSensReader
- HIGH_BIT - Enum constant in enum class loci.formats.dicom.DicomAttribute
- HIGH_PRIORITY - Static variable in interface loci.formats.cache.ICacheStrategy
- HIGH_RR_VALUE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- HIS_MAGIC_STRING - Static variable in class loci.formats.in.HISReader
- HISReader - Class in loci.formats.in
-
HISReader is the file format reader for Hamamatsu .his files.
- HISReader() - Constructor for class loci.formats.in.HISReader
-
Constructs a new Hamamatsu .his reader.
- HISTOLOGY_DOMAIN - Static variable in class loci.formats.FormatTools
-
Identifies the histology domain.
- HISTORY_KEYS - Static variable in class loci.formats.in.ICSReader
- HitachiReader - Class in loci.formats.in
-
HitachiReader is the file format reader for S-4800 files.
- HitachiReader() - Constructor for class loci.formats.in.HitachiReader
-
Constructs a new Hitachi reader.
- HORIZONTAL_FLIP - Static variable in class loci.formats.in.FluoviewReader
- HORIZONTAL_LINE - Enum constant in enum class loci.formats.in.BaseZeissReader.FillStyle
- HOST_COMPUTER - Static variable in class loci.formats.tiff.IFD
- hostnames - Variable in class loci.formats.in.FlexReader.MeaHandler
- HOT_PIXEL_CORRECTION - Static variable in class loci.formats.in.CellSensReader
- HRDGDFReader - Class in loci.formats.in
-
HRDGDFReader is the file format reader for the Gridded Data Format used by NOAA's Hurricane Research Division.
- HRDGDFReader() - Constructor for class loci.formats.in.HRDGDFReader
-
Constructs a new Gridded Data Format reader.
- HTM_SUFFIX - Static variable in class loci.formats.in.PerkinElmerReader
- HTML_REGEX - Static variable in class loci.formats.in.PerkinElmerReader
- HTML_SUFFIX - Static variable in class loci.formats.in.VisitechReader
- HUE - Static variable in class loci.formats.in.NikonReader
- HuffmanCodec - Class in loci.formats.codec
-
This class implements Huffman decoding.
- HuffmanCodec() - Constructor for class loci.formats.codec.HuffmanCodec
- HuffmanCodecOptions - Class in loci.formats.codec
-
Options for compressing and decompressing Huffman data.
- HuffmanCodecOptions() - Constructor for class loci.formats.codec.HuffmanCodecOptions
- humidity - Variable in class loci.formats.in.ZeissCZIReader
- HW_ACCUM - Enum constant in enum class loci.formats.in.SPEReader.SpeHeaderEntry
- HxRLE(int, long) - Constructor for class loci.formats.in.AmiraReader.HxRLE
- HxZip(long) - Constructor for class loci.formats.in.AmiraReader.HxZip
I
- i(String) - Method in class loci.formats.in.PrairieMetadata
-
Converts the given string to an
Integer, or null if incompatible. - I2IReader - Class in loci.formats.in
-
I2IReader is the file format reader for I2I files.
- I2IReader() - Constructor for class loci.formats.in.I2IReader
-
Constructs a new I2I reader.
- ICacheSource - Interface in loci.formats.cache
-
Interface for cache sources.
- ICacheStrategy - Interface in loci.formats.cache
-
Interface for cache strategies.
- ICC_ENABLED - Static variable in class loci.formats.in.CellSensReader
- ICC_PROFILE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- ICompressedTileReader - Interface in loci.formats
-
Interface for reading pre-compressed image tiles.
- ICompressedTileWriter - Interface in loci.formats
-
Interface for writing pre-compressed image tiles.
- icon - Variable in class loci.formats.gui.ImageViewer
- icon - Variable in class loci.formats.gui.PreviewPane
- ICON_IMAGE_SEQUENCE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- iconLabel - Variable in class loci.formats.gui.ImageViewer
- iconLabel - Variable in class loci.formats.gui.PreviewPane
-
Labels containing thumbnail and dimensional information.
- iconText - Variable in class loci.formats.gui.PreviewPane
- iconTip - Variable in class loci.formats.gui.PreviewPane
- ICSReader - Class in loci.formats.in
-
ICSReader is the file format reader for ICS (Image Cytometry Standard) files.
- ICSReader() - Constructor for class loci.formats.in.ICSReader
-
Constructs a new ICSReader.
- ICSWriter - Class in loci.formats.out
-
ICSWriter is the file format writer for ICS files.
- ICSWriter() - Constructor for class loci.formats.out.ICSWriter
- id - Static variable in class loci.formats.filter.LZ4Filter
- id - Variable in class loci.formats.gui.CacheComponent
-
File name that the cache is working with (debugging only).
- id - Variable in class loci.formats.in.BaseZeissReader.Shape
- id - Variable in class loci.formats.in.FlexReader.FilterGroup
- id - Variable in class loci.formats.in.LeicaHandler.Laser
- id - Variable in enum class loci.formats.in.LeicaMicrosystemsMetadata.Dimension.DimensionKey
- id - Variable in class loci.formats.in.LeicaReader.Detector
- id - Variable in class loci.formats.in.LIFReader.MemoryBlock
- id - Variable in class loci.formats.in.OIRReader.Channel
- id - Variable in class loci.formats.in.OIRReader.Detector
- id - Variable in class loci.formats.in.OIRReader.Laser
- id - Variable in class loci.formats.in.OMETiffReader.OMETiffPlane
-
File containing this plane.
- id - Variable in class loci.formats.in.TissueFAXSReader.Channel
- id - Variable in class loci.formats.in.TissueFAXSReader.ScanRegion
- id - Variable in class loci.formats.in.ZeissCZIReader.Segment
- id - Variable in class loci.plugins.util.BFVirtualStack
- idatCount - Variable in class loci.formats.in.APNGReader
- IdDialog - Class in loci.plugins.in
-
Bio-Formats Importer id chooser dialog box.
- IdDialog(ImportProcess) - Constructor for class loci.plugins.in.IdDialog
-
Creates an id chooser dialog for the Bio-Formats Importer.
- IDENTIFIER - Static variable in class loci.formats.in.OIRReader
- idLoc - Variable in class loci.plugins.in.ImportProcess
- idName - Variable in class loci.plugins.in.ImportProcess
- idx1Pos - Variable in class loci.formats.out.AVIWriter
- IExtraMetadataWriter - Interface in loci.formats.out
- ifd - Variable in class loci.formats.in.LeicaSCNReader.Dimension
- ifd - Variable in class loci.formats.in.OMETiffReader.OMETiffPlane
-
IFD number of this plane.
- ifd - Variable in class loci.formats.in.VentanaReader.TIFFTile
- IFD - Class in loci.formats.tiff
-
Data structure for working with TIFF Image File Directories (IFDs).
- IFD - Enum constant in enum class loci.formats.tiff.IFDType
- IFD() - Constructor for class loci.formats.tiff.IFD
- IFD(IFD) - Constructor for class loci.formats.tiff.IFD
- IFD8 - Enum constant in enum class loci.formats.tiff.IFDType
- ifdBuffer - Variable in class loci.formats.tiff.TiffSaver
- ifdCounts - Variable in class loci.formats.out.OMETiffWriter
- ifdIndex - Variable in class loci.formats.in.SVSCoreMetadata
- ifdList - Variable in class loci.formats.tiff.TiffParser
-
Cached list of IFDs in the current file.
- IFDList - Class in loci.formats.tiff
-
Data structure for working with a list of TIFF
IFDs. - IFDList() - Constructor for class loci.formats.tiff.IFDList
- IFDMap - Variable in class loci.formats.in.LeicaSCNReader.LeicaSCNHandler
- ifdOffsets - Variable in class loci.formats.in.FlowSightReader
- ifds - Variable in class loci.formats.in.APLReader
- ifds - Variable in class loci.formats.in.CellSensReader
- ifds - Variable in class loci.formats.in.EPSReader
- ifds - Variable in class loci.formats.in.FlexReader.FlexFile
- ifds - Variable in class loci.formats.in.FV1000Reader
- ifds - Variable in class loci.formats.in.LeicaReader
- ifds - Variable in class loci.formats.in.MinimalTiffReader
-
List of IFDs for the current TIFF.
- ifds - Variable in class loci.formats.out.DicomWriter
- ifdsList - Variable in class loci.formats.in.ZeissLSMReader
- IFDType - Enum Class in loci.formats.tiff
-
An enumeration of IFD types.
- IFDType(int, int) - Constructor for enum class loci.formats.tiff.IFDType
-
Default constructor.
- IFormatHandler - Interface in loci.formats
-
Interface for all biological file format readers and writers.
- IFormatReader - Interface in loci.formats
-
Interface for all biological file format readers.
- IFormatWidgets - Interface in loci.plugins.config
-
Interface for defining custom widgets for a specific file format reader.
- IFormatWriter - Interface in loci.formats
-
Interface for all biological file format writers.
- ignore - Variable in class loci.plugins.util.SearchableWindow.SearchBox
- IGNORE - Enum constant in enum class loci.formats.dicom.ResolutionStrategy
- ignoreCase - Variable in class loci.plugins.util.SearchableWindow.SearchBox
- ih - Variable in class loci.formats.in.GIFReader
-
Current image rectangle.
- IJStatusEchoer - Class in loci.plugins.util
-
Echoes status messages to the ImageJ status bar.
- IJStatusEchoer() - Constructor for class loci.plugins.util.IJStatusEchoer
- IllegalBlockException - Exception Class in loci.formats
-
Exception thrown when
FilePatternBlockencounters an invalid pattern. - IllegalBlockException() - Constructor for exception class loci.formats.IllegalBlockException
- IllegalBlockException(String) - Constructor for exception class loci.formats.IllegalBlockException
- IllegalBlockException(String, Throwable) - Constructor for exception class loci.formats.IllegalBlockException
- IllegalBlockException(Throwable) - Constructor for exception class loci.formats.IllegalBlockException
- ILLUM_CHANNEL_ACQUIRE - Static variable in class loci.formats.in.ZeissLSMReader
- ILLUM_CHANNEL_ATTENUATION - Static variable in class loci.formats.in.ZeissLSMReader
- ILLUM_CHANNEL_NAME - Static variable in class loci.formats.in.ZeissLSMReader
- ILLUM_CHANNEL_WAVELENGTH - Static variable in class loci.formats.in.ZeissLSMReader
- illumination - Variable in class loci.formats.in.ZeissCZIReader.Channel
- ILLUMINATION - Static variable in class loci.formats.FormatTools
-
Identifies the Illumination dimensional type, representing a dimension consisting of illuminations.
- ILLUMINATION_COLOR_CODE_SEQUENCE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- ILLUMINATION_TYPE_CODE_SEQUENCE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- ILLUMINATION_WAVELENGTH - Enum constant in enum class loci.formats.dicom.DicomAttribute
- IlluminationChannel() - Constructor for class loci.formats.in.ZeissLSMReader.IlluminationChannel
- illuminationLabels - Variable in class loci.formats.in.ZeissCZIReader
- illuminations - Variable in class loci.formats.in.FV1000Reader
- illuminations - Variable in class loci.formats.in.ZeissCZIReader
- illuminations - Variable in class loci.formats.in.ZeissLSMReader
- ILLUMINATOR_TYPE_CODE_SEQUENCE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- illumNA - Variable in class loci.formats.in.LeicaSCNReader.Image
- illumSource - Variable in class loci.formats.in.LeicaSCNReader.Image
- IM3Reader - Class in loci.formats.in
- IM3Reader() - Constructor for class loci.formats.in.IM3Reader
-
Construct an uninitialized reader of .im3 files.
- IM3Reader.BooleanIM3Record - Class in loci.formats.in
-
A record containing boolean values
- IM3Reader.ContainerRecord - Class in loci.formats.in
- IM3Reader.FloatIM3Record - Class in loci.formats.in
- IM3Reader.IM3Record - Class in loci.formats.in
- IM3Reader.IntIM3Record - Class in loci.formats.in
- IM3Reader.Spectrum - Class in loci.formats.in
- IM3Reader.StringIM3Record - Class in loci.formats.in
- IM3Record(String, int, long, int) - Constructor for class loci.formats.in.IM3Reader.IM3Record
- ImaconHandler() - Constructor for class loci.formats.in.ImaconReader.ImaconHandler
- ImaconReader - Class in loci.formats.in
-
ImaconReader is the file format reader for Imacon .fff (TIFF) files.
- ImaconReader() - Constructor for class loci.formats.in.ImaconReader
-
Constructs a new Imacon reader.
- ImaconReader.ImaconHandler - Class in loci.formats.in
- image - Variable in class loci.formats.in.VeecoReader
- Image() - Constructor for class loci.formats.in.InCellReader.Image
- Image() - Constructor for class loci.formats.in.TecanReader.Image
- Image(Attributes) - Constructor for class loci.formats.in.LeicaSCNReader.Image
- IMAGE - Static variable in class loci.formats.in.CellH5Reader.CellH5Constants
- IMAGE_AREA_DOSE_PRODUCT - Enum constant in enum class loci.formats.dicom.DicomAttribute
- IMAGE_BOUNDARY - Static variable in class loci.formats.in.CellSensReader
- IMAGE_COLLECTION_PROPERTIES - Static variable in class loci.formats.in.CellSensReader
- IMAGE_DESCRIPTION - Static variable in class loci.formats.tiff.IFD
- IMAGE_DETAILS - Static variable in class loci.formats.in.ZeissXRMReader
- IMAGE_FRAME_VOLUME - Static variable in class loci.formats.in.CellSensReader
- IMAGE_GEOMETRY_TYPE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- IMAGE_HEADER - Enum constant in enum class loci.formats.codec.JPEG2000BoxType
- IMAGE_ID - Enum constant in enum class loci.formats.dicom.DicomAttribute
- IMAGE_INFO_PATH - Static variable in class loci.formats.in.ZeissXRMReader
- IMAGE_LENGTH - Static variable in class loci.formats.tiff.IFD
- IMAGE_ORIENTATION_PATIENT - Enum constant in enum class loci.formats.dicom.DicomAttribute
- IMAGE_PATH - Static variable in class loci.formats.in.CellH5Reader.CellH5Constants
- IMAGE_PATH_FILTER_PASS_BAND - Enum constant in enum class loci.formats.dicom.DicomAttribute
- IMAGE_PATH_FILTER_PASSTHROUGH_WAVELENGTH - Enum constant in enum class loci.formats.dicom.DicomAttribute
- IMAGE_PATH_FILTER_TYPE_STACK_CODE_SEQUENCE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- IMAGE_POSITION - Enum constant in enum class loci.formats.dicom.DicomAttribute
- IMAGE_POSITION_PATIENT - Enum constant in enum class loci.formats.dicom.DicomAttribute
- IMAGE_PRO_TAG_1 - Static variable in class loci.formats.in.SEQReader
-
An array of shorts (length 12) with identical values in all of our samples; assuming this is some sort of format identifier.
- IMAGE_PRO_TAG_2 - Static variable in class loci.formats.in.SEQReader
-
Frame rate.
- IMAGE_PRO_TAG_3 - Static variable in class loci.formats.in.SEQReader
- IMAGE_SEPARATOR - Static variable in class loci.formats.in.GIFReader
- IMAGE_SOURCE_DATA - Static variable in class loci.formats.in.PhotoshopTiffReader
- IMAGE_TRIGGER_DELAY - Enum constant in enum class loci.formats.dicom.DicomAttribute
- IMAGE_TYPE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- IMAGE_TYPE_1 - Static variable in class loci.formats.in.OpenlabReader
-
Tag types.
- IMAGE_TYPE_2 - Static variable in class loci.formats.in.OpenlabReader
- IMAGE_TYPES - Static variable in class loci.formats.in.DeltavisionReader
- IMAGE_WIDTH - Static variable in class loci.formats.tiff.IFD
- ImageCollection(Attributes) - Constructor for class loci.formats.in.LeicaSCNReader.ImageCollection
- imageCount - Variable in class loci.formats.CoreMetadata
-
Total number of images.
- imageCount - Variable in class loci.formats.in.ZeissCZIReader.Coordinate
- imageCreationDate - Variable in class loci.formats.in.MetamorphReader
-
The TIFF's creation date
- IMAGED_NUCLEUS - Enum constant in enum class loci.formats.dicom.DicomAttribute
- IMAGED_VOLUME_DEPTH - Enum constant in enum class loci.formats.dicom.DicomAttribute
- IMAGED_VOLUME_HEIGHT - Enum constant in enum class loci.formats.dicom.DicomAttribute
- IMAGED_VOLUME_WIDTH - Enum constant in enum class loci.formats.dicom.DicomAttribute
- imageDepth - Variable in class loci.formats.in.FV1000Reader
- imageDescription - Variable in class loci.formats.in.BaseZeissReader
- imageDescription - Variable in class loci.formats.in.FEITiffReader
- imageDescription - Variable in class loci.formats.in.MicroCTReader
- imageDescriptions - Variable in class loci.formats.in.SlidebookReader
- imageDimensions - Variable in class loci.formats.services.JPEGTurboServiceImpl
- imageDirectory - Variable in class loci.formats.in.TecanReader
- imageFile - Variable in class loci.formats.in.PCORAWReader
- imageFileCSV - Variable in class loci.formats.in.JDCEReader
- imageFiles - Variable in class loci.formats.in.BaseZeissReader
- imageFiles - Variable in class loci.formats.in.InCellReader
- imageFiles - Variable in class loci.formats.in.IPWReader
-
List of embedded image file names (one per image plane).
- imageFiles - Variable in class loci.formats.in.PCIReader
- imageFolder - Variable in class loci.formats.in.CellVoyagerReader
- imageFormat - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.MultipleImagesReader
- imageFormat - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.XlifDocument
- ImageFormat() - Constructor for enum class loci.formats.in.LeicaMicrosystemsMetadata.LMSFileReader.ImageFormat
- imageHeight - Variable in class loci.formats.in.InCellReader
- imageHeight - Variable in class loci.formats.services.JPEGTurboServiceImpl
- imageIFD(int) - Method in class loci.formats.in.LeicaSCNReader
- imageIndex - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.MultipleImagesReader
- ImageIOReader - Class in loci.formats.in
-
ImageIOReader is the superclass for file format readers that use the javax.imageio package.
- ImageIOReader(String, String) - Constructor for class loci.formats.in.ImageIOReader
-
Constructs a new ImageIOReader.
- ImageIOReader(String, String[]) - Constructor for class loci.formats.in.ImageIOReader
-
Constructs a new ImageIOReader.
- ImageIOWriter - Class in loci.formats.out
-
ImageIOWriter is the superclass for file format writers that use the javax.imageio library.
- ImageIOWriter(String, String[], String) - Constructor for class loci.formats.out.ImageIOWriter
-
Constructs an ImageIO-based writer with the given name, default suffixes and output type (e.g., png, jpeg).
- ImageIOWriter(String, String, String) - Constructor for class loci.formats.out.ImageIOWriter
-
Constructs an ImageIO-based writer with the given name, default suffix and output type (e.g., png, jpeg).
- IMAGEJ_MSG - Static variable in class loci.plugins.util.LibraryChecker
-
Message to be displayed if ImageJ is too old for Bio-Formats plugins.
- IMAGEJ_TAG - Static variable in class loci.formats.in.TiffReader
- IMAGEJ_VERSION - Static variable in class loci.plugins.util.LibraryChecker
-
Minimum version of ImageJ necessary for Bio-Formats plugins.
- imageLocations - Variable in class loci.formats.out.OMETiffWriter
- imageMap - Variable in class loci.formats.in.LeicaSCNReader.LeicaSCNHandler
- imageMetadataLVExists - Variable in class loci.formats.in.ND2Handler
- imageMetadataLVOrder - Variable in class loci.formats.in.ND2Reader
- imageMetadataLVProcessed - Variable in class loci.formats.in.ND2Reader
- imageName - Variable in class loci.formats.in.BioRadSCNReader
- imageName - Variable in class loci.formats.in.FEITiffReader
- imageName - Variable in class loci.formats.in.ImaconReader
- imageName - Variable in class loci.formats.in.MetamorphHandler
- imageName - Variable in class loci.formats.in.MetamorphReader
-
The TIFF's name
- imageName - Variable in class loci.formats.in.SISReader
- imageName - Variable in class loci.formats.in.ZeissCZIReader
- imageNames - Variable in class loci.formats.in.BrukerReader
- imageNames - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataTempBuffer
- imageNames - Variable in class loci.formats.in.LIFReader
- imageNames - Variable in class loci.formats.in.TillVisionReader
- imageNames - Variable in class loci.formats.in.ZeissCZIReader
- imageNames - Variable in class loci.formats.in.ZeissLSMReader
- imageNumber - Variable in class loci.formats.in.APNGReader.PNGInputStream
- imageNumEnd - Variable in class loci.formats.in.LeicaSCNReader.Image
- imageNumStart - Variable in class loci.formats.in.LeicaSCNReader.Image
- imageOffset - Variable in class loci.formats.in.IvisionReader
- imagePaths - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.XlifDocument
- imagePaths - Variable in class loci.formats.in.ZeissXRMReader
- ImagePlusReader - Class in loci.plugins.in
-
A high-level reader for
ImagePlusobjects. - ImagePlusReader() - Constructor for class loci.plugins.in.ImagePlusReader
-
Constructs an ImagePlusReader with the default options.
- ImagePlusReader(ImportProcess) - Constructor for class loci.plugins.in.ImagePlusReader
-
Constructs an ImagePlusReader with the given complete import preparation process.
- ImageProcessorReader - Class in loci.plugins.util
-
A low-level reader for
ImageProcessorobjects. - ImageProcessorReader() - Constructor for class loci.plugins.util.ImageProcessorReader
-
Constructs an ImageProcessorReader around a new image reader.
- ImageProcessorReader(IFormatReader) - Constructor for class loci.plugins.util.ImageProcessorReader
-
Constructs an ImageProcessorReader with the given reader.
- ImageProcessorSource - Class in loci.plugins.util
-
Retrieves ImageJ image processors from an image reader.
- ImageProcessorSource(IFormatReader) - Constructor for class loci.plugins.util.ImageProcessorSource
- IMAGER_PIXEL_SPACING - Enum constant in enum class loci.formats.dicom.DicomAttribute
- imageReader - Variable in class loci.plugins.in.ImportProcess
- ImageReader - Class in loci.formats
-
ImageReader is the master file format reader for all supported formats.
- ImageReader() - Constructor for class loci.formats.ImageReader
-
Constructs a new ImageReader with the default list of reader classes from readers.txt.
- ImageReader(ClassList<IFormatReader>) - Constructor for class loci.formats.ImageReader
-
Constructs a new ImageReader from the given list of reader classes.
- imageROIs - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataTempBuffer
- imageROIs - Variable in class loci.formats.in.LIFReader
- imageRX - Variable in class loci.formats.in.SDTInfo
- imageRY - Variable in class loci.formats.in.SDTInfo
- images - Variable in class loci.formats.gui.ImageViewer
- images - Variable in class loci.formats.in.GIFReader
- images - Variable in class loci.formats.in.LeicaSCNReader.ImageCollection
- images - Variable in class loci.formats.in.TecanReader
- IMAGES - Static variable in class loci.formats.in.LeicaReader
- imagesDir - Variable in class loci.formats.in.OperettaReader
- imageSequence - Variable in class loci.formats.in.DeltavisionReader
- imagesNumber - Variable in class loci.formats.in.InCellReader
- imagesPerFile - Variable in class loci.formats.FileStitcher.ExternalSeries
- imagesPerFile - Variable in class loci.formats.in.DicomReader
- imageThumbnail - Variable in class loci.formats.in.LeicaSCNReader.Image
- ImageTools - Class in loci.formats
-
A utility class with convenience methods for manipulating images in primitive array form.
- ImageTools() - Constructor for class loci.formats.ImageTools
- imageType - Variable in class loci.formats.dicom.DicomFileInfo
- imageType - Variable in class loci.formats.in.DicomReader
- ImageViewer - Class in loci.formats.gui
-
ImageViewer is a simple viewer/converter for the Bio-Formats image formats.
- ImageViewer() - Constructor for class loci.formats.gui.ImageViewer
-
Constructs an image viewer.
- ImageViewer(boolean) - Constructor for class loci.formats.gui.ImageViewer
-
Constructs an image viewer.
- imageWidth - Variable in class loci.formats.in.InCellReader
- imageWidth - Variable in class loci.formats.services.JPEGTurboServiceImpl
- ImageWriter - Class in loci.formats
-
ImageWriter is the master file format writer for all supported formats.
- ImageWriter() - Constructor for class loci.formats.ImageWriter
-
Constructs a new ImageWriter with the default list of writer classes from writers.txt.
- ImageWriter(ClassList<IFormatWriter>) - Constructor for class loci.formats.ImageWriter
-
Constructs a new ImageWriter from the given list of writer classes.
- imageX - Variable in class loci.formats.in.SDTInfo
-
4 subsequent fields valid only for Camera mode or FIFO_IMAGE mode.
- imageY - Variable in class loci.formats.in.SDTInfo
- ImagicReader - Class in loci.formats.in
-
ImagicReader is the file format reader for IMAGIC files.
- ImagicReader() - Constructor for class loci.formats.in.ImagicReader
-
Constructs a new IMAGIC reader.
- IMAGING_FREQUENCY - Enum constant in enum class loci.formats.dicom.DicomAttribute
- IMARIS_MAGIC_BYTES - Static variable in class loci.formats.in.ImarisReader
-
Magic number; present in all files.
- ImarisHDFReader - Class in loci.formats.in
-
Reader for Bitplane Imaris 5.5 (HDF) files.
- ImarisHDFReader() - Constructor for class loci.formats.in.ImarisHDFReader
-
Constructs a new Imaris HDF reader.
- ImarisReader - Class in loci.formats.in
-
ImarisReader is the file format reader for Bitplane Imaris files.
- ImarisReader() - Constructor for class loci.formats.in.ImarisReader
-
Constructs a new Imaris reader.
- ImarisTiffReader - Class in loci.formats.in
-
ImarisTiffReader is the file format reader for Bitplane Imaris 3 files (TIFF variant).
- ImarisTiffReader() - Constructor for class loci.formats.in.ImarisTiffReader
-
Constructs a new Imaris TIFF reader.
- IMetadata - Interface in loci.formats.meta
- IMetadataConfigurable - Interface in loci.formats
- img - Variable in class loci.formats.in.ImageIOReader
-
Transient reference to a
BufferedImagefor thisFormatHandler.currentId. - img - Variable in class loci.formats.tools.AsciiImage
- IMinMaxStore - Interface in loci.formats.meta
-
Interface for consumers of minima and maxima pixel intensities across a given wavelength.
- immersion - Variable in class loci.formats.in.ND2Handler
- immersion - Variable in class loci.formats.in.NikonTiffReader
- immersion - Variable in class loci.formats.in.OIRReader.Objective
- immersion - Variable in class loci.formats.in.SimplePCITiffReader
- immersion - Variable in class loci.formats.in.ZeissLSMReader.Recording
- immersions - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataTempBuffer
- immersions - Variable in class loci.formats.in.LIFReader
- IMODReader - Class in loci.formats.in
-
Reader for IMOD binary files.
- IMODReader() - Constructor for class loci.formats.in.IMODReader
-
Constructs a new IMOD reader.
- IMODSTAMP_OFFSET - Static variable in class loci.formats.in.MRCReader
- imp - Variable in class loci.plugins.out.Exporter
-
Current stack.
- imp - Variable in class loci.plugins.Slicer
-
Current image stack.
- IMPLANT_PRESENT - Enum constant in enum class loci.formats.dicom.DicomAttribute
- IMPLEMENTATION_UID - Enum constant in enum class loci.formats.dicom.DicomAttribute
- IMPLEMENTATION_VERSION - Enum constant in enum class loci.formats.dicom.DicomAttribute
- implementationUID - Variable in class loci.formats.out.DicomWriter
- IMPLICIT - Enum constant in enum class loci.formats.dicom.DicomVR
- importData(JComponent, Transferable) - Method in class loci.plugins.shortcut.ShortcutTransferHandler
- Importer - Class in loci.plugins.in
-
Core logic for the Bio-Formats Importer ImageJ plugin.
- Importer(LociImporter) - Constructor for class loci.plugins.in.Importer
- ImporterDialog - Class in loci.plugins.in
-
Abstract superclass of importer dialogs.
- ImporterDialog(ImportProcess) - Constructor for class loci.plugins.in.ImporterDialog
- ImporterMetadata - Class in loci.plugins.in
-
Helper class for storing original metadata key/value pairs.
- ImporterMetadata(IFormatReader, ImportProcess, boolean) - Constructor for class loci.plugins.in.ImporterMetadata
- ImporterOptions - Class in loci.plugins.in
-
Helper class for managing Bio-Formats Importer options.
- ImporterOptions() - Constructor for class loci.plugins.in.ImporterOptions
- ImporterPrompter - Class in loci.plugins.in
-
Helper class for presenting the user with dialog boxes for configuring importer options.
- ImporterPrompter(ImportProcess) - Constructor for class loci.plugins.in.ImporterPrompter
- ImportProcess - Class in loci.plugins.in
-
Manages the import preparation process.
- ImportProcess() - Constructor for class loci.plugins.in.ImportProcess
- ImportProcess(ImporterOptions) - Constructor for class loci.plugins.in.ImportProcess
- ImportStep - Enum Class in loci.plugins.in
-
An enumeration of the steps in the import preparation process.
- ImportStep(int, String) - Constructor for enum class loci.plugins.in.ImportStep
- IMPROVISION_MAGIC_STRING - Static variable in class loci.formats.in.ImprovisionTiffReader
- ImprovisionTiffReader - Class in loci.formats.in
-
ImprovisionTiffReader is the file format reader for Improvision TIFF files.
- ImprovisionTiffReader() - Constructor for class loci.formats.in.ImprovisionTiffReader
- ImspectorReader - Class in loci.formats.in
-
ImspectorReader is the file format reader for Imspector .msr files.
- ImspectorReader() - Constructor for class loci.formats.in.ImspectorReader
-
Constructs a new Imspector reader.
- in - Variable in class loci.formats.FormatReader
-
Current file.
- in - Variable in class loci.formats.gui.ImageViewer
- in - Variable in class loci.formats.in.JPEG2000MetadataParser
-
Stream that we're parsing metadata from.
- in - Variable in class loci.formats.out.TiffWriter
-
Input stream to use when overwriting data.
- in - Variable in class loci.formats.services.JPEGTurboServiceImpl
- in - Variable in class loci.formats.tiff.TiffParser
-
Input source from which to parse TIFF data.
- in - Variable in class loci.formats.tools.AmiraParameters
- IN_CONCATENATION_NUMBER - Enum constant in enum class loci.formats.dicom.DicomAttribute
- inCache - Variable in class loci.formats.cache.Cache
-
Whether each position is currently supposed to be cached.
- INCELL_MAGIC_STRING - Static variable in class loci.formats.in.InCellReader
- InCell3000Reader - Class in loci.formats.in
-
InCell3000Reader is the file format reader for InCell 3000.
- InCell3000Reader() - Constructor for class loci.formats.in.InCell3000Reader
-
Constructs a new InCell 3000 reader.
- InCellHandler(MetadataStore) - Constructor for class loci.formats.in.InCellReader.InCellHandler
- InCellReader - Class in loci.formats.in
-
InCellReader is the file format reader for InCell 1000/2000 datasets.
- InCellReader() - Constructor for class loci.formats.in.InCellReader
-
Constructs a new InCell 1000/2000 reader.
- InCellReader.Image - Class in loci.formats.in
- InCellReader.InCellHandler - Class in loci.formats.in
-
SAX handler for parsing XML.
- InCellReader.MinimalInCellHandler - Class in loci.formats.in
- INCLUDE_ATTACHMENTS_DEFAULT - Static variable in class loci.formats.in.ZeissCZIReader
- INCLUDE_ATTACHMENTS_KEY - Static variable in class loci.formats.in.ZeissCZIReader
- includeC - Variable in class loci.formats.gui.DataConverter
- includeCZIAttachments() - Static method in class loci.plugins.util.LociPrefs
- includeT - Variable in class loci.formats.gui.DataConverter
- includeZ - Variable in class loci.formats.gui.DataConverter
- incr - Variable in class loci.formats.in.SDTInfo
- index - Variable in class loci.formats.cache.CacheEvent
-
Relevant index to the event, if any.
- index - Variable in class loci.formats.in.BaseZeissReader.Tag
- index - Variable in class loci.formats.in.CellVoyagerReader.AreaInfo
- index - Variable in class loci.formats.in.CellVoyagerReader.FieldInfo
- index - Variable in class loci.formats.in.CV7000Reader.Channel
- index - Variable in class loci.formats.in.LeicaHandler.Laser
- index - Variable in class loci.formats.in.LeicaReader.Detector
- index - Variable in class loci.formats.in.PrairieMetadata.Frame
-
indexof this<Frame>. - index - Variable in class loci.formats.in.TecanReader.Channel
- index - Variable in class loci.formats.in.VentanaReader.AreaOfInterest
- index - Variable in class loci.formats.in.ZeissTIFFHandler.Tag
- index - Variable in class loci.formats.Resolution
- index - Variable in class loci.plugins.in.ThumbLoader.SeriesInfo
- index - Variable in class loci.plugins.util.SearchableWindow
- Index(int[]) - Constructor for class loci.formats.in.MicromanagerReader.Index
- Index16ColorModel - Class in loci.formats.gui
-
ColorModel that handles 16 bits per channel lookup tables.
- Index16ColorModel(int, int, short[][], boolean) - Constructor for class loci.formats.gui.Index16ColorModel
- indexed - Variable in class loci.formats.CoreMetadata
-
Indicates whether or not the images are stored as indexed color.
- INDEXED - Static variable in class loci.formats.in.APNGReader
- indexedAsRGB - Variable in class loci.formats.FormatReader
-
Whether or not MetadataStore sets C = 3 for indexed color images.
- indexedToRGB(byte[][], byte[]) - Static method in class loci.formats.ImageTools
-
Converts a LUT and an array of indices into an array of RGB tuples.
- indexedToRGB(short[][], byte[], boolean) - Static method in class loci.formats.ImageTools
-
Converts a LUT and an array of indices into an array of RGB tuples.
- indexedToRGB(BufferedImage, boolean) - Static method in class loci.formats.gui.AWTImageTools
-
Converts an indexed color BufferedImage to an RGB BufferedImage.
- indexIntoPlanes - Variable in class loci.formats.in.ZeissCZIReader
- indexMax - Variable in class loci.formats.in.PrairieMetadata.Sequence
-
Maximum index value.
- indexMin - Variable in class loci.formats.in.PrairieMetadata.Sequence
-
Minimum index value.
- indexToValue - Variable in class loci.formats.in.FakeReader
-
For indexed color, mapping from indices to values and vice versa.
- inDimensionProperties - Variable in class loci.formats.in.CellSensReader
- INDIVIDUAL_JARS - Static variable in class loci.formats.UpgradeChecker
-
Names of the individual JARs.
- infFile - Variable in class loci.formats.in.FujiReader
- infFiles - Variable in class loci.formats.in.TillVisionReader
- inflateInputBuffer - Variable in class loci.formats.in.OBFReader.State
- inflater - Variable in class loci.formats.in.OBFReader.State
- info - Variable in class loci.formats.in.GatanReader
- info - Variable in class loci.formats.in.OMETiffReader
-
Mapping from series and plane numbers to files and IFD entries.
- info - Variable in class loci.formats.in.SDTInfo
- info - Variable in class loci.formats.in.SDTReader
-
Object containing SDT header information.
- info - Variable in class loci.plugins.prefs.Option
-
Documentation about the option, in HTML.
- INFO_DEFAULT - Static variable in class loci.plugins.in.MainDialog
-
Initial message to display in help text box.
- INFO_TABLE - Static variable in class loci.formats.in.LiFlimReader
- infoLength - Variable in class loci.formats.in.SDTInfo
-
Length of the info part.
- infoOffs - Variable in class loci.formats.in.SDTInfo
-
Offset of the info part which contains general text information (Title, date, time, contents etc.).
- infoPane - Variable in class loci.plugins.in.MainDialog
- infoTable - Variable in class loci.plugins.in.MainDialog
- ini - Variable in class loci.formats.in.LiFlimReader
-
Parsed configuration data.
- INI_DEFAULT - Static variable in class loci.plugins.prefs.Option
-
INI key indicating option's default value.
- INI_INFO - Static variable in class loci.plugins.prefs.Option
-
INI key indicating option's info.
- INI_KEY - Static variable in class loci.plugins.prefs.Option
-
INI key indicating option's key.
- INI_LABEL - Static variable in class loci.plugins.prefs.Option
-
INI key indicating option's label.
- INI_POSSIBLE - Static variable in class loci.plugins.prefs.StringOption
-
INI key indicating option's possible values.
- INI_SAVE - Static variable in class loci.plugins.prefs.Option
-
INI key indicating whether option should be saved to prefs file.
- INI_TYPE - Static variable in class loci.plugins.prefs.OptionsList
-
INI key indicating option's type.
- iniFile - Variable in class loci.formats.in.FakeReader
-
Properties companion file which can be associated with this fake file
- init() - Method in class loci.formats.services.NetCDFServiceImpl
- init() - Method in class org.libjpegturbo.turbojpeg.TJCompressor
- init() - Method in class org.libjpegturbo.turbojpeg.TJDecompressor
- init() - Method in class org.libjpegturbo.turbojpeg.TJTransformer
- initAlternateMetadata() - Method in class loci.formats.in.FluoviewReader
- initAlternateMetadataStore() - Method in class loci.formats.in.FluoviewReader
- initChildren() - Method in class loci.formats.in.LeicaMicrosystemsMetadata.LMSCollectionXmlDocument
-
Adds all referenced xlcfs and valid xlifs as children
- initCoreMetadata() - Method in class loci.formats.in.LiFlimReader
- initCoreMetadata(int, int) - Method in class loci.formats.in.LeicaSCNReader
- initDecompressor() - Method in class loci.formats.in.AmiraReader.HxZip
- initDetectorModels(int) - Method in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataStoreInitializer
-
Adds detector and channel color details from the reader's
MetadataTempBufferto itsMetadataStore - initExtraMetadata() - Method in class loci.formats.in.DeltavisionReader
- initFile(String) - Method in class loci.formats.FileStitcher
-
Initializes the given file or file pattern.
- initFile(String) - Method in class loci.formats.FormatReader
-
Initializes the given file (parsing header information, etc.).
- initFile(String) - Method in class loci.formats.in.AFIReader
- initFile(String) - Method in class loci.formats.in.AIMReader
- initFile(String) - Method in class loci.formats.in.AliconaReader
- initFile(String) - Method in class loci.formats.in.AmiraReader
- initFile(String) - Method in class loci.formats.in.AnalyzeReader
- initFile(String) - Method in class loci.formats.in.APLReader
- initFile(String) - Method in class loci.formats.in.APNGReader
- initFile(String) - Method in class loci.formats.in.ARFReader
- initFile(String) - Method in class loci.formats.in.AVIReader
- initFile(String) - Method in class loci.formats.in.BaseTiffReader
- initFile(String) - Method in class loci.formats.in.BDReader
- initFile(String) - Method in class loci.formats.in.BDVReader
- initFile(String) - Method in class loci.formats.in.BioRadGelReader
- initFile(String) - Method in class loci.formats.in.BioRadReader
- initFile(String) - Method in class loci.formats.in.BioRadSCNReader
- initFile(String) - Method in class loci.formats.in.BMPReader
- initFile(String) - Method in class loci.formats.in.BrukerReader
- initFile(String) - Method in class loci.formats.in.BurleighReader
- initFile(String) - Method in class loci.formats.in.CanonRawReader
- initFile(String) - Method in class loci.formats.in.CellH5Reader
- initFile(String) - Method in class loci.formats.in.CellomicsReader
- initFile(String) - Method in class loci.formats.in.CellSensReader
- initFile(String) - Method in class loci.formats.in.CellVoyagerReader
- initFile(String) - Method in class loci.formats.in.CellWorxReader
- initFile(String) - Method in class loci.formats.in.ColumbusReader
- initFile(String) - Method in class loci.formats.in.CV7000Reader
- initFile(String) - Method in class loci.formats.in.DCIMGReader
- initFile(String) - Method in class loci.formats.in.DeltavisionReader
- initFile(String) - Method in class loci.formats.in.DicomReader
- initFile(String) - Method in class loci.formats.in.DNGReader
- initFile(String) - Method in class loci.formats.in.Ecat7Reader
- initFile(String) - Method in class loci.formats.in.EPSReader
- initFile(String) - Method in class loci.formats.in.FakeReader
- initFile(String) - Method in class loci.formats.in.FEIReader
- initFile(String) - Method in class loci.formats.in.FilePatternReader
- initFile(String) - Method in class loci.formats.in.FitsReader
- initFile(String) - Method in class loci.formats.in.FlexReader
- initFile(String) - Method in class loci.formats.in.FlowSightReader
- initFile(String) - Method in class loci.formats.in.FujiReader
- initFile(String) - Method in class loci.formats.in.FV1000Reader
- initFile(String) - Method in class loci.formats.in.GatanDM2Reader
- initFile(String) - Method in class loci.formats.in.GatanReader
- initFile(String) - Method in class loci.formats.in.GIFReader
- initFile(String) - Method in class loci.formats.in.HamamatsuVMSReader
- initFile(String) - Method in class loci.formats.in.HISReader
- initFile(String) - Method in class loci.formats.in.HitachiReader
- initFile(String) - Method in class loci.formats.in.HRDGDFReader
- initFile(String) - Method in class loci.formats.in.I2IReader
- initFile(String) - Method in class loci.formats.in.ICSReader
- initFile(String) - Method in class loci.formats.in.IM3Reader
- initFile(String) - Method in class loci.formats.in.ImageIOReader
- initFile(String) - Method in class loci.formats.in.ImagicReader
- initFile(String) - Method in class loci.formats.in.ImarisHDFReader
- initFile(String) - Method in class loci.formats.in.ImarisReader
- initFile(String) - Method in class loci.formats.in.ImarisTiffReader
- initFile(String) - Method in class loci.formats.in.IMODReader
- initFile(String) - Method in class loci.formats.in.ImspectorReader
- initFile(String) - Method in class loci.formats.in.InCell3000Reader
- initFile(String) - Method in class loci.formats.in.InCellReader
- initFile(String) - Method in class loci.formats.in.INRReader
- initFile(String) - Method in class loci.formats.in.InveonReader
- initFile(String) - Method in class loci.formats.in.IPLabReader
- initFile(String) - Method in class loci.formats.in.IPWReader
- initFile(String) - Method in class loci.formats.in.IvisionReader
- initFile(String) - Method in class loci.formats.in.JDCEReader
- initFile(String) - Method in class loci.formats.in.JEOLReader
- initFile(String) - Method in class loci.formats.in.JPEG2000Reader
- initFile(String) - Method in class loci.formats.in.JPEGReader.DefaultJPEGReader
- initFile(String) - Method in class loci.formats.in.JPXReader
- initFile(String) - Method in class loci.formats.in.KhorosReader
- initFile(String) - Method in class loci.formats.in.KLBReader
- initFile(String) - Method in class loci.formats.in.KodakReader
- initFile(String) - Method in class loci.formats.in.L2DReader
- initFile(String) - Method in class loci.formats.in.LeicaReader
- initFile(String) - Method in class loci.formats.in.LiFlimReader
- initFile(String) - Method in class loci.formats.in.LIFReader
- initFile(String) - Method in class loci.formats.in.LIMReader
- initFile(String) - Method in class loci.formats.in.LOFReader
- initFile(String) - Method in class loci.formats.in.MetamorphReader
- initFile(String) - Method in class loci.formats.in.MetamorphTiffReader
- initFile(String) - Method in class loci.formats.in.MIASReader
- initFile(String) - Method in class loci.formats.in.MicroCTReader
- initFile(String) - Method in class loci.formats.in.MicromanagerReader
- initFile(String) - Method in class loci.formats.in.MINCReader
- initFile(String) - Method in class loci.formats.in.MinimalTiffReader
- initFile(String) - Method in class loci.formats.in.MNGReader
- initFile(String) - Method in class loci.formats.in.MolecularImagingReader
- initFile(String) - Method in class loci.formats.in.MRCReader
- initFile(String) - Method in class loci.formats.in.MRWReader
- initFile(String) - Method in class loci.formats.in.NAFReader
- initFile(String) - Method in class loci.formats.in.ND2Reader
- initFile(String) - Method in class loci.formats.in.NDPIReader
- initFile(String) - Method in class loci.formats.in.NDPISReader
- initFile(String) - Method in class loci.formats.in.NiftiReader
- initFile(String) - Method in class loci.formats.in.NikonReader
- initFile(String) - Method in class loci.formats.in.NRRDReader
- initFile(String) - Method in class loci.formats.in.OBFReader
- initFile(String) - Method in class loci.formats.in.OIRReader
- initFile(String) - Method in class loci.formats.in.OlympusTileReader
- initFile(String) - Method in class loci.formats.in.OMETiffReader
- initFile(String) - Method in class loci.formats.in.OMEXMLReader
- initFile(String) - Method in class loci.formats.in.OpenlabRawReader
- initFile(String) - Method in class loci.formats.in.OpenlabReader
- initFile(String) - Method in class loci.formats.in.OperettaReader
- initFile(String) - Method in class loci.formats.in.OxfordInstrumentsReader
- initFile(String) - Method in class loci.formats.in.PCIReader
- initFile(String) - Method in class loci.formats.in.PCORAWReader
- initFile(String) - Method in class loci.formats.in.PCXReader
- initFile(String) - Method in class loci.formats.in.PDSReader
- initFile(String) - Method in class loci.formats.in.PerkinElmerReader
- initFile(String) - Method in class loci.formats.in.PGMReader
- initFile(String) - Method in class loci.formats.in.PhotoshopTiffReader
- initFile(String) - Method in class loci.formats.in.PictReader
- initFile(String) - Method in class loci.formats.in.PovrayReader
- initFile(String) - Method in class loci.formats.in.PQBinReader
- initFile(String) - Method in class loci.formats.in.PrairieReader
- initFile(String) - Method in class loci.formats.in.PSDReader
- initFile(String) - Method in class loci.formats.in.QTReader
- initFile(String) - Method in class loci.formats.in.QuesantReader
- initFile(String) - Method in class loci.formats.in.RHKReader
- initFile(String) - Method in class loci.formats.in.SBIGReader
- initFile(String) - Method in class loci.formats.in.ScanrReader
- initFile(String) - Method in class loci.formats.in.SDTReader
- initFile(String) - Method in class loci.formats.in.SeikoReader
- initFile(String) - Method in class loci.formats.in.SEQReader
- initFile(String) - Method in class loci.formats.in.SIFReader
- initFile(String) - Method in class loci.formats.in.SlideBook7Reader
- initFile(String) - Method in class loci.formats.in.SlidebookReader
- initFile(String) - Method in class loci.formats.in.SMCameraReader
- initFile(String) - Method in class loci.formats.in.SPCReader
- initFile(String) - Method in class loci.formats.in.SPEReader
- initFile(String) - Method in class loci.formats.in.SpiderReader
- initFile(String) - Method in class loci.formats.in.TargaReader
- initFile(String) - Method in class loci.formats.in.TCSReader
- initFile(String) - Method in class loci.formats.in.TecanReader
- initFile(String) - Method in class loci.formats.in.TextReader
- initFile(String) - Method in class loci.formats.in.TiffJAIReader
- initFile(String) - Method in class loci.formats.in.TileJPEGReader
- initFile(String) - Method in class loci.formats.in.TillVisionReader
- initFile(String) - Method in class loci.formats.in.TissueFAXSReader
- initFile(String) - Method in class loci.formats.in.TopometrixReader
- initFile(String) - Method in class loci.formats.in.TrestleReader
- initFile(String) - Method in class loci.formats.in.UBMReader
- initFile(String) - Method in class loci.formats.in.UnisokuReader
- initFile(String) - Method in class loci.formats.in.VarianFDFReader
- initFile(String) - Method in class loci.formats.in.VeecoReader
- initFile(String) - Method in class loci.formats.in.VGSAMReader
- initFile(String) - Method in class loci.formats.in.VisitechReader
- initFile(String) - Method in class loci.formats.in.VolocityClippingReader
- initFile(String) - Method in class loci.formats.in.VolocityReader
- initFile(String) - Method in class loci.formats.in.WATOPReader
- initFile(String) - Method in class loci.formats.in.XLEFReader
- initFile(String) - Method in class loci.formats.in.ZeissCZIReader
- initFile(String) - Method in class loci.formats.in.ZeissLMSReader
- initFile(String) - Method in class loci.formats.in.ZeissLSMReader
- initFile(String) - Method in class loci.formats.in.ZeissTIFFReader
- initFile(String) - Method in class loci.formats.in.ZeissXRMReader
- initFile(String) - Method in class loci.formats.in.ZeissZVIReader
- initFile(String) - Method in class loci.formats.in.ZipReader
- initFile(String) - Method in class loci.formats.SubResolutionFormatReader
-
Initializes the given file (parsing header information, etc.).
- initFileMain(String) - Method in class loci.formats.in.BaseZeissReader
- initFilterModels(int) - Method in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataStoreInitializer
-
Adds filter details from the reader's
MetadataTempBufferto itsMetadataStore - initFlexFile(String) - Method in class loci.formats.in.FlexReader
- InitFrom() - Constructor for enum class loci.formats.in.LeicaMicrosystemsMetadata.LMSXmlDocument.InitFrom
- initFromFilepath(String) - Method in class loci.formats.in.LeicaMicrosystemsMetadata.LMSXmlDocument
- initFromXmlString(String) - Method in class loci.formats.in.LeicaMicrosystemsMetadata.LMSXmlDocument
- initialize() - Method in class loci.formats.codec.JPEGXRCodec
-
Initializes the JPEG-XR dependency service.
- initialize(String) - Method in interface loci.formats.services.EXIFService
- initialize(String) - Method in class loci.formats.services.EXIFServiceImpl
- initialize(String) - Method in interface loci.formats.services.MDBService
-
Prepare the given .mdb file for reading.
- initialize(String) - Method in class loci.formats.services.MDBServiceImpl
- initialize(String) - Method in interface loci.formats.services.MetakitService
- initialize(String) - Method in class loci.formats.services.MetakitServiceImpl
- initialize(String) - Method in interface loci.formats.services.POIService
-
Construct a new POI filesystem around the given file.
- initialize(String) - Method in class loci.formats.services.POIServiceImpl
- initialize(String, int) - Method in class loci.formats.codec.JPEGTileDecoder
- initialize(RandomAccessInputStream) - Method in interface loci.formats.services.MetakitService
- initialize(RandomAccessInputStream) - Method in class loci.formats.services.MetakitServiceImpl
- initialize(RandomAccessInputStream) - Method in interface loci.formats.services.POIService
-
Construct a new POI filesystem around the given stream.
- initialize(RandomAccessInputStream) - Method in class loci.formats.services.POIServiceImpl
- initialize(RandomAccessInputStream, int) - Method in class loci.formats.codec.JPEGTileDecoder
- initialize(RandomAccessInputStream, int, int) - Method in interface loci.formats.services.JPEGTurboService
-
Initialize the given stream, which represents an image of the given width and height.
- initialize(RandomAccessInputStream, int, int) - Method in class loci.formats.services.JPEGTurboServiceImpl
- initialize(RandomAccessInputStream, int, int, int) - Method in class loci.formats.codec.JPEGTileDecoder
- Initialize(long, int, int, int, int, int) - Method in class loci.formats.in.SlideBook7Reader.CCompressionBase
- Initialize(long, int, int, int, int, int, int) - Method in class loci.formats.in.SlideBook7Reader.CCompressionBase
- initializeColors() - Method in class loci.plugins.in.ImportProcess
-
Performed following ImportStep.COLORS notification.
- initializeCrop() - Method in class loci.plugins.in.ImportProcess
-
Performed following ImportStep.CROP notification.
- initialized - Variable in class loci.formats.FormatWriter
-
Whether each plane in each series of the current file has been prepped for writing.
- initializedFile - Variable in class loci.formats.in.HamamatsuVMSReader
- initializeDimOrder() - Method in class loci.plugins.in.ImportProcess
-
Performed following ImportStep.DIM_ORDER notification.
- initializedPlane - Variable in class loci.formats.in.HamamatsuVMSReader
- initializedPlane - Variable in class loci.formats.in.NDPIReader
- initializedSeries - Variable in class loci.formats.in.HamamatsuVMSReader
- initializedSeries - Variable in class loci.formats.in.NDPIReader
- initializeFile() - Method in class loci.plugins.in.ImportProcess
-
Performed following ImportStep.FILE notification.
- initializeHelper - Variable in class loci.formats.in.NRRDReader
- initializeJHDFService(String) - Method in class loci.formats.in.BDVReader
- initializeJHDFService(String) - Method in class loci.formats.in.CellH5Reader
- initializeMetadata() - Method in class loci.plugins.in.ImportProcess
-
Performed following ImportStep.METADATA notification.
- initializeRange() - Method in class loci.plugins.in.ImportProcess
-
Performed following ImportStep.RANGE notification.
- initializeReader() - Method in class loci.plugins.in.ImportProcess
-
Performed following ImportStep.READER notification.
- initializeReader(IFormatReader, String) - Method in class loci.formats.in.OMETiffReader
- initializeSeries() - Method in class loci.plugins.in.ImportProcess
-
Performed following ImportStep.SERIES notification.
- initializeStack() - Method in class loci.plugins.in.ImportProcess
-
Performed following ImportStep.STACK notification.
- initialUseLegacy - Variable in class loci.formats.in.JPEGReader
-
setId may alter the "useLegacy" variable depending upon the type of JPEG encountered.
- initImage() - Method in class loci.formats.in.ImageIOReader
- initImageDetails(int) - Method in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataStoreInitializer
-
Adds image and ROI details from the reader's
MetadataTempBufferto itsMetadataStore - initImagePaths() - Method in class loci.formats.in.LeicaMicrosystemsMetadata.XlifDocument
-
Searches the xml for referenced images and adds image paths
- initIntArray(String, long[], long) - Method in interface loci.formats.services.JHDFService
-
Creates an HDF5 dataset in path consisting of integers specified by bytes per pixel bpp.
- initIntArray(String, long[], long) - Method in class loci.formats.services.JHDFServiceImpl
- initLasers(int) - Method in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataStoreInitializer
-
Adds laser and light source details from the reader's
MetadataTempBufferto itsMetadataStore - initMeaFile(String) - Method in class loci.formats.in.FlexReader
-
Initialize the dataset from a .mea file.
- initMetadata() - Method in class loci.formats.in.BaseTiffReader
-
Populates the metadata hashtable and metadata store.
- initMetadata() - Method in class loci.formats.in.GelReader
- initMetadata(int) - Method in class loci.formats.in.ZeissLSMReader
- initMetadata(String) - Method in class loci.formats.in.LIFReader
-
Parses a string of XML and puts the values in a Hashtable.
- initMetadataStore() - Method in class loci.formats.in.BaseTiffReader
-
Populates the metadata store using the data parsed in
BaseTiffReader.initStandardMetadata()along with some further parsing done in the method itself. - initMetadataStore() - Method in class loci.formats.in.FEITiffReader
- initMetadataStore() - Method in class loci.formats.in.FluoviewReader
- initMetadataStore() - Method in class loci.formats.in.ImaconReader
- initMetadataStore() - Method in class loci.formats.in.ImprovisionTiffReader
- initMetadataStore() - Method in class loci.formats.in.IonpathMIBITiffReader
- initMetadataStore() - Method in class loci.formats.in.JPKReader
- initMetadataStore() - Method in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataStoreInitializer
-
Translates metadata information from the reader's
MetadataTempBufferand adds it to itsMetadataStore - initMetadataStore() - Method in class loci.formats.in.LeicaSCNReader
- initMetadataStore() - Method in class loci.formats.in.LEOReader
- initMetadataStore() - Method in class loci.formats.in.NDPIReader
- initMetadataStore() - Method in class loci.formats.in.NikonElementsTiffReader
- initMetadataStore() - Method in class loci.formats.in.NikonTiffReader
- initMetadataStore() - Method in class loci.formats.in.PyramidTiffReader
- initMetadataStore() - Method in class loci.formats.in.SimplePCITiffReader
- initMetadataStore() - Method in class loci.formats.in.SISReader
- initMetadataStore() - Method in class loci.formats.in.SlidebookTiffReader
- initMetadataStore() - Method in class loci.formats.in.SVSReader
- initMetadataStore() - Method in class loci.formats.in.TiffReader
- initMetadataStore() - Method in class loci.formats.in.TrestleReader
- initMetadataStore() - Method in class loci.formats.in.VectraReader
- initMetadataStore() - Method in class loci.formats.in.VentanaReader
- initMinMax() - Method in class loci.formats.MinMaxCalculator
-
Ensures internal min/max variables are initialized properly.
- initOMEMetadata() - Method in class loci.formats.in.LiFlimReader
- initOriginalMetadata() - Method in class loci.formats.in.LiFlimReader
- initPixels() - Method in class loci.formats.in.DeltavisionReader
- initPlaneReader() - Method in class loci.formats.in.AmiraReader
- initPOIService() - Method in class loci.formats.in.FV1000Reader
- initPOIService() - Method in class loci.formats.in.IPWReader
- initPOIService() - Method in class loci.formats.in.PCIReader
- initPOIService() - Method in class loci.formats.in.ZeissXRMReader
- initPOIService() - Method in class loci.formats.in.ZeissZVIReader
- initReader(int, int) - Method in class loci.formats.FileStitcher
- initReader(IFormatReader, String, boolean) - Method in class loci.formats.in.CellWorxReader
- initReaders(List<String>) - Method in class loci.formats.in.LeicaMicrosystemsMetadata.MultipleImagesReader
-
Creates an internal reader for each image file
- initResFile(String) - Method in class loci.formats.in.FlexReader
-
Initialize the dataset from a .res file.
- initStack(long) - Method in class loci.formats.in.OBFReader
- initStandardMetadata() - Method in class loci.formats.in.BaseTiffReader
-
Parses standard metadata.
- initStandardMetadata() - Method in class loci.formats.in.DNGReader
- initStandardMetadata() - Method in class loci.formats.in.FEITiffReader
- initStandardMetadata() - Method in class loci.formats.in.FluoviewReader
- initStandardMetadata() - Method in class loci.formats.in.ImaconReader
- initStandardMetadata() - Method in class loci.formats.in.ImprovisionTiffReader
- initStandardMetadata() - Method in class loci.formats.in.IonpathMIBITiffReader
- initStandardMetadata() - Method in class loci.formats.in.JPKReader
- initStandardMetadata() - Method in class loci.formats.in.LeicaSCNReader
- initStandardMetadata() - Method in class loci.formats.in.LEOReader
- initStandardMetadata() - Method in class loci.formats.in.MetamorphReader
- initStandardMetadata() - Method in class loci.formats.in.NDPIReader
- initStandardMetadata() - Method in class loci.formats.in.NikonElementsTiffReader
- initStandardMetadata() - Method in class loci.formats.in.NikonReader
- initStandardMetadata() - Method in class loci.formats.in.NikonTiffReader
- initStandardMetadata() - Method in class loci.formats.in.PyramidTiffReader
- initStandardMetadata() - Method in class loci.formats.in.SEQReader
- initStandardMetadata() - Method in class loci.formats.in.SimplePCITiffReader
- initStandardMetadata() - Method in class loci.formats.in.SISReader
- initStandardMetadata() - Method in class loci.formats.in.SlidebookTiffReader
- initStandardMetadata() - Method in class loci.formats.in.SVSReader
- initStandardMetadata() - Method in class loci.formats.in.TiffReader
- initStandardMetadata() - Method in class loci.formats.in.TrestleReader
- initStandardMetadata() - Method in class loci.formats.in.VectraReader
- initStandardMetadata() - Method in class loci.formats.in.VentanaReader
- initStandDetails(int) - Method in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataStoreInitializer
-
Adds microscope and objective details from the reader's
MetadataTempBufferto itsMetadataStore - initTiffParser() - Method in class loci.formats.in.LeicaSCNReader
- initTiffParser() - Method in class loci.formats.in.LEOReader
- initTiffParser() - Method in class loci.formats.in.MinimalTiffReader
-
Reinitialize the underlying TiffParser.
- initVars(String) - Method in class loci.formats.in.BaseZeissReader
- initVars(String) - Method in class loci.formats.in.ZeissTIFFReader
- initVars(String) - Method in class loci.formats.in.ZeissZVIReader
- INK_NAMES - Static variable in class loci.formats.tiff.IFD
- INK_SET - Static variable in class loci.formats.tiff.IFD
- inPixels - Variable in class loci.formats.in.BDVReader.BDVXMLHandler
- inPixels - Variable in class loci.formats.in.OMEXMLReader.OMEXMLHandler
- INPLANE_PHASE_ENCODING_DIRECTION - Enum constant in enum class loci.formats.dicom.DicomAttribute
- input - Variable in class loci.formats.gui.DataConverter
- input - Variable in class loci.formats.Memoizer.KryoDeser
- inputOrder - Variable in class loci.formats.SwappableMetadata
-
Order in which dimensions are stored.
- inputOrder - Variable in class loci.plugins.in.ImporterOptions
- INR_MAGIC - Static variable in class loci.formats.in.INRReader
- INRReader - Class in loci.formats.in
-
INRReader is the file format reader for INR files.
- INRReader() - Constructor for class loci.formats.in.INRReader
-
Constructs a new INR reader.
- insert(ImageProcessor, int, int) - Method in class loci.plugins.util.RecordedImageProcessor
- insertChannel(int, OIRReader.Channel) - Method in class loci.formats.in.OIRReader
-
Insert the given Channel into the list of channels, at the given index.
- insertResolution(OMEPyramidStore.Resolution, int, int) - Method in class loci.formats.ome.OMEPyramidStore
-
Store the given Resolution object at the given indices.
- insertWarningComment(String) - Method in class loci.formats.out.OMETiffWriter
- install(String) - Static method in class loci.plugins.Updater
-
Install the tools bundle which can be retrieved from the specified path.
- install(String, String) - Method in class loci.formats.UpgradeChecker
-
Download and install a JAR file from the given URL.
- installButton - Variable in class loci.plugins.config.ConfigWindow
- installIndividualJars(String, String) - Method in class loci.formats.UpgradeChecker
-
Download and install all of the individual JAR files into the given directory.
- InstallWizard - Class in loci.plugins.config
-
A wizard for walking users through installation of third party libraries and plugins used by the Bio-Formats plugins.
- InstallWizard() - Constructor for class loci.plugins.config.InstallWizard
- INSTANCE_AVAILABILITY - Enum constant in enum class loci.formats.dicom.DicomAttribute
- INSTANCE_CREATOR - Enum constant in enum class loci.formats.dicom.DicomAttribute
- INSTANCE_NUMBER - Enum constant in enum class loci.formats.dicom.DicomAttribute
- instanceUID - Variable in class loci.formats.in.DicomReader
- instanceUIDValue - Variable in class loci.formats.out.DicomWriter
- INSTITUTION_ADDRESS - Enum constant in enum class loci.formats.dicom.DicomAttribute
- INSTITUTION_CODE_SEQUENCE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- INSTITUTION_NAME - Enum constant in enum class loci.formats.dicom.DicomAttribute
- INSTITUTIONAL_DEPARTMENT_NAME - Enum constant in enum class loci.formats.dicom.DicomAttribute
- institutions - Variable in class loci.formats.in.BrukerReader
- instrumentModel - Variable in class loci.formats.in.NDPIReader
- instrumentType - Variable in class loci.formats.in.OperettaReader.OperettaHandler
- INT - Enum constant in enum class loci.formats.in.SPEReader.SpeHeaderType
- INT - Static variable in class loci.formats.in.CellSensReader
- INT - Static variable in class loci.formats.in.GatanReader
- INT_2 - Static variable in class loci.formats.in.CellSensReader
- INT_3 - Static variable in class loci.formats.in.CellSensReader
- INT_4 - Static variable in class loci.formats.in.CellSensReader
- INT_ARRAY_2 - Static variable in class loci.formats.in.CellSensReader
- INT_ARRAY_3 - Static variable in class loci.formats.in.CellSensReader
- INT_ARRAY_4 - Static variable in class loci.formats.in.CellSensReader
- INT_ARRAY_5 - Static variable in class loci.formats.in.CellSensReader
- INT_INTERVAL - Static variable in class loci.formats.in.CellSensReader
- INT_RECT - Static variable in class loci.formats.in.CellSensReader
- INT16 - Static variable in class loci.formats.FormatTools
-
Identifies the INT16 data type used to store pixel values.
- INT16 - Static variable in class loci.formats.in.SPEReader
- INT16_TYPE - Static variable in class loci.formats.in.KLBReader
- INT32 - Static variable in class loci.formats.FormatTools
-
Identifies the INT32 data type used to store pixel values.
- INT32 - Static variable in class loci.formats.in.SPEReader
- INT32_TYPE - Static variable in class loci.formats.in.KLBReader
- INT64_TYPE - Static variable in class loci.formats.in.KLBReader
- INT8 - Static variable in class loci.formats.FormatTools
-
Identifies the INT8 data type used to store pixel values.
- INT8_TYPE - Static variable in class loci.formats.in.KLBReader
- INTARRAY - Enum constant in enum class loci.formats.in.SPEReader.SpeHeaderType
- INTELLECTUAL_PROPERTY - Enum constant in enum class loci.formats.codec.JPEG2000BoxType
- intenScaling - Variable in class loci.formats.in.DeltavisionReader.DVExtHdrFields
-
Intensity scaling factor.
- INTENSIFIER_SIZE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- intensity - Variable in class loci.formats.in.LeicaHandler.Laser
- intensity - Variable in class loci.formats.in.SDTReader
-
Whether to combine lifetime bins into single intensity image planes.
- intensity - Variable in class loci.formats.in.TecanReader.Channel
- intensity - Variable in class loci.formats.in.ZeissCZIReader.Channel
- INTENSITY_STRING - Enum constant in enum class loci.formats.in.SPEReader.SpeHeaderEntry
- INTERFACE_TYPE - Enum constant in enum class loci.formats.in.SPEReader.SpeHeaderEntry
- interlace - Variable in class loci.formats.in.APNGReader
- interlace - Variable in class loci.formats.in.GIFReader
-
Interlace flag.
- interlaced - Variable in class loci.formats.codec.MJPBCodecOptions
-
Indicates whether or not channels are interlaced.
- interlaced - Variable in class loci.formats.in.QTReader
-
Set to true if the scanlines in a plane are interlaced (mjpb only).
- interleaved - Variable in class loci.formats.codec.CodecOptions
-
Indicates whether or not channels are interleaved.
- interleaved - Variable in class loci.formats.CoreMetadata
-
True if channels are stored RGBRGBRGB...; false if channels are stored RRR...GGG...BBB...
- interleaved - Variable in class loci.formats.FormatWriter
-
Whether the channels in an RGB image are interleaved.
- internalOffsets - Variable in class loci.formats.in.AmiraReader.HxRLE
- internalStamps - Variable in class loci.formats.in.MetamorphReader
- interpolate(short[], byte[], int[], int, int, boolean) - Static method in class loci.formats.ImageTools
- INTERVALS_ACQUIRED - Enum constant in enum class loci.formats.dicom.DicomAttribute
- INTERVALS_REJECTED - Enum constant in enum class loci.formats.dicom.DicomAttribute
- INTERVENTION_DESCRIPTION - Enum constant in enum class loci.formats.dicom.DicomAttribute
- INTERVENTION_DRUG_DOSE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- INTERVENTION_DRUG_INFORMATION_SEQUENCE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- INTERVENTION_DRUG_NAME - Enum constant in enum class loci.formats.dicom.DicomAttribute
- INTERVENTION_DRUG_SEQUENCE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- INTERVENTION_DRUG_START_TIME - Enum constant in enum class loci.formats.dicom.DicomAttribute
- INTERVENTION_DRUG_STOP_TIME - Enum constant in enum class loci.formats.dicom.DicomAttribute
- INTERVENTION_SEQUENCE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- INTERVENTION_STATUS - Enum constant in enum class loci.formats.dicom.DicomAttribute
- intFormat(int, int) - Static method in class loci.formats.in.MetamorphReader
-
Formats an integer value with leading 0s if needed.
- intFormatMax(int, int) - Static method in class loci.formats.in.MetamorphReader
-
Formats an integer with leading 0 using maximum sequence number.
- IntIM3Record(String, int, long, int) - Constructor for class loci.formats.in.IM3Reader.IntIM3Record
- IntIntPair(Integer, Integer) - Constructor for class loci.formats.in.SlideBook7Reader.IntIntPair
- intValue() - Method in class loci.formats.tiff.TiffRational
-
Returns the value of the specified number as an int.
- INVALID - Enum constant in enum class loci.formats.dicom.DicomAttribute
- INVALID_PIXEL_DATA - Enum constant in enum class loci.formats.dicom.DicomAttribute
- INVALID_PIXELS - Static variable in class loci.formats.in.FEIReader
- invalidAndMark(int) - Method in class loci.formats.in.SPCReader
- invalidAndMarkInit(int) - Method in class loci.formats.in.SPCReader
- InveonReader - Class in loci.formats.in
-
InveonReader is the file format reader for Inveon files.
- InveonReader() - Constructor for class loci.formats.in.InveonReader
-
Constructs a new Inveon reader.
- inverseRgb - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataTempBuffer
- INVERSION_TIME - Enum constant in enum class loci.formats.dicom.DicomAttribute
- invert() - Method in class loci.plugins.util.RecordedImageProcessor
- inverted - Variable in class loci.formats.in.DicomReader
- invertLut() - Method in class loci.plugins.util.RecordedImageProcessor
- invertX - Variable in class loci.formats.in.RHKReader
- invertY - Variable in class loci.formats.in.BMPReader
- invertY - Variable in class loci.formats.in.ICSReader
-
Whether or not the image is inverted along the Y axis.
- invertY - Variable in class loci.formats.in.RHKReader
- invokeMethod(String, String, FormatEntry, boolean) - Method in class loci.plugins.config.ConfigWindow
- IONPATH_MIBI_SOFTWARE_PREFIX - Static variable in class loci.formats.in.IonpathMIBITiffReader
-
TIFF software tag prefix for Ionpath MIBI files.
- IonpathMIBITiffReader - Class in loci.formats.in
-
IonpathMIBITiffReader is the file format reader for Ionpath MIBI TIFF files.
- IonpathMIBITiffReader() - Constructor for class loci.formats.in.IonpathMIBITiffReader
-
Constructs a new Ionpath MIBI reader.
- IPLabReader - Class in loci.formats.in
-
IPLabReader is the file format reader for IPLab (.IPL) files.
- IPLabReader() - Constructor for class loci.formats.in.IPLabReader
-
Constructs a new IPLab reader.
- IPW_MAGIC_BYTES - Static variable in class loci.formats.in.IPWReader
- IPWReader - Class in loci.formats.in
-
IPWReader is the file format reader for Image-Pro Workspace (IPW) files.
- IPWReader() - Constructor for class loci.formats.in.IPWReader
-
Constructs a new IPW reader.
- IPyramidHandler - Interface in loci.formats
-
Interface for defining image pyramids.
- IPyramidStore - Interface in loci.formats.meta
-
Interface for defining pyramid resolutions.
- ir - Variable in class loci.plugins.in.ThumbLoader
- iris - Variable in class loci.formats.in.ZeissLSMReader.Recording
- IS - Enum constant in enum class loci.formats.dicom.DicomVR
- IS_GLITCHED - Static variable in class loci.plugins.prefs.OptionsDialog
-
Flag indicating whether to invoke workaround for AWT refresh bug.
- IS_LITTLE - Static variable in class loci.formats.in.DCIMGReader
- IS_LITTLE - Static variable in class loci.formats.in.ImarisReader
-
Specifies endianness.
- IS_TRANSMISSION - Static variable in class loci.formats.in.CellSensReader
- isAllowedKey(String) - Method in class loci.formats.ClassList
-
Returns whether a given key is an allowed option.
- isAutoscale() - Method in class loci.plugins.in.ImporterOptions
- isBGR(short[]) - Method in class loci.formats.services.JPEGXRServiceImpl
- isBigTiff - Variable in class loci.formats.out.TiffWriter
-
Whether or not the output file is a BigTIFF file.
- isBigTiff() - Method in class loci.formats.tiff.IFD
-
Gets whether this is a BigTIFF IFD.
- isBigTiff() - Method in class loci.formats.tiff.TiffParser
-
Returns whether or not the current TIFF file contains BigTIFF data.
- isBigTiff() - Method in class loci.formats.tiff.TiffSaver
-
Returns whether or not we are writing BigTIFF data.
- isBitOnByteBoundary() - Method in class loci.formats.codec.BitBuffer
-
Deprecated.Checks if the current position is on a byte boundary, that is the next bit in the byte array is the first bit in a byte.
- isCellsensFailOnMissing() - Static method in class loci.plugins.util.LociPrefs
- isCertain() - Method in class loci.formats.AxisGuesser
-
Gets whether the guesser is confident that all axes are correct.
- isColorLut() - Method in class loci.plugins.util.RecordedImageProcessor
- isColorModeColorized() - Method in class loci.plugins.in.ImporterOptions
- isColorModeComposite() - Method in class loci.plugins.in.ImporterOptions
- isColorModeCustom() - Method in class loci.plugins.in.ImporterOptions
- isColorModeDefault() - Method in class loci.plugins.in.ImporterOptions
- isColorModeGrayscale() - Method in class loci.plugins.in.ImporterOptions
- isCompatibleRaster(Raster) - Method in class loci.formats.gui.Index16ColorModel
- isCompatibleRaster(Raster) - Method in class loci.formats.gui.SignedColorModel
- isCompatibleRaster(Raster) - Method in class loci.formats.gui.UnsignedIntColorModel
- isCompressed - Variable in class loci.formats.in.LIMReader
- isConcatenate() - Method in class loci.plugins.in.ImporterOptions
- isContainer(String) - Method in class loci.formats.in.QTReader
-
Checks if the given String is a container atom type.
- isCorrectionImage(TissueFAXSReader.ScanRegion) - Method in class loci.formats.in.TissueFAXSReader
- isCS_sRGB() - Method in class loci.formats.gui.TwoChannelColorSpace
- isCurrentFile(String) - Method in class loci.formats.in.OIRReader
- isDeflate - Variable in class loci.formats.dicom.DicomTile
- isDeflate - Variable in class loci.formats.in.DicomReader
- isDimensions(String) - Method in class loci.formats.in.ND2Handler
-
Returns whether or not the specified key is denotes dimensions.
- isEnabled - Variable in class loci.formats.in.CellVoyagerReader.ChannelInfo
- isEqual(OMEXMLMetadata, OMEXMLMetadata) - Method in interface loci.formats.services.OMEXMLService
-
Determine whether or not two OMEXMLMetadata objects are equal.
- isEqual(OMEXMLMetadata, OMEXMLMetadata) - Method in class loci.formats.services.OMEXMLServiceImpl
- isExtendedDepthOfField() - Method in class loci.formats.in.DicomReader
- isFalseColor() - Method in class loci.formats.FileStitcher
- isFalseColor() - Method in class loci.formats.FormatReader
- isFalseColor() - Method in interface loci.formats.IFormatReader
-
Returns false if
IFormatReader.isIndexed()is false, or ifIFormatReader.isIndexed()is true and the lookup table represents "real" color data. - isFalseColor() - Method in class loci.formats.ImageReader
- isFalseColor() - Method in class loci.formats.ReaderWrapper
- isFalseColor() - Method in class loci.formats.WrappedReader
- isFiji() - Static method in class loci.plugins.Updater
-
Returns true if the current ImageJ instance is actually a Fiji instance.
- isFilled() - Method in class loci.formats.ChannelFiller
-
Returns true if the indices are being factored out.
- isFirstTime() - Method in class loci.plugins.in.ImporterOptions
- isFixed() - Method in class loci.formats.FilePatternBlock
-
Whether or not this is a fixed-width block.
- isFLIM - Variable in class loci.formats.in.ImspectorReader
-
Whether or not this file contains FLIM data.
- isFLIMLabel(String) - Method in class loci.formats.in.OBFReader
- isFloat - Variable in class loci.formats.in.BrukerReader
- isFloatingPoint(int) - Static method in class loci.formats.FormatTools
-
Determines whether the given pixel type is floating point or integer.
- isFloatingPoint(IFormatReader) - Static method in class loci.formats.FormatTools
-
Determines whether the given reader represents any floating point data.
- isForceThumbnails() - Method in class loci.plugins.in.ImporterOptions
- isFullPlane(int, int, int, int) - Method in class loci.formats.FormatWriter
-
Returns true if the given rectangle coordinates correspond to a full image in the given series.
- isGreaterThanEpsilon(double) - Method in class loci.formats.in.SlidebookReader
-
Returns true if the given double is greater than epsilon (defined here as 0.000001), i.e.
- isGroupFiles() - Method in class loci.formats.FileStitcher
- isGroupFiles() - Method in class loci.formats.FormatReader
- isGroupFiles() - Method in interface loci.formats.IFormatReader
-
Returns true if we should group files in multi-file formats.
- isGroupFiles() - Method in class loci.formats.ImageReader
- isGroupFiles() - Method in class loci.formats.in.FilePatternReader
- isGroupFiles() - Method in class loci.formats.ReaderWrapper
- isGroupFiles() - Method in class loci.plugins.in.ImporterOptions
- isGroupFiles(String[]) - Method in class loci.plugins.macro.LociFunctions
- isHarmony - Variable in class loci.formats.in.OperettaReader.OperettaHandler
- isHCS - Variable in class loci.formats.in.MetamorphReader
- isHTTP() - Method in class loci.plugins.in.ImporterOptions
- isInCache(int) - Method in class loci.formats.cache.Cache
-
Returns true if the object at the given index is in the cache.
- isInCache(int[]) - Method in class loci.formats.cache.Cache
-
Returns true if the object at the given dimensional position is in the cache.
- isIndexed() - Method in class loci.formats.ChannelFiller
- isIndexed() - Method in class loci.formats.ChannelMerger
- isIndexed() - Method in class loci.formats.FileStitcher
- isIndexed() - Method in class loci.formats.FormatReader
- isIndexed() - Method in interface loci.formats.IFormatReader
-
Gets whether the image planes are indexed color.
- isIndexed() - Method in class loci.formats.ImageReader
- isIndexed() - Method in class loci.formats.ReaderWrapper
- isIndexed() - Method in class loci.formats.WrappedReader
- isIndexed(String[]) - Method in class loci.plugins.macro.LociFunctions
- isIntensity() - Method in class loci.formats.in.SDTReader
-
Gets whether the reader is combining each lifetime histogram into a summed intensity image plane.
- isInterleaved() - Method in class loci.formats.ChannelMerger
- isInterleaved() - Method in class loci.formats.FileStitcher
- isInterleaved() - Method in class loci.formats.FormatReader
- isInterleaved() - Method in class loci.formats.FormatWriter
- isInterleaved() - Method in interface loci.formats.IFormatReader
-
Gets whether or not the channels are interleaved.
- isInterleaved() - Method in interface loci.formats.IFormatWriter
-
Gets whether or not the channels in an image are interleaved.
- isInterleaved() - Method in class loci.formats.ImageReader
- isInterleaved() - Method in class loci.formats.ImageWriter
- isInterleaved() - Method in class loci.formats.ReaderWrapper
- isInterleaved() - Method in class loci.formats.WrappedReader
- isInterleaved() - Method in class loci.formats.WriterWrapper
- isInterleaved(int) - Method in class loci.formats.FileStitcher
- isInterleaved(int) - Method in class loci.formats.FormatReader
- isInterleaved(int) - Method in interface loci.formats.IFormatReader
-
Gets whether or not the given sub-channel is interleaved.
- isInterleaved(int) - Method in class loci.formats.ImageReader
- isInterleaved(int) - Method in class loci.formats.in.ICSReader
- isInterleaved(int) - Method in class loci.formats.in.SDTReader
- isInterleaved(int) - Method in class loci.formats.ReaderWrapper
- isInterleaved(int) - Method in class loci.formats.WrappedReader
- isInterleaved(String[]) - Method in class loci.plugins.macro.LociFunctions
- isInterleavedSubC(Double, String[]) - Method in class loci.plugins.macro.LociFunctions
- isInvertedLut() - Method in class loci.plugins.util.RecordedImageProcessor
- isInvertX() - Method in class loci.formats.in.PrairieMetadata
-
Gets whether the stage position X coordinates are inverted (i.e., left-to-right).
- isInvertY() - Method in class loci.formats.in.PrairieMetadata
-
Gets whether the stage position Y coordinates are inverted (i.e., bottom-to-top).
- isJNG - Variable in class loci.formats.in.MNGReader
- isJP2K - Variable in class loci.formats.dicom.DicomTile
- isJP2K - Variable in class loci.formats.in.DicomReader
- isJPEG - Variable in class loci.formats.dicom.DicomTile
- isJPEG - Variable in class loci.formats.in.BaseZeissReader
- isJPEG - Variable in class loci.formats.in.DicomReader
- isJPEG - Variable in class loci.formats.in.ND2Reader
-
Whether or not the pixel data is compressed using JPEG 2000.
- isLegacy() - Method in class loci.formats.DelegateReader
-
Gets whether to use the legacy reader by default.
- isLeicaLIFPhysicalSizeBackwardsCompatible() - Static method in class loci.plugins.util.LociPrefs
- isLibraryLoaded() - Method in interface loci.formats.services.JPEGTurboService
- isLibraryLoaded() - Method in class loci.formats.services.JPEGTurboServiceImpl
- isLittleEndian() - Method in class loci.formats.FileStitcher
- isLittleEndian() - Method in class loci.formats.FormatReader
- isLittleEndian() - Method in interface loci.formats.IFormatReader
-
Gets whether the data is in little-endian format.
- isLittleEndian() - Method in class loci.formats.ImageReader
- isLittleEndian() - Method in class loci.formats.ReaderWrapper
- isLittleEndian() - Method in class loci.formats.tiff.IFD
-
Gets whether the TIFF information in this IFD is little-endian.
- isLittleEndian() - Method in class loci.formats.tiff.TiffSaver
-
Returns whether or not we are writing little-endian data.
- isLittleEndian() - Method in class loci.formats.WrappedReader
- isLittleEndian(String[]) - Method in class loci.plugins.macro.LociFunctions
- isLoadedFromMemo() - Method in class loci.formats.Memoizer
-
Returns whether the
ReaderWrapper.readerinstance currently active was loaded from the memo file duringMemoizer.setId(String). - isLocal() - Method in class loci.plugins.in.ImporterOptions
- isLossless - Variable in class loci.formats.in.ND2Handler
- isLossless - Variable in class loci.formats.in.ND2Reader
-
Whether or not the pixel data is losslessly compressed.
- isLossless() - Method in class loci.formats.in.ND2Handler
- isLutInverted - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.Channel
- isMetadataComplete() - Method in class loci.formats.FormatReader
- isMetadataComplete() - Method in interface loci.formats.IFormatReader
-
Returns true if this format's metadata is completely parsed.
- isMetadataComplete() - Method in class loci.formats.ImageReader
- isMetadataComplete() - Method in class loci.formats.ReaderWrapper
- isMetadataComplete() - Method in class loci.formats.WrappedReader
- isMetadataComplete(String[]) - Method in class loci.plugins.macro.LociFunctions
- isMetadataFiltered() - Method in class loci.formats.FormatReader
- isMetadataFiltered() - Method in interface loci.formats.IFormatReader
-
Returns true if ugly metadata (entries with unprintable characters, and extremely large entries) are discarded from the metadata table.
- isMetadataFiltered() - Method in class loci.formats.ImageReader
- isMetadataFiltered() - Method in class loci.formats.in.FilePatternReader
- isMetadataFiltered() - Method in class loci.formats.ReaderWrapper
- isMetadataFiltered(String[]) - Method in class loci.plugins.macro.LociFunctions
- isMINC2 - Variable in class loci.formats.in.MINCReader
- isMinimumMetadata() - Method in class loci.formats.in.PrairieReader
-
Gets whether to populate only the minimum required metadata.
- isMinMaxPopulated() - Method in class loci.formats.MinMaxCalculator
-
Returns true if the values returned by getChannelGlobalMinimum/Maximum can be trusted.
- isModulo - Variable in class loci.formats.tools.MakeTestOmeTiff
- isNormalized() - Method in class loci.formats.FormatReader
- isNormalized() - Method in interface loci.formats.IFormatReader
-
Returns true if we should normalize float data.
- isNormalized() - Method in class loci.formats.ImageReader
- isNormalized() - Method in class loci.formats.in.FilePatternReader
- isNormalized() - Method in class loci.formats.ReaderWrapper
- isNormalized(Boolean[]) - Method in class loci.plugins.macro.LociFunctions
- isNumeric() - Method in class loci.formats.FilePatternBlock
-
Whether or not this is a numeric block.
- ISO - Static variable in class loci.formats.in.NikonReader
- ISO_SENSITIVITY - Static variable in class loci.formats.in.CellSensReader
- ISO_SPEED_RATINGS - Static variable in class loci.formats.tiff.IFD
- isOIB - Variable in class loci.formats.in.FV1000Reader
-
Flag indicating this is an OIB dataset.
- isOmero(String) - Method in class loci.formats.FormatReader
- isOmero(String) - Method in class loci.formats.ImageReader
- isOMERO() - Method in class loci.plugins.in.ImporterOptions
- isOMEXMLMetadata(Object) - Method in interface loci.formats.services.OMEXMLService
-
Checks whether the given object is an OME-XML metadata object.
- isOMEXMLMetadata(Object) - Method in class loci.formats.services.OMEXMLServiceImpl
- isOMEXMLRoot(Object) - Method in interface loci.formats.services.OMEXMLService
-
Checks whether the given object is an OME-XML root object.
- isOMEXMLRoot(Object) - Method in class loci.formats.services.OMEXMLServiceImpl
- isOne() - Method in class org.libjpegturbo.turbojpeg.TJScalingFactor
-
Returns true or false, depending on whether this instance is equal to 1/1.
- isOrderCertain() - Method in class loci.formats.FileStitcher
- isOrderCertain() - Method in class loci.formats.FormatReader
- isOrderCertain() - Method in interface loci.formats.IFormatReader
-
Gets whether the dimension order and sizes are known, or merely guesses.
- isOrderCertain() - Method in class loci.formats.ImageReader
- isOrderCertain() - Method in class loci.formats.ReaderWrapper
- isOrderCertain() - Method in class loci.formats.WrappedReader
- isOrderCertain(String[]) - Method in class loci.plugins.macro.LociFunctions
- isOriginalMetadataPopulated() - Method in class loci.formats.FormatReader
- isOriginalMetadataPopulated() - Method in interface loci.formats.IFormatReader
-
Returns true if we should save proprietary metadata in the MetadataStore.
- isOriginalMetadataPopulated() - Method in class loci.formats.ImageReader
- isOriginalMetadataPopulated() - Method in class loci.formats.in.FilePatternReader
- isOriginalMetadataPopulated() - Method in class loci.formats.ReaderWrapper
- isOriginalMetadataPopulated(Boolean[]) - Method in class loci.plugins.macro.LociFunctions
- isPositiveValue(Double) - Static method in class loci.formats.FormatTools
- isPossible(String, String) - Method in class loci.plugins.prefs.OptionsList
-
Gets whether the specified value is a possible one for the string option with the given key.
- isPreviewName(String) - Method in class loci.formats.in.FV1000Reader
- isPrivateContentCreator() - Method in class loci.formats.dicom.DicomTag
-
See https://dicom.nema.org/dicom/2013/output/chtml/part05/sect_7.8.html
- isPseudoColorLut() - Method in class loci.plugins.util.RecordedImageProcessor
- isPyramidResolution(int, int) - Method in class loci.formats.in.NDPISReader
- isQuiet() - Method in class loci.plugins.in.ImporterOptions
- isRawCodestream - Variable in class loci.formats.in.JPEG2000MetadataParser
-
Whether or not the codestream is raw and not JP2 boxed.
- isRawCodestream() - Method in class loci.formats.in.JPEG2000MetadataParser
-
Whether or not the codestream is raw and not JP2 boxed.
- isReaderEnabled(Class<? extends IFormatReader>) - Static method in class loci.plugins.util.LociPrefs
- isReaderEnabled(FormatEntry) - Method in class loci.plugins.config.ConfigWindow
- isReaderPref(String, FormatEntry, boolean) - Method in class loci.plugins.config.ConfigWindow
- isReaderWindowless(FormatEntry) - Method in class loci.plugins.config.ConfigWindow
- isReallySequential() - Method in class loci.formats.out.DicomWriter
- isRegex - Variable in class loci.formats.FilePattern
-
Whether or not this FilePattern represents a regular expression.
- isRegex() - Method in class loci.formats.FilePattern
-
Returns whether or not this pattern is a regular expression.
- isRGB() - Method in class loci.formats.ChannelFiller
- isRGB() - Method in class loci.formats.ChannelMerger
- isRGB() - Method in class loci.formats.ChannelSeparator
- isRGB() - Method in class loci.formats.FileStitcher
- isRGB() - Method in class loci.formats.FormatReader
- isRGB() - Method in interface loci.formats.IFormatReader
-
Checks if the image planes in the file have more than one channel per
IFormatReader.openBytes(int)call. - isRGB() - Method in class loci.formats.ImageReader
- isRGB() - Method in class loci.formats.in.LeicaMicrosystemsMetadata.MultipleImagesReader
- isRGB() - Method in class loci.formats.ReaderWrapper
- isRGB() - Method in class loci.formats.WrappedReader
- isRLE - Variable in class loci.formats.dicom.DicomTile
- isRLE - Variable in class loci.formats.in.DicomReader
- isSaved() - Method in class loci.plugins.prefs.Option
-
Gets whether option should be saved to ImageJ preferences file.
- isSaved(String) - Method in class loci.plugins.prefs.OptionsList
-
Gets whether the option with the given key is saved to the ImageJ preferences file.
- isSavedToMemo() - Method in class loci.formats.Memoizer
-
Returns whether the
ReaderWrapper.readerinstance currently active was saved to the memo file duringMemoizer.setId(String). - isSDTIntensity() - Static method in class loci.plugins.util.LociPrefs
- isSeriesOn(int) - Method in class loci.plugins.in.ImporterOptions
- isSet(String) - Method in class loci.plugins.prefs.OptionsList
-
Gets the value of the boolean option with the given key.
- isSetByDefault(String) - Method in class loci.plugins.prefs.OptionsList
-
Gets the default value of the boolean option with the given key.
- IsSFMT(String) - Method in class loci.formats.in.SlideBook7Reader.CImageGroup
- isShowMetadata() - Method in class loci.plugins.in.ImporterOptions
- isShowOMEXML() - Method in class loci.plugins.in.ImporterOptions
- isSigned(int) - Static method in class loci.formats.FormatTools
-
Determines whether the given pixel type is signed or unsigned.
- isSIM - Variable in class loci.formats.in.ZeissLSMReader
- isSingleFile(String) - Method in class loci.formats.FormatReader
- isSingleFile(String) - Method in interface loci.formats.IFormatReader
-
Returns true if the named file is expected to be the only file in the dataset.
- isSingleFile(String) - Method in class loci.formats.ImageReader
- isSingleFile(String) - Method in class loci.formats.in.AFIReader
- isSingleFile(String) - Method in class loci.formats.in.AnalyzeReader
- isSingleFile(String) - Method in class loci.formats.in.APLReader
- isSingleFile(String) - Method in class loci.formats.in.BDReader
- isSingleFile(String) - Method in class loci.formats.in.BioRadReader
- isSingleFile(String) - Method in class loci.formats.in.BrukerReader
- isSingleFile(String) - Method in class loci.formats.in.CellSensReader
- isSingleFile(String) - Method in class loci.formats.in.CellVoyagerReader
- isSingleFile(String) - Method in class loci.formats.in.ColumbusReader
- isSingleFile(String) - Method in class loci.formats.in.CV7000Reader
- isSingleFile(String) - Method in class loci.formats.in.DCIMGReader
- isSingleFile(String) - Method in class loci.formats.in.DeltavisionReader
- isSingleFile(String) - Method in class loci.formats.in.FakeReader
- isSingleFile(String) - Method in class loci.formats.in.FilePatternReader
- isSingleFile(String) - Method in class loci.formats.in.FlexReader
- isSingleFile(String) - Method in class loci.formats.in.FujiReader
- isSingleFile(String) - Method in class loci.formats.in.FV1000Reader
- isSingleFile(String) - Method in class loci.formats.in.HitachiReader
- isSingleFile(String) - Method in class loci.formats.in.ICSReader
- isSingleFile(String) - Method in class loci.formats.in.ImagicReader
- isSingleFile(String) - Method in class loci.formats.in.InCellReader
- isSingleFile(String) - Method in class loci.formats.in.JDCEReader
- isSingleFile(String) - Method in class loci.formats.in.L2DReader
- isSingleFile(String) - Method in class loci.formats.in.LeicaReader
- isSingleFile(String) - Method in class loci.formats.in.MetamorphReader
- isSingleFile(String) - Method in class loci.formats.in.MIASReader
- isSingleFile(String) - Method in class loci.formats.in.MicroCTReader
- isSingleFile(String) - Method in class loci.formats.in.MicromanagerReader
- isSingleFile(String) - Method in class loci.formats.in.NDPISReader
- isSingleFile(String) - Method in class loci.formats.in.NiftiReader
- isSingleFile(String) - Method in class loci.formats.in.NRRDReader
- isSingleFile(String) - Method in class loci.formats.in.OIRReader
- isSingleFile(String) - Method in class loci.formats.in.OlympusTileReader
- isSingleFile(String) - Method in class loci.formats.in.OMETiffReader
- isSingleFile(String) - Method in class loci.formats.in.OperettaReader
- isSingleFile(String) - Method in class loci.formats.in.PerkinElmerReader
- isSingleFile(String) - Method in class loci.formats.in.PrairieReader
- isSingleFile(String) - Method in class loci.formats.in.ScanrReader
- isSingleFile(String) - Method in class loci.formats.in.SlideBook7Reader
- isSingleFile(String) - Method in class loci.formats.in.SPCReader
- isSingleFile(String) - Method in class loci.formats.in.TCSReader
- isSingleFile(String) - Method in class loci.formats.in.TecanReader
- isSingleFile(String) - Method in class loci.formats.in.TillVisionReader
- isSingleFile(String) - Method in class loci.formats.in.VisitechReader
- isSingleFile(String) - Method in class loci.formats.in.XLEFReader
- isSingleFile(String) - Method in class loci.formats.in.ZeissLSMReader
- isSingleFile(String) - Method in class loci.formats.in.ZeissTIFFReader
- isSingleFile(String) - Method in class loci.formats.ReaderWrapper
- isSingleFile(String) - Method in class loci.formats.WrappedReader
- isSpecifyRanges() - Method in class loci.plugins.in.ImporterOptions
- isSpectralMode() - Method in class loci.formats.in.PrairieMetadata.Sequence
- isSplitChannels() - Method in class loci.plugins.in.ImporterOptions
- isSplitFocalPlanes() - Method in class loci.plugins.in.ImporterOptions
- isSplitTimepoints() - Method in class loci.plugins.in.ImporterOptions
- isSpool - Variable in class loci.formats.in.SlidebookReader
- isSPWStructure(String) - Method in class loci.formats.in.FakeReader
- ISSUER_OF_PATIENT_ID - Enum constant in enum class loci.formats.dicom.DicomAttribute
- isSupportedType(int) - Method in class loci.formats.FormatWriter
- isSupportedType(int) - Method in interface loci.formats.IFormatWriter
-
Checks if the given pixel type is supported.
- isSupportedType(int) - Method in class loci.formats.ImageWriter
- isSupportedType(int) - Method in class loci.formats.WriterWrapper
- isSwapDimensions() - Method in class loci.plugins.in.ImporterOptions
- isTable() - Method in interface loci.formats.in.PrairieMetadata.Value
- isTable() - Method in class loci.formats.in.PrairieMetadata.ValueItem
- isTable() - Method in class loci.formats.in.PrairieMetadata.ValueTable
- isThisType(byte[]) - Method in class loci.formats.FormatReader
- isThisType(byte[]) - Method in interface loci.formats.IFormatReader
-
Checks if the given block is a valid header for this file format.
- isThisType(byte[]) - Method in class loci.formats.ImageReader
- isThisType(byte[]) - Method in class loci.formats.ReaderWrapper
- isThisType(String) - Method in class loci.formats.FormatHandler
-
Checks if a file matches the type of this format handler.
- isThisType(String) - Method in class loci.formats.FormatReader
- isThisType(String) - Method in interface loci.formats.IFormatHandler
-
Checks if the given string is a valid filename for this file format.
- isThisType(String) - Method in class loci.formats.ImageReader
- isThisType(String) - Method in class loci.formats.ImageWriter
- isThisType(String) - Method in class loci.formats.out.PyramidOMETiffWriter
- isThisType(String) - Method in class loci.formats.ReaderWrapper
- isThisType(String) - Method in class loci.formats.WriterWrapper
- isThisType(String, boolean) - Method in class loci.formats.DelegateReader
- isThisType(String, boolean) - Method in class loci.formats.FormatReader
-
Checks if a file matches the type of this format reader.
- isThisType(String, boolean) - Method in interface loci.formats.IFormatReader
-
Checks if the given file is a valid instance of this file format.
- isThisType(String, boolean) - Method in class loci.formats.ImageReader
- isThisType(String, boolean) - Method in class loci.formats.in.AnalyzeReader
- isThisType(String, boolean) - Method in class loci.formats.in.APLReader
- isThisType(String, boolean) - Method in class loci.formats.in.BDReader
- isThisType(String, boolean) - Method in class loci.formats.in.BDVReader
- isThisType(String, boolean) - Method in class loci.formats.in.BioRadReader
- isThisType(String, boolean) - Method in class loci.formats.in.BrukerReader
- isThisType(String, boolean) - Method in class loci.formats.in.CellH5Reader
- isThisType(String, boolean) - Method in class loci.formats.in.CellVoyagerReader
- isThisType(String, boolean) - Method in class loci.formats.in.CellWorxReader
- isThisType(String, boolean) - Method in class loci.formats.in.ColumbusReader
- isThisType(String, boolean) - Method in class loci.formats.in.DeltavisionReader
- isThisType(String, boolean) - Method in class loci.formats.in.DicomReader
- isThisType(String, boolean) - Method in class loci.formats.in.FakeReader
- isThisType(String, boolean) - Method in class loci.formats.in.FujiReader
- isThisType(String, boolean) - Method in class loci.formats.in.FV1000Reader
- isThisType(String, boolean) - Method in class loci.formats.in.HitachiReader
- isThisType(String, boolean) - Method in class loci.formats.in.ImagicReader
- isThisType(String, boolean) - Method in class loci.formats.in.InCellReader
- isThisType(String, boolean) - Method in class loci.formats.in.InveonReader
- isThisType(String, boolean) - Method in class loci.formats.in.JEOLReader
- isThisType(String, boolean) - Method in class loci.formats.in.JPEGReader.DefaultJPEGReader
- isThisType(String, boolean) - Method in class loci.formats.in.JPKReader
- isThisType(String, boolean) - Method in class loci.formats.in.L2DReader
- isThisType(String, boolean) - Method in class loci.formats.in.LeicaReader
- isThisType(String, boolean) - Method in class loci.formats.in.LeicaSCNReader
- isThisType(String, boolean) - Method in class loci.formats.in.MetamorphReader
- isThisType(String, boolean) - Method in class loci.formats.in.MetaxpressTiffReader
- isThisType(String, boolean) - Method in class loci.formats.in.MIASReader
- isThisType(String, boolean) - Method in class loci.formats.in.MicromanagerReader
- isThisType(String, boolean) - Method in class loci.formats.in.MikroscanTiffReader
- isThisType(String, boolean) - Method in class loci.formats.in.NDPIReader
- isThisType(String, boolean) - Method in class loci.formats.in.NiftiReader
- isThisType(String, boolean) - Method in class loci.formats.in.NikonReader
- isThisType(String, boolean) - Method in class loci.formats.in.NRRDReader
- isThisType(String, boolean) - Method in class loci.formats.in.OMETiffReader
- isThisType(String, boolean) - Method in class loci.formats.in.OMEXMLReader
- isThisType(String, boolean) - Method in class loci.formats.in.OperettaReader
- isThisType(String, boolean) - Method in class loci.formats.in.PCORAWReader
- isThisType(String, boolean) - Method in class loci.formats.in.PDSReader
- isThisType(String, boolean) - Method in class loci.formats.in.PerkinElmerReader
- isThisType(String, boolean) - Method in class loci.formats.in.PrairieReader
- isThisType(String, boolean) - Method in class loci.formats.in.RCPNLReader
- isThisType(String, boolean) - Method in class loci.formats.in.ScanrReader
- isThisType(String, boolean) - Method in class loci.formats.in.SEQReader
- isThisType(String, boolean) - Method in class loci.formats.in.SlideBook7Reader
- isThisType(String, boolean) - Method in class loci.formats.in.SPCReader
- isThisType(String, boolean) - Method in class loci.formats.in.SVSReader
- isThisType(String, boolean) - Method in class loci.formats.in.TCSReader
- isThisType(String, boolean) - Method in class loci.formats.in.TecanReader
- isThisType(String, boolean) - Method in class loci.formats.in.TillVisionReader
- isThisType(String, boolean) - Method in class loci.formats.in.TrestleReader
- isThisType(String, boolean) - Method in class loci.formats.in.UnisokuReader
- isThisType(String, boolean) - Method in class loci.formats.in.VectraReader
- isThisType(String, boolean) - Method in class loci.formats.in.VentanaReader
- isThisType(String, boolean) - Method in class loci.formats.in.VisitechReader
- isThisType(String, boolean) - Method in class loci.formats.in.VolocityReader
- isThisType(String, boolean) - Method in class loci.formats.in.ZeissTIFFReader
- isThisType(String, boolean) - Method in class loci.formats.ReaderWrapper
- isThisType(String, String[]) - Method in class loci.plugins.macro.LociFunctions
- isThisType(RandomAccessInputStream) - Method in class loci.formats.DelegateReader
- isThisType(RandomAccessInputStream) - Method in class loci.formats.FormatReader
- isThisType(RandomAccessInputStream) - Method in interface loci.formats.IFormatReader
-
Checks if the given stream is a valid stream for this file format.
- isThisType(RandomAccessInputStream) - Method in class loci.formats.ImageReader
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.AFIReader
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.AliconaReader
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.AmiraReader
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.AnalyzeReader
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.APNGReader
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.ARFReader
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.AVIReader
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.BDReader
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.BDVReader
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.BioRadGelReader
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.BioRadReader
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.BioRadSCNReader
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.BMPReader
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.BrukerReader
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.BurleighReader
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.CanonRawReader
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.CellH5Reader
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.CellomicsReader
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.ColumbusReader
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.DCIMGReader
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.DeltavisionReader
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.DicomReader
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.DNGReader
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.Ecat7Reader
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.FEIReader
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.FEITiffReader
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.FlowSightReader
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.FluoviewReader
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.FujiReader
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.FV1000Reader
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.GatanDM2Reader
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.GatanReader
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.GelReader
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.GIFReader
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.HISReader
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.HitachiReader
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.HRDGDFReader
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.I2IReader
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.IM3Reader
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.ImaconReader
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.ImarisHDFReader
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.ImarisReader
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.IMODReader
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.ImprovisionTiffReader
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.ImspectorReader
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.InCell3000Reader
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.InCellReader
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.INRReader
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.InveonReader
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.IonpathMIBITiffReader
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.IPLabReader
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.IPWReader
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.IvisionReader
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.JEOLReader
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.JPEG2000Reader
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.JPEGReader.DefaultJPEGReader
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.JPXReader
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.KhorosReader
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.KodakReader
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.L2DReader
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.LeicaReader
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.LEOReader
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.LIFReader
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.LOFReader
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.MetamorphReader
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.MetamorphTiffReader
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.MIASReader
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.MicroCTReader
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.MicromanagerReader
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.MinimalTiffReader
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.MNGReader
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.MolecularImagingReader
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.MRCReader
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.MRWReader
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.ND2Reader
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.NDPISReader
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.NiftiReader
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.NikonElementsTiffReader
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.NikonReader
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.NikonTiffReader
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.NRRDReader
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.OBFReader
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.OIRReader
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.OMETiffReader
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.OMEXMLReader
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.OpenlabRawReader
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.OpenlabReader
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.OperettaReader
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.OxfordInstrumentsReader
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.PCIReader
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.PCORAWReader
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.PCXReader
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.PDSReader
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.PGMReader
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.PhotoshopTiffReader
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.PQBinReader
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.PrairieReader
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.PSDReader
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.PyramidTiffReader
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.QTReader
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.SBIGReader
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.ScanrReader
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.SEQReader
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.SIFReader
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.SimplePCITiffReader
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.SISReader
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.SlideBook7Reader
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.SlidebookReader
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.SlidebookTiffReader
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.SMCameraReader
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.SPEReader
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.SpiderReader
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.TCSReader
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.TextReader
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.TopometrixReader
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.TrestleReader
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.UnisokuReader
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.VarianFDFReader
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.VGSAMReader
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.VolocityClippingReader
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.VolocityReader
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.WATOPReader
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.ZeissCZIReader
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.ZeissLMSReader
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.ZeissLSMReader
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.ZeissXRMReader
- isThisType(RandomAccessInputStream) - Method in class loci.formats.in.ZeissZVIReader
- isThisType(RandomAccessInputStream) - Method in class loci.formats.ReaderWrapper
- isThisType(IFormatReader, byte[]) - Method in class loci.formats.ImageReader
- isThisType(IFormatReader, String, boolean) - Method in class loci.formats.ImageReader
- isThisType(IFormatReader, RandomAccessInputStream) - Method in class loci.formats.ImageReader
- isThisTypeFast(String, String[]) - Method in class loci.plugins.macro.LociFunctions
- isThumbnailSeries() - Method in class loci.formats.FileStitcher
- isThumbnailSeries() - Method in class loci.formats.FormatReader
- isThumbnailSeries() - Method in interface loci.formats.IFormatReader
-
Gets whether the current series is a lower resolution copy of a different series.
- isThumbnailSeries() - Method in class loci.formats.ImageReader
- isThumbnailSeries() - Method in class loci.formats.ReaderWrapper
- isThumbnailSeries() - Method in class loci.formats.WrappedReader
- isTiff - Variable in class loci.formats.in.EPSReader
- isTiff - Variable in class loci.formats.in.InCellReader.Image
- isTiff - Variable in class loci.formats.in.PerkinElmerReader
-
Flag indicating that the image data is in TIFF format.
- isTiffImageIO() - Static method in class loci.plugins.util.LociPrefs
- isTiled() - Method in class loci.formats.tiff.IFD
- isTimeSeries() - Method in class loci.formats.in.PrairieMetadata.Sequence
-
Gets whether this
Sequenceshould be considered a time series. - isUngroupFiles() - Method in class loci.plugins.in.ImporterOptions
- isUsedFile(String) - Method in class loci.formats.FormatReader
-
Returns true if the given file name is in the used files list.
- isUsingPatternIds() - Method in class loci.formats.FileStitcher
-
Gets whether the reader is using file patterns for IDs.
- isUsingPatternIds() - Method in class loci.plugins.in.ImporterOptions
- isValid() - Method in class loci.formats.FilePattern
-
Returns whether or not the file pattern is valid.
- isValid() - Method in class loci.formats.in.LeicaMicrosystemsMetadata.XlifDocument
- isValidate() - Method in class loci.formats.in.DefaultMetadataOptions
- isValidate() - Method in class loci.formats.in.DynamicMetadataOptions
- isValidate() - Method in interface loci.formats.in.MetadataOptions
-
Checks whether file validation has been set.
- isValidHeader() - Method in class loci.formats.tiff.TiffParser
-
Tests this stream to see if it represents a TIFF file.
- isValidRange(int, int, int) - Static method in class loci.formats.tools.FakeImage
- isVersionChecking() - Method in class loci.formats.Memoizer
-
Returns whether or not version checking is done based upon major/minor version numbers.
- isViewBrowser() - Method in class loci.plugins.in.ImporterOptions
- isViewHyperstack() - Method in class loci.plugins.in.ImporterOptions
- isViewImage5D() - Method in class loci.plugins.in.ImporterOptions
- isViewNone() - Method in class loci.plugins.in.ImporterOptions
- isViewStandard() - Method in class loci.plugins.in.ImporterOptions
- isViewView5D() - Method in class loci.plugins.in.ImporterOptions
- isVirtual() - Method in class loci.plugins.in.ImporterOptions
- isWellAcquired(int, int) - Method in class loci.formats.in.CV7000Reader
- isWhitelistedKey(String) - Method in class loci.formats.ClassList
-
Deprecated.Use
ClassList.isAllowedKey(String)instead. - isWindowless() - Method in class loci.plugins.in.ImporterOptions
- isWindowless() - Method in class loci.plugins.in.ImportProcess
- isWindowless(IFormatReader) - Static method in class loci.plugins.util.LociPrefs
-
Gets whether windowless mode should be used when opening this reader's currently initialized dataset.
- isWritableDirectory(File) - Method in class loci.formats.Memoizer
-
Test if the given
Fileinstance is a writable directory. - isZlib - Variable in class loci.formats.in.BaseZeissReader
- ITagProvider - Interface in loci.formats.dicom
-
Interface used to provide DICOM tags.
- italic - Variable in class loci.formats.in.BaseZeissReader.Shape
- ITEM - Enum constant in enum class loci.formats.dicom.DicomAttribute
- ITEM_DELIMITATION_ITEM - Enum constant in enum class loci.formats.dicom.DicomAttribute
- itemStateChanged(ItemEvent) - Method in class loci.plugins.config.CellSensWidgets
- itemStateChanged(ItemEvent) - Method in class loci.plugins.config.ConfigWindow
- itemStateChanged(ItemEvent) - Method in class loci.plugins.config.LIFWidgets
- itemStateChanged(ItemEvent) - Method in class loci.plugins.config.ND2Widgets
- itemStateChanged(ItemEvent) - Method in class loci.plugins.config.SDTWidgets
- itemStateChanged(ItemEvent) - Method in class loci.plugins.config.TiffDelegateWidgets
- itemStateChanged(ItemEvent) - Method in class loci.plugins.config.ZeissCZIWidgets
- itemStateChanged(ItemEvent) - Method in class loci.plugins.in.MainDialog
-
Handles toggling of mutually exclusive options.
- itemStateChanged(ItemEvent) - Method in class loci.plugins.in.SwapDialog
- iterateIn(RandomAccessInputStream, Long) - Method in class loci.formats.in.ND2Reader
-
Function for iterating through ND2 metaAttributes
- iterateIn(RandomAccessInputStream, Long, boolean) - Method in class loci.formats.in.ND2Reader
-
Function for iterating through ND2 metaAttributes
- IvisionHandler() - Constructor for class loci.formats.in.IvisionReader.IvisionHandler
- IvisionReader - Class in loci.formats.in
-
IvisionReader is the file format reader for IVision (.IPM) files.
- IvisionReader() - Constructor for class loci.formats.in.IvisionReader
-
Constructs a new Ivision reader.
- IvisionReader.IvisionHandler - Class in loci.formats.in
- IVUS_ACQUISITION - Enum constant in enum class loci.formats.dicom.DicomAttribute
- IVUS_GATED_RATE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- IVUS_PULLBACK_RATE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- IVUS_PULLBACK_START_FRAME_NUMBER - Enum constant in enum class loci.formats.dicom.DicomAttribute
- IVUS_PULLBACK_STOP_FRAME_NUMBER - Enum constant in enum class loci.formats.dicom.DicomAttribute
- iw - Variable in class loci.formats.in.GIFReader
-
Current image rectangle.
- ix - Variable in class loci.formats.in.GIFReader
-
Current image rectangle.
- iy - Variable in class loci.formats.in.GIFReader
-
Current image rectangle.
J
- J2K - Enum constant in enum class loci.formats.codec.CompressionType
- J2K_LOSSY - Enum constant in enum class loci.formats.codec.CompressionType
- j2kCodecOptions - Variable in class loci.formats.in.MinimalTiffReader
-
Codec options to use when decoding JPEG 2000 data.
- JAIIIOService - Interface in loci.formats.services
-
Interface defining methods for reading data using JAI Image I/O.
- JAIIIOServiceImpl - Class in loci.formats.services
-
Implementation of JAIIIOService for reading and writing JPEG-2000 data.
- JAIIIOServiceImpl() - Constructor for class loci.formats.services.JAIIIOServiceImpl
-
Default constructor.
- JavaWriter - Class in loci.formats.out
-
JavaWriter is the file format writer for Java source code.
- JavaWriter() - Constructor for class loci.formats.out.JavaWriter
- JDCEReader - Class in loci.formats.in
-
JDCEReader is the file format reader for Molecular Devices JDCE plates.
- JDCEReader() - Constructor for class loci.formats.in.JDCEReader
-
Constructs a new JDCE reader.
- JDCEReader.JDCEWell - Class in loci.formats.in
- JDCEReader.PlaneMetadata - Class in loci.formats.in
- JDCEWell(int, int, int) - Constructor for class loci.formats.in.JDCEReader.JDCEWell
- JEOLReader - Class in loci.formats.in
-
JEOLReader is the file format reader for JEOL files.
- JEOLReader() - Constructor for class loci.formats.in.JEOLReader
-
Constructs a new JEOL reader.
- jhdf - Variable in class loci.formats.in.BDVReader
- jhdf - Variable in class loci.formats.in.CellH5Reader
- jhdf - Variable in class loci.formats.out.CellH5Writer
- JHDFService - Interface in loci.formats.services
-
Utility class for working with NetCDF/HDF files.
- JHDFServiceImpl - Class in loci.formats.services
-
Utility class for working with HDF files.
- JHDFServiceImpl() - Constructor for class loci.formats.services.JHDFServiceImpl
-
Default constructor.
- jpeg - Variable in class loci.formats.in.CellSensReader
- JPEG - Enum constant in enum class loci.formats.codec.CompressionType
- JPEG - Enum constant in enum class loci.formats.in.LeicaMicrosystemsMetadata.LMSFileReader.ImageFormat
- JPEG - Enum constant in enum class loci.formats.tiff.TiffCompression
- JPEG - Static variable in class loci.formats.in.AVIReader
- JPEG - Static variable in class loci.formats.in.CellSensReader
- JPEG - Static variable in class loci.formats.in.ZeissCZIReader
- JPEG_2000 - Enum constant in enum class loci.formats.tiff.TiffCompression
- JPEG_2000 - Static variable in class loci.formats.in.CellSensReader
- JPEG_2000_LOSSY - Enum constant in enum class loci.formats.tiff.TiffCompression
- JPEG_AC_TABLES - Static variable in class loci.formats.tiff.IFD
- JPEG_DC_TABLES - Static variable in class loci.formats.tiff.IFD
- JPEG_INTERCHANGE_FORMAT - Static variable in class loci.formats.tiff.IFD
- JPEG_INTERCHANGE_FORMAT_LENGTH - Static variable in class loci.formats.tiff.IFD
- JPEG_LOSSLESS - Static variable in class loci.formats.in.CellSensReader
- JPEG_LOSSLESS_PREDICTORS - Static variable in class loci.formats.tiff.IFD
- JPEG_POINT_TRANSFORMS - Static variable in class loci.formats.tiff.IFD
- JPEG_PROC - Static variable in class loci.formats.tiff.IFD
- JPEG_Q_TABLES - Static variable in class loci.formats.tiff.IFD
- JPEG_QUALITY - Static variable in class loci.formats.in.NDPIReader
- JPEG_RESTART_INTERVAL - Static variable in class loci.formats.tiff.IFD
- JPEG_TABLES - Static variable in class loci.formats.tiff.IFD
- JPEG2000BoxType - Enum Class in loci.formats.codec
-
An enumeration of JPEG 2000 box types.
- JPEG2000BoxType(int, String) - Constructor for enum class loci.formats.codec.JPEG2000BoxType
-
Default constructor.
- JPEG2000Codec - Class in loci.formats.codec
-
This class implements JPEG 2000 compression and decompression.
- JPEG2000Codec() - Constructor for class loci.formats.codec.JPEG2000Codec
- JPEG2000CodecOptions - Class in loci.formats.codec
-
Options for compressing and decompressing JPEG-2000 data.
- JPEG2000CodecOptions() - Constructor for class loci.formats.codec.JPEG2000CodecOptions
-
Creates a new instance.
- JPEG2000CodecOptions(CodecOptions) - Constructor for class loci.formats.codec.JPEG2000CodecOptions
-
Creates a new instance with options.
- JPEG2000MetadataParser - Class in loci.formats.in
-
A parser for JPEG 2000 metadata.
- JPEG2000MetadataParser(RandomAccessInputStream) - Constructor for class loci.formats.in.JPEG2000MetadataParser
-
Constructs a new JPEG2000MetadataParser.
- JPEG2000MetadataParser(RandomAccessInputStream, long) - Constructor for class loci.formats.in.JPEG2000MetadataParser
-
Constructs a new JPEG2000MetadataParser.
- JPEG2000Reader - Class in loci.formats.in
-
JPEG2000Reader is the file format reader for JPEG-2000 images.
- JPEG2000Reader() - Constructor for class loci.formats.in.JPEG2000Reader
-
Constructs a new JPEG2000Reader.
- JPEG2000SegmentMarker - Enum Class in loci.formats.codec
-
An enumeration of JPEG 2000 segment markers.
- JPEG2000SegmentMarker(int, String) - Constructor for enum class loci.formats.codec.JPEG2000SegmentMarker
-
Default constructor.
- JPEG2000Writer - Class in loci.formats.out
-
JPEG2000Writer is the file format writer for JPEG2000 files.
- JPEG2000Writer() - Constructor for class loci.formats.out.JPEG2000Writer
-
Creates a new instance.
- jpegBuf - Variable in class org.libjpegturbo.turbojpeg.TJDecompressor
- jpegBufSize - Variable in class org.libjpegturbo.turbojpeg.TJDecompressor
- JPEGCodec - Class in loci.formats.codec
-
This class implements JPEG compression and decompression.
- JPEGCodec() - Constructor for class loci.formats.codec.JPEGCodec
- jpegHeight - Variable in class org.libjpegturbo.turbojpeg.TJDecompressor
- jpegOffsets - Variable in class loci.formats.in.PictReader
- jpegQuality - Variable in class org.libjpegturbo.turbojpeg.TJCompressor
- JPEGReader - Class in loci.formats.in
-
JPEGReader is the file format reader for JPEG images.
- JPEGReader() - Constructor for class loci.formats.in.JPEGReader
-
Constructs a new JPEGReader.
- JPEGReader.DefaultJPEGReader - Class in loci.formats.in
- jpegSubsamp - Variable in class org.libjpegturbo.turbojpeg.TJDecompressor
- JPEGTileDecoder - Class in loci.formats.codec
- JPEGTileDecoder() - Constructor for class loci.formats.codec.JPEGTileDecoder
- JPEGTurboService - Interface in loci.formats.services
- JPEGTurboServiceImpl - Class in loci.formats.services
-
Based upon the NDPI to OME-TIFF converter by Matthias Baldauf: http://matthias-baldauf.at/software/ndpi_converter/
- JPEGTurboServiceImpl() - Constructor for class loci.formats.services.JPEGTurboServiceImpl
- jpegWidth - Variable in class org.libjpegturbo.turbojpeg.TJDecompressor
- JPEGWriter - Class in loci.formats.out
-
JPEGWriter is the file format writer for JPEG files.
- JPEGWriter() - Constructor for class loci.formats.out.JPEGWriter
- JPEGXR - Enum constant in enum class loci.formats.tiff.TiffCompression
- JPEGXR - Static variable in class loci.formats.in.ZeissCZIReader
- JPEGXRCodec - Class in loci.formats.codec
- JPEGXRCodec() - Constructor for class loci.formats.codec.JPEGXRCodec
- JPEGXRService - Interface in loci.formats.services
-
Interface defining methods for working with JPEG-XR data
- JPEGXRServiceImpl - Class in loci.formats.services
-
Interface defining methods for working with JPEG-XR data
- JPEGXRServiceImpl() - Constructor for class loci.formats.services.JPEGXRServiceImpl
- JPKReader - Class in loci.formats.in
-
JPKReader is the file format reader for JPK Instruments files.
- JPKReader() - Constructor for class loci.formats.in.JPKReader
-
Constructs a new JPK reader.
- JPXReader - Class in loci.formats.in
-
JPXReader is the file format reader for JPX (3D JPEG-2000) images.
- JPXReader() - Constructor for class loci.formats.in.JPXReader
-
Constructs a new JPX Reader.
- JSON_TAG - Static variable in class loci.formats.in.MicromanagerReader
K
- kAnnotationRecordFilename - Static variable in class loci.formats.in.SlideBook7Reader.CSBFile70
- kAuxDataFilename - Static variable in class loci.formats.in.SlideBook7Reader.CSBFile70
- kBinaryFileSuffix - Static variable in class loci.formats.in.SlideBook7Reader.CSBFile70
- kChannelRecordFilename - Static variable in class loci.formats.in.SlideBook7Reader.CSBFile70
- kElapsedTimesFilename - Static variable in class loci.formats.in.SlideBook7Reader.CSBFile70
- key - Variable in class loci.formats.dicom.DicomTag
- key - Variable in class loci.formats.in.BaseZeissReader.Layer
- key - Variable in class loci.formats.in.BioRadSCNReader.SCNHandler
- key - Variable in class loci.formats.in.FEITiffReader.FEIHandler
- key - Variable in class loci.formats.in.ImaconReader.ImaconHandler
- key - Variable in class loci.formats.in.IvisionReader.IvisionHandler
- key - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.Dimension
- key - Variable in class loci.formats.in.ScanrReader.ScanrHandler
- key - Variable in class loci.formats.in.ZeissTIFFHandler.Scaling
- key - Variable in class loci.formats.in.ZeissTIFFHandler.Tag
- key - Variable in class loci.formats.meta.OriginalMetadataAnnotation
- key - Variable in class loci.plugins.prefs.Option
-
Key name for ImageJ preferences file.
- KEY_AUTOSCALE - Static variable in class loci.plugins.in.ImporterOptions
- KEY_COLOR_MODE - Static variable in class loci.plugins.in.ImporterOptions
- KEY_CONCATENATE - Static variable in class loci.plugins.in.ImporterOptions
- KEY_CROP - Static variable in class loci.plugins.in.ImporterOptions
- KEY_FIRST - Static variable in class loci.plugins.in.ImporterOptions
- KEY_FORCE_THUMBS - Static variable in class loci.plugins.in.ImporterOptions
- KEY_GROUP_FILES - Static variable in class loci.plugins.in.ImporterOptions
- KEY_ID - Static variable in class loci.plugins.in.ImporterOptions
- KEY_LOCATION - Static variable in class loci.plugins.in.ImporterOptions
- KEY_MUST_GROUP - Static variable in class loci.plugins.in.ImporterOptions
- KEY_OPEN_ALL_SERIES - Static variable in class loci.plugins.in.ImporterOptions
- KEY_PREFIX - Static variable in class loci.plugins.prefs.Option
-
Prefix to use for all plugins preferences.
- KEY_QUIET - Static variable in class loci.plugins.in.ImporterOptions
- KEY_ROIS_MODE - Static variable in class loci.plugins.in.ImporterOptions
- KEY_SHOW_METADATA - Static variable in class loci.plugins.in.ImporterOptions
- KEY_SHOW_OME_XML - Static variable in class loci.plugins.in.ImporterOptions
- KEY_SHOW_ROIS - Static variable in class loci.plugins.in.ImporterOptions
- KEY_SPECIFY_RANGES - Static variable in class loci.plugins.in.ImporterOptions
- KEY_SPLIT_C - Static variable in class loci.plugins.in.ImporterOptions
- KEY_SPLIT_T - Static variable in class loci.plugins.in.ImporterOptions
- KEY_SPLIT_Z - Static variable in class loci.plugins.in.ImporterOptions
- KEY_STACK_FORMAT - Static variable in class loci.plugins.in.ImporterOptions
- KEY_STACK_ORDER - Static variable in class loci.plugins.in.ImporterOptions
- KEY_STITCH_TILES - Static variable in class loci.plugins.in.ImporterOptions
- KEY_SWAP_DIMS - Static variable in class loci.plugins.in.ImporterOptions
- KEY_UNGROUP_FILES - Static variable in class loci.plugins.in.ImporterOptions
- KEY_UPGRADE_CHECK - Static variable in class loci.plugins.in.ImporterOptions
- KEY_VIRTUAL - Static variable in class loci.plugins.in.ImporterOptions
- KEY_WINDOWLESS - Static variable in class loci.plugins.in.ImporterOptions
- keyid - Variable in class loci.formats.in.BaseZeissReader.Tag
- keyPressed(KeyEvent) - Method in class loci.formats.gui.ImageViewer
-
Handles key presses.
- keyReleased(KeyEvent) - Method in class loci.formats.gui.ImageViewer
- keys(Hashtable<String, Object>) - Static method in class loci.formats.MetadataTools
-
Gets a sorted list of keys from the given hashtable.
- KEYS - Static variable in class loci.formats.ClassList
- keyTyped(KeyEvent) - Method in class loci.formats.gui.ImageViewer
- KHOROS_MAGIC_BYTES - Static variable in class loci.formats.in.KhorosReader
- KhorosReader - Class in loci.formats.in
-
Reader for Khoros XV files.
- KhorosReader() - Constructor for class loci.formats.in.KhorosReader
-
Constructs a new Khoros reader.
- kImageDirSuffix - Static variable in class loci.formats.in.SlideBook7Reader.CSBFile70
- kImageRecordFilename - Static variable in class loci.formats.in.SlideBook7Reader.CSBFile70
- kind - Variable in class loci.formats.out.ImageIOWriter
- KINETIC_CYCLE_TIME - Static variable in class loci.formats.in.FluoviewReader
- KINETIC_TRIGGER - Enum constant in enum class loci.formats.in.SPEReader.SpeHeaderEntry
- KLB_DATA_DIMS - Static variable in class loci.formats.in.KLBReader
- KLB_DEFAULT_HEADER_VERSION - Static variable in class loci.formats.in.KLBReader
- KLB_METADATA_SIZE - Static variable in class loci.formats.in.KLBReader
- KLBReader - Class in loci.formats.in
-
Reader for Keller Lab Block (KLB) files.
- KLBReader() - Constructor for class loci.formats.in.KLBReader
-
Constructs a new BDV reader.
- kMaskRecordFilename - Static variable in class loci.formats.in.SlideBook7Reader.CSBFile70
- kMaxNumberOpenFiles - Static variable in class loci.formats.in.SlideBook7Reader.DataLoader
- KNOWN_VERSIONS - Static variable in class loci.formats.in.LiFlimReader
- kNumDigitsInTimepoint - Static variable in class loci.formats.in.SlideBook7Reader.CSBFile70
- KodakReader - Class in loci.formats.in
-
KodakReader is the file format reader for Kodak Molecular Imaging .bip files.
- KodakReader() - Constructor for class loci.formats.in.KodakReader
-
Constructs a new Kodak reader.
- kRootDirSuffix - Static variable in class loci.formats.in.SlideBook7Reader.CSBFile70
- kryo - Variable in class loci.formats.Memoizer.KryoDeser
- KryoDeser() - Constructor for class loci.formats.Memoizer.KryoDeser
- kSAPositionDataFilename - Static variable in class loci.formats.in.SlideBook7Reader.CSBFile70
- kSlideSuffix - Static variable in class loci.formats.in.SlideBook7Reader.CSBFile70
- kStagePositionDataFilename - Static variable in class loci.formats.in.SlideBook7Reader.CSBFile70
- KVP - Enum constant in enum class loci.formats.dicom.DicomAttribute
- kZBinaryFileSuffix - Static variable in class loci.formats.in.SlideBook7Reader.CSBFile70
- kZSlideSuffix - Static variable in class loci.formats.in.SlideBook7Reader.CSBFile70
L
- L2DReader - Class in loci.formats.in
-
L2DReader is the file format reader for Li-Cor L2D datasets.
- L2DReader() - Constructor for class loci.formats.in.L2DReader
-
Construct a new L2D reader.
- label - Variable in class loci.plugins.prefs.Option
-
Label describing the option, for use with ImageJ dialogs.
- LABEL - Enum constant in enum class loci.formats.codec.JPEG2000BoxType
- LABEL_OBSCURED - Static variable in class loci.formats.in.NDPIReader
- LABEL_TEXT - Enum constant in enum class loci.formats.dicom.DicomAttribute
- LABEL_X - Static variable in class loci.formats.in.TextReader
- LABEL_Y - Static variable in class loci.formats.in.TextReader
- labelIndex - Variable in class loci.formats.in.SVSReader
- labelPlanes - Variable in class loci.formats.in.FakeReader
- labels - Variable in class loci.formats.in.FakeReader
- labels - Variable in class loci.formats.in.ICSReader
-
Dimensional reordering for lifetime data
- labels - Variable in class loci.formats.Modulo
- labels - Variable in class loci.plugins.config.CellSensWidgets
- labels - Variable in class loci.plugins.config.FormatEntry
- labels - Variable in class loci.plugins.config.LIFWidgets
- labels - Variable in class loci.plugins.config.ND2Widgets
- labels - Variable in class loci.plugins.config.SDTWidgets
- labels - Variable in class loci.plugins.config.TiffDelegateWidgets
- labels - Variable in class loci.plugins.config.ZeissCZIWidgets
- LAMBDA - Static variable in class loci.formats.in.CellSensReader
- LAMBDA_INCREMENT - Static variable in class loci.formats.in.CellSensReader
- LAMBDA_START - Static variable in class loci.formats.in.CellSensReader
- LAMBDA_VALUE - Static variable in class loci.formats.in.CellSensReader
- LAMP_AGE - Static variable in class loci.formats.in.NDPIReader
- LARGEST_IMAGE_PIXEL_VALUE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- LARGEST_IMAGE_PIXEL_VALUE_IN_PLANE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- LARGEST_PIXEL_VALUE_IN_SERIES - Enum constant in enum class loci.formats.dicom.DicomAttribute
- Laser() - Constructor for class loci.formats.in.LeicaHandler.Laser
- Laser() - Constructor for class loci.formats.in.OIRReader.Laser
- Laser() - Constructor for class loci.formats.in.ZeissLSMReader.Laser
- LASER_ACQUIRE - Static variable in class loci.formats.in.ZeissLSMReader
- LASER_NAME - Static variable in class loci.formats.in.ZeissLSMReader
- LASER_POWER - Static variable in class loci.formats.in.ZeissLSMReader
- laserActive - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataTempBuffer
- laserActive - Variable in class loci.formats.in.LIFReader
- laserCount - Variable in class loci.formats.in.LeicaHandler
- laserFrap - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataTempBuffer
- laserFrap - Variable in class loci.formats.in.LIFReader
- laserIDs - Variable in class loci.formats.in.NikonTiffReader
- laserIndex - Variable in class loci.formats.in.OIRReader.Channel
- laserIntensity - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataTempBuffer
- laserIntensity - Variable in class loci.formats.in.LIFReader
- lasers - Variable in class loci.formats.in.LeicaHandler
- lasers - Variable in class loci.formats.in.OIRReader
- laserWavelength - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataTempBuffer
- laserWavelength - Variable in class loci.formats.in.LIFReader
- last - Variable in class loci.formats.dicom.DicomTile
- LAST_MENSTRUAL_DATE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- LAST_VALUE - Enum constant in enum class loci.formats.in.SPEReader.SpeHeaderEntry
- lastChannel - Variable in class loci.formats.in.BDVReader
- lastChannel - Variable in class loci.formats.in.BioRadReader
- lastChannel - Variable in class loci.formats.in.CellH5Reader
- lastChannel - Variable in class loci.formats.in.FV1000Reader
- lastChannel - Variable in class loci.formats.in.ImarisHDFReader
- lastChannel - Variable in class loci.formats.in.LIFReader
- lastChannel - Variable in class loci.formats.in.LOFReader
- lastChannel - Variable in class loci.formats.in.ND2Reader
- lastChannel - Variable in class loci.formats.in.OIRReader
- lastCodeOffset - Variable in class loci.formats.in.AmiraReader.HxRLE
- lastDispose - Variable in class loci.formats.in.GIFReader
- lastFile - Variable in class loci.formats.in.CellWorxReader
- lastFile - Variable in class loci.formats.in.ImprovisionTiffReader
- lastFile - Variable in class loci.formats.in.SlidebookTiffReader
- lastId - Variable in class loci.formats.gui.PreviewPane
-
Last ID loaded.
- lastIFD - Variable in class loci.formats.in.LeicaSCNReader.Pixels
- lastImage - Variable in class loci.formats.ChannelSeparator
-
Last image opened.
- lastImage - Variable in class loci.formats.in.APNGReader
- lastImage - Variable in class loci.formats.in.AVIReader
- lastImage - Variable in class loci.formats.in.InCellReader.MinimalInCellHandler
- lastImageHeight - Variable in class loci.formats.ChannelSeparator
-
Height of last image opened.
- lastImageIndex - Variable in class loci.formats.ChannelSeparator
-
Index of last image opened.
- lastImageIndex - Variable in class loci.formats.in.APNGReader
- lastImageNo - Variable in class loci.formats.in.AVIReader
- lastImageRow - Variable in class loci.formats.in.APNGReader
- lastImageSeries - Variable in class loci.formats.ChannelSeparator
-
Series of last image opened.
- lastImageWidth - Variable in class loci.formats.ChannelSeparator
-
Width of last image opened.
- lastImageX - Variable in class loci.formats.ChannelSeparator
-
X index of last image opened.
- lastImageY - Variable in class loci.formats.ChannelSeparator
-
Y index of last image opened.
- lastIndex - Variable in class loci.formats.in.DNGReader
- lastIndex - Variable in class loci.formats.in.NikonReader
- lastMaxZ - Variable in class loci.formats.in.ImarisHDFReader
- lastMinZ - Variable in class loci.formats.in.ImarisHDFReader
- lastPlane - Variable in class loci.formats.in.BaseZeissReader
- lastPlane - Variable in class loci.formats.in.DNGReader
- lastPlane - Variable in class loci.formats.in.JPXReader
- lastPlane - Variable in class loci.formats.in.LeicaReader
- lastPlane - Variable in class loci.formats.in.MinimalTiffReader
- lastPlane - Variable in class loci.formats.in.NikonReader
- lastPlane - Variable in class loci.formats.in.NRRDReader
- lastPlane - Variable in class loci.formats.in.OMETiffReader
- lastPlane - Variable in class loci.formats.in.OpenlabReader
- lastPlane - Variable in class loci.formats.in.TCSReader
- lastPlane - Variable in class loci.formats.out.ICSWriter
- lastPlane - Variable in class loci.formats.out.V3DrawWriter
- lastReader - Variable in class loci.formats.in.CellWorxReader
- lastRes - Variable in class loci.formats.in.ImarisHDFReader
- lastSeries - Variable in class loci.formats.in.BrukerReader
- lastSeries - Variable in class loci.formats.in.JPEG2000Reader
- lastSeries - Variable in class loci.formats.in.JPXReader
- lastSeriesPlane - Variable in class loci.formats.in.JPEG2000Reader
- lastSeriesPlane - Variable in class loci.formats.in.JPXReader
- lastT - Variable in class loci.formats.in.ImarisHDFReader
- lastTimepoint - Variable in class loci.formats.in.BDVReader
- LATEST_VERSION - Static variable in class loci.formats.services.OMEXMLServiceImpl
-
Latest OME-XML version namespace.
- Layer() - Constructor for class loci.formats.in.BaseZeissReader.Layer
- layer_count - Variable in class loci.formats.in.ZeissTIFFHandler
- LAYER_INFO_PROPERTIES - Static variable in class loci.formats.in.CellSensReader
- LAYER_SELECTION - Static variable in class loci.formats.in.CellSensReader
- LAYER_SELECTION_INDEX - Static variable in class loci.formats.in.CellSensReader
- LAYER_XY_FIXED - Static variable in class loci.formats.in.CellSensReader
- layerNames - Variable in class loci.formats.in.PhotoshopTiffReader
- layerOffset - Variable in class loci.formats.in.PhotoshopTiffReader
- layers - Variable in class loci.formats.in.BaseZeissReader
- layers - Variable in class loci.formats.in.ZeissTIFFHandler
- LAYOUT_KEYS - Static variable in class loci.formats.in.ICSReader
- LAYOUT_TABLE - Static variable in class loci.formats.in.LiFlimReader
- lblockNo - Variable in class loci.formats.in.SDTInfo
-
Long blockNo - see remarks below.
- LEFT - Enum constant in enum class loci.formats.in.BaseZeissReader.LineEndPositions
- LEFT - Enum constant in enum class loci.formats.in.BaseZeissReader.TextAlignment
- legacyReader - Variable in class loci.formats.DelegateReader
-
Legacy reader.
- legacyReaderInitialized - Variable in class loci.formats.DelegateReader
-
Flag indicating that the legacy reader was successfully initialized.
- LEI_SUFFIX - Static variable in class loci.formats.in.LeicaReader
- LEICA_MAGIC_TAG - Static variable in class loci.formats.in.LeicaReader
-
All Leica TIFFs have this tag.
- LeicaHandler - Class in loci.formats.in
-
SAX handler for parsing XML in Leica LIF and Leica TCS files.
- LeicaHandler(MetadataStore, MetadataLevel) - Constructor for class loci.formats.in.LeicaHandler
- LeicaHandler(MetadataStore, MetadataLevel, boolean) - Constructor for class loci.formats.in.LeicaHandler
- LeicaHandler.Channel - Class in loci.formats.in
- LeicaHandler.Detector - Class in loci.formats.in
- LeicaHandler.Laser - Class in loci.formats.in
- LeicaHandler.MultiBand - Class in loci.formats.in
- LeicaHandler.ROI - Class in loci.formats.in
- LeicaReader - Class in loci.formats.in
-
LeicaReader is the file format reader for Leica files.
- LeicaReader() - Constructor for class loci.formats.in.LeicaReader
-
Constructs a new Leica reader.
- LeicaReader.Detector - Class in loci.formats.in
- LeicaSCNHandler() - Constructor for class loci.formats.in.LeicaSCNReader.LeicaSCNHandler
- LeicaSCNReader - Class in loci.formats.in
-
LeicaSCNReader is the file format reader for Leica SCN TIFF files.
- LeicaSCNReader() - Constructor for class loci.formats.in.LeicaSCNReader
-
Constructs a new LeicaSCN reader.
- LeicaSCNReader.Dimension - Class in loci.formats.in
- LeicaSCNReader.Image - Class in loci.formats.in
- LeicaSCNReader.ImageCollection - Class in loci.formats.in
- LeicaSCNReader.LeicaSCNHandler - Class in loci.formats.in
-
SAX handler for parsing XML in Leica SCN files.
- LeicaSCNReader.Pixels - Class in loci.formats.in
- leiFilename - Variable in class loci.formats.in.LeicaReader
-
Name of current LEI file
- len - Variable in class loci.plugins.util.BFVirtualStack
- lenC - Variable in class loci.formats.FileStitcher
-
Component lengths for each axis type.
- length - Variable in class loci.formats.in.APNGReader.PNGBlock
- length - Variable in class loci.formats.in.IM3Reader.IM3Record
- length - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.Dimension
- length - Variable in class loci.formats.in.ND2Reader.ChunkMapEntry
- length - Variable in class loci.formats.in.OBFReader.Stack
- length - Variable in class loci.formats.in.OIRReader.PixelBlock
- length() - Method in class loci.formats.cache.CacheStrategy
-
Shortcut for computing total number of positions.
- length() - Method in class loci.formats.Modulo
- LENGTH - Enum constant in enum class loci.formats.in.BaseZeissReader.FeatureType
- lengths - Variable in class loci.formats.cache.CacheStrategy
-
Length of each dimensional axis.
- lengths - Variable in class loci.formats.gui.CacheComponent
-
Length of each dimensional axis, obtained from cache strategy.
- lengths - Variable in class loci.formats.in.AVIReader
-
Number of bytes in each plane.
- lengths - Variable in class loci.formats.in.DeltavisionReader
- lengths - Variable in class loci.formats.in.MNGReader.SeriesInfo
- lens - Variable in class loci.formats.in.PSDReader
- LENS - Static variable in class loci.formats.in.NikonReader
- LENS_TYPE - Static variable in class loci.formats.in.NikonReader
- LENSES_CODE_SEQUENCE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- lensNA - Variable in class loci.formats.in.FluoviewReader
- lensNA - Variable in class loci.formats.in.FV1000Reader
- lensNA - Variable in class loci.formats.in.IvisionReader
- lensNA - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataTempBuffer
- lensNA - Variable in class loci.formats.in.LIFReader
- lensNA - Variable in class loci.formats.in.MetamorphHandler
- lensNA - Variable in class loci.formats.in.ND2Reader
- lensNA - Variable in class loci.formats.in.NikonTiffReader
- lensNA - Variable in class loci.formats.in.OperettaReader.Channel
- lensNA - Variable in class loci.formats.in.OperettaReader.Plane
- lensNA - Variable in class loci.formats.in.ZeissLSMReader.Recording
- lensRI - Variable in class loci.formats.in.MetamorphHandler
- lenT - Variable in class loci.formats.FileStitcher
-
Component lengths for each axis type.
- lenZ - Variable in class loci.formats.FileStitcher
-
Component lengths for each axis type.
- LEO_TAG - Static variable in class loci.formats.in.LEOReader
- LEOReader - Class in loci.formats.in
-
LEOReader is the file format reader for LEO EM files.
- LEOReader() - Constructor for class loci.formats.in.LEOReader
-
Constructs a new LEO reader.
- LESION_NUMBER - Enum constant in enum class loci.formats.dicom.DicomAttribute
- letter - Variable in class loci.formats.ResourceNamer
- level - Variable in class loci.formats.in.BioRadReader.Note
- level - Variable in class loci.formats.in.FlexReader.FlexHandler
- level - Variable in class loci.formats.in.LeicaHandler
- LEXPOS - Enum constant in enum class loci.formats.in.SPEReader.SpeHeaderEntry
- LFLOAT - Enum constant in enum class loci.formats.in.SPEReader.SpeHeaderEntry
- libClass - Variable in class loci.plugins.config.LibraryEntry
- Library() - Constructor for enum class loci.plugins.util.LibraryChecker.Library
- LibraryChecker - Class in loci.plugins.util
-
Utility methods for verifying that classes are present and versions are correct.
- LibraryChecker() - Constructor for class loci.plugins.util.LibraryChecker
- LibraryChecker.Library - Enum Class in loci.plugins.util
-
List of possible libraries for which to check.
- LibraryEntry - Class in loci.plugins.config
-
A list entry for the configuration window's Libraries tab.
- LibraryEntry(PrintWriter, String, String, String, String, String, String, String) - Constructor for class loci.plugins.config.LibraryEntry
- LibraryEntry(PrintWriter, HashMap<String, String>) - Constructor for class loci.plugins.config.LibraryEntry
- libraryLoaded - Static variable in class loci.formats.services.JPEGTurboServiceImpl
- libsList - Variable in class loci.plugins.config.ConfigWindow
- libsListModel - Variable in class loci.plugins.config.ConfigWindow
- license - Variable in class loci.plugins.config.ConfigWindow
- license - Variable in class loci.plugins.config.LibraryEntry
- LICOR_MAGIC_STRING - Static variable in class loci.formats.in.L2DReader
- LIF_MAGIC_BYTE - Static variable in class loci.formats.in.LIFReader
- LIF_MEMORY_BYTE - Static variable in class loci.formats.in.LIFReader
- lifetime - Variable in class loci.formats.in.ICSReader
-
Whether or not the channels represent lifetime histogram bins.
- LIFETIME - Static variable in class loci.formats.FormatTools
-
Identifies the Lifetime dimensional type, representing a dimension consisting of a lifetime histogram.
- LIFF_MAGIC_BYTES - Static variable in class loci.formats.in.OpenlabReader
- LiFlimReader - Class in loci.formats.in
-
LiFlimReader is the file format reader for LI-FLIM files.
- LiFlimReader() - Constructor for class loci.formats.in.LiFlimReader
-
Constructs a new LI-FLIM reader.
- LiFlimReader.ROI - Class in loci.formats.in
- LIFReader - Class in loci.formats.in
-
LIFReader is the file format reader for Leica LIF files.
- LIFReader() - Constructor for class loci.formats.in.LIFReader
-
Constructs a new Leica LIF reader.
- LIFReader.MemoryBlock - Class in loci.formats.in
- LIFReader.ROI - Class in loci.formats.in
- LIFWidgets - Class in loci.plugins.config
-
Custom widgets for configuring Bio-Formats Leica LIF support.
- LIFWidgets() - Constructor for class loci.plugins.config.LIFWidgets
- LIGHT_PATH_FILTER_PASS_BAND - Enum constant in enum class loci.formats.dicom.DicomAttribute
- LIGHT_PATH_FILTER_PASSTHROUGH_WAVELENGTH - Enum constant in enum class loci.formats.dicom.DicomAttribute
- LIGHT_PATH_FILTER_TYPE_STACK_CODE_SEQUENCE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- LIGHT_SOURCE - Static variable in class loci.formats.tiff.IFD
- LIGHT_TYPE - Static variable in class loci.formats.in.NikonReader
- LightSource() - Constructor for class loci.formats.in.CV7000Reader.LightSource
- lightSourceCombinationIDs - Variable in class loci.formats.in.FlexReader
- lightSourceCombinationRefs - Variable in class loci.formats.in.FlexReader
- lightSourceID - Variable in class loci.formats.in.FlexReader.FlexHandler
- lightSourceIDs - Variable in class loci.formats.in.FlexReader
- lightSourceIDs - Variable in class loci.formats.in.ZeissCZIReader
- lightSourceRef - Variable in class loci.formats.in.ZeissCZIReader.Channel
- lightSourceRefs - Variable in class loci.formats.in.CV7000Reader.Channel
- lightSources - Variable in class loci.formats.in.CV7000Reader
- limitHeight(JComponent) - Method in class loci.formats.gui.DataConverter
- LIMReader - Class in loci.formats.in
-
LIMReader is the file format reader for Laboratory Imaging/Nikon LIM files.
- LIMReader() - Constructor for class loci.formats.in.LIMReader
-
Constructs a new LIM reader.
- line - Variable in class loci.formats.in.FakeReader.TextLine
- line - Variable in class loci.formats.in.FV1000Reader
- line - Variable in class loci.formats.tools.MakeTestOmeTiff.TextLine
- LINE - Enum constant in enum class loci.formats.in.BaseZeissReader.FeatureType
- LINE - Static variable in class loci.formats.in.FV1000Reader
- LINE - Static variable in class loci.formats.in.GatanReader
-
Shape types
- LINE - Static variable in class loci.formats.in.LeicaHandler.ROI
- LINE - Static variable in class loci.formats.in.LeicaMicrosystemsMetadata.ROI
- LINE - Static variable in class loci.formats.in.LIFReader.ROI
- LINE - Static variable in class loci.formats.in.ZeissLSMReader
- LINE_LENGTH - Static variable in class loci.formats.in.FitsReader
- LINEAR - Static variable in class loci.formats.in.GelReader
- linediv - Variable in class loci.formats.in.SDTInfo
-
Line predivider = 2 ** (linediv).
- lineEndPositions - Variable in class loci.formats.in.BaseZeissReader.Shape
- LineEndPositions(int) - Constructor for enum class loci.formats.in.BaseZeissReader.LineEndPositions
- lineEndSize - Variable in class loci.formats.in.BaseZeissReader.Shape
- lineEndStyle - Variable in class loci.formats.in.BaseZeissReader.Shape
- LineEndStyle(int) - Constructor for enum class loci.formats.in.BaseZeissReader.LineEndStyle
- lineMode - Variable in class loci.formats.in.SPCReader
- lines - Variable in class loci.formats.in.FakeReader
- lineTo(int, int) - Method in class loci.plugins.util.RecordedImageProcessor
- linewidth - Variable in class loci.formats.in.LeicaHandler.ROI
- linewidth - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.ROI
- linewidth - Variable in class loci.formats.in.LIFReader.ROI
- lineWidth - Variable in class loci.formats.in.BaseZeissReader.Shape
- linkedInstruments - Variable in class loci.formats.in.LeicaHandler
- LIPixelFormat - Class in loci.formats.in
- LIPixelFormat() - Constructor for class loci.formats.in.LIPixelFormat
- listeners - Variable in class loci.formats.cache.Cache
-
List of cache event listeners.
- listeners - Variable in class loci.formats.cache.CacheStrategy
-
List of cache event listeners.
- listeners - Variable in class loci.plugins.in.ImagePlusReader
- listeners - Variable in class loci.plugins.in.ImportProcess
- listFakeSeries(String) - Method in class loci.formats.in.FakeReader
-
Traverses a fake file folder structure indicated by traversedDirectory
- listString - Variable in class loci.formats.in.AVIReader
- LITTLE - Static variable in class loci.formats.tiff.TiffConstants
- LITTLE_ENDIAN - Static variable in class loci.formats.in.BioRadReader
-
Always little endian.
- LITTLE_ENDIAN - Static variable in class loci.formats.in.DeltavisionReader
- LITTLE_ENDIAN - Static variable in class loci.formats.in.OBFReader
- LITTLE_ENDIAN - Static variable in class loci.formats.in.TextReader
- LITTLE_ENDIAN - Static variable in class loci.formats.tiff.IFD
- littleEndian - Variable in class loci.formats.codec.CodecOptions
-
Indicates endianness of pixel data.
- littleEndian - Variable in class loci.formats.CoreMetadata
-
Indicates whether or not each pixel's bytes are in little endian order.
- littleEndian - Variable in class loci.formats.out.APNGWriter
- littleEndian - Variable in class loci.formats.tools.AmiraParameters
- LIVE_OVERFLOW - Static variable in class loci.formats.in.CellSensReader
- LM_DOMAIN - Static variable in class loci.formats.FormatTools
-
Identifies the light microscopy domain.
- LMSCollectionXmlDocument - Class in loci.formats.in.LeicaMicrosystemsMetadata
-
This class represents an LMS xml file that references other LMS xml files such as xlcfs and xlifs.
- LMSCollectionXmlDocument(String, LMSCollectionXmlDocument) - Constructor for class loci.formats.in.LeicaMicrosystemsMetadata.LMSCollectionXmlDocument
- LMSFileReader - Class in loci.formats.in.LeicaMicrosystemsMetadata
-
This class can be extended by readers of Leica Microsystems file formats that include LASX generated XML (e.g.
- LMSFileReader(String, String) - Constructor for class loci.formats.in.LeicaMicrosystemsMetadata.LMSFileReader
- LMSFileReader.ImageFormat - Enum Class in loci.formats.in.LeicaMicrosystemsMetadata
-
file format in which actual image bytes are stored
- LMSImageXmlDocument - Class in loci.formats.in.LeicaMicrosystemsMetadata
-
This class loads and represents a Leica Microsystems image XML document that contains image metadata
- LMSImageXmlDocument(String) - Constructor for class loci.formats.in.LeicaMicrosystemsMetadata.LMSImageXmlDocument
- LMSImageXmlDocument(String, LMSCollectionXmlDocument) - Constructor for class loci.formats.in.LeicaMicrosystemsMetadata.LMSImageXmlDocument
- LMSMetadataExtractor - Class in loci.formats.in.LeicaMicrosystemsMetadata
-
This class extracts metadata information from Leica Microsystems image XML and stores it in the reader's CoreMetadata and MetadataTempBuffer
- LMSMetadataExtractor(LMSFileReader) - Constructor for class loci.formats.in.LeicaMicrosystemsMetadata.LMSMetadataExtractor
- LMSXmlDocument - Class in loci.formats.in.LeicaMicrosystemsMetadata
-
This class loads and represents a Leica Microsystems XML document (from file or xml string)
- LMSXmlDocument(String) - Constructor for class loci.formats.in.LeicaMicrosystemsMetadata.LMSXmlDocument
- LMSXmlDocument(String, LMSCollectionXmlDocument) - Constructor for class loci.formats.in.LeicaMicrosystemsMetadata.LMSXmlDocument
- LMSXmlDocument.InitFrom - Enum Class in loci.formats.in.LeicaMicrosystemsMetadata
- LNOSCAN - Enum constant in enum class loci.formats.in.SPEReader.SpeHeaderEntry
- LO - Enum constant in enum class loci.formats.dicom.DicomVR
- load() - Static method in class org.libjpegturbo.turbojpeg.TJLoader
- load(String, File, boolean) - Static method in class loci.formats.Memoizer
- Load() - Method in class loci.formats.in.SlideBook7Reader.CImageGroup
- LoadAnnotations() - Method in class loci.formats.in.SlideBook7Reader.CImageGroup
- LoadAuxData() - Method in class loci.formats.in.SlideBook7Reader.CImageGroup
- LoadChannelRecord() - Method in class loci.formats.in.SlideBook7Reader.CImageGroup
- loadedFromMemo - Variable in class loci.formats.Memoizer
-
Whether the
ReaderWrapper.readerinstance currently active was loaded from the memo file duringMemoizer.setId(String). - LoadElapsedTimes() - Method in class loci.formats.in.SlideBook7Reader.CImageGroup
- loader - Variable in class loci.formats.gui.PreviewPane
-
Thumbnail loading thread.
- loader - Variable in class loci.plugins.in.ThumbLoader
- loaderAlive - Variable in class loci.formats.gui.PreviewPane
-
Flag indicating whether loader thread should keep running.
- loadId - Variable in class loci.formats.gui.PreviewPane
-
Current ID to load.
- loadImage(Image) - Static method in class loci.formats.gui.AWTImageTools
-
Ensures the given AWT image is fully loaded.
- LoadImageRecord() - Method in class loci.formats.in.SlideBook7Reader.CImageGroup
- LoadMaks() - Method in class loci.formats.in.SlideBook7Reader.CImageGroup
- loadManifest() - Static method in class loci.formats.FormatTools
- loadMemo() - Method in class loci.formats.Memoizer
-
Load a memo file if possible, returning a null if not.
- LoadMetadata() - Method in class loci.formats.in.SlideBook7Reader.DataLoader
- loadOption() - Method in class loci.plugins.prefs.BooleanOption
- loadOption() - Method in class loci.plugins.prefs.DoubleOption
- loadOption() - Method in class loci.plugins.prefs.Option
-
Loads the option's value from the ImageJ preferences file.
- loadOption() - Method in class loci.plugins.prefs.StringOption
- loadOptions() - Method in class loci.plugins.prefs.OptionsList
-
Loads option values from the ImageJ preferences file.
- loadOptions(String, ArrayList<String>) - Method in class loci.formats.in.DynamicMetadataOptions
- loadProperties() - Static method in class loci.formats.FormatTools
-
Deprecated.This method should no longer be used. The properties are now obtained from the jar manifest.
- loadReader() - Method in interface loci.formats.Memoizer.Deser
- loadReader() - Method in class loci.formats.Memoizer.KryoDeser
- loadReader() - Method in class loci.formats.Memoizer.RandomAccessDeser
- loadReleaseVersion() - Method in interface loci.formats.Memoizer.Deser
- loadReleaseVersion() - Method in class loci.formats.Memoizer.KryoDeser
- loadReleaseVersion() - Method in class loci.formats.Memoizer.RandomAccessDeser
- loadRevision() - Method in interface loci.formats.Memoizer.Deser
- loadRevision() - Method in class loci.formats.Memoizer.KryoDeser
- loadRevision() - Method in class loci.formats.Memoizer.RandomAccessDeser
- LoadSAPositions() - Method in class loci.formats.in.SlideBook7Reader.CImageGroup
- LoadStagePosition() - Method in class loci.formats.in.SlideBook7Reader.CImageGroup
- loadStart(File) - Method in interface loci.formats.Memoizer.Deser
- loadStart(File) - Method in class loci.formats.Memoizer.KryoDeser
- loadStart(File) - Method in class loci.formats.Memoizer.RandomAccessDeser
- loadStop() - Method in interface loci.formats.Memoizer.Deser
- loadStop() - Method in class loci.formats.Memoizer.KryoDeser
- loadStop() - Method in class loci.formats.Memoizer.RandomAccessDeser
- loadStream - Variable in class loci.formats.Memoizer.RandomAccessDeser
- loadThumb(BufferedImageReader, int, Panel, boolean) - Static method in class loci.plugins.in.ThumbLoader
- loadVersion() - Method in interface loci.formats.Memoizer.Deser
- loadVersion() - Method in class loci.formats.Memoizer.KryoDeser
- loadVersion() - Method in class loci.formats.Memoizer.RandomAccessDeser
- locateExperimentFile(String) - Method in class loci.formats.in.BDReader
- locateFirstValidFile() - Method in class loci.formats.in.MetamorphReader
-
Locates the first valid file in the STK arrays.
- LOCATION - Enum constant in enum class loci.formats.dicom.DicomAttribute
- LOCATION_HTTP - Static variable in class loci.plugins.in.ImporterOptions
- LOCATION_LOCAL - Static variable in class loci.plugins.in.ImporterOptions
- LOCATION_OMERO - Static variable in class loci.plugins.in.ImporterOptions
- LocationDialog - Class in loci.plugins.in
-
Bio-Formats Importer location chooser dialog box.
- LocationDialog(ImportProcess) - Constructor for class loci.plugins.in.LocationDialog
-
Creates a location chooser dialog for the Bio-Formats Importer.
- locator - Variable in class loci.formats.in.OMEXMLReader.OMEXMLHandler
- loci.formats - package loci.formats
-
Bio-Formats: a library for reading and writing popular microscopy file formats.
- loci.formats.cache - package loci.formats.cache
-
Package containing Bio-Formats caching logic, for managing subsets of large collections of image planes in memory.
- loci.formats.codec - package loci.formats.codec
- loci.formats.dicom - package loci.formats.dicom
- loci.formats.filter - package loci.formats.filter
- loci.formats.gui - package loci.formats.gui
-
Package containing Bio-Formats graphical user interface code.
- loci.formats.in - package loci.formats.in
-
Package containing Bio-Formats file format readers.
- loci.formats.in.LeicaMicrosystemsMetadata - package loci.formats.in.LeicaMicrosystemsMetadata
- loci.formats.internal - package loci.formats.internal
-
Package containing common classes for internal use by Bio-Formats readers/writers.
- loci.formats.meta - package loci.formats.meta
-
Package containing core Bio-Formats metadata interfaces for the OME data model.
- loci.formats.ome - package loci.formats.ome
-
Package containing Bio-Formats OME-related logic for OME-XML metadata, and database import, upload and download.
- loci.formats.out - package loci.formats.out
-
Package containing Bio-Formats file format writers.
- loci.formats.services - package loci.formats.services
- loci.formats.tiff - package loci.formats.tiff
-
Package containing Bio-Formats TIFF code of general utility.
- loci.formats.tools - package loci.formats.tools
-
Package containing utility methods corresponding to the Bio-Formats command line tools.
- loci.plugins - package loci.plugins
-
Bio-Formats Plugins: a collection of plugins for ImageJ, including the Bio-Formats Importer, Bio-Formats Exporter, Bio-Formats Macro Extensions, Data Browser and Stack Slicer.
- loci.plugins.config - package loci.plugins.config
-
Bio-Formats Plugins Configuration plugin for ImageJ.
- loci.plugins.in - package loci.plugins.in
-
Bio-Formats Importer plugin for ImageJ.
- loci.plugins.macro - package loci.plugins.macro
-
Bio-Formats Macro Extensions plugin for ImageJ.
- loci.plugins.out - package loci.plugins.out
-
Bio-Formats Exporter plugin for ImageJ.
- loci.plugins.prefs - package loci.plugins.prefs
-
Classes for managing Bio-Formats plugins preferences.
- loci.plugins.shortcut - package loci.plugins.shortcut
-
Bio-Formats Plugins Shortcut Window plugin for ImageJ.
- loci.plugins.util - package loci.plugins.util
-
Utility classes and methods for the Bio-Formats plugins for ImageJ.
- LociConfig - Class in loci.plugins.config
-
An ImageJ plugin for displaying the Bio-Formats plugins configuration dialog.
- LociConfig() - Constructor for class loci.plugins.config.LociConfig
- LociExporter - Class in loci.plugins
-
ImageJ plugin for writing files using the OME Bio-Formats package.
- LociExporter() - Constructor for class loci.plugins.LociExporter
- LociFunctions - Class in loci.plugins.macro
-
This class provides macro extensions in ImageJ for Bio-Formats.
- LociFunctions() - Constructor for class loci.plugins.macro.LociFunctions
- LociImporter - Class in loci.plugins
-
ImageJ plugin for reading files using the OME Bio-Formats package.
- LociImporter() - Constructor for class loci.plugins.LociImporter
- LociInstaller - Class in loci.plugins.config
-
An ImageJ plugin for installing and upgrading libraries related to the Bio-Formats plugins.
- LociInstaller() - Constructor for class loci.plugins.config.LociInstaller
- LociPrefs - Class in loci.plugins.util
-
Utility methods for ImageJ preferences for Bio-Formats plugins.
- LociPrefs() - Constructor for class loci.plugins.util.LociPrefs
- LOF - Enum constant in enum class loci.formats.in.LeicaMicrosystemsMetadata.LMSFileReader.ImageFormat
- LOF - Enum constant in enum class loci.formats.in.LOFReader.MetadataSource
- LOF_MAGIC_BYTE - Static variable in class loci.formats.in.LOFReader
- LOF_MEMORY_BYTE - Static variable in class loci.formats.in.LOFReader
- LOFReader - Class in loci.formats.in
-
LOFReader is the file format reader for Leica Microsystems' LOF files.
- LOFReader() - Constructor for class loci.formats.in.LOFReader
-
Constructs a new Leica LOF reader.
- LOFReader(XlifDocument) - Constructor for class loci.formats.in.LOFReader
- LOFReader.MetadataSource - Enum Class in loci.formats.in
- LofXmlDocument - Class in loci.formats.in.LeicaMicrosystemsMetadata
-
This class loads and represents a Leica Microsystems XML document that has been extracted from a LOF file
- LofXmlDocument(String, String) - Constructor for class loci.formats.in.LeicaMicrosystemsMetadata.LofXmlDocument
- log - Static variable in class loci.formats.in.LeicaMicrosystemsMetadata.LMSFileReader
- log - Variable in class loci.plugins.config.ConfigWindow
- log() - Method in class loci.plugins.util.RecordedImageProcessor
- logFile - Variable in class loci.formats.in.DeltavisionReader
- logFiles - Variable in class loci.formats.in.CellWorxReader
- logger - Variable in class loci.formats.services.JPEGTurboServiceImpl
- LOGGER - Static variable in class loci.formats.cache.CacheUpdater
- LOGGER - Static variable in class loci.formats.ChannelMerger
- LOGGER - Static variable in class loci.formats.ClassList
- LOGGER - Static variable in class loci.formats.codec.BaseCodec
- LOGGER - Static variable in class loci.formats.dicom.DicomJSONProvider
- LOGGER - Static variable in class loci.formats.FileStitcher
- LOGGER - Static variable in class loci.formats.FormatHandler
- LOGGER - Static variable in class loci.formats.FormatTools
- LOGGER - Static variable in class loci.formats.gui.AWTImageTools
- LOGGER - Static variable in class loci.formats.gui.CacheComponent
- LOGGER - Static variable in class loci.formats.gui.DataConverter
- LOGGER - Static variable in class loci.formats.gui.ImageViewer
- LOGGER - Static variable in class loci.formats.gui.PreviewPane
- LOGGER - Static variable in class loci.formats.ImageReader
- LOGGER - Static variable in class loci.formats.ImageWriter
- LOGGER - Static variable in class loci.formats.in.BaseTiffReader
-
Logger for this class.
- LOGGER - Static variable in class loci.formats.in.CV7000Reader
- LOGGER - Static variable in class loci.formats.in.DNGReader
-
Logger for this class.
- LOGGER - Static variable in class loci.formats.in.DynamicMetadataOptions
- LOGGER - Static variable in class loci.formats.in.IM3Reader
-
Logger for outputting summary diagnostics.
- LOGGER - Static variable in class loci.formats.in.ImarisTiffReader
-
Logger for this class.
- LOGGER - Static variable in class loci.formats.in.JPEG2000MetadataParser
-
Logger for this class.
- LOGGER - Static variable in class loci.formats.in.JPEG2000Reader
-
Logger for this class.
- LOGGER - Static variable in class loci.formats.in.JPXReader
-
Logger for this class.
- LOGGER - Static variable in class loci.formats.in.LeicaHandler
-
Logger for this class.
- LOGGER - Static variable in class loci.formats.in.LeicaMicrosystemsMetadata.LMSXmlDocument
- LOGGER - Static variable in class loci.formats.in.LeicaReader
- LOGGER - Static variable in class loci.formats.in.LeicaSCNReader
-
Logger for this class.
- LOGGER - Static variable in class loci.formats.in.MetamorphHandler
- LOGGER - Static variable in class loci.formats.in.MetamorphReader
-
Logger for this class.
- LOGGER - Static variable in class loci.formats.in.MikroscanTiffReader
-
Logger for this class.
- LOGGER - Static variable in class loci.formats.in.MinimalTiffReader
-
Logger for this class.
- LOGGER - Static variable in class loci.formats.in.ND2Handler
- LOGGER - Static variable in class loci.formats.in.NikonReader
-
Logger for this class.
- LOGGER - Static variable in class loci.formats.in.PyramidTiffReader
-
Logger for this class.
- LOGGER - Static variable in class loci.formats.in.SlideBook7Reader
- LOGGER - Static variable in class loci.formats.in.SVSReader
-
Logger for this class.
- LOGGER - Static variable in class loci.formats.in.TecanReader
- LOGGER - Static variable in class loci.formats.in.TiffReader
-
Logger for this class.
- LOGGER - Static variable in class loci.formats.in.TissueFAXSReader
- LOGGER - Static variable in class loci.formats.in.TrestleReader
-
Logger for this class.
- LOGGER - Static variable in class loci.formats.in.VectraReader
-
Logger for this class.
- LOGGER - Static variable in class loci.formats.in.VentanaReader
-
Logger for this class.
- LOGGER - Static variable in class loci.formats.in.ZeissTIFFHandler
- LOGGER - Static variable in class loci.formats.Memoizer
-
Default
Loggerfor the memoizer class - LOGGER - Static variable in class loci.formats.MetadataTools
- LOGGER - Static variable in class loci.formats.services.JPEGTurboServiceImpl
- LOGGER - Static variable in class loci.formats.services.JPEGXRServiceImpl
- LOGGER - Static variable in class loci.formats.services.OMEXMLServiceImpl
-
Logger for this class.
- LOGGER - Static variable in class loci.formats.tiff.IFD
- LOGGER - Static variable in enum class loci.formats.tiff.TiffCompression
- LOGGER - Static variable in class loci.formats.tiff.TiffParser
- LOGGER - Static variable in class loci.formats.tiff.TiffSaver
- LOGGER - Static variable in class loci.formats.TileStitcher
- LOGGER - Static variable in class loci.formats.tools.AmiraParameters
- LOGGER - Static variable in class loci.formats.tools.EditTiffG
- LOGGER - Static variable in class loci.formats.tools.FakeImage
- LOGGER - Static variable in class loci.formats.UpgradeChecker
- LOGIC_OUTPUT - Enum constant in enum class loci.formats.in.SPEReader.SpeHeaderEntry
- logIsThisTypeError(IFormatReader, Exception) - Method in class loci.formats.ImageReader
- LOGO_FILE - Static variable in class loci.formats.in.LIFReader
- LONG - Enum constant in enum class loci.formats.in.SPEReader.SpeHeaderType
- LONG - Enum constant in enum class loci.formats.tiff.IFDType
- LONG - Static variable in class loci.formats.in.CellSensReader
- LONG_DATE_FORMAT - Static variable in class loci.formats.in.MetamorphReader
- LONG8 - Enum constant in enum class loci.formats.tiff.IFDType
- LONGARRAY - Enum constant in enum class loci.formats.in.SPEReader.SpeHeaderType
- longValue() - Method in class loci.formats.tiff.TiffRational
-
Returns the value of the specified number as a long.
- lookup - Static variable in enum class loci.formats.codec.CompressionType
-
Map used to retrieve the compression type corresponding to the code.
- lookup - Static variable in enum class loci.formats.codec.JPEG2000BoxType
-
Map used to retrieve the box type corresponding to the code.
- lookup - Static variable in enum class loci.formats.codec.JPEG2000SegmentMarker
-
Map used to retrieve the segment marker corresponding to the code.
- lookup - Static variable in enum class loci.formats.dicom.DicomAttribute
- lookup - Static variable in enum class loci.formats.dicom.DicomVR
- lookup - Static variable in enum class loci.formats.in.BaseZeissReader.Charset
- lookup - Static variable in enum class loci.formats.in.BaseZeissReader.DrawStyle
- lookup - Static variable in enum class loci.formats.in.BaseZeissReader.FeatureType
- lookup - Static variable in enum class loci.formats.in.BaseZeissReader.FillStyle
- lookup - Static variable in enum class loci.formats.in.BaseZeissReader.LineEndPositions
- lookup - Static variable in enum class loci.formats.in.BaseZeissReader.LineEndStyle
- lookup - Static variable in enum class loci.formats.in.BaseZeissReader.PointStyle
- lookup - Static variable in enum class loci.formats.in.BaseZeissReader.TextAlignment
- lookup - Variable in class loci.formats.in.PictReader
-
Color lookup table for palette color images.
- lookup - Static variable in enum class loci.formats.tiff.IFDType
- lookup - Static variable in enum class loci.formats.tiff.PhotoInterp
- lookup - Static variable in enum class loci.formats.tiff.TiffCompression
-
Reverse lookup of code to TIFF compression enumerate value.
- lookup(String) - Method in class loci.formats.in.ZeissTIFFReader
-
Translate a file path from the XML file to an actual path on disk.
- lookupChannel(CV7000Reader.Plane) - Method in class loci.formats.in.CV7000Reader
- lookupChannelIndex(String) - Method in class loci.formats.in.TecanReader
- lookupChild(DicomAttribute) - Method in class loci.formats.dicom.DicomTag
-
Find the first child tag with the given attribute, or null if one does not exist.
- lookupDimension(int, int, int) - Method in class loci.formats.in.LeicaSCNReader.Pixels
- lookupFile(int) - Method in class loci.formats.in.FlexReader
- lookupFile(int) - Method in class loci.formats.in.PerkinElmerReader
- lookupFile(int, int) - Method in class loci.formats.in.CellomicsReader
- lookupFile(int, int, int) - Method in class loci.formats.in.FlexReader
- lookupImage(int, int, boolean, boolean) - Method in class loci.formats.in.TecanReader
- lookupPlane(int, int) - Method in class loci.formats.in.CV7000Reader
- lookupPlane(int, int, int, int, int, int) - Method in class loci.formats.in.ColumbusReader
- lookupResolution(int, int) - Method in class loci.formats.ome.OMEPyramidStore
-
Find the Resolution object for the given indices.
- lookupResolution(int, int, boolean) - Method in class loci.formats.ome.OMEPyramidStore
-
Find the Resolution object for the given indices.
- lookupTag(String, JSONObject) - Method in class loci.formats.dicom.DicomJSONProvider
-
Get the tag code corresponding to the given JSON object.
- lookupTag(List<DicomTag>, DicomTag) - Method in class loci.formats.out.DicomWriter
- lookupVR(Integer, JSONObject) - Method in class loci.formats.dicom.DicomJSONProvider
-
Get the VR associated with the given tag code and JSON object.
- lookupWell(int, int, int) - Method in class loci.formats.in.JDCEReader
- lossless - Variable in class loci.formats.codec.CodecOptions
-
Used with codecs allowing lossy and lossless compression.
- LOSSLESS_DECODER_CONFIGURATION_12 - Static variable in class loci.formats.codec.NikonCodec
- LOSSLESS_DECODER_CONFIGURATION_14 - Static variable in class loci.formats.codec.NikonCodec
- LosslessJPEGCodec - Class in loci.formats.codec
-
Decompresses lossless JPEG images.
- LosslessJPEGCodec() - Constructor for class loci.formats.codec.LosslessJPEGCodec
- LOSSY_DECODER_CONFIGURATION_12 - Static variable in class loci.formats.codec.NikonCodec
- LOSSY_DECODER_CONFIGURATION_14 - Static variable in class loci.formats.codec.NikonCodec
- LOSSY_IMAGE_COMPRESSION - Enum constant in enum class loci.formats.dicom.DicomAttribute
- LOSSY_IMAGE_COMPRESSION_METHOD - Enum constant in enum class loci.formats.dicom.DicomAttribute
- LOSSY_IMAGE_COMPRESSION_RATIO - Enum constant in enum class loci.formats.dicom.DicomAttribute
- lossyCompression - Variable in class loci.formats.in.NikonReader
- LOW_PRIORITY - Static variable in interface loci.formats.cache.ICacheStrategy
- LOW_RR_VALUE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- lPad - Variable in class loci.formats.gui.CacheIndicator
- lsmFilenames - Variable in class loci.formats.in.ZeissLSMReader
- LT - Enum constant in enum class loci.formats.dicom.DicomVR
- LUMA_BLUE - Static variable in enum class loci.formats.tiff.PhotoInterp
- LUMA_GREEN - Static variable in enum class loci.formats.tiff.PhotoInterp
- LUMA_RED - Static variable in enum class loci.formats.tiff.PhotoInterp
-
Default luminance values for YCbCr data.
- lut - Variable in class loci.formats.in.AmiraReader
- lut - Variable in class loci.formats.in.APNGReader
- lut - Variable in class loci.formats.in.AVIReader
- lut - Variable in class loci.formats.in.BioRadReader
- lut - Variable in class loci.formats.in.DicomReader
- lut - Variable in class loci.formats.in.FV1000Reader
- lut - Variable in class loci.formats.in.IvisionReader
- lut - Variable in class loci.formats.in.JPEG2000MetadataParser
-
Color lookup table stored in the file.
- lut - Variable in class loci.formats.in.JPEG2000Reader
-
The color lookup table associated with this file.
- lut - Variable in class loci.formats.in.JPXReader
-
The color lookup table associated with this file.
- lut - Variable in class loci.formats.in.KhorosReader
-
Global lookup table.
- lut - Variable in class loci.formats.in.OIRReader.Channel
- lut - Variable in class loci.formats.in.PCXReader
- lut - Variable in class loci.formats.in.PSDReader
-
Lookup table.
- lut - Variable in class loci.formats.in.ZeissLMSReader
- lut - Variable in class loci.formats.in.ZeissLSMReader
- LUT - Enum constant in enum class loci.formats.in.BaseZeissReader.FeatureType
- LUT_DATA - Enum constant in enum class loci.formats.dicom.DicomAttribute
- LUT_DESCRIPTOR - Enum constant in enum class loci.formats.dicom.DicomAttribute
- LUT_EXPLANATION - Enum constant in enum class loci.formats.dicom.DicomAttribute
- LUT_LENGTH - Static variable in class loci.formats.in.BioRadReader
- LUT_SIZE - Static variable in class loci.formats.in.NAFReader
- lut16 - Variable in class loci.formats.in.FakeReader
-
16-bit lookup table, if indexed color, one per channel.
- lut8 - Variable in class loci.formats.in.FakeReader
-
8-bit lookup table, if indexed color, one per channel.
- LUTDESC - Static variable in class loci.formats.in.LeicaReader
- lutIndex - Variable in class loci.formats.in.PDSReader
- lutLength - Variable in class loci.formats.ChannelFiller
-
Number of LUT components.
- lutName - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.Channel
- lutNames - Variable in class loci.formats.in.FV1000Reader
- lutNames - Variable in class loci.formats.in.LeicaHandler
- lutNames - Variable in class loci.formats.in.LIFReader
- luts - Variable in class loci.formats.in.OpenlabReader
- luts - Variable in class loci.plugins.util.VirtualImagePlus
- LZ4Filter - Class in loci.formats.filter
- LZ4Filter(Map<String, Object>) - Constructor for class loci.formats.filter.LZ4Filter
- LZ4Filter.LZ4FilterProvider - Class in loci.formats.filter
- LZ4FilterProvider() - Constructor for class loci.formats.filter.LZ4Filter.LZ4FilterProvider
- LZOCodec - Class in loci.formats.codec
-
This class implements LZO decompression.
- LZOCodec() - Constructor for class loci.formats.codec.LZOCodec
- LZW - Enum constant in enum class loci.formats.codec.CompressionType
- LZW - Enum constant in enum class loci.formats.tiff.TiffCompression
- LZW - Static variable in class loci.formats.in.ZeissCZIReader
- LZWCodec - Class in loci.formats.codec
-
This is an optimized LZW codec for use with TIFF files.
- LZWCodec() - Constructor for class loci.formats.codec.LZWCodec
M
- MAC_1_BIT - Static variable in class loci.formats.in.OpenlabReader
-
Image types.
- MAC_16_BIT_COLOR - Static variable in class loci.formats.in.OpenlabReader
- MAC_16_COLORS - Static variable in class loci.formats.in.OpenlabReader
- MAC_16_GREYS - Static variable in class loci.formats.in.OpenlabReader
- MAC_24_BIT_COLOR - Static variable in class loci.formats.in.OpenlabReader
- MAC_256_COLORS - Static variable in class loci.formats.in.OpenlabReader
- MAC_256_GREYS - Static variable in class loci.formats.in.OpenlabReader
- MAC_4_GREYS - Static variable in class loci.formats.in.OpenlabReader
- MAC_CHARSET - Enum constant in enum class loci.formats.in.BaseZeissReader.Charset
- MACRO_IMAGE - Static variable in class loci.formats.in.CellSensReader
- macroFile - Variable in class loci.formats.in.HamamatsuVMSReader
- MacroFunctions - Class in loci.plugins.macro
-
Convenience class that simplifies implemention of ImageJ macro extensions.
- MacroFunctions() - Constructor for class loci.plugins.macro.MacroFunctions
- macroIndex - Variable in class loci.formats.in.SVSReader
- mActualMagnification - Variable in class loci.formats.in.SlideBook7Reader.CLensDef70
- mag - Variable in class loci.formats.in.FluoviewReader
- mag - Variable in class loci.formats.in.GatanReader
- mag - Variable in class loci.formats.in.ND2Handler
- MAG_MULTIPLIER - Static variable in class loci.formats.in.FEITiffReader
- MAGIC - Static variable in class loci.formats.in.AnalyzeReader
- MAGIC - Static variable in class loci.formats.in.BioRadSCNReader
- MAGIC - Static variable in class loci.formats.in.ColumbusReader
- MAGIC - Static variable in class loci.formats.in.HitachiReader
- MAGIC_BYTES - Static variable in class loci.formats.in.BioRadGelReader
- MAGIC_NUMBER - Static variable in class loci.formats.in.OBFReader
- MAGIC_NUMBER - Static variable in class loci.formats.tiff.TiffConstants
- MAGIC_STRING - Static variable in class loci.formats.in.HRDGDFReader
- MAGIC_STRING - Static variable in class loci.formats.in.IMODReader
- MAGIC_STRING - Static variable in class loci.formats.in.ImspectorReader
-
The header for each file contains this string.
- MAGIC_STRING - Static variable in class loci.formats.in.KodakReader
- MAGIC_STRING - Static variable in class loci.formats.in.MolecularImagingReader
- MAGIC_STRING - Static variable in class loci.formats.in.SIFReader
- MAGIC_STRING - Static variable in class loci.formats.in.SimplePCITiffReader
- MAGNETIC_FIELD_STRENGTH - Enum constant in enum class loci.formats.dicom.DicomAttribute
- magnification - Variable in class loci.formats.in.CellSensReader.Pyramid
- magnification - Variable in class loci.formats.in.CV7000Reader.Channel
- magnification - Variable in class loci.formats.in.FEITiffReader
- magnification - Variable in class loci.formats.in.FV1000Reader
- magnification - Variable in class loci.formats.in.IvisionReader
- magnification - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataTempBuffer
- magnification - Variable in class loci.formats.in.LIFReader
- magnification - Variable in class loci.formats.in.NDPIReader
- magnification - Variable in class loci.formats.in.NikonTiffReader
- magnification - Variable in class loci.formats.in.OIRReader.Objective
- magnification - Variable in class loci.formats.in.OperettaReader.Channel
- magnification - Variable in class loci.formats.in.OperettaReader.Plane
- magnification - Variable in class loci.formats.in.SimplePCITiffReader
- magnification - Variable in class loci.formats.in.SISReader
- magnification - Variable in class loci.formats.in.SVSReader
- magnification - Variable in class loci.formats.in.VentanaReader
- magnification - Variable in class loci.formats.in.VolocityReader.Stack
- magnification - Variable in class loci.formats.in.ZeissLSMReader.Recording
- MAGNIFICATION - Static variable in class loci.formats.in.CellSensReader
- MAGNIFICATION_TAG - Static variable in class loci.formats.in.SlidebookTiffReader
- magnitudes - Variable in class loci.formats.in.IM3Reader.Spectrum
- main(String[]) - Static method in class loci.formats.codec.BitBuffer
-
Deprecated.Testing method.
- main(String[]) - Static method in class loci.formats.codec.BitWriter
-
Deprecated.Tests the BitWriter class.
- main(String[]) - Static method in class loci.formats.gui.DataConverter
- main(String[]) - Static method in class loci.formats.gui.ImageViewer
- main(String[]) - Static method in class loci.formats.gui.XMLWindow
- main(String[]) - Static method in class loci.formats.in.IM3Reader
-
Write a summary of each record to STDOUT
- main(String[]) - Static method in class loci.formats.Memoizer
- main(String[]) - Static method in class loci.formats.tools.AmiraParameters
- main(String[]) - Static method in class loci.formats.tools.BioFormatsExtensionPrinter
- main(String[]) - Static method in class loci.formats.tools.CacheConsole
-
Interactive interpreter for testing Bio-Formats caching implementation.
- main(String[]) - Static method in class loci.formats.tools.EditTiffG
- main(String[]) - Static method in class loci.formats.tools.MakeTestOmeTiff
- main(String[]) - Static method in class loci.formats.tools.UpgradeCheck
- main(String[]) - Static method in class loci.plugins.About
- main(String[]) - Static method in class loci.plugins.config.LociConfig
- main(String[]) - Static method in class loci.plugins.in.Importer
-
Main method, for testing.
- MAIN - Enum constant in enum class loci.formats.in.BaseZeissReader.Context
- main_tagset - Variable in class loci.formats.in.ZeissTIFFHandler
- MainDialog - Class in loci.plugins.in
-
Bio-Formats Importer general options dialog box.
- MainDialog(ImportProcess) - Constructor for class loci.plugins.in.MainDialog
-
Creates a general options dialog for the Bio-Formats Importer.
- majorVersion - Variable in class loci.formats.in.ZeissCZIReader.FileHeader
- MAKE - Static variable in class loci.formats.tiff.IFD
- make24Bits(Object, int, int, boolean) - Static method in class loci.formats.ImageTools
-
Convert an arbitrary primitive type array with 3 samples per pixel to an int array, i.e.
- make24Bits(Object, int, int, boolean, boolean) - Static method in class loci.formats.ImageTools
-
Convert an arbitrary primitive type array with 3 samples per pixel to a 3 x (width * height) byte array.
- make24Bits(Object, int, int, boolean, boolean, Double, Double) - Static method in class loci.formats.ImageTools
-
Convert an arbitrary primitive type array with 3 samples per pixel to a 3 x (width * height) byte array.
- make24Bits(Object, int, int, boolean, Double, Double) - Static method in class loci.formats.ImageTools
-
Convert an arbitrary primitive type array with 3 samples per pixel to an int array, i.e.
- makeBitArray(int, int) - Static method in class loci.formats.gui.SignedColorModel
- makeBitArray(int, int) - Static method in class loci.formats.gui.UnsignedIntColorModel
- makeBuffered(Image) - Static method in class loci.formats.gui.AWTImageTools
-
Creates a buffered image from the given AWT image object.
- makeBuffered(Image, ColorModel) - Static method in class loci.formats.gui.AWTImageTools
-
Creates a buffered image possessing the given color model, from the specified AWT image object.
- makeBufferedImageReader(IFormatReader) - Static method in class loci.formats.gui.BufferedImageReader
-
Converts the given reader into a BufferedImageReader, wrapping if needed.
- makeBufferedImageWriter(IFormatWriter) - Static method in class loci.formats.gui.BufferedImageWriter
-
Converts the given writer into a BufferedImageWriter, wrapping if needed.
- makeChannelFiller(IFormatReader) - Static method in class loci.formats.ChannelFiller
-
Converts the given reader into a ChannelFiller, wrapping if needed.
- makeChannelMerger(IFormatReader) - Static method in class loci.formats.ChannelMerger
-
Converts the given reader into a ChannelMerger, wrapping if needed.
- makeChannelSeparator(IFormatReader) - Static method in class loci.formats.ChannelSeparator
-
Converts the given reader into a ChannelSeparator, wrapping if needed.
- makeColorModel(int, int) - Static method in class loci.formats.gui.AWTImageTools
-
Gets a color model for the given number of color components.
- makeColorSpace(int) - Static method in class loci.formats.gui.AWTImageTools
-
Gets a color space for the given number of color components.
- makeComboFilter(FileFilter[]) - Static method in class loci.formats.gui.GUITools
-
Creates an "All supported file types" combo filter encompassing all of the given filters.
- makeCompactGrid(Container, int, int, int, int, int, int) - Static method in class loci.plugins.config.SpringUtilities
-
Aligns the first
rows*colscomponents ofparentin a grid. - makeCompatible(BufferedImage, GraphicsConfiguration) - Static method in class loci.formats.gui.AWTImageTools
-
Creates a buffered image compatible with the given graphics configuration, using the given buffered image as a source.
- makeDimensionSwapper(IFormatReader) - Static method in class loci.formats.DimensionSwapper
-
Converts the given reader into a DimensionSwapper, wrapping if needed.
- makeDimensionTable() - Static method in class loci.formats.in.LeicaReader
- makeDummySlider() - Static method in class loci.plugins.util.DataBrowser
- makeFileList() - Method in class loci.formats.in.DicomReader
-
Build a list of files that belong with the current file.
- makeFilterMetadata() - Method in class loci.formats.FormatReader
-
Return a properly configured loci.formats.meta.FilterMetadata.
- makeFilterMetadata() - Method in class loci.formats.in.LeicaMicrosystemsMetadata.LMSFileReader
- makeGrid(Container, int, int, int, int, int, int) - Static method in class loci.plugins.config.SpringUtilities
-
Aligns the first
rows*colscomponents ofparentin a grid. - makeHeavyPanel(Component) - Static method in class loci.plugins.util.DataBrowser
-
Makes AWT play nicely with Swing components.
- makeIFD() - Method in class loci.formats.out.PyramidOMETiffWriter
- makeIFD() - Method in class loci.formats.out.TiffWriter
- makeImage(byte[][], int, int, boolean) - Static method in class loci.formats.gui.AWTImageTools
-
Creates an image from the given byte data.
- makeImage(byte[][], int, int, int, boolean, boolean, boolean) - Static method in class loci.formats.gui.AWTImageTools
-
Creates an image from the given raw byte array, performing any necessary type conversions.
- makeImage(byte[], boolean, MetadataRetrieve, int) - Static method in class loci.formats.gui.AWTImageTools
-
Creates an image from the given raw byte array, obtaining the dimensional parameters from the specified metadata object.
- makeImage(byte[], int, int, boolean) - Static method in class loci.formats.gui.AWTImageTools
-
Creates an image from the given single-channel byte data.
- makeImage(byte[], int, int, int, boolean, boolean) - Static method in class loci.formats.gui.AWTImageTools
-
Creates an image from the given byte data.
- makeImage(byte[], int, int, int, boolean, int, boolean, boolean, boolean) - Static method in class loci.formats.gui.AWTImageTools
-
Creates an image from the given raw byte array, performing any necessary type conversions.
- makeImage(double[][], int, int) - Static method in class loci.formats.gui.AWTImageTools
-
Creates an image from the given double-precision floating point data.
- makeImage(double[], int, int) - Static method in class loci.formats.gui.AWTImageTools
-
Creates an image from the given single-channel double data.
- makeImage(double[], int, int, int, boolean) - Static method in class loci.formats.gui.AWTImageTools
-
Creates an image from the given double data.
- makeImage(float[][], int, int) - Static method in class loci.formats.gui.AWTImageTools
-
Creates an image from the given single-precision floating point data.
- makeImage(float[], int, int) - Static method in class loci.formats.gui.AWTImageTools
-
Creates an image from the given single-channel float data.
- makeImage(float[], int, int, int, boolean) - Static method in class loci.formats.gui.AWTImageTools
-
Creates an image from the given float data.
- makeImage(int[][], int, int, boolean) - Static method in class loci.formats.gui.AWTImageTools
-
Creates an image from the given int data.
- makeImage(int[], int, int, boolean) - Static method in class loci.formats.gui.AWTImageTools
-
Creates an image from the given single-channel int data.
- makeImage(int[], int, int, int, boolean, boolean) - Static method in class loci.formats.gui.AWTImageTools
-
Creates an image from the given int data.
- makeImage(short[][], int, int, boolean) - Static method in class loci.formats.gui.AWTImageTools
-
Creates an image from the given short data.
- makeImage(short[], int, int, boolean) - Static method in class loci.formats.gui.AWTImageTools
-
Creates an image from the given single-channel short data.
- makeImage(short[], int, int, int, boolean, boolean) - Static method in class loci.formats.gui.AWTImageTools
-
Creates an image from the given short data.
- makeImage(String) - Method in class loci.formats.gui.PreviewPane
-
Creates a blank image with the given message painted on top (e.g., a loading or error message), matching the size of the active reader's thumbnails.
- makeImageName(int) - Method in class loci.formats.in.MetamorphReader
-
Create an appropriate name for the given series.
- makeImageProcessorReader(IFormatReader) - Static method in class loci.plugins.util.ImageProcessorReader
-
Converts the given reader into a ImageProcessorReader, wrapping if needed.
- makeImageReader() - Static method in class loci.plugins.util.LociPrefs
-
Creates an image reader according to the current configuration settings, including which format readers are currently enabled, as well as format-specific configuration settings.
- makeItem() - Method in class loci.formats.out.DicomWriter
- makeItemDelimitation() - Method in class loci.formats.out.DicomWriter
- makeJTree(Document) - Static method in class loci.formats.gui.XMLCellRenderer
-
Constructs a Swing JTree that displays the given XML DOM document.
- makeLabel(String, boolean) - Method in class loci.plugins.config.ConfigWindow
- makeLabel(String, int, int) - Method in class loci.plugins.in.ColorDialog
- makeList(DefaultListModel) - Method in class loci.plugins.config.ConfigWindow
- makeLUT(int, int) - Method in class loci.plugins.in.Colorizer
- makeLUT(Color) - Method in class loci.plugins.in.Colorizer
- makeLUTs(int) - Method in class loci.plugins.in.Colorizer
- makeLUTs(ColorModel[], boolean) - Method in class loci.plugins.in.Colorizer
- makeMinMaxCalculator(IFormatReader) - Static method in class loci.formats.MinMaxCalculator
-
Converts the given reader into a MinMaxCalculator, wrapping if needed.
- makeModuloElement(Document) - Method in class loci.formats.meta.ModuloAnnotation
-
Construct a DOM element for this annotation using the given Document as the root.
- makeOmeTiff(String...) - Method in class loci.formats.tools.MakeTestOmeTiff
- makeOmeTiff(String, CoreMetadata) - Method in class loci.formats.tools.MakeTestOmeTiff
- makeOmeTiffExtensions(String...) - Method in class loci.formats.tools.MakeTestOmeTiff
- makeOriginalMetadata(Document) - Method in class loci.formats.meta.OriginalMetadataAnnotation
-
Create a DOM element for this annotation with the given document as the parent.
- makePixelTypes() - Static method in class loci.formats.FormatTools
- MAKER_NOTE - Static variable in class loci.formats.tiff.IFD
- MAKER_WHITE_BALANCE - Static variable in class loci.formats.in.NikonReader
- makeRGBImage(byte[][], int, int) - Static method in class loci.formats.gui.AWTImageTools
- makeRGBImage(byte[], int, int, int, boolean) - Static method in class loci.formats.gui.AWTImageTools
- makerNoteOffset - Variable in class loci.formats.in.NikonReader
-
Offset to the Nikon Maker Note.
- makeSamples() - Method in class loci.formats.tools.MakeTestOmeTiff
- makeSaneDimensionOrder(String) - Static method in class loci.formats.MetadataTools
-
Adjusts the given dimension order as needed so that it contains exactly one of each of the following characters: 'X', 'Y', 'Z', 'C', 'T'.
- makeShortArray(int) - Method in class loci.formats.out.DicomWriter
- makeSplitPane(JList, JPanel) - Method in class loci.plugins.config.ConfigWindow
- makeStack(ImageStack) - Method in class loci.plugins.Slicer
-
Returns a new ImageStack using the given ImageStack as a template.
- MakeTestOmeTiff - Class in loci.formats.tools
-
Creates sample OME-TIFF datasets according to the given parameters.
- MakeTestOmeTiff() - Constructor for class loci.formats.tools.MakeTestOmeTiff
- MakeTestOmeTiff.TextLine - Class in loci.formats.tools
- makeTextField() - Static method in class loci.plugins.config.ConfigWindow
- makeTileStitcher(IFormatReader) - Static method in class loci.formats.TileStitcher
-
Converts the given reader into a TileStitcher, wrapping if needed.
- makeTreeNode(Node) - Static method in class loci.formats.gui.XMLCellRenderer
-
Recursively builds JTree node structure from DOM node structure.
- makeUnsigned(BufferedImage) - Static method in class loci.formats.gui.AWTImageTools
-
Converts the given BufferedImage into an image with unsigned pixel data.
- makeValidIFD(IFD, int, int) - Method in class loci.formats.tiff.TiffSaver
-
Makes a valid IFD.
- makeWellLabel(int, int) - Method in class loci.formats.in.TecanReader
- mAlgorythm - Variable in class loci.formats.in.SlideBook7Reader.CCompressionBase
- mAlignManipRecordList - Variable in class loci.formats.in.SlideBook7Reader.CImageGroup
- mAltSourcePosition - Variable in class loci.formats.in.SlideBook7Reader.CFluorDef70
- mAnn - Variable in class loci.formats.in.SlideBook7Reader.CCubeAnnotation70
- mAnn - Variable in class loci.formats.in.SlideBook7Reader.CFRAPRegionAnnotation70
- mAnn - Variable in class loci.formats.in.SlideBook7Reader.CUnknownAnnotation70
- mAnnotationList - Variable in class loci.formats.in.SlideBook7Reader.CImageGroup
- mAnnotationTablePtr - Variable in class loci.formats.in.SlideBook7Reader.CImageRecord70
- MANUFACTURER - Enum constant in enum class loci.formats.dicom.DicomAttribute
- MANUFACTURER_MODEL_NAME - Enum constant in enum class loci.formats.dicom.DicomAttribute
- map - Variable in class loci.formats.in.EPSReader
- map - Variable in class loci.formats.tools.AmiraParameters
- mapFile - Variable in class loci.formats.in.HamamatsuVMSReader
- mapOIBFiles() - Method in class loci.formats.in.FV1000Reader
- mappedFiles - Variable in class loci.formats.in.ZipReader
- MAPPING_RESOURCE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- mapServer(String, String) - Static method in class loci.formats.in.FlexReader
-
Map the server named 'alias' to the path 'realName'.
- mapServer(String, String[]) - Static method in class loci.formats.in.FlexReader
-
Map the server named 'alias' to the paths in 'realNames'.
- mapServersFromConfigurationFile(String) - Static method in class loci.formats.in.FlexReader
-
Read a configuration file with lines of the form: <server alias>=<real server name> and call mapServer(String, String) accordingly.
- Marker() - Constructor for class loci.formats.in.ZeissLSMReader.Marker
- MARKER - Static variable in class loci.formats.in.ZeissLMSReader
- MARKER_0 - Static variable in class loci.formats.in.TillVisionReader
- MARKER_1 - Static variable in class loci.formats.in.TillVisionReader
- MARKER_2 - Static variable in class loci.formats.in.TillVisionReader
- MARKER_3 - Static variable in class loci.formats.in.TillVisionReader
- MARKER_TAG - Static variable in class loci.formats.in.NDPIReader
- MARKER_TAG_HIGH_BYTES - Static variable in class loci.formats.in.NDPIReader
- MASK_FRAME_NUMBERS - Enum constant in enum class loci.formats.dicom.DicomAttribute
- MASK_OPERATION - Enum constant in enum class loci.formats.dicom.DicomAttribute
- MASK_OPERATION_EXPLANATION - Enum constant in enum class loci.formats.dicom.DicomAttribute
- MASK_SUBPIXEL_SHIFT - Enum constant in enum class loci.formats.dicom.DicomAttribute
- MASK_SUBTRACTION_SEQUENCE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- masks - Variable in class loci.formats.in.FakeReader
- masterClock - Variable in class loci.formats.in.SDTInfo
-
Use or not Master Clock (SPC140 multi-module).
- matchFilename(String) - Method in class loci.formats.in.CellomicsReader
- matchFiles(String[], NumberFilter) - Static method in class loci.formats.FilePattern
- matrix - Variable in class loci.formats.in.ZeissTIFFHandler.Scaling
- mAuxCaptureFlags - Variable in class loci.formats.in.SlideBook7Reader.CExposureRecord70
- mAuxDataTablePtr - Variable in class loci.formats.in.SlideBook7Reader.CImageRecord70
- mAuxDoubleDataList - Variable in class loci.formats.in.SlideBook7Reader.CImageGroup
- mAuxFilterWheel2Pos - Variable in class loci.formats.in.SlideBook7Reader.CFluorDef70
- mAuxFilterWheel3Pos - Variable in class loci.formats.in.SlideBook7Reader.CFluorDef70
- mAuxFilterWheel4Pos - Variable in class loci.formats.in.SlideBook7Reader.CFluorDef70
- mAuxFilterWheel5Pos - Variable in class loci.formats.in.SlideBook7Reader.CFluorDef70
- mAuxFilterWheel6Pos - Variable in class loci.formats.in.SlideBook7Reader.CFluorDef70
- mAuxFilterWheel7Pos - Variable in class loci.formats.in.SlideBook7Reader.CFluorDef70
- mAuxFilterWheelPos - Variable in class loci.formats.in.SlideBook7Reader.CFluorDef70
- mAuxFloatDataList - Variable in class loci.formats.in.SlideBook7Reader.CImageGroup
- mAuxNDPos - Variable in class loci.formats.in.SlideBook7Reader.CFluorDef70
- mAuxSInt32DataList - Variable in class loci.formats.in.SlideBook7Reader.CImageGroup
- mAuxSInt64DataList - Variable in class loci.formats.in.SlideBook7Reader.CImageGroup
- mAuxXmlDataList - Variable in class loci.formats.in.SlideBook7Reader.CImageGroup
- mAuxZStageIncreaseTowardsSample - Variable in class loci.formats.in.SlideBook7Reader.CAnnotation70
- mAuxZStageMicrons - Variable in class loci.formats.in.SlideBook7Reader.CAnnotation70
- mAuxZStageMicronsSet - Variable in class loci.formats.in.SlideBook7Reader.CAnnotation70
- mAuxZStartPosition - Variable in class loci.formats.in.SlideBook7Reader.CExposureRecord70
- max - Variable in class loci.formats.gui.SignedColorModel
- max - Variable in class loci.formats.in.InCellReader.Image
- max - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.Channel
- max(double) - Method in class loci.plugins.util.RecordedImageProcessor
- MAX_APERTURE_VALUE - Static variable in class loci.formats.tiff.IFD
- MAX_BLOCK_SIZE - Static variable in class loci.formats.services.POIServiceImpl
- MAX_CHANNELS - Static variable in class loci.formats.in.DeltavisionReader
- MAX_COMPONENTS - Static variable in class loci.plugins.in.SeriesDialog
- MAX_HEADER_SIZE - Static variable in class loci.formats.in.QuesantReader
- MAX_INTENSITY - Enum constant in enum class loci.formats.in.SPEReader.SpeHeaderEntry
- MAX_JPEG_SIZE - Static variable in class loci.formats.in.HamamatsuVMSReader
- MAX_LEN - Static variable in class loci.formats.out.DicomWriter.UIDCreator
- MAX_MAJOR_VERSION - Static variable in class loci.formats.in.MicromanagerReader
-
Defines maximum Micro-Manager version supported.
- MAX_PRIORITY - Static variable in interface loci.formats.cache.ICacheStrategy
- MAX_READERS - Static variable in class loci.formats.FileStitcher
- MAX_SAMPLE_VALUE - Static variable in class loci.formats.tiff.IFD
- MAX_SERIES_THUMBS - Static variable in class loci.plugins.in.SeriesDialog
- MAX_SERIES_TOGGLES - Static variable in class loci.plugins.in.SeriesDialog
- MAX_SIZE - Static variable in class loci.formats.in.HamamatsuVMSReader
- MAX_SIZE - Static variable in class loci.formats.in.JPEGReader
- MAX_SIZE - Static variable in class loci.formats.in.NDPIReader
- MAX_STACK_SIZE - Static variable in class loci.formats.in.GIFReader
-
Maximum buffer size.
- MAX_VERSION - Static variable in class loci.formats.in.MicromanagerReader
- maxAdcRate - Variable in class loci.formats.in.SDTInfo
- maxBufferSize - Variable in class loci.formats.in.ImarisHDFReader
- maxBytes - Variable in class loci.formats.codec.CodecOptions
-
If compressing, this is the maximum number of raw bytes to compress.
- maxC - Variable in class loci.formats.in.CV7000Reader.MinMax
- maxCfdRate - Variable in class loci.formats.in.SDTInfo
-
(-1.0 - not set).
- maxCycle - Variable in class loci.formats.in.TecanReader
- maxField - Variable in class loci.formats.in.TecanReader
- MAXIMAL_NUMBER_OF_DIMENSIONS - Static variable in class loci.formats.in.OBFReader
- maximumReadOffset - Variable in class loci.formats.in.JPEG2000MetadataParser
-
Maximum read offset within in the stream.
- maxInten - Variable in class loci.formats.in.DeltavisionReader.DVExtHdrFields
-
Maxiumum intensity.
- maxOffsetIndex - Variable in class loci.formats.in.AmiraReader.HxRLE
- maxPixelRange - Variable in class loci.formats.in.DicomReader
- maxResolution - Variable in class loci.formats.in.ZeissCZIReader
- maxSyncRate - Variable in class loci.formats.in.SDTInfo
-
Maximum rates during the measurement.
- maxT - Variable in class loci.formats.in.CV7000Reader.MinMax
- maxTacRate - Variable in class loci.formats.in.SDTInfo
- maxValue() - Method in class loci.plugins.util.RecordedImageProcessor
- maxX - Variable in class loci.formats.in.ImarisHDFReader
- maxY - Variable in class loci.formats.in.ImarisHDFReader
- maxZ - Variable in class loci.formats.in.CV7000Reader.MinMax
- maxZ - Variable in class loci.formats.in.ImarisHDFReader
- mBackX1 - Variable in class loci.formats.in.SlideBook7Reader.CRatioManipRecord70
- mBackX2 - Variable in class loci.formats.in.SlideBook7Reader.CRatioManipRecord70
- mBackY1 - Variable in class loci.formats.in.SlideBook7Reader.CRatioManipRecord70
- mBackY2 - Variable in class loci.formats.in.SlideBook7Reader.CRatioManipRecord70
- mBaseAnnotationList - Variable in class loci.formats.in.SlideBook7Reader.CImageGroup.CAnnotations
- mBeta - Variable in class loci.formats.in.SlideBook7Reader.CRatioManipRecord70
- mBinning - Variable in class loci.formats.in.SlideBook7Reader.CExposureRecord70
- mBitDepth - Variable in class loci.formats.in.SlideBook7Reader.CMainViewRecord70
- mBkgndChannel - Variable in class loci.formats.in.SlideBook7Reader.CMainViewRecord70
- mBlendFraction - Variable in class loci.formats.in.SlideBook7Reader.CMainViewRecord70
- mBlockDictionary - Variable in class loci.formats.in.SlideBook7Reader.CCompressionBase
- mBlockDictionarySize - Variable in class loci.formats.in.SlideBook7Reader.CCompressionBase
- mBlueChannel - Variable in class loci.formats.in.SlideBook7Reader.CMainViewRecord70
- mBorderFillPixels - Variable in class loci.formats.in.SlideBook7Reader.CAnnotation70
- mBottomX - Variable in class loci.formats.in.SlideBook7Reader.CCube
- mBottomY - Variable in class loci.formats.in.SlideBook7Reader.CCube
- mBottomZ - Variable in class loci.formats.in.SlideBook7Reader.CCube
- mBrightfieldPos - Variable in class loci.formats.in.SlideBook7Reader.CLensDef70
- mBufLenBY - Variable in class loci.formats.in.SlideBook7Reader.CCompressionBase
- mBuiltTable - Variable in class loci.formats.in.SlideBook7Reader.CRemapChannelLUT70
- mByteOrdering - Variable in class loci.formats.in.SlideBook7Reader.CAlignManipRecord70
- mByteOrdering - Variable in class loci.formats.in.SlideBook7Reader.CAnnotation70
- mByteOrdering - Variable in class loci.formats.in.SlideBook7Reader.CChannelDef70
- mByteOrdering - Variable in class loci.formats.in.SlideBook7Reader.CChannelRecord70
- mByteOrdering - Variable in class loci.formats.in.SlideBook7Reader.CDataTableHeaderRecord70
- mByteOrdering - Variable in class loci.formats.in.SlideBook7Reader.CExposureRecord70
- mByteOrdering - Variable in class loci.formats.in.SlideBook7Reader.CFluorDef70
- mByteOrdering - Variable in class loci.formats.in.SlideBook7Reader.CFRETManipRecord70
- mByteOrdering - Variable in class loci.formats.in.SlideBook7Reader.CHistogramRecord70
- mByteOrdering - Variable in class loci.formats.in.SlideBook7Reader.CImageRecord70
- mByteOrdering - Variable in class loci.formats.in.SlideBook7Reader.CLensDef70
- mByteOrdering - Variable in class loci.formats.in.SlideBook7Reader.CMainViewRecord70
- mByteOrdering - Variable in class loci.formats.in.SlideBook7Reader.CMaskRecord70
- mByteOrdering - Variable in class loci.formats.in.SlideBook7Reader.COptovarDef70
- mByteOrdering - Variable in class loci.formats.in.SlideBook7Reader.CRatioManipRecord70
- mByteOrdering - Variable in class loci.formats.in.SlideBook7Reader.CRemapManipRecord70
- mByteOrdering - Variable in class loci.formats.in.SlideBook7Reader.CSlideRecord70
- mBytesPerPixel - Variable in class loci.formats.in.SlideBook7Reader.CNpyHeader
- mCalibDataPtrHigh - Variable in class loci.formats.in.SlideBook7Reader.CRemapManipRecord70
- mCalibDataPtrLow - Variable in class loci.formats.in.SlideBook7Reader.CRemapManipRecord70
- mCamera - Variable in class loci.formats.in.SlideBook7Reader.CFluorDef70
- mCameraBitDepth - Variable in class loci.formats.in.SlideBook7Reader.CFluorDef70
- mCameraGain - Variable in class loci.formats.in.SlideBook7Reader.CFluorDef70
- mCameraIntensification - Variable in class loci.formats.in.SlideBook7Reader.CFluorDef70
- mCameraMagnificationChange - Variable in class loci.formats.in.SlideBook7Reader.CLensDef70
- mCameraName - Variable in class loci.formats.in.SlideBook7Reader.CChannelDef70
- mCameraName - Variable in class loci.formats.in.SlideBook7Reader.CLensDef70
- mCameraParameter1 - Variable in class loci.formats.in.SlideBook7Reader.CFluorDef70
- mCameraPixelSize - Variable in class loci.formats.in.SlideBook7Reader.CLensDef70
- mCameraPort - Variable in class loci.formats.in.SlideBook7Reader.CFluorDef70
- mCameraSpeed - Variable in class loci.formats.in.SlideBook7Reader.CFluorDef70
- mCameraVideoTurretPos - Variable in class loci.formats.in.SlideBook7Reader.CFluorDef70
- mCaptureFlags - Variable in class loci.formats.in.SlideBook7Reader.CExposureRecord70
- mCaptureSetId - Variable in class loci.formats.in.SlideBook7Reader.CExposureRecord70
- mCaptureStatus - Variable in class loci.formats.in.SlideBook7Reader.CSlideRecord70
- mCaptureType - Variable in class loci.formats.in.SlideBook7Reader.CExposureRecord70
- mCentroidChannel - Variable in class loci.formats.in.SlideBook7Reader.CMaskRecord70
- mCentroidFeature - Variable in class loci.formats.in.SlideBook7Reader.CMaskRecord70
- mChannelDef - Variable in class loci.formats.in.SlideBook7Reader.CChannelRecord70
- mChannelEnabled - Variable in class loci.formats.in.SlideBook7Reader.CMainViewRecord70
- mChannelIndex - Variable in class loci.formats.in.SlideBook7Reader.CDataTableHeaderRecord70
- mChannelIndex - Variable in class loci.formats.in.SlideBook7Reader.CHistogramRecord70
- mChannelMask - Variable in class loci.formats.in.SlideBook7Reader.CAnnotation70
- mChannelPtr - Variable in class loci.formats.in.SlideBook7Reader.CImageRecord70
- mChannelRecordList - Variable in class loci.formats.in.SlideBook7Reader.CImageGroup
- mChannelType - Variable in class loci.formats.in.SlideBook7Reader.CFluorDef70
- mCheckpointImagePtr - Variable in class loci.formats.in.SlideBook7Reader.CSlideRecord70
- mCheckpointMaxImages - Variable in class loci.formats.in.SlideBook7Reader.CSlideRecord70
- mCheckpointNumImages - Variable in class loci.formats.in.SlideBook7Reader.CSlideRecord70
- mCImageGroupList - Variable in class loci.formats.in.SlideBook7Reader.DataLoader
- mCoefficients - Variable in class loci.formats.in.SlideBook7Reader.CRemapChannelLUT70
- mColorDisplay - Variable in class loci.formats.in.SlideBook7Reader.CMainViewRecord70
- mColumns - Variable in class loci.formats.in.SlideBook7Reader.CDataTableHeaderRecord70
- mCompressedSizes - Variable in class loci.formats.in.SlideBook7Reader.CImageGroup.CMaskPositions
- mCompressionFlag - Variable in class loci.formats.in.SlideBook7Reader.CImageGroup
- mCompressionFlag - Variable in class loci.formats.in.SlideBook7Reader.CNpyHeader
- mCompressor - Variable in class loci.formats.in.SlideBook7Reader.CImageGroup
- mCounterToPathMap - Variable in class loci.formats.in.SlideBook7Reader.DataLoader
- mcsPoints - Variable in class loci.formats.in.SDTInfo
-
No of MCS values.
- mcstaPoints - Variable in class loci.formats.in.SDTInfo
-
Number of MCS_TA points.
- mcsTime - Variable in class loci.formats.in.SDTInfo
-
Interval time [ms] for MCS histogram.
- mCube - Variable in class loci.formats.in.SlideBook7Reader.CRemapPoint
- mCubeAnnotationList - Variable in class loci.formats.in.SlideBook7Reader.CImageGroup.CAnnotations
- mcuHeight - Variable in class loci.formats.services.JPEGTurboServiceImpl
- mcuHeight - Static variable in class org.libjpegturbo.turbojpeg.TJ
- mCurrentFileCounter - Variable in class loci.formats.in.SlideBook7Reader.DataLoader
- mcuWidth - Variable in class loci.formats.services.JPEGTurboServiceImpl
- mcuWidth - Static variable in class org.libjpegturbo.turbojpeg.TJ
- MD_FILE_UNITS - Static variable in class loci.formats.in.GelReader
- MD_FILETAG - Static variable in class loci.formats.in.GelReader
- MD_LAB_NAME - Static variable in class loci.formats.in.GelReader
- MD_PREP_DATE - Static variable in class loci.formats.in.GelReader
- MD_PREP_TIME - Static variable in class loci.formats.in.GelReader
- MD_SAMPLE_INFO - Static variable in class loci.formats.in.GelReader
- MD_SCALE_PIXEL - Static variable in class loci.formats.in.GelReader
- mDarkfieldPos - Variable in class loci.formats.in.SlideBook7Reader.CLensDef70
- mDarkValue - Variable in class loci.formats.in.SlideBook7Reader.CFRETManipRecord70
- mDataBlockSize - Variable in class loci.formats.in.SlideBook7Reader.CHistogramRecord70
- mDataLenBY - Variable in class loci.formats.in.SlideBook7Reader.CCompressionBase
- mDataLoader - Variable in class loci.formats.in.SlideBook7Reader
- mDataPosition - Variable in class loci.formats.in.SlideBook7Reader.CCompressionBase
- mDataTablePtr - Variable in class loci.formats.in.SlideBook7Reader.CChannelRecord70
- mDataType - Variable in class loci.formats.in.SlideBook7Reader.CChannelRecord70
- mDataType - Variable in class loci.formats.in.SlideBook7Reader.CNpyHeader
- mDay - Variable in class loci.formats.in.SlideBook7Reader.CImageRecord70
- mdb - Variable in class loci.formats.services.MDBServiceImpl
- MDB_SUFFIX - Static variable in class loci.formats.in.ZeissLSMReader
- MDBService - Interface in loci.formats.services
-
Interface defining methods for parsing MDB database files.
- MDBServiceImpl - Class in loci.formats.services
-
Implementation of
MDBServicefor parsing MDB database files. - MDBServiceImpl() - Constructor for class loci.formats.services.MDBServiceImpl
-
Default constructor.
- mDefault - Variable in class loci.formats.in.SlideBook7Reader.CLensDef70
- mDefault - Variable in class loci.formats.in.SlideBook7Reader.COptovarDef70
- mDefaultColor - Variable in class loci.formats.in.SlideBook7Reader.CFluorDef70
- mDefaultColorDisplay - Variable in class loci.formats.in.SlideBook7Reader.CFluorDef70
- mDemoFlag - Variable in class loci.formats.in.SlideBook7Reader.CSlideRecord70
- mDenBackground - Variable in class loci.formats.in.SlideBook7Reader.CRatioManipRecord70
- mDenMax - Variable in class loci.formats.in.SlideBook7Reader.CRatioManipRecord70
- mDenMin - Variable in class loci.formats.in.SlideBook7Reader.CRatioManipRecord70
- mDependencyRef - Variable in class loci.formats.in.SlideBook7Reader.CAnnotation70
- mDependencyType70 - Variable in class loci.formats.in.SlideBook7Reader.CAnnotation70
- mDeprecatedMagnification - Variable in class loci.formats.in.SlideBook7Reader.CLensDef70
- mDescriptorFileOffset - Variable in class loci.formats.in.SlideBook7Reader.CDataTableHeaderRecord70
- mDescriptorSize - Variable in class loci.formats.in.SlideBook7Reader.CDataTableHeaderRecord70
- mDescriptorVersion - Variable in class loci.formats.in.SlideBook7Reader.CDataTableHeaderRecord70
- mDesiredValue - Variable in class loci.formats.in.SlideBook7Reader.CRemapPoint
- mdf - Variable in class loci.formats.in.SlideBook7Reader.CLensDef70
- mDICPos - Variable in class loci.formats.in.SlideBook7Reader.CLensDef70
- mDICPrismPos - Variable in class loci.formats.in.SlideBook7Reader.CLensDef70
- mDictionaryPosition - Variable in class loci.formats.in.SlideBook7Reader.CCompressionBase
- mDictionaryRead - Variable in class loci.formats.in.SlideBook7Reader.CCompressionBase
- mDisplayHigh - Variable in class loci.formats.in.SlideBook7Reader.CFRETManipRecord70
- mDisplayLow - Variable in class loci.formats.in.SlideBook7Reader.CFRETManipRecord70
- mDisplayNormalization - Variable in class loci.formats.in.SlideBook7Reader.CFRETManipRecord70
- mDonor1Lifetime - Variable in class loci.formats.in.SlideBook7Reader.CFRETManipRecord70
- mDonor1X - Variable in class loci.formats.in.SlideBook7Reader.CFRETManipRecord70
- mDonor1Y - Variable in class loci.formats.in.SlideBook7Reader.CFRETManipRecord70
- mDonor2Lifetime - Variable in class loci.formats.in.SlideBook7Reader.CFRETManipRecord70
- mDoubleData - Variable in class loci.formats.in.SlideBook7Reader.CImageGroup.CAuxDoubleData
- MEA_SUFFIX - Static variable in class loci.formats.in.FlexReader
- MeaHandler() - Constructor for class loci.formats.in.FlexReader.MeaHandler
- MEAS_ALIGNED_RECTANGLE - Enum constant in enum class loci.formats.in.BaseZeissReader.FeatureType
- MEAS_ANGLE3 - Enum constant in enum class loci.formats.in.BaseZeissReader.FeatureType
- MEAS_ANGLE4 - Enum constant in enum class loci.formats.in.BaseZeissReader.FeatureType
- MEAS_CALIPER - Enum constant in enum class loci.formats.in.BaseZeissReader.FeatureType
- MEAS_CIRCLE - Enum constant in enum class loci.formats.in.BaseZeissReader.FeatureType
- MEAS_DISTANCE - Enum constant in enum class loci.formats.in.BaseZeissReader.FeatureType
- MEAS_ELLIPSE - Enum constant in enum class loci.formats.in.BaseZeissReader.FeatureType
- MEAS_LENGTH - Enum constant in enum class loci.formats.in.BaseZeissReader.FeatureType
- MEAS_LINE - Enum constant in enum class loci.formats.in.BaseZeissReader.FeatureType
- MEAS_MULTIPLE_CALIPER - Enum constant in enum class loci.formats.in.BaseZeissReader.FeatureType
- MEAS_MULTIPLE_DISTANCE - Enum constant in enum class loci.formats.in.BaseZeissReader.FeatureType
- MEAS_POINT - Enum constant in enum class loci.formats.in.BaseZeissReader.FeatureType
- MEAS_POINTS - Enum constant in enum class loci.formats.in.BaseZeissReader.FeatureType
- MEAS_POLYLINE_CLOSED - Enum constant in enum class loci.formats.in.BaseZeissReader.FeatureType
- MEAS_POLYLINE_OPEN - Enum constant in enum class loci.formats.in.BaseZeissReader.FeatureType
- MEAS_PROFILE - Enum constant in enum class loci.formats.in.BaseZeissReader.FeatureType
- MEAS_RECTANGLE - Enum constant in enum class loci.formats.in.BaseZeissReader.FeatureType
- MEAS_SPLINE_CLOSED - Enum constant in enum class loci.formats.in.BaseZeissReader.FeatureType
- MEAS_SPLINE_OPEN - Enum constant in enum class loci.formats.in.BaseZeissReader.FeatureType
- measDescBlockLength - Variable in class loci.formats.in.SDTInfo
- measDescBlockNo - Variable in class loci.formats.in.SDTInfo
-
Number of the measurement description block corresponding to this data block.
- measDescBlockOffs - Variable in class loci.formats.in.SDTInfo
- measMode - Variable in class loci.formats.in.SDTInfo
- MEASUREMENT_DETAIL - Static variable in class loci.formats.in.CV7000Reader
- MEASUREMENT_FILE - Static variable in class loci.formats.in.CV7000Reader
- MEASUREMENT_SUFFIXES - Static variable in class loci.formats.in.FlexReader
- MeasurementDataHandler(String) - Constructor for class loci.formats.in.CV7000Reader.MeasurementDataHandler
- MeasurementDetailHandler() - Constructor for class loci.formats.in.CV7000Reader.MeasurementDetailHandler
- measurementFiles - Variable in class loci.formats.in.FlexReader
- MeasurementHandler() - Constructor for class loci.formats.in.ColumbusReader.MeasurementHandler
- measurementID - Variable in class loci.formats.in.ColumbusReader.MeasurementHandler
- measurementID - Variable in class loci.formats.in.OperettaReader.OperettaHandler
- measurementName - Variable in class loci.formats.in.ColumbusReader.MeasurementHandler
- measurementPath - Variable in class loci.formats.in.CV7000Reader
- measurementResultFile - Variable in class loci.formats.in.CellVoyagerReader
- MeasurementSettingsHandler() - Constructor for class loci.formats.in.CV7000Reader.MeasurementSettingsHandler
- measurementTime - Variable in class loci.formats.in.OperettaReader.OperettaHandler
- MECHANICAL_INDEX - Enum constant in enum class loci.formats.dicom.DicomAttribute
- MEDIA_SOP_CLASS_UID - Enum constant in enum class loci.formats.dicom.DicomAttribute
- MEDIA_SOP_INSTANCE_UID - Enum constant in enum class loci.formats.dicom.DicomAttribute
- medianFilter() - Method in class loci.plugins.util.RecordedImageProcessor
- MEDICAL_ALERTS - Enum constant in enum class loci.formats.dicom.DicomAttribute
- MEDICAL_DOMAIN - Static variable in class loci.formats.FormatTools
-
Identifies the medical imaging domain.
- MEDICAL_RECORD_LOCATOR - Enum constant in enum class loci.formats.dicom.DicomAttribute
- medium - Variable in class loci.formats.in.ZeissCZIReader
- medium - Variable in class loci.formats.in.ZeissLSMReader.Laser
- mElapsedTimeOffset - Variable in class loci.formats.in.SlideBook7Reader.CImageRecord70
- mElapsedTimes - Variable in class loci.formats.in.SlideBook7Reader.CImageGroup
- mElapsedTimeTablePtr - Variable in class loci.formats.in.SlideBook7Reader.CImageRecord70
- MEM_MODEL - Static variable in class loci.formats.in.CellSensReader
- memBank - Variable in class loci.formats.in.SDTInfo
- mEmissionWheelPos - Variable in class loci.formats.in.SlideBook7Reader.CFluorDef70
- memoFile - Variable in class loci.formats.Memoizer
- Memoizer - Class in loci.formats
-
ReaderWrapperimplementation which caches the state of the delegate (including and otherReaderWrapperinstances) afterMemoizer.setId(String)has been called. - Memoizer() - Constructor for class loci.formats.Memoizer
-
Constructs a memoizer around a new
ImageReadercreating memo files under the same directory as the original file only if the call toMemoizer.setId(java.lang.String)takes longer than 100L in milliseconds. - Memoizer(long) - Constructor for class loci.formats.Memoizer
-
Constructs a memoizer around a new
ImageReadercreating memo files under the same directory as the original file only if the call toMemoizer.setId(java.lang.String)takes longer thanminimumElapsedin milliseconds. - Memoizer(long, File) - Constructor for class loci.formats.Memoizer
-
Constructs a memoizer around a new
ImageReadercreating memo files under thedirectoryargument including the full path of the original file only if the call toMemoizer.setId(java.lang.String)takes longer thanminimumElapsedin milliseconds. - Memoizer(IFormatReader) - Constructor for class loci.formats.Memoizer
-
Constructs a memoizer around the given
IFormatReadercreating memo files under the same directory as the original file only if the call toMemoizer.setId(java.lang.String)takes longer than 100L in milliseconds. - Memoizer(IFormatReader, long) - Constructor for class loci.formats.Memoizer
-
Constructs a memoizer around the given
IFormatReadercreating memo files under the same directory as the original file only if the call toMemoizer.setId(java.lang.String)takes longer thanminimumElapsedin milliseconds. - Memoizer(IFormatReader, long, File) - Constructor for class loci.formats.Memoizer
-
Constructs a memoizer around the given
IFormatReadercreating memo files under thedirectoryargument including the full path of the original file only if the call toMemoizer.setId(java.lang.String)takes longer thanminimumElapsedin milliseconds. - Memoizer(IFormatReader, File) - Constructor for class loci.formats.Memoizer
-
Constructs a memoizer around the given
IFormatReadercreating memo file under thedirectoryargument including the full path of the original file only if the call toMemoizer.setId(java.lang.String)takes longer than 100L in milliseconds. - Memoizer.Deser - Interface in loci.formats
- Memoizer.KryoDeser - Class in loci.formats
- Memoizer.RandomAccessDeser - Class in loci.formats
-
Helper implementation that can be used to implement
Memoizer.Deserclasses for libraries working solely with byte arrays. - MemoryBlock(long, String) - Constructor for class loci.formats.in.LIFReader.MemoryBlock
- memoryBlocks - Variable in class loci.formats.in.LIFReader
-
Memory blocks including offsets and ID
- MemoryDialog - Class in loci.plugins.in
-
Bio-Formats Importer memory usage confirmation dialog box.
- MemoryDialog(ImportProcess) - Constructor for class loci.plugins.in.MemoryDialog
-
Creates a memory confirmation dialog for the Bio-Formats Importer.
- mEquationString - Variable in class loci.formats.in.SlideBook7Reader.CRemapChannelLUT70
- merge - Variable in class loci.plugins.util.BFVirtualStack
- merge(Map<String, Object>, Map<String, Object>, String) - Static method in class loci.formats.MetadataTools
-
Merges the given lists of metadata, prepending the specified prefix for the destination keys.
- MERGE_NAMES - Static variable in class loci.formats.in.BioRadReader
-
List of merge types.
- mergeChannels(BufferedImage[]) - Static method in class loci.formats.gui.AWTImageTools
-
Merges the given images into a single multi-channel image.
- mergeSubIFDs - Variable in class loci.formats.in.MinimalTiffReader
-
Merge SubIFDs into the main IFD list.
- mErrorMessage - Variable in class loci.formats.in.SlideBook7Reader.CCompressionBase
- mErrorMessage - Variable in class loci.formats.in.SlideBook7Reader.DataLoader
- message - Variable in enum class loci.plugins.in.ImportStep
- meta - Variable in class loci.formats.in.OMETiffReader
-
Represents OME-XML stored in the current OME-TIFF file(s).
- meta - Variable in class loci.formats.in.PrairieReader
-
Format-specific metadata.
- meta - Variable in class loci.plugins.in.ImportProcess
- META_EXT - Static variable in class loci.formats.in.BDReader
- metadata - Variable in class loci.formats.FormatReader
-
Hashtable containing metadata key/value pairs.
- metadata - Variable in class loci.formats.in.MetamorphHandler
- metadata - Variable in class loci.formats.in.ND2Handler
- metadata - Variable in class loci.formats.in.ZeissCZIReader.SubBlock
- metadata - Variable in class loci.plugins.in.ImportProcess
- metadata - Variable in class loci.plugins.util.DataBrowser
- Metadata() - Constructor for class loci.formats.in.ZeissCZIReader.Metadata
- METADATA - Enum constant in enum class loci.plugins.in.ImportStep
- METADATA - Static variable in class loci.formats.in.MicromanagerReader
-
File containing extra metadata.
- METADATA_KEYS - Static variable in class loci.formats.in.ZeissLSMReader
- METADATA_LEVEL_DEFAULT - Static variable in class loci.formats.in.DynamicMetadataOptions
- METADATA_LEVEL_KEY - Static variable in class loci.formats.in.DynamicMetadataOptions
- METADATA_SUFFIXES - Static variable in class loci.formats.in.APLReader
- METADATA_SUFFIXES - Static variable in class loci.formats.in.InCellReader
- METADATA_SUFFIXES - Static variable in class loci.formats.in.ScanrReader
- METADATA_TAG - Static variable in class loci.formats.in.NDPIReader
- METADATA_TAG - Static variable in class loci.formats.in.NDPISReader
- METADATA_XML_TAG - Static variable in class loci.formats.in.FlowSightReader
- metadataComplete - Variable in class loci.formats.CoreMetadata
-
Indicates whether or not we are confident that all of the metadata stored within the file has been parsed.
- MetadataConverter - Class in loci.formats.meta
-
Deprecated.Use ome.xml.meta.MetadataConverter.
- MetadataConverter() - Constructor for class loci.formats.meta.MetadataConverter
-
Deprecated.Private constructor; all methods in MetadataConverter are static, so this should not be called.
- metadataFile - Variable in class loci.formats.in.MicromanagerReader.Position
- metadataFile - Variable in class loci.formats.in.OMETiffReader
- metadataFiles - Variable in class loci.formats.in.BDReader
- metadataFiles - Variable in class loci.formats.in.CellomicsReader
- metadataFiles - Variable in class loci.formats.in.ColumbusReader
- metadataFiles - Variable in class loci.formats.in.InCellReader
- metadataFiles - Variable in class loci.formats.in.L2DReader
-
List of all metadata files in the dataset.
- metadataFiles - Variable in class loci.formats.in.MicroCTReader
- metadataFiles - Variable in class loci.formats.in.OperettaReader
- metadataFiles - Variable in class loci.formats.in.ScanrReader
- metadataIndex - Variable in class loci.formats.in.CellSensReader
- metadataInPlanes - Variable in class loci.formats.in.SlidebookReader
- metadataLevel - Variable in class loci.formats.in.DefaultMetadataOptions
- MetadataLevel - Enum Class in loci.formats.in
- MetadataLevel() - Constructor for enum class loci.formats.in.MetadataLevel
- MetadataList<T> - Class in loci.formats
-
A container of metadata for FormatReader and other reader implementations.
- MetadataList() - Constructor for class loci.formats.MetadataList
- MetadataList(int) - Constructor for class loci.formats.MetadataList
-
Construct a list containing a specified number of primary elements.
- MetadataList(int[]) - Constructor for class loci.formats.MetadataList
-
Construct a list containing a specified number of primary and secondary elements.
- MetadataList(int, int) - Constructor for class loci.formats.MetadataList
-
Construct a list containing a specified number of primary elements and a fixed number of secondary elements.
- MetadataList(MetadataList<T>) - Constructor for class loci.formats.MetadataList
-
Copy a list.
- metadataMap - Variable in class loci.formats.in.JDCEReader.JDCEWell
- metadataOffsets - Variable in class loci.formats.in.SlidebookReader
- metadataOptions - Variable in class loci.formats.FormatHandler
-
Metadata parsing options.
- MetadataOptions - Interface in loci.formats.in
-
Holds metadata-related options.
- metadataPosition - Variable in class loci.formats.in.ZeissCZIReader.FileHeader
- metadataRetrieve - Variable in class loci.formats.FormatWriter
-
Current metadata retrieval object.
- MetadataRetrieve - Interface in loci.formats.meta
- metadataSize - Variable in class loci.formats.in.ZeissCZIReader.SubBlock
- metadataSource - Variable in class loci.formats.in.LOFReader
- MetadataSource() - Constructor for enum class loci.formats.in.LOFReader.MetadataSource
- metadataStore - Variable in class loci.formats.FormatReader
-
Current metadata store.
- MetadataStore - Interface in loci.formats.meta
- MetadataStoreInitializer - Class in loci.formats.in.LeicaMicrosystemsMetadata
- MetadataStoreInitializer(LMSFileReader) - Constructor for class loci.formats.in.LeicaMicrosystemsMetadata.MetadataStoreInitializer
- MetadataTempBuffer - Class in loci.formats.in.LeicaMicrosystemsMetadata
-
This class is used to temporarily store metadata information extracted from Leica XML before it is written to the reader's MetadataStore
- MetadataTempBuffer(int) - Constructor for class loci.formats.in.LeicaMicrosystemsMetadata.MetadataTempBuffer
-
Constructs a MetadataTempBuffer for a given number of images.
- MetadataTools - Class in loci.formats
-
A utility class for working with metadata objects, including
MetadataStore,MetadataRetrieve, and OME-XML strings. - MetadataTools() - Constructor for class loci.formats.MetadataTools
- metadataType - Variable in enum class loci.formats.tiff.PhotoInterp
-
Metadata type of the photometric interpretation.
- metaFile - Variable in class loci.formats.in.OMETiffReader
- MetakitService - Interface in loci.formats.services
-
Interface defining methods for interacting with the OME Metakit library.
- MetakitServiceImpl - Class in loci.formats.services
-
Implementation of MetakitService for interacting with the OME Metakit library.
- MetakitServiceImpl() - Constructor for class loci.formats.services.MetakitServiceImpl
- METAMORPH_ID - Static variable in class loci.formats.in.MetamorphReader
- MetamorphHandler - Class in loci.formats.in
-
MetamorphTiffReader is the file format reader for TIFF files produced by Metamorph software version 7.5 and above.
- MetamorphHandler() - Constructor for class loci.formats.in.MetamorphHandler
- MetamorphHandler(Hashtable) - Constructor for class loci.formats.in.MetamorphHandler
- MetamorphReader - Class in loci.formats.in
-
Reader is the file format reader for Metamorph STK files.
- MetamorphReader() - Constructor for class loci.formats.in.MetamorphReader
-
Constructs a new Metamorph reader.
- MetamorphTiffReader - Class in loci.formats.in
-
MetamorphTiffReader is the file format reader for TIFF files produced by Metamorph software version 7.5 and above.
- MetamorphTiffReader() - Constructor for class loci.formats.in.MetamorphTiffReader
-
Constructs a new Metamorph TIFF reader.
- MetamorphTiffReader.NumericComparator - Class in loci.formats.in
- MetamorphTiffReader.Well - Class in loci.formats.in
- metaTemp - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.LMSFileReader
- metaWindow - Variable in class loci.plugins.util.DataBrowser
- MetaxpressTiffReader - Class in loci.formats.in
-
MetaxpressTiffReader is the file format reader for MetaXpress .htd + TIFF files.
- MetaxpressTiffReader() - Constructor for class loci.formats.in.MetaxpressTiffReader
-
Constructs a new MetaXpress TIFF reader.
- METER_MULTIPLY - Static variable in class loci.formats.in.LeicaMicrosystemsMetadata.Dimension
- METER_MULTIPLY - Static variable in class loci.formats.in.LeicaMicrosystemsMetadata.LMSMetadataExtractor
- METER_MULTIPLY - Static variable in class loci.formats.in.LeicaMicrosystemsMetadata.ROI
- METER_MULTIPLY - Static variable in class loci.formats.in.LIFReader
- METERING_MODE - Static variable in class loci.formats.tiff.IFD
- method - Variable in class loci.plugins.util.RecordedImageProcessor.MethodEntry
- MethodEntry() - Constructor for class loci.plugins.util.RecordedImageProcessor.MethodEntry
- methodStack - Variable in class loci.plugins.util.RecordedImageProcessor
- methodStacks - Variable in class loci.plugins.util.BFVirtualStack
- mExcitationLambda - Variable in class loci.formats.in.SlideBook7Reader.CFluorDef70
- mExcitationWheelPos - Variable in class loci.formats.in.SlideBook7Reader.CFluorDef70
- mExposureFactor - Variable in class loci.formats.in.SlideBook7Reader.CRatioManipRecord70
- mExposureRecord - Variable in class loci.formats.in.SlideBook7Reader.CChannelRecord70
- mExposureTime - Variable in class loci.formats.in.SlideBook7Reader.CExposureRecord70
- mFaAa - Variable in class loci.formats.in.SlideBook7Reader.CFRETManipRecord70
- mFdDd - Variable in class loci.formats.in.SlideBook7Reader.CFRETManipRecord70
- mFieldMicronsPerPixel - Variable in class loci.formats.in.SlideBook7Reader.CAnnotation70
- mFieldOffsetMicrons - Variable in class loci.formats.in.SlideBook7Reader.CAnnotation70
- mFieldOffsetSet - Variable in class loci.formats.in.SlideBook7Reader.CAnnotation70
- mFile - Variable in class loci.formats.in.SlideBook7Reader.CImageGroup
- mFile - Variable in class loci.formats.in.SlideBook7Reader.DataLoader
- mFileOffsets - Variable in class loci.formats.in.SlideBook7Reader.CImageGroup.CMaskPositions
- mFileVersion - Variable in class loci.formats.in.SlideBook7Reader.CSlideRecord70
- mFilterSet - Variable in class loci.formats.in.SlideBook7Reader.CFluorDef70
- mFloatData - Variable in class loci.formats.in.SlideBook7Reader.CCubeAnnotation70
- mFloatData - Variable in class loci.formats.in.SlideBook7Reader.CImageGroup.CAuxFloatData
- mFluorDef - Variable in class loci.formats.in.SlideBook7Reader.CChannelDef70
- mFortranOrder - Variable in class loci.formats.in.SlideBook7Reader.CNpyHeader
- mFRAPDevice - Variable in class loci.formats.in.SlideBook7Reader.CCubeAnnotation70
- mFRAPRegionAnnotationList - Variable in class loci.formats.in.SlideBook7Reader.CImageGroup.CAnnotations
- mFRETAddParameter - Variable in class loci.formats.in.SlideBook7Reader.CFRETManipRecord70
- mFRETManipRecList - Variable in class loci.formats.in.SlideBook7Reader.CImageGroup
- mFRETMethod - Variable in class loci.formats.in.SlideBook7Reader.CFRETManipRecord70
- mFRETParadigm - Variable in class loci.formats.in.SlideBook7Reader.CFRETManipRecord70
- mGamma - Variable in class loci.formats.in.SlideBook7Reader.CMainViewRecord70
- mGivenValue - Variable in class loci.formats.in.SlideBook7Reader.CRemapPoint
- mGraphicType70 - Variable in class loci.formats.in.SlideBook7Reader.CAnnotation70
- mGreenChannel - Variable in class loci.formats.in.SlideBook7Reader.CMainViewRecord70
- mGroupId - Variable in class loci.formats.in.SlideBook7Reader.CAnnotation70
- mHardwareFileLen - Variable in class loci.formats.in.SlideBook7Reader.CSlideRecord70
- mHardwareFileOffset - Variable in class loci.formats.in.SlideBook7Reader.CSlideRecord70
- mHeaderSize - Variable in class loci.formats.in.SlideBook7Reader.CNpyHeader
- mHeight - Variable in class loci.formats.in.SlideBook7Reader.CImageRecord70
- mHigh - Variable in class loci.formats.in.SlideBook7Reader.CMainViewRecord70
- mHighDesired - Variable in class loci.formats.in.SlideBook7Reader.CRemapChannelLUT70
- mHighestCount - Variable in class loci.formats.in.SlideBook7Reader.CSlideRecord70
- mHighGiven - Variable in class loci.formats.in.SlideBook7Reader.CRemapChannelLUT70
- mHistogramRecordList - Variable in class loci.formats.in.SlideBook7Reader.CImageGroup
- mHistogramSummaryPtr - Variable in class loci.formats.in.SlideBook7Reader.CChannelRecord70
- mHistogramTablePtr - Variable in class loci.formats.in.SlideBook7Reader.CChannelRecord70
- mHistogramType - Variable in class loci.formats.in.SlideBook7Reader.CHistogramRecord70
- mHour - Variable in class loci.formats.in.SlideBook7Reader.CImageRecord70
- mHue - Variable in class loci.formats.in.SlideBook7Reader.CFluorDef70
- mHue - Variable in class loci.formats.in.SlideBook7Reader.CMainViewRecord70
- MIASReader - Class in loci.formats.in
-
MIASReader is the file format reader for Maia Scientific MIAS-2 datasets.
- MIASReader() - Constructor for class loci.formats.in.MIASReader
-
Constructs a new MIAS reader.
- MIASReader.AnalysisFile - Class in loci.formats.in
- MicroCTReader - Class in loci.formats.in
-
MicroCTReader is the file format reader for VFF files from a GE MicroCT scanner.
- MicroCTReader() - Constructor for class loci.formats.in.MicroCTReader
-
Constructs a new MicroCT reader.
- MicromanagerHandler() - Constructor for class loci.formats.in.MicromanagerReader.MicromanagerHandler
- MicromanagerReader - Class in loci.formats.in
-
MicromanagerReader is the file format reader for Micro-Manager files.
- MicromanagerReader() - Constructor for class loci.formats.in.MicromanagerReader
-
Constructs a new Micromanager reader.
- MicromanagerReader.Index - Class in loci.formats.in
- MicromanagerReader.MicromanagerHandler - Class in loci.formats.in
-
SAX handler for parsing Acqusition.xml.
- MicromanagerReader.Position - Class in loci.formats.in
- microscopeModel - Variable in class loci.formats.in.FEITiffReader
- microscopeModels - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataTempBuffer
- microscopeModels - Variable in class loci.formats.in.LIFReader
- microscopyMode - Variable in class loci.formats.in.ImarisHDFReader
- microSecPerFrame - Variable in class loci.formats.out.AVIWriter
- MIKROSCAN_IMAGE_DESCRIPTION_PREFIX - Static variable in class loci.formats.in.MikroscanTiffReader
-
TIFF image description prefix for Mikroscan TIF files.
- MikroscanTiffReader - Class in loci.formats.in
-
MikroscanTiffReader is the file format reader for Mikroscan TIFF files.
- MikroscanTiffReader() - Constructor for class loci.formats.in.MikroscanTiffReader
-
Constructs a new Mikroscan TIF reader.
- MILITARY_RANK - Enum constant in enum class loci.formats.dicom.DicomAttribute
- mIlluminationMode - Variable in class loci.formats.in.SlideBook7Reader.CFluorDef70
- mImageDataList - Variable in class loci.formats.in.SlideBook7Reader.CImageGroup
- mImageGroupIndex - Variable in class loci.formats.in.SlideBook7Reader.CImageRecord70
- mImageIndex - Variable in class loci.formats.in.SlideBook7Reader.CHistogramRecord70
- mImagePtr - Variable in class loci.formats.in.SlideBook7Reader.CSlideRecord70
- mImageRecord - Variable in class loci.formats.in.SlideBook7Reader.CImageGroup
- mImageTitle - Variable in class loci.formats.in.SlideBook7Reader.CImageGroup
- mImagingMode - Variable in class loci.formats.in.SlideBook7Reader.CFluorDef70
- mImported - Variable in class loci.formats.in.SlideBook7Reader.CImageRecord70
- min - Variable in class loci.formats.in.InCellReader.Image
- min - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.Channel
- min(double) - Method in class loci.plugins.util.RecordedImageProcessor
- MIN_BLK - Enum constant in enum class loci.formats.in.SPEReader.SpeHeaderEntry
- MIN_BROWSER_WIDTH - Static variable in class loci.plugins.util.DataBrowser
- MIN_INTENSITY - Enum constant in enum class loci.formats.in.SPEReader.SpeHeaderEntry
- MIN_PRIORITY - Static variable in interface loci.formats.cache.ICacheStrategy
- MIN_SAMPLE_VALUE - Static variable in class loci.formats.tiff.IFD
- minAdcRate - Variable in class loci.formats.in.SDTInfo
- minC - Variable in class loci.formats.in.CV7000Reader.MinMax
- minCfdRate - Variable in class loci.formats.in.SDTInfo
-
(-1.0 - not set).
- MINCReader - Class in loci.formats.in
-
MINCReader is the file format reader for MINC MRI files.
- MINCReader() - Constructor for class loci.formats.in.MINCReader
-
Constructs a new MINC reader.
- mInfo - Variable in class loci.formats.in.SlideBook7Reader.CImageRecord70
- MINIMAL_TAGS - Static variable in class loci.formats.in.FlowSightReader
-
The tags that must be present for this reader to function properly
- MinimalInCellHandler() - Constructor for class loci.formats.in.InCellReader.MinimalInCellHandler
- MinimalTiffReader - Class in loci.formats.in
-
MinimalTiffReader is the superclass for file format readers compatible with or derived from the TIFF 6.0 file format.
- MinimalTiffReader() - Constructor for class loci.formats.in.MinimalTiffReader
-
Constructs a new MinimalTiffReader.
- MinimalTiffReader(String, String) - Constructor for class loci.formats.in.MinimalTiffReader
-
Constructs a new MinimalTiffReader.
- MinimalTiffReader(String, String[]) - Constructor for class loci.formats.in.MinimalTiffReader
-
Constructs a new MinimalTiffReader.
- MINIMUM - Enum constant in enum class loci.formats.in.MetadataLevel
- MINIMUM_MEMORY_PADDING - Static variable in class loci.plugins.in.MemoryDialog
-
Minimum amount of wiggle room for available memory, in bytes.
- minimumElapsed - Variable in class loci.formats.Memoizer
-
Minimum number of milliseconds which must elapse during the call to
Memoizer.setId(java.lang.String)before a memo file will be created. - minInten - Variable in class loci.formats.in.DeltavisionReader.DVExtHdrFields
-
Minimum intensity
- mInitialOffset - Variable in class loci.formats.in.SlideBook7Reader.CExposureRecord70
- MinMax() - Constructor for class loci.formats.in.CV7000Reader.MinMax
- minMaxCalculator - Variable in class loci.plugins.in.ImportProcess
- MinMaxCalculator - Class in loci.formats
-
Logic to compute minimum and maximum values for each channel.
- MinMaxCalculator() - Constructor for class loci.formats.MinMaxCalculator
-
Constructs a MinMaxCalculator around a new image reader.
- MinMaxCalculator(IFormatReader) - Constructor for class loci.formats.MinMaxCalculator
-
Constructs a MinMaxCalculator with the given reader.
- minMaxDone - Variable in class loci.formats.MinMaxCalculator
-
Number of planes for which min/max computations have been completed.
- minMaxStore - Variable in class loci.formats.MinMaxCalculator
-
Consumer of channel global minima and maxima
- minorVersion - Variable in class loci.formats.in.ZeissCZIReader.FileHeader
- mInsideRange - Variable in class loci.formats.in.SlideBook7Reader.CRemapChannelLUT70
- minSyncRate - Variable in class loci.formats.in.SDTInfo
-
Minimum rates during the measurement.
- minT - Variable in class loci.formats.in.CV7000Reader.MinMax
- minT - Variable in class loci.formats.in.OIRReader
- mInt - Variable in class loci.formats.in.SlideBook7Reader.StrIntPair
- mInt1 - Variable in class loci.formats.in.SlideBook7Reader.IntIntPair
- mInt2 - Variable in class loci.formats.in.SlideBook7Reader.IntIntPair
- minTacRate - Variable in class loci.formats.in.SDTInfo
- mIntData - Variable in class loci.formats.in.SlideBook7Reader.CCubeAnnotation70
- mIntegerData - Variable in class loci.formats.in.SlideBook7Reader.CImageGroup.CAuxSInt32Data
- mInterplaneSpacing - Variable in class loci.formats.in.SlideBook7Reader.CExposureRecord70
- minValue() - Method in class loci.plugins.util.RecordedImageProcessor
- minX - Variable in class loci.formats.in.ImarisHDFReader
- minY - Variable in class loci.formats.in.ImarisHDFReader
- minZ - Variable in class loci.formats.in.CV7000Reader.MinMax
- minZ - Variable in class loci.formats.in.ImarisHDFReader
- minZ - Variable in class loci.formats.in.OIRReader
- mipmapLevel - Variable in class loci.formats.in.BDVReader.H5Coordinate
- MIRROR_H - Static variable in class loci.formats.in.CellSensReader
- MIRROR_V - Static variable in class loci.formats.in.CellSensReader
- mIsBackground - Variable in class loci.formats.in.SlideBook7Reader.CCubeAnnotation70
- mIsCompressed - Variable in class loci.formats.in.SlideBook7Reader.CSBFile70
- mIsFloatSet - Variable in class loci.formats.in.SlideBook7Reader.CCubeAnnotation70
- mIsFRAP - Variable in class loci.formats.in.SlideBook7Reader.CCubeAnnotation70
- mIsIntSet - Variable in class loci.formats.in.SlideBook7Reader.CCubeAnnotation70
- mIsLLS - Variable in class loci.formats.in.SlideBook7Reader.CCubeAnnotation70
- mIsNoLabel - Variable in class loci.formats.in.SlideBook7Reader.CCubeAnnotation70
- MISSING - Static variable in class loci.plugins.config.LibraryEntry
-
HTML markup for missing library.
- MISSING_VERSION_CODE - Static variable in class loci.plugins.config.LibraryEntry
-
Version code to indicate a missing library.
- MissingLibraryException - Exception Class in loci.formats
-
MissingLibraryException is the exception thrown when a particular data stream or filename requires a library that is not present on the system.
- MissingLibraryException() - Constructor for exception class loci.formats.MissingLibraryException
- MissingLibraryException(String) - Constructor for exception class loci.formats.MissingLibraryException
- MissingLibraryException(String, Throwable) - Constructor for exception class loci.formats.MissingLibraryException
- MissingLibraryException(Throwable) - Constructor for exception class loci.formats.MissingLibraryException
- mIsStimulation - Variable in class loci.formats.in.SlideBook7Reader.CCubeAnnotation70
- MJPBCodec - Class in loci.formats.codec
-
Methods for compressing and decompressing QuickTime Motion JPEG-B data.
- MJPBCodec() - Constructor for class loci.formats.codec.MJPBCodec
- MJPBCodecOptions - Class in loci.formats.codec
-
Options for compressing and decompressing MJPB data.
- MJPBCodecOptions() - Constructor for class loci.formats.codec.MJPBCodecOptions
- MJPEG_HUFFMAN_TABLE - Static variable in class loci.formats.in.AVIReader
-
Huffman table for MJPEG data.
- mKd - Variable in class loci.formats.in.SlideBook7Reader.CRatioManipRecord70
- mLambda - Variable in class loci.formats.in.SlideBook7Reader.CFluorDef70
- mLambdaOptions - Variable in class loci.formats.in.SlideBook7Reader.CFluorDef70
- mLaserPowerPos - Variable in class loci.formats.in.SlideBook7Reader.CFluorDef70
- mLastChannel - Variable in class loci.formats.in.SlideBook7Reader.CImageGroup
- mLastTimepoint - Variable in class loci.formats.in.SlideBook7Reader.CImageGroup
- mLCDPos - Variable in class loci.formats.in.SlideBook7Reader.CFluorDef70
- mLensDef - Variable in class loci.formats.in.SlideBook7Reader.CImageRecord70
- mLightSource - Variable in class loci.formats.in.SlideBook7Reader.CFluorDef70
- mLittleEndian - Variable in class loci.formats.in.SlideBook7Reader.CNpyHeader
- mLongData - Variable in class loci.formats.in.SlideBook7Reader.CImageGroup.CAuxSInt64Data
- mLow - Variable in class loci.formats.in.SlideBook7Reader.CMainViewRecord70
- mLowDesired - Variable in class loci.formats.in.SlideBook7Reader.CRemapChannelLUT70
- mLowGiven - Variable in class loci.formats.in.SlideBook7Reader.CRemapChannelLUT70
- MM_JSON_TAG - Static variable in class loci.formats.in.MicromanagerReader
- mMagnification - Variable in class loci.formats.in.SlideBook7Reader.COptovarDef70
- mMainFrequency - Variable in class loci.formats.in.SlideBook7Reader.CFRETManipRecord70
- mMainViewRecord - Variable in class loci.formats.in.SlideBook7Reader.CImageRecord70
- mMajorVersion - Variable in class loci.formats.in.SlideBook7Reader.CNpyHeader
- mManipID - Variable in class loci.formats.in.SlideBook7Reader.CAlignManipRecord70
- mManipID - Variable in class loci.formats.in.SlideBook7Reader.CFRETManipRecord70
- mManipID - Variable in class loci.formats.in.SlideBook7Reader.CRatioManipRecord70
- mManipID - Variable in class loci.formats.in.SlideBook7Reader.CRemapManipRecord70
- mManipPtr - Variable in class loci.formats.in.SlideBook7Reader.CChannelRecord70
- mManipPtr - Variable in class loci.formats.in.SlideBook7Reader.CMaskRecord70
- mMaskDataTablePtr - Variable in class loci.formats.in.SlideBook7Reader.CMaskRecord70
- mMaskPosList - Variable in class loci.formats.in.SlideBook7Reader.CImageGroup
- mMaskPtr - Variable in class loci.formats.in.SlideBook7Reader.CImageRecord70
- mMaskRecordList - Variable in class loci.formats.in.SlideBook7Reader.CImageGroup
- mMax - Variable in class loci.formats.in.SlideBook7Reader.CHistogramRecord70
- mMean - Variable in class loci.formats.in.SlideBook7Reader.CHistogramRecord70
- mMedium - Variable in class loci.formats.in.SlideBook7Reader.CLensDef70
- MMHEADER - Static variable in class loci.formats.in.FluoviewReader
-
Private TIFF tags
- mMicronPerPixel - Variable in class loci.formats.in.SlideBook7Reader.CLensDef70
- mMin - Variable in class loci.formats.in.SlideBook7Reader.CHistogramRecord70
- mMinorVersion - Variable in class loci.formats.in.SlideBook7Reader.CNpyHeader
- mMinute - Variable in class loci.formats.in.SlideBook7Reader.CImageRecord70
- mModulationFlatFieldCorrected - Variable in class loci.formats.in.SlideBook7Reader.CFRETManipRecord70
- mModZero - Variable in class loci.formats.in.SlideBook7Reader.CFRETManipRecord70
- mMonth - Variable in class loci.formats.in.SlideBook7Reader.CImageRecord70
- mMoveFieldDownSign - Variable in class loci.formats.in.SlideBook7Reader.CExposureRecord70
- mMoveFieldRightSign - Variable in class loci.formats.in.SlideBook7Reader.CExposureRecord70
- mmPlanes - Variable in class loci.formats.in.MetamorphReader
- MMSTAMP - Static variable in class loci.formats.in.FluoviewReader
- mNA - Variable in class loci.formats.in.SlideBook7Reader.CLensDef70
- mName - Variable in class loci.formats.in.SlideBook7Reader.CChannelDef70
- mName - Variable in class loci.formats.in.SlideBook7Reader.CFluorDef70
- mName - Variable in class loci.formats.in.SlideBook7Reader.CImageRecord70
- mName - Variable in class loci.formats.in.SlideBook7Reader.CLensDef70
- mName - Variable in class loci.formats.in.SlideBook7Reader.CMaskRecord70
- mName - Variable in class loci.formats.in.SlideBook7Reader.COptovarDef70
- mName - Variable in class loci.formats.in.SlideBook7Reader.CSlideRecord70
- mNDPos - Variable in class loci.formats.in.SlideBook7Reader.CFluorDef70
- mNextTableFileOffset - Variable in class loci.formats.in.SlideBook7Reader.CDataTableHeaderRecord70
- MNG_MAGIC_BYTES - Static variable in class loci.formats.in.MNGReader
- MNGReader - Class in loci.formats.in
-
MNGReader is the file format reader for Multiple-image Network Graphics (MNG) files.
- MNGReader() - Constructor for class loci.formats.in.MNGReader
-
Constructs a new MNG reader.
- MNGReader.SeriesInfo - Class in loci.formats.in
- mNotesLen - Variable in class loci.formats.in.SlideBook7Reader.CImageRecord70
- mNotesLen - Variable in class loci.formats.in.SlideBook7Reader.CSlideRecord70
- mNotesPtr - Variable in class loci.formats.in.SlideBook7Reader.CImageRecord70
- mNotesPtr - Variable in class loci.formats.in.SlideBook7Reader.CSlideRecord70
- mNpyHeader - Variable in class loci.formats.in.SlideBook7Reader.CImageGroup
- mNumAuxDataTables - Variable in class loci.formats.in.SlideBook7Reader.CImageRecord70
- mNumBackground - Variable in class loci.formats.in.SlideBook7Reader.CRatioManipRecord70
- mNumberOfThreads - Variable in class loci.formats.in.SlideBook7Reader.CCompressionBase
- mNumBins - Variable in class loci.formats.in.SlideBook7Reader.CHistogramRecord70
- mNumBlocks - Variable in class loci.formats.in.SlideBook7Reader.CCompressionBase
- mNumCalibPoints - Variable in class loci.formats.in.SlideBook7Reader.CRemapManipRecord70
- mNumChannels - Variable in class loci.formats.in.SlideBook7Reader.CImageRecord70
- mNumExposuresAverage - Variable in class loci.formats.in.SlideBook7Reader.CFluorDef70
- mNumImages - Variable in class loci.formats.in.SlideBook7Reader.CSlideRecord70
- mNumManip - Variable in class loci.formats.in.SlideBook7Reader.CChannelRecord70
- mNumManip - Variable in class loci.formats.in.SlideBook7Reader.CMaskRecord70
- mNumMasks - Variable in class loci.formats.in.SlideBook7Reader.CImageRecord70
- mNumMax - Variable in class loci.formats.in.SlideBook7Reader.CRatioManipRecord70
- mNumMin - Variable in class loci.formats.in.SlideBook7Reader.CRatioManipRecord70
- mNumPhases - Variable in class loci.formats.in.SlideBook7Reader.CFRETManipRecord70
- mNumPlanes - Variable in class loci.formats.in.SlideBook7Reader.CChannelRecord70
- mNumPlanes - Variable in class loci.formats.in.SlideBook7Reader.CExposureRecord70
- mNumPlanes - Variable in class loci.formats.in.SlideBook7Reader.CImageRecord70
- mNumTimepoints - Variable in class loci.formats.in.SlideBook7Reader.CImageRecord70
- mNumViews - Variable in class loci.formats.in.SlideBook7Reader.CImageRecord70
- mNumX - Variable in class loci.formats.in.SlideBook7Reader.CCompressionBase
- mNumY - Variable in class loci.formats.in.SlideBook7Reader.CCompressionBase
- mNumZ - Variable in class loci.formats.in.SlideBook7Reader.CCompressionBase
- mNuTSACSampleSize - Variable in class loci.formats.in.SlideBook7Reader.CExposureRecord70
- mObjectId - Variable in class loci.formats.in.SlideBook7Reader.CAnnotation70
- mOcularPhotoTurretPos - Variable in class loci.formats.in.SlideBook7Reader.CFluorDef70
- mod - Variable in class loci.formats.in.SDTInfo
-
Module number.
- MODALITIES_IN_STUDY - Enum constant in enum class loci.formats.dicom.DicomAttribute
- modality - Variable in class loci.formats.in.ND2Handler
- MODALITY - Enum constant in enum class loci.formats.dicom.DicomAttribute
- MODALITY_LUT_SEQUENCE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- MODALITY_LUT_TYPE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- MODE - Enum constant in enum class loci.formats.in.SPEReader.SpeHeaderEntry
- model - Variable in class loci.formats.in.BioRadSCNReader
- model - Variable in class loci.formats.in.FluoviewReader
- model - Variable in class loci.formats.in.LeicaHandler.Detector
- model - Variable in class loci.formats.in.ZeissLSMReader.Laser
- MODEL - Static variable in class loci.formats.in.FluoviewReader
- MODEL - Static variable in class loci.formats.tiff.IFD
- MODELS_WITHOUT_CORRECTION - Static variable in class loci.formats.in.LeicaSCNReader
- modFpgaVer - Variable in class loci.formats.in.SDTInfo
-
New in v.8.4.
- modSerNo - Variable in class loci.formats.in.SDTInfo
-
Serial number of the module.
- modType - Variable in class loci.formats.in.SDTInfo
-
Module type.
- modTypeCode - Variable in class loci.formats.in.SDTInfo
- modulo - Variable in class loci.formats.meta.ModuloAnnotation
- Modulo - Class in loci.formats
-
Represents a subdimension of Z, C, or T as needed for supporting Modulo annotations.
- Modulo(String) - Constructor for class loci.formats.Modulo
- Modulo(Modulo) - Constructor for class loci.formats.Modulo
- MODULO_NS - Static variable in class loci.formats.meta.ModuloAnnotation
- ModuloAnnotation - Class in loci.formats.meta
- ModuloAnnotation() - Constructor for class loci.formats.meta.ModuloAnnotation
- moduloC - Variable in class loci.formats.CoreMetadata
- moduloT - Variable in class loci.formats.CoreMetadata
- moduloZ - Variable in class loci.formats.CoreMetadata
- MolecularImagingReader - Class in loci.formats.in
-
MolecularImagingReader is the file format reader for Molecular Imaging files.
- MolecularImagingReader() - Constructor for class loci.formats.in.MolecularImagingReader
-
Constructs a new Molecular Imaging reader.
- MONO - Enum constant in enum class loci.formats.in.LeicaMicrosystemsMetadata.Channel.ChannelType
- montageIndex - Variable in class loci.formats.in.FluoviewReader
- montageOffsets - Variable in class loci.formats.in.FluoviewReader
- mOptovarDef - Variable in class loci.formats.in.SlideBook7Reader.CImageRecord70
- mosaics - Variable in class loci.formats.in.ZeissCZIReader
- mouseClicked(MouseEvent) - Method in class loci.plugins.in.MainDialog
- mouseDragged(MouseEvent) - Method in class loci.formats.gui.ImageViewer
-
Handles cursor probes.
- mouseEntered(MouseEvent) - Method in class loci.plugins.in.MainDialog
-
Focuses the component upon mouseover.
- mouseExited(MouseEvent) - Method in class loci.plugins.in.MainDialog
- mouseMoved(MouseEvent) - Method in class loci.formats.gui.ImageViewer
-
Handles cursor probes.
- mousePressed(MouseEvent) - Method in class loci.plugins.in.MainDialog
- mouseReleased(MouseEvent) - Method in class loci.plugins.in.MainDialog
- mouseWheelMoved(MouseWheelEvent) - Method in class loci.plugins.util.DataBrowser
- mOutputBuffer - Variable in class loci.formats.in.SlideBook7Reader.CCompressionBase
- moveTo(int, int) - Method in class loci.plugins.util.RecordedImageProcessor
- mParcentricOffsetX - Variable in class loci.formats.in.SlideBook7Reader.CLensDef70
- mParcentricOffsetY - Variable in class loci.formats.in.SlideBook7Reader.CLensDef70
- mParentRecordPtr - Variable in class loci.formats.in.SlideBook7Reader.CDataTableHeaderRecord70
- mParfocalOffset - Variable in class loci.formats.in.SlideBook7Reader.CLensDef70
- mParfocalOffset2 - Variable in class loci.formats.in.SlideBook7Reader.CLensDef70
- mPathToStreamMap - Variable in class loci.formats.in.SlideBook7Reader.DataLoader
- MPEG_4 - Enum constant in enum class loci.formats.codec.CompressionType
- mPersistentSubmasks - Variable in class loci.formats.in.SlideBook7Reader.CMaskRecord70
- mPhaseFlatFieldCorrected - Variable in class loci.formats.in.SlideBook7Reader.CFRETManipRecord70
- mPhasePos - Variable in class loci.formats.in.SlideBook7Reader.CLensDef70
- mPhaseZero - Variable in class loci.formats.in.SlideBook7Reader.CFRETManipRecord70
- mPlaneId - Variable in class loci.formats.in.SlideBook7Reader.CAnnotation70
- mPlanes - Variable in class loci.formats.in.SlideBook7Reader.CDataTableHeaderRecord70
- mPoints - Variable in class loci.formats.in.SlideBook7Reader.CRemapChannelLUT70
- mPolarizerPos - Variable in class loci.formats.in.SlideBook7Reader.CLensDef70
- mPrefsFileLen - Variable in class loci.formats.in.SlideBook7Reader.CSlideRecord70
- mPrefsOffset - Variable in class loci.formats.in.SlideBook7Reader.CSlideRecord70
- mProjectFolder - Variable in class loci.formats.in.SlideBook7Reader.CSlideRecord70
- mPseudoFrom - Variable in class loci.formats.in.SlideBook7Reader.CMainViewRecord70
- mPseudoTo - Variable in class loci.formats.in.SlideBook7Reader.CMainViewRecord70
- MR_ACQUISITION_TYPE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- mRatioManipRecordList - Variable in class loci.formats.in.SlideBook7Reader.CImageGroup
- MRC_SUFFIXES - Static variable in class loci.formats.in.MRCReader
- MRCReader - Class in loci.formats.in
-
MRCReader is the file format reader for MRC files.
- MRCReader() - Constructor for class loci.formats.in.MRCReader
-
Constructs a new MRC reader.
- MRDR_RECORD_OFFSET - Enum constant in enum class loci.formats.dicom.DicomAttribute
- mRedChannel - Variable in class loci.formats.in.SlideBook7Reader.CMainViewRecord70
- mRegionIndex - Variable in class loci.formats.in.SlideBook7Reader.CCubeAnnotation70
- mRegions - Variable in class loci.formats.in.SlideBook7Reader.CFRAPRegionAnnotation70
- mRelativePower - Variable in class loci.formats.in.SlideBook7Reader.CAnnotation70
- mRemapChannelLUTList - Variable in class loci.formats.in.SlideBook7Reader.CImageGroup
- mRemapManipRecList - Variable in class loci.formats.in.SlideBook7Reader.CImageGroup
- mRemapType - Variable in class loci.formats.in.SlideBook7Reader.CRemapChannelLUT70
- mRemapType - Variable in class loci.formats.in.SlideBook7Reader.CRemapManipRecord70
- mReserved1 - Variable in class loci.formats.in.SDTInfo
- mReserved2 - Variable in class loci.formats.in.SDTInfo
- mReserved2 - Variable in class loci.formats.in.SlideBook7Reader.CRemapManipRecord70
- mReservedBuf - Variable in class loci.formats.in.SlideBook7Reader.CCubeAnnotation70
- mRGBFactor - Variable in class loci.formats.in.SlideBook7Reader.CFluorDef70
- mRhigh - Variable in class loci.formats.in.SlideBook7Reader.CRatioManipRecord70
- mRlow - Variable in class loci.formats.in.SlideBook7Reader.CRatioManipRecord70
- mRmax - Variable in class loci.formats.in.SlideBook7Reader.CRatioManipRecord70
- mRmin - Variable in class loci.formats.in.SlideBook7Reader.CRatioManipRecord70
- mRows - Variable in class loci.formats.in.SlideBook7Reader.CDataTableHeaderRecord70
- MRW_MAGIC_STRING - Static variable in class loci.formats.in.MRWReader
- MRWReader - Class in loci.formats.in
-
MRWReader is the file format reader for Minolta MRW files.
- MRWReader() - Constructor for class loci.formats.in.MRWReader
-
Constructs a new MRW reader.
- MS_VIDEO - Static variable in class loci.formats.in.AVIReader
- mSamplingStdDev - Variable in class loci.formats.in.SlideBook7Reader.CRemapPoint
- mSAPositionList - Variable in class loci.formats.in.SlideBook7Reader.CImageGroup
- mSAPositionTablePtr - Variable in class loci.formats.in.SlideBook7Reader.CImageRecord70
- mSaturation - Variable in class loci.formats.in.SlideBook7Reader.CFluorDef70
- mSaturation - Variable in class loci.formats.in.SlideBook7Reader.CMainViewRecord70
- mScanning - Variable in class loci.formats.in.SlideBook7Reader.CExposureRecord70
- mSecond - Variable in class loci.formats.in.SlideBook7Reader.CImageRecord70
- mSequenceId - Variable in class loci.formats.in.SlideBook7Reader.CAnnotation70
- msg - Variable in class loci.formats.FilePattern
-
Error message generated during file pattern construction.
- msg(String) - Method in class loci.formats.gui.DataConverter
- mShape - Variable in class loci.formats.in.SlideBook7Reader.CNpyHeader
- mSignalThreshold - Variable in class loci.formats.in.SlideBook7Reader.CFRETManipRecord70
- mSingleTimepointFile - Variable in class loci.formats.in.SlideBook7Reader.CImageGroup
- mSlidePath - Variable in class loci.formats.in.SlideBook7Reader.CSBFile70
- mSlidePath - Variable in class loci.formats.in.SlideBook7Reader.DataLoader
- mSlideRecord - Variable in class loci.formats.in.SlideBook7Reader.DataLoader
- mSpecialBuildStr - Variable in class loci.formats.in.SlideBook7Reader.CSlideRecord70
- MSRLE - Static variable in class loci.formats.in.AVIReader
-
Supported compression types.
- MSRLECodec - Class in loci.formats.codec
-
Methods for compressing and decompressing data using Microsoft RLE.
- MSRLECodec() - Constructor for class loci.formats.codec.MSRLECodec
- mStageOffsetMicrons - Variable in class loci.formats.in.SlideBook7Reader.CAnnotation70
- mStageOffsetSet - Variable in class loci.formats.in.SlideBook7Reader.CAnnotation70
- mStagePositions - Variable in class loci.formats.in.SlideBook7Reader.CImageGroup
- mStagePositionTablePtr - Variable in class loci.formats.in.SlideBook7Reader.CImageRecord70
- mStartTime - Variable in class loci.formats.in.SlideBook7Reader.CDataTableHeaderRecord70
- mStoreMicronPositions - Variable in class loci.formats.in.SlideBook7Reader.CAnnotation70
- mStr - Variable in class loci.formats.in.SlideBook7Reader.StrIntPair
- mStructID - Variable in class loci.formats.in.SlideBook7Reader.CAlignManipRecord70
- mStructID - Variable in class loci.formats.in.SlideBook7Reader.CChannelDef70
- mStructID - Variable in class loci.formats.in.SlideBook7Reader.CChannelRecord70
- mStructID - Variable in class loci.formats.in.SlideBook7Reader.CDataTableHeaderRecord70
- mStructID - Variable in class loci.formats.in.SlideBook7Reader.CExposureRecord70
- mStructID - Variable in class loci.formats.in.SlideBook7Reader.CFluorDef70
- mStructID - Variable in class loci.formats.in.SlideBook7Reader.CFRETManipRecord70
- mStructID - Variable in class loci.formats.in.SlideBook7Reader.CHistogramRecord70
- mStructID - Variable in class loci.formats.in.SlideBook7Reader.CImageRecord70
- mStructID - Variable in class loci.formats.in.SlideBook7Reader.CLensDef70
- mStructID - Variable in class loci.formats.in.SlideBook7Reader.CMainViewRecord70
- mStructID - Variable in class loci.formats.in.SlideBook7Reader.CMaskRecord70
- mStructID - Variable in class loci.formats.in.SlideBook7Reader.COptovarDef70
- mStructID - Variable in class loci.formats.in.SlideBook7Reader.CRatioManipRecord70
- mStructID - Variable in class loci.formats.in.SlideBook7Reader.CRemapManipRecord70
- mStructLen - Variable in class loci.formats.in.SlideBook7Reader.CAlignManipRecord70
- mStructLen - Variable in class loci.formats.in.SlideBook7Reader.CChannelDef70
- mStructLen - Variable in class loci.formats.in.SlideBook7Reader.CChannelRecord70
- mStructLen - Variable in class loci.formats.in.SlideBook7Reader.CDataTableHeaderRecord70
- mStructLen - Variable in class loci.formats.in.SlideBook7Reader.CExposureRecord70
- mStructLen - Variable in class loci.formats.in.SlideBook7Reader.CFluorDef70
- mStructLen - Variable in class loci.formats.in.SlideBook7Reader.CFRETManipRecord70
- mStructLen - Variable in class loci.formats.in.SlideBook7Reader.CHistogramRecord70
- mStructLen - Variable in class loci.formats.in.SlideBook7Reader.CImageRecord70
- mStructLen - Variable in class loci.formats.in.SlideBook7Reader.CLensDef70
- mStructLen - Variable in class loci.formats.in.SlideBook7Reader.CMainViewRecord70
- mStructLen - Variable in class loci.formats.in.SlideBook7Reader.CMaskRecord70
- mStructLen - Variable in class loci.formats.in.SlideBook7Reader.COptovarDef70
- mStructLen - Variable in class loci.formats.in.SlideBook7Reader.CRatioManipRecord70
- mStructLen - Variable in class loci.formats.in.SlideBook7Reader.CRemapManipRecord70
- mStructLen - Variable in class loci.formats.in.SlideBook7Reader.CSlideRecord70
- mStructVersion - Variable in class loci.formats.in.SlideBook7Reader.CAlignManipRecord70
- mStructVersion - Variable in class loci.formats.in.SlideBook7Reader.CChannelDef70
- mStructVersion - Variable in class loci.formats.in.SlideBook7Reader.CChannelRecord70
- mStructVersion - Variable in class loci.formats.in.SlideBook7Reader.CDataTableHeaderRecord70
- mStructVersion - Variable in class loci.formats.in.SlideBook7Reader.CExposureRecord70
- mStructVersion - Variable in class loci.formats.in.SlideBook7Reader.CFluorDef70
- mStructVersion - Variable in class loci.formats.in.SlideBook7Reader.CFRETManipRecord70
- mStructVersion - Variable in class loci.formats.in.SlideBook7Reader.CHistogramRecord70
- mStructVersion - Variable in class loci.formats.in.SlideBook7Reader.CImageRecord70
- mStructVersion - Variable in class loci.formats.in.SlideBook7Reader.CLensDef70
- mStructVersion - Variable in class loci.formats.in.SlideBook7Reader.CMainViewRecord70
- mStructVersion - Variable in class loci.formats.in.SlideBook7Reader.CMaskRecord70
- mStructVersion - Variable in class loci.formats.in.SlideBook7Reader.COptovarDef70
- mStructVersion - Variable in class loci.formats.in.SlideBook7Reader.CRatioManipRecord70
- mStructVersion - Variable in class loci.formats.in.SlideBook7Reader.CRemapManipRecord70
- mStructVersion - Variable in class loci.formats.in.SlideBook7Reader.CSlideRecord70
- MSVideoCodec - Class in loci.formats.codec
-
Methods for compressing and decompressing data using Microsoft Video 1.
- MSVideoCodec() - Constructor for class loci.formats.codec.MSVideoCodec
- mTableType - Variable in class loci.formats.in.SlideBook7Reader.CDataTableHeaderRecord70
- mText - Variable in class loci.formats.in.SlideBook7Reader.CAnnotation70
- mThumbNail - Variable in class loci.formats.in.SlideBook7Reader.CImageRecord70
- mThumbPlane - Variable in class loci.formats.in.SlideBook7Reader.CMainViewRecord70
- mThumbTimePoint - Variable in class loci.formats.in.SlideBook7Reader.CMainViewRecord70
- mTimeBasis - Variable in class loci.formats.in.SlideBook7Reader.CDataTableHeaderRecord70
- mTimeInterval - Variable in class loci.formats.in.SlideBook7Reader.CDataTableHeaderRecord70
- mTimeLapse - Variable in class loci.formats.in.SlideBook7Reader.CExposureRecord70
- mTimeLapseInterval - Variable in class loci.formats.in.SlideBook7Reader.CExposureRecord70
- mTimePointsTableSize - Variable in class loci.formats.in.SlideBook7Reader.CDataTableHeaderRecord70
- mTimePointsWritten - Variable in class loci.formats.in.SlideBook7Reader.CDataTableHeaderRecord70
- mTIRFPos - Variable in class loci.formats.in.SlideBook7Reader.CFluorDef70
- mTLApertureDiaphramPos - Variable in class loci.formats.in.SlideBook7Reader.CLensDef70
- mTLFieldDiaphramPos - Variable in class loci.formats.in.SlideBook7Reader.CLensDef70
- mTopLensPos - Variable in class loci.formats.in.SlideBook7Reader.CLensDef70
- mTopX - Variable in class loci.formats.in.SlideBook7Reader.CCube
- mTopY - Variable in class loci.formats.in.SlideBook7Reader.CCube
- mTopZ - Variable in class loci.formats.in.SlideBook7Reader.CCube
- mTransmittedModePrompt - Variable in class loci.formats.in.SlideBook7Reader.CFluorDef70
- mtResol - Variable in class loci.formats.in.SDTInfo
-
Macro time clock in 0.1 ns units.
- mTurretPosition - Variable in class loci.formats.in.SlideBook7Reader.CFluorDef70
- mTurretPosition - Variable in class loci.formats.in.SlideBook7Reader.CLensDef70
- mTurretPosition - Variable in class loci.formats.in.SlideBook7Reader.COptovarDef70
- mTwoLifetimeRatio - Variable in class loci.formats.in.SlideBook7Reader.CFRETManipRecord70
- mUint16Size - Variable in class loci.formats.in.SlideBook7Reader.CCompressionBase
- MultiBand() - Constructor for class loci.formats.in.LeicaHandler.MultiBand
- multiBands - Variable in class loci.formats.in.LeicaHandler
- MULTIDIM_IMAGE_VOLUME - Static variable in class loci.formats.in.CellSensReader
- MULTIDIM_STACK_PROPERTIES - Static variable in class loci.formats.in.CellSensReader
- multifile - Variable in class loci.formats.in.ZeissTIFFReader.TIFFInfo
- MULTIPLE_CALIPER - Enum constant in enum class loci.formats.in.BaseZeissReader.FeatureType
- MULTIPLE_DISTANCE - Enum constant in enum class loci.formats.in.BaseZeissReader.FeatureType
- MultipleImagesReader - Class in loci.formats.in.LeicaMicrosystemsMetadata
-
MultipleImagesReader presents a number of image files as one image reference
- MultipleImagesReader(XlifDocument, int) - Constructor for class loci.formats.in.LeicaMicrosystemsMetadata.MultipleImagesReader
- MULTIPLEX_GROUP_TIME_OFFSET - Enum constant in enum class loci.formats.dicom.DicomAttribute
- multiply(double) - Method in class loci.plugins.util.RecordedImageProcessor
- mUncompactedSpace - Variable in class loci.formats.in.SlideBook7Reader.CSlideRecord70
- mUniqueId - Variable in class loci.formats.in.SlideBook7Reader.CImageRecord70
- mUnknownAnnotationList - Variable in class loci.formats.in.SlideBook7Reader.CImageGroup.CAnnotations
- MUST_GROUP - Static variable in class loci.formats.FormatTools
-
File grouping options.
- MUST_GROUP - Static variable in interface loci.formats.IFormatReader
-
File grouping options.
- mUV - Variable in class loci.formats.in.SlideBook7Reader.CFluorDef70
- mUV - Variable in class loci.formats.in.SlideBook7Reader.CLensDef70
- mValue - Variable in class loci.formats.in.SlideBook7Reader.CFluorDef70
- mValue - Variable in class loci.formats.in.SlideBook7Reader.CMainViewRecord70
- mValues - Variable in class loci.formats.in.SlideBook7Reader.CRemapChannelLUT70
- mValueType - Variable in class loci.formats.in.SlideBook7Reader.CDataTableHeaderRecord70
- mVersion - Variable in class loci.formats.in.SlideBook7Reader.CAnnotation70
- mVertexes - Variable in class loci.formats.in.SlideBook7Reader.CAnnotation70
- mViewID - Variable in class loci.formats.in.SlideBook7Reader.CMainViewRecord70
- mViewOptions - Variable in class loci.formats.in.SlideBook7Reader.CMainViewRecord70
- mViewPtr - Variable in class loci.formats.in.SlideBook7Reader.CImageRecord70
- mWidth - Variable in class loci.formats.in.SlideBook7Reader.CImageRecord70
- mX - Variable in class loci.formats.in.SlideBook7Reader.CSBPoint
- mXExtent - Variable in class loci.formats.in.SlideBook7Reader.CExposureRecord70
- mXFactor - Variable in class loci.formats.in.SlideBook7Reader.CExposureRecord70
- mXML - Variable in class loci.formats.in.SlideBook7Reader.CFRAPRegionAnnotation70
- mXmlData - Variable in class loci.formats.in.SlideBook7Reader.CImageGroup.CAuxXmlData
- mXmlDescriptor - Variable in class loci.formats.in.SlideBook7Reader.CImageGroup.CAuxDoubleData
- mXmlDescriptor - Variable in class loci.formats.in.SlideBook7Reader.CImageGroup.CAuxFloatData
- mXmlDescriptor - Variable in class loci.formats.in.SlideBook7Reader.CImageGroup.CAuxSInt32Data
- mXmlDescriptor - Variable in class loci.formats.in.SlideBook7Reader.CImageGroup.CAuxSInt64Data
- mXOffset - Variable in class loci.formats.in.SlideBook7Reader.CAlignManipRecord70
- mXOffset - Variable in class loci.formats.in.SlideBook7Reader.CExposureRecord70
- mXStartPosition - Variable in class loci.formats.in.SlideBook7Reader.CExposureRecord70
- mXYInterpolationFactor - Variable in class loci.formats.in.SlideBook7Reader.CImageRecord70
- mY - Variable in class loci.formats.in.SlideBook7Reader.CSBPoint
- mYear - Variable in class loci.formats.in.SlideBook7Reader.CImageRecord70
- mYExtent - Variable in class loci.formats.in.SlideBook7Reader.CExposureRecord70
- mYFactor - Variable in class loci.formats.in.SlideBook7Reader.CExposureRecord70
- mYOffset - Variable in class loci.formats.in.SlideBook7Reader.CAlignManipRecord70
- mYOffset - Variable in class loci.formats.in.SlideBook7Reader.CExposureRecord70
- myReader - Variable in class loci.formats.gui.ImageViewer
-
Current format reader.
- mYStartPosition - Variable in class loci.formats.in.SlideBook7Reader.CExposureRecord70
- myWriter - Variable in class loci.formats.gui.ImageViewer
-
Current format writer.
- mZ - Variable in class loci.formats.in.SlideBook7Reader.CSBPoint
- mZInterpolationFactor - Variable in class loci.formats.in.SlideBook7Reader.CImageRecord70
- mZOffset - Variable in class loci.formats.in.SlideBook7Reader.CAlignManipRecord70
- mZStageDirectionsValid - Variable in class loci.formats.in.SlideBook7Reader.CAnnotation70
- mZStageIncreaseTowardsSample - Variable in class loci.formats.in.SlideBook7Reader.CAnnotation70
- mZStartPosition - Variable in class loci.formats.in.SlideBook7Reader.CExposureRecord70
N
- N_ACCUMULATIONS - Static variable in class loci.formats.in.FluoviewReader
- N_FRAMES - Static variable in class loci.formats.in.FluoviewReader
- na - Variable in class loci.formats.in.ND2Handler
- na - Variable in class loci.formats.in.OIRReader.Objective
- NAFReader - Class in loci.formats.in
-
NAFReader is the file format reader for Hamamatsu Aquacosmos NAF files.
- NAFReader() - Constructor for class loci.formats.in.NAFReader
-
Constructs a new NAF reader.
- name - Variable in enum class loci.formats.codec.JPEG2000BoxType
-
The name of the box type.
- name - Variable in enum class loci.formats.codec.JPEG2000SegmentMarker
-
The name of the segment marker.
- name - Static variable in class loci.formats.filter.LZ4Filter
- name - Variable in enum class loci.formats.in.BaseZeissReader.Charset
- name - Variable in class loci.formats.in.BaseZeissReader.Layer
- name - Variable in class loci.formats.in.BaseZeissReader.Shape
- name - Variable in class loci.formats.in.CellSensReader.Pyramid
- name - Variable in class loci.formats.in.CellVoyagerReader.ChannelInfo
- name - Variable in class loci.formats.in.CV7000Reader.LightSource
- name - Variable in class loci.formats.in.CV7000Reader.WPIHandler
- name - Variable in class loci.formats.in.FV1000Reader.ChannelData
- name - Variable in class loci.formats.in.IM3Reader.IM3Record
- name - Variable in class loci.formats.in.IM3Reader.Spectrum
- name - Variable in class loci.formats.in.LeicaHandler.Channel
- name - Variable in class loci.formats.in.LeicaHandler.ROI
- name - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.LofXmlDocument
- name - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.ROI
- name - Variable in class loci.formats.in.LeicaReader.Detector
- name - Variable in class loci.formats.in.LeicaSCNReader.Image
- name - Variable in class loci.formats.in.LeicaSCNReader.ImageCollection
- name - Variable in class loci.formats.in.LiFlimReader.ROI
- name - Variable in class loci.formats.in.LIFReader.ROI
- name - Variable in class loci.formats.in.MicromanagerReader.Position
- name - Variable in class loci.formats.in.ND2Reader.ChunkMapEntry
- name - Variable in class loci.formats.in.OIRReader.Channel
- name - Variable in class loci.formats.in.OIRReader.Laser
- name - Variable in class loci.formats.in.OIRReader.Objective
- name - Variable in class loci.formats.in.TecanReader.Channel
- name - Variable in class loci.formats.in.TissueFAXSReader.Channel
- name - Variable in class loci.formats.in.ZeissCZIReader.AttachmentEntry
- name - Variable in class loci.formats.in.ZeissCZIReader.Channel
- name - Variable in class loci.formats.in.ZeissLSMReader.DataChannel
- name - Variable in class loci.formats.in.ZeissLSMReader.IlluminationChannel
- name - Variable in class loci.formats.in.ZeissLSMReader.Recording
- name - Variable in enum class loci.formats.tiff.PhotoInterp
-
Given name of the photometric interpretation.
- name - Variable in class loci.plugins.config.LibraryEntry
- name - Variable in class loci.plugins.in.IdDialog
- name - Variable in class loci.plugins.util.RecordedImageProcessor.MethodEntry
- nameLength - Variable in class loci.formats.in.LeicaReader
- nameLookup - Static variable in enum class loci.formats.dicom.DicomAttribute
- nameOfMeasuredQuantity - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.Channel
- names - Variable in class loci.formats.in.FlexReader.FlexHandler
- names - Static variable in class loci.plugins.shortcut.ShortcutPanel
-
Details for installed plugins.
- NAMESPACE - Static variable in class loci.formats.ome.OMEPyramidStore
- nameStack - Variable in class loci.formats.in.LeicaHandler
- nameStack - Variable in class loci.formats.in.LeicaSCNReader.LeicaSCNHandler
- nameStack - Variable in class loci.formats.in.ZeissTIFFHandler
- NATIVE_LIB_CLASS - Static variable in class loci.formats.services.JPEGTurboServiceImpl
- nativeReader - Variable in class loci.formats.DelegateReader
-
Native reader.
- nativeReaderInitialized - Variable in class loci.formats.DelegateReader
-
Flag indicating that the native reader was successfully initialized.
- nBuffers - Variable in class loci.formats.in.SPCReader
- nChannels - Variable in class loci.formats.gui.SignedColorModel
- nChannels - Variable in class loci.formats.gui.UnsignedIntColorModel
- nChannels - Variable in class loci.formats.in.InCellReader.MinimalInCellHandler
- nChannels - Variable in class loci.formats.in.SPCReader
-
Number of spectral nChannels.
- nColorPlanes - Variable in class loci.formats.in.PCXReader
- nCols - Variable in class loci.formats.in.FlexReader
- nCols - Variable in class loci.formats.in.HamamatsuVMSReader
- ncx - Variable in class loci.formats.in.SDTInfo
- ncy - Variable in class loci.formats.in.SDTInfo
- ND_ENCODING - Static variable in class loci.formats.in.MetamorphReader
- ND_SUFFIX - Static variable in class loci.formats.in.MetamorphReader
- ND2_MAGIC_BYTES_1 - Static variable in class loci.formats.in.ND2Reader
- ND2_MAGIC_BYTES_2 - Static variable in class loci.formats.in.ND2Reader
- ND2Handler - Class in loci.formats.in
-
DefaultHandler implementation for handling XML produced by Nikon Elements.
- ND2Handler(CoreMetadataList, boolean, int) - Constructor for class loci.formats.in.ND2Handler
- ND2Handler(CoreMetadataList, int) - Constructor for class loci.formats.in.ND2Handler
- ND2Reader - Class in loci.formats.in
-
ND2Reader is the file format reader for Nikon ND2 files.
- ND2Reader() - Constructor for class loci.formats.in.ND2Reader
-
Constructs a new ND2 reader.
- ND2Reader.ChunkMapEntry - Class in loci.formats.in
- ND2Widgets - Class in loci.plugins.config
-
Custom widgets for configuring Bio-Formats ND2 support.
- ND2Widgets() - Constructor for class loci.plugins.config.ND2Widgets
- ndFilename - Variable in class loci.formats.in.MetamorphReader
- ndFilter - Variable in class loci.formats.in.DeltavisionReader.DVExtHdrFields
-
Neutral density value.
- ndFilters - Variable in class loci.formats.in.DeltavisionReader
- ndFilters - Variable in class loci.formats.in.SlidebookReader
- nDimensions - Variable in class loci.formats.in.CellSensReader
- nDimensions - Variable in class loci.formats.in.NiftiReader
- NDINFOFILE_VER1 - Static variable in class loci.formats.in.MetamorphReader
- NDINFOFILE_VER2 - Static variable in class loci.formats.in.MetamorphReader
- ndpiFiles - Variable in class loci.formats.in.NDPISReader
- NDPIReader - Class in loci.formats.in
-
NDPIReader is the file format reader for Hamamatsu .ndpi files.
- NDPIReader() - Constructor for class loci.formats.in.NDPIReader
-
Constructs a new NDPI reader.
- NDPISReader - Class in loci.formats.in
-
NDPISReader is the file format reader for Hamamatsu .ndpis files.
- NDPISReader() - Constructor for class loci.formats.in.NDPISReader
-
Constructs a new NDPIS reader.
- needMem - Variable in class loci.plugins.in.MemoryDialog
-
Required memory for the dataset, in bytes.
- needPrompt() - Method in class loci.plugins.in.ColorDialog
- needPrompt() - Method in class loci.plugins.in.CropDialog
- needPrompt() - Method in class loci.plugins.in.FilePatternDialog
- needPrompt() - Method in class loci.plugins.in.IdDialog
- needPrompt() - Method in class loci.plugins.in.ImporterDialog
- needPrompt() - Method in class loci.plugins.in.LocationDialog
- needPrompt() - Method in class loci.plugins.in.MainDialog
- needPrompt() - Method in class loci.plugins.in.MemoryDialog
- needPrompt() - Method in class loci.plugins.in.RangeDialog
- needPrompt() - Method in class loci.plugins.in.SeriesDialog
- needPrompt() - Method in class loci.plugins.in.SwapDialog
- needPrompt() - Method in class loci.plugins.in.UpgradeDialog
- NEF_SUFFIX - Static variable in class loci.formats.in.NikonReader
- netcdf - Variable in class loci.formats.in.ImarisHDFReader
- netcdf - Variable in class loci.formats.in.MINCReader
- netcdf - Variable in class loci.formats.in.VeecoReader
- netCDFFile - Variable in class loci.formats.services.NetCDFServiceImpl
-
NetCDF file instance.
- NetCDFService - Interface in loci.formats.services
-
Utility class for working with NetCDF/HDF files.
- NetCDFServiceImpl - Class in loci.formats.services
-
Utility class for working with NetCDF/HDF files.
- NetCDFServiceImpl() - Constructor for class loci.formats.services.NetCDFServiceImpl
-
Default constructor.
- NEW_MDIM_VOLUME_HEADER - Static variable in class loci.formats.in.CellSensReader
- NEW_SUBFILE_TYPE - Static variable in class loci.formats.tiff.IFD
- NEW_TYPE - Static variable in class loci.formats.in.DeltavisionReader
- NEW_VOLUME_HEADER - Static variable in class loci.formats.in.CellSensReader
- newFileType - Variable in class loci.formats.in.DeltavisionReader
- newOrder - Variable in class loci.formats.AxisGuesser
-
Adjusted ordering of internal dimensional axes.
- newVersionAvailable(String) - Method in class loci.formats.UpgradeChecker
-
Contact the OME registry and return true if a new version is available.
- newVersionAvailable(String, String) - Method in class loci.formats.UpgradeChecker
-
Contact the OME registry and return true if a new version is available.
- nextBlockOffs - Variable in class loci.formats.in.SDTInfo
-
Offset to the data block header of the next data block.
- nextCamera - Variable in class loci.formats.in.FlexReader.FlexHandler
- nextChannel - Variable in class loci.formats.in.LeicaHandler
- nextChannel - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataStoreInitializer
- nextChannel - Variable in class loci.formats.in.LeicaReader
- nextChName - Variable in class loci.formats.in.BaseZeissReader
- nextDetectChannel - Variable in class loci.formats.in.ZeissLSMReader
- nextDetector - Variable in class loci.formats.in.LeicaReader
- nextDetector - Variable in class loci.formats.in.ZeissLSMReader
- nextDichroic - Variable in class loci.formats.in.FlexReader.FlexHandler
- nextDichroic - Variable in class loci.formats.in.ZeissLSMReader
- nextDichroicChannel - Variable in class loci.formats.in.ZeissLSMReader
- nextEmWave - Variable in class loci.formats.in.BaseZeissReader
- nextExWave - Variable in class loci.formats.in.BaseZeissReader
- nextFilter - Variable in class loci.formats.in.FlexReader.FlexHandler
- nextFilter - Variable in class loci.formats.in.LeicaHandler
- nextFilter - Variable in class loci.formats.in.ZeissLSMReader
- nextFilterSet - Variable in class loci.formats.in.FlexReader.FlexHandler
- nextIFDPointer - Variable in class loci.formats.out.DicomWriter
- nextIllumChannel - Variable in class loci.formats.in.ZeissLSMReader
- nextImage - Variable in class loci.formats.in.FlexReader.FlexHandler
- nextLaser - Variable in class loci.formats.in.FlexReader.FlexHandler
- nextLaser - Variable in class loci.formats.in.ZeissLSMReader
- nextLetter() - Method in class loci.formats.ResourceNamer
-
Increments the internal alphabet pointer to the next element of the alphabet.
- nextObjective - Variable in class loci.formats.in.FlexReader.FlexHandler
- nextPlate - Variable in class loci.formats.in.FlexReader.FlexHandler
- nextPlate - Variable in class loci.formats.in.InCellReader.InCellHandler
- nextReadPosition - Variable in class loci.formats.in.OBFReader.State
- nextROI - Variable in class loci.formats.in.LeicaHandler
- nextSequenceNumber - Variable in class loci.formats.out.APNGWriter
- nextSliderRef - Variable in class loci.formats.in.FlexReader.FlexHandler
- nextTag - Variable in class loci.formats.in.OpenlabReader
- nextXPos - Variable in class loci.formats.in.ScanrReader.ScanrHandler
- nextYPos - Variable in class loci.formats.in.ScanrReader.ScanrHandler
- nFields - Variable in class loci.formats.in.ColumbusReader
- nFiles - Variable in class loci.formats.in.FlexReader
- nFrames - Variable in class loci.formats.in.SPCReader
- ni - Variable in class loci.formats.in.BrukerReader
- NiftiReader - Class in loci.formats.in
-
NiftiReader is the file format reader for NIfTI files.
- NiftiReader() - Constructor for class loci.formats.in.NiftiReader
-
Constructs a new NIfTI reader.
- NIKON - Enum constant in enum class loci.formats.tiff.TiffCompression
- NIKON_XML_TAG - Static variable in class loci.formats.in.NikonElementsTiffReader
- NIKON_XML_TAG_2 - Static variable in class loci.formats.in.NikonElementsTiffReader
- NikonCodec - Class in loci.formats.codec
-
This class implements Nikon decompression.
- NikonCodec() - Constructor for class loci.formats.codec.NikonCodec
- NikonCodecOptions - Class in loci.formats.codec
-
Options for compressing and decompressing Nikon NEF data.
- NikonCodecOptions() - Constructor for class loci.formats.codec.NikonCodecOptions
- NikonElementsTiffReader - Class in loci.formats.in
-
NikonElementsTiffReader is the file format reader for TIFF files produced by Nikon Elements.
- NikonElementsTiffReader() - Constructor for class loci.formats.in.NikonElementsTiffReader
- NikonReader - Class in loci.formats.in
-
NikonReader is the file format reader for Nikon NEF (TIFF) files.
- NikonReader() - Constructor for class loci.formats.in.NikonReader
-
Constructs a new Nikon reader.
- NikonTiffReader - Class in loci.formats.in
-
NikonTiffReader is the file format reader for Nikon TIFF files.
- NikonTiffReader() - Constructor for class loci.formats.in.NikonTiffReader
- nImages - Variable in class loci.formats.in.ND2Handler
- NL - Static variable in class loci.formats.in.ICSReader
-
Newline characters.
- NL - Static variable in class loci.formats.tools.AsciiImage
- nLines - Variable in class loci.formats.in.SPCReader
- no - Variable in class loci.formats.in.CV7000Reader.Plane
- NO_ASSOC_ERROR - Static variable in class org.libjpegturbo.turbojpeg.TJCompressor
- NO_ASSOC_ERROR - Static variable in class org.libjpegturbo.turbojpeg.TJDecompressor
- NO_J2K_MSG - Static variable in class loci.formats.services.JAIIIOServiceImpl
- NO_JAI_MSG - Static variable in class loci.formats.in.TiffJAIReader
- NO_JHDF_MSG - Static variable in class loci.formats.services.JHDFServiceImpl
- NO_LINE - Enum constant in enum class loci.formats.in.BaseZeissReader.DrawStyle
- NO_NETCDF_MSG - Static variable in class loci.formats.services.NetCDFServiceImpl
- NO_OME_XML_MSG - Static variable in class loci.formats.services.OMEXMLServiceImpl
- NO_OVERLAYS - Enum constant in enum class loci.formats.in.MetadataLevel
- node - Variable in class loci.formats.gui.XMLCellRenderer.XMLItem
- nodeToString(Node) - Method in class loci.formats.in.LeicaMicrosystemsMetadata.LMSXmlDocument
- NoExtensionFileFilter - Class in loci.formats.gui
-
A file filter that selects files with no extension, for use with a JFileChooser.
- NoExtensionFileFilter() - Constructor for class loci.formats.gui.NoExtensionFileFilter
- noise(double) - Method in class loci.plugins.util.RecordedImageProcessor
- NOISE_REDUCTION - Static variable in class loci.formats.in.CellSensReader
- NOMINAL_INTERVAL - Enum constant in enum class loci.formats.dicom.DicomAttribute
- NOMINAL_SCANNED_PIXEL_SPACING - Enum constant in enum class loci.formats.dicom.DicomAttribute
- NON_GRAPHICS_DOMAINS - Static variable in class loci.formats.FormatTools
-
List of non-graphics domains.
- NON_HCS_DOMAINS - Static variable in class loci.formats.FormatTools
-
List of non-HCS domains.
- NON_SPECIAL_DOMAINS - Static variable in class loci.formats.FormatTools
-
List of domains that do not require special handling.
- NONE - Enum constant in enum class loci.formats.in.BaseZeissReader.FillStyle
- NONE - Enum constant in enum class loci.formats.in.BaseZeissReader.LineEndPositions
- NONE - Enum constant in enum class loci.formats.in.BaseZeissReader.LineEndStyle
- NONE - Enum constant in enum class loci.formats.in.BaseZeissReader.PointStyle
- NONE - Enum constant in enum class loci.formats.in.BaseZeissReader.TextAlignment
- NONE - Static variable in class loci.formats.in.APNGReader
-
Filter types.
- noOfDataBlocks - Variable in class loci.formats.in.SDTInfo
-
no_of_data_blocks valid only when in 0 ..
- noOfMeasDescBlocks - Variable in class loci.formats.in.SDTInfo
- NORMAL_MENU - Static variable in class loci.plugins.shortcut.ShortcutPanel
-
Name of the 'Bio-Formats' submenu.
- NORMAL_PRIORITY - Static variable in interface loci.formats.cache.ICacheStrategy
- normalize() - Method in class loci.formats.in.LeicaHandler.ROI
-
Vertices and transformation values are not stored in pixel coordinates.
- normalize() - Method in class loci.formats.in.LeicaMicrosystemsMetadata.ROI
-
Vertices and transformation values are not stored in pixel coordinates.
- normalize() - Method in class loci.formats.in.LIFReader.ROI
-
Vertices and transformation values are not stored in pixel coordinates.
- normalizeColor(String) - Method in class loci.formats.in.ZeissCZIReader
- normalized - Variable in class loci.formats.in.LeicaHandler.ROI
- normalized - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.ROI
- normalized - Variable in class loci.formats.in.LIFReader.ROI
- normalizeData - Variable in class loci.formats.FormatReader
-
Whether or not to normalize float data.
- normalizeFilename(String, String) - Method in class loci.formats.in.OMETiffReader
- NOSCAN - Enum constant in enum class loci.formats.in.SPEReader.SpeHeaderEntry
- noStitch - Variable in class loci.formats.FileStitcher
- noSubresolutions - Variable in class loci.formats.in.MinimalTiffReader
- Note() - Constructor for class loci.formats.in.BioRadReader.Note
- NOTE_NAMES - Static variable in class loci.formats.in.BioRadReader
-
List of note types.
- NOTE_TYPE_4D_SERIES - Static variable in class loci.formats.in.BioRadReader
- NOTE_TYPE_ARROW - Static variable in class loci.formats.in.BioRadReader
- NOTE_TYPE_COLLECT - Static variable in class loci.formats.in.BioRadReader
- NOTE_TYPE_FILE1 - Static variable in class loci.formats.in.BioRadReader
- NOTE_TYPE_FILE2 - Static variable in class loci.formats.in.BioRadReader
- NOTE_TYPE_LINE - Static variable in class loci.formats.in.BioRadReader
- NOTE_TYPE_LIVE - Static variable in class loci.formats.in.BioRadReader
- NOTE_TYPE_MERGE - Static variable in class loci.formats.in.BioRadReader
- NOTE_TYPE_NUMBER - Static variable in class loci.formats.in.BioRadReader
- NOTE_TYPE_SCALEBAR - Static variable in class loci.formats.in.BioRadReader
- NOTE_TYPE_STRUCTURE - Static variable in class loci.formats.in.BioRadReader
- NOTE_TYPE_THRUVIEW - Static variable in class loci.formats.in.BioRadReader
- NOTE_TYPE_USER - Static variable in class loci.formats.in.BioRadReader
- NOTE_TYPE_VARIABLE - Static variable in class loci.formats.in.BioRadReader
- notes - Variable in class loci.plugins.config.ConfigWindow
- notes - Variable in class loci.plugins.config.LibraryEntry
- noteStrings - Variable in class loci.formats.in.BioRadReader
- notifyListeners(StatusEvent) - Method in class loci.plugins.in.ImagePlusReader
- notifyListeners(StatusEvent) - Method in class loci.plugins.in.ImportProcess
- notifyListeners(CacheEvent) - Method in class loci.formats.cache.Cache
-
Informs listeners of a cache update.
- notifyListeners(CacheEvent) - Method in class loci.formats.cache.CacheStrategy
-
Informs listeners of a cache update.
- nPixels - Variable in class loci.formats.in.SPCReader
- nr - Variable in class loci.formats.in.BrukerReader
- nRows - Variable in class loci.formats.in.FlexReader
- nRows - Variable in class loci.formats.in.HamamatsuVMSReader
- NRRD_MAGIC_STRING - Static variable in class loci.formats.in.NRRDReader
- NRRDReader - Class in loci.formats.in
-
File format reader for NRRD files; see http://teem.sourceforge.net/nrrd.
- NRRDReader() - Constructor for class loci.formats.in.NRRDReader
-
Constructs a new NRRD reader.
- ns - Variable in class loci.formats.in.BrukerReader
- nSlider - Variable in class loci.formats.gui.ImageViewer
- nStreams - Variable in class loci.formats.tools.AmiraParameters
- nTimebins - Variable in class loci.formats.in.SPCReader
-
Number of time bins in lifetime histogram.
- nTimepoints - Variable in class loci.formats.in.CellWorxReader
- NTP_SOURCE_ADDRESS - Enum constant in enum class loci.formats.dicom.DicomAttribute
- num - Variable in class loci.formats.in.BioRadReader.Note
- num - Variable in class org.libjpegturbo.turbojpeg.TJScalingFactor
-
Numerator
- NUM_COMPONENTS - Static variable in class loci.formats.gui.TwoChannelColorSpace
- NUM_DIMENSIONS - Static variable in class loci.formats.in.FV1000Reader
- NUM_EXP_ROIS - Enum constant in enum class loci.formats.in.SPEReader.SpeHeaderEntry
- NUM_FRAMES - Enum constant in enum class loci.formats.in.SPEReader.SpeHeaderEntry
- NUM_IN_BLK - Enum constant in enum class loci.formats.in.SPEReader.SpeHeaderEntry
- NUM_ROIS - Enum constant in enum class loci.formats.in.SPEReader.SpeHeaderEntry
- number - Variable in class loci.formats.in.CellVoyagerReader.WellInfo
- NUMBER_OF_AVERAGES - Enum constant in enum class loci.formats.dicom.DicomAttribute
- NUMBER_OF_DETECTORS - Enum constant in enum class loci.formats.dicom.DicomAttribute
- NUMBER_OF_ENERGY_WINDOWS - Enum constant in enum class loci.formats.dicom.DicomAttribute
- NUMBER_OF_EVENT_TIMERS - Enum constant in enum class loci.formats.dicom.DicomAttribute
- NUMBER_OF_FOCAL_PLANES - Enum constant in enum class loci.formats.dicom.DicomAttribute
- NUMBER_OF_FRAMES - Enum constant in enum class loci.formats.dicom.DicomAttribute
- NUMBER_OF_INKS - Static variable in class loci.formats.tiff.IFD
- NUMBER_OF_PHASE_ENCODING_STEPS - Enum constant in enum class loci.formats.dicom.DicomAttribute
- NUMBER_OF_REFERENCES - Enum constant in enum class loci.formats.dicom.DicomAttribute
- NUMBER_OF_ROTATIONS - Enum constant in enum class loci.formats.dicom.DicomAttribute
- NUMBER_OF_SLICES - Enum constant in enum class loci.formats.dicom.DicomAttribute
- NUMBER_OF_STAGES - Enum constant in enum class loci.formats.dicom.DicomAttribute
- NUMBER_OF_TABLE_BREAK_POINTS - Enum constant in enum class loci.formats.dicom.DicomAttribute
- NUMBER_OF_TABLE_ENTRIES - Enum constant in enum class loci.formats.dicom.DicomAttribute
- NUMBER_OF_TOMOSYNTHESIS_SOURCE_IMAGES - Enum constant in enum class loci.formats.dicom.DicomAttribute
- NUMBER_OF_VIEWS_STAGE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- NUMBER_OPTICAL_PATHS - Enum constant in enum class loci.formats.dicom.DicomAttribute
- numberBuffer - Variable in class loci.formats.in.AmiraReader.ASCII
- NumberFilter - Class in loci.formats
-
NumberFilter is a helper filter for FilePattern.findPattern().
- NumberFilter(String, String) - Constructor for class loci.formats.NumberFilter
-
Creates a filter for files containing a numerical block, sandwiched between the given strings.
- NUMBEROFDARKIMAGES_KEY - Static variable in class loci.formats.in.LiFlimReader
- NUMBEROFFRAMES_KEY - Static variable in class loci.formats.in.LiFlimReader
- numBlocks - Variable in class loci.formats.in.KLBReader
- numBytes - Variable in class loci.formats.in.AliconaReader
-
Number of bytes per pixel (either 1 or 2).
- numBytes - Variable in class loci.formats.out.QTWriter
-
Total number of pixel bytes.
- numChannels - Variable in class loci.formats.in.LeicaHandler
- numDatasets - Variable in class loci.formats.in.LeicaHandler
- numDecompositionLevels - Variable in class loci.formats.codec.JPEG2000CodecOptions
-
The number of decomposition levels as would be provided to:
J2KImageWriteParam.setNumDecompositionLevels(int)(WRITE). - numer - Variable in class loci.formats.tiff.TiffRational
-
Components of the rational's fractional representation.
- numeric - Variable in class loci.formats.FilePatternBlock
-
Whether or not this is a numeric block.
- NUMERICAL_APERTURE - Static variable in class loci.formats.in.CellSensReader
- numericalAperture - Variable in class loci.formats.in.CellSensReader.Pyramid
- NumericComparator() - Constructor for class loci.formats.in.MetamorphTiffReader.NumericComparator
- numFloatsPerSection - Variable in class loci.formats.in.DeltavisionReader
- numFrames - Variable in class loci.formats.out.APNGWriter
- numFramesPointer - Variable in class loci.formats.out.APNGWriter
- numIntsPerSection - Variable in class loci.formats.in.DeltavisionReader
-
The number of ints in each extended header section.
- NUMOP - Static variable in class org.libjpegturbo.turbojpeg.TJTransform
-
The number of lossless transform operations
- NUMPF - Static variable in class org.libjpegturbo.turbojpeg.TJ
-
The number of pixel formats
- numPixelBytes - Variable in class loci.formats.in.GatanReader
- numRegions - Variable in class loci.formats.in.LiFlimReader
- NUMSAMP - Static variable in class org.libjpegturbo.turbojpeg.TJ
-
The number of chrominance subsampling options
- numSeries - Variable in class loci.formats.in.LeicaReader
-
Number of series in the file.
- numSeries - Variable in class loci.formats.in.ND2Handler
- numWritten - Variable in class loci.formats.out.QTWriter
- nXFields - Variable in class loci.formats.in.ND2Handler
- nXFields - Variable in class loci.formats.in.ND2Reader
- nYFields - Variable in class loci.formats.in.ND2Handler
O
- OB - Enum constant in enum class loci.formats.dicom.DicomVR
- OBFReader - Class in loci.formats.in
-
OBFReader is the file format reader for Imspector OBF files.
- OBFReader() - Constructor for class loci.formats.in.OBFReader
- OBFReader.Stack - Class in loci.formats.in
- OBFReader.State - Class in loci.formats.in
- OBJECT - Static variable in class loci.formats.in.BDVReader.H5Constants
- OBJECT - Static variable in class loci.formats.in.CellH5Reader.CellH5Constants
- OBJECT_DROPPED - Static variable in class loci.formats.cache.CacheEvent
-
Event type indicating an object has been removed from the cache.
- OBJECT_LOADED - Static variable in class loci.formats.cache.CacheEvent
-
Event type indicating an object has been added to the cache.
- objective - Variable in class loci.formats.in.BDReader
- objective - Variable in class loci.formats.in.CV7000Reader.Channel
- Objective() - Constructor for class loci.formats.in.OIRReader.Objective
- OBJECTIVE_LENS_NA - Enum constant in enum class loci.formats.dicom.DicomAttribute
- OBJECTIVE_LENS_POWER - Enum constant in enum class loci.formats.dicom.DicomAttribute
- OBJECTIVE_MAG - Static variable in class loci.formats.in.CellSensReader
- OBJECTIVE_NAME - Static variable in class loci.formats.in.CellSensReader
- OBJECTIVE_TYPE - Static variable in class loci.formats.in.CellSensReader
- objectiveID - Variable in class loci.formats.in.CV7000Reader.Channel
- objectiveIDs - Variable in class loci.formats.in.FlexReader
- objectiveMag - Variable in class loci.formats.in.ND2Reader
- objectiveManufacturer - Variable in class loci.formats.in.FluoviewReader
- objectiveModel - Variable in class loci.formats.in.ND2Handler
- objectiveModel - Variable in class loci.formats.in.ND2Reader
- objectiveModels - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataTempBuffer
- objectiveModels - Variable in class loci.formats.in.LIFReader
- objectiveName - Variable in class loci.formats.in.CellSensReader.Pyramid
- objectiveName - Variable in class loci.formats.in.FV1000Reader
- objectiveNames - Variable in class loci.formats.in.CellSensReader.Pyramid
- objectiveRefs - Variable in class loci.formats.in.FlexReader
- objectives - Variable in class loci.formats.in.OIRReader
- objectiveSettingsID - Variable in class loci.formats.in.ZeissCZIReader
- objectiveTypes - Variable in class loci.formats.in.CellSensReader.Pyramid
- objMag - Variable in class loci.formats.in.LeicaSCNReader.Image
- OBS - Static variable in class loci.formats.gui.AWTImageTools
-
ImageObserver for working with AWT images.
- OCCUPATION - Enum constant in enum class loci.formats.dicom.DicomAttribute
- ocr - Variable in class loci.formats.in.LeicaSCNReader.ImageCollection
- od - Variable in class loci.plugins.in.IdDialog
- OD - Enum constant in enum class loci.formats.dicom.DicomVR
- oddLocations - Variable in class loci.formats.dicom.DicomTag
- OECF - Static variable in class loci.formats.tiff.IFD
- OF - Enum constant in enum class loci.formats.dicom.DicomVR
- offByOneLength - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.Dimension
- offset - Variable in class loci.formats.in.APNGReader.PNGBlock
- offset - Variable in class loci.formats.in.BDReader
- offset - Variable in class loci.formats.in.BioRadGelReader
- offset - Variable in class loci.formats.in.BioRadReader
- offset - Variable in class loci.formats.in.CellSensReader.Pyramid
- offset - Variable in class loci.formats.in.ICSReader
-
Offset to pixel data.
- offset - Variable in class loci.formats.in.IM3Reader.IM3Record
- offset - Variable in class loci.formats.in.IvisionReader
- offset - Variable in class loci.formats.in.KhorosReader
-
Image offset.
- offset - Variable in class loci.formats.in.LeicaHandler.Detector
- offset - Variable in class loci.formats.in.LeicaReader.Detector
- offset - Variable in class loci.formats.in.MRWReader
-
Offset to image data.
- offset - Variable in class loci.formats.in.NRRDReader
-
Offset to pixel data.
- offset - Variable in class loci.formats.in.OIRReader.Detector
- offset - Variable in class loci.formats.in.OIRReader.PixelBlock
- offset - Variable in class loci.formats.in.PCXReader
-
Offset to pixel data.
- offset - Variable in class loci.formats.in.PGMReader
-
Offset to pixel data.
- offset - Variable in class loci.formats.in.PSDReader
-
Offset to pixel data.
- offset - Variable in class loci.formats.in.SDTInfo
- offset - Variable in enum class loci.formats.in.SPEReader.SpeHeaderEntry
- offset - Variable in class loci.formats.in.TargaReader
- offset - Variable in class loci.formats.in.VentanaReader.TIFFTile
- offset - Variable in class loci.formats.services.JPEGTurboServiceImpl
- OFFSET_FIRST_DIRECTORY_RECORD - Enum constant in enum class loci.formats.dicom.DicomAttribute
- OFFSET_HIGH_BYTES - Static variable in class loci.formats.in.NDPIReader
- OFFSET_LAST_DIRECTORY_RECORD - Enum constant in enum class loci.formats.dicom.DicomAttribute
- OFFSET_OF_NEXT_DIRECTORY_RECORD - Enum constant in enum class loci.formats.dicom.DicomAttribute
- OFFSET_OF_REFERENCED_DIRECTORY - Enum constant in enum class loci.formats.dicom.DicomAttribute
- offsetFilePointer - Variable in class loci.formats.in.KLBReader
- offsetOfFirstStream - Variable in class loci.formats.in.AmiraReader
- offsetOfStream - Variable in class loci.formats.in.AmiraReader.HxZip
- offsetPointCounter - Variable in class loci.formats.in.InCellReader
- offsets - Variable in class loci.formats.in.AmiraReader.ASCII
- offsets - Variable in class loci.formats.in.AmiraReader.HxRLE
- offsets - Variable in class loci.formats.in.AVIReader
-
Offset to each plane.
- offsets - Variable in class loci.formats.in.BaseZeissReader
- offsets - Variable in class loci.formats.in.FlexReader.FlexFile
- offsets - Variable in class loci.formats.in.FluoviewReader
- offsets - Variable in class loci.formats.in.ImarisReader
-
Offsets to each image.
- offsets - Variable in class loci.formats.in.LOFReader
-
Offsets to memory blocks, paired with their corresponding description.
- offsets - Variable in class loci.formats.in.MNGReader.SeriesInfo
- offsets - Variable in class loci.formats.in.NAFReader
- offsets - Variable in class loci.formats.in.ND2Reader
-
Array of image offsets.
- offsets - Variable in class loci.formats.in.OpenlabRawReader
-
Offset to each image's pixel data.
- offsets - Variable in class loci.formats.in.QTReader
-
Offsets to each plane's pixel data.
- offsets - Variable in class loci.formats.in.ZeissLMSReader
- offsets - Variable in class loci.formats.out.QTWriter
-
Vector of plane offsets.
- offsetToFooter - Variable in class loci.formats.in.DCIMGReader
- offsetToFourPixels - Variable in class loci.formats.in.DCIMGReader
- OIB_SUFFIX - Static variable in class loci.formats.in.FV1000Reader
- oibMapping - Variable in class loci.formats.in.FV1000Reader
-
File mappings for OIB file.
- OIF_SUFFIX - Static variable in class loci.formats.in.FV1000Reader
- OIRReader - Class in loci.formats.in
-
OIRReader is the file format reader for Olympus .oir files.
- OIRReader() - Constructor for class loci.formats.in.OIRReader
-
Constructs a new OIR reader.
- OIRReader.Channel - Class in loci.formats.in
- OIRReader.CZTKey - Class in loci.formats.in
-
This is a class that wraps three numbers c,z,t and an object can be used as a key in a hashmap.
- OIRReader.Detector - Class in loci.formats.in
- OIRReader.Laser - Class in loci.formats.in
- OIRReader.Objective - Class in loci.formats.in
- OIRReader.PixelBlock - Class in loci.formats.in
- OL - Enum constant in enum class loci.formats.dicom.DicomVR
- OLD_JPEG - Enum constant in enum class loci.formats.tiff.TiffCompression
- OLD_PHYSICAL_SIZE_DEFAULT - Static variable in class loci.formats.in.LeicaMicrosystemsMetadata.LMSFileReader
- OLD_PHYSICAL_SIZE_DEFAULT - Static variable in class loci.formats.in.LIFReader
- OLD_PHYSICAL_SIZE_KEY - Static variable in class loci.formats.in.LeicaMicrosystemsMetadata.LMSFileReader
- OLD_PHYSICAL_SIZE_KEY - Static variable in class loci.formats.in.LIFReader
- OLD_TOOLS - Static variable in class loci.formats.UpgradeChecker
-
Deprecated.Removed in Bio-Formats 6.9.0
- oldPhysicalSize - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.Dimension
- OLYMPUS_JPEG2000 - Enum constant in enum class loci.formats.tiff.TiffCompression
- OlympusTileReader - Class in loci.formats.in
-
OlympusTileReader is the file format reader for Olympus .omp2info files.
- OlympusTileReader() - Constructor for class loci.formats.in.OlympusTileReader
-
Constructs a new Olympus .omp2info reader.
- OlympusTileReader.Tile - Class in loci.formats.in
- OME_JAVA_XML - Enum constant in enum class loci.plugins.util.LibraryChecker.Library
- ome_meta_data - Variable in class loci.formats.in.OBFReader
- OME_TIFF_SUFFIXES - Static variable in class loci.formats.in.OMETiffReader
- OME_TOOLS - Static variable in class loci.formats.UpgradeChecker
-
Name of the OME tools JAR.
- OMEHandler() - Constructor for class loci.formats.out.OMEXMLWriter.OMEHandler
- omeMeasurementFile - Variable in class loci.formats.in.CellVoyagerReader
- omeMeta - Variable in class loci.formats.gui.ImageViewer
-
Attached OME metadata store, if available.
- omeMeta - Variable in class loci.formats.out.OMETiffWriter
- OMEPyramidStore - Class in loci.formats.ome
-
Extension of OMEXMLMetadataImpl that allows for pyramid resolution storage and retrieval.
- OMEPyramidStore() - Constructor for class loci.formats.ome.OMEPyramidStore
- OMEPyramidStore.Resolution - Class in loci.formats.ome
- OMETiffCoreMetadata() - Constructor for class loci.formats.in.OMETiffReader.OMETiffCoreMetadata
- OMETiffCoreMetadata(CoreMetadata) - Constructor for class loci.formats.in.OMETiffReader.OMETiffCoreMetadata
- OMETiffCoreMetadata(OMETiffReader.OMETiffCoreMetadata) - Constructor for class loci.formats.in.OMETiffReader.OMETiffCoreMetadata
- OMETiffPlane() - Constructor for class loci.formats.in.OMETiffReader.OMETiffPlane
- OMETiffReader - Class in loci.formats.in
-
OMETiffReader is the file format reader for OME-TIFF files.
- OMETiffReader() - Constructor for class loci.formats.in.OMETiffReader
-
Constructs a new OME-TIFF reader.
- OMETiffReader(String, String[]) - Constructor for class loci.formats.in.OMETiffReader
- OMETiffReader.OMETiffCoreMetadata - Class in loci.formats.in
- OMETiffReader.OMETiffPlane - Class in loci.formats.in
-
Structure containing details on where to find a particular image plane.
- OMETiffWriter - Class in loci.formats.out
-
OMETiffWriter is the file format writer for OME-TIFF files.
- OMETiffWriter() - Constructor for class loci.formats.out.OMETiffWriter
- omexml - Variable in class loci.formats.in.OMEXMLReader
- omeXML - Variable in class loci.plugins.in.ImportProcess
- OMEXMLHandler() - Constructor for class loci.formats.in.OMEXMLReader.OMEXMLHandler
- omeXmlMetadata - Variable in class loci.formats.in.FakeReader
- OMEXMLMetadata - Interface in loci.formats.ome
- OMEXMLMetadataImpl - Class in loci.formats.ome
- OMEXMLMetadataImpl() - Constructor for class loci.formats.ome.OMEXMLMetadataImpl
- OMEXMLReader - Class in loci.formats.in
-
OMEXMLReader is the file format reader for OME-XML files.
- OMEXMLReader() - Constructor for class loci.formats.in.OMEXMLReader
-
Constructs a new OME-XML reader.
- OMEXMLReader.BinData - Class in loci.formats.in
- OMEXMLReader.OMEXMLHandler - Class in loci.formats.in
- omexmlService - Variable in class loci.formats.gui.ImageViewer
-
Service for working with OME-XML metadata.
- omeXmlService - Variable in class loci.formats.in.FakeReader
- OMEXMLService - Interface in loci.formats.services
- OMEXMLServiceImpl - Class in loci.formats.services
- OMEXMLServiceImpl() - Constructor for class loci.formats.services.OMEXMLServiceImpl
-
Default constructor.
- OMEXMLWriter - Class in loci.formats.out
-
OMEXMLWriter is the file format writer for OME-XML files.
- OMEXMLWriter() - Constructor for class loci.formats.out.OMEXMLWriter
- OMEXMLWriter.OMEHandler - Class in loci.formats.out
- OnDemandLongArray - Class in loci.formats.tiff
- OnDemandLongArray(RandomAccessInputStream) - Constructor for class loci.formats.tiff.OnDemandLongArray
- ONE - Static variable in class loci.formats.AxisGuesser
- oneHeaderPerSlice - Variable in class loci.formats.in.SpiderReader
- oneTimepointPerSeries - Variable in class loci.formats.in.InCellReader
- op - Variable in class org.libjpegturbo.turbojpeg.TJTransform
-
Transform operation (one of
OP_*) - OP_HFLIP - Static variable in class org.libjpegturbo.turbojpeg.TJTransform
-
Flip (mirror) image horizontally.
- OP_NONE - Static variable in class org.libjpegturbo.turbojpeg.TJTransform
-
Do not transform the position of the image pixels.
- OP_ROT180 - Static variable in class org.libjpegturbo.turbojpeg.TJTransform
-
Rotate image 180 degrees.
- OP_ROT270 - Static variable in class org.libjpegturbo.turbojpeg.TJTransform
-
Rotate image counter-clockwise by 90 degrees.
- OP_ROT90 - Static variable in class org.libjpegturbo.turbojpeg.TJTransform
-
Rotate image clockwise by 90 degrees.
- OP_TRANSPOSE - Static variable in class org.libjpegturbo.turbojpeg.TJTransform
-
Transpose image (flip/mirror along upper left to lower right axis).
- OP_TRANSVERSE - Static variable in class org.libjpegturbo.turbojpeg.TJTransform
-
Transverse transpose image (flip/mirror along upper right to lower left axis).
- OP_VFLIP - Static variable in class org.libjpegturbo.turbojpeg.TJTransform
-
Flip (mirror) image vertically.
- open() - Method in class loci.formats.tools.EditTiffG
- open(String) - Method in class loci.formats.gui.ImageViewer
-
Opens the given data source using the current format reader.
- open(String) - Static method in class loci.formats.tools.EditTiffG
- open(String) - Method in class loci.plugins.shortcut.ShortcutPanel
-
Opens the given location (e.g., file) with the Bio-Formats Importer plugin.
- open(String, IFormatReader) - Method in class loci.formats.gui.ImageViewer
-
Opens from the given data source using the specified reader in a separate thread.
- OPEN_ARROW - Static variable in class loci.formats.in.ZeissLSMReader
- OPEN_BEZIER - Static variable in class loci.formats.in.ZeissLSMReader
- OPEN_POLYLINE - Static variable in class loci.formats.in.ZeissLSMReader
- openAllSeries() - Method in class loci.plugins.in.ImporterOptions
- openAllSeriesBox - Variable in class loci.plugins.in.MainDialog
- openBitmaskBytes(IFD, int, int) - Method in class loci.formats.in.FlowSightReader
-
Decode the whole IFD plane using bitmask compression
- openBufferedImage(int) - Method in class loci.formats.in.TiffJAIReader
-
Obtains a BufferedImage from the given data source using JAI.
- openBytes(int) - Method in class loci.formats.ChannelFiller
- openBytes(int) - Method in class loci.formats.ChannelMerger
- openBytes(int) - Method in class loci.formats.ChannelSeparator
- openBytes(int) - Method in class loci.formats.DimensionSwapper
- openBytes(int) - Method in class loci.formats.FileStitcher
- openBytes(int) - Method in class loci.formats.FormatReader
- openBytes(int) - Method in interface loci.formats.IFormatReader
-
Obtains the specified image plane from the current file as a byte array.
- openBytes(int) - Method in class loci.formats.ImageReader
- openBytes(int) - Method in class loci.formats.MinMaxCalculator
- openBytes(int) - Method in class loci.formats.ReaderWrapper
- openBytes(int) - Method in class loci.formats.TileStitcher
- openBytes(int) - Method in class loci.formats.WrappedReader
- openBytes(int, byte[]) - Method in class loci.formats.ChannelFiller
- openBytes(int, byte[]) - Method in class loci.formats.ChannelMerger
- openBytes(int, byte[]) - Method in class loci.formats.ChannelSeparator
- openBytes(int, byte[]) - Method in class loci.formats.DimensionSwapper
- openBytes(int, byte[]) - Method in class loci.formats.FileStitcher
- openBytes(int, byte[]) - Method in class loci.formats.FormatReader
- openBytes(int, byte[]) - Method in interface loci.formats.IFormatReader
-
Obtains the specified image plane from the current file into a pre-allocated byte array of (sizeX * sizeY * bytesPerPixel * RGB channel count).
- openBytes(int, byte[]) - Method in class loci.formats.ImageReader
- openBytes(int, byte[]) - Method in class loci.formats.MinMaxCalculator
- openBytes(int, byte[]) - Method in class loci.formats.ReaderWrapper
- openBytes(int, byte[]) - Method in class loci.formats.TileStitcher
- openBytes(int, byte[]) - Method in class loci.formats.WrappedReader
- openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.ChannelFiller
- openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.ChannelMerger
- openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.ChannelSeparator
- openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.DelegateReader
- openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.DimensionSwapper
- openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.FileStitcher
- openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.FormatReader
- openBytes(int, byte[], int, int, int, int) - Method in interface loci.formats.IFormatReader
-
Obtains a sub-image of the specified image plane into a pre-allocated byte array.
- openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.ImageReader
- openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.AFIReader
- openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.AIMReader
- openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.AliconaReader
- openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.AmiraReader
- openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.AnalyzeReader
- openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.APLReader
- openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.APNGReader
- openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.ARFReader
- openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.AVIReader
- openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.BDReader
- openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.BDVReader
- openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.BIFormatReader
- openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.BioRadGelReader
- openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.BioRadReader
- openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.BioRadSCNReader
- openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.BMPReader
- openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.BrukerReader
- openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.BurleighReader
- openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.CanonRawReader
- openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.CellH5Reader
- openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.CellomicsReader
- openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.CellSensReader
- openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.CellVoyagerReader
- openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.CellWorxReader
- openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.ColumbusReader
- openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.CV7000Reader
- openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.DCIMGReader
- openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.DeltavisionReader
- openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.DicomReader
- openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.DNGReader
- openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.Ecat7Reader
- openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.EPSReader
- openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.FakeReader
- openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.FEIReader
- openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.FitsReader
- openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.FlexReader
- openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.FlowSightReader
- openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.FluoviewReader
- openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.FujiReader
- openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.FV1000Reader
- openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.GatanDM2Reader
- openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.GatanReader
- openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.GelReader
- openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.GIFReader
- openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.HamamatsuVMSReader
- openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.HISReader
- openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.HitachiReader
- openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.HRDGDFReader
- openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.I2IReader
- openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.ICSReader
- openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.IM3Reader
- openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.ImaconReader
- openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.ImagicReader
- openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.ImarisHDFReader
- openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.ImarisReader
- openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.IMODReader
- openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.ImprovisionTiffReader
- openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.ImspectorReader
- openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.InCell3000Reader
- openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.InCellReader
- openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.INRReader
- openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.InveonReader
- openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.IonpathMIBITiffReader
- openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.IPLabReader
- openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.IPWReader
- openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.IvisionReader
- openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.JDCEReader
- openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.JEOLReader
- openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.JPEG2000Reader
- openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.JPKReader
- openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.JPXReader
- openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.KhorosReader
- openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.KLBReader
- openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.KodakReader
- openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.L2DReader
- openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.LeicaMicrosystemsMetadata.MultipleImagesReader
- openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.LeicaReader
- openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.LeicaSCNReader
- openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.LiFlimReader
- openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.LIFReader
- openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.LIMReader
- openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.LOFReader
- openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.MetamorphReader
- openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.MetamorphTiffReader
- openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.MIASReader
- openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.MicroCTReader
- openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.MicromanagerReader
- openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.MINCReader
- openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.MinimalTiffReader
- openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.MolecularImagingReader
- openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.MRCReader
- openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.MRWReader
- openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.NAFReader
- openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.ND2Reader
- openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.NDPIReader
- openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.NDPISReader
- openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.NiftiReader
- openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.NikonReader
- openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.NRRDReader
- openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.OBFReader
- openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.OIRReader
- openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.OlympusTileReader
- openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.OMETiffReader
- openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.OMEXMLReader
- openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.OpenlabRawReader
- openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.OpenlabReader
- openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.OperettaReader
- openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.OxfordInstrumentsReader
- openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.PCIReader
- openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.PCORAWReader
- openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.PCXReader
- openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.PDSReader
- openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.PerkinElmerReader
- openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.PGMReader
- openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.PhotoshopTiffReader
- openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.PictReader
- openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.PovrayReader
- openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.PQBinReader
- openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.PrairieReader
- openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.PSDReader
- openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.PyramidTiffReader
- openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.QTReader
- openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.QuesantReader
- openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.RHKReader
- openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.SBIGReader
- openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.ScanrReader
- openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.SDTReader
- openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.SeikoReader
- openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.SEQReader
- openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.SIFReader
- openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.SimplePCITiffReader
- openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.SlideBook7Reader
- openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.SlidebookReader
- openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.SlidebookTiffReader
- openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.SMCameraReader
- openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.SPCReader
- openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.SPEReader
- openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.SpiderReader
- openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.SVSReader
- openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.TargaReader
- openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.TCSReader
- openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.TecanReader
- openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.TextReader
- openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.TiffDelegateReader
- openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.TileJPEGReader
- openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.TillVisionReader
- openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.TissueFAXSReader
- openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.TopometrixReader
- openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.TrestleReader
- openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.UBMReader
- openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.UnisokuReader
- openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.VarianFDFReader
- openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.VectraReader
- openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.VeecoReader
- openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.VentanaReader
- openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.VGSAMReader
- openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.VisitechReader
- openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.VolocityClippingReader
- openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.VolocityReader
- openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.WATOPReader
- openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.XLEFReader
- openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.ZeissCZIReader
- openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.ZeissLMSReader
- openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.ZeissLSMReader
- openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.ZeissTIFFReader
- openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.ZeissXRMReader
- openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.ZeissZVIReader
- openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.ZipReader
- openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.MinMaxCalculator
- openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.ReaderWrapper
- openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.TileStitcher
- openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.WrappedReader
- openBytes(int, int, int, int, int) - Method in class loci.formats.ChannelFiller
- openBytes(int, int, int, int, int) - Method in class loci.formats.ChannelMerger
- openBytes(int, int, int, int, int) - Method in class loci.formats.ChannelSeparator
- openBytes(int, int, int, int, int) - Method in class loci.formats.DimensionSwapper
- openBytes(int, int, int, int, int) - Method in class loci.formats.FileStitcher
- openBytes(int, int, int, int, int) - Method in class loci.formats.FormatReader
- openBytes(int, int, int, int, int) - Method in interface loci.formats.IFormatReader
-
Obtains a sub-image of the specified image plane, whose upper-left corner is given by (x, y).
- openBytes(int, int, int, int, int) - Method in class loci.formats.ImageReader
- openBytes(int, int, int, int, int) - Method in class loci.formats.in.XLEFReader
- openBytes(int, int, int, int, int) - Method in class loci.formats.MinMaxCalculator
- openBytes(int, int, int, int, int) - Method in class loci.formats.ReaderWrapper
- openBytes(int, int, int, int, int) - Method in class loci.formats.TileStitcher
- openBytes(int, int, int, int, int) - Method in class loci.formats.WrappedReader
- openBytesJpeg(int, byte[], int, int, int, int) - Method in class loci.formats.in.XLEFReader
-
Gets bytes of jpeg images.
- openCompressedBytes(int, byte[], int, int) - Method in class loci.formats.ChannelFiller
- openCompressedBytes(int, byte[], int, int) - Method in class loci.formats.ChannelMerger
- openCompressedBytes(int, byte[], int, int) - Method in class loci.formats.ChannelSeparator
- openCompressedBytes(int, byte[], int, int) - Method in class loci.formats.DimensionSwapper
- openCompressedBytes(int, byte[], int, int) - Method in class loci.formats.FileStitcher
- openCompressedBytes(int, byte[], int, int) - Method in interface loci.formats.ICompressedTileReader
-
Retrieve the specified tile without performing any decompression.
- openCompressedBytes(int, byte[], int, int) - Method in class loci.formats.ImageReader
- openCompressedBytes(int, byte[], int, int) - Method in class loci.formats.in.DicomReader
- openCompressedBytes(int, byte[], int, int) - Method in class loci.formats.in.NDPIReader
- openCompressedBytes(int, byte[], int, int) - Method in class loci.formats.in.SVSReader
- openCompressedBytes(int, byte[], int, int) - Method in class loci.formats.ReaderWrapper
- openCompressedBytes(int, byte[], int, int) - Method in class loci.formats.TileStitcher
- openCompressedBytes(int, int, int) - Method in class loci.formats.ChannelFiller
- openCompressedBytes(int, int, int) - Method in class loci.formats.ChannelMerger
- openCompressedBytes(int, int, int) - Method in class loci.formats.ChannelSeparator
- openCompressedBytes(int, int, int) - Method in class loci.formats.DimensionSwapper
- openCompressedBytes(int, int, int) - Method in class loci.formats.FileStitcher
- openCompressedBytes(int, int, int) - Method in interface loci.formats.ICompressedTileReader
-
Retrieve the specified tile without performing any decompression.
- openCompressedBytes(int, int, int) - Method in class loci.formats.ImageReader
- openCompressedBytes(int, int, int) - Method in class loci.formats.in.DicomReader
- openCompressedBytes(int, int, int) - Method in class loci.formats.in.NDPIReader
- openCompressedBytes(int, int, int) - Method in class loci.formats.in.SVSReader
- openCompressedBytes(int, int, int) - Method in class loci.formats.ReaderWrapper
- openCompressedBytes(int, int, int) - Method in class loci.formats.TileStitcher
- openConnection() - Method in class loci.formats.in.TecanReader
- openConnection(String) - Method in class loci.formats.in.TecanReader
- openConnection(String) - Method in class loci.formats.in.TissueFAXSReader
- OPENER_PLUGIN - Static variable in class loci.plugins.shortcut.ShortcutPanel
-
Name of plugin to use for opening dropped files.
- openerIndex - Static variable in class loci.plugins.shortcut.ShortcutPanel
-
Index of plugin to use to open dropped files.
- openFile(int, int) - Method in class loci.formats.out.DicomWriter
- openFile(File) - Method in class loci.formats.tools.EditTiffG
- openFile(File, RandomAccessInputStream) - Method in class loci.formats.tools.EditTiffG
- openFile(String) - Static method in class loci.formats.tools.EditTiffG
-
Deprecated.
- openFiles - Variable in class loci.formats.in.MetamorphReader
- openGreyscaleBytes(IFD, int, int) - Method in class loci.formats.in.FlowSightReader
-
Decode the whole IFD plane using greyscale compression
- openImage - Variable in class loci.formats.in.InCellReader.InCellHandler
- openImage(byte[], IFormatReader, int, int) - Static method in class loci.formats.gui.AWTImageTools
-
Creates an image from the given byte array, using the given IFormatReader to retrieve additional information.
- openImage(byte[], IFormatReader, int, int, boolean) - Static method in class loci.formats.gui.AWTImageTools
-
Creates an image from the given byte array, using the given IFormatReader to retrieve additional information.
- openImage(int) - Method in class loci.formats.gui.BufferedImageReader
-
Obtains the specified image from the current file.
- openImage(int, int, int, int, int) - Method in class loci.formats.gui.BufferedImageReader
-
Obtains a sub-image of the specified image, whose upper-left corner is given by (x, y).
- openImage(String, Double) - Method in class loci.plugins.macro.LociFunctions
- openImagePlus() - Method in class loci.plugins.in.ImagePlusReader
-
Opens one or more
ImagePlusobjects corresponding to the reader's associated options. - openImagePlus(String) - Static method in class loci.plugins.BF
- openImagePlus(String) - Method in class loci.plugins.macro.LociFunctions
- openImagePlus(ImporterOptions) - Static method in class loci.plugins.BF
- OPENLAB_RAW_MAGIC_STRING - Static variable in class loci.formats.in.OpenlabRawReader
- OpenlabRawReader - Class in loci.formats.in
-
OpenlabRawReader is the file format reader for Openlab RAW files.
- OpenlabRawReader() - Constructor for class loci.formats.in.OpenlabRawReader
-
Constructs a new RAW reader.
- OpenlabReader - Class in loci.formats.in
-
OpenlabReader is the file format reader for Openlab LIFF files.
- OpenlabReader() - Constructor for class loci.formats.in.OpenlabReader
-
Constructs a new OpenlabReader.
- OpenlabReader.PlaneInfo - Class in loci.formats.in
-
Helper class for storing plane info.
- openPixelTag() - Method in class loci.formats.in.PhotoshopTiffReader
- openPlane(int, int, int, int, int) - Method in class loci.formats.FileStitcher
- openPlane(int, int, int, int, int) - Method in class loci.formats.FormatReader
- openPlane(int, int, int, int, int) - Method in interface loci.formats.IFormatReader
-
Obtains the specified image plane (or sub-image thereof) in the reader's native data structure.
- openPlane(int, int, int, int, int) - Method in class loci.formats.ImageReader
- openPlane(int, int, int, int, int) - Method in class loci.formats.in.ImageIOReader
- openPlane(int, int, int, int, int) - Method in class loci.formats.in.MNGReader
- openPlane(int, int, int, int, int) - Method in class loci.formats.in.TextReader
- openPlane(int, int, int, int, int) - Method in class loci.formats.in.TiffJAIReader
- openPlane(int, int, int, int, int) - Method in class loci.formats.ReaderWrapper
- openPlane(int, int, int, int, int) - Method in class loci.formats.WrappedReader
- openPlane(int, int, int, int, int) - Method in class loci.plugins.util.ImageProcessorReader
- openProcessors(int) - Method in class loci.plugins.util.ImageProcessorReader
-
Creates an ImageJ image processor object for the image plane at the given position.
- openProcessors(int, int, int, int, int) - Method in class loci.plugins.util.ImageProcessorReader
-
Returns an array of ImageProcessors that represent the given slice.
- openRaw() - Method in class loci.formats.in.IM3Reader
-
Open the current series in raw-mode, returning the interleaved image bytes.
- openROIs(IMetadata, ImagePlus[]) - Static method in class loci.plugins.util.ROIHandler
-
Look for ROIs in the given OMEXMLMetadata; if any are present, apply them to the given images and display them in the ROI manager.
- openROIs(IMetadata, ImagePlus[], boolean) - Static method in class loci.plugins.util.ROIHandler
-
Opens the rois and converts them into ImageJ Rois.
- openROIs(IMetadata, ImagePlus[], boolean, String) - Static method in class loci.plugins.util.ROIHandler
-
Opens the rois and converts them into ImageJ Rois.
- openSubImage(String, Double, Double, Double, Double, Double) - Method in class loci.plugins.macro.LociFunctions
- openThumbBytes(int) - Method in class loci.formats.ChannelSeparator
- openThumbBytes(int) - Method in class loci.formats.DimensionSwapper
- openThumbBytes(int) - Method in class loci.formats.FileStitcher
- openThumbBytes(int) - Method in class loci.formats.FormatReader
- openThumbBytes(int) - Method in interface loci.formats.IFormatReader
-
Obtains a thumbnail for the specified image plane from the current file, as a byte array.
- openThumbBytes(int) - Method in class loci.formats.ImageReader
- openThumbBytes(int) - Method in class loci.formats.in.AFIReader
- openThumbBytes(int) - Method in class loci.formats.in.CellSensReader
- openThumbBytes(int) - Method in class loci.formats.in.LeicaSCNReader
- openThumbBytes(int) - Method in class loci.formats.in.MinimalTiffReader
- openThumbBytes(int) - Method in class loci.formats.in.NDPIReader
- openThumbBytes(int) - Method in class loci.formats.in.SVSReader
- openThumbBytes(int) - Method in class loci.formats.in.VectraReader
- openThumbBytes(int) - Method in class loci.formats.in.VentanaReader
- openThumbBytes(int) - Method in class loci.formats.ReaderWrapper
- openThumbBytes(int) - Method in class loci.formats.WrappedReader
- openThumbBytes(IFormatReader, int) - Static method in class loci.formats.FormatTools
-
Default implementation for
IFormatReader.openThumbBytes(int). - openThumbImage(int) - Method in class loci.formats.gui.BufferedImageReader
-
Obtains a thumbnail for the specified image from the current file.
- openThumbImage(String, Double) - Method in class loci.plugins.macro.LociFunctions
- openThumbImagePlus() - Method in class loci.plugins.in.ImagePlusReader
- openThumbImagePlus(String) - Static method in class loci.plugins.BF
- openThumbImagePlus(String) - Method in class loci.plugins.macro.LociFunctions
- openThumbImagePlus(ImporterOptions) - Static method in class loci.plugins.BF
- openThumbProcessors(int) - Method in class loci.plugins.util.ImageProcessorReader
- OPERATOR_ID - Enum constant in enum class loci.formats.dicom.DicomAttribute
- OPERATOR_NAME - Enum constant in enum class loci.formats.dicom.DicomAttribute
- OPERETTA_MAGIC - Static variable in class loci.formats.in.OperettaReader
- OperettaHandler() - Constructor for class loci.formats.in.OperettaReader.OperettaHandler
- OperettaReader - Class in loci.formats.in
-
OperettaReader is the file format reader for PerkinElmer Operetta data.
- OperettaReader() - Constructor for class loci.formats.in.OperettaReader
-
Constructs a new Operetta reader.
- OperettaReader.Channel - Class in loci.formats.in
- OperettaReader.OperettaHandler - Class in loci.formats.in
- OperettaReader.Plane - Class in loci.formats.in
- OPT_CROP - Static variable in class org.libjpegturbo.turbojpeg.TJTransform
-
This option will enable lossless cropping.
- OPT_GRAY - Static variable in class org.libjpegturbo.turbojpeg.TJTransform
-
This option will discard the color data in the input image and produce a grayscale output image.
- OPT_NOOUTPUT - Static variable in class org.libjpegturbo.turbojpeg.TJTransform
-
This option will prevent
TJTransformer.transform()from outputting a JPEG image for this particular transform. - OPT_PERFECT - Static variable in class org.libjpegturbo.turbojpeg.TJTransform
-
This option will cause
TJTransformer.transform()to throw an exception if the transform is not perfect. - OPT_TRIM - Static variable in class org.libjpegturbo.turbojpeg.TJTransform
-
This option will discard any partial MCU blocks that cannot be transformed.
- OPTICAL_PATH - Static variable in class loci.formats.in.CellSensReader
- OPTICAL_PATH_DESCRIPTION - Enum constant in enum class loci.formats.dicom.DicomAttribute
- OPTICAL_PATH_ID - Enum constant in enum class loci.formats.dicom.DicomAttribute
- OPTICAL_PATH_ID_SEQUENCE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- OPTICAL_PATH_SEQUENCE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- optimalTileHeight - Variable in class loci.formats.in.OIRReader
- Option - Class in loci.plugins.prefs
-
Base class for an option for one of the plugins.
- Option(String, boolean, String, String) - Constructor for class loci.plugins.prefs.Option
-
Constructs an option with the given parameters.
- options - Variable in class loci.formats.ClassList
-
List of options.
- options - Variable in class loci.formats.FormatWriter
-
The options if required.
- options - Variable in class loci.formats.tiff.TiffSaver
-
The codec options if set.
- options - Variable in class loci.plugins.in.DisplayHandler
- options - Variable in class loci.plugins.in.ImporterDialog
- options - Variable in class loci.plugins.in.ImportProcess
-
Associated importer options.
- options - Variable in class loci.plugins.prefs.OptionsList
-
Table of options defining this set of preferences.
- options - Variable in class loci.plugins.util.DataBrowser
- options - Variable in class org.libjpegturbo.turbojpeg.TJTransform
-
Transform options (bitwise OR of one or more of
OPT_*) - OptionsDialog - Class in loci.plugins.prefs
-
Base class for options dialogs.
- OptionsDialog(OptionsList) - Constructor for class loci.plugins.prefs.OptionsDialog
-
Creates a new options dialog with the given associated options.
- optionsList - Variable in class loci.plugins.prefs.OptionsDialog
-
Options list associated with the dialog.
- OptionsList - Class in loci.plugins.prefs
-
Base class for ImageJ preferences for plugins.
- OptionsList(String, Class<?>) - Constructor for class loci.plugins.prefs.OptionsList
- OptionsList(IniList) - Constructor for class loci.plugins.prefs.OptionsList
- optionsWindow - Variable in class loci.plugins.util.DataBrowser
- or(int) - Method in class loci.plugins.util.RecordedImageProcessor
- order - Variable in class loci.formats.cache.CacheStrategy
-
The order in which planes should be loaded along each axis.
- order - Variable in class loci.formats.gui.CacheComponent
-
Combo boxes for choosing planar ordering.
- ORDER - Static variable in class loci.plugins.out.Exporter
- ORDER_CHANGED - Static variable in class loci.formats.cache.CacheEvent
-
Event type indicating new planar ordering.
- ORDER_DEFAULT - Static variable in class loci.plugins.in.ImporterOptions
- ORDER_VALUES - Static variable in class loci.formats.gui.CacheComponent
- ORDER_XYCTZ - Static variable in class loci.plugins.in.ImporterOptions
- ORDER_XYCZT - Static variable in class loci.plugins.in.ImporterOptions
- ORDER_XYTCZ - Static variable in class loci.plugins.in.ImporterOptions
- ORDER_XYTZC - Static variable in class loci.plugins.in.ImporterOptions
- ORDER_XYZCT - Static variable in class loci.plugins.in.ImporterOptions
- ORDER_XYZTC - Static variable in class loci.plugins.in.ImporterOptions
- orderCertain - Variable in class loci.formats.CoreMetadata
-
Indicates whether or not we are confident that the dimension order is correct.
- orderIndex(int) - Method in class loci.formats.gui.CacheComponent
-
Converts enumerated order value to order chooser index.
- ordering - Variable in class loci.formats.in.BrukerReader
- ORDERS - Static variable in class loci.formats.gui.CacheComponent
- orderValue(int) - Method in class loci.formats.gui.CacheComponent
-
Converts order chooser index to enumerated order value.
- org.libjpegturbo.turbojpeg - package org.libjpegturbo.turbojpeg
- orientation - Variable in class loci.formats.in.TargaReader
- ORIENTATION - Static variable in class loci.formats.tiff.IFD
- orientationMatrix - Variable in class loci.formats.in.OperettaReader.Channel
- orientationMatrix - Variable in class loci.formats.in.OperettaReader.Plane
- origin - Variable in class loci.formats.in.ZeissTIFFHandler.Scaling.Dimension
- original - Variable in class loci.formats.in.DNGReader
-
The original IFD.
- original - Variable in class loci.formats.in.NikonReader
-
The original IFD.
- ORIGINAL_FRAME_RATE - Static variable in class loci.formats.in.CellSensReader
- ORIGINAL_METADATA_NS - Static variable in class loci.formats.meta.OriginalMetadataAnnotation
- ORIGINAL_SOP_CLASS_UID - Enum constant in enum class loci.formats.dicom.DicomAttribute
- originalDate - Variable in class loci.formats.in.DicomReader
- originalID - Variable in class loci.plugins.in.FilePatternDialog
- originalInstance - Variable in class loci.formats.in.DicomReader
- originalMetadata - Variable in class loci.formats.in.CellSensReader.Pyramid
- OriginalMetadataAnnotation - Class in loci.formats.meta
- OriginalMetadataAnnotation() - Constructor for class loci.formats.meta.OriginalMetadataAnnotation
- originalName - Variable in class loci.formats.in.TecanReader.Channel
- originalOrder - Variable in class loci.formats.FileStitcher.ExternalSeries
- originalSeries - Variable in class loci.formats.in.DicomReader
- originalSpecimen - Variable in class loci.formats.in.DicomReader
- originalStudyTime - Variable in class loci.formats.in.DicomReader
- originalTime - Variable in class loci.formats.in.DicomReader
- originalX - Variable in class loci.formats.in.DicomReader
- originalY - Variable in class loci.formats.in.DicomReader
- originX - Variable in class loci.formats.in.CellSensReader.Pyramid
- originX - Variable in class loci.formats.in.PerkinElmerReader
- originX - Variable in class loci.formats.in.VarianFDFReader
- originX - Variable in class loci.formats.in.ZeissLSMReader
- originY - Variable in class loci.formats.in.CellSensReader.Pyramid
- originY - Variable in class loci.formats.in.PerkinElmerReader
- originY - Variable in class loci.formats.in.VarianFDFReader
- originY - Variable in class loci.formats.in.ZeissLSMReader
- originZ - Variable in class loci.formats.in.PerkinElmerReader
- originZ - Variable in class loci.formats.in.VarianFDFReader
- originZ - Variable in class loci.formats.in.ZeissLSMReader
- origname - Variable in class loci.formats.in.ZeissTIFFReader.TIFFInfo
- OTHER_KEYS - Static variable in class loci.formats.in.ICSReader
- OTHER_PATIENT_IDS - Enum constant in enum class loci.formats.dicom.DicomAttribute
- OTHER_PATIENT_NAMES - Enum constant in enum class loci.formats.dicom.DicomAttribute
- otherChannels - Variable in class loci.plugins.util.RecordedImageProcessor
- otherExposureTimes - Variable in class loci.formats.in.CellSensReader.Pyramid
- out - Variable in class loci.formats.FormatWriter
-
Current file.
- out - Variable in class loci.formats.tiff.TiffSaver
-
Output stream to use when saving TIFF data.
- output - Variable in class loci.formats.gui.DataConverter
- output - Variable in class loci.formats.Memoizer.KryoDeser
- OUTPUT_POWER - Enum constant in enum class loci.formats.dicom.DicomAttribute
- outputOrder - Variable in class loci.formats.out.ICSWriter
- outputOrder - Variable in class loci.formats.out.V3DrawWriter
- outputPath - Variable in class loci.formats.out.CellH5Writer
- OV - Enum constant in enum class loci.formats.dicom.DicomVR
- overfl - Variable in class loci.formats.in.SDTInfo
- overflowCorrFactor - Variable in class loci.formats.in.SDTInfo
- Overlap() - Constructor for class loci.formats.in.VentanaReader.Overlap
- overlaps - Variable in class loci.formats.in.TrestleReader
- overlaps - Variable in class loci.formats.in.VentanaReader.AreaOfInterest
- overlapX - Variable in class loci.formats.in.TissueFAXSReader.ScanRegion
- overlapY - Variable in class loci.formats.in.TissueFAXSReader.ScanRegion
- overlay - Variable in class loci.formats.in.TecanReader.Image
- OVERLAY_DATE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- OVERLAY_TIME - Enum constant in enum class loci.formats.dicom.DicomAttribute
- overlayFiles - Variable in class loci.formats.in.MIASReader
- overlayPlanes - Variable in class loci.formats.in.MIASReader
- overruns - Variable in class loci.formats.in.SDTInfo
-
No of Fifo overruns when > 0 fcs curve & endTime are not valid.
- OVERVIEW_IMAGE - Static variable in class loci.formats.in.CellSensReader
- overwriteComment(RandomAccessInputStream, Object) - Method in class loci.formats.tiff.TiffSaver
-
Convenience method for overwriting a file's first ImageDescription.
- overwriteDimensions(MetadataRetrieve) - Method in class loci.formats.out.ICSWriter
- overwriteIFDOffset(RandomAccessInputStream, long, long) - Method in class loci.formats.tiff.TiffSaver
- overwriteIFDValue(RandomAccessInputStream, int, int, Object) - Method in class loci.formats.tiff.TiffSaver
-
Surgically overwrites an existing IFD value with the given one.
- overwriteIFDValue(RandomAccessInputStream, long, int, Object) - Method in class loci.formats.tiff.TiffSaver
-
Surgically overwrites an existing IFD value with the given one.
- overwriteIFDValue(RandomAccessInputStream, long, int, Object, boolean) - Method in class loci.formats.tiff.TiffSaver
-
Surgically overwrites an existing IFD value with the given one.
- overwriteLastIFDOffset(RandomAccessInputStream) - Method in class loci.formats.tiff.TiffSaver
- OW - Enum constant in enum class loci.formats.dicom.DicomVR
- OXFORD_MAGIC_STRING - Static variable in class loci.formats.in.OxfordInstrumentsReader
- OxfordInstrumentsReader - Class in loci.formats.in
-
OxfordInstrumentsReader is the file format reader for Oxford Instruments .top files.
- OxfordInstrumentsReader() - Constructor for class loci.formats.in.OxfordInstrumentsReader
-
Constructs a new Oxford Instruments reader.
P
- p - Variable in class loci.formats.in.BioRadReader.Note
- p - Variable in class loci.plugins.in.SeriesDialog
- p - Variable in class loci.plugins.in.ThumbLoader
- P_KEY - Static variable in class loci.formats.in.LiFlimReader
- pack() - Method in class loci.plugins.util.DataBrowser
-
Overridden pack method to allow us to delay initial window sizing.
- PACK_BITS - Enum constant in enum class loci.formats.tiff.TiffCompression
- PACKBITS - Static variable in class loci.formats.in.PhotoshopTiffReader
- PackbitsCodec - Class in loci.formats.codec
-
This class implements packbits decompression.
- PackbitsCodec() - Constructor for class loci.formats.codec.PackbitsCodec
- packing - Variable in class loci.formats.in.LiFlimReader
- PACKING_KEY - Static variable in class loci.formats.in.LiFlimReader
- pad - Variable in class loci.formats.out.QTWriter
-
Number of padding bytes in each row.
- PAD - Static variable in class loci.plugins.config.ConfigWindow
- padding - Variable in class loci.formats.in.UBMReader
- PADDING_BYTES - Static variable in class loci.formats.out.AVIWriter
- paddingZeros - Variable in class loci.plugins.in.FilePatternDialog
- padImage(byte[], boolean, int, int, int, int) - Static method in class loci.formats.ImageTools
-
Pads (or crops) the byte array to the given width and height.
- padImage(double[], boolean, int, int, int, int) - Static method in class loci.formats.ImageTools
-
Pads (or crops) the double array to the given width and height.
- padImage(float[], boolean, int, int, int, int) - Static method in class loci.formats.ImageTools
-
Pads (or crops) the float array to the given width and height.
- padImage(int[], boolean, int, int, int, int) - Static method in class loci.formats.ImageTools
-
Pads (or crops) the int array to the given width and height.
- padImage(short[], boolean, int, int, int, int) - Static method in class loci.formats.ImageTools
-
Pads (or crops) the short array to the given width and height.
- padImage(BufferedImage, int, int) - Static method in class loci.formats.gui.AWTImageTools
-
Pads (or crops) the image to the given width and height.
- padString(String) - Method in class loci.formats.out.DicomWriter
-
Pad the given string so that the length is a multiple of 2.
- padString(String, String) - Method in class loci.formats.out.DicomWriter
- padString(String, String, int) - Method in class loci.formats.out.DicomWriter
- padTagValues(DicomTag) - Method in class loci.formats.out.DicomWriter
- padUID(String) - Method in class loci.formats.out.DicomWriter
-
Pad the given string so that the length is a multiple of 2.
- PAETH - Static variable in class loci.formats.in.APNGReader
- page - Variable in class loci.formats.in.PrairieMetadata.PFile
-
pageattribute of this<File>. - page - Variable in class loci.formats.in.SDTInfo
- PAGE_NAME - Static variable in class loci.formats.tiff.IFD
- PAGE_NUMBER - Static variable in class loci.formats.tiff.IFD
- PAGE_NUMBER_VECTOR - Enum constant in enum class loci.formats.dicom.DicomAttribute
- paintComponent(Graphics) - Method in class loci.formats.gui.CacheIndicator
- palette - Variable in class loci.formats.in.BMPReader
-
The palette for indexed color images.
- PALETTE - Enum constant in enum class loci.formats.codec.JPEG2000BoxType
- PALETTE - Static variable in class loci.formats.in.ZeissLSMReader
- PALETTE_COLOR_LUT_SEQUENCE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- PALETTE_LUT_UID - Enum constant in enum class loci.formats.dicom.DicomAttribute
- pane - Variable in class loci.formats.gui.ImageViewer
- panel - Variable in class loci.plugins.util.SearchableWindow
- panelSize - Variable in class loci.formats.in.DeltavisionReader
- PARAMETER_KEYS - Static variable in class loci.formats.in.ICSReader
- parameterFile - Variable in class loci.formats.in.JEOLReader
- paramFile - Variable in class loci.formats.in.PCORAWReader
- PARAMS - Static variable in class loci.plugins.config.ConfigWindow
- parent - Variable in class loci.formats.dicom.DicomTag
- parent - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.LMSXmlDocument
- parentDimension - Variable in class loci.formats.Modulo
- parentDir - Variable in class loci.formats.in.CV7000Reader.MeasurementDataHandler
- parentNames - Variable in class loci.formats.in.FEITiffReader.FEIHandler
- parentQName - Variable in class loci.formats.in.FlexReader.FlexHandler
- parentType - Variable in class loci.formats.Modulo
- parse(int, long, long) - Method in class loci.formats.in.QTReader
-
Parse all of the atoms in the file.
- parse(Element) - Method in class loci.formats.in.PrairieMetadata.Frame
-
Parses metadata from the given
Frameelement. - parse(Element) - Method in class loci.formats.in.PrairieMetadata.PFile
-
Parses metadata from the given
Fileelement. - parse(Element) - Method in class loci.formats.in.PrairieMetadata.Sequence
-
Parses metadata from the given
Sequenceelement. - parseApplicationTags() - Method in class loci.formats.in.ZeissLSMReader
- parseArg(String) - Method in class loci.plugins.in.ImporterOptions
-
Parses the plugin argument for parameter values.
- parseArray(String) - Method in class loci.formats.in.VarianFDFReader
-
Split a String that represents an array into individual elements.
- parseAttributes() - Method in class loci.formats.in.ImarisHDFReader
- parseAttributesAndVariables(List<Group>) - Method in class loci.formats.services.NetCDFServiceImpl
-
Recursively parses attribute and variable paths, filling
attributeListandvariableList. - parseAxis(Element) - Method in class loci.formats.in.OIRReader
- parseBoxes() - Method in class loci.formats.in.JPEG2000MetadataParser
-
Parses the JPEG 2000 JP2 metadata boxes.
- parseCellObjects() - Method in class loci.formats.in.CellH5Reader
- parseCFG(Document) - Method in class loci.formats.in.PrairieMetadata
-
Parses metadata from Prairie CFG file.
- parseChannel(Element, boolean) - Method in class loci.formats.in.OIRReader
- parseChannelData(Location) - Method in class loci.formats.in.BDReader
- parseChannels() - Method in class loci.formats.in.PrairieMetadata
-
Parses details of the activated channels into the
PrairieMetadata.activeChannelsdata structure from the "channel" entry of the configuration. - parseChannelTag() - Method in class loci.formats.in.LeicaReader
- parseChunks(IRandomAccess) - Method in class loci.formats.in.IM3Reader.ContainerRecord
-
Parse and return the sub-records for the record container
- parseColor(byte, byte, byte) - Static method in class loci.formats.in.BaseZeissReader
- parseColor(byte, byte, byte) - Static method in class loci.formats.in.ZeissTIFFHandler
- parseColor(String) - Method in class loci.formats.in.FakeReader
- parseComment() - Method in class loci.formats.in.FluoviewReader
- parseCommentGeneric(String) - Method in class loci.formats.in.TiffReader
- parseCommentImageJ(String) - Method in class loci.formats.in.TiffReader
- parseCommentMetamorph(String) - Method in class loci.formats.in.TiffReader
- parseContiguousCodestream(long) - Method in class loci.formats.in.JPEG2000MetadataParser
-
Parses the JPEG 2000 codestream metadata.
- parseCSVFile(String) - Method in class loci.formats.in.PerkinElmerReader
- parseDatabase() - Method in interface loci.formats.services.MDBService
-
Read all tables from a pre-initialized .mdb files.
- parseDatabase() - Method in class loci.formats.services.MDBServiceImpl
- parseDCAMVersion0Footer(RandomAccessInputStream) - Method in class loci.formats.in.DCIMGReader
- parseDCAMVersion0Header(RandomAccessInputStream) - Method in class loci.formats.in.DCIMGReader
- parseDCAMVersion1Header(RandomAccessInputStream) - Method in class loci.formats.in.DCIMGReader
- parseDeconvolutionLog(RandomAccessInputStream, MetadataStore) - Method in class loci.formats.in.DeltavisionReader
-
Parse deconvolution output, if it exists.
- parseDimension(String) - Method in class loci.formats.in.APLReader
-
Parse an integer from the given dimension String.
- parseDimensionSizes(String[], String[]) - Method in class loci.formats.in.NikonTiffReader
- parseDimensionTag(int) - Method in class loci.formats.in.LeicaReader
- parseDOM(Location) - Method in class loci.formats.in.PrairieReader
-
Parses a
Documentfrom the data in the given file. - parseDouble(String) - Method in class loci.formats.in.LeicaHandler
- parseDouble(String) - Method in class loci.formats.in.LeicaMicrosystemsMetadata.LMSMetadataExtractor
- parseDouble(String) - Method in class loci.formats.in.MetamorphHandler
-
Remove '+' before parsing doubles.
- parseDouble(String) - Method in class loci.formats.in.TiffReader
- parseDouble(String) - Static method in class loci.formats.in.ZeissTIFFHandler
-
Parse a Double from a String.
- parseENV(Document) - Method in class loci.formats.in.PrairieMetadata
-
Parses metadata from Prairie ENV file.
- parseETSFile(RandomAccessInputStream, String, int, boolean) - Method in class loci.formats.in.CellSensReader
- parseExperimentTag() - Method in class loci.formats.in.LeicaReader
- parseExtraTags() - Method in class loci.formats.in.GatanDM2Reader
- parseFDF(String) - Method in class loci.formats.in.VarianFDFReader
- parseFile(String, Class<?>) - Method in class loci.formats.ClassList
-
Parses a list of classes from a configuration file.
- parseFile(String, MetamorphHandler) - Method in class loci.formats.in.MetamorphTiffReader
- parseFile(DirectoryEntry) - Method in class loci.formats.services.POIServiceImpl
- parseFileHeader(List<String>) - Method in class loci.formats.in.TextReader
-
Parses the file looking for the file header.
- parseFilename(String[], int, int) - Method in class loci.formats.in.APLReader
- parseFilenames(int) - Method in class loci.formats.in.LeicaReader
- parseFilePath(String) - Method in class loci.formats.in.LeicaMicrosystemsMetadata.LMSXmlDocument
-
Translates Leica XML file paths to absolute url decoded paths
- parseFlexFile(int, int, int, int, boolean, MetadataStore) - Method in class loci.formats.in.FlexReader
-
Parses XML metadata from the Flex file corresponding to the given well.
- parseFrameProperties(Element) - Method in class loci.formats.in.OIRReader
- parseHeader() - Method in class loci.formats.in.LiFlimReader
- parseHeaderRow(String[]) - Method in class loci.formats.in.TextReader
-
Populates rowLength, xIndex, yIndex, and channels.
- parseHTD() - Method in class loci.formats.in.CellWorxReader
- parseImageNames(int) - Method in class loci.formats.in.OpenlabReader
- parseImageProperties(Element) - Method in class loci.formats.in.OIRReader
- parseImageTag(int) - Method in class loci.formats.in.LeicaReader
- parseImageXML(String, int) - Method in class loci.formats.in.ColumbusReader
- parseInstrumentData(MetadataStore, int) - Method in class loci.formats.in.LeicaReader
- parseInt(String) - Static method in class loci.formats.in.BaseZeissReader
-
Parse an Integer from a String.
- parseInt(String) - Method in class loci.formats.in.LeicaMicrosystemsMetadata.LMSMetadataExtractor
- parseInt(String) - Method in class loci.formats.in.TiffReader
- parseInt(String, int) - Static method in class loci.formats.in.BaseZeissReader
-
Parse an Integer from a String.
- parseIntegerString(String) - Method in class loci.formats.in.BDVReader.BDVXMLHandler
- parseIntValue(Number, int) - Method in class loci.formats.in.DicomReader
- parseJSON() - Method in class loci.formats.in.TissueFAXSReader.ScanRegion
- parseKeyAndValue(String, String, int, int, int) - Method in class loci.formats.in.MicromanagerReader
- parseKeyAndValue(String, String, String) - Method in class loci.formats.in.ND2Handler
- parseKeys(Element, PrairieMetadata.ValueTable) - Method in class loci.formats.in.PrairieMetadata
-
Parses
<Key>elements beneath the given element, into the specified table. - parseKeyValue(String, String) - Method in class loci.formats.in.LEOReader
- parseKeyValue(String, String) - Method in class loci.formats.in.PerkinElmerReader
- parseLength(String) - Static method in class loci.formats.FormatTools
-
Parse a length composed of a value and an optional unit
- parseLength(String, String) - Static method in class loci.formats.FormatTools
-
Parse a length composed of a value and an optional unit
- parseLine(String) - Method in class loci.formats.ClassList
-
Parses a class from a string including options and comments.
- parseLines(String[]) - Method in class loci.formats.in.BrukerReader
- parseList(String) - Static method in class loci.plugins.prefs.StringOption
-
Parses a string of comma-separated values into a list of tokens.
- parseLogFile(MetadataStore) - Method in class loci.formats.in.DeltavisionReader
-
Extract metadata from associated log file, if it exists.
- parseLong(String) - Method in class loci.formats.in.LeicaMicrosystemsMetadata.LMSMetadataExtractor
- parseLUT(int) - Method in class loci.formats.in.LeicaReader
- parseLUT(Element, String) - Method in class loci.formats.in.OIRReader
- parseMainTags(int, MetadataStore, ArrayList<BaseZeissReader.Tag>) - Method in class loci.formats.in.BaseZeissReader
- parseMasks - Variable in class loci.formats.in.MIASReader
-
Whether or not mask pixel data should be parsed in setId.
- parseMasks(MetadataStore) - Method in class loci.formats.in.MIASReader
-
Parse masks into a separate overlay-specific MetadataStore.
- parseMasks(MetadataStore, int, int, String) - Method in class loci.formats.in.MIASReader
-
Parse Mask ROIs from the given TIFF and place them in the given MetadataStore.
- parseMDB(String) - Method in class loci.formats.in.ZeissLSMReader
-
Parse a .mdb file and return a list of referenced .lsm files.
- parseMetadata() - Method in class loci.formats.in.ZeissCZIReader.SubBlock
- parseNotes(MetadataStore) - Method in class loci.formats.in.BioRadReader
- ParseNpyHeader(RandomAccessInputStream) - Method in class loci.formats.in.SlideBook7Reader.CNpyHeader
- parseObjectives(NodeList) - Method in class loci.formats.in.ZeissCZIReader
- parseOption(String) - Method in class loci.plugins.prefs.BooleanOption
- parseOption(String) - Method in class loci.plugins.prefs.DoubleOption
- parseOption(String) - Method in class loci.plugins.prefs.Option
-
Parses the option's value from the given argument string.
- parseOption(String) - Method in class loci.plugins.prefs.StringOption
- parseOptions(String) - Method in class loci.formats.ClassList
-
Parses one or more options from a string.
- parseOptions(String) - Method in class loci.plugins.in.Importer
-
Parses core options.
- parseOptions(String) - Method in class loci.plugins.prefs.OptionsList
-
Parses option values from the given argument string.
- parseOriginalMetadata(Node) - Method in class loci.formats.in.OIRReader
- parseOriginalMetadata(Node) - Method in class loci.formats.in.OlympusTileReader
- parseOverlays(int, long, String, MetadataStore) - Method in class loci.formats.in.ZeissLSMReader
-
Parses overlay-related fields.
- parsePageName() - Method in class loci.formats.in.FluoviewReader
- parsePhysicalSize(String, String) - Method in class loci.formats.in.FakeReader
- parsePixelSize(int) - Method in class loci.formats.in.NRRDReader
- parsePixelSpacing(String) - Method in class loci.formats.in.DicomReader
- parsePixelsSizeZFromKey(String) - Method in class loci.formats.in.ND2Handler
-
Parses the physical size from a key.
- parsePoints(String) - Static method in class loci.plugins.util.ROIHandler
-
Parse (x, y) coordinates from a String returned by MetadataRetrieve.getPolygonpoints(...) or MetadataRetrieve.getPolylinepoints(...)
- parsePosition(int) - Method in class loci.formats.in.MicromanagerReader
- parsePosition(String, int) - Method in class loci.formats.in.MicromanagerReader
- parsePosition(String, int, int, IniTable) - Method in class loci.formats.in.FakeReader
- parsePrairieMetadata() - Method in class loci.formats.in.PrairieReader
-
This step parses the Prairie metadata files into the Prairie-specific metadata structure,
PrairieReader.meta. - parsePVStateShard(Element, PrairieMetadata.ValueTable) - Method in class loci.formats.in.PrairieMetadata
-
Parses the
<PVStateShard>element beneath the given element, into the specified table. - parser - Variable in class loci.formats.in.APLReader
- parser - Variable in class loci.formats.in.CellSensReader
- parser - Variable in class loci.formats.in.FV1000Reader
- parser - Variable in class loci.formats.in.ZeissCZIReader
- parseRecord(IRandomAccess) - Static method in class loci.formats.in.IM3Reader
-
Parse an IM3 record at the current file pointer location
- parseResFile(String) - Method in class loci.formats.in.FlexReader
- parseROIFile(String, MetadataStore, int, int) - Method in class loci.formats.in.FV1000Reader
- parseROIs(int) - Method in class loci.formats.in.BDVReader
- parseROIs(int) - Method in class loci.formats.in.CellH5Reader
- parseROIs(RandomAccessInputStream, int, String, MetadataStore) - Method in class loci.formats.in.ZeissZVIReader
-
Parse ROI data from the given RandomAccessInputStream and store it in the given MetadataStore.
- parseROIs(MetadataStore) - Method in class loci.formats.in.BDReader
- parseROIs(MetadataStore) - Method in class loci.formats.in.TrestleReader
- parseROIString(RandomAccessInputStream) - Method in class loci.formats.in.ZeissZVIReader
- parseSeriesTable(IniTable, MetadataStore, int) - Method in class loci.formats.in.FakeReader
-
Translate key/value pairs from the INI table for the specified series.
- parseSeriesTag() - Method in class loci.formats.in.LeicaReader
- parseSetup(String, String) - Method in class loci.formats.in.SPCReader
- parseSOF() - Method in class loci.formats.services.JPEGTurboServiceImpl
- parseSpectrumRecord(IRandomAccess, IM3Reader.ContainerRecord) - Method in class loci.formats.in.IM3Reader.Spectrum
-
Parse the spectrum record
- parseSpreadsheet() - Method in class loci.formats.in.TecanReader
- parseString(IRandomAccess) - Static method in class loci.formats.in.IM3Reader
-
Parse a string from the IM3 file at the current file pointer loc
- parseStructure() - Method in class loci.formats.in.BDVReader
- parseStructure() - Method in class loci.formats.in.CellH5Reader
- parseTable(String) - Method in interface loci.formats.services.MDBService
-
Read named table from a pre-initialized .mdb files.
- parseTable(String) - Method in class loci.formats.services.MDBServiceImpl
- parseTableData(List<String>, int) - Method in class loci.formats.in.TextReader
-
Reads the tabular data into the data array.
- parseTags(int, String, String) - Method in class loci.formats.in.GatanReader
-
Parses Gatan DM3 tags.
- parseTags(int, String, MetadataStore) - Method in class loci.formats.in.ZeissZVIReader
-
Parse all of the tags in a stream.
- parseTags(MetadataStore) - Method in class loci.formats.in.IPLabReader
- parseTemplateFile(MetadataStore) - Method in class loci.formats.in.MIASReader
-
Parse metadata from the Nugenesistemplate.txt file.
- parseText(String, int, boolean) - Method in class loci.formats.in.ND2Reader
- parseTimestamp(String) - Method in class loci.formats.in.BaseZeissReader
-
Parse timestamp from string.
- parseTimeTag(int) - Method in class loci.formats.in.LeicaReader
- parseTimFile(String) - Method in class loci.formats.in.PerkinElmerReader
- parseUIC1Tags(long, int) - Method in class loci.formats.in.MetamorphReader
-
UIC1 entry parser
- parseUIC2Tags(long) - Method in class loci.formats.in.MetamorphReader
-
Populates metadata fields with some contained in MetaMorph UIC2 Tag.
- parseUIC4Tags(long) - Method in class loci.formats.in.MetamorphReader
-
UIC4 metadata parser UIC4 Table contains per-plane blocks of metadata stage X/Y positions, camera chip offsets, stage labels...
- parseWavelength(String, String) - Method in class loci.formats.in.FakeReader
- parseWellLogFile(int, MetadataStore) - Method in class loci.formats.in.CellWorxReader
-
Parse metadata from a well log file.
- parseWellLogFile(int, MetadataStore) - Method in class loci.formats.in.MetaxpressTiffReader
- parseXML(String) - Method in class loci.formats.in.VentanaReader
- parseXML(RandomAccessInputStream, String, long) - Method in class loci.formats.in.OIRReader
- parseXML(Document) - Method in class loci.formats.in.PrairieMetadata
-
Parses metadata from Prairie XML file.
- parseXMLFile() - Method in class loci.formats.in.MicromanagerReader
-
Parse metadata values from the Acqusition.xml file.
- parseZpoFile(String) - Method in class loci.formats.in.PerkinElmerReader
- parsingAttributes - Variable in class loci.formats.in.BDVReader.BDVXMLHandler
- parsingId - Variable in class loci.formats.in.BDVReader.BDVXMLHandler
- parsingTimepoints - Variable in class loci.formats.in.BDVReader.BDVXMLHandler
- parsingViewSetups - Variable in class loci.formats.in.BDVReader.BDVXMLHandler
- parsingVoxelSizes - Variable in class loci.formats.in.BDVReader.BDVXMLHandler
- PARTIAL_VIEW - Enum constant in enum class loci.formats.dicom.DicomAttribute
- PARTIAL_VIEW_DESCRIPTION - Enum constant in enum class loci.formats.dicom.DicomAttribute
- PASS_HEIGHTS - Static variable in class loci.formats.in.APNGReader
- PASS_WIDTHS - Static variable in class loci.formats.in.APNGReader
-
Interlacing pass dimensions.
- PassthroughCodec - Class in loci.formats.codec
-
A codec which just returns the exact data it was given, performing no compression or decompression.
- PassthroughCodec() - Constructor for class loci.formats.codec.PassthroughCodec
- path - Variable in class loci.formats.in.PerkinElmerReader.PixelsFile
- path - Variable in class loci.plugins.config.ConfigWindow
- path - Variable in class loci.plugins.config.LibraryEntry
- PathComparator() - Constructor for class loci.formats.in.XLEFReader.PathComparator
- pathPrefix - Variable in class loci.formats.in.ImarisHDFReader
- pathToImageData - Variable in class loci.formats.in.BDVReader.H5Coordinate
- pathToPosition - Variable in class loci.formats.in.BDVReader.H5Coordinate
- pathToPosition - Variable in class loci.formats.in.CellH5Reader.CellH5Coordinate
- PATIENT_ADDRESS - Enum constant in enum class loci.formats.dicom.DicomAttribute
- PATIENT_AGE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- PATIENT_BIRTH_DATE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- PATIENT_BIRTH_NAME - Enum constant in enum class loci.formats.dicom.DicomAttribute
- PATIENT_BIRTH_TIME - Enum constant in enum class loci.formats.dicom.DicomAttribute
- PATIENT_COMMENTS - Enum constant in enum class loci.formats.dicom.DicomAttribute
- PATIENT_ID - Enum constant in enum class loci.formats.dicom.DicomAttribute
- PATIENT_INSURANCE_PLAN_CODE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- PATIENT_MOTHER_BIRTH_NAME - Enum constant in enum class loci.formats.dicom.DicomAttribute
- PATIENT_NAME - Enum constant in enum class loci.formats.dicom.DicomAttribute
- PATIENT_ORIENTATION - Enum constant in enum class loci.formats.dicom.DicomAttribute
- PATIENT_POSITION - Enum constant in enum class loci.formats.dicom.DicomAttribute
- PATIENT_PRIMARY_LANGUAGE_CODE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- PATIENT_PRIMARY_LANGUAGE_MODIFIER - Enum constant in enum class loci.formats.dicom.DicomAttribute
- PATIENT_RELIGIOUS_PREFERENCE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- PATIENT_SEX - Enum constant in enum class loci.formats.dicom.DicomAttribute
- PATIENT_SIZE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- PATIENT_TELEPHONE_NUMBER - Enum constant in enum class loci.formats.dicom.DicomAttribute
- PATIENT_WEIGHT - Enum constant in enum class loci.formats.dicom.DicomAttribute
- pattern - Variable in class loci.formats.FilePattern
-
The file pattern string.
- pattern - Variable in class loci.formats.FileStitcher.ExternalSeries
- PATTERN_D - Static variable in class loci.formats.in.CellomicsReader
- PATTERN_O - Static variable in class loci.formats.in.CellomicsReader
- patternIds - Variable in class loci.formats.FileStitcher
-
Whether string ids given should be treated as file patterns rather than single file paths.
- PBGRA_32 - Static variable in class loci.formats.services.JPEGXRServiceImpl
- PCI_MAGIC_BYTES - Static variable in class loci.formats.in.PCIReader
- PCIReader - Class in loci.formats.in
-
PCIReader is the file format reader for SimplePCI (Compix) .cxd files.
- PCIReader() - Constructor for class loci.formats.in.PCIReader
-
Constructs a new SimplePCI reader.
- PCORAWReader - Class in loci.formats.in
-
PCORAWReader is the file format reader for PCORAW files.
- PCORAWReader() - Constructor for class loci.formats.in.PCORAWReader
-
Constructs a new PCORAW reader.
- PCX_MAGIC_BYTE - Static variable in class loci.formats.in.PCXReader
- PCXReader - Class in loci.formats.in
-
PCXReader is the file format reader for PCX files (originally used by PC Paintbrush; now used in Zeiss' LSM Image Browser).
- PCXReader() - Constructor for class loci.formats.in.PCXReader
-
Constructs a new PCX reader.
- PDS_MAGIC_STRING - Static variable in class loci.formats.in.PDSReader
- PDSReader - Class in loci.formats.in
-
PDSReader is the file format reader for Perkin Elmer densitometer files.
- PDSReader() - Constructor for class loci.formats.in.PDSReader
-
Constructs a new PDS reader.
- PER_FRAME_FUNCTIONAL_GROUPS_SEQUENCE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- PERCENT_PHASE_FOV - Enum constant in enum class loci.formats.dicom.DicomAttribute
- PERCENT_SAMPLING - Enum constant in enum class loci.formats.dicom.DicomAttribute
- PerkinElmerReader - Class in loci.formats.in
-
PerkinElmerReader is the file format reader for PerkinElmer files.
- PerkinElmerReader() - Constructor for class loci.formats.in.PerkinElmerReader
-
Constructs a new PerkinElmer reader.
- PerkinElmerReader.PixelsFile - Class in loci.formats.in
- pf(Double, String) - Method in class loci.formats.in.PrairieReader
-
Converts the given
doubleto aPositiveFloat, ornullif incompatible. - PF_ABGR - Static variable in class org.libjpegturbo.turbojpeg.TJ
-
ABGR pixel format.
- PF_ARGB - Static variable in class org.libjpegturbo.turbojpeg.TJ
-
ARGB pixel format.
- PF_BGR - Static variable in class org.libjpegturbo.turbojpeg.TJ
-
BGR pixel format.
- PF_BGRA - Static variable in class org.libjpegturbo.turbojpeg.TJ
-
BGRA pixel format.
- PF_BGRX - Static variable in class org.libjpegturbo.turbojpeg.TJ
-
BGRX pixel format.
- PF_GRAY - Static variable in class org.libjpegturbo.turbojpeg.TJ
-
Grayscale pixel format.
- PF_RGB - Static variable in class org.libjpegturbo.turbojpeg.TJ
-
RGB pixel format.
- PF_RGBA - Static variable in class org.libjpegturbo.turbojpeg.TJ
-
RGBA pixel format.
- PF_RGBX - Static variable in class org.libjpegturbo.turbojpeg.TJ
-
RGBX pixel format.
- PF_XBGR - Static variable in class org.libjpegturbo.turbojpeg.TJ
-
XBGR pixel format.
- PF_XRGB - Static variable in class org.libjpegturbo.turbojpeg.TJ
-
XRGB pixel format.
- PFile(PrairieMetadata.Frame, Element) - Constructor for class loci.formats.in.PrairieMetadata.PFile
-
Creates a new file by parsing the given
<File>element. - pfsOffset - Variable in class loci.formats.in.ND2Reader
- pfsStateOffset - Variable in class loci.formats.in.ND2Reader
- PGM_MAGIC_CHAR - Static variable in class loci.formats.in.PGMReader
- PGMReader - Class in loci.formats.in
-
PGMReader is the file format reader for Portable Gray Map (PGM) images.
- PGMReader() - Constructor for class loci.formats.in.PGMReader
-
Constructs a new PGMReader.
- PHASE - Static variable in class loci.formats.FormatTools
-
Identifies the Phase dimensional type, representing a dimension consisting of phases.
- PHASE - Static variable in class loci.formats.in.CellSensReader
- phaseLabels - Variable in class loci.formats.in.ZeissCZIReader
- phases - Variable in class loci.formats.in.LiFlimReader
- phases - Variable in class loci.formats.in.ZeissCZIReader
- phases - Variable in class loci.formats.in.ZeissLSMReader
- PHENIX_MAGIC - Static variable in class loci.formats.in.OperettaReader
- PHOSPHOR_TYPE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- PHOTOBLEACHING - Static variable in class loci.formats.in.CellSensReader
- PhotoInterp - Enum Class in loci.formats.tiff
-
Utility class for working with TIFF photometric interpretations.
- PhotoInterp(int, String, String) - Constructor for enum class loci.formats.tiff.PhotoInterp
-
Default constructor.
- PHOTOMETRIC_INTERPRETATION - Enum constant in enum class loci.formats.dicom.DicomAttribute
- PHOTOMETRIC_INTERPRETATION - Static variable in class loci.formats.tiff.IFD
- photon(int) - Method in class loci.formats.in.SPCReader
- PHOTON_IMAGING_MODE - Static variable in class loci.formats.in.CellSensReader
- photosensorReading - Variable in class loci.formats.in.DeltavisionReader.DVExtHdrFields
-
Photosensor reading.
- PhotoshopTiffReader - Class in loci.formats.in
-
PhotoshopTiffReader is the file format reader for Adobe Photoshop TIFF files.
- PhotoshopTiffReader() - Constructor for class loci.formats.in.PhotoshopTiffReader
-
Constructs a new Photoshop TIFF reader.
- PHYSICAL_DELTA_X - Enum constant in enum class loci.formats.dicom.DicomAttribute
- PHYSICAL_DELTA_Y - Enum constant in enum class loci.formats.dicom.DicomAttribute
- PHYSICAL_SIZE_TAG - Static variable in class loci.formats.in.SlidebookTiffReader
- PHYSICAL_UNITS_X_DIRECTION - Enum constant in enum class loci.formats.dicom.DicomAttribute
- PHYSICAL_UNITS_Y_DIRECTION - Enum constant in enum class loci.formats.dicom.DicomAttribute
- physicalDistanceFromLeftEdge - Variable in class loci.formats.in.SVSReader
- physicalDistanceFromTopEdge - Variable in class loci.formats.in.SVSReader
- physicalPixelSize - Variable in class loci.formats.in.VentanaReader
- physicalSizes - Variable in class loci.formats.in.LeicaReader
- physicalSizeX - Variable in class loci.formats.in.BaseZeissReader
- physicalSizeX - Variable in class loci.formats.in.BioRadSCNReader
- physicalSizeX - Variable in class loci.formats.in.CellSensReader.Pyramid
- physicalSizeX - Variable in class loci.formats.in.FakeReader
- physicalSizeX - Variable in class loci.formats.in.LeicaHandler
- physicalSizeX - Variable in class loci.formats.in.NikonTiffReader
- physicalSizeX - Variable in class loci.formats.in.OIRReader
- physicalSizeX - Variable in class loci.formats.in.SISReader
- physicalSizeXs - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataTempBuffer
- physicalSizeXs - Variable in class loci.formats.in.LIFReader
- physicalSizeY - Variable in class loci.formats.in.BaseZeissReader
- physicalSizeY - Variable in class loci.formats.in.BioRadSCNReader
- physicalSizeY - Variable in class loci.formats.in.CellSensReader.Pyramid
- physicalSizeY - Variable in class loci.formats.in.FakeReader
- physicalSizeY - Variable in class loci.formats.in.LeicaHandler
- physicalSizeY - Variable in class loci.formats.in.NikonTiffReader
- physicalSizeY - Variable in class loci.formats.in.OIRReader
- physicalSizeY - Variable in class loci.formats.in.SISReader
- physicalSizeYs - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataTempBuffer
- physicalSizeYs - Variable in class loci.formats.in.LIFReader
- physicalSizeZ - Variable in class loci.formats.in.BaseZeissReader
- physicalSizeZ - Variable in class loci.formats.in.FakeReader
- physicalSizeZ - Variable in class loci.formats.in.NikonTiffReader
- physicalSizeZ - Variable in class loci.formats.in.OIRReader
- physicalSizeZ - Variable in class loci.formats.in.TiffReader
- physicalX - Variable in class loci.formats.in.VolocityReader.Stack
- physicalY - Variable in class loci.formats.in.VolocityReader.Stack
- physicalZ - Variable in class loci.formats.in.VolocityReader.Stack
- PHYSICIAN_ID - Enum constant in enum class loci.formats.dicom.DicomAttribute
- PHYSICIAN_NAME - Enum constant in enum class loci.formats.dicom.DicomAttribute
- PHYSICIAN_READING - Enum constant in enum class loci.formats.dicom.DicomAttribute
- PHYSICIAN_READING_ID - Enum constant in enum class loci.formats.dicom.DicomAttribute
- PHYSICIANS - Enum constant in enum class loci.formats.dicom.DicomAttribute
- PHYSICIANS_ID - Enum constant in enum class loci.formats.dicom.DicomAttribute
- PI_MAX_2NS_BRD - Enum constant in enum class loci.formats.in.SPEReader.SpeHeaderEntry
- PI_MAX_GAIN - Enum constant in enum class loci.formats.in.SPEReader.SpeHeaderEntry
- PI_MAX_MODE - Enum constant in enum class loci.formats.in.SPEReader.SpeHeaderEntry
- PI_MAX_USED - Enum constant in enum class loci.formats.in.SPEReader.SpeHeaderEntry
- PIC_FILE_ID - Static variable in class loci.formats.in.BioRadReader
-
Numerical ID of a valid Bio-Rad PIC file.
- PIC_SUFFIX - Static variable in class loci.formats.in.BioRadReader
- picFiles - Variable in class loci.formats.in.BioRadReader
- pict - Variable in class loci.formats.in.OpenlabReader
-
Helper reader to read PICT data.
- pict - Variable in class loci.formats.in.OpenlabReader.PlaneInfo
- PICT_9A - Static variable in class loci.formats.in.PictReader
- PICT_BITSRECT - Static variable in class loci.formats.in.PictReader
- PICT_BITSRGN - Static variable in class loci.formats.in.PictReader
- PICT_CLIP_RGN - Static variable in class loci.formats.in.PictReader
- PICT_END - Static variable in class loci.formats.in.PictReader
- PICT_JPEG - Static variable in class loci.formats.in.PictReader
- PICT_LONGCOMMENT - Static variable in class loci.formats.in.PictReader
- PICT_PACKBITSRECT - Static variable in class loci.formats.in.PictReader
- PICT_PACKBITSRGN - Static variable in class loci.formats.in.PictReader
- PICT_TYPE_1 - Static variable in class loci.formats.in.PictReader
- PICT_TYPE_2 - Static variable in class loci.formats.in.PictReader
- PictReader - Class in loci.formats.in
-
PictReader is the file format reader for Apple PICT files.
- PictReader() - Constructor for class loci.formats.in.PictReader
-
Constructs a new PICT reader.
- pinhole - Variable in class loci.formats.in.ImarisHDFReader
- pinhole - Variable in class loci.formats.in.LeicaHandler
- pinhole - Variable in class loci.formats.in.LeicaReader
- pinhole - Variable in class loci.formats.in.OIRReader.Channel
- pinhole - Variable in class loci.formats.in.ZeissCZIReader.Channel
- pinhole - Variable in class loci.formats.in.ZeissLSMReader.DetectionChannel
- pinholes - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataTempBuffer
- pinholes - Variable in class loci.formats.in.LIFReader
- pinholeSize - Variable in class loci.formats.in.FV1000Reader
- pinholeSize - Variable in class loci.formats.in.ND2Handler
- pinholeSize - Variable in class loci.formats.in.NikonTiffReader
- pix - Variable in class loci.formats.in.CanonRawReader
- pixClk - Variable in class loci.formats.in.SDTInfo
- PIXEL_ASPECT_RATIO - Enum constant in enum class loci.formats.dicom.DicomAttribute
- PIXEL_BANDWIDTH - Enum constant in enum class loci.formats.dicom.DicomAttribute
- PIXEL_CLOCK - Static variable in class loci.formats.in.CellSensReader
- PIXEL_COMPONENT_DATA_TYPE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- PIXEL_COMPONENT_MASK - Enum constant in enum class loci.formats.dicom.DicomAttribute
- PIXEL_COMPONENT_ORGANIZATION - Enum constant in enum class loci.formats.dicom.DicomAttribute
- PIXEL_COMPONENT_PHYSICAL_UNITS - Enum constant in enum class loci.formats.dicom.DicomAttribute
- PIXEL_COMPONENT_RANGE_START - Enum constant in enum class loci.formats.dicom.DicomAttribute
- PIXEL_COMPONENT_RANGE_STOP - Enum constant in enum class loci.formats.dicom.DicomAttribute
- PIXEL_DATA - Enum constant in enum class loci.formats.dicom.DicomAttribute
- PIXEL_DATA_LENGTH - Enum constant in enum class loci.formats.dicom.DicomAttribute
- PIXEL_FORMAT_TAG - Static variable in class loci.formats.services.JPEGXRServiceImpl
- PIXEL_INFO_TYPE - Static variable in class loci.formats.in.CellSensReader
- PIXEL_INTENSITY_RELATIONSHIP - Enum constant in enum class loci.formats.dicom.DicomAttribute
- PIXEL_MEASURES_SEQUENCE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- PIXEL_OFFSET - Static variable in class loci.formats.in.BioRadGelReader
- PIXEL_OFFSET - Static variable in class loci.formats.in.VGSAMReader
- PIXEL_PADDING_VALUE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- PIXEL_PRESENTATION - Enum constant in enum class loci.formats.dicom.DicomAttribute
- PIXEL_REPRESENTATION - Enum constant in enum class loci.formats.dicom.DicomAttribute
- PIXEL_SIGN - Enum constant in enum class loci.formats.dicom.DicomAttribute
- PIXEL_SPACING - Enum constant in enum class loci.formats.dicom.DicomAttribute
- PIXEL_VALUE_TRANSFORMATION_SEQUENCE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- PIXEL_X_DIMENSION - Static variable in class loci.formats.tiff.IFD
- PIXEL_Y_DIMENSION - Static variable in class loci.formats.tiff.IFD
- pixelBits - Variable in class loci.formats.gui.SignedColorModel
- PixelBlock() - Constructor for class loci.formats.in.OIRReader.PixelBlock
- pixelBlocks - Variable in class loci.formats.in.OIRReader
- pixelBytes - Variable in class loci.formats.in.QTReader
-
Total number of bytes of pixel data.
- pixelData - Variable in class loci.formats.in.MINCReader
- pixelDataLengthPointer - Variable in class loci.formats.out.DicomWriter
- pixelDataSize - Variable in class loci.formats.out.DicomWriter
- pixelFile - Variable in class loci.formats.in.AnalyzeReader
-
File containing the pixel data.
- pixelFile - Variable in class loci.formats.in.NiftiReader
-
File containing the pixel data.
- PIXELFORMAT_BAYERBG12 - Static variable in class loci.formats.in.LIPixelFormat
- PIXELFORMAT_BAYERBG12P - Static variable in class loci.formats.in.LIPixelFormat
- PIXELFORMAT_BAYERBG12PMSB - Static variable in class loci.formats.in.LIPixelFormat
- PIXELFORMAT_BAYERBG16 - Static variable in class loci.formats.in.LIPixelFormat
- PIXELFORMAT_BAYERBG8 - Static variable in class loci.formats.in.LIPixelFormat
- PIXELFORMAT_BAYERGB12 - Static variable in class loci.formats.in.LIPixelFormat
- PIXELFORMAT_BAYERGB12P - Static variable in class loci.formats.in.LIPixelFormat
- PIXELFORMAT_BAYERGB12PMSB - Static variable in class loci.formats.in.LIPixelFormat
- PIXELFORMAT_BAYERGB16 - Static variable in class loci.formats.in.LIPixelFormat
- PIXELFORMAT_BAYERGB8 - Static variable in class loci.formats.in.LIPixelFormat
- PIXELFORMAT_BAYERGR10 - Static variable in class loci.formats.in.LIPixelFormat
- PIXELFORMAT_BAYERGR12 - Static variable in class loci.formats.in.LIPixelFormat
- PIXELFORMAT_BAYERGR12P - Static variable in class loci.formats.in.LIPixelFormat
- PIXELFORMAT_BAYERGR12PMSB - Static variable in class loci.formats.in.LIPixelFormat
- PIXELFORMAT_BAYERGR16 - Static variable in class loci.formats.in.LIPixelFormat
- PIXELFORMAT_BAYERGR8 - Static variable in class loci.formats.in.LIPixelFormat
- PIXELFORMAT_BAYERRG10 - Static variable in class loci.formats.in.LIPixelFormat
- PIXELFORMAT_BAYERRG12 - Static variable in class loci.formats.in.LIPixelFormat
- PIXELFORMAT_BAYERRG12P - Static variable in class loci.formats.in.LIPixelFormat
- PIXELFORMAT_BAYERRG12PACKED - Static variable in class loci.formats.in.LIPixelFormat
- PIXELFORMAT_BAYERRG12PMSB - Static variable in class loci.formats.in.LIPixelFormat
- PIXELFORMAT_BAYERRG16 - Static variable in class loci.formats.in.LIPixelFormat
- PIXELFORMAT_BAYERRG8 - Static variable in class loci.formats.in.LIPixelFormat
- PIXELFORMAT_BGR8 - Static variable in class loci.formats.in.LIPixelFormat
- PIXELFORMAT_BGR8PACKED - Static variable in class loci.formats.in.LIPixelFormat
- PIXELFORMAT_KEY - Static variable in class loci.formats.in.LiFlimReader
- PIXELFORMAT_MONO10 - Static variable in class loci.formats.in.LIPixelFormat
- PIXELFORMAT_MONO10P - Static variable in class loci.formats.in.LIPixelFormat
- PIXELFORMAT_MONO10PMSB - Static variable in class loci.formats.in.LIPixelFormat
- PIXELFORMAT_MONO12 - Static variable in class loci.formats.in.LIPixelFormat
- PIXELFORMAT_MONO12P - Static variable in class loci.formats.in.LIPixelFormat
- PIXELFORMAT_MONO12PACKED - Static variable in class loci.formats.in.LIPixelFormat
- PIXELFORMAT_MONO12PMSB - Static variable in class loci.formats.in.LIPixelFormat
- PIXELFORMAT_MONO14 - Static variable in class loci.formats.in.LIPixelFormat
- PIXELFORMAT_MONO14P - Static variable in class loci.formats.in.LIPixelFormat
- PIXELFORMAT_MONO16 - Static variable in class loci.formats.in.LIPixelFormat
- PIXELFORMAT_MONO8 - Static variable in class loci.formats.in.LIPixelFormat
- PIXELFORMAT_RGB8 - Static variable in class loci.formats.in.LIPixelFormat
- PIXELFORMAT_RGB8PACKED - Static variable in class loci.formats.in.LIPixelFormat
- pixelFormatEqualsBitSize(Integer, String) - Static method in class loci.formats.in.LIPixelFormat
- pixelLengths - Variable in class loci.formats.in.SlidebookReader
- pixelOffset - Variable in class loci.formats.in.AIMReader
- pixelOffset - Variable in class loci.formats.in.AnalyzeReader
-
Offset to the pixel data in the .img file.
- pixelOffset - Variable in class loci.formats.in.FitsReader
- pixelOffset - Variable in class loci.formats.in.GatanReader
-
Offset to pixel data.
- pixelOffset - Variable in class loci.formats.in.HISReader
-
Offsets to pixel data for each series.
- pixelOffset - Variable in class loci.formats.in.JEOLReader
- pixelOffset - Variable in class loci.formats.in.KodakReader
- pixelOffset - Variable in class loci.formats.in.MolecularImagingReader
- pixelOffset - Variable in class loci.formats.in.NiftiReader
-
Offset to the pixel data in the .img file.
- pixelOffset - Variable in class loci.formats.in.QTReader
-
Offset to start of pixel data.
- pixelOffset - Variable in class loci.formats.in.RHKReader
- pixelOffset - Variable in class loci.formats.in.SIFReader
- pixelOffset - Variable in class loci.formats.in.TopometrixReader
- pixelOffset - Variable in class loci.formats.in.VolocityClippingReader
- pixelOffset - Variable in class loci.formats.out.ICSWriter
- pixelOffset - Variable in class loci.formats.out.V3DrawWriter
- pixelOffsets - Variable in class loci.formats.in.JPXReader
- pixelOffsets - Variable in class loci.formats.in.SlidebookReader
- pixelOffsets - Variable in class loci.formats.in.VarianFDFReader
- pixelOffsets - Variable in class loci.formats.in.VisitechReader
- pixels - Variable in class loci.formats.in.AFIReader
- pixels - Variable in class loci.formats.in.GIFReader
- pixels - Variable in class loci.formats.in.ImagicReader
- pixels - Variable in class loci.formats.in.LeicaSCNReader.Image
- pixels - Variable in class loci.formats.in.ZeissCZIReader
- pixels - Variable in class loci.formats.out.ICSWriter
- pixels - Variable in class loci.formats.out.V3DrawWriter
- Pixels(Attributes) - Constructor for class loci.formats.in.LeicaSCNReader.Pixels
- PIXELS_MARKER - Static variable in class loci.formats.in.VisitechReader
- PIXELS_OFFSET - Static variable in class loci.formats.in.ARFReader
- PIXELS_OFFSET - Static variable in class loci.formats.in.LIMReader
- PIXELS_STRING - Static variable in class loci.formats.in.KodakReader
- PIXELS_SUFFIXES - Static variable in class loci.formats.in.InCellReader
- PIXELS_TAG - Static variable in class loci.formats.in.ImaconReader
- pixelsFile - Variable in class loci.formats.in.FujiReader
- pixelsFile - Variable in class loci.formats.in.ImagicReader
- pixelsFile - Variable in class loci.formats.in.PDSReader
- PixelsFile() - Constructor for class loci.formats.in.PerkinElmerReader.PixelsFile
- pixelsFilename - Variable in class loci.formats.in.AnalyzeReader
- pixelsFilename - Variable in class loci.formats.in.NiftiReader
- pixelsFiles - Variable in class loci.formats.in.BrukerReader
- pixelsFiles - Variable in class loci.formats.in.TillVisionReader
- pixelsFiles - Variable in class loci.formats.in.TissueFAXSReader
- pixelsFiles - Variable in class loci.formats.in.VolocityReader.Stack
- pixelSize - Variable in class loci.formats.in.FV1000Reader
- pixelSize - Variable in class loci.formats.in.IPLabReader
- pixelSize - Variable in class loci.formats.in.MicromanagerReader.Position
- pixelSize - Variable in class loci.formats.in.ScanrReader
- pixelSize - Variable in class loci.formats.in.SVSCoreMetadata
- pixelSize - Variable in class loci.formats.in.TecanReader.Image
- pixelSize - Variable in class loci.formats.in.ZeissXRMReader
- pixelSize - Static variable in class org.libjpegturbo.turbojpeg.TJ
- pixelSizes - Variable in class loci.formats.in.GatanReader
-
List of pixel sizes.
- pixelSizes - Variable in class loci.formats.in.NRRDReader
- pixelSizeT - Variable in class loci.formats.in.FV1000Reader
- pixelSizeT - Variable in class loci.formats.in.ImprovisionTiffReader
- pixelSizeUnits - Variable in class loci.formats.in.GatanDM2Reader
- pixelSizeX - Variable in class loci.formats.dicom.DicomFileInfo
- pixelSizeX - Variable in class loci.formats.in.DicomReader
- pixelSizeX - Variable in class loci.formats.in.FV1000Reader
- pixelSizeX - Variable in class loci.formats.in.GatanDM2Reader
- pixelSizeX - Variable in class loci.formats.in.ImarisHDFReader
- pixelSizeX - Variable in class loci.formats.in.ImprovisionTiffReader
- pixelSizeX - Variable in class loci.formats.in.MetamorphHandler
- pixelSizeX - Variable in class loci.formats.in.ND2Handler
- pixelSizeX - Variable in class loci.formats.in.PerkinElmerReader
- pixelSizeX - Variable in class loci.formats.in.VarianFDFReader
- pixelSizeX - Variable in class loci.formats.in.ZeissLSMReader
- pixelSizeY - Variable in class loci.formats.dicom.DicomFileInfo
- pixelSizeY - Variable in class loci.formats.in.DicomReader
- pixelSizeY - Variable in class loci.formats.in.FV1000Reader
- pixelSizeY - Variable in class loci.formats.in.GatanDM2Reader
- pixelSizeY - Variable in class loci.formats.in.ImarisHDFReader
- pixelSizeY - Variable in class loci.formats.in.ImprovisionTiffReader
- pixelSizeY - Variable in class loci.formats.in.MetamorphHandler
- pixelSizeY - Variable in class loci.formats.in.ND2Handler
- pixelSizeY - Variable in class loci.formats.in.PerkinElmerReader
- pixelSizeY - Variable in class loci.formats.in.VarianFDFReader
- pixelSizeY - Variable in class loci.formats.in.ZeissLSMReader
- pixelSizeZ - Variable in class loci.formats.dicom.DicomFileInfo
- pixelSizeZ - Variable in class loci.formats.in.DicomReader
- pixelSizeZ - Variable in class loci.formats.in.FV1000Reader
- pixelSizeZ - Variable in class loci.formats.in.ImarisHDFReader
- pixelSizeZ - Variable in class loci.formats.in.ImprovisionTiffReader
- pixelSizeZ - Variable in class loci.formats.in.ND2Handler
- pixelSizeZ - Variable in class loci.formats.in.VarianFDFReader
- pixelSizeZ - Variable in class loci.formats.in.ZeissLSMReader
- pixelsOffset - Variable in class loci.formats.in.BioRadSCNReader
- pixelsOffset - Variable in class loci.formats.in.BurleighReader
- pixelsOffset - Variable in class loci.formats.in.InCell3000Reader
- pixelsOffset - Variable in class loci.formats.in.JPEG2000Reader
- pixelsOffset - Variable in class loci.formats.in.QuesantReader
- pixelsOffsets - Variable in class loci.formats.in.ImspectorReader
-
List of offsets to each block of pixel data.
- pixelsPerPlane - Variable in class loci.formats.in.AmiraReader.ASCII
- pixelsStream - Variable in class loci.formats.in.TillVisionReader
- pixelStack - Variable in class loci.formats.in.GIFReader
- pixelType - Variable in class loci.formats.CoreMetadata
-
Describes the number of bytes per pixel.
- pixelType - Variable in class loci.formats.in.AmiraReader.ASCII
- pixelType - Variable in class loci.formats.in.DCIMGReader
- pixelType - Variable in class loci.formats.in.ZeissCZIReader.DirectoryEntry
- pixelTypeFromBytes(int, boolean, boolean) - Static method in class loci.formats.FormatTools
-
Returns an appropriate pixel type given the number of bytes per pixel.
- pixelTypeFromString(String) - Static method in class loci.formats.FormatTools
-
Takes a string value and maps it to one of the pixel type enumerations.
- pixelTypeIndex - Variable in class loci.formats.in.ZeissCZIReader.SubBlock
- pixelTypes - Static variable in class loci.formats.FormatTools
-
Human readable pixel type.
- pixTime - Variable in class loci.formats.in.SDTInfo
- PLACEHOLDER - Enum constant in enum class loci.formats.codec.JPEG2000BoxType
- placeWindow(Window) - Static method in class loci.plugins.util.WindowTools
-
Places the given window at a nice location on screen, either centered below the ImageJ window if there is one, or else centered on screen.
- PLANAR_CONFIGURATION - Enum constant in enum class loci.formats.dicom.DicomAttribute
- PLANAR_CONFIGURATION - Static variable in class loci.formats.tiff.IFD
- plane - Variable in class loci.formats.in.CanonRawReader
- plane - Variable in class loci.formats.in.TecanReader.Image
- plane - Variable in class loci.formats.in.ZeissCZIReader.Coordinate
- Plane() - Constructor for class loci.formats.in.ColumbusReader.Plane
- Plane() - Constructor for class loci.formats.in.CV7000Reader.Plane
- Plane() - Constructor for class loci.formats.in.OperettaReader.Plane
- Plane() - Constructor for class loci.formats.in.ZeissTIFFReader.Plane
- Plane(String, ZeissTIFFHandler.TagSet) - Constructor for class loci.formats.in.ZeissTIFFHandler.Plane
-
Constructor
- PLANE - Enum constant in enum class loci.formats.in.BaseZeissReader.Context
- PLANE_ORIGIN_RWC - Static variable in class loci.formats.in.CellSensReader
- PLANE_POSITION_SLIDE_SEQUENCE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- PLANE_SCALE_RWC - Static variable in class loci.formats.in.CellSensReader
- PLANE_UNIT - Static variable in class loci.formats.in.CellSensReader
- planeCount - Variable in class loci.formats.in.JDCEReader.JDCEWell
- planeCount() - Method in class loci.formats.out.OMETiffWriter
- planeData - Variable in class loci.formats.in.CV7000Reader
- PlaneData() - Constructor for class loci.formats.in.FV1000Reader.PlaneData
- planeDeltaT - Variable in class loci.formats.in.FlexReader
- planeExposureTime - Variable in class loci.formats.in.FlexReader
- planeIndex - Variable in class loci.formats.dicom.DicomTile
- planeIndex - Variable in class loci.formats.in.ZeissCZIReader.SubBlock
- planeIndexes - Variable in class loci.plugins.util.BFVirtualStack
- PlaneInfo() - Constructor for class loci.formats.in.OpenlabReader.PlaneInfo
- planeMax - Variable in class loci.formats.MinMaxCalculator
-
Max values for each plane.
- PlaneMetadata() - Constructor for class loci.formats.in.JDCEReader.PlaneMetadata
- planeMin - Variable in class loci.formats.MinMaxCalculator
-
Min values for each plane.
- planeName - Variable in class loci.formats.in.OpenlabReader.PlaneInfo
- planeNames - Variable in class loci.formats.in.ZeissTIFFHandler
- planeOffset - Variable in class loci.formats.in.OpenlabReader.PlaneInfo
- planeOffset - Variable in class loci.formats.in.SlidebookReader
- planeOffset - Variable in class loci.formats.out.EPSWriter
- PlaneOffset() - Constructor for class loci.formats.out.DicomWriter.PlaneOffset
- planeOffsets - Variable in class loci.formats.in.OpenlabReader
- planeOffsets - Variable in class loci.formats.out.DicomWriter
- planePadding - Variable in class loci.formats.in.VolocityReader.Stack
- planePositionX - Variable in class loci.formats.in.FlexReader
- planePositionY - Variable in class loci.formats.in.FlexReader
- planePositionZ - Variable in class loci.formats.in.FlexReader
- planeReader - Variable in class loci.formats.in.AmiraReader
- planes - Variable in class loci.formats.in.ColumbusReader
- planes - Variable in class loci.formats.in.CV7000Reader.MeasurementDataHandler
- planes - Variable in class loci.formats.in.FV1000Reader
- planes - Variable in class loci.formats.in.OpenlabReader
- planes - Variable in class loci.formats.in.OperettaReader.OperettaHandler
- planes - Variable in class loci.formats.in.OperettaReader
- planes - Variable in class loci.formats.in.ZeissCZIReader
- planes - Variable in class loci.formats.in.ZeissTIFFHandler
- planes - Variable in class loci.formats.in.ZeissTIFFReader
-
Image planes
- PLANES - Enum constant in enum class loci.formats.dicom.DicomAttribute
- planeSize - Variable in class loci.formats.in.AmiraReader.HxRLE
- planeSize - Variable in class loci.formats.in.AmiraReader.HxZip
- planesPerBlock - Variable in class loci.formats.in.ImspectorReader
-
Number of planes in each block of pixel data.
- planesRead - Variable in class loci.formats.in.GIFReader
- planesWritten - Variable in class loci.formats.out.AVIWriter
- plate - Variable in class loci.formats.in.CellH5Reader.CellH5Coordinate
- plate - Variable in class loci.formats.in.MIASReader.AnalysisFile
- PLATE - Static variable in class loci.formats.in.CellH5Reader.CellH5Constants
- PLATE - Static variable in class loci.formats.ResourceNamer
- PLATE_ID - Enum constant in enum class loci.formats.dicom.DicomAttribute
- PLATE_TYPE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- plateAcqs - Variable in class loci.formats.in.FakeReader
- plateAcqStartTime - Variable in class loci.formats.in.FlexReader
- plateAcquisitionIndex - Variable in class loci.formats.internal.WellContainer
- plateBarcode - Variable in class loci.formats.in.FlexReader
- plateCols - Variable in class loci.formats.in.FakeReader
- plateCols - Variable in class loci.formats.in.OperettaReader.OperettaHandler
- plateColumns - Variable in class loci.formats.in.ColumbusReader.MeasurementHandler
- plateColumns - Variable in class loci.formats.in.CV7000Reader.WPIHandler
- plateColumns - Variable in class loci.formats.in.TecanReader
- plateColumns - Variable in class loci.formats.in.ZeissCZIReader
- plateCount - Variable in class loci.formats.in.FlexReader
- plateDescription - Variable in class loci.formats.in.BDReader
- plateDescription - Variable in class loci.formats.in.OperettaReader.OperettaHandler
- plateID - Variable in class loci.formats.in.CV7000Reader.WPIHandler
- plateID - Variable in class loci.formats.in.OperettaReader.OperettaHandler
- plateLogFile - Variable in class loci.formats.in.CellWorxReader
- plateMap - Variable in class loci.formats.in.InCellReader
- plateName - Variable in class loci.formats.in.BDReader
- plateName - Variable in class loci.formats.in.ColumbusReader.MeasurementHandler
- plateName - Variable in class loci.formats.in.FlexReader
- plateName - Variable in class loci.formats.in.OperettaReader.OperettaHandler
- plateName - Variable in class loci.formats.in.ScanrReader
- plateName - Variable in class loci.formats.in.TecanReader
- platePositions - Variable in class loci.formats.in.ZeissCZIReader
- plateRows - Variable in class loci.formats.in.ColumbusReader.MeasurementHandler
- plateRows - Variable in class loci.formats.in.CV7000Reader.WPIHandler
- plateRows - Variable in class loci.formats.in.FakeReader
- plateRows - Variable in class loci.formats.in.OperettaReader.OperettaHandler
- plateRows - Variable in class loci.formats.in.TecanReader
- plateRows - Variable in class loci.formats.in.ZeissCZIReader
- plates - Variable in class loci.formats.in.FakeReader
- plateType - Variable in class loci.formats.in.ColumbusReader.MeasurementHandler
- PLM - Enum constant in enum class loci.formats.codec.JPEG2000SegmentMarker
- PLT - Enum constant in enum class loci.formats.codec.JPEG2000SegmentMarker
- plugin - Variable in class loci.plugins.in.Importer
-
A handle to the plugin wrapper, for toggling the canceled and success flags.
- plugin - Variable in class loci.plugins.out.Exporter
- plugins - Static variable in class loci.plugins.shortcut.ShortcutPanel
-
Details for installed plugins.
- PLUS - Enum constant in enum class loci.formats.in.BaseZeissReader.PointStyle
- PN - Enum constant in enum class loci.formats.dicom.DicomVR
- PNG - Enum constant in enum class loci.formats.in.LeicaMicrosystemsMetadata.LMSFileReader.ImageFormat
- PNG - Static variable in class loci.formats.in.CellSensReader
- PNG_SIG - Static variable in class loci.formats.out.APNGWriter
- PNGBlock() - Constructor for class loci.formats.in.APNGReader.PNGBlock
- PNGInputStream(String) - Constructor for class loci.formats.in.APNGReader.PNGInputStream
- PNGInputStream(String, int) - Constructor for class loci.formats.in.APNGReader.PNGInputStream
- POC - Enum constant in enum class loci.formats.codec.JPEG2000SegmentMarker
- poi - Variable in class loci.formats.in.FV1000Reader
- poi - Variable in class loci.formats.in.IPWReader
-
Helper reader - parses embedded files from the OLE document.
- poi - Variable in class loci.formats.in.PCIReader
- poi - Variable in class loci.formats.in.ZeissXRMReader
- poi - Variable in class loci.formats.in.ZeissZVIReader
- POI_MAGIC_BYTES - Static variable in class loci.formats.services.POIServiceImpl
- POINT - Enum constant in enum class loci.formats.in.BaseZeissReader.FeatureType
- POINT - Static variable in class loci.formats.in.FV1000Reader
-
ROI types.
- pointCount - Variable in class loci.formats.in.BaseZeissReader.Shape
- points - Variable in enum class loci.formats.in.BaseZeissReader.FeatureType
- points - Variable in class loci.formats.in.BaseZeissReader.Shape
- points - Variable in class loci.formats.in.FakeReader
- points - Variable in class loci.formats.in.IMODReader
- points - Variable in class loci.formats.in.LiFlimReader.ROI
- POINTS - Enum constant in enum class loci.formats.in.BaseZeissReader.FeatureType
- pointsToString() - Method in class loci.formats.in.LiFlimReader.ROI
- pointStyle - Variable in class loci.formats.in.BaseZeissReader.Shape
- PointStyle(int) - Constructor for enum class loci.formats.in.BaseZeissReader.PointStyle
- POIService - Interface in loci.formats.services
-
Interface defining methods for reading Microsoft OLE2 documents using OME's fork of Apache POI.
- POIServiceImpl - Class in loci.formats.services
- POIServiceImpl() - Constructor for class loci.formats.services.POIServiceImpl
-
Default constructor.
- polarityF - Variable in class loci.formats.in.SDTInfo
- polarityL - Variable in class loci.formats.in.SDTInfo
-
2 = disabled line markers.
- polarityP - Variable in class loci.formats.in.SDTInfo
- POLARIZATION - Static variable in class loci.formats.FormatTools
-
Identifies the Polarization dimensional type, representing a dimension consisting of polarization states.
- POLYGON - Static variable in class loci.formats.in.FV1000Reader
- POLYGON - Static variable in class loci.formats.in.LeicaHandler.ROI
- POLYGON - Static variable in class loci.formats.in.LeicaMicrosystemsMetadata.ROI
- POLYGON - Static variable in class loci.formats.in.LIFReader.ROI
- polygons - Variable in class loci.formats.in.FakeReader
- POLYLINE - Static variable in class loci.formats.in.FV1000Reader
- POLYLINE_ARROW - Static variable in class loci.formats.in.ZeissLSMReader
- POLYLINE_CLOSED - Enum constant in enum class loci.formats.in.BaseZeissReader.FeatureType
- POLYLINE_OPEN - Enum constant in enum class loci.formats.in.BaseZeissReader.FeatureType
- polylines - Variable in class loci.formats.in.FakeReader
- populateCircles(NodeList, int, int) - Method in class loci.formats.in.ZeissCZIReader
- populateCore - Variable in class loci.formats.in.FlexReader.FlexHandler
- populateCoreMetadata() - Method in class loci.formats.in.PrairieReader
-
This step populates the
CoreMetadataby extracting relevant values from the parsedPrairieReader.metastructure. - populateCoreMetadata(int, int, int, int, int) - Method in class loci.formats.in.TextReader
-
Populates the
CoreMetadatavalues. - populateCoreMetadata(int, int, int, List<String>) - Method in class loci.formats.in.FlexReader
-
Populate core metadata using the given list of image names.
- populateExtendedMetadata() - Method in class loci.formats.in.NiftiReader
- populateGlobalMetaData() - Method in class loci.formats.in.SPEReader
-
This function is used to populate values not contained in Core Meta Data to the Global Meta Data
- populateImage(OMEXMLMetadata, int) - Method in class loci.formats.out.OMETiffWriter
- populateInstrument(MetadataStore) - Method in class loci.formats.in.FakeReader
- populateLines(NodeList, int, int) - Method in class loci.formats.in.ZeissCZIReader
- populateMaskPixels(int, int, int, MetadataStore) - Method in class loci.formats.in.MIASReader
-
Populate the MaskPixels.BinData attribute for the Mask identified by the given Image index, ROI index, and Shape index.
- populateMetadata() - Method in class loci.formats.in.CellWorxReader
- populateMetadata() - Method in class loci.formats.in.MicromanagerReader
- populateMetadata(MetadataStore, int, String, boolean, String, String, int, int, int, int, int, int) - Static method in class loci.formats.MetadataTools
-
Populates the given
MetadataStore, for the specified series, using the provided values. - populateMetadata(MetadataStore, int, String, CoreMetadata) - Static method in class loci.formats.MetadataTools
-
Populates the given
MetadataStore, for the specified series, using the values from the providedCoreMetadata. - populateMetadata(MetadataStore, String, int, String, boolean, String, String, int, int, int, int, int, int) - Static method in class loci.formats.MetadataTools
-
Populates the given
MetadataStore, for the specified series, using the provided values. - populateMetadataStore() - Method in class loci.formats.in.TillVisionReader
- populateMetadataStore(String[]) - Method in class loci.formats.in.MicromanagerReader
- populateMetadataStore(ND2Handler) - Method in class loci.formats.in.ND2Reader
- populateMetadataStore(ZeissLSMReader.SubBlock, MetadataStore, int) - Method in class loci.formats.in.ZeissLSMReader
- populateMetadataStore(MetadataStore) - Method in class loci.formats.in.FlexReader
- populateMetadataStore(MetadataStore, String) - Method in class loci.formats.in.FV1000Reader
- populateMetadataStoreImageJ(MetadataStore) - Method in class loci.formats.in.TiffReader
-
Checks the original metadata table for ImageJ-specific information to propagate into the metadata store.
- populateObjective(MetadataStore, int) - Method in class loci.formats.in.DeltavisionReader
-
Populate an Objective based upon the lens ID.
- populateObjective(MetadataStore, int) - Method in class loci.formats.in.RCPNLReader
- populateOMEMetadata() - Method in class loci.formats.in.PrairieReader
-
This step populates the OME
MetadataStoreby extracting relevant values from the parsedPrairieReader.metastructure. - populateOMEMetadata(IniTable, MetadataStore) - Method in class loci.formats.in.HitachiReader
- populateOriginalMetadata() - Method in class loci.formats.in.PrairieReader
-
This steps populates the original metadata table (the tables returned by
FormatReader.getGlobalMetadata()andFormatReader.getSeriesMetadata()). - populateOriginalMetadata(OMEXMLMetadata, String, String) - Method in interface loci.formats.services.OMEXMLService
-
Adds the specified key/value pair as a new OriginalMetadata node to the given OME-XML metadata object.
- populateOriginalMetadata(OMEXMLMetadata, String, String) - Method in class loci.formats.services.OMEXMLServiceImpl
- populateOriginalMetadata(OMEXMLMetadata, Hashtable<String, Object>) - Method in interface loci.formats.services.OMEXMLService
-
Adds the key/value pairs in the specified Hashtable as new OriginalMetadata annotations in the given OME-XML metadata object.
- populateOriginalMetadata(OMEXMLMetadata, Hashtable<String, Object>) - Method in class loci.formats.services.OMEXMLServiceImpl
- populateOriginalMetadata(Element, Deque<String>) - Method in class loci.formats.in.LeicaMicrosystemsMetadata.LMSMetadataExtractor
-
Creates key value pairs from attributes of the root's child nodes (tag | attribute name : attribute value) and adds them to reader's
CoreMetadata - populateOriginalMetadata(Element, Deque<String>) - Method in class loci.formats.in.ZeissCZIReader
- populateOriginalMetadata(Element, Deque<String>, int[], int) - Method in class loci.formats.in.LIFReader
- populatePixels(MetadataStore, IFormatReader) - Static method in class loci.formats.MetadataTools
-
Populates the Pixels element of the given metadata store, using core metadata from the given reader.
- populatePixels(MetadataStore, IFormatReader, boolean) - Static method in class loci.formats.MetadataTools
-
Populates the Pixels element of the given metadata store, using core metadata from the given reader.
- populatePixels(MetadataStore, IFormatReader, boolean, boolean) - Static method in class loci.formats.MetadataTools
-
Populates the Pixels element of the given metadata store, using core metadata from the given reader.
- populatePixelsOnly(MetadataStore, int, boolean, String, String, int, int, int, int, int, int) - Static method in class loci.formats.MetadataTools
- populatePixelsOnly(MetadataStore, IFormatReader) - Static method in class loci.formats.MetadataTools
- populatePixelType(int) - Method in class loci.formats.in.NiftiReader
- populatePolylines(NodeList, int, int, boolean) - Method in class loci.formats.in.ZeissCZIReader
- populateRectangles(NodeList, int, int) - Method in class loci.formats.in.ZeissCZIReader
- populateROI(List<String>, String[], int, int, int, int, MetadataStore) - Method in class loci.formats.in.MIASReader
- populateRoiMetaData(MetadataStore) - Method in class loci.formats.in.SPEReader
-
Reads and populates ROI Meta Data values.
- populateROIs(MetadataStore) - Method in class loci.formats.in.ND2Handler
- populateSPW(MetadataStore, int, int, int, int, int, int, boolean) - Method in class loci.formats.in.FakeReader
- populateTiffData(OMEXMLMetadata, int[], int, int, int) - Method in class loci.formats.out.OMETiffWriter
- populateXY - Variable in class loci.formats.in.ND2Handler
- pos - Variable in class loci.formats.in.AVIReader
- pos(int) - Method in class loci.formats.cache.CacheStrategy
-
Shortcut for converting rasterized position to N-D position.
- pos(int, int[]) - Method in class loci.formats.cache.CacheStrategy
-
Shortcut for converting rasterized position to N-D position, using the given array instead of allocating a new one.
- position - Variable in class loci.formats.in.MicromanagerReader.Index
- position - Variable in class loci.formats.in.ND2Reader.ChunkMapEntry
- position - Variable in class loci.formats.in.OBFReader.Stack
- Position() - Constructor for class loci.formats.in.MicromanagerReader.Position
- POSITION_CHANGED - Static variable in class loci.formats.cache.CacheEvent
-
Event type indicating an updated current dimensional position.
- positionCount - Variable in class loci.formats.in.ND2Reader
- POSITIONER_MOTION - Enum constant in enum class loci.formats.dicom.DicomAttribute
- POSITIONER_PRIMARY_ANGLE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- POSITIONER_PRIMARY_ANGLE_INCREMENT - Enum constant in enum class loci.formats.dicom.DicomAttribute
- POSITIONER_SECONDARY_ANGLE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- POSITIONER_SECONDARY_ANGLE_INCREMENT - Enum constant in enum class loci.formats.dicom.DicomAttribute
- POSITIONER_TYPE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- positionInT - Variable in class loci.formats.in.DeltavisionReader
- positions - Variable in class loci.formats.cache.CacheStrategy
-
The list of dimensional positions to consider caching, in order of preference based on strategy, axis priority and planar ordering.
- positions - Variable in class loci.formats.in.MicromanagerReader.Position
- positions - Variable in class loci.formats.in.MicromanagerReader
- positions - Variable in class loci.formats.in.ZeissCZIReader
- POSITIONS - Static variable in class loci.formats.in.ZeissXRMReader
- positionsMatch(int, int) - Method in class loci.formats.in.PrairieReader
-
Verifies that stage coordinates match for all (P, Z) across time.
- positionsX - Variable in class loci.formats.in.ZeissCZIReader
- positionsY - Variable in class loci.formats.in.ZeissCZIReader
- positionsZ - Variable in class loci.formats.in.ZeissCZIReader
- positionToRaster(int[], int[]) - Static method in class loci.formats.FormatTools
-
Computes a unique 1-D index corresponding to the given multidimensional position.
- positionX - Variable in class loci.formats.dicom.DicomFileInfo
- positionX - Variable in class loci.formats.in.ColumbusReader.Plane
- positionX - Variable in class loci.formats.in.DicomReader
- positionX - Variable in class loci.formats.in.FV1000Reader.PlaneData
- positionX - Variable in class loci.formats.in.JDCEReader.PlaneMetadata
- positionX - Variable in class loci.formats.in.MetamorphHandler
- positionX - Variable in class loci.formats.in.OperettaReader.Plane
- positionY - Variable in class loci.formats.dicom.DicomFileInfo
- positionY - Variable in class loci.formats.in.ColumbusReader.Plane
- positionY - Variable in class loci.formats.in.DicomReader
- positionY - Variable in class loci.formats.in.FV1000Reader.PlaneData
- positionY - Variable in class loci.formats.in.JDCEReader.PlaneMetadata
- positionY - Variable in class loci.formats.in.MetamorphHandler
- positionY - Variable in class loci.formats.in.OperettaReader.Plane
- positionZ - Variable in class loci.formats.dicom.DicomFileInfo
- positionZ - Variable in class loci.formats.in.ColumbusReader.Plane
- positionZ - Variable in class loci.formats.in.DicomReader
- positionZ - Variable in class loci.formats.in.FV1000Reader.PlaneData
- positionZ - Variable in class loci.formats.in.JDCEReader.PlaneMetadata
- positionZ - Variable in class loci.formats.in.OperettaReader.Plane
- posMap - Variable in class loci.formats.in.JDCEReader.JDCEWell
- posNames - Variable in class loci.formats.in.ND2Handler
- possibleValues - Variable in class loci.plugins.prefs.StringOption
-
List of possible values.
- post - Variable in class loci.formats.NumberFilter
-
String appearing after the numerical block.
- POST_PROCESS - Static variable in class loci.formats.in.CV7000Reader
- POSTPROCESSING_FUNCTION - Enum constant in enum class loci.formats.dicom.DicomAttribute
- posX - Variable in class loci.formats.in.GatanReader
- posX - Variable in class loci.formats.in.InCellReader
- posX - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataTempBuffer
- posX - Variable in class loci.formats.in.LIFReader
- posX - Variable in class loci.formats.in.ND2Handler
- posX - Variable in class loci.formats.in.ND2Reader
- posY - Variable in class loci.formats.in.GatanReader
- posY - Variable in class loci.formats.in.InCellReader
- posY - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataTempBuffer
- posY - Variable in class loci.formats.in.LIFReader
- posY - Variable in class loci.formats.in.ND2Handler
- posY - Variable in class loci.formats.in.ND2Reader
- posZ - Variable in class loci.formats.in.GatanReader
- posZ - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataTempBuffer
- posZ - Variable in class loci.formats.in.LIFReader
- posZ - Variable in class loci.formats.in.ND2Handler
- posZ - Variable in class loci.formats.in.ND2Reader
- PovrayReader - Class in loci.formats.in
-
PovrayReader is the file format reader for POV-Ray .df3 files.
- PovrayReader() - Constructor for class loci.formats.in.PovrayReader
-
Constructs a new POV-Ray reader.
- power - Variable in class loci.formats.in.CV7000Reader.LightSource
- power - Variable in class loci.formats.in.ND2Handler
- power - Variable in class loci.formats.in.OIRReader.Laser
- power - Variable in class loci.formats.in.ZeissLSMReader.Laser
- PPM - Enum constant in enum class loci.formats.codec.JPEG2000SegmentMarker
- PPT - Enum constant in enum class loci.formats.codec.JPEG2000SegmentMarker
- PQBinReader - Class in loci.formats.in
-
PQBinReader is the file format reader for PicoQuant .bin files.
- PQBinReader() - Constructor for class loci.formats.in.PQBinReader
-
Constructs a new PQBin reader.
- PRAIRIE_SUFFIXES - Static variable in class loci.formats.in.PrairieReader
- PRAIRIE_TAG_1 - Static variable in class loci.formats.in.PrairieReader
- PRAIRIE_TAG_2 - Static variable in class loci.formats.in.PrairieReader
- PRAIRIE_TAG_3 - Static variable in class loci.formats.in.PrairieReader
- PrairieMetadata - Class in loci.formats.in
-
Metadata structure for Prairie Technologies' TIFF-based format.
- PrairieMetadata(Document, Document, Document) - Constructor for class loci.formats.in.PrairieMetadata
-
Creates a new Prairie metadata by parsing the given XML, CFG and/or ENV documents.
- PrairieMetadata.Frame - Class in loci.formats.in
-
A Prairie
<Frame>, beneath a<Sequence>. - PrairieMetadata.PFile - Class in loci.formats.in
-
A Prairie
<File>beneath a<Frame>. - PrairieMetadata.Sequence - Class in loci.formats.in
-
A Prairie
<Sequence>. - PrairieMetadata.Value - Interface in loci.formats.in
-
A value in a Prairie metadata dictionary.
- PrairieMetadata.ValueItem - Class in loci.formats.in
-
A leaf value with an actual
PrairieMetadata.ValueItem.value()as well as an optionalPrairieMetadata.ValueItem.description(). - PrairieMetadata.ValueTable - Class in loci.formats.in
-
A table of values.
- PrairieReader - Class in loci.formats.in
-
PrairieReader is the file format reader for Prairie Technologies' TIFF variant.
- PrairieReader() - Constructor for class loci.formats.in.PrairieReader
-
Constructs a new Prairie TIFF reader.
- pre - Variable in class loci.formats.NumberFilter
-
String appearing before the numerical block.
- PRE_AMP_SETTING - Static variable in class loci.formats.in.FluoviewReader
- PREAMP_GAIN_VALUE - Static variable in class loci.formats.in.CellSensReader
- PREDICTED_CLASS_LABELS - Static variable in class loci.formats.in.BDVReader.H5Constants
- PREDICTED_CLASS_LABELS - Static variable in class loci.formats.in.CellH5Reader.CellH5Constants
- PREDICTOR - Static variable in class loci.formats.tiff.IFD
- PREF_CELLSENS_FAIL - Static variable in class loci.plugins.util.LociPrefs
- PREF_CZI_ATTACHMENT - Static variable in class loci.plugins.util.LociPrefs
- PREF_CZI_AUTOSTITCH - Static variable in class loci.plugins.util.LociPrefs
- PREF_LEICA_LIF_PHYSICAL_SIZE - Static variable in class loci.plugins.util.LociPrefs
- PREF_ND2_CHUNKMAP - Static variable in class loci.plugins.util.LociPrefs
- PREF_READER_ENABLED - Static variable in class loci.plugins.util.LociPrefs
- PREF_READER_WINDOWLESS - Static variable in class loci.plugins.util.LociPrefs
- PREF_SDT_INTENSITY - Static variable in class loci.plugins.util.LociPrefs
- PREF_SLICE_LABEL_BASE_INDEX - Static variable in class loci.plugins.util.LociPrefs
- PREF_SLICE_LABEL_PATTERN - Static variable in class loci.plugins.util.LociPrefs
- PREF_TIFF_IMAGEIO - Static variable in class loci.plugins.util.LociPrefs
- PREFERRED_PLAYBACK_SEQUENCING - Enum constant in enum class loci.formats.dicom.DicomAttribute
- prefix - Variable in class loci.formats.in.GIFReader
- prefix - Variable in class loci.formats.in.ND2Handler
- prefix - Variable in class loci.formats.in.ZeissTIFFReader.TIFFInfo
- PREFIX - Static variable in class loci.formats.in.TCSReader
- PREFIX_PATH - Static variable in class loci.formats.in.CellH5Reader.CellH5Constants
- PREGNANCY_STATUS - Enum constant in enum class loci.formats.dicom.DicomAttribute
- preLoad - Variable in class loci.formats.in.SDTReader
-
Whether to pre-load all lifetime bins for faster loading.
- prepareGZipStream(int) - Method in class loci.formats.in.LiFlimReader
- prepareToWriteImage(int, byte[], IFD, int, int, int, int) - Method in class loci.formats.out.TiffWriter
-
Performs the preparation for work prior to the usage of the TIFF saver.
- prepareUINT12Stream(int) - Method in class loci.formats.in.LiFlimReader
-
Similar to Gzip, make a DataInputstream for UINT12 data
- prepend(List<Class<? extends T>>) - Method in class loci.formats.ClassList
-
Prepends a list of classes which must be assignable to the base class
- prepend(ClassList<T>) - Method in class loci.formats.ClassList
-
Prepends a class list which must be assignable to the base class
- preprocess(RandomAccessInputStream) - Method in class loci.formats.codec.JPEGTileDecoder
-
Pre-process the stream to make sure that the image width and height are non-zero.
- PRESCANS - Static variable in class loci.formats.in.FluoviewReader
- PRESENT - Static variable in class loci.plugins.config.LibraryEntry
-
HTML markup for installed library.
- PRESENTATION_INTENT_TYPE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- PRESENTATION_LUT_SHAPE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- preserveCreator() - Method in class loci.formats.out.OMETiffWriter
-
Get the value of the
OMETiffWriter.CREATOR_KEYoption. - preserveCreator() - Method in class loci.formats.out.OMEXMLWriter
-
Get the value of the
OMEXMLWriter.CREATOR_KEYoption. - prestitched - Variable in class loci.formats.in.ZeissCZIReader
- prevBuf - Variable in class loci.formats.in.ZeissLSMReader
- prevChannel - Variable in class loci.formats.in.ZeissLSMReader
- prevElement - Variable in class loci.formats.in.ND2Handler
- PREVIEWNAME_PREFIXES - Static variable in class loci.formats.in.FV1000Reader
- previewNames - Variable in class loci.formats.in.FV1000Reader
- PreviewPane - Class in loci.formats.gui
-
PreviewPane is a panel for use as a JFileChooser accessory, displaying a thumbnail for the selected image, loaded in a separate thread.
- PreviewPane(JFileChooser) - Constructor for class loci.formats.gui.PreviewPane
-
Constructs a preview pane for the given file chooser.
- prevImage - Variable in class loci.formats.in.ICSReader
- previousChannel - Variable in class loci.formats.in.ZeissCZIReader
- previousImage - Variable in class loci.formats.codec.CodecOptions
-
Pixels for preceding image (READ/WRITE).
- previousTag - Variable in class loci.formats.in.CellSensReader
- prevPixels - Variable in class loci.formats.in.QTReader
-
Pixel data for the previous image plane.
- prevPlane - Variable in class loci.formats.in.QTReader
-
Previous plane number.
- prevPlane - Variable in class loci.formats.in.ZeissLSMReader
- prevRegion - Variable in class loci.formats.in.ZeissLSMReader
- prevRuntype - Variable in class loci.formats.in.ND2Handler
- PRIMARY_ANATOMIC_STRUCTURE_MODIFIER - Enum constant in enum class loci.formats.dicom.DicomAttribute
- PRIMARY_ANATOMIC_STRUCTURE_SEQUENCE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- PRIMARY_CHROMATICITIES - Static variable in class loci.formats.tiff.IFD
- primaryFileGUID - Variable in class loci.formats.in.ZeissCZIReader.FileHeader
- print(int, long, String) - Method in class loci.formats.in.QTReader
-
Debugging method; prints information on an atom.
- printArray(String, int[]) - Static method in class loci.formats.tools.CacheConsole
-
Helper utility for outputing contents of an int array, used by main.
- printIFD() - Method in class loci.formats.tiff.IFD
-
Prints the contents of this IFD.
- printOrder(String, Cache) - Static method in class loci.formats.tools.CacheConsole
-
Helper utility for outputing cache strategy's order, used by main.
- printReferences() - Method in class loci.formats.in.LeicaMicrosystemsMetadata.XlefDocument
- printSizes(Component) - Static method in class loci.plugins.config.SpringUtilities
-
A debugging utility that prints to stdout the component's minimum, preferred, and maximum sizes.
- printSource(String, Cache) - Static method in class loci.formats.tools.CacheConsole
-
Helper utility for outputing cache's associated source, used by main.
- printStrategy(String, Cache) - Static method in class loci.formats.tools.CacheConsole
-
Helper utility for outputing cache's associated strategy, used by main.
- printXlifInfo() - Method in class loci.formats.in.LeicaMicrosystemsMetadata.XlifDocument
- priorities - Variable in class loci.formats.cache.CacheStrategy
-
Priority for caching each axis.
- PRIORITIES - Static variable in class loci.formats.gui.CacheComponent
- PRIORITIES_CHANGED - Static variable in class loci.formats.cache.CacheEvent
-
Event type indicating new axis priorities.
- priority - Variable in class loci.formats.gui.CacheComponent
-
Combo boxes for choosing axis priority.
- PRIORITY_VALUES - Static variable in class loci.formats.gui.CacheComponent
- priorityIndex(int) - Method in class loci.formats.gui.CacheComponent
-
Converts enumerated priority value to priority chooser index.
- priorityValue(int) - Method in class loci.formats.gui.CacheComponent
-
Converts priority chooser index to enumerated priority value.
- PRIVATE_RECORD_UID - Enum constant in enum class loci.formats.dicom.DicomAttribute
- privateContentHighWords - Variable in class loci.formats.in.DicomReader
- probeLabel - Variable in class loci.formats.gui.ImageViewer
- proc - Variable in class loci.plugins.util.RecordedImageProcessor
- PROCEDURE_CODE_SEQUENCE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- process - Variable in class loci.plugins.in.Calibrator
- process - Variable in class loci.plugins.in.Colorizer
- process - Variable in class loci.plugins.in.DisplayHandler
- process - Variable in class loci.plugins.in.ImagePlusReader
-
Import preparation process managing Bio-Formats readers and other state.
- process - Variable in class loci.plugins.in.ImporterDialog
- process - Variable in class loci.plugins.in.ImporterPrompter
- processBuffer(int) - Method in class loci.formats.in.SPCReader
- processElement(String) - Method in class loci.formats.in.FEITiffReader.FEIHandler
- PROCESSING_FUNCTION - Enum constant in enum class loci.formats.dicom.DicomAttribute
- processKey(String, String) - Method in class loci.formats.in.MicroCTReader
-
Takes a key/value pair from disparate metadata files, and attempts to stores it in the original metadata table and/or MetadataStore as appropriate.
- processParentNode(Node, String) - Method in class loci.formats.in.VectraReader
- profileXML - Variable in class loci.formats.in.VectraReader
- progress - Variable in class loci.formats.gui.DataConverter
- progress(boolean, int, int) - Static method in class loci.plugins.BF
- PROJECTION - Static variable in class loci.formats.in.ZeissXRMReader
- PROJECTION_EPONYMOUS_NAME_CODE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- PROJECTION_PREFIX - Static variable in class loci.formats.in.KLBReader
- PROJECTION_SUFFIX - Static variable in class loci.formats.in.KLBReader
- promptColors() - Method in class loci.plugins.in.ImporterPrompter
-
Prompts for color details, if necessary.
- promptCrop() - Method in class loci.plugins.in.ImporterPrompter
-
Prompts for cropping details, if necessary.
- promptFilePattern() - Method in class loci.plugins.in.ImporterPrompter
-
Prompts for the file pattern, if necessary.
- promptId() - Method in class loci.plugins.in.ImporterPrompter
- promptLocation() - Method in class loci.plugins.in.ImporterPrompter
- promptMain() - Method in class loci.plugins.in.ImporterPrompter
- promptMemory() - Method in class loci.plugins.in.ImporterPrompter
-
Prompts for confirmation of memory usage, if necessary.
- promptRange() - Method in class loci.plugins.in.ImporterPrompter
-
Prompts for the range of planes to import, if necessary.
- promptSeries() - Method in class loci.plugins.in.ImporterPrompter
-
Prompts for which series to import, if necessary.
- promptSwap() - Method in class loci.plugins.in.ImporterPrompter
-
Prompts for dimension swapping parameters, if necessary.
- promptUpgrade() - Method in class loci.plugins.in.ImporterPrompter
- PROP_LUT - Static variable in class loci.plugins.in.ImagePlusReader
-
Special property prefix for storing planar LUTs.
- PROP_SERIES - Static variable in class loci.plugins.in.ImagePlusReader
-
Special property for storing series number associated with the image.
- PROPERTY_FILE - Static variable in class loci.formats.FormatTools
-
Deprecated.The property file is no longer used.
- PROPERTY_SET_VOLUME - Static variable in class loci.formats.in.CellSensReader
- propertyChange(PropertyChangeEvent) - Method in class loci.formats.gui.PreviewPane
-
Property change event, to listen for when a new file is selected, or the file chooser closes.
- PROPRIETARY_DEFLATE - Enum constant in enum class loci.formats.tiff.TiffCompression
- props - Variable in class loci.formats.in.DynamicMetadataOptions
- PROTOCOL_NAME - Enum constant in enum class loci.formats.dicom.DicomAttribute
- PSD_MAGIC_STRING - Static variable in class loci.formats.in.PSDReader
- PSDReader - Class in loci.formats.in
-
PSDReader is the file format reader for Photoshop PSD files.
- PSDReader() - Constructor for class loci.formats.in.PSDReader
-
Constructs a new PSD reader.
- ptyEnd - Variable in class loci.formats.in.FV1000Reader
- ptyPattern - Variable in class loci.formats.in.FV1000Reader
- ptyStart - Variable in class loci.formats.in.FV1000Reader
- PULSAR_TYPE - Enum constant in enum class loci.formats.in.SPEReader.SpeHeaderEntry
- PULSE_AMP_FAST - Enum constant in enum class loci.formats.in.SPEReader.SpeHeaderEntry
- PULSE_AMP_SLOW - Enum constant in enum class loci.formats.in.SPEReader.SpeHeaderEntry
- PULSE_BRACKET_TYPE - Enum constant in enum class loci.formats.in.SPEReader.SpeHeaderEntry
- PULSE_BRACKET_USED - Enum constant in enum class loci.formats.in.SPEReader.SpeHeaderEntry
- PULSE_BURST_COUNT - Enum constant in enum class loci.formats.in.SPEReader.SpeHeaderEntry
- PULSE_BURST_PERIOD - Enum constant in enum class loci.formats.in.SPEReader.SpeHeaderEntry
- PULSE_BURST_USED - Enum constant in enum class loci.formats.in.SPEReader.SpeHeaderEntry
- PULSE_END_DELAY - Enum constant in enum class loci.formats.in.SPEReader.SpeHeaderEntry
- PULSE_END_WIDTH - Enum constant in enum class loci.formats.in.SPEReader.SpeHeaderEntry
- PULSE_FILENAME - Enum constant in enum class loci.formats.in.SPEReader.SpeHeaderEntry
- PULSE_INC_MODE - Enum constant in enum class loci.formats.in.SPEReader.SpeHeaderEntry
- PULSE_REP_DELAY - Enum constant in enum class loci.formats.in.SPEReader.SpeHeaderEntry
- PULSE_REP_EXP - Enum constant in enum class loci.formats.in.SPEReader.SpeHeaderEntry
- PULSE_REP_WIDTH - Enum constant in enum class loci.formats.in.SPEReader.SpeHeaderEntry
- PULSE_REPETITION_FREQUENCY - Enum constant in enum class loci.formats.dicom.DicomAttribute
- PULSE_START_DELAY - Enum constant in enum class loci.formats.in.SPEReader.SpeHeaderEntry
- PULSE_START_WIDTH - Enum constant in enum class loci.formats.in.SPEReader.SpeHeaderEntry
- PULSE_TIMECONST_FAST - Enum constant in enum class loci.formats.in.SPEReader.SpeHeaderEntry
- PULSE_TIMECONST_SLOW - Enum constant in enum class loci.formats.in.SPEReader.SpeHeaderEntry
- PULSER_CHIP_ACCUMS - Enum constant in enum class loci.formats.in.SPEReader.SpeHeaderEntry
- PULSER_MODE - Enum constant in enum class loci.formats.in.SPEReader.SpeHeaderEntry
- put(String, boolean) - Method in class loci.formats.in.BaseTiffReader
- put(String, byte) - Method in class loci.formats.in.BaseTiffReader
- put(String, char) - Method in class loci.formats.in.BaseTiffReader
- put(String, double) - Method in class loci.formats.in.BaseTiffReader
- put(String, float) - Method in class loci.formats.in.BaseTiffReader
- put(String, int) - Method in class loci.formats.in.BaseTiffReader
- put(String, long) - Method in class loci.formats.in.BaseTiffReader
- put(String, short) - Method in class loci.formats.in.BaseTiffReader
- put(String, Object) - Method in class loci.formats.in.BaseTiffReader
- put(String, IFD, int) - Method in class loci.formats.in.BaseTiffReader
- putColumn(int, int, int[], int) - Method in class loci.plugins.util.RecordedImageProcessor
- putDouble(String, IFD, int) - Method in class loci.formats.in.BaseTiffReader
- putIFDValue(int, int) - Method in class loci.formats.tiff.IFD
-
Adds a directory entry of type SHORT to this IFD.
- putIFDValue(int, long) - Method in class loci.formats.tiff.IFD
-
Adds a directory entry of type LONG to this IFD.
- putIFDValue(int, short) - Method in class loci.formats.tiff.IFD
-
Adds a directory entry of type BYTE to this IFD.
- putIFDValue(int, Object) - Method in class loci.formats.tiff.IFD
-
Adds a directory entry to this IFD.
- putInt(String, IFD, int) - Method in class loci.formats.in.BaseTiffReader
- putPixel(int, int, int) - Method in class loci.plugins.util.RecordedImageProcessor
- putPixel(int, int, int[]) - Method in class loci.plugins.util.RecordedImageProcessor
- putPixelValue(int, int, double) - Method in class loci.plugins.util.RecordedImageProcessor
- putRow(int, int, int[], int) - Method in class loci.plugins.util.RecordedImageProcessor
- putString(String, IFD, int) - Method in class loci.formats.in.BaseTiffReader
- PVC_REJECTION - Enum constant in enum class loci.formats.dicom.DicomAttribute
- Pyramid() - Constructor for class loci.formats.in.CellSensReader.Pyramid
- pyramidDepth - Variable in class loci.formats.in.VectraReader
- pyramidHeight - Variable in class loci.formats.in.NDPIReader
- PyramidOMETiffWriter - Class in loci.formats.out
-
PyramidOMETiffWriter is the file format writer for pyramid OME-TIFF files.
- PyramidOMETiffWriter() - Constructor for class loci.formats.out.PyramidOMETiffWriter
- pyramids - Variable in class loci.formats.in.CellSensReader
- PyramidTiffReader - Class in loci.formats.in
-
PyramidTiffReader is the file format reader for pyramid TIFFs.
- PyramidTiffReader() - Constructor for class loci.formats.in.PyramidTiffReader
-
Constructs a new pyramid TIFF reader.
- pyramidType - Variable in class loci.formats.in.ZeissCZIReader.DirectoryEntry
Q
- QCC - Enum constant in enum class loci.formats.codec.JPEG2000SegmentMarker
- QCD - Enum constant in enum class loci.formats.codec.JPEG2000SegmentMarker
- qName - Variable in class loci.formats.in.ImaconReader.ImaconHandler
- qName - Variable in class loci.formats.in.ScanrReader.ScanrHandler
- QQ - Enum constant in enum class loci.formats.dicom.DicomVR
- QTReader - Class in loci.formats.in
-
QTReader is the file format reader for QuickTime movie files.
- QTReader() - Constructor for class loci.formats.in.QTReader
-
Constructs a new QuickTime reader.
- QTRLECodec - Class in loci.formats.codec
-
Methods for compressing and decompressing data using QuickTime RLE.
- QTRLECodec() - Constructor for class loci.formats.codec.QTRLECodec
- QTWriter - Class in loci.formats.out
-
QTWriter is the file format writer for uncompressed QuickTime movie files.
- QTWriter() - Constructor for class loci.formats.out.QTWriter
- quality - Variable in class loci.formats.codec.CodecOptions
-
Compression quality level as it would be provided to:
ImageWriteParam.compressionQuality(WRITE). - quality - Variable in class loci.formats.out.QTWriter
-
The quality to use.
- QUALITY - Static variable in class loci.formats.in.NikonReader
- QUALITY_CONTROL_IMAGE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- QUALITY_HIGH - Static variable in class loci.formats.out.QTWriter
-
Value indicating High quality.
- QUALITY_LOW - Static variable in class loci.formats.out.QTWriter
-
Value indicating Low quality.
- QUALITY_MAXIMUM - Static variable in class loci.formats.out.QTWriter
-
Value indicating Maximum quality.
- QUALITY_NORMAL - Static variable in class loci.formats.out.QTWriter
-
Value indicating Normal quality.
- QUERY_LEVEL - Enum constant in enum class loci.formats.dicom.DicomAttribute
- QuesantReader - Class in loci.formats.in
-
QuesantReader is the file format reader for Quesant .afm files.
- QuesantReader() - Constructor for class loci.formats.in.QuesantReader
-
Constructs a new Quesant reader.
- quit - Variable in class loci.formats.cache.CacheUpdater
- quit() - Method in class loci.formats.cache.CacheUpdater
R
- r - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.LMSMetadataExtractor
- r - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataStoreInitializer
- r - Variable in class loci.formats.in.LeicaSCNReader.Dimension
- r - Variable in class loci.formats.in.TiffJAIReader
-
Reflection tool for JAI calls.
- r - Variable in class loci.plugins.macro.LociFunctions
- r - Variable in class loci.plugins.util.VirtualImagePlus
- R_WAVE_POINTER - Enum constant in enum class loci.formats.dicom.DicomAttribute
- R_WAVE_TIME_VECTOR - Enum constant in enum class loci.formats.dicom.DicomAttribute
- RADIAL_POSITION - Enum constant in enum class loci.formats.dicom.DicomAttribute
- RADIATION_MODE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- RADIATION_SETTING - Enum constant in enum class loci.formats.dicom.DicomAttribute
- RADIONUCLIDE_HALF_LIFE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- RADIONUCLIDE_POSITRON_FRACTION - Enum constant in enum class loci.formats.dicom.DicomAttribute
- RADIONUCLIDE_TOTAL_DOSE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- RADIOPHARMACEUTICAL - Enum constant in enum class loci.formats.dicom.DicomAttribute
- RADIOPHARMACEUTICAL_ROUTE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- RADIOPHARMACEUTICAL_SPECIFIC_ACTIVITY - Enum constant in enum class loci.formats.dicom.DicomAttribute
- RADIOPHARMACEUTICAL_START_TIME - Enum constant in enum class loci.formats.dicom.DicomAttribute
- RADIOPHARMACEUTICAL_STOP_TIME - Enum constant in enum class loci.formats.dicom.DicomAttribute
- RADIOPHARMACEUTICAL_VOLUME - Enum constant in enum class loci.formats.dicom.DicomAttribute
- RADIUS_OF_CIRCULAR_COLLIMATOR - Enum constant in enum class loci.formats.dicom.DicomAttribute
- RADIUS_OF_CIRCULAR_SHUTTER - Enum constant in enum class loci.formats.dicom.DicomAttribute
- raisedException - Static variable in class loci.formats.ImageReader
- RandomAccessDeser() - Constructor for class loci.formats.Memoizer.RandomAccessDeser
- range - Variable in class loci.formats.cache.CacheStrategy
-
Number of planes to cache along each axis.
- range - Variable in class loci.formats.gui.CacheComponent
-
Spinners for choosing range of slices to cache.
- RANGE - Enum constant in enum class loci.plugins.in.ImportStep
- RANGE_CHANGED - Static variable in class loci.formats.cache.CacheEvent
-
Event type indicating new planar ordering.
- RangeDialog - Class in loci.plugins.in
-
Bio-Formats Importer range chooser dialog box.
- RangeDialog(ImportProcess) - Constructor for class loci.plugins.in.RangeDialog
-
Creates a range chooser dialog for the Bio-Formats Importer.
- raster(int[]) - Method in class loci.formats.cache.CacheStrategy
-
Shortcut for converting N-D position to rasterized position.
- rasterToPosition(int[], int) - Static method in class loci.formats.FormatTools
-
Computes a unique N-D position corresponding to the given rasterized index value.
- rasterToPosition(int[], int, int[]) - Static method in class loci.formats.FormatTools
-
Computes a unique N-D position corresponding to the given rasterized index value.
- RATIONAL - Enum constant in enum class loci.formats.tiff.IFDType
- RAW - Static variable in class loci.formats.in.BMPReader
-
Compression types.
- RAW - Static variable in class loci.formats.in.CellSensReader
- rawBits - Variable in class loci.formats.in.PGMReader
- rawBuf - Variable in class loci.formats.in.SPCReader
- rawCount - Variable in class loci.formats.in.BaseZeissReader
- rawSize - Variable in class loci.formats.in.QTReader
-
Raw plane size, in bytes.
- rc - Variable in class loci.formats.gui.DataConverter
- RCPNLReader - Class in loci.formats.in
- RCPNLReader() - Constructor for class loci.formats.in.RCPNLReader
- read() - Method in class loci.formats.in.APNGReader.PNGInputStream
- read() - Method in class loci.formats.in.ZeissLSMReader.BeamSplitter
- read() - Method in class loci.formats.in.ZeissLSMReader.DataChannel
- read() - Method in class loci.formats.in.ZeissLSMReader.DetectionChannel
- read() - Method in class loci.formats.in.ZeissLSMReader.IlluminationChannel
- read() - Method in class loci.formats.in.ZeissLSMReader.Laser
- read() - Method in class loci.formats.in.ZeissLSMReader.Recording
- read() - Method in class loci.formats.in.ZeissLSMReader.SubBlock
- read() - Method in class loci.formats.in.ZeissLSMReader.Track
- read(byte[], int) - Method in class loci.formats.in.AmiraReader.HxRLE
- read(byte[], int, int) - Method in class loci.formats.in.APNGReader.PNGInputStream
- read(int, byte[]) - Method in class loci.formats.in.AmiraReader.ASCII
- read(int, byte[]) - Method in class loci.formats.in.AmiraReader.HxRLE
- read(int, byte[]) - Method in class loci.formats.in.AmiraReader.HxZip
- read(int, byte[]) - Method in interface loci.formats.in.AmiraReader.PlaneReader
- read(Kryo, Input) - Method in class loci.formats.services.NetCDFServiceImpl
- readAbsoluteZValid() - Method in class loci.formats.in.MetamorphReader
- readArea(Element, int, double, double, int, int) - Method in class loci.formats.in.CellVoyagerReader
- readAsDoubles(RandomAccessInputStream) - Method in class loci.formats.in.ZeissXRMReader
- readAsString(RandomAccessInputStream) - Method in class loci.formats.in.ZeissXRMReader
- readAttachments() - Method in class loci.formats.in.ZeissCZIReader
- readBlock() - Method in class loci.formats.in.GIFReader
-
Reads the next variable length block.
- readByte() - Method in class loci.formats.in.APNGReader.PNGInputStream
- readByte() - Method in class loci.formats.tools.AmiraParameters
- readByteArray(String) - Method in interface loci.formats.services.JHDFService
-
Reads a multi-dimensional byte array from path.
- readByteArray(String) - Method in class loci.formats.services.JHDFServiceImpl
- readByteBlockArray(String, int[], int[]) - Method in interface loci.formats.services.JHDFService
-
Reads a multi-dimensional sub-block byte array from path.
- readByteBlockArray(String, int[], int[]) - Method in class loci.formats.services.JHDFServiceImpl
- readChannel(Element) - Method in class loci.formats.in.CellVoyagerReader
- readChunk() - Method in class loci.formats.in.AVIReader
- readChunkHeader() - Method in class loci.formats.in.AVIReader
- readCompoundArrayDataMap(String) - Method in interface loci.formats.services.JHDFService
-
Reads Compound array of any type
- readCompoundArrayDataMap(String) - Method in class loci.formats.services.JHDFServiceImpl
- readCString() - Method in class loci.formats.in.OpenlabReader
- readCString() - Method in class loci.formats.in.SlidebookReader
- readCString(RandomAccessInputStream, int) - Static method in class loci.formats.in.MetamorphReader
-
Read a null-terminated string.
- ReadData(RandomAccessInputStream, int) - Method in class loci.formats.in.SlideBook7Reader.CCompressionBase
- readDate() - Method in class loci.formats.in.OxfordInstrumentsReader
- ReadDictionary(RandomAccessInputStream) - Method in class loci.formats.in.SlideBook7Reader.CCompressionBase
- readDoubleArray(int) - Method in class loci.formats.tools.AmiraParameters
- readEntry() - Method in class loci.formats.in.ZeissLSMReader
- reader - Variable in class loci.formats.cache.CacheSource
-
Reader from which to draw image planes.
- reader - Variable in class loci.formats.FileInfo
-
IFormatReader implementation that would be used to read this file.
- reader - Variable in class loci.formats.gui.BufferedImageSource
-
Image reader from which to draw BufferedImages.
- reader - Variable in class loci.formats.gui.DataConverter
- reader - Variable in class loci.formats.gui.FormatFileFilter
-
Associated file format reader.
- reader - Variable in class loci.formats.gui.PreviewPane
-
Reader for use when loading thumbnails.
- reader - Variable in class loci.formats.in.AFIReader
- reader - Variable in class loci.formats.in.BDReader
- reader - Variable in class loci.formats.in.ColumbusReader
- reader - Variable in class loci.formats.in.CV7000Reader
- reader - Variable in class loci.formats.in.L2DReader
- reader - Variable in class loci.formats.in.OMETiffReader.OMETiffPlane
-
Reader to use for accessing this plane.
- reader - Variable in class loci.formats.in.OperettaReader
- reader - Variable in class loci.formats.in.PCORAWReader
- reader - Variable in class loci.formats.in.ScanrReader
- reader - Variable in class loci.formats.in.ZeissTIFFHandler
- reader - Variable in class loci.formats.in.ZipReader
- reader - Variable in class loci.formats.ReaderWrapper
-
FormatReader used to read the file.
- reader - Variable in class loci.formats.services.MetakitServiceImpl
- reader - Variable in class loci.plugins.config.FormatEntry
- reader - Variable in class loci.plugins.in.ImportProcess
- reader - Variable in class loci.plugins.util.BFVirtualStack
- reader - Variable in class loci.plugins.util.ImageProcessorSource
-
Image reader from which to draw ImageProcessors.
- READER - Enum constant in enum class loci.plugins.in.ImportStep
- READER_VALIDATE_DEFAULT - Static variable in class loci.formats.in.DynamicMetadataOptions
- READER_VALIDATE_KEY - Static variable in class loci.formats.in.DynamicMetadataOptions
- readerFromBytes(Class<IFormatReader>, byte[]) - Method in class loci.formats.Memoizer.RandomAccessDeser
- readerName - Variable in class loci.plugins.config.FormatEntry
- readers - Variable in class loci.formats.FileStitcher.ExternalSeries
- readers - Variable in class loci.formats.ImageReader
-
List of supported file format readers.
- readers - Variable in class loci.formats.in.ImprovisionTiffReader
- readers - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.MultipleImagesReader
- readers - Variable in class loci.formats.in.MIASReader
-
Delegate readers.
- readers - Variable in class loci.formats.in.NDPISReader
- readers - Variable in class loci.formats.in.SlidebookTiffReader
- readers - Variable in class loci.formats.in.XLEFReader
- ReaderWrapper - Class in loci.formats
-
Abstract superclass of reader logic that wraps other readers.
- ReaderWrapper() - Constructor for class loci.formats.ReaderWrapper
-
Constructs a reader wrapper around a new image reader.
- ReaderWrapper(IFormatReader) - Constructor for class loci.formats.ReaderWrapper
-
Constructs a reader wrapper around the given reader.
- readExtraMetadata(MetadataStore) - Method in class loci.formats.in.KodakReader
- readField(Element) - Method in class loci.formats.in.CellVoyagerReader
- readFile(String) - Method in class loci.formats.in.TextReader
- readFile(String) - Method in class loci.formats.tools.AmiraParameters
- readFile(RandomAccessInputStream) - Method in class loci.formats.tools.AmiraParameters
- readFileInfoMetadata(MetadataStore) - Method in class loci.formats.in.KodakReader
- readFlimFrame(OBFReader.Stack, int, byte[], int, int, int, int) - Method in class loci.formats.in.OBFReader
- readFloat32() - Method in class loci.formats.in.KLBReader
- readFrameInterval(Document) - Method in class loci.formats.in.CellVoyagerReader
- readFromOverlays() - Static method in class loci.plugins.util.ROIHandler
-
Returns rois if any from the overlay.
- readFromRoiManager() - Static method in class loci.plugins.util.ROIHandler
-
Returns the rois if any stored in the ROI manager.
- readFromStack(OBFReader.Stack, byte[], int, int) - Method in class loci.formats.in.OBFReader
- readFromStackRaw(OBFReader.Stack, byte[], int, int) - Method in class loci.formats.in.OBFReader
- readGZIPPlane(String, int, byte[], int, int, int, int) - Method in class loci.formats.in.NRRDReader
-
Read a tile in the specified plane from a GZIP-compressed file.
- readHeader(CoreMetadata) - Method in class loci.formats.in.KLBReader
- readImage(int, boolean) - Method in class loci.plugins.in.ImagePlusReader
- readImage(long) - Method in class loci.formats.in.MNGReader
- readImage(InputStream) - Method in interface loci.formats.services.JAIIIOService
-
Reads an image using JAI Image I/O using the JPEG 2000 codec.
- readImage(InputStream) - Method in class loci.formats.services.JAIIIOServiceImpl
- readImage(InputStream, JPEG2000CodecOptions) - Method in interface loci.formats.services.JAIIIOService
-
Reads an image using JAI Image I/O using the JPEG 2000 codec.
- readImage(InputStream, JPEG2000CodecOptions) - Method in class loci.formats.services.JAIIIOServiceImpl
- readImageBlock() - Method in class loci.formats.in.GIFReader
- readImageHeader(int) - Method in class loci.formats.in.PictReader
- readImages() - Method in class loci.plugins.in.ImagePlusReader
- readImages(boolean) - Method in class loci.plugins.in.ImagePlusReader
- readInfo(Document, Document) - Method in class loci.formats.in.CellVoyagerReader
- readIntArray() - Method in class loci.formats.tools.AmiraParameters
- readIntArray(int) - Method in class loci.formats.tools.AmiraParameters
- readIntArray(String) - Method in interface loci.formats.services.JHDFService
-
Reads a multi-dimensional int array from path.
- readIntArray(String) - Method in class loci.formats.services.JHDFServiceImpl
- readIntBlockArray(String, int[], int[]) - Method in interface loci.formats.services.JHDFService
-
Reads a multi-dimensional sub-block int array from path.
- readIntBlockArray(String, int[], int[]) - Method in class loci.formats.services.JHDFServiceImpl
- readKey() - Method in class loci.formats.tools.AmiraParameters
- readLine() - Method in class loci.formats.in.EPSReader
- readLookupTables(RandomAccessInputStream) - Method in class loci.formats.in.BioRadReader
-
Read all lookup tables from the given file into the 'lut' variable.
- readLut(int) - Method in class loci.formats.in.GIFReader
-
Read a color lookup table of the specified size.
- readMap() - Method in class loci.formats.tools.AmiraParameters
- readMetadata(String) - Method in class loci.formats.in.OlympusTileReader
- readMetaData(String) - Method in class loci.formats.in.BDReader
- readMetadataFile() - Method in class loci.formats.in.OMETiffReader
-
Extracts the OME-XML from the current
OMETiffReader.metadataFile. - readNotes(RandomAccessInputStream, boolean) - Method in class loci.formats.in.BioRadReader
-
Read all of the note strings from the given file.
- readNumber() - Method in class loci.formats.tools.AmiraParameters
- readNumberArray() - Method in class loci.formats.tools.AmiraParameters
- readNumberString() - Method in class loci.formats.in.AmiraReader.ASCII
- READOUT_MODE - Enum constant in enum class loci.formats.in.SPEReader.SpeHeaderEntry
- READOUT_TIME - Enum constant in enum class loci.formats.in.SPEReader.SpeHeaderEntry
- READOUT_TIME - Static variable in class loci.formats.in.FluoviewReader
- readOutRate - Variable in class loci.formats.in.MetamorphHandler
- readoutTime - Variable in class loci.formats.in.FluoviewReader
- readPixelData() - Method in class loci.formats.in.ZeissCZIReader.SubBlock
- readPixelData(RandomAccessInputStream) - Method in class loci.formats.in.ZeissCZIReader.SubBlock
- readPixelData(RandomAccessInputStream, Region, byte[]) - Method in class loci.formats.in.ZeissCZIReader.SubBlock
- readPixels(byte[], RandomAccessInputStream, ZipInputStream, long) - Method in class loci.formats.in.SDTReader
- readPixels(ImagePlusReader, ImporterOptions, DisplayHandler) - Method in class loci.plugins.in.Importer
- readPixelsFile(String, RandomAccessInputStream) - Method in class loci.formats.in.OIRReader
- readPlane(RandomAccessInputStream, int, int, int, int, byte[]) - Method in class loci.formats.FormatReader
-
Reads a raw plane from disk.
- readPlane(RandomAccessInputStream, int, int, int, int, int, byte[]) - Method in class loci.formats.FormatReader
-
Reads a raw plane from disk.
- readPlane(RandomAccessInputStream, int, int, int, int, int, int, int, byte[]) - Method in class loci.formats.FormatReader
- ReadPlane(int, byte[], int, int, int, int) - Method in class loci.formats.in.SlideBook7Reader.DataLoader
- readPlaneData() - Method in class loci.formats.in.MetamorphReader
- readPlanes(ImportProcess, int, List<LUT>, boolean) - Method in class loci.plugins.in.ImagePlusReader
- readQuotedString() - Method in class loci.formats.tools.AmiraParameters
- readRaster(InputStream) - Method in interface loci.formats.services.JAIIIOService
-
Reads an image into a raster using JAI Image I/O using the JPEG 2000 codec.
- readRaster(InputStream) - Method in class loci.formats.services.JAIIIOServiceImpl
- readRaster(InputStream, JPEG2000CodecOptions) - Method in interface loci.formats.services.JAIIIOService
-
Reads an image into a raster using JAI Image I/O using the JPEG 2000 codec.
- readRaster(InputStream, JPEG2000CodecOptions) - Method in class loci.formats.services.JAIIIOServiceImpl
- readRational(RandomAccessInputStream) - Method in class loci.formats.in.MetamorphReader
- readRational(RandomAccessInputStream, long) - Method in class loci.formats.in.MetamorphReader
- readRationals(String[]) - Method in class loci.formats.in.MetamorphReader
- readSanitizedXML(String) - Method in class loci.formats.in.CV7000Reader
- readSegment(String) - Method in class loci.formats.in.ZeissCZIReader
- readSegments(String) - Method in class loci.formats.in.ZeissCZIReader
- readSequence(JSONObject, DicomTag) - Method in class loci.formats.dicom.DicomJSONProvider
- readShortBlockArray(String, int[], int[]) - Method in interface loci.formats.services.JHDFService
-
Reads a multi-dimensional sub-block short array from path.
- readShortBlockArray(String, int[], int[]) - Method in class loci.formats.services.JHDFServiceImpl
- ReadSld() - Method in class loci.formats.in.SlideBook7Reader.DataLoader
- ReadSld(InputStream) - Method in class loci.formats.in.SlideBook7Reader.DataLoader
- readSpecialPixels(byte[]) - Static method in class loci.formats.in.FakeReader
-
Read byte-encoded metadata from the given plane.
- readSpecialPixels(byte[], int, boolean) - Static method in class loci.formats.in.FakeReader
-
Read byte-encoded metadata from the given plane.
- readSpecialPixels(byte[], int, boolean, int, boolean) - Static method in class loci.formats.in.FakeReader
-
Read byte-encoded metadata from the given plane.
- readStackFrame(OBFReader.Stack, long, byte[], int, int, int) - Method in class loci.formats.in.OBFReader
- readStackHeader() - Method in class loci.formats.in.ImspectorReader
-
Read the header for an image stack.
- readStageLabels() - Method in class loci.formats.in.MetamorphReader
- readStagePositions() - Method in class loci.formats.in.MetamorphReader
- readStamps() - Method in class loci.formats.in.FluoviewReader
- readString() - Method in class loci.formats.in.OBFReader
- readStringArray(String) - Method in interface loci.formats.services.JHDFService
-
Reads String array array from path.
- readStringArray(String) - Method in class loci.formats.services.JHDFServiceImpl
- readTagHeader() - Method in class loci.formats.in.OpenlabReader
-
Read the next tag.
- readTags(RandomAccessInputStream, boolean, String) - Method in class loci.formats.in.CellSensReader
- readTagSource(String) - Method in class loci.formats.dicom.DicomJSONProvider
- readTagSource(String) - Method in interface loci.formats.dicom.ITagProvider
-
Read tags from the given location.
- readThumbImages() - Method in class loci.plugins.in.ImagePlusReader
- readTiffIFDEntry() - Method in class loci.formats.tiff.TiffParser
- readTimePoints(Document) - Method in class loci.formats.in.CellVoyagerReader
- readTopLevel() - Method in class loci.formats.tools.AmiraParameters
- readTypeAndSize() - Method in class loci.formats.in.AVIReader
- readUInt32() - Method in class loci.formats.in.KLBReader
- readUInt64() - Method in class loci.formats.in.KLBReader
- readUnsignedLong(RandomAccessInputStream) - Method in class loci.formats.in.SDTInfo
- readValue() - Method in class loci.formats.in.ZeissLSMReader
- readValue(int) - Method in class loci.formats.in.GatanReader
- readVariable() - Method in class loci.formats.in.OpenlabReader
- readVariable() - Method in class loci.formats.in.QuesantReader
- readVarint(RandomAccessInputStream) - Method in class loci.formats.in.ZeissCZIReader
- readWavelength(int, MetadataStore) - Method in class loci.formats.in.DeltavisionReader
- readWellInfo(Element, double, double, int, int) - Method in class loci.formats.in.CellVoyagerReader
- readXMLBlock(String, RandomAccessInputStream) - Method in class loci.formats.in.OIRReader
- realChannel - Variable in class loci.formats.in.LIFReader
- realColors - Variable in class loci.formats.in.ND2Handler
- realFile - Variable in class loci.formats.Memoizer
- realHeight - Variable in class loci.formats.in.BaseZeissReader
- realWidth - Variable in class loci.formats.in.BaseZeissReader
- realX - Variable in class loci.formats.in.VentanaReader.TIFFTile
- realY - Variable in class loci.formats.in.VentanaReader.TIFFTile
- rebuild(GenericDialog) - Method in class loci.plugins.in.FilePatternDialog
- rebuildDialog(GenericDialog) - Method in class loci.plugins.in.MainDialog
-
Fancies up the importer dialog to look much nicer.
- rebuildDialog(GenericDialog, int) - Method in class loci.plugins.in.SeriesDialog
- REC_BOOLEAN - Static variable in class loci.formats.in.IM3Reader
- REC_CONTAINER - Static variable in class loci.formats.in.IM3Reader
-
A record that is a container of other records.
- REC_FLOAT - Static variable in class loci.formats.in.IM3Reader
- REC_IMAGE - Static variable in class loci.formats.in.IM3Reader
-
Image format int: pixel type? 3 = RGBA int: width int: height int: depth data bytes follow
- REC_INT - Static variable in class loci.formats.in.IM3Reader
-
32-bit integer values
- REC_NESTED - Static variable in class loci.formats.in.IM3Reader
-
A nested record of records
- REC_STRING - Static variable in class loci.formats.in.IM3Reader
-
A string int: ? int: length 8-byte characters follow
- REC_SUFFIX - Static variable in class loci.formats.in.PerkinElmerReader
- recache() - Method in class loci.formats.cache.Cache
-
Updates all planes on the load list.
- recache(int) - Method in class loci.formats.cache.Cache
-
Updates the given plane.
- reCalculateBlockOffsets(int) - Method in class loci.formats.in.KLBReader
- RECEIVE_COIL_NAME - Enum constant in enum class loci.formats.dicom.DicomAttribute
- RECOGNITION_CODE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- RECOMMENDED_ABSENT_PIXEL_CIELAB_VALUE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- RECOMMENDED_DISPLAY_FRAMERATE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- RECOMMENDED_VIEWING_MODE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- RECON_SETTINGS - Static variable in class loci.formats.in.ZeissXRMReader
- RECON_SETTINGS_PATH - Static variable in class loci.formats.in.ZeissXRMReader
- RECONSTRUCTION_DIAMETER - Enum constant in enum class loci.formats.dicom.DicomAttribute
- record - Variable in class loci.plugins.util.BFVirtualStack
- record(String) - Method in class loci.plugins.util.RecordedImageProcessor
- record(String, Object[], Class<?>[]) - Method in class loci.plugins.util.RecordedImageProcessor
- record(String, Object, Class<?>) - Method in class loci.plugins.util.RecordedImageProcessor
- RECORD_IN_USE_FLAG - Enum constant in enum class loci.formats.dicom.DicomAttribute
- RecordedImageProcessor - Class in loci.plugins.util
-
Image processor extension that records commands executed upon it.
- RecordedImageProcessor(ImageProcessor) - Constructor for class loci.plugins.util.RecordedImageProcessor
- RecordedImageProcessor(ImageProcessor, int, ImageProcessor[]) - Constructor for class loci.plugins.util.RecordedImageProcessor
- RecordedImageProcessor.MethodEntry - Class in loci.plugins.util
- Recording() - Constructor for class loci.formats.in.ZeissLSMReader.Recording
- RECORDING_CAMERA_BINNING - Static variable in class loci.formats.in.ZeissLSMReader
- RECORDING_DESCRIPTION - Static variable in class loci.formats.in.ZeissLSMReader
- RECORDING_NAME - Static variable in class loci.formats.in.ZeissLSMReader
-
Data types.
- RECORDING_OBJECTIVE - Static variable in class loci.formats.in.ZeissLSMReader
- RECORDING_SAMPLE_0TIME - Static variable in class loci.formats.in.ZeissLSMReader
- RECORDING_ZOOM - Static variable in class loci.formats.in.ZeissLSMReader
- records - Variable in class loci.formats.in.IM3Reader
- recordWidth - Variable in class loci.formats.in.PDSReader
- RECTANGLE - Enum constant in enum class loci.formats.in.BaseZeissReader.FeatureType
- RECTANGLE - Static variable in class loci.formats.in.FV1000Reader
- RECTANGLE - Static variable in class loci.formats.in.GatanReader
- RECTANGLE - Static variable in class loci.formats.in.LeicaHandler.ROI
- RECTANGLE - Static variable in class loci.formats.in.LeicaMicrosystemsMetadata.ROI
- RECTANGLE - Static variable in class loci.formats.in.LIFReader.ROI
- RECTANGLE - Static variable in class loci.formats.in.ZeissLSMReader
- rectangles - Variable in class loci.formats.in.FakeReader
- RectangleStrategy - Class in loci.formats.cache
-
A rectangle strategy caches planes extending from the the current dimensional position along each axis and combination of axes.
- RectangleStrategy(int[]) - Constructor for class loci.formats.cache.RectangleStrategy
-
Constructs a rectangle strategy.
- RECTIFICATION_TYPE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- RED - Enum constant in enum class loci.formats.in.LeicaMicrosystemsMetadata.Channel.ChannelType
- RED_GAIN - Static variable in class loci.formats.in.CellSensReader
- RED_LUT_DATA - Enum constant in enum class loci.formats.dicom.DicomAttribute
- RED_LUT_DESCRIPTOR - Enum constant in enum class loci.formats.dicom.DicomAttribute
- RED_MAX - Static variable in class loci.plugins.in.Colorizer
- RED_MULTIPLIER - Static variable in class loci.formats.in.NDPIReader
- RED_OFFSET - Static variable in class loci.formats.in.CellSensReader
- redGain - Variable in class loci.formats.in.CellSensReader.Pyramid
- redOffset - Variable in class loci.formats.in.CellSensReader.Pyramid
- redOffset - Static variable in class org.libjpegturbo.turbojpeg.TJ
- redShort - Variable in class loci.formats.gui.Index16ColorModel
-
Lookup tables.
- reduce() - Method in class loci.formats.tiff.TiffRational
-
Reduces this rational's fraction to lowest terms.
- refCount - Variable in class loci.plugins.util.VirtualReader
- REFERENCE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- REFERENCE - Static variable in class loci.formats.in.NDPIReader
- REFERENCE_BLACK_WHITE - Static variable in class loci.formats.tiff.IFD
- REFERENCE_GRAYSCALE_PRESENTATION_STATE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- REFERENCE_PATH - Static variable in class loci.formats.in.ZeissXRMReader
- REFERENCE_PIXEL_PHYSICAL_VALUE_X - Enum constant in enum class loci.formats.dicom.DicomAttribute
- REFERENCE_PIXEL_PHYSICAL_VALUE_Y - Enum constant in enum class loci.formats.dicom.DicomAttribute
- REFERENCE_PIXEL_X0 - Enum constant in enum class loci.formats.dicom.DicomAttribute
- REFERENCE_PIXEL_Y0 - Enum constant in enum class loci.formats.dicom.DicomAttribute
- REFERENCED_CURVE_SEQUENCE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- REFERENCED_FILE_ID - Enum constant in enum class loci.formats.dicom.DicomAttribute
- REFERENCED_FRAME_NUMBER - Enum constant in enum class loci.formats.dicom.DicomAttribute
- REFERENCED_IMAGE_EVIDENCE_SEQUENCE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- REFERENCED_IMAGE_NAVIGATION_SEQUENCE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- REFERENCED_IMAGE_SEQUENCE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- REFERENCED_INSTANCE_SEQUENCE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- REFERENCED_OVERLAY_SEQUENCE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- REFERENCED_PATIENT_SEQUENCE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- REFERENCED_PERFORMED_PROCEDURE_STEP - Enum constant in enum class loci.formats.dicom.DicomAttribute
- REFERENCED_RAW_DATA_SEQUENCE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- REFERENCED_RELATED_SOP_CLASS_UID_FILE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- REFERENCED_RESULTS_SEQUENCE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- REFERENCED_SERIES_SEQUENCE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- REFERENCED_SOP_CLASS_UID - Enum constant in enum class loci.formats.dicom.DicomAttribute
- REFERENCED_SOP_CLASS_UID_FILE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- REFERENCED_SOP_INSTANCE_UID - Enum constant in enum class loci.formats.dicom.DicomAttribute
- REFERENCED_SOP_INSTANCE_UID_FILE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- REFERENCED_SOP_SEQUENCE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- REFERENCED_STUDY_SEQUENCE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- REFERENCED_TRANSFER_SYNTAX_UID_FILE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- REFERENCED_VISIT_SEQUENCE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- REFERENCED_WAVEFORM_SEQUENCE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- REFERRING_PHYSICIAN_ADDRESS - Enum constant in enum class loci.formats.dicom.DicomAttribute
- REFERRING_PHYSICIAN_ID - Enum constant in enum class loci.formats.dicom.DicomAttribute
- REFERRING_PHYSICIAN_NAME - Enum constant in enum class loci.formats.dicom.DicomAttribute
- REFERRING_PHYSICIAN_TELEPHONE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- REFOCUS_INTERVAL - Static variable in class loci.formats.in.NDPIReader
- refractive - Variable in class loci.formats.in.InCellReader
- REFRACTIVE_INDEX - Static variable in class loci.formats.in.CellSensReader
- refractiveIndex - Variable in class loci.formats.in.CellSensReader.Pyramid
- refractiveIndex - Variable in class loci.formats.in.IvisionReader
- refractiveIndex - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataTempBuffer
- refractiveIndex - Variable in class loci.formats.in.LIFReader
- refractiveIndex - Variable in class loci.formats.in.ND2Handler
- refractiveIndex - Variable in class loci.formats.in.ND2Reader
- refractiveIndex - Variable in class loci.formats.in.ZeissCZIReader
- refresher - Variable in class loci.formats.gui.PreviewPane
-
Method for syncing the view to the model.
- region - Variable in class loci.formats.dicom.DicomTile
- region - Variable in class loci.formats.in.OlympusTileReader.Tile
- REGION_DATA_TYPE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- REGION_FLAGS - Enum constant in enum class loci.formats.dicom.DicomAttribute
- REGION_LOCATION_MAX_X1 - Enum constant in enum class loci.formats.dicom.DicomAttribute
- REGION_LOCATION_MAX_Y1 - Enum constant in enum class loci.formats.dicom.DicomAttribute
- REGION_LOCATION_MIN_X0 - Enum constant in enum class loci.formats.dicom.DicomAttribute
- REGION_LOCATION_MIN_Y0 - Enum constant in enum class loci.formats.dicom.DicomAttribute
- REGION_OF_RESIDENCE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- REGION_SPATIAL_FORMAT - Enum constant in enum class loci.formats.dicom.DicomAttribute
- regionMetadata - Variable in class loci.formats.in.TissueFAXSReader.ScanRegion
- regions - Variable in class loci.formats.in.TissueFAXSReader
- registerServiceProviders() - Static method in class loci.formats.services.JAIIIOServiceImpl
-
Register the JPEG-2000 readers with the reader service.
- REGISTRY - Static variable in class loci.formats.UpgradeChecker
-
Location of the OME registry.
- REGISTRY_IMAGEJ - Static variable in class loci.formats.UpgradeChecker
-
Registry ID identifying usage of Bio-Formats in ImageJ.
- REGISTRY_LIBRARY - Static variable in class loci.formats.UpgradeChecker
-
Registry ID identifying usage of Bio-Formats as a library in general.
- REGISTRY_PROPERTIES - Static variable in class loci.formats.UpgradeChecker
-
Properties that are sent to the OME registry.
- RELATED_SERIES_SEQUENCE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- RELATED_SOP_CLASS_UID - Enum constant in enum class loci.formats.dicom.DicomAttribute
- RELATED_SOUND_FILE - Static variable in class loci.formats.tiff.IFD
- RELATIVE_POSITIONS_DEFAULT - Static variable in class loci.formats.in.ZeissCZIReader
- RELATIVE_POSITIONS_KEY - Static variable in class loci.formats.in.ZeissCZIReader
- RELATIVE_XRAY_EXPOSURE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- relativeTime - Variable in class loci.formats.in.PrairieMetadata.Frame
-
relativeTimeattribute of this<Frame>. - remainingBytesInChunk(OBFReader.Stack) - Method in class loci.formats.in.OBFReader
- remove(int) - Method in class loci.formats.MetadataList
-
Remove the entire primary array element at the specified index.
- remove(int, int) - Method in class loci.formats.MetadataList
-
Remove the array element at the specified indexes.
- REMOVE_THUMBNAIL_DEFAULT - Static variable in class loci.formats.in.SVSReader
- REMOVE_THUMBNAIL_KEY - Static variable in class loci.formats.in.SVSReader
- removeBinData(OMEXMLMetadata) - Method in interface loci.formats.services.OMEXMLService
-
Remove all of the BinData elements from the given OME-XML metadata object.
- removeBinData(OMEXMLMetadata) - Method in class loci.formats.services.OMEXMLServiceImpl
- removeCacheListener(CacheListener) - Method in class loci.formats.cache.Cache
- removeCacheListener(CacheListener) - Method in interface loci.formats.cache.CacheReporter
-
Removes a listener for status update events.
- removeCacheListener(CacheListener) - Method in class loci.formats.cache.CacheStrategy
- removeChannels(OMEXMLMetadata, int, int) - Method in interface loci.formats.services.OMEXMLService
-
Remove all but the first sizeC valid Channel elements from the given OME-XML metadata object.
- removeChannels(OMEXMLMetadata, int, int) - Method in class loci.formats.services.OMEXMLServiceImpl
- removeClass(Class<? extends T>) - Method in class loci.formats.ClassList
-
Removes the given class from the list.
- removeExtension(String) - Method in class loci.plugins.out.Exporter
-
Removes the extension of the specified name.
- removeGST(String) - Method in class loci.formats.in.FV1000Reader
- removeIFDComments(IFormatReader) - Method in class loci.formats.in.OMETiffReader
- removePossible(String) - Method in class loci.plugins.prefs.StringOption
-
Removes a possible value from the list.
- removeStatusListener(StatusListener) - Method in class loci.plugins.in.ImagePlusReader
- removeStatusListener(StatusListener) - Method in class loci.plugins.in.ImportProcess
- removeThumbnail() - Method in class loci.formats.in.SVSReader
- removeTiffData(OMEXMLMetadata) - Method in interface loci.formats.services.OMEXMLService
-
Remove all of the TiffData elements from the given OME-XML metadata object.
- removeTiffData(OMEXMLMetadata) - Method in class loci.formats.services.OMEXMLServiceImpl
- RenamePathToTimepoint0(String) - Method in class loci.formats.in.SlideBook7Reader.CSBFile70
- RENDER_OPERATION_ID - Static variable in class loci.formats.in.CellSensReader
- reopenFile() - Method in class loci.formats.DelegateReader
- reopenFile() - Method in class loci.formats.FileStitcher
- reopenFile() - Method in class loci.formats.FormatReader
- reopenFile() - Method in interface loci.formats.IFormatReader
-
Reopen any files that were closed, and which are expected to be open while the reader is open.
- reopenFile() - Method in class loci.formats.ImageReader
- reopenFile() - Method in class loci.formats.in.AnalyzeReader
- reopenFile() - Method in class loci.formats.in.BDVReader
- reopenFile() - Method in class loci.formats.in.CellH5Reader
- reopenFile() - Method in class loci.formats.in.CellSensReader
- reopenFile() - Method in class loci.formats.in.FakeReader
- reopenFile() - Method in class loci.formats.in.FlowSightReader
- reopenFile() - Method in class loci.formats.in.HitachiReader
- reopenFile() - Method in class loci.formats.in.ICSReader
- reopenFile() - Method in class loci.formats.in.ImagicReader
- reopenFile() - Method in class loci.formats.in.LeicaMicrosystemsMetadata.MultipleImagesReader
- reopenFile() - Method in class loci.formats.in.MinimalTiffReader
- reopenFile() - Method in class loci.formats.in.NiftiReader
- reopenFile() - Method in class loci.formats.in.OMETiffReader
- reopenFile() - Method in class loci.formats.in.SPCReader
- reopenFile() - Method in class loci.formats.in.TileJPEGReader
- reopenFile() - Method in class loci.formats.in.XLEFReader
- reopenFile() - Method in class loci.formats.in.ZipReader
- reopenFile() - Method in class loci.formats.ReaderWrapper
- reopenFile() - Method in class loci.formats.WrappedReader
- reorder() - Method in class loci.formats.CoreMetadataList
- reorder(int) - Method in class loci.formats.DimensionSwapper
- reorder(ImagePlus, String, String) - Static method in class loci.plugins.Slicer
-
Reorder the given ImagePlus's stack.
- reorderXSLT - Static variable in class loci.formats.services.OMEXMLServiceImpl
-
Reordering stylesheet.
- REPETITION_TIME - Enum constant in enum class loci.formats.dicom.DicomAttribute
- REPLACE - Enum constant in enum class loci.formats.dicom.ResolutionStrategy
- replaceExtension(String, String, String) - Method in class loci.formats.in.FV1000Reader
- replacementMetadataStore - Variable in class loci.formats.Memoizer
-
MetadataStorecreated internally. - reportException(Throwable) - Static method in class loci.plugins.util.WindowTools
-
Reports the given exception with stack trace in an ImageJ error dialog.
- reportException(Throwable, boolean) - Static method in class loci.plugins.util.WindowTools
-
Reports the given exception with stack trace in an ImageJ error dialog.
- reportException(Throwable, boolean, String) - Static method in class loci.plugins.util.WindowTools
-
Reports the given exception with stack trace in an ImageJ error dialog.
- REPRESENTATION_KEYS - Static variable in class loci.formats.in.ICSReader
- REPRESENTATIVE_FRAME_NUMBER - Enum constant in enum class loci.formats.dicom.DicomAttribute
- repT - Variable in class loci.formats.in.SDTInfo
- RES_SUFFIX - Static variable in class loci.formats.in.FlexReader
- rescale(int) - Method in class loci.formats.gui.SignedColorModel
- rescale(int, int) - Method in class loci.formats.gui.SignedColorModel
- RESCALE_INTERCEPT - Enum constant in enum class loci.formats.dicom.DicomAttribute
- RESCALE_SLOPE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- RESCALE_TYPE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- RESERVED - Enum constant in enum class loci.formats.dicom.DicomVR
- RESERVED_DELIMITER_MARKER_MAX - Enum constant in enum class loci.formats.codec.JPEG2000SegmentMarker
- RESERVED_DELIMITER_MARKER_MIN - Enum constant in enum class loci.formats.codec.JPEG2000SegmentMarker
- reserved1 - Variable in class loci.formats.in.SDTInfo
- reserved2 - Variable in class loci.formats.in.SDTInfo
- reset() - Method in class loci.formats.cache.Cache
-
Reallocates the cache.
- reset() - Method in class loci.plugins.util.RecordedImageProcessor
- reset(ImageProcessor) - Method in class loci.plugins.util.RecordedImageProcessor
- resetBinaryThreshold() - Method in class loci.plugins.util.RecordedImageProcessor
- resetMinAndMax() - Method in class loci.plugins.util.RecordedImageProcessor
- resetRoi() - Method in class loci.plugins.util.RecordedImageProcessor
- resetSliceLabelButton - Variable in class loci.plugins.config.ConfigWindow
- resetStream(IFD) - Method in class loci.formats.in.NDPIReader
- resetThreshold() - Method in class loci.plugins.util.RecordedImageProcessor
- ResHandler() - Constructor for class loci.formats.in.FlexReader.ResHandler
- resize(int) - Method in class loci.plugins.util.RecordedImageProcessor
- resize(int, int) - Method in class loci.plugins.util.RecordedImageProcessor
- resLabel - Variable in class loci.formats.gui.PreviewPane
-
Labels containing thumbnail and dimensional information.
- reslice(ImagePlus, boolean, boolean, boolean, String) - Method in class loci.plugins.Slicer
- resolution - Variable in class loci.formats.codec.JPEG2000CodecOptions
-
The resolution level as would be provided to:
J2KImageReadParam.setResolution(int)(READ). - resolution - Variable in class loci.formats.FormatReader
-
The number of the current resolution.
- resolution - Variable in class loci.formats.FormatWriter
-
Current pyramid resolution.
- resolution - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.Channel
- Resolution - Class in loci.formats
-
Represents a single subresolution in a pyramid.
- Resolution() - Constructor for class loci.formats.ome.OMEPyramidStore.Resolution
- Resolution(int, int, int) - Constructor for class loci.formats.Resolution
- Resolution(int, int, int, int) - Constructor for class loci.formats.Resolution
- Resolution(String) - Constructor for class loci.formats.ome.OMEPyramidStore.Resolution
- RESOLUTION - Enum constant in enum class loci.formats.codec.JPEG2000BoxType
- RESOLUTION_UNIT - Static variable in class loci.formats.tiff.IFD
- resolutionCount - Variable in class loci.formats.CoreMetadata
- resolutionCount - Variable in class loci.formats.in.LeicaSCNReader.LeicaSCNHandler
- resolutionData - Variable in class loci.formats.FormatWriter
- resolutionIndex - Variable in class loci.formats.in.ZeissCZIReader.SubBlock
- resolutionLevels - Variable in class loci.formats.in.JPEG2000MetadataParser
-
Number of JPEG 2000 resolution levels the file has.
- resolutionLevels - Variable in class loci.formats.in.JPEG2000Reader
-
The number of JPEG 2000 resolution levels the file has.
- resolutionLevels - Variable in class loci.formats.in.JPXReader
-
The number of JPEG 2000 resolution levels the file has.
- resolutionLevels - Variable in class loci.formats.in.MinimalTiffReader
-
Number of JPEG 2000 resolution levels.
- resolutions - Variable in class loci.formats.in.TissueFAXSReader.ScanRegion
- resolutions - Variable in class loci.formats.in.VentanaReader
- resolutions - Variable in class loci.formats.ome.OMEPyramidStore
- ResolutionStrategy - Enum Class in loci.formats.dicom
- ResolutionStrategy() - Constructor for enum class loci.formats.dicom.ResolutionStrategy
- resolutionX - Variable in class loci.formats.in.OperettaReader.Channel
- resolutionX - Variable in class loci.formats.in.OperettaReader.Plane
- resolutionY - Variable in class loci.formats.in.OperettaReader.Channel
- resolutionY - Variable in class loci.formats.in.OperettaReader.Plane
- resourceCount - Variable in class loci.formats.ResourceNamer
- resourceNamer - Variable in class loci.formats.tools.FakeImage
- ResourceNamer - Class in loci.formats
-
Utility class helping with generating human-readable resource names based on alphanumeric indexing.
- ResourceNamer(int) - Constructor for class loci.formats.ResourceNamer
- RESPONSIBLE_ORGANIZATION - Enum constant in enum class loci.formats.dicom.DicomAttribute
- restartAlphabet() - Method in class loci.formats.ResourceNamer
-
Resets the internal state of the class so that it starts alphabet generation from the first letter (ASCII A).
- restartInterval - Variable in class loci.formats.services.JPEGTurboServiceImpl
- restartMarkers - Variable in class loci.formats.in.HamamatsuVMSReader
- restartMarkers - Variable in class loci.formats.services.JPEGTurboServiceImpl
- resText - Variable in class loci.formats.gui.PreviewPane
- resTip - Variable in class loci.formats.gui.PreviewPane
- RestoreSpecialCharacters(String) - Method in class loci.formats.in.SlideBook7Reader.ClassDecoder
- result - Variable in class loci.formats.in.TecanReader.Image
- resultFile - Variable in class loci.formats.in.MIASReader
-
Path to file containing analysis results for all plates.
- RETRIEVE_TITLE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- REUSE - Static variable in class loci.formats.tiff.IFD
- reverseFileMapping - Variable in class loci.formats.in.FlexReader
- reversePlaneLookup - Variable in class loci.formats.in.CV7000Reader
- reverseX - Variable in class loci.formats.in.PDSReader
- reverseY - Variable in class loci.formats.in.PDSReader
- revision - Variable in class loci.formats.in.SDTInfo
-
Software revision number (lower 4 bits >= 10(decimal)).
- rgb - Variable in class loci.formats.CoreMetadata
-
Indicates whether or not the images are stored as RGB (multiple channels per plane).
- RGB - Enum constant in enum class loci.formats.tiff.PhotoInterp
- RGB - Static variable in class loci.formats.in.CellSensReader
- RGB_MASK - Static variable in class loci.formats.in.BMPReader
- RGB_PALETTE - Enum constant in enum class loci.formats.tiff.PhotoInterp
- RGN - Enum constant in enum class loci.formats.codec.JPEG2000SegmentMarker
- RHKReader - Class in loci.formats.in
-
RHKReader is the file format reader for RHK Technologies files.
- RHKReader() - Constructor for class loci.formats.in.RHKReader
-
Constructs a new RHK reader.
- ri - Variable in class loci.formats.in.OIRReader.Objective
- RIGHT - Enum constant in enum class loci.formats.in.BaseZeissReader.LineEndPositions
- RIGHT - Enum constant in enum class loci.formats.in.BaseZeissReader.TextAlignment
- RLE_4 - Static variable in class loci.formats.in.BMPReader
- RLE_8 - Static variable in class loci.formats.in.BMPReader
- roi - Variable in class loci.formats.in.LeicaHandler
- ROI - Class in loci.formats.in.LeicaMicrosystemsMetadata
-
This class helps saving ROI information to a reader's MetadataStore
- ROI() - Constructor for class loci.formats.in.LeicaHandler.ROI
- ROI() - Constructor for class loci.formats.in.LeicaMicrosystemsMetadata.ROI
- ROI() - Constructor for class loci.formats.in.LiFlimReader.ROI
- ROI() - Constructor for class loci.formats.in.LIFReader.ROI
- ROI_BEGIN - Enum constant in enum class loci.formats.in.SPEReader.SpeHeaderEntry
- ROI_PREFIX - Static variable in class loci.formats.in.FakeReader
- ROI_SIGNATURE - Static variable in class loci.formats.in.ZeissZVIReader
- ROI_SPACING - Static variable in class loci.formats.in.FakeReader
- ROIARRAY - Enum constant in enum class loci.formats.in.SPEReader.SpeHeaderType
- roiCount - Variable in class loci.formats.in.FakeReader
- roiDrawFile - Variable in class loci.formats.in.TrestleReader
- roiFile - Variable in class loci.formats.in.BDReader
- roiFile - Variable in class loci.formats.in.TrestleReader
- roiFilenames - Variable in class loci.formats.in.FV1000Reader
- roiFiles - Variable in class loci.formats.in.MIASReader
- ROIHandler - Class in loci.plugins.util
-
Utility class for managing regions of interest within ImageJ.
- ROIHandler() - Constructor for class loci.plugins.util.ROIHandler
- roiIDs - Variable in class loci.formats.in.BaseZeissReader
- rois - Variable in class loci.formats.in.LiFlimReader
- rois - Variable in class loci.formats.in.ND2Handler
- ROIS_MODE_MANAGER - Static variable in class loci.plugins.in.ImporterOptions
- ROIS_MODE_OVERLAY - Static variable in class loci.plugins.in.ImporterOptions
- ROIShape() - Constructor for class loci.formats.in.GatanReader.ROIShape
- roisModeChoice - Variable in class loci.plugins.in.MainDialog
- root - Variable in class loci.formats.services.NetCDFServiceImpl
-
Root of the NetCDF file.
- root - Variable in class loci.formats.services.POIServiceImpl
- rootList - Variable in class loci.formats.in.BDReader
- rotate(double) - Method in class loci.plugins.util.RecordedImageProcessor
- rotateLeft() - Method in class loci.plugins.util.RecordedImageProcessor
- rotateRight() - Method in class loci.plugins.util.RecordedImageProcessor
- rotation - Variable in class loci.formats.in.LeicaHandler.ROI
- rotation - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.ROI
- rotation - Variable in class loci.formats.in.LIFReader.ROI
- ROTATION - Static variable in class loci.formats.FormatTools
-
Identifies the Rotation dimensional type, representing a dimension consisting of rotations.
- ROTATION - Static variable in class loci.formats.in.FV1000Reader
- ROTATION_DIRECTION - Enum constant in enum class loci.formats.dicom.DicomAttribute
- ROTATION_OF_SCANNED_FILM - Enum constant in enum class loci.formats.dicom.DicomAttribute
- rotationLabels - Variable in class loci.formats.in.ZeissCZIReader
- rotations - Variable in class loci.formats.in.ZeissCZIReader
- rotations - Variable in class loci.formats.in.ZeissLSMReader
- row - Variable in class loci.formats.in.CellomicsReader.ChannelFile
- row - Variable in class loci.formats.in.CellVoyagerReader.WellInfo
- row - Variable in class loci.formats.in.ColumbusReader.Plane
- row - Variable in class loci.formats.in.CV7000Reader.Field
- row - Variable in class loci.formats.in.FlexReader.FlexFile
- row - Variable in class loci.formats.in.OMEXMLReader.BinData
- row - Variable in class loci.formats.in.OperettaReader.Plane
- row - Variable in class loci.formats.in.TextReader
-
Current row number.
- row - Variable in class loci.formats.in.ZeissCZIReader.SubBlock
- row - Variable in class loci.formats.tools.AmiraParameters
- ROW_POSITION_IN_MATRIX - Enum constant in enum class loci.formats.dicom.DicomAttribute
- rowBytes - Variable in class loci.formats.in.PictReader
-
Number of bytes in a row of pixel data (variable).
- rowCount - Variable in class loci.formats.in.BaseZeissReader
- rowIndex - Variable in class loci.formats.internal.WellContainer
- rowLength - Variable in class loci.formats.in.TextReader
-
Number of tokens per row.
- rowName - Variable in class loci.formats.in.InCellReader
- RowPanel() - Constructor for class loci.formats.gui.DataConverter.RowPanel
- rows - Variable in class loci.formats.in.CellSensReader
- ROWS - Enum constant in enum class loci.formats.dicom.DicomAttribute
- ROWS_PER_STRIP - Static variable in class loci.formats.tiff.IFD
- rPad - Variable in class loci.formats.gui.CacheIndicator
- RPZACodec - Class in loci.formats.codec
-
Implements encoding and decoding methods for Apple RPZA.
- RPZACodec() - Constructor for class loci.formats.codec.RPZACodec
- RST0 - Static variable in class loci.formats.services.JPEGTurboServiceImpl
- RST7 - Static variable in class loci.formats.services.JPEGTurboServiceImpl
- run() - Method in class loci.formats.cache.CacheUpdater
- run() - Method in class loci.formats.gui.DataConverter
- run() - Method in class loci.formats.gui.ImageViewer
-
Handles animation.
- run() - Method in class loci.formats.gui.PreviewPane
-
Thumbnail loading routine.
- run() - Method in class loci.plugins.config.ConfigWindow
-
Populate configuration information in a separate thread.
- run() - Method in class loci.plugins.in.ThumbLoader
-
Does the work of loading the thumbnails.
- run() - Method in class loci.plugins.out.Exporter
-
Executes the plugin.
- run(ImageProcessor) - Method in class loci.plugins.LociExporter
-
Executes the plugin.
- run(ImageProcessor) - Method in class loci.plugins.Slicer
- run(String) - Method in class loci.plugins.About
- run(String) - Method in class loci.plugins.config.LociConfig
-
Executes the plugin.
- run(String) - Method in class loci.plugins.config.LociInstaller
-
Executes the plugin.
- run(String) - Method in class loci.plugins.in.Importer
-
Executes the plugin.
- run(String) - Method in class loci.plugins.LociImporter
-
Executes the plugin.
- run(String) - Method in class loci.plugins.macro.LociFunctions
- run(String) - Method in class loci.plugins.macro.MacroFunctions
- run(String) - Method in class loci.plugins.shortcut.ShortcutPanel
-
Executes the plugin.
- run(String) - Method in class loci.plugins.Updater
- RUN - Static variable in class loci.formats.ResourceNamer
- runPlugIn(String, String) - Static method in class loci.plugins.shortcut.ShortcutPanel
-
Executes the given plugin, in a separate thread.
- RUSSIAN_CHARSET - Enum constant in enum class loci.formats.in.BaseZeissReader.Charset
- RWC_FRAME_ORIGIN - Static variable in class loci.formats.in.CellSensReader
- RWC_FRAME_SCALE - Static variable in class loci.formats.in.CellSensReader
- RWC_FRAME_UNIT - Static variable in class loci.formats.in.CellSensReader
S
- S - Enum constant in enum class loci.formats.in.LeicaMicrosystemsMetadata.Dimension.DimensionKey
- S_AXIS - Static variable in class loci.formats.AxisGuesser
-
Axis type for series.
- S_MAX_SAMPLE_VALUE - Static variable in class loci.formats.tiff.IFD
- S_MIN_SAMPLE_VALUE - Static variable in class loci.formats.tiff.IFD
- S_PREFIXES - Static variable in class loci.formats.AxisGuesser
-
Prefixes indicating series dimension.
- safeSkip(InputStream, long) - Method in class loci.formats.in.NRRDReader
-
Skip a specified number of bytes in a stream.
- SAMP_420 - Static variable in class org.libjpegturbo.turbojpeg.TJ
-
4:2:0 chrominance subsampling.
- SAMP_422 - Static variable in class org.libjpegturbo.turbojpeg.TJ
-
4:2:2 chrominance subsampling.
- SAMP_440 - Static variable in class org.libjpegturbo.turbojpeg.TJ
-
4:4:0 chrominance subsampling.
- SAMP_444 - Static variable in class org.libjpegturbo.turbojpeg.TJ
-
4:4:4 chrominance subsampling (no chrominance subsampling).
- SAMP_GRAY - Static variable in class org.libjpegturbo.turbojpeg.TJ
-
Grayscale.
- SAMPLE_FLAGS_LIST - Static variable in class loci.formats.in.CellSensReader
- SAMPLE_FORMAT - Static variable in class loci.formats.tiff.IFD
- SAMPLE_ID_LIST - Static variable in class loci.formats.in.CellSensReader
- SAMPLE_MASK - Static variable in class loci.formats.in.CellSensReader
- SAMPLES_PER_PIXEL - Enum constant in enum class loci.formats.dicom.DicomAttribute
- SAMPLES_PER_PIXEL - Static variable in class loci.formats.tiff.IFD
- SAMPLES_PER_PIXEL_USED - Enum constant in enum class loci.formats.dicom.DicomAttribute
- samplesWritten - Variable in class loci.formats.in.OBFReader.Stack
- sampleTable - Variable in class loci.formats.in.VolocityReader
- sampleTime - Variable in class loci.formats.in.GatanReader
- sanitize(String, boolean) - Method in class loci.formats.gui.XMLCellRenderer.XMLItem
-
Sanitizes strings to appear correctly in HTML.
- sanitizeControl(String) - Static method in class loci.formats.in.ND2Reader
-
Remove control and invalid characters from the given string.
- sanitizeFile(String, String) - Method in class loci.formats.in.FV1000Reader
- sanitizeValue(String) - Method in class loci.formats.in.FV1000Reader
- SAR - Enum constant in enum class loci.formats.dicom.DicomAttribute
- SATURATION - Static variable in class loci.formats.in.CellSensReader
- SATURATION - Static variable in class loci.formats.tiff.IFD
- save - Variable in class loci.plugins.prefs.Option
-
Whether option state should be saved to ImageJ preferences file.
- save() - Method in class loci.formats.tools.EditTiffG
- save(String) - Method in class loci.formats.gui.ImageViewer
-
Saves the current images to the given destination using the current format writer.
- save(String, IFormatWriter) - Method in class loci.formats.gui.ImageViewer
-
Saves to the given data destination using the specified writer in a separate thread.
- SAVE_FILE_SIZE - Static variable in class loci.formats.out.AVIWriter
- SAVE_JUNK_SIG - Static variable in class loci.formats.out.AVIWriter
- SAVE_LIST1_SIZE - Static variable in class loci.formats.out.AVIWriter
- SAVE_LIST1_SUBSIZE - Static variable in class loci.formats.out.AVIWriter
- SAVE_LIST2_SIZE - Static variable in class loci.formats.out.AVIWriter
- SAVE_MOVI - Static variable in class loci.formats.out.AVIWriter
- SAVE_STRF_SIZE - Static variable in class loci.formats.out.AVIWriter
- SAVE_STRN_POS - Static variable in class loci.formats.out.AVIWriter
- saveBytes(int, byte[]) - Method in class loci.formats.FormatWriter
- saveBytes(int, byte[]) - Method in interface loci.formats.IFormatWriter
-
Saves the given image to the current series in the current file.
- saveBytes(int, byte[]) - Method in class loci.formats.ImageWriter
- saveBytes(int, byte[]) - Method in class loci.formats.out.CellH5Writer
-
Saves the given image to the specified (possibly already open) file.
- saveBytes(int, byte[]) - Method in class loci.formats.WriterWrapper
- saveBytes(int, byte[], int, int, int, int) - Method in interface loci.formats.IFormatWriter
-
Saves the given image tile to the current series in the current file.
- saveBytes(int, byte[], int, int, int, int) - Method in class loci.formats.ImageWriter
- saveBytes(int, byte[], int, int, int, int) - Method in class loci.formats.out.APNGWriter
- saveBytes(int, byte[], int, int, int, int) - Method in class loci.formats.out.AVIWriter
- saveBytes(int, byte[], int, int, int, int) - Method in class loci.formats.out.CellH5Writer
- saveBytes(int, byte[], int, int, int, int) - Method in class loci.formats.out.DicomWriter
- saveBytes(int, byte[], int, int, int, int) - Method in class loci.formats.out.EPSWriter
- saveBytes(int, byte[], int, int, int, int) - Method in class loci.formats.out.ICSWriter
- saveBytes(int, byte[], int, int, int, int) - Method in class loci.formats.out.ImageIOWriter
- saveBytes(int, byte[], int, int, int, int) - Method in class loci.formats.out.JavaWriter
- saveBytes(int, byte[], int, int, int, int) - Method in class loci.formats.out.JPEG2000Writer
- saveBytes(int, byte[], int, int, int, int) - Method in class loci.formats.out.OMETiffWriter
- saveBytes(int, byte[], int, int, int, int) - Method in class loci.formats.out.OMEXMLWriter
- saveBytes(int, byte[], int, int, int, int) - Method in class loci.formats.out.QTWriter
- saveBytes(int, byte[], int, int, int, int) - Method in class loci.formats.out.TiffWriter
- saveBytes(int, byte[], int, int, int, int) - Method in class loci.formats.out.V3DrawWriter
- saveBytes(int, byte[], int, int, int, int) - Method in class loci.formats.WriterWrapper
- saveBytes(int, byte[], Region) - Method in class loci.formats.FormatWriter
- saveBytes(int, byte[], Region) - Method in interface loci.formats.IFormatWriter
-
Saves the given image tile to the current series in the current file.
- saveBytes(int, byte[], Region) - Method in class loci.formats.ImageWriter
- saveBytes(int, byte[], Region) - Method in class loci.formats.WriterWrapper
- saveBytes(int, byte[], IFD) - Method in class loci.formats.out.TiffWriter
-
Saves the given image to the specified (possibly already open) file.
- saveBytes(int, byte[], IFD, int, int, int, int) - Method in class loci.formats.out.OMETiffWriter
- saveBytes(int, byte[], IFD, int, int, int, int) - Method in class loci.formats.out.PyramidOMETiffWriter
- saveBytes(int, byte[], IFD, int, int, int, int) - Method in class loci.formats.out.TiffWriter
-
Saves the given image to the specified series in the current file.
- saveComment(String, String) - Method in class loci.formats.out.OMETiffWriter
- saveCompressedBytes(int, byte[], int, int, int, int) - Method in interface loci.formats.ICompressedTileWriter
-
Save a compressed tile to the current output file.
- saveCompressedBytes(int, byte[], int, int, int, int) - Method in class loci.formats.ImageWriter
- saveCompressedBytes(int, byte[], int, int, int, int) - Method in class loci.formats.out.DicomWriter
- saveCompressedBytes(int, byte[], int, int, int, int) - Method in class loci.formats.out.OMETiffWriter
- saveCompressedBytes(int, byte[], int, int, int, int) - Method in class loci.formats.out.TiffWriter
- saveCompressedBytes(int, byte[], int, int, int, int) - Method in class loci.formats.WriterWrapper
- savedbLength - Variable in class loci.formats.out.AVIWriter
- saveDefaults() - Method in class loci.plugins.in.ImportProcess
-
Performed following ImportStep.FILE notification.
- savedToMemo - Variable in class loci.formats.Memoizer
-
Whether the
ReaderWrapper.readerinstance was saved to a memo file onMemoizer.setId(String). - saveFile(File) - Method in class loci.formats.tools.EditTiffG
- saveidx1Length - Variable in class loci.formats.out.AVIWriter
- saveImage(int, BufferedImage) - Method in class loci.formats.gui.BufferedImageWriter
-
Saves the given BufferedImage to the current file.
- saveImage(int, BufferedImage, int, int, int, int) - Method in class loci.formats.gui.BufferedImageWriter
-
Saves the given BufferedImage to the current file.
- saveLUTs(ImagePlus, List<LUT>) - Static method in class loci.plugins.in.ImagePlusReader
- saveMemo() - Method in class loci.formats.Memoizer
-
Save a reader including all reader wrappers inside a memo file.
- saveOption() - Method in class loci.plugins.prefs.BooleanOption
- saveOption() - Method in class loci.plugins.prefs.DoubleOption
- saveOption() - Method in class loci.plugins.prefs.Option
-
Saves the option's value to the ImageJ preferences file.
- saveOption() - Method in class loci.plugins.prefs.StringOption
- saveOptions() - Method in class loci.plugins.prefs.OptionsList
-
Saves option values to the ImageJ preferences file.
- saveOriginalMetadata - Variable in class loci.formats.FormatReader
-
Whether or not to save proprietary metadata in the MetadataStore.
- savePlane(int, Object) - Method in class loci.formats.FormatWriter
- savePlane(int, Object) - Method in interface loci.formats.IFormatWriter
-
Saves the given image plane to the current series in the current file.
- savePlane(int, Object) - Method in class loci.formats.ImageWriter
- savePlane(int, Object) - Method in class loci.formats.WriterWrapper
- savePlane(int, Object, int, int, int, int) - Method in class loci.formats.FormatWriter
- savePlane(int, Object, int, int, int, int) - Method in interface loci.formats.IFormatWriter
-
Saves the given image plane to the current series in the current file.
- savePlane(int, Object, int, int, int, int) - Method in class loci.formats.ImageWriter
- savePlane(int, Object, int, int, int, int) - Method in class loci.formats.out.ImageIOWriter
- savePlane(int, Object, int, int, int, int) - Method in class loci.formats.WriterWrapper
- savePlane(int, Object, Region) - Method in class loci.formats.FormatWriter
- savePlane(int, Object, Region) - Method in interface loci.formats.IFormatWriter
-
Saves the given image plane to the current series in the current file.
- savePlane(int, Object, Region) - Method in class loci.formats.ImageWriter
- savePlane(int, Object, Region) - Method in class loci.formats.WriterWrapper
- saveReader(IFormatReader) - Method in interface loci.formats.Memoizer.Deser
- saveReader(IFormatReader) - Method in class loci.formats.Memoizer.KryoDeser
- saveReader(IFormatReader) - Method in class loci.formats.Memoizer.RandomAccessDeser
- saveReleaseVersion(String) - Method in interface loci.formats.Memoizer.Deser
- saveReleaseVersion(String) - Method in class loci.formats.Memoizer.KryoDeser
- saveReleaseVersion(String) - Method in class loci.formats.Memoizer.RandomAccessDeser
- saveRevision(String) - Method in interface loci.formats.Memoizer.Deser
- saveRevision(String) - Method in class loci.formats.Memoizer.KryoDeser
- saveRevision(String) - Method in class loci.formats.Memoizer.RandomAccessDeser
- saveROIs(MetadataStore) - Static method in class loci.plugins.util.ROIHandler
-
Save ROIs in the ROI manager to the given MetadataStore.
- saveStart(File) - Method in interface loci.formats.Memoizer.Deser
- saveStart(File) - Method in class loci.formats.Memoizer.KryoDeser
- saveStart(File) - Method in class loci.formats.Memoizer.RandomAccessDeser
- saveStop() - Method in interface loci.formats.Memoizer.Deser
- saveStop() - Method in class loci.formats.Memoizer.KryoDeser
- saveStop() - Method in class loci.formats.Memoizer.RandomAccessDeser
- saveStream - Variable in class loci.formats.Memoizer.RandomAccessDeser
- saveVersion(Integer) - Method in interface loci.formats.Memoizer.Deser
- saveVersion(Integer) - Method in class loci.formats.Memoizer.KryoDeser
- saveVersion(Integer) - Method in class loci.formats.Memoizer.RandomAccessDeser
- sb - Variable in class loci.formats.gui.ImageViewer
- sb - Variable in class loci.formats.in.FEITiffReader.FEIHandler
- SBIGReader - Class in loci.formats.in
-
SBIGReader is the file format reader for SBIG files.
- SBIGReader() - Constructor for class loci.formats.in.SBIGReader
-
Constructs a new SBIG reader.
- SBYTE - Enum constant in enum class loci.formats.tiff.IFDType
- scale - Variable in class loci.formats.in.QTReader
-
Amount to subtract from each offset.
- scale(double, double) - Method in class loci.plugins.util.RecordedImageProcessor
- scale(BufferedImage, int, int, boolean) - Static method in class loci.formats.gui.AWTImageTools
-
Scales the image using the most appropriate API, with the resultant image having the same color model as the original image.
- SCALE - Static variable in class loci.formats.in.FV1000Reader
- SCALE_BAR - Enum constant in enum class loci.formats.in.BaseZeissReader.FeatureType
- SCALE_BAR - Static variable in class loci.formats.in.LeicaHandler.ROI
- SCALE_BAR - Static variable in class loci.formats.in.LeicaMicrosystemsMetadata.ROI
- SCALE_BAR - Static variable in class loci.formats.in.LIFReader.ROI
- SCALE_BAR - Static variable in class loci.formats.in.ZeissLSMReader
- scale2D(BufferedImage, int, int, Object, GraphicsConfiguration) - Static method in class loci.formats.gui.AWTImageTools
-
Scales the image using the Java2D API, with the resultant image optimized for the given graphics configuration.
- scale2D(BufferedImage, int, int, Object, ColorModel) - Static method in class loci.formats.gui.AWTImageTools
-
Scales the image using the Java2D API, with the resultant image having the given color model.
- scaleAWT(BufferedImage, int, int, int) - Static method in class loci.formats.gui.AWTImageTools
-
Scales the image using the AWT Image API.
- scaleCoordinate(int, int) - Method in class loci.formats.in.VentanaReader
- scaleFactor - Variable in class loci.formats.in.FakeReader
-
Scale factor for gradient, if any.
- scaleFactor - Variable in class loci.formats.in.TissueFAXSReader.ScanRegion
- scaleFactor - Variable in class loci.formats.in.ZeissCZIReader
- scaleX - Variable in class loci.formats.in.LeicaHandler.ROI
- scaleX - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.ROI
- scaleX - Variable in class loci.formats.in.LIFReader.ROI
- scaleY - Variable in class loci.formats.in.LeicaHandler.ROI
- scaleY - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.ROI
- scaleY - Variable in class loci.formats.in.LIFReader.ROI
- scaling - Variable in class loci.formats.in.SimplePCITiffReader
- Scaling() - Constructor for class loci.formats.in.ZeissTIFFHandler.Scaling
- SCALING - Enum constant in enum class loci.formats.in.BaseZeissReader.Context
- scalings - Variable in class loci.formats.in.ZeissTIFFHandler
- SCAN_ARC - Enum constant in enum class loci.formats.dicom.DicomAttribute
- SCAN_LENGTH - Enum constant in enum class loci.formats.dicom.DicomAttribute
- SCAN_OPTIONS - Enum constant in enum class loci.formats.dicom.DicomAttribute
- SCAN_TIME - Static variable in class loci.formats.in.NDPIReader
- SCAN_VELOCITY - Enum constant in enum class loci.formats.dicom.DicomAttribute
- scanData(byte[], int, boolean) - Static method in class loci.formats.ImageTools
-
Scan a plane for the channel min and max values.
- scanDim - Variable in class loci.formats.in.ZeissCZIReader
- scanDirectory(Location) - Method in class loci.formats.in.DCIMGReader
- scanDirectory(Location, boolean) - Method in class loci.formats.in.DicomReader
-
Scan the given directory for files that belong to this dataset.
- scanFormat(String, String) - Static method in class loci.formats.in.FV1000Reader
- SCANNERSET - Static variable in class loci.formats.in.LeicaReader
- SCANNING_SEQUENCE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- ScanRegion() - Constructor for class loci.formats.in.TissueFAXSReader.ScanRegion
- ScanrHandler() - Constructor for class loci.formats.in.ScanrReader.ScanrHandler
- ScanrReader - Class in loci.formats.in
-
ScanrReader is the file format reader for Olympus ScanR datasets.
- ScanrReader() - Constructor for class loci.formats.in.ScanrReader
-
Constructs a new ScanR reader.
- ScanrReader.ScanrHandler - Class in loci.formats.in
- scanRX - Variable in class loci.formats.in.SDTInfo
- scanRY - Variable in class loci.formats.in.SDTInfo
- scanValues - Variable in class loci.formats.in.PrairieMetadata
-
Table of key/value pairs at the top level.
- scanX - Variable in class loci.formats.in.SDTInfo
- scanY - Variable in class loci.formats.in.SDTInfo
- SCENE_CAPTURE_TYPE - Static variable in class loci.formats.tiff.IFD
- SCENE_TYPE - Static variable in class loci.formats.tiff.IFD
- SCHEMA_2010_03 - Static variable in class loci.formats.in.LeicaSCNReader
- SCHEMA_2010_10 - Static variable in class loci.formats.in.LeicaSCNReader
- SCHEMA_CLASSPATH_READER - Static variable in class loci.formats.services.OMEXMLServiceImpl
-
Finds OME-XML schema definitions in specifications.jar.
- SCHEMA_PATH - Static variable in class loci.formats.services.OMEXMLServiceImpl
- SCHEMA_URL_PATTERN - Static variable in class loci.formats.services.OMEXMLServiceImpl
-
The pattern of system ID URLs for OME-XML schema definitions.
- schemaType - Variable in class loci.formats.in.ZeissCZIReader.AttachmentEntry
- schemaType - Variable in class loci.formats.in.ZeissCZIReader.DirectoryEntry
- SCNHandler() - Constructor for class loci.formats.in.BioRadSCNReader.SCNHandler
- SCRAMBLE - Enum constant in enum class loci.formats.in.SPEReader.SpeHeaderEntry
- SCREENING - Static variable in class loci.formats.in.FlexReader
- screenName - Variable in class loci.formats.in.ColumbusReader.MeasurementHandler
- screens - Variable in class loci.formats.in.FakeReader
- SDTInfo - Class in loci.formats.in
-
SDTInfo encapsulates the header information for Becker & Hickl SPC-Image SDT files.
- SDTInfo(RandomAccessInputStream, Hashtable) - Constructor for class loci.formats.in.SDTInfo
-
Constructs a new SDT header by reading values from the given input source, populating the given metadata table.
- SDTReader - Class in loci.formats.in
-
SDTReader is the file format reader for Becker & Hickl SPC-Image SDT files.
- SDTReader() - Constructor for class loci.formats.in.SDTReader
-
Constructs a new SDT reader.
- SDTWidgets - Class in loci.plugins.config
-
Custom widgets for configuring Bio-Formats SDT support.
- SDTWidgets() - Constructor for class loci.plugins.config.SDTWidgets
- SearchableWindow - Class in loci.plugins.util
-
Text panel with search capabilities.
- SearchableWindow(String, String, String, int, int) - Constructor for class loci.plugins.util.SearchableWindow
- SearchableWindow.SearchBox - Class in loci.plugins.util
- searchBox - Variable in class loci.plugins.util.SearchableWindow.SearchBox
- SearchBox(SearchableWindow) - Constructor for class loci.plugins.util.SearchableWindow.SearchBox
- searchPane - Variable in class loci.plugins.util.SearchableWindow.SearchBox
- SECONDARY_CAPTURE_DEVICE_ID - Enum constant in enum class loci.formats.dicom.DicomAttribute
- SECONDARY_CAPTURE_DEVICE_MANUFACTURER - Enum constant in enum class loci.formats.dicom.DicomAttribute
- SECONDARY_CAPTURE_DEVICE_MODEL_NAME - Enum constant in enum class loci.formats.dicom.DicomAttribute
- SECONDARY_CAPTURE_DEVICE_SOFTWARE_VERSION - Enum constant in enum class loci.formats.dicom.DicomAttribute
- SEED - Static variable in class loci.formats.in.FakeReader
- seekStartOfPlane(int, long, long) - Method in class loci.formats.in.LIFReader
- seekStartOfPlane(int, long, long) - Method in class loci.formats.in.LOFReader
- seekToFrameStart(OBFReader.Stack, long) - Method in class loci.formats.in.OBFReader
- seekToNextMarker() - Method in class loci.formats.in.ZeissLMSReader
- seekToPlaneOffset(long, int, int) - Method in class loci.formats.FormatWriter
-
Seek to the given (x, y) coordinate of the image that starts at the given offset.
- Segment() - Constructor for class loci.formats.in.ZeissCZIReader.Segment
- Segment(String) - Constructor for class loci.formats.in.ZeissCZIReader.Segment
- Segment(ZeissCZIReader.Segment) - Constructor for class loci.formats.in.ZeissCZIReader.Segment
- SEGMENTATION_PATH - Static variable in class loci.formats.in.BDVReader.H5Constants
- SEGMENTATION_PATH - Static variable in class loci.formats.in.CellH5Reader.CellH5Constants
- SEGMENTED_BLUE_LUT_DATA - Enum constant in enum class loci.formats.dicom.DicomAttribute
- SEGMENTED_GREEN_LUT_DATA - Enum constant in enum class loci.formats.dicom.DicomAttribute
- SEGMENTED_RED_LUT_DATA - Enum constant in enum class loci.formats.dicom.DicomAttribute
- segments - Variable in class loci.formats.in.ZeissCZIReader
- SeikoReader - Class in loci.formats.in
-
SeikoReader is the file format reader for Seiko .xqd/.xqf files.
- SeikoReader() - Constructor for class loci.formats.in.SeikoReader
-
Constructs a new Seiko reader.
- SELECTED_CHANNELS - Static variable in class loci.formats.in.CellSensReader
- SELECTED_FRAMES - Static variable in class loci.formats.in.CellSensReader
- selectLine(int) - Method in class loci.plugins.util.SearchableWindow
- SEM_DOMAIN - Static variable in class loci.formats.FormatTools
-
Identifies the scanning electron microscopy domain.
- SENSING_METHOD - Static variable in class loci.formats.tiff.IFD
- SENSITIVITY - Enum constant in enum class loci.formats.dicom.DicomAttribute
- SENSOR_KEYS - Static variable in class loci.formats.in.ICSReader
- sensorHeight - Variable in class loci.formats.in.MRWReader
- sensorWidth - Variable in class loci.formats.in.MRWReader
- separatedFork - Variable in class loci.formats.in.QTReader
-
Flag indicating whether the resource and data fork are separated.
- SEQ_FILTERSET - Static variable in class loci.formats.in.LeicaReader
- SEQ_FILTERSET_END - Static variable in class loci.formats.in.LeicaReader
- SEQ_SCANNERSET - Static variable in class loci.formats.in.LeicaReader
- SEQ_SCANNERSET_END - Static variable in class loci.formats.in.LeicaReader
- SEQReader - Class in loci.formats.in
-
SEQReader is the file format reader for Image-Pro Sequence files.
- SEQReader() - Constructor for class loci.formats.in.SEQReader
-
Constructs a new Image-Pro SEQ reader.
- sequence - Variable in class loci.formats.in.PrairieMetadata.Frame
-
The
<Sequence>containing this<Frame>. - sequence(int) - Method in class loci.formats.in.PrairieReader
-
Gets the first sequence associated with the given series.
- sequence(int, int) - Method in class loci.formats.in.PrairieReader
-
Gets the sequence associated with the given series and time point.
- sequence(int, int, int) - Method in class loci.formats.in.PrairieReader
-
Gets the sequence associated with the given time point and stage position.
- Sequence(Element) - Constructor for class loci.formats.in.PrairieMetadata.Sequence
-
Creates a new sequence by parsing the given
<Sequence>element. - SEQUENCE_DELIMITATION_ITEM - Enum constant in enum class loci.formats.dicom.DicomAttribute
- SEQUENCE_NAME - Enum constant in enum class loci.formats.dicom.DicomAttribute
- SEQUENCE_OF_ULTRASOUND_REGIONS - Enum constant in enum class loci.formats.dicom.DicomAttribute
- SEQUENCE_VARIANT - Enum constant in enum class loci.formats.dicom.DicomAttribute
- sequences - Variable in class loci.formats.in.PrairieMetadata
-
<Sequence>elements, keyed on each sequence'scycle. - sequences - Variable in class loci.formats.in.PrairieReader
-
List of Prairie metadata
Sequences, ordered by cycle. - sequenceValues - Variable in class loci.formats.in.PrairieMetadata.Sequence
-
Table of key/value pairs for this
<Sequence>. - sequential - Variable in class loci.formats.FormatWriter
-
Whether or not we are writing planes sequentially.
- sequential - Variable in class loci.formats.in.LeicaReader
- SEQUENTIALSET - Static variable in class loci.formats.in.LeicaReader
- sequentialTileByteCounts - Variable in class loci.formats.tiff.TiffSaver
- sequentialTileFilePointer - Variable in class loci.formats.tiff.TiffSaver
- sequentialTileOffsets - Variable in class loci.formats.tiff.TiffSaver
-
Store tile offsets and original file pointer when writing sequentially.
- sequentialWrite - Variable in class loci.formats.tiff.TiffSaver
- ser - Variable in class loci.formats.Memoizer
- SERIAL_NUMBER - Static variable in class loci.formats.in.NDPIReader
- SERIALIZED_MASK - Static variable in class loci.formats.in.CellSensReader
- serialNumber - Variable in class loci.formats.in.BioRadSCNReader
- serialNumber - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataTempBuffer
- serialNumber - Variable in class loci.formats.in.LIFReader
- serialNumber - Variable in class loci.formats.in.NDPIReader
- serialVersionUID - Static variable in class org.libjpegturbo.turbojpeg.TJTransform
- series - Variable in class loci.formats.FileStitcher
-
The number of the current series (non flat).
- series - Variable in class loci.formats.FormatReader
-
The number of the current series (non flat).
- series - Variable in class loci.formats.FormatWriter
-
Current series.
- series - Variable in class loci.formats.gui.DataConverter
- series - Variable in class loci.formats.in.CellomicsReader.ChannelFile
- series - Variable in class loci.formats.in.ColumbusReader.Plane
- series - Variable in class loci.formats.in.CV7000Reader.Plane
- series - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.MultipleImagesReader
- series - Variable in class loci.formats.in.OBFReader.State
- series - Variable in class loci.formats.in.OpenlabReader.PlaneInfo
- series - Variable in class loci.formats.in.TecanReader.Image
- series - Variable in class loci.formats.in.ZeissCZIReader.Coordinate
- series - Variable in class loci.plugins.macro.LociFunctions
- series - Variable in class loci.plugins.util.BFVirtualStack
- SERIES - Enum constant in enum class loci.plugins.in.ImportStep
- SERIES - Static variable in class loci.formats.in.LeicaReader
-
IFD tags.
- SERIES_DATE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- SERIES_DESCRIPTION - Enum constant in enum class loci.formats.dicom.DicomAttribute
- SERIES_INSTANCE_UID - Enum constant in enum class loci.formats.dicom.DicomAttribute
- SERIES_NAME - Static variable in class loci.formats.FormatTools
- SERIES_NUM - Static variable in class loci.formats.FormatTools
-
Patterns to be used when constructing a pattern for output filenames.
- SERIES_NUMBER - Enum constant in enum class loci.formats.dicom.DicomAttribute
- SERIES_PREFIXES - Static variable in class loci.formats.in.KLBReader
- SERIES_TIME - Enum constant in enum class loci.formats.dicom.DicomAttribute
- seriesCount - Variable in class loci.formats.in.BDVReader
- seriesCount - Variable in class loci.formats.in.ImarisHDFReader
- seriesCounts - Variable in class loci.formats.in.ZeissLSMReader
- seriesDescriptions - Variable in class loci.formats.in.LeicaReader
- SeriesDialog - Class in loci.plugins.in
-
Bio-Formats Importer series chooser dialog box.
- SeriesDialog(ImportProcess) - Constructor for class loci.plugins.in.SeriesDialog
-
Creates a series chooser dialog for the Bio-Formats Importer.
- seriesFiles - Variable in class loci.formats.in.ScanrReader
- seriesIFDs - Variable in class loci.formats.in.IonpathMIBITiffReader
- seriesIndex - Variable in class loci.formats.in.LeicaSCNReader.LeicaSCNHandler
- seriesInfo - Variable in class loci.formats.in.MNGReader
- SeriesInfo() - Constructor for class loci.formats.in.MNGReader.SeriesInfo
- SeriesInfo(int, int) - Constructor for class loci.plugins.in.ThumbLoader.SeriesInfo
- seriesLabels - Variable in class loci.plugins.in.ImportProcess
-
A descriptive label for each series.
- seriesMetadata - Variable in class loci.formats.CoreMetadata
-
Non-core metadata associated with this series.
- seriesNames - Variable in class loci.formats.in.LeicaReader
- seriesOn - Variable in class loci.plugins.in.ImporterOptions
- seriesRow - Variable in class loci.formats.gui.DataConverter
- seriesStream - Variable in class loci.formats.in.BrukerReader
- seriesToCoreIndex(int) - Method in class loci.formats.FileStitcher
- seriesToCoreIndex(int) - Method in class loci.formats.FormatReader
- seriesToCoreIndex(int) - Method in interface loci.formats.IFormatReader
-
Deprecated.This method is no longer required for sub-resolution support.
- seriesToCoreIndex(int) - Method in class loci.formats.ImageReader
- seriesToCoreIndex(int) - Method in class loci.formats.ReaderWrapper
- seriesToCoreIndex(int) - Method in class loci.formats.SubResolutionFormatReader
- seriesToCoreIndex(int) - Method in class loci.formats.WrappedReader
- seriesToIFD - Variable in class loci.formats.in.MinimalTiffReader
- seriesToWellArea(int) - Method in class loci.formats.in.CellVoyagerReader
-
Returns the well index (in the field
CellVoyagerReader.wells) and the area index (in the fieldCellVoyagerReader.WellInfo.areascorresponding to the specified series. - seriesTypes - Variable in class loci.formats.in.IonpathMIBITiffReader
- serverMap - Static variable in class loci.formats.in.FlexReader
-
Mapping from server names stored in the .mea file to actual server names.
- service - Variable in class loci.formats.codec.JPEGXRCodec
- service - Variable in class loci.formats.FormatReader
- service - Variable in class loci.formats.in.CellWorxReader
- service - Variable in class loci.formats.in.HamamatsuVMSReader
- service - Variable in class loci.formats.in.NDPIReader
- service - Variable in class loci.formats.in.OMETiffReader
-
OMEXMLService that can be used to manipulate OME-XML.
- service - Variable in class loci.formats.in.TileJPEGReader
- service - Variable in class loci.formats.Memoizer
- service - Variable in class loci.formats.out.OMETiffWriter
- service - Variable in class loci.formats.out.OMEXMLWriter
- serviceRegistry - Variable in class loci.formats.services.JAIIIOServiceImpl
- set(int, int) - Method in class loci.plugins.util.RecordedImageProcessor
- set(int, int, int) - Method in class loci.plugins.util.RecordedImageProcessor
- set(int, int, T) - Method in class loci.formats.MetadataList
-
Set the array element for the specified indexes.
- set(String, String) - Method in class loci.formats.in.DynamicMetadataOptions
-
Set property
nametovalue. - set(List<T>, int, T, T) - Method in class loci.plugins.in.ImporterOptions
- setAllowOpenFiles(boolean) - Method in class loci.formats.ImageReader
-
Toggles whether or not file system access is allowed when doing type detection.
- setAntialiasedText(boolean) - Method in class loci.plugins.util.RecordedImageProcessor
- setAssumeEqualStrips(boolean) - Method in class loci.formats.tiff.TiffParser
-
Sets whether or not to assume that strips are of equal size.
- setAutomaticallyParseMasks(boolean) - Method in class loci.formats.in.MIASReader
-
Toggle whether or not Mask pixel data should be parsed in setId.
- setAutoscale(boolean) - Method in class loci.plugins.in.ImporterOptions
- setAutoThreshold(int, int) - Method in class loci.plugins.util.RecordedImageProcessor
- setAxisTypes(int[]) - Method in class loci.formats.AxisGuesser
-
Sets the axis type for each dimensional block.
- setAxisTypes(int[]) - Method in class loci.formats.FileStitcher
-
Sets the axis type for each dimensional block.
- setBackgroundValue(double) - Method in class loci.plugins.util.RecordedImageProcessor
- setBigTiff(boolean) - Method in class loci.formats.out.DicomWriter
-
Sets whether or not BigTIFF files should be written.
- setBigTiff(boolean) - Method in class loci.formats.out.TiffWriter
-
Sets whether or not BigTIFF files should be written.
- setBigTiff(boolean) - Method in class loci.formats.tiff.TiffSaver
-
Sets whether or not BigTIFF data should be written.
- setBoolean(String, Boolean) - Method in class loci.formats.in.DynamicMetadataOptions
-
Set property
nameto Booleanvalue. - setByte(int, int) - Method in class loci.formats.in.SPEReader.SpeHeader
-
Private method used to set a Byte value in the SPE header
- setCalibrationTable(float[]) - Method in class loci.plugins.util.RecordedImageProcessor
- setCanChangePattern(boolean) - Method in class loci.formats.FileStitcher
- setCanDetectBigTiff(boolean) - Method in class loci.formats.out.TiffWriter
-
Sets whether or not BigTIFF can be used automatically based upon the input data size (true by default).
- setCanDoUpgradeCheck(boolean) - Method in class loci.formats.UpgradeChecker
-
Set whether or not we are ever allowed to perform an upgrade check.
- setCanLookForND(boolean) - Method in class loci.formats.in.MetamorphReader
- setCategory(int) - Method in class loci.formats.in.BaseZeissReader.Tag
- setCBegin(int, int) - Method in class loci.plugins.in.ImporterOptions
- setCEnd(int, int) - Method in class loci.plugins.in.ImporterOptions
- setChannelGlobalMinMax(int, double, double, int) - Method in interface loci.formats.meta.IMinMaxStore
-
Populates the channel global minimum and maximum.
- setChannelType() - Method in class loci.formats.in.LeicaMicrosystemsMetadata.Channel
- setClass(String, Class<?>) - Method in class loci.formats.in.DynamicMetadataOptions
-
Set property
nameto Classvalue. - setClipRect(Rectangle) - Method in class loci.plugins.util.RecordedImageProcessor
- setCodec() - Method in class loci.formats.out.QTWriter
- setCodec(int) - Method in class loci.formats.out.QTWriter
-
Sets the encoded movie's codec.
- setCodecOptions(CodecOptions) - Method in class loci.formats.FormatWriter
- setCodecOptions(CodecOptions) - Method in interface loci.formats.IFormatWriter
-
Sets the codec options.
- setCodecOptions(CodecOptions) - Method in class loci.formats.ImageWriter
- setCodecOptions(CodecOptions) - Method in class loci.formats.tiff.TiffParser
-
Sets the codec options to be used when decompressing pixel data.
- setCodecOptions(CodecOptions) - Method in class loci.formats.tiff.TiffSaver
-
Sets the codec options.
- setCodecOptions(CodecOptions) - Method in class loci.formats.WriterWrapper
- setColor(int) - Method in class loci.plugins.util.RecordedImageProcessor
- setColor(Color) - Method in class loci.plugins.util.RecordedImageProcessor
- setColorMode(String) - Method in class loci.plugins.in.ImporterOptions
- setColorModel(ColorModel) - Method in class loci.formats.FormatWriter
- setColorModel(ColorModel) - Method in interface loci.formats.IFormatWriter
-
Sets the color model.
- setColorModel(ColorModel) - Method in class loci.formats.ImageWriter
- setColorModel(ColorModel) - Method in class loci.formats.WriterWrapper
- setColorModel(ColorModel) - Method in class loci.plugins.util.RecordedImageProcessor
- setColumnIndex(int) - Method in class loci.formats.internal.WellContainer
- setCompression(String) - Method in class loci.formats.FormatWriter
- setCompression(String) - Method in interface loci.formats.IFormatWriter
-
Sets the current compression type.
- setCompression(String) - Method in class loci.formats.ImageWriter
- setCompression(String) - Method in class loci.formats.WriterWrapper
- setConcatenate(boolean) - Method in class loci.plugins.in.ImporterOptions
- setCore(ArrayList<CoreMetadata>) - Method in class loci.formats.in.LeicaMicrosystemsMetadata.LMSFileReader
- setCoreDimensionSizes(int) - Method in class loci.formats.in.LeicaMicrosystemsMetadata.LMSMetadataExtractor
-
Writes extracted dimension sizes to CoreMetadata
- setCoreIndex(int) - Method in class loci.formats.DelegateReader
- setCoreIndex(int) - Method in class loci.formats.FileStitcher
- setCoreIndex(int) - Method in class loci.formats.FormatReader
- setCoreIndex(int) - Method in interface loci.formats.IFormatReader
-
Deprecated.This method is no longer required for sub-resolution support.
- setCoreIndex(int) - Method in class loci.formats.ImageReader
- setCoreIndex(int) - Method in class loci.formats.in.ZeissLSMReader
- setCoreIndex(int) - Method in class loci.formats.ReaderWrapper
- setCoreIndex(int) - Method in class loci.formats.SubResolutionFormatReader
- setCoreIndex(int) - Method in class loci.formats.WrappedReader
- setCoreMetadata(CoreMetadata) - Method in class loci.formats.in.LeicaMicrosystemsMetadata.MultipleImagesReader
- setCreator(OMEXMLMetadataRoot) - Method in class loci.formats.out.OMETiffWriter
-
Set the Creator attribute on the given OME-XML root object.
- setCrop(boolean) - Method in class loci.plugins.in.ImporterOptions
- setCropRegion(int, Region) - Method in class loci.plugins.in.ImporterOptions
- setCStep(int, int) - Method in class loci.plugins.in.ImporterOptions
- setCurrentPos(int[]) - Method in class loci.formats.cache.Cache
-
Sets the current dimensional position.
- setCustomColor(int, int, Color) - Method in class loci.plugins.in.ImporterOptions
- setDataType(String) - Method in class loci.formats.in.InveonReader
- setDefaultCreationDate(MetadataStore, String, int) - Static method in class loci.formats.MetadataTools
-
Sets a default creation date.
- setDefaultDateEnabled(boolean) - Static method in class loci.formats.MetadataTools
-
Disables the setting of a default creation date.
- setDimensions(int, int, int) - Method in class loci.formats.in.ND2Reader
- setDoCaching(boolean) - Method in class loci.formats.tiff.TiffParser
-
Sets whether or not IFD entries should be cached.
- setDocument(Document) - Method in class loci.formats.gui.XMLWindow
-
Displays XML from the given document.
- setDocumentLocator(Locator) - Method in class loci.formats.in.OMEXMLReader.OMEXMLHandler
- setDoRecording(boolean) - Method in class loci.plugins.util.RecordedImageProcessor
- setDouble(String, Double) - Method in class loci.formats.in.DynamicMetadataOptions
-
Set property
nameto Doublevalue. - setElem(int, int) - Method in class loci.formats.gui.SignedByteBuffer
- setElem(int, int) - Method in class loci.formats.gui.UnsignedIntBuffer
- setElem(int, int, int) - Method in class loci.formats.gui.SignedByteBuffer
- setElem(int, int, int) - Method in class loci.formats.gui.SignedShortBuffer
- setElem(int, int, int) - Method in class loci.formats.gui.UnsignedIntBuffer
- setElemDouble(int, double) - Method in class loci.formats.gui.UnsignedIntBuffer
- setElemDouble(int, int, double) - Method in class loci.formats.gui.UnsignedIntBuffer
- setElemFloat(int, float) - Method in class loci.formats.gui.UnsignedIntBuffer
- setElemFloat(int, int, float) - Method in class loci.formats.gui.UnsignedIntBuffer
- setEncoding(String) - Method in class loci.formats.tiff.TiffParser
-
Sets the encoding to use for tags with ASCII values.
- setEnum(String, T) - Method in class loci.formats.in.DynamicMetadataOptions
-
Set property
nameto enumerated typevalue. - setExtraMetadata(String) - Method in class loci.formats.out.DicomWriter
- setExtraMetadata(String) - Method in interface loci.formats.out.IExtraMetadataWriter
-
Provide additional metadata that should be written as part of this dataset.
- setf(int, float) - Method in class loci.plugins.util.RecordedImageProcessor
- setf(int, int, float) - Method in class loci.plugins.util.RecordedImageProcessor
- setFieldCount(int) - Method in class loci.formats.internal.WellContainer
- setFile(String) - Method in interface loci.formats.services.JHDFService
-
Initializes the service on a given file path.
- setFile(String) - Method in class loci.formats.services.JHDFServiceImpl
- setFile(String) - Method in interface loci.formats.services.NetCDFService
-
Initializes the service on a given file path.
- setFile(String) - Method in class loci.formats.services.NetCDFServiceImpl
- setFile(String, File) - Method in class loci.formats.in.DynamicMetadataOptions
-
Set property
nameto file objectvalue. - setFileForWrite(String) - Method in interface loci.formats.services.JHDFService
-
Initializes the service on a given file path.
- setFileForWrite(String) - Method in class loci.formats.services.JHDFServiceImpl
- setFillColor(Byte) - Method in class loci.formats.FormatReader
- setFillColor(Byte) - Method in interface loci.formats.IFormatReader
-
Set the fill value for undefined pixels.
- setFillColor(Byte) - Method in class loci.formats.ImageReader
- setFillColor(Byte) - Method in class loci.formats.ReaderWrapper
- setFilled(boolean) - Method in class loci.formats.ChannelFiller
-
Toggles whether the indices should be factored out.
- setFirstTime(boolean) - Method in class loci.plugins.in.ImporterOptions
- setFixed() - Method in class loci.formats.FilePatternBlock
- setFlattenedList(List<CoreMetadata>) - Method in class loci.formats.CoreMetadataList
- setFlattenedResolutions(boolean) - Method in class loci.formats.DelegateReader
- setFlattenedResolutions(boolean) - Method in class loci.formats.FileStitcher
- setFlattenedResolutions(boolean) - Method in class loci.formats.FormatReader
- setFlattenedResolutions(boolean) - Method in interface loci.formats.IFormatReader
-
Set whether or not to flatten resolutions into individual series.
- setFlattenedResolutions(boolean) - Method in class loci.formats.ImageReader
- setFlattenedResolutions(boolean) - Method in class loci.formats.in.FilePatternReader
- setFlattenedResolutions(boolean) - Method in class loci.formats.ReaderWrapper
- setFloat(String, Float) - Method in class loci.formats.in.DynamicMetadataOptions
-
Set property
nameto Floatvalue. - setFloatArray(float[][]) - Method in class loci.plugins.util.RecordedImageProcessor
- setFont(Font) - Method in class loci.plugins.util.RecordedImageProcessor
- setForceThumbnails(boolean) - Method in class loci.plugins.in.ImporterOptions
- setFramesPerSecond(int) - Method in class loci.formats.FormatWriter
- setFramesPerSecond(int) - Method in interface loci.formats.IFormatWriter
-
Sets the frames per second to use when writing.
- setFramesPerSecond(int) - Method in class loci.formats.ImageWriter
- setFramesPerSecond(int) - Method in class loci.formats.WriterWrapper
- setGroupFiles(boolean) - Method in class loci.formats.DelegateReader
- setGroupFiles(boolean) - Method in class loci.formats.FileStitcher
- setGroupFiles(boolean) - Method in class loci.formats.FormatReader
- setGroupFiles(boolean) - Method in interface loci.formats.IFormatReader
-
Specifies whether or not to force grouping in multi-file formats.
- setGroupFiles(boolean) - Method in class loci.formats.ImageReader
- setGroupFiles(boolean) - Method in class loci.formats.in.FilePatternReader
- setGroupFiles(boolean) - Method in class loci.formats.in.ZipReader
- setGroupFiles(boolean) - Method in class loci.formats.ReaderWrapper
- setGroupFiles(boolean) - Method in class loci.plugins.in.ImporterOptions
- setGroupFiles(String) - Method in class loci.plugins.macro.LociFunctions
- setHeader(byte[]) - Method in class loci.formats.in.SPEReader.SpeHeader
- setHistogramRange(double, double) - Method in class loci.plugins.util.RecordedImageProcessor
- setHistogramSize(int) - Method in class loci.plugins.util.RecordedImageProcessor
- setId(String) - Method in class loci.formats.ChannelFiller
- setId(String) - Method in class loci.formats.ChannelMerger
- setId(String) - Method in class loci.formats.ChannelSeparator
- setId(String) - Method in class loci.formats.DelegateReader
- setId(String) - Method in class loci.formats.DimensionSwapper
- setId(String) - Method in class loci.formats.FileStitcher
- setId(String) - Method in class loci.formats.FormatReader
-
Initialize a reader from the input file name.
- setId(String) - Method in class loci.formats.FormatWriter
-
Initializes a writer from the input file name.
- setId(String) - Method in interface loci.formats.IFormatHandler
-
Sets the current file name.
- setId(String) - Method in class loci.formats.ImageReader
- setId(String) - Method in class loci.formats.ImageWriter
- setId(String) - Method in class loci.formats.in.JPEGReader
- setId(String) - Method in class loci.formats.in.TiffDelegateReader
- setId(String) - Method in class loci.formats.Memoizer
- setId(String) - Method in class loci.formats.out.APNGWriter
- setId(String) - Method in class loci.formats.out.AVIWriter
- setId(String) - Method in class loci.formats.out.CellH5Writer
- setId(String) - Method in class loci.formats.out.DicomWriter
- setId(String) - Method in class loci.formats.out.ICSWriter
- setId(String) - Method in class loci.formats.out.JavaWriter
- setId(String) - Method in class loci.formats.out.OMETiffWriter
- setId(String) - Method in class loci.formats.out.OMEXMLWriter
- setId(String) - Method in class loci.formats.out.QTWriter
- setId(String) - Method in class loci.formats.out.TiffWriter
- setId(String) - Method in class loci.formats.out.V3DrawWriter
- setId(String) - Method in class loci.formats.ReaderWrapper
- setId(String) - Method in class loci.formats.TileStitcher
- setId(String) - Method in class loci.formats.WriterWrapper
- setId(String) - Method in class loci.plugins.in.ImporterOptions
- setId(String) - Method in class loci.plugins.macro.LociFunctions
- setIdWithMetadata(String, XlifDocument) - Method in class loci.formats.in.LOFReader
-
Inits the LOFReader using passed xml (from XLIF) for metadata initiation, instead of reading the LOF's included xml
- setImages(BufferedImage[]) - Method in class loci.formats.gui.ImageViewer
-
Sets the viewer to display the given images.
- setImages(IFormatReader, BufferedImage[]) - Method in class loci.formats.gui.ImageViewer
-
Sets the viewer to display the given images, obtaining corresponding core metadata from the specified format reader.
- setIndex(int) - Method in class loci.formats.in.BaseZeissReader.Tag
- setInputOrder(int, String) - Method in class loci.plugins.in.ImporterOptions
- setInt(int, int) - Method in class loci.formats.in.SPEReader.SpeHeader
-
Private method used to set an Integer value in the SPE header
- setIntArray(int[][]) - Method in class loci.plugins.util.RecordedImageProcessor
- setInteger(String, Integer) - Method in class loci.formats.in.DynamicMetadataOptions
-
Set property
nameto Integervalue. - setIntensity(boolean) - Method in class loci.formats.in.SDTReader
-
Toggles whether the reader should return intensity data only (the sum of each lifetime histogram).
- setInterleaved(boolean) - Method in class loci.formats.FormatWriter
- setInterleaved(boolean) - Method in interface loci.formats.IFormatWriter
-
Sets whether or not the channels in an image are interleaved.
- setInterleaved(boolean) - Method in class loci.formats.ImageWriter
- setInterleaved(boolean) - Method in class loci.formats.WriterWrapper
- setInterpolate(boolean) - Method in class loci.plugins.util.RecordedImageProcessor
- setJPEGImage(byte[], int) - Method in class org.libjpegturbo.turbojpeg.TJDecompressor
-
Associate the JPEG image of length
imageSizebytes stored injpegImagewith this decompressor instance. - setJPEGQuality(int) - Method in class org.libjpegturbo.turbojpeg.TJCompressor
-
Set the JPEG image quality level for subsequent compress operations.
- setJustification(int) - Method in class loci.plugins.util.RecordedImageProcessor
- setKey(int) - Method in class loci.formats.in.BaseZeissReader.Tag
- setKeyValue(String, String) - Method in class loci.formats.meta.OriginalMetadataAnnotation
-
Set the key/value metadata pair for this annotation.
- setLegacy(boolean) - Method in class loci.formats.DelegateReader
-
Sets whether to use the legacy reader by default.
- setLength(Double) - Method in class loci.formats.in.LeicaMicrosystemsMetadata.Dimension
- setLineWidth(int) - Method in class loci.plugins.util.RecordedImageProcessor
- setLittleEndian(boolean) - Method in class loci.formats.tiff.TiffSaver
-
Sets whether or not little-endian data should be written.
- setLittleEndian(RandomAccessInputStream) - Method in class loci.formats.in.MRCReader
-
Detect the correct endianness and set the stream accordingly.
- setLocation(String) - Method in class loci.plugins.in.ImporterOptions
- setLong(int, int) - Method in class loci.formats.in.SPEReader.SpeHeader
-
Private method used to set a Long value in the SPE header
- setLong(String, Long) - Method in class loci.formats.in.DynamicMetadataOptions
-
Set property
nameto Longvalue. - setLutAnimation(boolean) - Method in class loci.plugins.util.RecordedImageProcessor
- setLUTs(LUT[]) - Method in class loci.plugins.util.VirtualImagePlus
- setMask(ImageProcessor) - Method in class loci.plugins.util.RecordedImageProcessor
- setMetadataFiltered(boolean) - Method in class loci.formats.DelegateReader
- setMetadataFiltered(boolean) - Method in class loci.formats.FormatReader
- setMetadataFiltered(boolean) - Method in interface loci.formats.IFormatReader
-
Specifies whether ugly metadata (entries with unprintable characters, and extremely large entries) should be discarded from the metadata table.
- setMetadataFiltered(boolean) - Method in class loci.formats.ImageReader
- setMetadataFiltered(boolean) - Method in class loci.formats.in.FilePatternReader
- setMetadataFiltered(boolean) - Method in class loci.formats.ReaderWrapper
- setMetadataFiltered(String) - Method in class loci.plugins.macro.LociFunctions
- setMetadataLevel(MetadataLevel) - Method in class loci.formats.in.DefaultMetadataOptions
- setMetadataLevel(MetadataLevel) - Method in class loci.formats.in.DynamicMetadataOptions
- setMetadataLevel(MetadataLevel) - Method in interface loci.formats.in.MetadataOptions
-
Set the metadata level.
- setMetadataOfMultipleImagesReaders() - Method in class loci.formats.in.XLEFReader
- setMetadataOptions(MetadataOptions) - Method in class loci.formats.DelegateReader
- setMetadataOptions(MetadataOptions) - Method in class loci.formats.FileStitcher
- setMetadataOptions(MetadataOptions) - Method in class loci.formats.FormatHandler
- setMetadataOptions(MetadataOptions) - Method in class loci.formats.ImageReader
- setMetadataOptions(MetadataOptions) - Method in class loci.formats.ImageWriter
- setMetadataOptions(MetadataOptions) - Method in interface loci.formats.IMetadataConfigurable
- setMetadataOptions(MetadataOptions) - Method in class loci.formats.ReaderWrapper
- setMetadataOptions(MetadataOptions) - Method in class loci.formats.WriterWrapper
- setMetadataRetrieve(MetadataRetrieve) - Method in class loci.formats.FormatWriter
- setMetadataRetrieve(MetadataRetrieve) - Method in interface loci.formats.IFormatWriter
-
Sets the metadata retrieval object from which to retrieve standardized metadata.
- setMetadataRetrieve(MetadataRetrieve) - Method in class loci.formats.ImageWriter
- setMetadataRetrieve(MetadataRetrieve) - Method in class loci.formats.WriterWrapper
- setMetadataStore(MetadataStore) - Method in class loci.formats.DelegateReader
- setMetadataStore(MetadataStore) - Method in class loci.formats.FileStitcher
- setMetadataStore(MetadataStore) - Method in class loci.formats.FormatReader
- setMetadataStore(MetadataStore) - Method in interface loci.formats.IFormatReader
-
Sets the default metadata store for this reader.
- setMetadataStore(MetadataStore) - Method in class loci.formats.ImageReader
- setMetadataStore(MetadataStore) - Method in class loci.formats.in.FilePatternReader
- setMetadataStore(MetadataStore) - Method in class loci.formats.Memoizer
- setMetadataStore(MetadataStore) - Method in class loci.formats.ReaderWrapper
- setMetadataTempBuffer(MetadataTempBuffer) - Method in class loci.formats.in.LeicaMicrosystemsMetadata.MultipleImagesReader
- setMinAndMax(double, double) - Method in class loci.plugins.util.RecordedImageProcessor
- setMinMaxStore(IMinMaxStore) - Method in class loci.formats.MinMaxCalculator
-
Sets the active min-max store for the calculator.
- setModulo(OMEXMLMetadata, Modulo) - Method in class loci.formats.meta.ModuloAnnotation
-
Set the value of this annotation using the given Modulo object
- setMustGroup(boolean) - Method in class loci.plugins.in.ImporterOptions
- setNormalized(boolean) - Method in class loci.formats.DelegateReader
- setNormalized(boolean) - Method in class loci.formats.FileStitcher
- setNormalized(boolean) - Method in class loci.formats.FormatReader
- setNormalized(boolean) - Method in interface loci.formats.IFormatReader
-
Specifies whether or not to normalize float data.
- setNormalized(boolean) - Method in class loci.formats.ImageReader
- setNormalized(boolean) - Method in class loci.formats.in.FilePatternReader
- setNormalized(boolean) - Method in class loci.formats.ReaderWrapper
- setNormalized(Boolean) - Method in class loci.plugins.macro.LociFunctions
- setNumeric() - Method in class loci.formats.FilePatternBlock
- setOffsetInfo(int, int, int, int) - Method in class loci.formats.in.DeltavisionReader
-
This method calculates the size of a w, t, z section depending on which sequence is being used
- setOffsets(String, long[][]) - Method in class loci.formats.in.ND2Reader
-
Change the underlying file path and pixel data offsets, keeping all other metadata the same.
- setOpenAllSeries(boolean) - Method in class loci.plugins.in.ImporterOptions
- setOrder(int, int) - Method in class loci.formats.cache.CacheStrategy
- setOrder(int, int) - Method in interface loci.formats.cache.ICacheStrategy
-
Sets the order in which objects should be loaded along each axis.
- setOriginalMetadataPopulated(boolean) - Method in class loci.formats.DelegateReader
- setOriginalMetadataPopulated(boolean) - Method in class loci.formats.FileStitcher
- setOriginalMetadataPopulated(boolean) - Method in class loci.formats.FormatReader
- setOriginalMetadataPopulated(boolean) - Method in interface loci.formats.IFormatReader
-
Specifies whether or not to save proprietary metadata in the MetadataStore.
- setOriginalMetadataPopulated(boolean) - Method in class loci.formats.ImageReader
- setOriginalMetadataPopulated(boolean) - Method in class loci.formats.in.FilePatternReader
- setOriginalMetadataPopulated(boolean) - Method in class loci.formats.ReaderWrapper
- setOriginalMetadataPopulated(Boolean) - Method in class loci.plugins.macro.LociFunctions
- setOutputOrder(String) - Method in class loci.formats.DimensionSwapper
-
Sets the output dimension order according to the given string (e.g., "XYZCT").
- setOutputOrder(String) - Method in class loci.formats.out.ICSWriter
-
Set the order in which dimensions should be written to the file.
- setOutputOrder(String) - Method in class loci.formats.out.V3DrawWriter
-
Set the order in which dimensions should be written to the file.
- setPixels() - Method in class loci.formats.in.GIFReader
- setPixels(int, FloatProcessor) - Method in class loci.plugins.util.RecordedImageProcessor
- setPixels(Object) - Method in class loci.plugins.util.RecordedImageProcessor
- setPixelType(int) - Method in class loci.formats.in.LeicaMicrosystemsMetadata.LMSMetadataExtractor
-
Sets CoreMetadata.pixelType depending on extracted x bytesInc
- setPlaneIndexes(int[]) - Method in class loci.plugins.util.BFVirtualStack
- setPlaneMetadataInStore - Variable in class loci.formats.in.LeicaHandler
- setPlateAcquisition(int) - Method in class loci.formats.internal.WellContainer
- setPreLoad(boolean) - Method in class loci.formats.in.SDTReader
-
Toggles whether the reader should pre-load data for increased performance.
- setPriority(int, int) - Method in class loci.formats.cache.CacheStrategy
- setPriority(int, int) - Method in interface loci.formats.cache.ICacheStrategy
-
Sets the priority for caching the given axis.
- setProgressBar(ProgressBar) - Method in class loci.plugins.util.RecordedImageProcessor
- setQuality(int) - Method in class loci.formats.out.QTWriter
-
Sets the quality of the encoded movie.
- setQuiet(boolean) - Method in class loci.plugins.in.ImporterOptions
- setRange(int, int) - Method in class loci.formats.cache.CacheStrategy
- setRange(int, int) - Method in interface loci.formats.cache.ICacheStrategy
-
Sets the number of objects to cache along the given axis.
- setReader(IFormatReader) - Method in class loci.plugins.util.VirtualImagePlus
- setReaderClassList(ClassList<IFormatReader>) - Method in class loci.formats.FileStitcher
-
Set the ClassList object to use when constructing any helper readers.
- setReaderEnabled(FormatEntry, boolean) - Method in class loci.plugins.config.ConfigWindow
- setReaderPref(String, FormatEntry, boolean) - Method in class loci.plugins.config.ConfigWindow
- setReaderWindowless(FormatEntry, boolean) - Method in class loci.plugins.config.ConfigWindow
- setRefCount(int) - Method in class loci.plugins.util.VirtualReader
- setResolution(int) - Method in class loci.formats.DelegateReader
- setResolution(int) - Method in class loci.formats.FileStitcher
- setResolution(int) - Method in class loci.formats.FormatReader
- setResolution(int) - Method in class loci.formats.FormatWriter
- setResolution(int) - Method in class loci.formats.ImageReader
- setResolution(int) - Method in class loci.formats.ImageWriter
- setResolution(int) - Method in interface loci.formats.IPyramidHandler
-
Set the resolution level.
- setResolution(int) - Method in class loci.formats.out.DicomWriter
- setResolution(int) - Method in class loci.formats.ReaderWrapper
- setResolution(int) - Method in class loci.formats.SubResolutionFormatReader
- setResolution(int) - Method in class loci.formats.WrappedReader
- setResolution(int) - Method in class loci.formats.WriterWrapper
- setResolutionLevel(IFD) - Method in class loci.formats.in.MinimalTiffReader
-
Sets the resolution level when we have JPEG 2000 compressed data.
- setResolutions(List<Resolution>) - Method in class loci.formats.FormatWriter
- setResolutions(List<Resolution>) - Method in interface loci.formats.IFormatWriter
-
Specify a list of resolution objects for the current series.
- setResolutions(List<Resolution>) - Method in class loci.formats.ImageWriter
- setResolutions(List<Resolution>) - Method in class loci.formats.WriterWrapper
- setResolutionSizeX(PositiveInteger, int, int) - Method in interface loci.formats.meta.IPyramidStore
-
Define the image width in pixels of the given pyramid resolution.
- setResolutionSizeX(PositiveInteger, int, int) - Method in class loci.formats.ome.OMEPyramidStore
- setResolutionSizeY(PositiveInteger, int, int) - Method in interface loci.formats.meta.IPyramidStore
-
Define the image height in pixels of the given pyramid resolution.
- setResolutionSizeY(PositiveInteger, int, int) - Method in class loci.formats.ome.OMEPyramidStore
- setRestartMarkers(long[]) - Method in interface loci.formats.services.JPEGTurboService
- setRestartMarkers(long[]) - Method in class loci.formats.services.JPEGTurboServiceImpl
- setRoi(int, int, int, int) - Method in class loci.plugins.util.RecordedImageProcessor
- setRoi(Roi) - Method in class loci.plugins.util.RecordedImageProcessor
- setRoi(Polygon) - Method in class loci.plugins.util.RecordedImageProcessor
- setRoi(Rectangle) - Method in class loci.plugins.util.RecordedImageProcessor
- setROIsMode(String) - Method in class loci.plugins.in.ImporterOptions
- setRoot(MetadataRoot) - Method in class loci.formats.ome.OMEPyramidStore
- setRowIndex(int) - Method in class loci.formats.internal.WellContainer
- setSeries(int) - Method in class loci.formats.DelegateReader
- setSeries(int) - Method in class loci.formats.FileStitcher
- setSeries(int) - Method in class loci.formats.FormatReader
- setSeries(int) - Method in class loci.formats.FormatWriter
- setSeries(int) - Method in interface loci.formats.IFormatReader
-
Activates the specified series.
- setSeries(int) - Method in interface loci.formats.IFormatWriter
-
Sets the current series.
- setSeries(int) - Method in class loci.formats.ImageReader
- setSeries(int) - Method in class loci.formats.ImageWriter
- setSeries(int) - Method in class loci.formats.in.IM3Reader
- setSeries(int) - Method in class loci.formats.in.LeicaMicrosystemsMetadata.MultipleImagesReader
-
Sets the field MultipleImagesReader.series.
- setSeries(int) - Method in class loci.formats.in.OMETiffReader
- setSeries(int) - Method in class loci.formats.in.ZeissLSMReader
- setSeries(int) - Method in class loci.formats.out.DicomWriter
- setSeries(int) - Method in class loci.formats.ReaderWrapper
- setSeries(int) - Method in class loci.formats.SubResolutionFormatReader
- setSeries(int) - Method in class loci.formats.WrappedReader
- setSeries(int) - Method in class loci.formats.WriterWrapper
- setSeries(Double) - Method in class loci.plugins.macro.LociFunctions
- setSeriesList(String) - Method in class loci.plugins.in.ImportProcess
- setSeriesOn(int, boolean) - Method in class loci.plugins.in.ImporterOptions
- setShort(int, int) - Method in class loci.formats.in.SPEReader.SpeHeader
-
Private method used to set a Short value in the SPE header
- setShowMetadata(boolean) - Method in class loci.plugins.in.ImporterOptions
- setShowOMEXML(boolean) - Method in class loci.plugins.in.ImporterOptions
- setShowROIs(boolean) - Method in class loci.plugins.in.ImporterOptions
- setSize(int) - Method in class loci.formats.tiff.OnDemandLongArray
- setSlice(int) - Method in class loci.plugins.util.VirtualImagePlus
- setSliceLabelButton - Variable in class loci.plugins.config.ConfigWindow
- setSnapshotCopyMode(boolean) - Method in class loci.plugins.util.RecordedImageProcessor
- setSnapshotPixels(Object) - Method in class loci.plugins.util.RecordedImageProcessor
- setSource(ICacheSource) - Method in class loci.formats.cache.Cache
-
Sets the cache's caching source.
- setSourceImage(byte[], int, int, int, int) - Method in class org.libjpegturbo.turbojpeg.TJCompressor
-
Associate an uncompressed source image with this compressor instance.
- setSpecifyRanges(boolean) - Method in class loci.plugins.in.ImporterOptions
- setSplitChannels(boolean) - Method in class loci.plugins.in.ImporterOptions
- setSplitFocalPlanes(boolean) - Method in class loci.plugins.in.ImporterOptions
- setSplitTimepoints(boolean) - Method in class loci.plugins.in.ImporterOptions
- setStackFormat(String) - Method in class loci.plugins.in.ImporterOptions
- setStackOrder(String) - Method in class loci.plugins.in.ImporterOptions
- setStitchTiles(boolean) - Method in class loci.plugins.in.ImporterOptions
- setStrategy(ICacheStrategy) - Method in class loci.formats.cache.Cache
-
Sets the cache's caching strategy.
- setStream(RandomAccessInputStream) - Method in class loci.formats.tiff.OnDemandLongArray
- setString(int, String) - Method in class loci.formats.in.SPEReader.SpeHeader
-
Private method used to set a String value in the SPE header
- setSubsamp(int) - Method in class org.libjpegturbo.turbojpeg.TJCompressor
-
Set the level of chrominance subsampling for subsequent compress/encode operations.
- setSwapDimensions(boolean) - Method in class loci.plugins.in.ImporterOptions
- setTBegin(int, int) - Method in class loci.plugins.in.ImporterOptions
- setTEnd(int, int) - Method in class loci.plugins.in.ImporterOptions
- setThreshold(double, double, int) - Method in class loci.plugins.util.RecordedImageProcessor
- setTileSizeX(int) - Method in class loci.formats.FormatWriter
- setTileSizeX(int) - Method in interface loci.formats.IFormatWriter
-
Will attempt to set the tile width to the desired value and return the actual value which will be used
- setTileSizeX(int) - Method in class loci.formats.ImageWriter
- setTileSizeX(int) - Method in class loci.formats.out.DicomWriter
- setTileSizeX(int) - Method in class loci.formats.out.TiffWriter
- setTileSizeX(int) - Method in class loci.formats.WriterWrapper
- setTileSizeY(int) - Method in class loci.formats.FormatWriter
- setTileSizeY(int) - Method in interface loci.formats.IFormatWriter
-
Will attempt to set the tile height to the desired value and return the actual value which will be used
- setTileSizeY(int) - Method in class loci.formats.ImageWriter
- setTileSizeY(int) - Method in class loci.formats.out.DicomWriter
- setTileSizeY(int) - Method in class loci.formats.out.TiffWriter
- setTileSizeY(int) - Method in class loci.formats.WriterWrapper
- settingsPath - Variable in class loci.formats.in.CV7000Reader
- setTruncatedFileFlag(boolean) - Method in class loci.formats.in.DeltavisionReader
-
This flag indicates if the file is known to be truncated.
- setTStep(int, int) - Method in class loci.plugins.in.ImporterOptions
- setUngroupFiles(boolean) - Method in class loci.plugins.in.ImporterOptions
- setup - Variable in class loci.formats.in.BDVReader.H5Coordinate
- setup - Variable in class loci.formats.in.SDTInfo
- setup(String, ImagePlus) - Method in class loci.plugins.LociExporter
-
Sets up the writer.
- setup(String, ImagePlus) - Method in class loci.plugins.Slicer
- SETUP_IDENTIFIER - Static variable in class loci.formats.in.SDTInfo
-
For .set files (setup only).
- setupAttributeList - Variable in class loci.formats.in.BDVReader
- setUpgradeCheck(boolean) - Method in class loci.plugins.in.ImporterOptions
- setupLength - Variable in class loci.formats.in.SDTInfo
-
Length of the setup data.
- setupOffs - Variable in class loci.formats.in.SDTInfo
-
Offset of the setup text data (system parameters, display parameters, trace parameters etc.).
- setupReader() - Method in class loci.formats.in.MicromanagerReader
-
Initialize the TIFF reader with the first non-null file in the current series.
- setupResolutionCounts - Variable in class loci.formats.in.BDVReader
- setupService() - Method in class loci.formats.FormatReader
-
Initialize the OMEXMLService needed by
FormatReader.setId(String) - setupService() - Method in class loci.formats.in.OMETiffReader
- setupServiceAndMetadata() - Method in class loci.formats.out.OMETiffWriter
- setupTiffSaver() - Method in class loci.formats.out.TiffWriter
- setupVoxelSizes - Variable in class loci.formats.in.BDVReader
- setUse64BitOffsets(boolean) - Method in class loci.formats.tiff.TiffParser
-
Sets whether or not 64-bit offsets are used for non-BigTIFF files.
- setUsingPatternIds(boolean) - Method in class loci.formats.FileStitcher
-
Sets whether the reader is using file patterns for IDs.
- setUsingPatternIds(boolean) - Method in class loci.plugins.in.ImporterOptions
- setValidate(boolean) - Method in class loci.formats.in.DefaultMetadataOptions
- setValidate(boolean) - Method in class loci.formats.in.DynamicMetadataOptions
- setValidate(boolean) - Method in interface loci.formats.in.MetadataOptions
-
Specifies whether or not to validate files when reading.
- setValidBitsPerPixel(int) - Method in class loci.formats.FormatWriter
- setValidBitsPerPixel(int) - Method in interface loci.formats.IFormatWriter
-
Sets the number of valid bits per pixel.
- setValidBitsPerPixel(int) - Method in class loci.formats.ImageWriter
- setValidBitsPerPixel(int) - Method in class loci.formats.WriterWrapper
- setValue(boolean) - Method in class loci.plugins.prefs.BooleanOption
-
Sets the current value of the option.
- setValue(double) - Method in class loci.plugins.prefs.DoubleOption
-
Sets the current value of the option.
- setValue(double) - Method in class loci.plugins.util.RecordedImageProcessor
- setValue(String) - Method in class loci.formats.in.BaseZeissReader.Tag
- setValue(String) - Method in class loci.plugins.prefs.StringOption
-
Sets the current value of the option.
- setValue(String, boolean) - Method in class loci.plugins.prefs.OptionsList
-
Sets the value of the boolean option with the given key.
- setValue(String, String) - Method in class loci.plugins.prefs.OptionsList
-
Sets the value of the string option with the given key.
- setVersionChecking(boolean) - Method in class loci.formats.Memoizer
-
Set whether version checking is done based upon major/minor version numbers.
- setView(Attributes) - Method in class loci.formats.in.LeicaSCNReader.Image
- setVirtual(boolean) - Method in class loci.plugins.in.ImporterOptions
- setVisible(boolean) - Method in class loci.formats.gui.ImageViewer
- setVisible(boolean) - Method in class loci.plugins.util.DataBrowser
-
Overridden show method to allow us to delay initial window display.
- setWellIndex(int) - Method in class loci.formats.internal.WellContainer
- setWindowless(boolean) - Method in class loci.plugins.in.ImporterOptions
- setWriteSequentially(boolean) - Method in class loci.formats.FormatWriter
- setWriteSequentially(boolean) - Method in interface loci.formats.IFormatWriter
-
Sets whether or not we know that planes will be written sequentially.
- setWriteSequentially(boolean) - Method in class loci.formats.ImageWriter
- setWriteSequentially(boolean) - Method in class loci.formats.WriterWrapper
- setWritingSequentially(boolean) - Method in class loci.formats.tiff.TiffSaver
-
Sets whether or not we know that the planes will be written sequentially.
- setXML(File) - Method in class loci.formats.gui.XMLWindow
-
Displays XML from the given file.
- setXML(String) - Method in class loci.formats.gui.XMLWindow
-
Displays XML from the given string.
- setXML(String) - Method in class loci.formats.tools.EditTiffG
- setXML(String) - Method in class loci.plugins.util.DataBrowser
-
Sets XML block associated with this window.
- setYCbCrCorrection(boolean) - Method in class loci.formats.tiff.TiffParser
-
Sets whether or not YCbCr color correction is allowed.
- setZBegin(int, int) - Method in class loci.plugins.in.ImporterOptions
- setZEnd(int, int) - Method in class loci.plugins.in.ImporterOptions
- setZStep(int, int) - Method in class loci.plugins.in.ImporterOptions
- SFEG_TAG - Static variable in class loci.formats.in.FEITiffReader
- SH - Enum constant in enum class loci.formats.dicom.DicomVR
- SHADING_MUL - Static variable in class loci.formats.in.CellSensReader
- SHADING_SUB - Static variable in class loci.formats.in.CellSensReader
- Shape() - Constructor for class loci.formats.in.BaseZeissReader.Shape
- shape_count - Variable in class loci.formats.in.ZeissTIFFHandler
- SHAPE_PREFIX - Static variable in class loci.formats.in.FakeReader
- shapes - Variable in class loci.formats.in.BaseZeissReader.Layer
- shapes - Variable in class loci.formats.in.GatanReader
- SHARED_FUNCTIONAL_GROUPS_SEQUENCE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- sharpen() - Method in class loci.plugins.util.RecordedImageProcessor
- SHARPENING - Static variable in class loci.formats.in.NikonReader
- SHARPNESS - Static variable in class loci.formats.in.CellSensReader
- SHARPNESS - Static variable in class loci.formats.tiff.IFD
- SHIFTJIS_CHARSET - Enum constant in enum class loci.formats.in.BaseZeissReader.Charset
- SHORT - Enum constant in enum class loci.formats.in.SPEReader.SpeHeaderType
- SHORT - Enum constant in enum class loci.formats.tiff.IFDType
- SHORT - Static variable in class loci.formats.in.CellSensReader
- SHORT - Static variable in class loci.formats.in.GatanReader
- SHORT_DATE_FORMAT - Static variable in class loci.formats.in.MetamorphReader
- SHORTARRAY - Enum constant in enum class loci.formats.in.SPEReader.SpeHeaderType
- shortArrayToBytes(short[]) - Method in class loci.formats.in.FluoviewReader
- SHORTCUT_PLUGIN - Static variable in class loci.plugins.shortcut.ShortcutPanel
-
Name of this plugin, ignored when parsing the plugins list.
- shortcutPanel - Variable in class loci.plugins.shortcut.ShortcutTransferHandler
-
Associated shortcut panel.
- ShortcutPanel - Class in loci.plugins.shortcut
-
A plugin that displays a small window containing shortcuts to the plugins, including the Bio-Formats Importer, Bio-Formats Exporter, Stack Colorizer and Stack Slicer.
- ShortcutPanel() - Constructor for class loci.plugins.shortcut.ShortcutPanel
-
Constructs a shortcut panel.
- ShortcutTransferHandler - Class in loci.plugins.shortcut
-
Drag and drop transfer handler for Bio-Formats Plugins Shortcut Window.
- ShortcutTransferHandler(ShortcutPanel) - Constructor for class loci.plugins.shortcut.ShortcutTransferHandler
-
Constructs a new shortcut panel drag and drop transfer handler.
- shortLut - Variable in class loci.formats.in.DicomReader
- shortValue() - Method in class loci.formats.tiff.TiffRational
-
Returns the value of the specified number as a short.
- showDialog() - Method in class loci.plugins.in.ImporterDialog
- showDialog() - Method in class loci.plugins.prefs.OptionsDialog
-
Displays the options dialog, returning the status of the operation.
- showDialogs(ImportProcess) - Method in class loci.plugins.in.Importer
- showError(Throwable) - Method in class loci.formats.tools.EditTiffG
- showMetadataBox - Variable in class loci.plugins.in.MainDialog
- showMetadataWindow() - Method in class loci.plugins.util.DataBrowser
-
Displays the OME-XML metadata window onscreen.
- showOMEXMLBox - Variable in class loci.plugins.in.MainDialog
- showOptionsWindow() - Method in class loci.plugins.util.DataBrowser
-
Displays the caching options window onscreen.
- showROIs() - Method in class loci.plugins.in.ImporterOptions
- showROIsBox - Variable in class loci.plugins.in.MainDialog
- shuffle(int, int[]) - Static method in class loci.formats.in.FakeReader
-
Fisher-Yates shuffle with constant seeds to ensure reproducibility.
- shuffleAllTypesToFront(FileFilter[]) - Static method in class loci.formats.gui.GUITools
-
Looks for an "All supported file types" combo filter and shuffles it to the front of the list.
- shutdown - Variable in class loci.formats.gui.DataConverter
- SHUTTER_COMP - Enum constant in enum class loci.formats.in.SPEReader.SpeHeaderEntry
- SHUTTER_CTRL - Enum constant in enum class loci.formats.in.SPEReader.SpeHeaderEntry
- SHUTTER_LEFT_VERTICAL_EDGE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- SHUTTER_LOWER_HORIZONTAL_EDGE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- SHUTTER_OVERLAY_GROUP - Enum constant in enum class loci.formats.dicom.DicomAttribute
- SHUTTER_PRESENTATION_VALUE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- SHUTTER_RIGHT_VERTICAL_EDGE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- SHUTTER_SHAPE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- SHUTTER_SPEED_VALUE - Static variable in class loci.formats.tiff.IFD
- SHUTTER_TYPE - Enum constant in enum class loci.formats.in.SPEReader.SpeHeaderEntry
- SHUTTER_UPPER_HORIZONTAL_EDGE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- SIFReader - Class in loci.formats.in
-
SIFReader is the file format reader for Andor SIF files.
- SIFReader() - Constructor for class loci.formats.in.SIFReader
-
Constructs a new SIF reader.
- SIGNAL_DOMAIN_COLUMNS - Enum constant in enum class loci.formats.dicom.DicomAttribute
- SIGNAL_DOMAIN_ROWS - Enum constant in enum class loci.formats.dicom.DicomAttribute
- SIGNAL_OUTPUT - Static variable in class loci.formats.in.CellSensReader
- SIGNATURE - Enum constant in enum class loci.formats.codec.JPEG2000BoxType
- SIGNATURE_SIZE - Static variable in class loci.formats.in.VolocityReader
- SIGNATURE_WRONG_ENDIANNESS - Enum constant in enum class loci.formats.codec.JPEG2000BoxType
- signed - Variable in class loci.formats.codec.CodecOptions
-
Indicates whether or not the pixel data is signed.
- signed - Variable in class loci.formats.in.BrukerReader
- signed - Variable in class loci.formats.in.GatanReader
- SignedByteBuffer - Class in loci.formats.gui
-
DataBuffer that stores signed bytes.
- SignedByteBuffer(byte[][], int) - Constructor for class loci.formats.gui.SignedByteBuffer
-
Construct a new buffer of signed bytes using the given 2D byte array.
- SignedByteBuffer(byte[], int) - Constructor for class loci.formats.gui.SignedByteBuffer
-
Construct a new buffer of signed bytes using the given byte array.
- SignedColorModel - Class in loci.formats.gui
-
ColorModel that handles 8, 16 and 32 bits per channel signed data.
- SignedColorModel(int, int, int) - Constructor for class loci.formats.gui.SignedColorModel
- SignedShortBuffer - Class in loci.formats.gui
-
DataBuffer that stores signed shorts.
- SignedShortBuffer(int) - Constructor for class loci.formats.gui.SignedShortBuffer
- SignedShortBuffer(int, int) - Constructor for class loci.formats.gui.SignedShortBuffer
- SignedShortBuffer(short[][], int) - Constructor for class loci.formats.gui.SignedShortBuffer
- SignedShortBuffer(short[][], int, int[]) - Constructor for class loci.formats.gui.SignedShortBuffer
- SignedShortBuffer(short[], int) - Constructor for class loci.formats.gui.SignedShortBuffer
- SignedShortBuffer(short[], int, int) - Constructor for class loci.formats.gui.SignedShortBuffer
- SimplePCITiffReader - Class in loci.formats.in
-
SimplePCITiffReader is the file format reader for TIFF files produced by SimplePCI software.
- SimplePCITiffReader() - Constructor for class loci.formats.in.SimplePCITiffReader
- simsDescription - Variable in class loci.formats.in.IonpathMIBITiffReader
- SINGLE_TIFF_PATH_BUILDER - Static variable in class loci.formats.in.CellVoyagerReader
- singleTiffMode - Variable in class loci.formats.in.PrairieReader
-
Flag indicating that the reader is operating in a mode where grouping of files is disallowed.
- SIS_INI_TAG - Static variable in class loci.formats.in.SISReader
- SIS_TAG - Static variable in class loci.formats.in.SISReader
- SIS_TAG_2 - Static variable in class loci.formats.in.SISReader
- SISReader - Class in loci.formats.in
-
SISReader is the file format reader for Olympus Soft Imaging Solutions TIFF files.
- SISReader() - Constructor for class loci.formats.in.SISReader
- site - Variable in class loci.formats.in.CellH5Reader.CellH5Coordinate
- site - Variable in class loci.formats.in.ZeissTIFFReader.Plane
- SITE - Static variable in class loci.formats.in.CellH5Reader.CellH5Constants
- SIZ - Enum constant in enum class loci.formats.codec.JPEG2000SegmentMarker
- size - Variable in class loci.formats.in.AVIReader
- size - Variable in class loci.formats.in.FV1000Reader
- size - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.Dimension
- size - Variable in class loci.formats.in.ZeissCZIReader.DimensionEntry
- size - Variable in class loci.formats.tiff.OnDemandLongArray
- size - Variable in class loci.plugins.in.ThumbLoader.SeriesInfo
- size() - Method in class loci.formats.codec.ByteVector
- size() - Method in class loci.formats.MetadataList
-
Get the size of the array (number of primary array elements).
- size() - Method in class loci.formats.tiff.OnDemandLongArray
- size(int) - Method in class loci.formats.MetadataList
-
Get the size of the specified primary array element (number of secondary array elements).
- sizeC - Variable in class loci.formats.CoreMetadata
-
Number of channels.
- sizeC - Variable in class loci.formats.FileStitcher
-
Dimensional axis lengths per file.
- sizeC - Variable in class loci.formats.gui.ImageViewer
- sizeC - Variable in class loci.formats.in.BDVReader
- sizeC - Variable in class loci.formats.in.FakeReader
- sizeC - Variable in class loci.formats.in.LeicaSCNReader.Pixels
- sizeCsub - Variable in class loci.formats.tools.MakeTestOmeTiff
- sizeR - Variable in class loci.formats.in.LeicaSCNReader.Pixels
- sizes - Variable in class loci.formats.in.BrukerReader
- sizes() - Method in class loci.formats.MetadataList
-
Get the sizes of all primary array elements.
- sizeT - Variable in class loci.formats.CoreMetadata
-
Number of timepoints.
- sizeT - Variable in class loci.formats.FileStitcher
-
Dimensional axis lengths per file.
- sizeT - Variable in class loci.formats.gui.ImageViewer
- sizeT - Variable in class loci.formats.in.FakeReader
- sizeTsub - Variable in class loci.formats.tools.MakeTestOmeTiff
- sizeX - Variable in class loci.formats.CoreMetadata
-
Width (in pixels) of images in this series.
- sizeX - Variable in class loci.formats.in.ColumbusReader.Plane
- sizeX - Variable in class loci.formats.in.FakeReader
- sizeX - Variable in class loci.formats.in.FEITiffReader
- sizeX - Variable in class loci.formats.in.JDCEReader.PlaneMetadata
- sizeX - Variable in class loci.formats.in.LeicaSCNReader.Dimension
- sizeX - Variable in class loci.formats.in.LeicaSCNReader.ImageCollection
- sizeX - Variable in class loci.formats.in.LeicaSCNReader.Pixels
- sizeX - Variable in class loci.formats.in.MetamorphReader
- sizeX - Variable in class loci.formats.in.TextReader
-
Image width.
- sizeX - Variable in class loci.formats.Resolution
- sizeY - Variable in class loci.formats.CoreMetadata
-
Height (in pixels) of images in this series.
- sizeY - Variable in class loci.formats.in.ColumbusReader.Plane
- sizeY - Variable in class loci.formats.in.FakeReader
- sizeY - Variable in class loci.formats.in.FEITiffReader
- sizeY - Variable in class loci.formats.in.JDCEReader.PlaneMetadata
- sizeY - Variable in class loci.formats.in.LeicaSCNReader.Dimension
- sizeY - Variable in class loci.formats.in.LeicaSCNReader.ImageCollection
- sizeY - Variable in class loci.formats.in.LeicaSCNReader.Pixels
- sizeY - Variable in class loci.formats.in.MetamorphReader
- sizeY - Variable in class loci.formats.in.TextReader
-
Image height.
- sizeY - Variable in class loci.formats.Resolution
- sizeZ - Variable in class loci.formats.CoreMetadata
-
Number of Z sections.
- sizeZ - Variable in class loci.formats.FileStitcher
-
Dimensional axis lengths per file.
- sizeZ - Variable in class loci.formats.gui.ImageViewer
- sizeZ - Variable in class loci.formats.in.FakeReader
- sizeZ - Variable in class loci.formats.in.LeicaSCNReader.Pixels
- sizeZ - Variable in class loci.formats.in.NDPIReader
- sizeZsub - Variable in class loci.formats.tools.MakeTestOmeTiff
- skip(InputStream, long) - Method in class loci.formats.in.LiFlimReader
- SKIP_BEATS - Enum constant in enum class loci.formats.dicom.DicomAttribute
- SKIP_MISSING_WELLS - Static variable in class loci.formats.in.ScanrReader
- SKIP_MISSING_WELLS_DEFAULT - Static variable in class loci.formats.in.ScanrReader
- skipBits(long) - Method in class loci.formats.codec.BitBuffer
-
Deprecated.Skips a number of bits in the BitBuffer.
- skipBlocks() - Method in class loci.formats.in.GIFReader
- skipBuffer - Variable in class loci.formats.in.OBFReader
- skipBytes(OBFReader.Stack, long) - Method in class loci.formats.in.OBFReader
- skipComment() - Method in class loci.formats.tools.AmiraParameters
- skipData() - Method in class loci.formats.in.ZeissCZIReader.Metadata
- skipHeader(RandomAccessInputStream) - Method in class loci.formats.in.MicroCTReader
-
Skip the VFF header, which consists of a variable number of LF-terminated lines.
- skipLoad - Variable in class loci.formats.Memoizer
- skipMissingWells() - Method in class loci.formats.in.ScanrReader
- skipPadding() - Method in class loci.formats.in.GatanReader
- skipPixelBlock(String, RandomAccessInputStream, boolean) - Method in class loci.formats.in.OIRReader
- skipSave - Variable in class loci.formats.Memoizer
- skipSave(boolean) - Method in class loci.formats.Memoizer
-
Set whether a memo file should be saved if a valid file is not present.
- skipTagBlock() - Method in class loci.formats.in.ImspectorReader
-
Skip an unknown tag.
- skipTags(int) - Method in class loci.formats.in.ImspectorReader
-
Skip a block of unknown string values.
- skipWhiteSpace() - Method in class loci.formats.in.AmiraReader.ASCII
- skipWhiteSpace() - Method in class loci.formats.tools.AmiraParameters
- SL - Enum constant in enum class loci.formats.dicom.DicomVR
- SLD_MAGIC_BYTES_1_0 - Static variable in class loci.formats.in.SlidebookReader
- SLD_MAGIC_BYTES_1_1 - Static variable in class loci.formats.in.SlidebookReader
- SLD_MAGIC_BYTES_1_2 - Static variable in class loci.formats.in.SlidebookReader
- SLD_MAGIC_BYTES_2_0 - Static variable in class loci.formats.in.SlidebookReader
- SLD_MAGIC_BYTES_2_1 - Static variable in class loci.formats.in.SlidebookReader
- SLD_MAGIC_BYTES_3 - Static variable in class loci.formats.in.SlidebookReader
- sleep(long) - Method in class loci.plugins.prefs.OptionsDialog
-
Blocks the current thread for the specified number of milliseconds.
- sleep(String, int) - Static method in class loci.formats.in.FakeReader
- sleepInitFile - Variable in class loci.formats.in.FakeReader
- sleepOpenBytes - Variable in class loci.formats.in.FakeReader
- SLICE_LOCATION - Enum constant in enum class loci.formats.dicom.DicomAttribute
- SLICE_LOCATION_VECTOR - Enum constant in enum class loci.formats.dicom.DicomAttribute
- SLICE_SPACING - Enum constant in enum class loci.formats.dicom.DicomAttribute
- SLICE_THICKNESS - Enum constant in enum class loci.formats.dicom.DicomAttribute
- SLICE_VECTOR - Enum constant in enum class loci.formats.dicom.DicomAttribute
- sliceLabel - Variable in class loci.plugins.config.ConfigWindow
- Slicer - Class in loci.plugins
-
A plugin for splitting an image stack into separate channels, focal planes and/or time points.
- Slicer() - Constructor for class loci.plugins.Slicer
- sliceSpace - Variable in class loci.formats.in.PerkinElmerReader
- sliceThickness - Variable in class loci.formats.in.MicromanagerReader.Position
- sliceThickness - Variable in class loci.formats.in.NiftiReader
- SLIDE_IMAGE_ORIENTATION - Enum constant in enum class loci.formats.dicom.DicomAttribute
- SLIDE_INFO - Static variable in class loci.formats.in.CellSensReader
- SLIDE_NAME - Static variable in class loci.formats.in.CellSensReader
- SLIDE_PREPARATION - Static variable in class loci.formats.in.CellSensReader
- SLIDE_PROPERTIES - Static variable in class loci.formats.in.CellSensReader
- SLIDE_SPECIMEN - Static variable in class loci.formats.in.CellSensReader
- SLIDE_STAINING - Static variable in class loci.formats.in.CellSensReader
- SLIDE_TISSUE - Static variable in class loci.formats.in.CellSensReader
- SLIDEBOOK_MAGIC_STRING - Static variable in class loci.formats.in.SlidebookTiffReader
- SlideBook7Reader - Class in loci.formats.in
- SlideBook7Reader() - Constructor for class loci.formats.in.SlideBook7Reader
- SlideBook7Reader.CAlignManipRecord70 - Class in loci.formats.in
- SlideBook7Reader.CAnnotation70 - Class in loci.formats.in
- SlideBook7Reader.CChannelDef70 - Class in loci.formats.in
- SlideBook7Reader.CChannelRecord70 - Class in loci.formats.in
- SlideBook7Reader.CCompressionBase - Class in loci.formats.in
- SlideBook7Reader.CCube - Class in loci.formats.in
- SlideBook7Reader.CCubeAnnotation70 - Class in loci.formats.in
- SlideBook7Reader.CDataTableHeaderRecord70 - Class in loci.formats.in
- SlideBook7Reader.CExposureRecord70 - Class in loci.formats.in
- SlideBook7Reader.CFluorDef70 - Class in loci.formats.in
- SlideBook7Reader.CFRAPRegionAnnotation70 - Class in loci.formats.in
- SlideBook7Reader.CFRETManipRecord70 - Class in loci.formats.in
- SlideBook7Reader.CHistogramRecord70 - Class in loci.formats.in
- SlideBook7Reader.CImageData - Class in loci.formats.in
- SlideBook7Reader.CImageGroup - Class in loci.formats.in
- SlideBook7Reader.CImageGroup.CAnnotations - Class in loci.formats.in
- SlideBook7Reader.CImageGroup.CAuxDoubleData - Class in loci.formats.in
- SlideBook7Reader.CImageGroup.CAuxFloatData - Class in loci.formats.in
- SlideBook7Reader.CImageGroup.CAuxSInt32Data - Class in loci.formats.in
- SlideBook7Reader.CImageGroup.CAuxSInt64Data - Class in loci.formats.in
- SlideBook7Reader.CImageGroup.CAuxXmlData - Class in loci.formats.in
- SlideBook7Reader.CImageGroup.CMaskPositions - Class in loci.formats.in
- SlideBook7Reader.CImageRecord70 - Class in loci.formats.in
- SlideBook7Reader.ClassDecoder - Class in loci.formats.in
- SlideBook7Reader.CLensDef70 - Class in loci.formats.in
- SlideBook7Reader.CMainViewRecord70 - Class in loci.formats.in
- SlideBook7Reader.CMaskRecord70 - Class in loci.formats.in
- SlideBook7Reader.CNpyHeader - Class in loci.formats.in
- SlideBook7Reader.COptovarDef70 - Class in loci.formats.in
- SlideBook7Reader.CRatioManipRecord70 - Class in loci.formats.in
- SlideBook7Reader.CRemapChannelLUT70 - Class in loci.formats.in
- SlideBook7Reader.CRemapManipRecord70 - Class in loci.formats.in
- SlideBook7Reader.CRemapPoint - Class in loci.formats.in
- SlideBook7Reader.CSBFile70 - Class in loci.formats.in
- SlideBook7Reader.CSBPoint<T> - Class in loci.formats.in
- SlideBook7Reader.CSlideRecord70 - Class in loci.formats.in
- SlideBook7Reader.CUnknownAnnotation70 - Class in loci.formats.in
- SlideBook7Reader.DataLoader - Class in loci.formats.in
- SlideBook7Reader.EGraphicType - Enum Class in loci.formats.in
- SlideBook7Reader.IntIntPair - Class in loci.formats.in
- SlideBook7Reader.StrIntPair - Class in loci.formats.in
- SlidebookReader - Class in loci.formats.in
-
SlidebookReader is the file format reader for 3I Slidebook files.
- SlidebookReader() - Constructor for class loci.formats.in.SlidebookReader
-
Constructs a new Slidebook reader.
- SlidebookTiffReader - Class in loci.formats.in
- SlidebookTiffReader() - Constructor for class loci.formats.in.SlidebookTiffReader
- sliderName - Variable in class loci.formats.in.FlexReader.FlexHandler
- sliderPanel - Variable in class loci.formats.gui.ImageViewer
- SLONG - Enum constant in enum class loci.formats.tiff.IFDType
- SLONG8 - Enum constant in enum class loci.formats.tiff.IFDType
- SMALLEST_IMAGE_PIXEL_VALUE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- SMALLEST_IMAGE_PIXEL_VALUE_IN_PLANE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- SMALLEST_PIXEL_VALUE_IN_SERIES - Enum constant in enum class loci.formats.dicom.DicomAttribute
- SMC_MAGIC - Static variable in class loci.formats.in.SMCameraReader
- SMCameraReader - Class in loci.formats.in
-
SMCameraReader is the file format reader for SM camera files.
- SMCameraReader() - Constructor for class loci.formats.in.SMCameraReader
-
Constructs a new SM camera reader.
- SMOKING_STATUS - Enum constant in enum class loci.formats.dicom.DicomAttribute
- smooth() - Method in class loci.plugins.util.RecordedImageProcessor
- snapshot() - Method in class loci.plugins.util.RecordedImageProcessor
- SOC - Enum constant in enum class loci.formats.codec.JPEG2000SegmentMarker
- SOC_WRONG_ENDIANNESS - Enum constant in enum class loci.formats.codec.JPEG2000SegmentMarker
- SOD - Enum constant in enum class loci.formats.codec.JPEG2000SegmentMarker
- SOF0 - Static variable in class loci.formats.services.JPEGTurboServiceImpl
- SOFT_TISSUE_FOCUS_THERMAL_INDEX - Enum constant in enum class loci.formats.dicom.DicomAttribute
- SOFT_TISSUE_SURFACE_THERMAL_INDEX - Enum constant in enum class loci.formats.dicom.DicomAttribute
- SOFT_TISSUE_THERMAL_INDEX - Enum constant in enum class loci.formats.dicom.DicomAttribute
- SOFTCOPY_VOI_LUT_SEQUENCE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- SOFTWARE - Enum constant in enum class loci.formats.in.SPEReader.SpeHeaderEntry
- SOFTWARE - Static variable in class loci.formats.tiff.IFD
- SOFTWARE_CHECK - Static variable in class loci.formats.in.VectraReader
-
TIFF image description prefix for PerkinElmer Vectra/QPTIFF files.
- SOFTWARE_VERSION - Enum constant in enum class loci.formats.dicom.DicomAttribute
- SOLID - Enum constant in enum class loci.formats.in.BaseZeissReader.DrawStyle
- SOLID - Enum constant in enum class loci.formats.in.BaseZeissReader.FillStyle
- SOP - Enum constant in enum class loci.formats.codec.JPEG2000SegmentMarker
- SOP_CLASS_UID - Enum constant in enum class loci.formats.dicom.DicomAttribute
- SOP_CLASS_UID_VALUE - Static variable in class loci.formats.out.DicomWriter
- SOP_CLASSES_SUPPORTED - Enum constant in enum class loci.formats.dicom.DicomAttribute
- SOP_INSTANCE_UID - Enum constant in enum class loci.formats.dicom.DicomAttribute
- SORENSON - Enum constant in enum class loci.formats.codec.CompressionType
- SORENSON_3 - Enum constant in enum class loci.formats.codec.CompressionType
- sortDimensions(int) - Method in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataTempBuffer
-
Sorts list of existing dimensions by increasing bytesInc, beginning with X and Y, ending with stage position
- sortFilters(Vector) - Static method in class loci.formats.gui.ComboFileFilter
-
Sorts the given list of file filters, and combines filters with identical descriptions into a combination filter that accepts anything any of its constituant filters do.
- sortFilters(Vector) - Static method in class loci.formats.gui.GUITools
-
Sorts the given list of file filters, keeping the "All supported file types" combo filter (if any) at the front of the list.
- sortFilters(FileFilter[]) - Static method in class loci.formats.gui.ComboFileFilter
-
Sorts the given list of file filters, and combines filters with identical descriptions into a combination filter that accepts anything any of its constituant filters do.
- sortFilters(FileFilter[]) - Static method in class loci.formats.gui.GUITools
-
Sorts the given list of file filters, keeping the "All supported file types" combo filter (if any) at the front of the list.
- sortMultipleImagesReaders() - Method in class loci.formats.in.XLEFReader
-
Sorts frames of all MultipleImagesReaders as per core dimension sizes and order
- sortPaths(List<String>) - Method in class loci.formats.in.XLEFReader
-
Sorts file paths by name and depth and moves current file path to the beginning
- sos - Variable in class loci.formats.services.JPEGTurboServiceImpl
- SOS - Static variable in class loci.formats.services.JPEGTurboServiceImpl
- SOT - Enum constant in enum class loci.formats.codec.JPEG2000SegmentMarker
- source - Variable in class loci.formats.cache.Cache
-
Current cache source.
- source - Variable in class loci.formats.cache.CacheEvent
-
Source of the cache update.
- SOURCE_APPLICATION - Enum constant in enum class loci.formats.dicom.DicomAttribute
- SOURCE_ASSEMBLY - Static variable in class loci.formats.in.ZeissXRMReader
- SOURCE_CHANGED - Static variable in class loci.formats.cache.CacheEvent
-
Event type indicating a new cache source.
- SOURCE_COMP - Enum constant in enum class loci.formats.in.SPEReader.SpeHeaderEntry
- SOURCE_IMAGE_EVIDENCE_SEQUENCE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- SOURCE_IMAGE_SEQUENCE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- SOURCE_LENS - Static variable in class loci.formats.in.NDPIReader
- SOURCE_PARAMS - Static variable in class loci.formats.gui.CacheComponent
- SOURCE_VALUES - Static variable in class loci.formats.gui.CacheComponent
- sourceChooser - Variable in class loci.formats.gui.CacheComponent
-
Combo box for choosing cache source.
- sourceIndex(ICacheSource) - Method in class loci.formats.gui.CacheComponent
-
Converts cache source to source chooser index.
- SOURCES - Static variable in class loci.formats.gui.CacheComponent
- sourceValue(int) - Method in class loci.formats.gui.CacheComponent
-
Generates a new cache source matching the source chooser index.
- SPARE4 - Enum constant in enum class loci.formats.in.SPEReader.SpeHeaderEntry
- SPARE6 - Enum constant in enum class loci.formats.in.SPEReader.SpeHeaderEntry
- SPATIAL_FREQUENCY_RESPONSE - Static variable in class loci.formats.tiff.IFD
- SPATIAL_RESOLUTION - Enum constant in enum class loci.formats.dicom.DicomAttribute
- spatialUnit - Variable in class loci.formats.in.NiftiReader
- spcId - Variable in class loci.formats.in.SPCReader
- SPCReader - Class in loci.formats.in
-
SPCReader is the file format reader for Becker & Hickl SPC-Image SPC FIFO files.
- SPCReader() - Constructor for class loci.formats.in.SPCReader
-
Constructs a new SPC reader.
- SPEC_CENTER_WAVELEN - Enum constant in enum class loci.formats.in.SPEReader.SpeHeaderEntry
- SPEC_GLUE_END - Enum constant in enum class loci.formats.in.SPEReader.SpeHeaderEntry
- SPEC_GLUE_FINAL_RES - Enum constant in enum class loci.formats.in.SPEReader.SpeHeaderEntry
- SPEC_GLUE_FLAG - Enum constant in enum class loci.formats.in.SPEReader.SpeHeaderEntry
- SPEC_GLUE_MIN_OVRLP - Enum constant in enum class loci.formats.in.SPEReader.SpeHeaderEntry
- SPEC_GLUE_START - Enum constant in enum class loci.formats.in.SPEReader.SpeHeaderEntry
- SPEC_GROOVES - Enum constant in enum class loci.formats.in.SPEReader.SpeHeaderEntry
- SPEC_MIRR_LOC - Enum constant in enum class loci.formats.in.SPEReader.SpeHeaderEntry
- SPEC_MIRROR_POS - Enum constant in enum class loci.formats.in.SPEReader.SpeHeaderEntry
- SPEC_MODEL - Enum constant in enum class loci.formats.in.SPEReader.SpeHeaderEntry
- SPEC_SLIT_LOC - Enum constant in enum class loci.formats.in.SPEReader.SpeHeaderEntry
- SPEC_SLIT_POS - Enum constant in enum class loci.formats.in.SPEReader.SpeHeaderEntry
- SPEC_SLIT_POS_UNITS - Enum constant in enum class loci.formats.in.SPEReader.SpeHeaderEntry
- SPEC_TYPE - Enum constant in enum class loci.formats.in.SPEReader.SpeHeaderEntry
- specialPlateNames - Variable in class loci.formats.in.OpenlabReader
- SPECIFIC_CHARSET - Enum constant in enum class loci.formats.dicom.DicomAttribute
- specifyRangesBox - Variable in class loci.plugins.in.MainDialog
- SPECIMEN_DESCRIPTION_SEQUENCE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- SPECIMEN_ID - Enum constant in enum class loci.formats.dicom.DicomAttribute
- SPECIMEN_ID_ISSUER_SEQUENCE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- SPECIMEN_LABEL_IN_IMAGE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- SPECIMEN_PREP_SEQUENCE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- SPECIMEN_UID - Enum constant in enum class loci.formats.dicom.DicomAttribute
- spectra - Variable in class loci.formats.in.IM3Reader
- SPECTRA - Static variable in class loci.formats.FormatTools
-
Identifies the Spectra dimensional type, representing a dimension consisting of spectral channels.
- SPECTRAL_SENSITIVITY - Static variable in class loci.formats.tiff.IFD
- spectralMode - Variable in class loci.formats.in.PrairieMetadata.Sequence
-
SpectralModeof this<Sequence>. - Spectrum(IRandomAccess, IM3Reader.ContainerRecord) - Constructor for class loci.formats.in.IM3Reader.Spectrum
-
Construct a spectrum by parsing a Spectrum record
- speed - Variable in class loci.formats.in.ND2Handler
- SpeHeader(byte[]) - Constructor for class loci.formats.in.SPEReader.SpeHeader
-
Constructor for SpeHeader
- SpeHeaderEntry(int, SPEReader.SpeHeaderType) - Constructor for enum class loci.formats.in.SPEReader.SpeHeaderEntry
-
Constructor for SpeHeaderEntry
- SpeHeaderType() - Constructor for enum class loci.formats.in.SPEReader.SpeHeaderType
- SPEReader - Class in loci.formats.in
-
SPEReader is the file format reader for Princeton Instruments SPE .spe files.
- SPEReader() - Constructor for class loci.formats.in.SPEReader
-
Constructs a new SPE reader.
- SPEReader.SpeHeader - Class in loci.formats.in
-
SpeHeader holds a byte array containing the SPE binary data header along with associated methods for reading SPE Header Entry values in various formats
- SPEReader.SpeHeaderEntry - Enum Class in loci.formats.in
-
SpeHeaderEntry is an Enum which provides a list of all available SPE header entries along with the offset value from the top of the header in bytes and their associated data type
- SPEReader.SpeHeaderType - Enum Class in loci.formats.in
-
SpeHeaderType is an Enum representing the available data types stored in the SPE header
- SPEReader.SpeROI - Class in loci.formats.in
-
Private class to represent the data for a single ROI in the SPE format
- SpeROI(int, int, int, int, int, int) - Constructor for class loci.formats.in.SPEReader.SpeROI
-
Constructor for SpeROI objects
- SpiderReader - Class in loci.formats.in
-
SpiderReader is the file format reader for SPIDER files.
- SpiderReader() - Constructor for class loci.formats.in.SpiderReader
-
Constructs a new SPIDER reader.
- spim - Variable in class loci.formats.in.MicromanagerReader
- SPLINE_CLOSED - Enum constant in enum class loci.formats.in.BaseZeissReader.FeatureType
- SPLINE_OPEN - Enum constant in enum class loci.formats.in.BaseZeissReader.FeatureType
- split - Variable in class loci.formats.codec.NikonCodecOptions
- split - Variable in class loci.formats.in.ND2Reader
- split - Variable in class loci.formats.in.NikonReader
- SPLIT_LOSSY_DECODER_CONFIGURATION_12 - Static variable in class loci.formats.codec.NikonCodec
- SPLIT_LOSSY_DECODER_CONFIGURATION_14 - Static variable in class loci.formats.codec.NikonCodec
- SPLIT_MONTAGE - Static variable in class loci.formats.in.GatanReader
- SPLIT_MONTAGE_DEFAULT - Static variable in class loci.formats.in.GatanReader
- SPLIT_TILES_DEFAULT - Static variable in class loci.formats.in.VentanaReader
-
Default value of
VentanaReader.SPLIT_TILES_KEY - SPLIT_TILES_KEY - Static variable in class loci.formats.in.VentanaReader
-
MetadataOptions key for determining whether to report each tile as a separate series.
- splitCBox - Variable in class loci.plugins.in.MainDialog
- splitChannels(byte[], byte[], int, int, int, boolean, boolean, int) - Static method in class loci.formats.ImageTools
-
Splits the given multi-channel array into a 2D array.
- splitChannels(byte[], int, int, int, boolean, boolean) - Static method in class loci.formats.ImageTools
-
Splits the given multi-channel array into a 2D array.
- splitChannels(BufferedImage) - Static method in class loci.formats.gui.AWTImageTools
-
Splits the given multi-channel image into single-channel images.
- splitDims(List<ImagePlus>) - Method in class loci.plugins.in.ImagePlusReader
- splitDoubles(String) - Method in class loci.formats.in.ICSReader
-
Splits the given string into a list of
Doubles. - splitFOVs(TissueFAXSReader.ScanRegion, byte[], int) - Method in class loci.formats.in.TissueFAXSReader
-
The largest resolution stores one field of view (FOV) per tile.
- splitIFD(IFD, int) - Method in class loci.formats.in.VentanaReader
-
Take the real IFD on disk and reshape it into something that represents only the given plane.
- splitMontage() - Method in class loci.formats.in.GatanReader
- splitPlanes - Variable in class loci.formats.in.ZeissLSMReader
- splitTBox - Variable in class loci.plugins.in.MainDialog
- splitTiles() - Method in class loci.formats.in.VentanaReader
- splitZBox - Variable in class loci.plugins.in.MainDialog
- SPM_DOMAIN - Static variable in class loci.formats.FormatTools
-
Identifies the scanning probe microscopy domain.
- SPREADSHEET_KEYS - Static variable in class loci.formats.in.TecanReader
- SpringUtilities - Class in loci.plugins.config
-
A 1.4 file that provides utility methods for creating form- or grid-style layouts with SpringLayout.
- SpringUtilities() - Constructor for class loci.plugins.config.SpringUtilities
- SPURIOUS_NOISE_REMOVAL - Static variable in class loci.formats.in.CellSensReader
- SQ - Enum constant in enum class loci.formats.dicom.DicomVR
- sqr() - Method in class loci.plugins.util.RecordedImageProcessor
- sqrt() - Method in class loci.plugins.util.RecordedImageProcessor
- SQUARE - Enum constant in enum class loci.formats.in.BaseZeissReader.PointStyle
- SQUARE_ROOT - Static variable in class loci.formats.in.GelReader
- squareRoot - Variable in class loci.formats.in.IvisionReader
- SRATIONAL - Enum constant in enum class loci.formats.tiff.IFDType
- srcBuf - Variable in class org.libjpegturbo.turbojpeg.TJCompressor
- srcHeight - Variable in class org.libjpegturbo.turbojpeg.TJCompressor
- srcPitch - Variable in class org.libjpegturbo.turbojpeg.TJCompressor
- srcPixelFormat - Variable in class org.libjpegturbo.turbojpeg.TJCompressor
- srcWidth - Variable in class org.libjpegturbo.turbojpeg.TJCompressor
- SS - Enum constant in enum class loci.formats.dicom.DicomVR
- SSHORT - Enum constant in enum class loci.formats.tiff.IFDType
- ST - Enum constant in enum class loci.formats.dicom.DicomVR
- STABLE - Static variable in class loci.plugins.Updater
- STABLE_BUILD - Static variable in class loci.formats.UpgradeChecker
-
Location of the JAR artifacts for the stable releases.
- STABLE_VERSION - Static variable in class loci.formats.UpgradeChecker
-
Deprecated.As of release 6.6.0
- Stack() - Constructor for class loci.formats.in.OBFReader.Stack
- Stack() - Constructor for class loci.formats.in.VolocityReader.Stack
- STACK - Enum constant in enum class loci.plugins.in.ImportStep
- STACK_DISPLAY_LUT - Static variable in class loci.formats.in.CellSensReader
- STACK_MAGIC_STRING - Static variable in class loci.formats.in.OBFReader
- STACK_NAME - Static variable in class loci.formats.in.CellSensReader
- STACK_TYPE - Static variable in class loci.formats.in.CellSensReader
- stackFormatChoice - Variable in class loci.plugins.in.MainDialog
- stackOrderChoice - Variable in class loci.plugins.in.MainDialog
- stacks - Variable in class loci.formats.in.OBFReader
- stacks - Variable in class loci.formats.in.VolocityReader
- STAGE_NAME - Enum constant in enum class loci.formats.dicom.DicomAttribute
- STAGE_NUMBER - Enum constant in enum class loci.formats.dicom.DicomAttribute
- stageLabel - Variable in class loci.formats.in.MetamorphHandler
- stageLabels - Variable in class loci.formats.in.MetamorphReader
- stageNames - Variable in class loci.formats.in.MetamorphReader
- stageX - Variable in class loci.formats.in.BaseZeissReader
- stageX - Variable in class loci.formats.in.FEITiffReader
- stageX - Variable in class loci.formats.in.GatanReader
- stageX - Variable in class loci.formats.in.MetamorphReader
- stageX - Variable in class loci.formats.in.ZeissCZIReader.SubBlock
- stageXCoord - Variable in class loci.formats.in.DeltavisionReader.DVExtHdrFields
-
X stage coordinates.
- stageY - Variable in class loci.formats.in.BaseZeissReader
- stageY - Variable in class loci.formats.in.FEITiffReader
- stageY - Variable in class loci.formats.in.GatanReader
- stageY - Variable in class loci.formats.in.MetamorphReader
- stageY - Variable in class loci.formats.in.ZeissCZIReader.SubBlock
- stageYCoord - Variable in class loci.formats.in.DeltavisionReader.DVExtHdrFields
-
Y stage coordinates.
- stageZ - Variable in class loci.formats.in.FEITiffReader
- stageZ - Variable in class loci.formats.in.GatanReader
- stageZ - Variable in class loci.formats.in.ZeissCZIReader.SubBlock
- stageZCoord - Variable in class loci.formats.in.DeltavisionReader.DVExtHdrFields
-
Z stage coordinates.
- stamps - Variable in class loci.formats.in.FluoviewReader
-
Timestamps for each plane, in seconds.
- stampValues - Variable in class loci.formats.in.LiFlimReader
- start - Variable in class loci.formats.dicom.DicomTag
- start - Variable in class loci.formats.in.EPSReader
-
Starting line of pixel data.
- start - Variable in class loci.formats.in.MicromanagerReader
- start - Variable in class loci.formats.in.ZeissCZIReader.DimensionEntry
- start - Variable in class loci.formats.Modulo
- start - Variable in class loci.formats.tiff.OnDemandLongArray
- START_OFFSET - Static variable in class loci.formats.in.BioRadGelReader
- START_TIME - Static variable in class loci.formats.in.ZeissLSMReader
- START_TRIM - Enum constant in enum class loci.formats.dicom.DicomAttribute
- startCoordinate - Variable in class loci.formats.in.ZeissCZIReader.DimensionEntry
- startElement(String, String, String, Attributes) - Method in class loci.formats.in.AFIReader.AFIHandler
- startElement(String, String, String, Attributes) - Method in class loci.formats.in.BDVReader.BDVXMLHandler
- startElement(String, String, String, Attributes) - Method in class loci.formats.in.BioRadReader.BioRadHandler
- startElement(String, String, String, Attributes) - Method in class loci.formats.in.BioRadSCNReader.SCNHandler
- startElement(String, String, String, Attributes) - Method in class loci.formats.in.ColumbusReader.MeasurementHandler
- startElement(String, String, String, Attributes) - Method in class loci.formats.in.CV7000Reader.MeasurementDataHandler
- startElement(String, String, String, Attributes) - Method in class loci.formats.in.CV7000Reader.MeasurementDetailHandler
- startElement(String, String, String, Attributes) - Method in class loci.formats.in.CV7000Reader.MeasurementSettingsHandler
- startElement(String, String, String, Attributes) - Method in class loci.formats.in.CV7000Reader.WPIHandler
- startElement(String, String, String, Attributes) - Method in class loci.formats.in.FEITiffReader.FEIHandler
- startElement(String, String, String, Attributes) - Method in class loci.formats.in.FlexReader.FlexHandler
- startElement(String, String, String, Attributes) - Method in class loci.formats.in.FlexReader.MeaHandler
- startElement(String, String, String, Attributes) - Method in class loci.formats.in.FlexReader.ResHandler
- startElement(String, String, String, Attributes) - Method in class loci.formats.in.ImaconReader.ImaconHandler
- startElement(String, String, String, Attributes) - Method in class loci.formats.in.InCellReader.InCellHandler
- startElement(String, String, String, Attributes) - Method in class loci.formats.in.InCellReader.MinimalInCellHandler
- startElement(String, String, String, Attributes) - Method in class loci.formats.in.IvisionReader.IvisionHandler
- startElement(String, String, String, Attributes) - Method in class loci.formats.in.LeicaHandler
- startElement(String, String, String, Attributes) - Method in class loci.formats.in.LeicaSCNReader.LeicaSCNHandler
- startElement(String, String, String, Attributes) - Method in class loci.formats.in.MetamorphHandler
- startElement(String, String, String, Attributes) - Method in class loci.formats.in.MicromanagerReader.MicromanagerHandler
- startElement(String, String, String, Attributes) - Method in class loci.formats.in.ND2Handler
- startElement(String, String, String, Attributes) - Method in class loci.formats.in.OMEXMLReader.OMEXMLHandler
- startElement(String, String, String, Attributes) - Method in class loci.formats.in.OperettaReader.OperettaHandler
- startElement(String, String, String, Attributes) - Method in class loci.formats.in.ScanrReader.ScanrHandler
- startElement(String, String, String, Attributes) - Method in class loci.formats.in.ZeissTIFFHandler
- startElement(String, String, String, Attributes) - Method in class loci.formats.out.OMEXMLWriter.OMEHandler
- startIndex - Variable in class loci.formats.FilePattern
-
Indices into the pattern indicating the start of a numerical block.
- startingPosition - Variable in class loci.formats.in.ZeissCZIReader.Segment
- startTime - Variable in class loci.formats.in.CV7000Reader
- startTime - Variable in class loci.formats.in.PerkinElmerReader
- startTime - Variable in class loci.formats.in.ZeissLSMReader.Recording
- startTime - Variable in class loci.plugins.in.ImagePlusReader
- startTiming() - Method in class loci.plugins.in.ImagePlusReader
- startX - Variable in class loci.formats.in.SPEReader.SpeROI
- startY - Variable in class loci.formats.in.SPEReader.SpeROI
- state - Variable in class loci.formats.in.OBFReader
- State(int) - Constructor for class loci.formats.in.OBFReader.State
- stateChanged(ChangeEvent) - Method in class loci.formats.gui.CacheComponent
-
Handles range spinner changes.
- stateChanged(ChangeEvent) - Method in class loci.formats.gui.DataConverter
- stateChanged(ChangeEvent) - Method in class loci.formats.gui.ImageViewer
-
Handles slider events.
- stateChanged(ChangeEvent) - Method in class loci.plugins.util.SearchableWindow.SearchBox
- STATION_NAME - Enum constant in enum class loci.formats.dicom.DicomAttribute
- status - Variable in class loci.formats.in.BioRadReader.Note
- status - Variable in class loci.formats.in.SDTInfo
-
Last SPC_test_state return value (status).
- status - Variable in class loci.plugins.config.ConfigWindow
- status - Variable in class loci.plugins.config.LibraryEntry
- status(boolean, String) - Static method in class loci.plugins.BF
- STATUS_CANCELED - Static variable in class loci.plugins.prefs.OptionsDialog
- STATUS_FINISHED - Static variable in class loci.plugins.prefs.OptionsDialog
- STATUS_OK - Static variable in class loci.plugins.prefs.OptionsDialog
- statusUpdated(StatusEvent) - Method in class loci.plugins.in.DisplayHandler
-
Reports status updates via ImageJ's status bar mechanism.
- statusUpdated(StatusEvent) - Method in class loci.plugins.in.ImporterPrompter
- STEERING_ANGLE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- step - Variable in class loci.formats.FilePatternBlock
- step - Variable in class loci.formats.Modulo
- step - Variable in class loci.plugins.in.ImportProcess
-
Current step in the import preparation process.
- step - Variable in enum class loci.plugins.in.ImportStep
- step(ImportStep) - Method in class loci.plugins.in.ImportProcess
- STEP_TABLE - Static variable in enum class loci.plugins.in.ImportStep
- steps - Variable in class loci.formats.in.SDTInfo
- stepSize - Variable in class loci.formats.in.MetamorphReader
- stitchTilesBox - Variable in class loci.plugins.in.MainDialog
- STK_SUFFIX - Static variable in class loci.formats.in.MetamorphReader
- stkReaders - Variable in class loci.formats.in.MetamorphReader
- stks - Variable in class loci.formats.in.MetamorphReader
-
List of STK files in the dataset.
- stop - Variable in class loci.plugins.in.ThumbLoader
- stop() - Method in class loci.plugins.in.ThumbLoader
-
Instructs the thumbnail loader to stop loading thumbnails.
- STOP_TRIM - Enum constant in enum class loci.formats.dicom.DicomAttribute
- stopt - Variable in class loci.formats.in.SDTInfo
- stopTime - Variable in class loci.formats.in.SDTInfo
-
Time from start to - disarm (simple measurement) - or to the end of the cycle (for complex measurement).
- stopWatch() - Method in class loci.formats.in.DicomReader
- stopWatch() - Method in class loci.formats.Memoizer
- stopWatch() - Method in class loci.formats.out.DicomWriter
- storageMethod - Variable in class loci.formats.in.MRWReader
- store - Variable in class loci.formats.FileStitcher
- store - Variable in class loci.formats.in.BDVReader
- store - Variable in class loci.formats.in.CellH5Reader
- store - Variable in class loci.formats.in.FlexReader.FlexHandler
- store - Variable in class loci.formats.in.InCellReader.InCellHandler
- store - Variable in class loci.formats.in.KLBReader
- store - Variable in class loci.formats.in.LeicaHandler
- store - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataStoreInitializer
- store - Variable in class loci.formats.in.ZeissCZIReader
- STORE_SYNC - Enum constant in enum class loci.formats.in.SPEReader.SpeHeaderEntry
- storedChannel - Variable in class loci.formats.in.SDTReader
- storedChannel - Variable in class loci.formats.in.SPCReader
- storedRGB - Variable in class loci.formats.in.ICSReader
- storedSeries - Variable in class loci.formats.in.SDTReader
- storedSize - Variable in class loci.formats.in.ZeissCZIReader.DimensionEntry
- storedT - Variable in class loci.formats.in.SPCReader
- storeKeyValue(Hashtable, String, String) - Method in class loci.formats.in.LeicaHandler
- storeLine(Line, MetadataStore, int, int, int, int, int) - Static method in class loci.plugins.util.ROIHandler
-
Stores the Line ROI into the specified metadata store.
- storeOval(OvalRoi, MetadataStore, int, int, int, int, int) - Static method in class loci.plugins.util.ROIHandler
-
Stores the Oval ROI into the specified metadata store.
- storePoint(PointRoi, MetadataStore, int, int, int, int, int) - Static method in class loci.plugins.util.ROIHandler
-
Stores the Point ROI into the specified metadata store.
- storePolygon(PolygonRoi, MetadataStore, int, int, int, int, int) - Static method in class loci.plugins.util.ROIHandler
-
Stores the Polygon ROI into the specified metadata store.
- storeRectangle(Roi, MetadataStore, int, int, int, int, int) - Static method in class loci.plugins.util.ROIHandler
-
Stores the Rectangle ROI into the specified metadata store.
- storeRelativePositions() - Method in class loci.formats.in.ZeissCZIReader
- storeROI(MetadataStore, int, int) - Method in class loci.formats.in.LeicaHandler.ROI
- storeROI(MetadataStore, int, int, int) - Method in class loci.formats.in.LIFReader.ROI
- storeROI(MetadataStore, int, int, int, int, int, boolean, MetadataLevel) - Method in class loci.formats.in.LeicaMicrosystemsMetadata.ROI
- storeROIs(MetadataStore) - Method in class loci.formats.in.BaseZeissReader
-
Store basic dimensions in model
- storeSeriesHashtable(int, Hashtable) - Method in class loci.formats.in.LeicaHandler
- storeText(TextRoi, MetadataStore, int, int, int, int, int) - Static method in class loci.plugins.util.ROIHandler
-
Stores the text ROI into the metadata stored.
- STRATEGIES - Static variable in class loci.formats.gui.CacheComponent
- strategy - Variable in class loci.formats.cache.Cache
-
Current cache strategy.
- strategy - Variable in class loci.formats.dicom.DicomTag
- STRATEGY_CHANGED - Static variable in class loci.formats.cache.CacheEvent
-
Event type indicating a new cache strategy.
- STRATEGY_PARAMS - Static variable in class loci.formats.gui.CacheComponent
- STRATEGY_VALUES - Static variable in class loci.formats.gui.CacheComponent
- strategyChooser - Variable in class loci.formats.gui.CacheComponent
-
Combo box for choosing cache strategy.
- strategyIndex(ICacheStrategy) - Method in class loci.formats.gui.CacheComponent
-
Converts cache strategy to strategy chooser index.
- strategyValue(int) - Method in class loci.formats.gui.CacheComponent
-
Generates a new cache strategy matching the strategy chooser index.
- stream - Variable in class loci.formats.in.ZeissCZIReader.Segment
- stream - Variable in class loci.formats.services.POIServiceImpl
- stream - Variable in class loci.formats.tiff.OnDemandLongArray
- streamNames - Variable in class loci.formats.tools.AmiraParameters
- streams - Variable in class loci.formats.tools.AmiraParameters
- streamTypes - Variable in class loci.formats.tools.AmiraParameters
- strikeout - Variable in class loci.formats.in.BaseZeissReader.Shape
- STRING - Enum constant in enum class loci.formats.in.SPEReader.SpeHeaderType
- StringIM3Record(String, int, long, int) - Constructor for class loci.formats.in.IM3Reader.StringIM3Record
- StringOption - Class in loci.plugins.prefs
-
A string option for one of the plugins.
- StringOption(String, boolean, String, String, String, Vector<String>) - Constructor for class loci.plugins.prefs.StringOption
-
Constructs a string option with the given parameters.
- StringOption(HashMap<String, String>) - Constructor for class loci.plugins.prefs.StringOption
-
Constructs a string option with the parameters from the given map.
- stringTable - Variable in class loci.formats.in.VolocityReader
- StrIntPair(String, Integer) - Constructor for class loci.formats.in.SlideBook7Reader.StrIntPair
- STRIP_BYTE_COUNTS - Static variable in class loci.formats.tiff.IFD
- STRIP_OFFSETS - Static variable in class loci.formats.tiff.IFD
- stripHeader() - Method in class loci.formats.in.QTReader
-
Cut off header bytes from a resource fork file.
- strips - Variable in class loci.formats.in.PictReader
-
Vector of byte arrays representing individual rows.
- strokeColor - Variable in class loci.formats.in.GatanReader.ROIShape
- STRUCTURE_LABELS_1 - Static variable in class loci.formats.in.BioRadReader
-
Structure labels.
- STRUCTURE_LABELS_2 - Static variable in class loci.formats.in.BioRadReader
- STRUCTURE_LABELS_3 - Static variable in class loci.formats.in.BioRadReader
- STRUCTURE_LABELS_4 - Static variable in class loci.formats.in.BioRadReader
- STRUCTURE_LABELS_5 - Static variable in class loci.formats.in.BioRadReader
- STRUCTURE_LABELS_6 - Static variable in class loci.formats.in.BioRadReader
- STUDIES_WITH_REFERENCED_INSTANCES - Enum constant in enum class loci.formats.dicom.DicomAttribute
- STUDY_DATE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- STUDY_DESCRIPTION - Enum constant in enum class loci.formats.dicom.DicomAttribute
- STUDY_ID - Enum constant in enum class loci.formats.dicom.DicomAttribute
- STUDY_INSTANCE_UID - Enum constant in enum class loci.formats.dicom.DicomAttribute
- STUDY_TIME - Enum constant in enum class loci.formats.dicom.DicomAttribute
- STYLESHEET_FILE - Static variable in class loci.formats.in.LIFReader
- SUB - Static variable in class loci.formats.in.APNGReader
- SUB_IFD - Static variable in class loci.formats.tiff.IFD
- SUB_SEC_TIME - Static variable in class loci.formats.tiff.IFD
- SUB_SEC_TIME_DIGITIZED - Static variable in class loci.formats.tiff.IFD
- SUB_SEC_TIME_ORIGINAL - Static variable in class loci.formats.tiff.IFD
- SubBlock() - Constructor for class loci.formats.in.ZeissCZIReader.SubBlock
- SubBlock() - Constructor for class loci.formats.in.ZeissLSMReader.SubBlock
- SubBlock(ZeissCZIReader.SubBlock) - Constructor for class loci.formats.in.ZeissCZIReader.SubBlock
- SUBBLOCK_BEAM_SPLITTER - Static variable in class loci.formats.in.ZeissLSMReader
- SUBBLOCK_DATA_CHANNEL - Static variable in class loci.formats.in.ZeissLSMReader
- SUBBLOCK_DETECTION_CHANNEL - Static variable in class loci.formats.in.ZeissLSMReader
- SUBBLOCK_END - Static variable in class loci.formats.in.ZeissLSMReader
- SUBBLOCK_ILLUMINATION_CHANNEL - Static variable in class loci.formats.in.ZeissLSMReader
- SUBBLOCK_LASER - Static variable in class loci.formats.in.ZeissLSMReader
- SUBBLOCK_MARKER - Static variable in class loci.formats.in.ZeissLSMReader
- SUBBLOCK_RECORDING - Static variable in class loci.formats.in.ZeissLSMReader
-
Subblock types.
- SUBBLOCK_TIMER - Static variable in class loci.formats.in.ZeissLSMReader
- SUBBLOCK_TRACK - Static variable in class loci.formats.in.ZeissLSMReader
- subdirectories - Variable in class loci.formats.in.CellWorxReader
- SUBFILE_TYPE - Static variable in class loci.formats.tiff.IFD
- SUBJECT_DISTANCE - Static variable in class loci.formats.tiff.IFD
- SUBJECT_DISTANCE_RANGE - Static variable in class loci.formats.tiff.IFD
- SUBJECT_LOCATION - Static variable in class loci.formats.tiff.IFD
- SubResolutionFormatReader - Class in loci.formats
-
Abstract superclass of all biological file format readers that can handle image pyramids.
- SubResolutionFormatReader(String, String) - Constructor for class loci.formats.SubResolutionFormatReader
-
Constructs a format reader with the given name and default suffix.
- SubResolutionFormatReader(String, String[]) - Constructor for class loci.formats.SubResolutionFormatReader
-
Constructs a format reader with the given name and default suffixes.
- subResolutionIFDs - Variable in class loci.formats.in.MinimalTiffReader
-
List of sub-resolution IFDs for each IFD in the current TIFF with the same order as
ifds. - subresolutionOffset - Variable in class loci.formats.in.OMETiffReader.OMETiffCoreMetadata
-
SubIFD offset for sub-resolution level; -1 if the main IFD.
- subsamp - Variable in class org.libjpegturbo.turbojpeg.TJCompressor
- substringsBetween(String, String, String) - Static method in class loci.plugins.in.ImagePlusReader
- subTag - Variable in class loci.formats.in.OpenlabReader
- success - Variable in class loci.plugins.LociImporter
-
Flag indicating whether last operation was successful.
- suffix - Variable in class loci.formats.in.GIFReader
- SUFFIX - Static variable in class loci.formats.in.TCSReader
- suffixes - Variable in class loci.formats.FormatHandler
-
Valid suffixes for this file format.
- suffixes - Variable in class loci.formats.ImageReader
-
Valid suffixes for this file format.
- suffixes - Variable in class loci.formats.ImageWriter
-
Valid suffixes for all file format writers.
- suffixes - Variable in class loci.plugins.config.FormatEntry
- SUFFIXES - Static variable in class loci.formats.in.FlexReader
- suffixNecessary - Variable in class loci.formats.FormatReader
-
Whether the file extension matching one of the reader's suffixes is necessary to identify the file as an instance of this format.
- suffixSufficient - Variable in class loci.formats.FormatReader
-
Whether the file extension matching one of the reader's suffixes is sufficient to identify the file as an instance of this format.
- sum(int[], int, int) - Method in class loci.formats.in.XLEFReader
-
Sums up all values of an array, from start index to (including) end index
- surfaceWind - Variable in class loci.formats.in.HRDGDFReader
- SV - Enum constant in enum class loci.formats.dicom.DicomVR
- SVSCoreMetadata - Class in loci.formats.in
- SVSCoreMetadata() - Constructor for class loci.formats.in.SVSCoreMetadata
- SVSReader - Class in loci.formats.in
-
SVSReader is the file format reader for Aperio SVS TIFF files.
- SVSReader() - Constructor for class loci.formats.in.SVSReader
-
Constructs a new SVS reader.
- SVSReader(String, String[]) - Constructor for class loci.formats.in.SVSReader
- swap - Variable in class loci.formats.gui.DataConverter
- SwapDialog - Class in loci.plugins.in
-
Bio-Formats Importer dimension swapper dialog box.
- SwapDialog(ImportProcess) - Constructor for class loci.plugins.in.SwapDialog
-
Creates a dimension swapper dialog for the Bio-Formats Importer.
- swapDimensions() - Method in class loci.formats.in.LeicaMicrosystemsMetadata.MultipleImagesReader
-
Rearranges frame order from ZSTC order (used in XLIFs) to desired CoreMetadata.dimensionOrder
- swapDimensions(String) - Method in class loci.formats.DimensionSwapper
-
Sets the input dimension order according to the given string (e.g., "XYZCT").
- swapDimsBox - Variable in class loci.plugins.in.MainDialog
- SwappableMetadata - Class in loci.formats
-
Extends
CoreMetadatato include the notion of an "input order" for planes: the input order being the order planes are stored on disk. - SwappableMetadata() - Constructor for class loci.formats.SwappableMetadata
- SwappableMetadata(IFormatReader, int) - Constructor for class loci.formats.SwappableMetadata
- SwappableMetadata(SwappableMetadata) - Constructor for class loci.formats.SwappableMetadata
- swapPixelArrays() - Method in class loci.plugins.util.RecordedImageProcessor
- swapXY - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataTempBuffer
- swapXY - Variable in class loci.formats.in.LIFReader
- SWATCH_SIZE - Static variable in class loci.plugins.in.ColorDialog
- switchChunk(OBFReader.Stack, int) - Method in class loci.formats.in.OBFReader
- SYNCHRONIZATION_CHANNEL - Enum constant in enum class loci.formats.dicom.DicomAttribute
- SYNCHRONIZATION_TRIGGER - Enum constant in enum class loci.formats.dicom.DicomAttribute
- syncPlane() - Method in class loci.plugins.util.DataBrowser
-
Updates the ImagePlus's displayed plane to match the slider values.
- syncSliders() - Method in class loci.plugins.util.DataBrowser
-
Updates the slider values to match the ImagePlus's displayed plane.
- synFD - Variable in class loci.formats.in.SDTInfo
- synHF - Variable in class loci.formats.in.SDTInfo
- syntaxError(String) - Method in class loci.formats.tools.AmiraParameters
- synTH - Variable in class loci.formats.in.SDTInfo
- synZC - Variable in class loci.formats.in.SDTInfo
- SYRINGE_COUNTS - Enum constant in enum class loci.formats.dicom.DicomAttribute
T
- t - Variable in class loci.formats.in.MicromanagerReader.Index
- t - Variable in class loci.formats.in.OIRReader.CZTKey
- t - Variable in class loci.formats.in.OperettaReader.Plane
- T - Enum constant in enum class loci.formats.in.LeicaMicrosystemsMetadata.Dimension.DimensionKey
- T - Static variable in class loci.formats.in.CellSensReader
- T_AXIS - Static variable in class loci.formats.AxisGuesser
-
Axis type for time points.
- T_KEY - Static variable in class loci.formats.in.LiFlimReader
- T_NUM - Static variable in class loci.formats.FormatTools
- T_PREFIXES - Static variable in class loci.formats.AxisGuesser
-
Prefixes indicating time dimension.
- T_STRING - Static variable in class loci.formats.in.SDTInfo
- T4_OPTIONS - Static variable in class loci.formats.tiff.IFD
- T6_OPTIONS - Static variable in class loci.formats.tiff.IFD
- table - Variable in class loci.formats.codec.HuffmanCodecOptions
- TABLE_ANGLE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- TABLE_HEIGHT - Enum constant in enum class loci.formats.dicom.DicomAttribute
- TABLE_LATERAL_INCREMENT - Enum constant in enum class loci.formats.dicom.DicomAttribute
- TABLE_LONGITUDINAL_INCREMENT - Enum constant in enum class loci.formats.dicom.DicomAttribute
- TABLE_MOTION - Enum constant in enum class loci.formats.dicom.DicomAttribute
- TABLE_OF_PARAMETER_VALUES - Enum constant in enum class loci.formats.dicom.DicomAttribute
- TABLE_OF_PIXEL_VALUES - Enum constant in enum class loci.formats.dicom.DicomAttribute
- TABLE_OF_X_BREAK_POINTS - Enum constant in enum class loci.formats.dicom.DicomAttribute
- TABLE_OF_Y_BREAK_POINTS - Enum constant in enum class loci.formats.dicom.DicomAttribute
- TABLE_TRAVERSE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- TABLE_TYPE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- TABLE_VERTICAL_INCREMENT - Enum constant in enum class loci.formats.dicom.DicomAttribute
- TAC_GAIN - Static variable in class loci.formats.in.SPCReader
- TAC_RANGE - Static variable in class loci.formats.in.SPCReader
- tacG - Variable in class loci.formats.in.SDTInfo
- tacLH - Variable in class loci.formats.in.SDTInfo
- tacLL - Variable in class loci.formats.in.SDTInfo
- tacOF - Variable in class loci.formats.in.SDTInfo
- tacR - Variable in class loci.formats.in.SDTInfo
- tag - Variable in enum class loci.formats.dicom.DicomAttribute
- tag - Variable in class loci.formats.dicom.DicomTag
- tag - Variable in class loci.formats.in.OpenlabReader
- tag - Variable in class loci.formats.in.PhotoshopTiffReader
- tag - Variable in class loci.formats.tiff.TiffIFDEntry
-
The Tag that identifies the field.
- Tag(int) - Constructor for class loci.formats.in.ZeissTIFFHandler.Tag
-
Constructor.
- Tag(int, String, BaseZeissReader.Context) - Constructor for class loci.formats.in.BaseZeissReader.Tag
-
Constructor.
- Tag(int, BaseZeissReader.Context) - Constructor for class loci.formats.in.BaseZeissReader.Tag
-
Constructor.
- TAG_CHANNEL - Static variable in class loci.formats.in.NDPISReader
- tag_count - Variable in class loci.formats.in.ZeissTIFFHandler
- TAG_EMISSION_WAVELENGTH - Static variable in class loci.formats.in.NDPISReader
- TAG_ENCODING - Static variable in class loci.formats.in.LEOReader
- tagEncoding - Variable in class loci.formats.tiff.TiffParser
- tagID - Variable in class loci.formats.in.BaseZeissReader.Shape
- taglist - Variable in class loci.formats.in.ZeissTIFFReader.Plane
- tagProviders - Variable in class loci.formats.out.DicomWriter
- tags - Variable in class loci.formats.dicom.DicomJSONProvider
- tags - Variable in class loci.formats.in.DicomReader
- tags - Variable in class loci.formats.in.ZeissTIFFHandler.TagSet
- tags - Variable in class loci.formats.in.ZeissTIFFReader.Plane
- tagset - Variable in class loci.formats.in.ZeissTIFFHandler.Plane
- tagset - Variable in class loci.formats.in.ZeissTIFFHandler.Scaling
- TagSet() - Constructor for class loci.formats.in.ZeissTIFFHandler.TagSet
- tagsToParse - Variable in class loci.formats.in.BaseZeissReader
- TargaReader - Class in loci.formats.in
-
File format reader for Truevision Targa files.
- TargaReader() - Constructor for class loci.formats.in.TargaReader
-
Constructs a new Targa reader.
- TargaRLECodec - Class in loci.formats.codec
-
This class implements Targa RLE decompression.
- TargaRLECodec() - Constructor for class loci.formats.codec.TargaRLECodec
- target - Variable in class loci.formats.in.CV7000Reader.Channel
- TARGET_PRINTER - Static variable in class loci.formats.tiff.IFD
- tBegin - Variable in class loci.plugins.in.ImporterOptions
- TCHAR - Static variable in class loci.formats.in.CellSensReader
- tChoice - Variable in class loci.formats.gui.DataConverter
- tChoice - Variable in class loci.plugins.in.SwapDialog
- TCSReader - Class in loci.formats.in
-
TCSReader is the file format reader for Leica TCS TIFF files and their companion XML file.
- TCSReader() - Constructor for class loci.formats.in.TCSReader
- tDim - Variable in class loci.formats.out.AVIWriter
- TecanReader - Class in loci.formats.in
- TecanReader() - Constructor for class loci.formats.in.TecanReader
-
Constructs a new Tecan Spark Cyto reader.
- TecanReader.Channel - Class in loci.formats.in
- TecanReader.Image - Class in loci.formats.in
- temperature - Variable in class loci.formats.in.FluoviewReader
- temperature - Variable in class loci.formats.in.InCellReader
- temperature - Variable in class loci.formats.in.MetamorphHandler
- temperature - Variable in class loci.formats.in.MicromanagerReader.Position
- temperature - Variable in class loci.formats.in.ND2Handler
- temperature - Variable in class loci.formats.in.ZeissCZIReader
- TEMPERATURE - Static variable in class loci.formats.in.FluoviewReader
- TEMPERATURE_TARGET - Static variable in class loci.formats.in.CellSensReader
- tempFile - Variable in class loci.formats.Memoizer
- templateFile - Variable in class loci.formats.in.MIASReader
- tempZ - Variable in class loci.formats.in.MetamorphReader
- tEnd - Variable in class loci.plugins.in.ImporterOptions
- test() - Method in class loci.formats.codec.BaseCodec
-
Main testing method default implementation.
- text - Variable in class loci.formats.in.BaseZeissReader.Shape
- text - Variable in class loci.formats.in.GatanReader.ROIShape
- text - Variable in class loci.formats.in.LeicaHandler.ROI
- text - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.ROI
- text - Variable in class loci.formats.in.LIFReader.ROI
- TEXT - Enum constant in enum class loci.formats.in.BaseZeissReader.FeatureType
- TEXT - Static variable in class loci.formats.in.GatanReader
- TEXT - Static variable in class loci.formats.in.LeicaHandler.ROI
- TEXT - Static variable in class loci.formats.in.LeicaMicrosystemsMetadata.ROI
- TEXT - Static variable in class loci.formats.in.LIFReader.ROI
- TEXT - Static variable in class loci.formats.in.ZeissLSMReader
-
Drawing element types.
- textAlignment - Variable in class loci.formats.in.BaseZeissReader.Shape
- TextAlignment(int) - Constructor for enum class loci.formats.in.BaseZeissReader.TextAlignment
- textArea - Variable in class loci.formats.tools.EditTiffG
- textArea - Variable in class loci.plugins.config.TextAreaWriter
-
Text area component to which output should be written.
- TextAreaWriter - Class in loci.plugins.config
-
Writer implementation that writes to a JTextArea document.
- TextAreaWriter(JTextArea) - Constructor for class loci.plugins.config.TextAreaWriter
-
Constructs a new TextAreaWriter around the given text area component.
- textChannelNames - Variable in class loci.formats.in.ND2Reader
- textColour - Variable in class loci.formats.in.BaseZeissReader.Shape
- textData - Variable in class loci.formats.in.ND2Reader
- textEmissionWavelengths - Variable in class loci.formats.in.ND2Reader
- TextLine(String, Font, int, int) - Constructor for class loci.formats.in.FakeReader.TextLine
- TextLine(String, Font, int, int) - Constructor for class loci.formats.tools.MakeTestOmeTiff.TextLine
- TextReader - Class in loci.formats.in
-
Reader for text files containing tables of data.
- TextReader() - Constructor for class loci.formats.in.TextReader
-
Constructs a new text reader.
- textureOffset - Variable in class loci.formats.in.AliconaReader
-
Image offset.
- THAI_CHARSET - Enum constant in enum class loci.formats.in.BaseZeissReader.Charset
- THIRD_ID - Static variable in class loci.formats.in.CellSensReader
- thisField - Variable in class loci.formats.in.FlexReader.FlexHandler
- THREE - Static variable in class loci.formats.AxisGuesser
- THRESHHOLDING - Static variable in class loci.formats.tiff.IFD
- threshold(int) - Method in class loci.plugins.util.RecordedImageProcessor
- THRESHOLD_MAX_LIVE - Enum constant in enum class loci.formats.in.SPEReader.SpeHeaderEntry
- THRESHOLD_MAX_VAL - Enum constant in enum class loci.formats.in.SPEReader.SpeHeaderEntry
- THRESHOLD_MIN_LIVE - Enum constant in enum class loci.formats.in.SPEReader.SpeHeaderEntry
- THRESHOLD_MIN_VAL - Enum constant in enum class loci.formats.in.SPEReader.SpeHeaderEntry
- throwBadBlock(String) - Method in class loci.formats.FilePatternBlock
- throwBadBlock(String, Throwable) - Method in class loci.formats.FilePatternBlock
- THUMB_TAG_2 - Static variable in class loci.formats.in.NDPIReader
- thumbId - Variable in class loci.formats.in.FV1000Reader
-
Name of thumbnail file.
- ThumbLoader - Class in loci.plugins.in
-
Loads thumbnails for Bio-Formats Importer series chooser in a separate thread.
- ThumbLoader(IFormatReader, Panel[], Dialog) - Constructor for class loci.plugins.in.ThumbLoader
-
Constructs a new thumbnail loader.
- ThumbLoader.SeriesInfo - Class in loci.plugins.in
-
Helper class for sorting series by image plane size.
- thumbnail - Variable in class loci.formats.CoreMetadata
-
Indicates whether or not this series is a lower-resolution copy of another series.
- THUMBNAIL_DIMENSION - Static variable in class loci.formats.FormatReader
-
Default thumbnail width and height.
- thumbnailFile - Variable in class loci.formats.in.InCellReader.Image
- thumbnailIFDs - Variable in class loci.formats.in.MinimalTiffReader
-
List of thumbnail IFDs for the current TIFF.
- thumbReader - Variable in class loci.formats.in.FV1000Reader
-
Helper reader for thumbnail.
- thumbReader - Variable in class loci.plugins.in.SeriesDialog
- thumbSizeX - Variable in class loci.formats.CoreMetadata
-
Width (in pixels) of thumbnail images in this series.
- thumbSizeX - Variable in class loci.formats.in.LeicaSCNReader.Image
- thumbSizeY - Variable in class loci.formats.CoreMetadata
-
Height (in pixels) of thumbnail images in this series.
- THUNDERSCAN - Enum constant in enum class loci.formats.tiff.TiffCompression
- TID_OFFSET - Enum constant in enum class loci.formats.dicom.DicomAttribute
- TIF - Enum constant in enum class loci.formats.in.LeicaMicrosystemsMetadata.LMSFileReader.ImageFormat
- tiff - Variable in class loci.formats.in.LeicaReader
-
Helper readers.
- tiff - Variable in class loci.formats.in.PerkinElmerReader
-
Helper reader.
- tiff - Variable in class loci.formats.in.PrairieReader
-
Helper reader for opening images.
- TIFF_EPS_STANDARD - Static variable in class loci.formats.in.DNGReader
- TIFF_EPS_STANDARD - Static variable in class loci.formats.in.NikonReader
- TIFF_IFD - Static variable in class loci.formats.in.CellSensReader
- TIFF_KEY - Static variable in class loci.formats.out.DicomWriter
-
Option for turning off TIFF metadata.
- TIFF_SUFFIXES - Static variable in class loci.formats.in.TiffReader
- TIFF_SUFFIXES - Static variable in class loci.formats.in.ZeissTIFFReader
- TiffCompression - Enum Class in loci.formats.tiff
-
Utility class for performing compression operations with a TIFF file.
- TiffCompression(int, Codec, String) - Constructor for enum class loci.formats.tiff.TiffCompression
-
Default constructor.
- TiffConstants - Class in loci.formats.tiff
-
Generally useful TIFF-related constants.
- TiffConstants() - Constructor for class loci.formats.tiff.TiffConstants
- TiffDelegateReader - Class in loci.formats.in
-
TiffDelegateReader is a file format reader for TIFF files.
- TiffDelegateReader() - Constructor for class loci.formats.in.TiffDelegateReader
-
Constructs a new TIFF reader.
- TiffDelegateWidgets - Class in loci.plugins.config
-
Custom widgets for configuring Bio-Formats TIFF support.
- TiffDelegateWidgets() - Constructor for class loci.plugins.config.TiffDelegateWidgets
- tiffFiles - Variable in class loci.formats.in.APLReader
- TiffIFDEntry - Class in loci.formats.tiff
-
This class represents a single raw TIFF IFD entry.
- TiffIFDEntry(int, IFDType, int, long) - Constructor for class loci.formats.tiff.TiffIFDEntry
- tiffInfo - Variable in class loci.formats.in.ZeissTIFFReader
- TIFFInfo() - Constructor for class loci.formats.in.ZeissTIFFReader.TIFFInfo
- TiffJAIReader - Class in loci.formats.in
-
TiffJAIReader is a file format reader for TIFF images.
- TiffJAIReader() - Constructor for class loci.formats.in.TiffJAIReader
-
Constructs a new TIFF reader that uses Java Image I/O.
- tiffParser - Variable in class loci.formats.in.FlowSightReader
- tiffParser - Variable in class loci.formats.in.MinimalTiffReader
- tiffParser - Variable in class loci.formats.in.TCSReader
- tiffParser - Variable in class loci.formats.in.ZeissLSMReader
- TiffParser - Class in loci.formats.tiff
-
Parses TIFF data from an input source.
- TiffParser(String) - Constructor for class loci.formats.tiff.TiffParser
-
Constructs a new TIFF parser from the given file name.
- TiffParser(RandomAccessInputStream) - Constructor for class loci.formats.tiff.TiffParser
-
Constructs a new TIFF parser from the given input source.
- TiffRational - Class in loci.formats.tiff
-
A rational number (numerator over denominator).
- TiffRational(long, long) - Constructor for class loci.formats.tiff.TiffRational
-
Constructs a rational number.
- tiffReader - Variable in class loci.formats.in.InCellReader
- tiffReader - Variable in class loci.formats.in.MicromanagerReader
-
Helper reader for TIFF files.
- tiffReader - Variable in class loci.formats.in.ZeissTIFFReader
-
Helper reader for TIFF files.
- TiffReader - Class in loci.formats.in
-
TiffReader is the file format reader for regular TIFF files, not of any specific TIFF variant.
- TiffReader() - Constructor for class loci.formats.in.TiffReader
-
Constructs a new Tiff reader.
- tiffReaders - Variable in class loci.formats.in.TCSReader
-
Helper readers.
- tiffs - Variable in class loci.formats.in.BDReader
- tiffs - Variable in class loci.formats.in.FV1000Reader
-
Names of every TIFF file to open.
- tiffs - Variable in class loci.formats.in.L2DReader
-
List of constituent TIFF files.
- tiffs - Variable in class loci.formats.in.MIASReader
-
TIFF files - indexed by well and file.
- tiffs - Variable in class loci.formats.in.MicromanagerReader.Position
- tiffs - Variable in class loci.formats.in.ScanrReader
- tiffs - Variable in class loci.formats.in.TCSReader
-
List of TIFF files.
- tiffSaver - Variable in class loci.formats.out.DicomWriter
- tiffSaver - Variable in class loci.formats.out.TiffWriter
-
The TiffSaver that will do most of the writing.
- TiffSaver - Class in loci.formats.tiff
-
Parses TIFF data from an input source.
- TiffSaver(String) - Constructor for class loci.formats.tiff.TiffSaver
-
Constructs a new TIFF saver from the given filename.
- TiffSaver(RandomAccessOutputStream, String) - Constructor for class loci.formats.tiff.TiffSaver
-
Constructs a new TIFF saver from the given output source.
- TiffSaver(RandomAccessOutputStream, ByteArrayHandle) - Constructor for class loci.formats.tiff.TiffSaver
-
Constructs a new TIFF saver from the given output source.
- TIFFTile() - Constructor for class loci.formats.in.VentanaReader.TIFFTile
- TiffWriter - Class in loci.formats.out
-
TiffWriter is the file format writer for TIFF files.
- TiffWriter() - Constructor for class loci.formats.out.TiffWriter
- TiffWriter(String, String[]) - Constructor for class loci.formats.out.TiffWriter
- Tile() - Constructor for class loci.formats.in.OlympusTileReader.Tile
- TILE_BYTE_COUNTS - Static variable in class loci.formats.tiff.IFD
- TILE_GRANULARITY - Static variable in class loci.formats.out.TiffWriter
-
TIFF tiles must be of a height and width divisible by 16.
- TILE_LENGTH - Static variable in class loci.formats.tiff.IFD
- TILE_NUM - Static variable in class loci.formats.FormatTools
- TILE_OFFSETS - Static variable in class loci.formats.tiff.IFD
- TILE_ORIGIN - Static variable in class loci.formats.in.CellSensReader
- TILE_SYSTEM - Static variable in class loci.formats.in.CellSensReader
- TILE_WIDTH - Static variable in class loci.formats.tiff.IFD
- TILE_X - Static variable in class loci.formats.FormatTools
- TILE_Y - Static variable in class loci.formats.FormatTools
- tileBytesInc - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataTempBuffer
- tileBytesInc - Variable in class loci.formats.in.LIFReader
- tileCols - Variable in class loci.formats.in.MIASReader
- tileColumns - Variable in class loci.formats.in.VentanaReader.AreaOfInterest
- TileCoordinate() - Constructor for class loci.formats.TileStitcher.TileCoordinate
- TileCoordinate(int) - Constructor for class loci.formats.in.CellSensReader.TileCoordinate
- tileCount - Variable in class loci.formats.in.ImspectorReader
-
The number of mosaic tiles stored in the file.
- tileCount - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataTempBuffer
- tileCount - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.MultipleImagesReader
- tileCount - Variable in class loci.formats.in.LIFReader
- tileCountPointer - Variable in class loci.formats.out.DicomWriter
- tileFiles - Variable in class loci.formats.in.HamamatsuVMSReader
- tileGridXOffset - Variable in class loci.formats.codec.CodecOptions
-
Horizontal offset of the tile grid as it would be provided to:
ImageWriteParam.setTiling(int, int, int, int)(WRITE). - tileGridYOffset - Variable in class loci.formats.codec.CodecOptions
-
Vertical offset of the tile grid as it would be provided to:
ImageWriteParam.setTiling(int, int, int, int)(WRITE). - tileHeight - Variable in class loci.formats.codec.CodecOptions
-
Tile height as it would be provided to:
ImageWriteParam.setTiling(int, int, int, int)(WRITE). - tileHeight - Variable in class loci.formats.in.CellVoyagerReader.ChannelInfo
- tileHeight - Variable in class loci.formats.in.L2DReader
- tileHeight - Variable in class loci.formats.in.LeicaReader
- tileHeight - Variable in class loci.formats.in.MIASReader
- tileHeight - Variable in class loci.formats.in.OMETiffReader.OMETiffCoreMetadata
-
Tile size Y.
- tileHeight - Variable in class loci.formats.in.ScanrReader
- tileHeight - Variable in class loci.formats.in.VentanaReader
- tileHeight - Variable in class loci.formats.in.ZeissCZIReader
- tileHeight - Variable in class loci.formats.out.DicomWriter
- tileHeight - Variable in class loci.formats.services.JPEGTurboServiceImpl
- tileHeightPointer - Variable in class loci.formats.out.DicomWriter
- tileIndices - Variable in class loci.formats.in.BaseZeissReader
- TileJPEGReader - Class in loci.formats.in
-
Reader for decoding JPEG images using java.awt.Toolkit and TurboJPEG.
- TileJPEGReader() - Constructor for class loci.formats.in.TileJPEGReader
- tileMap - Variable in class loci.formats.in.CellSensReader
- tileMap - Variable in class loci.formats.TileStitcher
- tileOffsets - Variable in class loci.formats.in.CellSensReader
- tileOriginX - Variable in class loci.formats.in.CellSensReader.Pyramid
- tileOriginY - Variable in class loci.formats.in.CellSensReader.Pyramid
- tilePositions - Variable in class loci.formats.in.DicomReader
- tileRangeX - Variable in class loci.formats.in.TissueFAXSReader.ScanRegion
- tileRangeY - Variable in class loci.formats.in.TissueFAXSReader.ScanRegion
- tileRows - Variable in class loci.formats.in.MIASReader
- tileRows - Variable in class loci.formats.in.VentanaReader.AreaOfInterest
- tiles - Variable in class loci.formats.dicom.DicomFileInfo
- tiles - Variable in class loci.formats.in.BaseZeissReader
- tiles - Variable in class loci.formats.in.OlympusTileReader
- tiles - Variable in class loci.formats.in.VentanaReader
- tileSizeX - Variable in class loci.formats.in.TissueFAXSReader.ScanRegion
- tileSizeX - Variable in class loci.formats.out.TiffWriter
-
The tile width which will be used for writing.
- tileSizeY - Variable in class loci.formats.in.TissueFAXSReader.ScanRegion
- tileSizeY - Variable in class loci.formats.out.TiffWriter
-
The tile height which will be used for writing.
- tileStitcher - Variable in class loci.plugins.in.ImportProcess
- TileStitcher - Class in loci.formats
- TileStitcher() - Constructor for class loci.formats.TileStitcher
-
Constructs a TileStitcher around a new image reader.
- TileStitcher(IFormatReader) - Constructor for class loci.formats.TileStitcher
-
Constructs a TileStitcher with the given reader.
- TileStitcher.TileCoordinate - Class in loci.formats
- tileWidth - Variable in class loci.formats.codec.CodecOptions
-
Tile width as it would be provided to:
ImageWriteParam.setTiling(int, int, int, int)(WRITE). - tileWidth - Variable in class loci.formats.in.CellVoyagerReader.ChannelInfo
- tileWidth - Variable in class loci.formats.in.L2DReader
- tileWidth - Variable in class loci.formats.in.LeicaReader
- tileWidth - Variable in class loci.formats.in.MIASReader
- tileWidth - Variable in class loci.formats.in.OMETiffReader.OMETiffCoreMetadata
-
Tile size X.
- tileWidth - Variable in class loci.formats.in.ScanrReader
- tileWidth - Variable in class loci.formats.in.VentanaReader
- tileWidth - Variable in class loci.formats.in.ZeissCZIReader
- tileWidth - Variable in class loci.formats.out.DicomWriter
- tileWidth - Variable in class loci.formats.services.JPEGTurboServiceImpl
- tileWidthPointer - Variable in class loci.formats.out.DicomWriter
- tileX - Variable in class loci.formats.in.CellSensReader
- tileX - Variable in class loci.formats.TileStitcher
- tileY - Variable in class loci.formats.in.CellSensReader
- tileY - Variable in class loci.formats.TileStitcher
- TillVisionReader - Class in loci.formats.in
-
TillVisionReader is the file format reader for TillVision files.
- TillVisionReader() - Constructor for class loci.formats.in.TillVisionReader
-
Constructs a new TillVision reader.
- TIM_SUFFIX - Static variable in class loci.formats.in.PerkinElmerReader
- time - Variable in class loci.formats.in.DicomReader
- time - Variable in class loci.formats.in.LEOReader
- time - Variable in class loci.formats.in.MicroCTReader
- time - Variable in class loci.formats.in.MicromanagerReader.Position
- time - Variable in class loci.formats.in.SDTInfo
-
Time of creation.
- time - Variable in class loci.formats.in.SVSReader
- time - Variable in class loci.plugins.in.ImagePlusReader
- TIME_DISTRIBUTION_PROTOCOL - Enum constant in enum class loci.formats.dicom.DicomAttribute
- TIME_FORMAT - Static variable in class loci.formats.in.GelReader
- TIME_INCREMENT - Static variable in class loci.formats.in.CellSensReader
- TIME_OF_LAST_CALIBRATION - Enum constant in enum class loci.formats.dicom.DicomAttribute
- TIME_OF_LAST_DETECTOR_CALIBRATION - Enum constant in enum class loci.formats.dicom.DicomAttribute
- TIME_OF_SECONDARY_CAPTURE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- TIME_OFFSET - Static variable in class loci.formats.in.TextReader
-
How often to report progress during initialization, in milliseconds.
- TIME_PREFIX - Static variable in class loci.formats.in.KLBReader
- TIME_SOURCE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- TIME_START - Static variable in class loci.formats.in.CellSensReader
- TIME_SUFFIX - Static variable in class loci.formats.in.KLBReader
- TIME_VALUE - Static variable in class loci.formats.in.CellSensReader
- timeBins - Variable in class loci.formats.in.PQBinReader
- timeBins - Variable in class loci.formats.in.SDTInfo
- timeBins - Variable in class loci.formats.in.SDTReader
-
Number of time bins in lifetime histogram.
- timeIncrement - Variable in class loci.formats.in.FEITiffReader
- timeIncrement - Variable in class loci.formats.in.IPLabReader
- timeIncrement - Variable in class loci.formats.in.TiffReader
- timeIncrement - Variable in class loci.formats.in.ZeissCZIReader
- timeIncrement - Variable in class loci.formats.in.ZeissLSMReader.Track
- timeIndex - Variable in class loci.formats.in.FluoviewReader
- TIMEINFO - Static variable in class loci.formats.in.LeicaReader
- timelineIndex - Variable in class loci.formats.in.CV7000Reader.Channel
- timelineIndex - Variable in class loci.formats.in.CV7000Reader.MeasurementSettingsHandler
- timelineIndex - Variable in class loci.formats.in.CV7000Reader.Plane
- timepoint - Variable in class loci.formats.in.BaseZeissReader
- timepoint - Variable in class loci.formats.in.BDVReader.H5Coordinate
- timepoint - Variable in class loci.formats.in.ColumbusReader.Plane
- timepoint - Variable in class loci.formats.in.CV7000Reader.Plane
- timepoint - Variable in class loci.formats.in.OpenlabReader.PlaneInfo
- timepoint - Variable in class loci.formats.in.TissueFAXSReader.ScanRegion
- timepointIncrement - Variable in class loci.formats.in.BDVReader
- timepointIndices - Variable in class loci.formats.in.BaseZeissReader
- timepoints - Variable in class loci.formats.in.SDTInfo
- timePoints - Variable in class loci.formats.in.CellVoyagerReader
- timepointUsePattern - Variable in class loci.formats.in.BDVReader
- Timer() - Constructor for class loci.formats.in.ZeissLSMReader.Timer
- times - Variable in class loci.formats.in.BDVReader
- timestamp - Variable in class loci.formats.dicom.DicomFileInfo
- timestamp - Variable in class loci.formats.in.CV7000Reader.Plane
- timestamp - Variable in class loci.formats.in.GatanReader
- timestamp - Variable in class loci.formats.in.InCellReader.InCellHandler
- timestamp - Variable in class loci.formats.in.JDCEReader.PlaneMetadata
- timestamp - Variable in class loci.formats.in.OpenlabReader.PlaneInfo
- timestamp - Variable in class loci.formats.in.TecanReader.Image
- timestamp - Variable in class loci.formats.in.ZeissCZIReader.SubBlock
- TIMESTAMP - Static variable in class loci.formats.FormatTools
- TIMESTAMP - Static variable in class loci.formats.in.CellSensReader
- TIMESTAMP_KEY - Static variable in class loci.formats.in.LiFlimReader
- timestampAdjustments - Variable in class loci.formats.in.OIRReader
- timestampFile - Variable in class loci.formats.in.VolocityReader.Stack
- timestamps - Variable in class loci.formats.in.BaseZeissReader
- timestamps - Variable in class loci.formats.in.BrukerReader
- timestamps - Variable in class loci.formats.in.CellWorxReader
- timestamps - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataTempBuffer
- timestamps - Variable in class loci.formats.in.LeicaReader
- timestamps - Variable in class loci.formats.in.LiFlimReader
- timestamps - Variable in class loci.formats.in.LIFReader
- timestamps - Variable in class loci.formats.in.MetamorphHandler
- timestamps - Variable in class loci.formats.in.MicromanagerReader.Position
- timestamps - Variable in class loci.formats.in.PCIReader
- timestamps - Variable in class loci.formats.in.VolocityReader
- timestamps - Variable in class loci.formats.in.ZeissCZIReader
- timestamps - Variable in class loci.formats.in.ZeissLSMReader
- timeStampSeconds - Variable in class loci.formats.in.DeltavisionReader.DVExtHdrFields
-
Time stamp in seconds since the experiment began.
- timeUnit - Variable in class loci.formats.in.NiftiReader
- TIMEZONE_OFFSET_UTC - Enum constant in enum class loci.formats.dicom.DicomAttribute
- TISSUE_INDEX - Static variable in class loci.formats.in.NDPIReader
- TissueFAXSReader - Class in loci.formats.in
-
Reader for TissueFAXS format from TissueGnostics.
- TissueFAXSReader() - Constructor for class loci.formats.in.TissueFAXSReader
-
Constructs a new TissueGnostics TissueFAXS reader.
- TissueFAXSReader.Channel - Class in loci.formats.in
- TissueFAXSReader.ScanRegion - Class in loci.formats.in
- TITAN_TAG - Static variable in class loci.formats.in.FEITiffReader
- TITLE - Static variable in class loci.formats.gui.DataConverter
- TITLE - Static variable in class loci.formats.gui.ImageViewer
- TITLE - Static variable in class loci.formats.tools.EditTiffG
- TJ - Class in org.libjpegturbo.turbojpeg
-
TurboJPEG utility class (cannot be instantiated)
- TJ() - Constructor for class org.libjpegturbo.turbojpeg.TJ
- TJCompressor - Class in org.libjpegturbo.turbojpeg
-
TurboJPEG compressor
- TJCompressor() - Constructor for class org.libjpegturbo.turbojpeg.TJCompressor
-
Create a TurboJPEG compressor instance.
- TJCompressor(byte[], int, int, int, int) - Constructor for class org.libjpegturbo.turbojpeg.TJCompressor
-
Create a TurboJPEG compressor instance and associate the uncompressed source image stored in
srcImagewith the newly-created instance. - TJCustomFilter - Interface in org.libjpegturbo.turbojpeg
-
Custom filter callback interface
- TJDecompressor - Class in org.libjpegturbo.turbojpeg
-
TurboJPEG decompressor
- TJDecompressor() - Constructor for class org.libjpegturbo.turbojpeg.TJDecompressor
-
Create a TurboJPEG decompresssor instance.
- TJDecompressor(byte[]) - Constructor for class org.libjpegturbo.turbojpeg.TJDecompressor
-
Create a TurboJPEG decompressor instance and associate the JPEG image stored in
jpegImagewith the newly-created instance. - TJDecompressor(byte[], int) - Constructor for class org.libjpegturbo.turbojpeg.TJDecompressor
-
Create a TurboJPEG decompressor instance and associate the JPEG image of length
imageSizebytes stored injpegImagewith the newly-created instance. - TJLoader - Class in org.libjpegturbo.turbojpeg
- TJLoader() - Constructor for class org.libjpegturbo.turbojpeg.TJLoader
- TJScalingFactor - Class in org.libjpegturbo.turbojpeg
-
Fractional scaling factor
- TJScalingFactor(int, int) - Constructor for class org.libjpegturbo.turbojpeg.TJScalingFactor
- TJTransform - Class in org.libjpegturbo.turbojpeg
-
Lossless transform parameters
- TJTransform() - Constructor for class org.libjpegturbo.turbojpeg.TJTransform
-
Create a new lossless transform instance.
- TJTransform(int, int, int, int, int, int, TJCustomFilter) - Constructor for class org.libjpegturbo.turbojpeg.TJTransform
-
Create a new lossless transform instance with the given parameters.
- TJTransform(Rectangle, int, int, TJCustomFilter) - Constructor for class org.libjpegturbo.turbojpeg.TJTransform
-
Create a new lossless transform instance with the given parameters.
- TJTransformer - Class in org.libjpegturbo.turbojpeg
-
TurboJPEG lossless transformer
- TJTransformer() - Constructor for class org.libjpegturbo.turbojpeg.TJTransformer
-
Create a TurboJPEG lossless transformer instance.
- TJTransformer(byte[]) - Constructor for class org.libjpegturbo.turbojpeg.TJTransformer
-
Create a TurboJPEG lossless transformer instance and associate the JPEG image stored in
jpegImagewith the newly-created instance. - TJTransformer(byte[], int) - Constructor for class org.libjpegturbo.turbojpeg.TJTransformer
-
Create a TurboJPEG lossless transformer instance and associate the JPEG image of length
imageSizebytes stored injpegImagewith the newly-created instance. - tLabel - Variable in class loci.formats.gui.DataConverter
- TLM - Enum constant in enum class loci.formats.codec.JPEG2000SegmentMarker
- TM - Enum constant in enum class loci.formats.dicom.DicomVR
- TM_LINE_POSITION_X0 - Enum constant in enum class loci.formats.dicom.DicomAttribute
- TM_LINE_POSITION_X1 - Enum constant in enum class loci.formats.dicom.DicomAttribute
- TM_LINE_POSITION_Y0 - Enum constant in enum class loci.formats.dicom.DicomAttribute
- TM_LINE_POSITION_Y1 - Enum constant in enum class loci.formats.dicom.DicomAttribute
- tmaX - Variable in class loci.formats.in.TissueFAXSReader.ScanRegion
- tmaY - Variable in class loci.formats.in.TissueFAXSReader.ScanRegion
- tmpLetter - Variable in class loci.formats.ResourceNamer
- toArray() - Method in class loci.formats.tiff.OnDemandLongArray
- toByteArray() - Method in class loci.formats.codec.BitWriter
-
Deprecated.Gets an array containing all bits written thus far.
- toByteArray() - Method in class loci.formats.codec.ByteVector
- toBytes(BufferedImage, IFormatWriter) - Static method in class loci.formats.gui.BufferedImageWriter
- toCIEXYZ(float[]) - Method in class loci.formats.gui.TwoChannelColorSpace
- toFloat(int, FloatProcessor) - Method in class loci.plugins.util.RecordedImageProcessor
- toggleAnimation() - Method in class loci.plugins.util.DataBrowser
-
Toggles whether the data browser is animating.
- token - Variable in enum class loci.formats.in.LeicaMicrosystemsMetadata.Dimension.DimensionKey
- token(String, String, int) - Method in class loci.formats.in.PrairieMetadata
-
Gets the
ith token of the given string, split according to the specific regular expression. - TOKEN_SEPARATOR - Static variable in class loci.formats.in.FakeReader
- tokenize(String) - Method in class loci.formats.in.ICSReader
- toLength(Double, boolean) - Method in class loci.formats.in.PrairieMetadata.Frame
-
Convert a position number to a length in the microscope reference frame.
- TOMO_ANGLE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- TOMO_CLASS - Enum constant in enum class loci.formats.dicom.DicomAttribute
- TOMO_LAYER_HEIGHT - Enum constant in enum class loci.formats.dicom.DicomAttribute
- TOMO_TIME - Enum constant in enum class loci.formats.dicom.DicomAttribute
- TOMO_TYPE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- TONE_COMPENSATION - Static variable in class loci.formats.in.NikonReader
- TOOLS - Static variable in class loci.formats.UpgradeChecker
-
Name of the ueber tools JAR.
- toOMExmlColor(Color) - Static method in class loci.plugins.util.ROIHandler
-
Converts the Java Color into an OME-XML Color.
- TOP_LEVEL_KEYS - Static variable in class loci.formats.in.NikonTiffReader
- TopometrixReader - Class in loci.formats.in
-
TopometrixReader is the file format reader for TopoMetrix .tfr, .ffr, .zfr, .zfp, and .2fl files.
- TopometrixReader() - Constructor for class loci.formats.in.TopometrixReader
-
Constructs a new TopoMetrix reader.
- toRGB(float[]) - Method in class loci.formats.gui.TwoChannelColorSpace
- toSPWCoordinates(int) - Method in class loci.formats.in.FakeReader
-
Convert the given series (Image) index to a WellSample, Well, and Plate index.
- toString() - Method in class loci.formats.cache.CacheEvent
- toString() - Method in class loci.formats.CoreMetadata
- toString() - Method in class loci.formats.dicom.DicomTag
- toString() - Method in class loci.formats.FileInfo
- toString() - Method in class loci.formats.gui.ComboFileFilter
-
Gets a string representation of this file filter.
- toString() - Method in class loci.formats.gui.ExtensionFileFilter
-
Gets a string representation of this file filter.
- toString() - Method in class loci.formats.gui.FormatFileFilter
-
Gets a string representation of this file filter.
- toString() - Method in class loci.formats.gui.NoExtensionFileFilter
-
Gets a string representation of this file filter.
- toString() - Method in class loci.formats.gui.XMLCellRenderer.XMLItem
-
Allows copy and paste from tree component.
- toString() - Method in class loci.formats.in.BaseZeissReader.Layer
- toString() - Method in class loci.formats.in.BaseZeissReader.Shape
- toString() - Method in class loci.formats.in.BaseZeissReader.Tag
- toString() - Method in class loci.formats.in.BDVReader.H5Coordinate
- toString() - Method in class loci.formats.in.BioRadReader.Note
- toString() - Method in class loci.formats.in.CellH5Reader.CellH5Coordinate
- toString() - Method in class loci.formats.in.CellSensReader.TileCoordinate
- toString() - Method in class loci.formats.in.CellVoyagerReader.AreaInfo
- toString() - Method in class loci.formats.in.CellVoyagerReader.ChannelInfo
- toString() - Method in class loci.formats.in.CellVoyagerReader.FieldInfo
- toString() - Method in class loci.formats.in.CellVoyagerReader.WellInfo
- toString() - Method in class loci.formats.in.CV7000Reader.Channel
- toString() - Method in class loci.formats.in.DeltavisionReader.DVExtHdrFields
-
Helper function which overrides toString, printing out the values in the header section.
- toString() - Method in class loci.formats.in.IM3Reader.IM3Record
- toString() - Method in class loci.formats.in.LeicaMicrosystemsMetadata.LMSXmlDocument
- toString() - Method in class loci.formats.in.LIFReader.MemoryBlock
- toString() - Method in class loci.formats.in.MicromanagerReader.Index
- toString() - Method in class loci.formats.in.ND2Reader.ChunkMapEntry
- toString() - Method in class loci.formats.in.OIRReader.CZTKey
- toString() - Method in class loci.formats.in.OlympusTileReader.Tile
- toString() - Method in class loci.formats.in.PrairieMetadata.ValueItem
- toString() - Method in class loci.formats.in.VentanaReader.AreaOfInterest
- toString() - Method in class loci.formats.in.VentanaReader.Overlap
- toString() - Method in class loci.formats.in.ZeissCZIReader.AttachmentEntry
- toString() - Method in class loci.formats.in.ZeissCZIReader.Coordinate
- toString() - Method in class loci.formats.in.ZeissCZIReader.DimensionEntry
- toString() - Method in class loci.formats.in.ZeissCZIReader.DirectoryEntry
- toString() - Method in class loci.formats.in.ZeissCZIReader.SubBlock
- toString() - Method in class loci.formats.in.ZeissTIFFHandler.Plane
- toString() - Method in class loci.formats.in.ZeissTIFFHandler.Scaling
- toString() - Method in class loci.formats.in.ZeissTIFFHandler.Tag
- toString() - Method in class loci.formats.in.ZeissTIFFHandler.TagSet
- toString() - Method in class loci.formats.in.ZeissTIFFHandler
- toString() - Method in class loci.formats.in.ZeissTIFFReader.Plane
- toString() - Method in class loci.formats.ome.OMEPyramidStore.Resolution
- toString() - Method in class loci.formats.tiff.TiffIFDEntry
- toString() - Method in class loci.formats.tiff.TiffRational
-
Returns a string representation of the object.
- toString() - Method in class loci.formats.tools.AmiraParameters
- toString() - Method in class loci.formats.tools.AsciiImage
- toString() - Method in class loci.plugins.config.FormatEntry
- toString() - Method in class loci.plugins.config.LibraryEntry
- toString() - Method in class loci.plugins.in.ImporterMetadata
- toString() - Method in class loci.plugins.util.RecordedImageProcessor
- toString(boolean) - Method in class loci.formats.gui.XMLCellRenderer.XMLItem
- toString(Map, String) - Static method in class loci.formats.tools.AmiraParameters
- TOTAL_PIXEL_MATRIX_COLUMNS - Enum constant in enum class loci.formats.dicom.DicomAttribute
- TOTAL_PIXEL_MATRIX_FOCAL_PLANES - Enum constant in enum class loci.formats.dicom.DicomAttribute
- TOTAL_PIXEL_MATRIX_ORIGIN_SEQUENCE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- TOTAL_PIXEL_MATRIX_ROWS - Enum constant in enum class loci.formats.dicom.DicomAttribute
- totalChannels - Variable in class loci.formats.in.InCellReader
- totalImages - Variable in class loci.formats.in.InCellReader
- totalROIs - Variable in class loci.formats.in.ZeissLSMReader
- toXMLAnnotation() - Method in class loci.formats.Modulo
- Track() - Constructor for class loci.formats.in.ZeissLSMReader.Track
- TRACK_ACQUIRE - Static variable in class loci.formats.in.ZeissLSMReader
- TRACK_TIME_BETWEEN_STACKS - Static variable in class loci.formats.in.ZeissLSMReader
- TRAILING_PADDING - Enum constant in enum class loci.formats.dicom.DicomAttribute
- TRANSACTION_UID - Enum constant in enum class loci.formats.dicom.DicomAttribute
- TRANSDUCER_DATA - Enum constant in enum class loci.formats.dicom.DicomAttribute
- TRANSDUCER_FREQUENCY - Enum constant in enum class loci.formats.dicom.DicomAttribute
- TRANSDUCER_ORIENTATION_MODIFIER - Enum constant in enum class loci.formats.dicom.DicomAttribute
- TRANSDUCER_ORIENTATION_SEQUENCE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- TRANSDUCER_POSITION_MODIFIER_SEQUENCE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- TRANSDUCER_POSITION_SEQUENCE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- TRANSDUCER_TYPE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- TRANSFER_FUNCTION - Static variable in class loci.formats.tiff.IFD
- TRANSFER_RANGE - Static variable in class loci.formats.tiff.IFD
- TRANSFER_SYNTAX_UID - Enum constant in enum class loci.formats.dicom.DicomAttribute
- transferSyntaxPointer - Variable in class loci.formats.out.DicomWriter
- transform(byte[][], TJTransform[], int) - Method in class org.libjpegturbo.turbojpeg.TJTransformer
-
Losslessly transform the JPEG image associated with this transformer instance into one or more JPEG images stored in the given destination buffers.
- transform(byte[], int, byte[][], TJTransform[], int) - Method in class org.libjpegturbo.turbojpeg.TJTransformer
- transform(TJTransform[], int) - Method in class org.libjpegturbo.turbojpeg.TJTransformer
-
Losslessly transform the JPEG image associated with this transformer instance and return an array of
TJDecompressorinstances, each of which has a transformed JPEG image associated with it. - transformAcquisitionMode(String) - Method in class loci.formats.in.InveonReader
- transformBedControl(String) - Method in class loci.formats.in.InveonReader
- transformBedMotion(String) - Method in class loci.formats.in.InveonReader
- transformBytes8To16(byte[], byte[], int) - Method in class loci.formats.in.XLEFReader
-
Transforms an 8bit byte array to a 16bit byte array, optionally with bit upscaling (8-16bit)
- transformCTProjectionInterpolation(String) - Method in class loci.formats.in.InveonReader
- transformCTWarping(String) - Method in class loci.formats.in.InveonReader
- transformedSizes - Variable in class org.libjpegturbo.turbojpeg.TJTransformer
- transformEventType(String) - Method in class loci.formats.in.InveonReader
- transformFileType(String) - Method in class loci.formats.in.InveonReader
- transformFilter(String) - Method in class loci.formats.in.InveonReader
- transformGantryRotation(String) - Method in class loci.formats.in.InveonReader
- transformModality(String) - Method in class loci.formats.in.InveonReader
- transformModalityConfiguration(String) - Method in class loci.formats.in.InveonReader
- transformModel(String) - Method in class loci.formats.in.InveonReader
- transformNormalizationApplied(String) - Method in class loci.formats.in.InveonReader
- transformReconAlgorithm(String) - Method in class loci.formats.in.InveonReader
- transformRegistrationAvailable(String) - Method in class loci.formats.in.InveonReader
- transformRotationDirection(String) - Method in class loci.formats.in.InveonReader
- transformSubjectLengthUnits(String) - Method in class loci.formats.in.InveonReader
- transformSubjectOrientation(String) - Method in class loci.formats.in.InveonReader
- transformSubjectWeightUnits(String) - Method in class loci.formats.in.InveonReader
- transformToLatestVersion(String) - Method in interface loci.formats.services.OMEXMLService
-
Transforms the given OME-XML string to the latest supported version of of the OME-XML schema.
- transformToLatestVersion(String) - Method in class loci.formats.services.OMEXMLServiceImpl
- transIndex - Variable in class loci.formats.in.GIFReader
-
Transparent color index.
- translate(int, int) - Method in class loci.plugins.util.RecordedImageProcessor
- translateAttachmentNodes(Element, int) - Method in class loci.formats.in.LeicaMicrosystemsMetadata.LMSMetadataExtractor
-
Extracts information from dimension descriptions and writes it to reader's
MetadataTempBuffer - translateAttachmentNodes(Element, int) - Method in class loci.formats.in.LIFReader
- translateChannelDescriptions(Element, int) - Method in class loci.formats.in.LeicaMicrosystemsMetadata.LMSMetadataExtractor
-
Extracts i.a.
- translateDetectors(Element, int) - Method in class loci.formats.in.LeicaMicrosystemsMetadata.LMSMetadataExtractor
-
Extracts detector information and writes it to reader's
MetadataTempBuffer - translateDetectors(Element, int) - Method in class loci.formats.in.LIFReader
- translateDimensionDescriptions(Element, int) - Method in class loci.formats.in.LeicaMicrosystemsMetadata.LMSMetadataExtractor
-
Extracts information from dimension descriptions and writes it to reader's
CoreMetadataandMetadataTempBuffer - translateDisplaySettings(Element) - Method in class loci.formats.in.ZeissCZIReader
- translateExperiment(Element) - Method in class loci.formats.in.ZeissCZIReader
- translateFilterSettings(Element, int) - Method in class loci.formats.in.LeicaMicrosystemsMetadata.LMSMetadataExtractor
-
Extracts filter information and writes it to reader's
MetadataTempBuffer - translateFilterSettings(Element, int) - Method in class loci.formats.in.LIFReader
- translateHardwareSettings(Element) - Method in class loci.formats.in.ZeissCZIReader
- translateImage(Element, int) - Method in class loci.formats.in.LeicaMicrosystemsMetadata.LMSMetadataExtractor
-
Extracts information from element node and writes it to reader's
CoreMetadataandMetadataTempBuffer - translateImageNames(Element, int) - Method in class loci.formats.in.LIFReader
- translateImageNodes(Element, int) - Method in class loci.formats.in.LIFReader
- translateInformation(Element) - Method in class loci.formats.in.ZeissCZIReader
- translateLaserLines(Element, int) - Method in class loci.formats.in.LeicaMicrosystemsMetadata.LMSMetadataExtractor
-
Extracts laser information and writes it to reader's
MetadataTempBuffer - translateLaserLines(Element, int) - Method in class loci.formats.in.LIFReader
- translateLayers(Element) - Method in class loci.formats.in.ZeissCZIReader
- translateLut(String) - Method in class loci.formats.in.LeicaMicrosystemsMetadata.LMSMetadataExtractor
-
Translates Leica XML lut name / value to Color
- translateLuts(List<String>, int) - Method in class loci.formats.in.LeicaMicrosystemsMetadata.LMSMetadataExtractor
-
Translates raw channel luts of an image to Colors and writes it to reader's
MetadataTempBuffer - translateMetadata(String) - Method in class loci.formats.in.ZeissCZIReader
- translateMetadata(List<LMSImageXmlDocument>) - Method in class loci.formats.in.LeicaMicrosystemsMetadata.LMSFileReader
-
Extracts metadata from a list of Leica image XML Documents and writes them to the reader's CoreMetadata,
MetadataTempBufferand MetadataStore - translateMetadata(List<LMSImageXmlDocument>) - Method in class loci.formats.in.LeicaMicrosystemsMetadata.LMSMetadataExtractor
-
Extracts all information from Leica image xml Documents and writes it to reader's
CoreMetadataandMetadataTempBuffer - translateMetadata(LMSImageXmlDocument) - Method in class loci.formats.in.LeicaMicrosystemsMetadata.LMSFileReader
- translateMetadata(Element) - Method in class loci.formats.in.LIFReader
- translateROIs(Element, int) - Method in class loci.formats.in.LeicaMicrosystemsMetadata.LMSMetadataExtractor
-
Extracts ROIs and writes them to reader's
MetadataTempBuffer - translateROIs(Element, int) - Method in class loci.formats.in.LIFReader
- translateScaling(Element) - Method in class loci.formats.in.ZeissCZIReader
- translateScannerSettings(Element, int) - Method in class loci.formats.in.LeicaMicrosystemsMetadata.LMSMetadataExtractor
-
Extracts scanner information and writes it to reader's
CoreMetadataandMetadataTempBuffer - translateScannerSettings(Element, int) - Method in class loci.formats.in.LIFReader
- translateSingleROIs(Element, int) - Method in class loci.formats.in.LeicaMicrosystemsMetadata.LMSMetadataExtractor
-
Extracts single ROIs and writes them to reader's
MetadataTempBuffer - translateSingleROIs(Element, int) - Method in class loci.formats.in.LIFReader
- translateSingleTimestamp(String) - Method in class loci.formats.in.LeicaMicrosystemsMetadata.LMSMetadataExtractor
-
Translates hex timestamp string to double value
- translateSingleTimestamp(String) - Method in class loci.formats.in.LIFReader
- translateSingleTimestamp(Element) - Method in class loci.formats.in.LeicaMicrosystemsMetadata.LMSMetadataExtractor
-
Translates the content of a timestamp node to double value
- translateSingleTimestamp(Element) - Method in class loci.formats.in.LIFReader
- translateTimestamps(Element, int) - Method in class loci.formats.in.LeicaMicrosystemsMetadata.LMSMetadataExtractor
-
Extracts timestamps and writes them to reader's
MetadataTempBuffer - translateTimestamps(Element, int) - Method in class loci.formats.in.LIFReader
- transmissivity - Variable in class loci.formats.in.OIRReader.Laser
- TRANSMIT_COIL_NAME - Enum constant in enum class loci.formats.dicom.DicomAttribute
- transparency - Variable in class loci.formats.in.GIFReader
-
Use transparent color.
- TRANSPARENCY_ID - Static variable in class loci.formats.in.CellSensReader
- TRANSPARENCY_MASK - Enum constant in enum class loci.formats.tiff.PhotoInterp
- TRANSPARENCY_VALUE - Static variable in class loci.formats.in.CellSensReader
- transX - Variable in class loci.formats.in.LeicaHandler.ROI
- transX - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.ROI
- transX - Variable in class loci.formats.in.LIFReader.ROI
- transY - Variable in class loci.formats.in.LeicaHandler.ROI
- transY - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.ROI
- transY - Variable in class loci.formats.in.LIFReader.ROI
- TrestleReader - Class in loci.formats.in
-
TrestleReader is the file format reader for Trestle slide datasets.
- TrestleReader() - Constructor for class loci.formats.in.TrestleReader
-
Constructs a new Trestle reader.
- trigger - Variable in class loci.formats.in.SDTInfo
- TRIGGER_DIODE - Enum constant in enum class loci.formats.in.SPEReader.SpeHeaderEntry
- TRIGGER_MODE - Enum constant in enum class loci.formats.in.SPEReader.SpeHeaderEntry
- TRIGGER_SAMPLE_POSITION - Enum constant in enum class loci.formats.dicom.DicomAttribute
- TRIGGER_SOURCE_OR_TYPE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- TRIGGER_TIME - Enum constant in enum class loci.formats.dicom.DicomAttribute
- TRIGGER_TIME_OFFSET - Enum constant in enum class loci.formats.dicom.DicomAttribute
- TRIGGER_WINDOW - Enum constant in enum class loci.formats.dicom.DicomAttribute
- TRIM_DIMENSIONS_DEFAULT - Static variable in class loci.formats.in.ZeissCZIReader
- TRIM_DIMENSIONS_KEY - Static variable in class loci.formats.in.ZeissCZIReader
- trimDimensions() - Method in class loci.formats.in.ZeissCZIReader
- TRUE_ALPHA - Static variable in class loci.formats.in.APNGReader
- TRUE_COLOR - Static variable in class loci.formats.in.APNGReader
- trueSizeX - Variable in class loci.formats.in.ND2Reader
- trueSizeY - Variable in class loci.formats.in.ND2Reader
- trueSizeZ - Variable in class loci.formats.in.ND2Reader
- truncatedFileFlag - Variable in class loci.formats.in.DeltavisionReader
- TRUNK - Static variable in class loci.plugins.Updater
- TRUNK_BUILD - Static variable in class loci.formats.UpgradeChecker
-
Location of the JAR artifacts for Bio-Formats' trunk build.
- ts - Variable in class loci.formats.in.ND2Handler
- tScroll - Variable in class loci.plugins.util.DataBrowser
- tSize - Variable in class loci.formats.in.DeltavisionReader
-
Size of one time element in the extended header.
- tSlider - Variable in class loci.formats.gui.ImageViewer
- tsT - Variable in class loci.formats.in.ND2Reader
- tStart - Variable in class loci.formats.in.OIRReader
- tStep - Variable in class loci.formats.in.OIRReader
- tStep - Variable in class loci.plugins.in.ImporterOptions
- tSteps - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataTempBuffer
- tSteps - Variable in class loci.formats.in.LIFReader
- Tstore - Variable in class loci.formats.in.SPCReader
- tstoreb - Variable in class loci.formats.in.SPCReader
- TURKISH_CHARSET - Enum constant in enum class loci.formats.in.BaseZeissReader.Charset
- tValues - Variable in class loci.formats.in.CellSensReader.Pyramid
- TWO - Static variable in class loci.formats.AxisGuesser
- TwoChannelColorSpace - Class in loci.formats.gui
-
ColorSpace for 2-channel images.
- TwoChannelColorSpace(int, int) - Constructor for class loci.formats.gui.TwoChannelColorSpace
- type - Variable in class loci.formats.cache.CacheEvent
-
Type of cache event.
- type - Variable in class loci.formats.in.APNGReader.PNGBlock
- type - Variable in class loci.formats.in.AVIReader
- type - Variable in class loci.formats.in.BaseZeissReader.Shape
- type - Variable in class loci.formats.in.BioRadReader.Note
- type - Variable in class loci.formats.in.CV7000Reader.LightSource
- type - Variable in class loci.formats.in.GatanReader.ROIShape
- type - Variable in class loci.formats.in.IM3Reader.IM3Record
- type - Variable in class loci.formats.in.LeicaHandler.Detector
- type - Variable in class loci.formats.in.LeicaHandler.ROI
- type - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.ROI
- type - Variable in class loci.formats.in.LIFReader.ROI
- type - Variable in class loci.formats.in.PrairieMetadata.Sequence
-
typeattribute of this<Sequence>. - type - Variable in enum class loci.formats.in.SPEReader.SpeHeaderEntry
- type - Variable in class loci.formats.in.ZeissLSMReader.Laser
- type - Variable in class loci.formats.in.ZeissTIFFHandler.Scaling.Dimension
- type - Variable in class loci.formats.Modulo
- type - Variable in class loci.formats.tiff.TiffIFDEntry
-
The field Type.
- type - Variable in class loci.plugins.config.ConfigWindow
- type - Variable in class loci.plugins.config.LibraryEntry
- TYPE - Enum constant in enum class loci.formats.in.SPEReader.SpeHeaderEntry
- TYPE_ASCII - Static variable in class loci.formats.in.ZeissLSMReader
- TYPE_BOOLEAN - Static variable in class loci.formats.in.ZeissLSMReader
- TYPE_BOOLEAN - Static variable in class loci.plugins.prefs.OptionsList
-
String indicating option is of type boolean.
- TYPE_DATE - Static variable in class loci.formats.in.ZeissLSMReader
- TYPE_LONG - Static variable in class loci.formats.in.ZeissLSMReader
- TYPE_OF_DETECTOR_MOTION - Enum constant in enum class loci.formats.dicom.DicomAttribute
- TYPE_OF_FILTERS - Enum constant in enum class loci.formats.dicom.DicomAttribute
- TYPE_RATIONAL - Static variable in class loci.formats.in.ZeissLSMReader
- TYPE_STRING - Static variable in class loci.plugins.prefs.OptionsList
-
String indicating option is of type string.
- TYPE_SUBBLOCK - Static variable in class loci.formats.in.ZeissLSMReader
-
Data types.
- typeDescription - Variable in class loci.formats.Modulo
- typeLabel - Variable in class loci.formats.gui.PreviewPane
-
Labels containing thumbnail and dimensional information.
- types - Variable in class loci.formats.in.TillVisionReader
- TYPES - Static variable in class loci.formats.in.MRCReader
- typeText - Variable in class loci.formats.gui.PreviewPane
- typeTip - Variable in class loci.formats.gui.PreviewPane
- TypeUINT12 - Variable in class loci.formats.in.LiFlimReader
-
if DataType is UINT12, data is compressed in 12 bits.
U
- UBMReader - Class in loci.formats.in
-
UBMReader is the file format reader for UBM .pr3 files.
- UBMReader() - Constructor for class loci.formats.in.UBMReader
-
Constructs a new UBM reader.
- UBYTE - Static variable in class loci.formats.in.GatanReader
- UC - Enum constant in enum class loci.formats.dicom.DicomVR
- UCHAR - Static variable in class loci.formats.in.CellSensReader
- UI - Enum constant in enum class loci.formats.dicom.DicomVR
- UIC1TAG - Static variable in class loci.formats.in.MetamorphReader
- UIC2TAG - Static variable in class loci.formats.in.MetamorphReader
- UIC3TAG - Static variable in class loci.formats.in.MetamorphReader
- UIC4TAG - Static variable in class loci.formats.in.MetamorphReader
- UID - Variable in class loci.formats.in.CellVoyagerReader.AreaInfo
- UID - Variable in class loci.formats.in.CellVoyagerReader.WellInfo
- UID_DEFAULT_ROOT - Static variable in class loci.formats.out.DicomWriter
- UID_ROOT_KEY - Static variable in class loci.formats.out.DicomWriter
-
Option for setting the organization root for UIDs.
- UIDCreator() - Constructor for class loci.formats.out.DicomWriter.UIDCreator
- uids - Variable in class loci.formats.out.DicomWriter
- UINT - Static variable in class loci.formats.in.CellSensReader
- UINT - Static variable in class loci.formats.in.GatanReader
- UINT12stream - Variable in class loci.formats.in.LiFlimReader
- UINT12streamPos - Variable in class loci.formats.in.LiFlimReader
- UINT12streamSeries - Variable in class loci.formats.in.LiFlimReader
- UINT16 - Static variable in class loci.formats.FormatTools
-
Identifies the UINT16 data type used to store pixel values.
- UINT16_TYPE - Static variable in class loci.formats.in.KLBReader
- UINT32 - Static variable in class loci.formats.FormatTools
-
Identifies the UINT32 data type used to store pixel values.
- UINT32_TYPE - Static variable in class loci.formats.in.KLBReader
- UINT64_TYPE - Static variable in class loci.formats.in.KLBReader
- UINT8 - Static variable in class loci.formats.FormatTools
-
Identifies the UINT8 data type used to store pixel values.
- UINT8_TYPE - Static variable in class loci.formats.in.KLBReader
- UL - Enum constant in enum class loci.formats.dicom.DicomVR
- ULONG - Static variable in class loci.formats.in.CellSensReader
- ULTRASOUND_COLOR_DATA_PRESENT - Enum constant in enum class loci.formats.dicom.DicomAttribute
- UN - Enum constant in enum class loci.formats.dicom.DicomVR
- uncompress(byte[], String) - Method in class loci.formats.in.QTReader
-
Uncompresses an image plane according to the the codec identifier.
- uncompress(int, byte[]) - Method in class loci.formats.in.AVIReader
- UNCOMPRESSED - Enum constant in enum class loci.formats.codec.CompressionType
- UNCOMPRESSED - Enum constant in enum class loci.formats.tiff.TiffCompression
- UNCOMPRESSED - Static variable in class loci.formats.in.ZeissCZIReader
-
Compression constants.
- UNDEFINED - Enum constant in enum class loci.formats.tiff.IFDType
- underline - Variable in class loci.formats.in.BaseZeissReader.Shape
- undifference(byte[], IFD) - Static method in enum class loci.formats.tiff.TiffCompression
-
Undoes in-place differencing according to the given predictor value.
- unfilter(byte[], byte[], int, int) - Method in class loci.formats.in.APNGReader
-
See http://www.w3.org/TR/PNG/#9Filters.
- ungroupFilesBox - Variable in class loci.plugins.in.MainDialog
- UNICODE_TCHAR - Static variable in class loci.formats.in.CellSensReader
- UNINT16 - Static variable in class loci.formats.in.SPEReader
- UNINT32 - Static variable in class loci.formats.in.SPEReader
- uniqueFiles - Variable in class loci.formats.in.DCIMGReader
- uniqueFiles - Variable in class loci.formats.out.ICSWriter
- uniquePMTs - Variable in class loci.formats.in.ImspectorReader
-
List of PMTs active during acquisition.
- uniqueZ - Variable in class loci.formats.in.PCIReader
- UNISOKU_MAGIC_STRING - Static variable in class loci.formats.in.UnisokuReader
- UnisokuReader - Class in loci.formats.in
-
UnisokuReader is the file format reader for Unisoku STM files.
- UnisokuReader() - Constructor for class loci.formats.in.UnisokuReader
-
Constructs a new Unisoku reader.
- unit - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.Channel
- unit - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.Dimension
- unit - Variable in class loci.formats.in.ZeissTIFFHandler.Scaling.Dimension
- unit - Variable in class loci.formats.Modulo
- units - Variable in class loci.formats.in.GatanReader
- units - Variable in class loci.formats.in.VarianFDFReader
- UNITS_METER - Static variable in class loci.formats.in.NiftiReader
-
Code for meters.
- UNITS_MM - Static variable in class loci.formats.in.NiftiReader
-
Code for millimeters.
- UNITS_MSEC - Static variable in class loci.formats.in.NiftiReader
-
Code for milliseconds.
- UNITS_USEC - Static variable in class loci.formats.in.NiftiReader
-
Code for microseconds.
- UNKNOWN - Enum constant in enum class loci.formats.in.BaseZeissReader.FeatureType
- UNKNOWN - Enum constant in enum class loci.formats.in.LeicaMicrosystemsMetadata.LMSFileReader.ImageFormat
- UNKNOWN - Static variable in class loci.formats.in.CellSensReader
- UNKNOWN - Static variable in class loci.formats.in.GatanReader
- UNKNOWN_AXIS - Static variable in class loci.formats.AxisGuesser
-
Axis type for unclassified axes.
- UNKNOWN_BLOBS_VOLUME - Static variable in class loci.formats.in.CellSensReader
- UNKNOWN_DOMAIN - Static variable in class loci.formats.FormatTools
-
Identifies an unknown domain.
- unknown1 - Variable in class loci.formats.in.BaseZeissReader.Shape
- unknown10 - Variable in class loci.formats.in.BaseZeissReader.Shape
- unknown11 - Variable in class loci.formats.in.BaseZeissReader.Shape
- unknown12 - Variable in class loci.formats.in.BaseZeissReader.Shape
- unknown13 - Variable in class loci.formats.in.BaseZeissReader.Shape
- unknown14 - Variable in class loci.formats.in.BaseZeissReader.Shape
- unknown15 - Variable in class loci.formats.in.BaseZeissReader.Shape
- unknown16 - Variable in class loci.formats.in.BaseZeissReader.Shape
- unknown17 - Variable in class loci.formats.in.BaseZeissReader.Shape
- unknown18 - Variable in class loci.formats.in.BaseZeissReader.Shape
- unknown19 - Variable in class loci.formats.in.BaseZeissReader.Shape
- unknown2 - Variable in class loci.formats.in.BaseZeissReader.Shape
- UNKNOWN2 - Static variable in class loci.formats.in.GatanReader
- unknown3 - Variable in class loci.formats.in.BaseZeissReader.Shape
- unknown4 - Variable in class loci.formats.in.BaseZeissReader.Shape
- unknown5 - Variable in class loci.formats.in.BaseZeissReader.Shape
- unknown6 - Variable in class loci.formats.in.BaseZeissReader.Shape
- unknown7 - Variable in class loci.formats.in.BaseZeissReader.Shape
- unknown8 - Variable in class loci.formats.in.BaseZeissReader.Shape
- UnknownFormatException - Exception Class in loci.formats
-
UnknownFormatException is the exception thrown when the format of a particular data stream or filename cannot be recognized or is unsupported.
- UnknownFormatException() - Constructor for exception class loci.formats.UnknownFormatException
- UnknownFormatException(String) - Constructor for exception class loci.formats.UnknownFormatException
- UnknownFormatException(String, Throwable) - Constructor for exception class loci.formats.UnknownFormatException
- UnknownFormatException(Throwable) - Constructor for exception class loci.formats.UnknownFormatException
- unmagnifiedPixelHeight - Variable in class loci.formats.in.CellVoyagerReader.ChannelInfo
- unmagnifiedPixelWidth - Variable in class loci.formats.in.CellVoyagerReader.ChannelInfo
- unpackBits(byte[], int[]) - Method in class loci.formats.in.PictReader
-
PackBits variant that outputs an int array.
- unpackBytes(byte[], int, byte[], IFD) - Static method in class loci.formats.tiff.TiffParser
-
Extracts pixel information from the given byte array according to the bits per sample, photometric interpretation and color map IFD directory entry values, and the specified byte ordering.
- unpackEndian - Variable in class loci.formats.in.VeecoReader
- UnsignedIntBuffer - Class in loci.formats.gui
-
DataBuffer that stores unsigned ints.
- UnsignedIntBuffer(int[][], int) - Constructor for class loci.formats.gui.UnsignedIntBuffer
-
Construct a new buffer of unsigned ints using the given 2D int array.
- UnsignedIntBuffer(int[], int) - Constructor for class loci.formats.gui.UnsignedIntBuffer
-
Construct a new buffer of unsigned ints using the given int array.
- UnsignedIntColorModel - Class in loci.formats.gui
-
ColorModel that handles unsigned 32 bit data.
- UnsignedIntColorModel(int, int, int) - Constructor for class loci.formats.gui.UnsignedIntColorModel
- UnsupportedCompressionException - Exception Class in loci.formats
-
UnsupportedCompressionException is the exception thrown when the compression scheme used in a particular file or stream is unsupported.
- UnsupportedCompressionException() - Constructor for exception class loci.formats.UnsupportedCompressionException
- UnsupportedCompressionException(String) - Constructor for exception class loci.formats.UnsupportedCompressionException
- UnsupportedCompressionException(String, Throwable) - Constructor for exception class loci.formats.UnsupportedCompressionException
- UnsupportedCompressionException(Throwable) - Constructor for exception class loci.formats.UnsupportedCompressionException
- unwrap() - Method in class loci.formats.ReaderWrapper
-
Unwraps nested wrapped readers until the core reader (i.e., not a
ReaderWrapperorImageReader) is found. - unwrap() - Method in class loci.formats.WriterWrapper
-
Unwraps nested wrapped writers until the core writer (i.e., not a
WriterWrapperorImageWriter) is found. - unwrap(int) - Static method in class loci.plugins.util.ROIHandler
-
Wraps the specified integer into a Non negative integer.
- unwrap(Class<? extends IFormatReader>, String) - Method in class loci.formats.ReaderWrapper
-
Unwraps nested wrapped readers until the given reader class is found.
- unwrap(Class<? extends IFormatWriter>, String) - Method in class loci.formats.WriterWrapper
-
Unwraps nested wrapped writers until the given writer class is found.
- unwrap(String) - Method in class loci.formats.ReaderWrapper
-
Unwraps nested wrapped readers until the core reader (i.e., not a
ReaderWrapperorImageReader) is found. - unwrap(String) - Method in class loci.formats.WriterWrapper
-
Unwraps nested wrapped writers until the core writer (i.e., not a
WriterWrapperorImageWriter) is found. - unwrapCodecException(CodecException) - Static method in class loci.formats.codec.WrappedCodec
- UP - Static variable in class loci.formats.in.APNGReader
- update() - Method in enum class loci.formats.dicom.DicomAttribute
- update2003FC - Static variable in class loci.formats.services.OMEXMLServiceImpl
-
Stylesheets for updating from previous schema releases.
- update200706 - Static variable in class loci.formats.services.OMEXMLServiceImpl
- update200802 - Static variable in class loci.formats.services.OMEXMLServiceImpl
- update200809 - Static variable in class loci.formats.services.OMEXMLServiceImpl
- update200909 - Static variable in class loci.formats.services.OMEXMLServiceImpl
- update201004 - Static variable in class loci.formats.services.OMEXMLServiceImpl
- update201006 - Static variable in class loci.formats.services.OMEXMLServiceImpl
- update201106 - Static variable in class loci.formats.services.OMEXMLServiceImpl
- update201206 - Static variable in class loci.formats.services.OMEXMLServiceImpl
- update201306 - Static variable in class loci.formats.services.OMEXMLServiceImpl
- update201501 - Static variable in class loci.formats.services.OMEXMLServiceImpl
- updateComposite(int[], int) - Method in class loci.plugins.util.RecordedImageProcessor
- updateCoreMetadata(CoreMetadata) - Method in class loci.formats.in.DicomReader
- updateIfGlitched() - Method in class loci.plugins.in.SeriesDialog
- updateLabel(int, int) - Method in class loci.formats.gui.ImageViewer
-
Updates cursor probe label.
- updateLabels(String) - Method in class loci.formats.gui.DataConverter
- updateMetadataLists(Hashtable<String, Object>) - Method in class loci.formats.FormatReader
-
For the given metadata hashtable, replace any value that is a list with one key/value pair per list entry.
- updateMinMax(int, byte[], int) - Method in class loci.formats.MinMaxCalculator
-
Updates min/max values based on the given byte array.
- updateOrder(int) - Method in class loci.formats.gui.CacheComponent
-
Updates cache order to match the state of the GUI.
- updatePending - Variable in class loci.formats.in.ZeissCZIReader.FileHeader
- updatePriority(int) - Method in class loci.formats.gui.CacheComponent
-
Updates cache priority to match the state of the GUI.
- Updater - Class in loci.plugins
-
A plugin for updating the Bio-Formats plugins.
- Updater() - Constructor for class loci.plugins.Updater
- updateRange(int) - Method in class loci.formats.gui.CacheComponent
-
Updates cache range to match the state of the GUI.
- updateSource() - Method in class loci.formats.gui.CacheComponent
-
Updates cache source to match the state of the GUI.
- updateStrategy() - Method in class loci.formats.gui.CacheComponent
-
Updates cache strategy to match the state of the GUI.
- updateTiming(int, int, int, int) - Method in class loci.plugins.in.ImagePlusReader
- UPGRADE_CHECK_ALLOWED_PROPERTY - Static variable in class loci.formats.UpgradeChecker
-
System property indicating whether the upgrade check is ever allowed.
- UPGRADE_CHECK_KEY - Static variable in class loci.plugins.config.ConfigWindow
- UPGRADE_CHECK_PROPERTY - Static variable in class loci.formats.UpgradeChecker
-
System property to set once the upgrade check is performed.
- upgradeBox - Variable in class loci.plugins.config.ConfigWindow
- UpgradeCheck - Class in loci.formats.tools
-
Utility that checks for a new stable version, and optionally installs a new version of Bio-Formats ueber tools.
- UpgradeCheck() - Constructor for class loci.formats.tools.UpgradeCheck
- UpgradeChecker - Class in loci.formats
-
Class that allows checking for new versions of Bio-Formats, as well as updating to the latest stable, daily, or trunk version.
- UpgradeChecker() - Constructor for class loci.formats.UpgradeChecker
- UpgradeDialog - Class in loci.plugins.in
-
Bio-Formats Importer upgrade checker dialog box.
- UpgradeDialog(ImportProcess) - Constructor for class loci.plugins.in.UpgradeDialog
-
Creates an upgrade checker dialog for the Bio-Formats Importer.
- UPWARDS_DIAGONAL - Enum constant in enum class loci.formats.in.BaseZeissReader.FillStyle
- UR - Enum constant in enum class loci.formats.dicom.DicomVR
- url - Variable in class loci.plugins.config.ConfigWindow
- url - Variable in class loci.plugins.config.LibraryEntry
- URL - Enum constant in enum class loci.formats.codec.JPEG2000BoxType
- URL_BF_SOFTWARE - Static variable in class loci.plugins.util.LibraryChecker
-
URL for Bio-Formats web page.
- URL_BIO_FORMATS - Static variable in class loci.formats.FormatTools
-
URL of Bio-Formats web page.
- URL_BIO_FORMATS_IMAGEJ - Static variable in class loci.plugins.About
-
URL of Bio-Formats ImageJ web page.
- URL_BIO_FORMATS_LIBRARIES - Static variable in class loci.formats.FormatTools
-
URL of 'Bio-Formats as a Java Library' web page.
- URL_DATA_BROWSER - Static variable in class loci.plugins.About
-
URL of Data Browser web page.
- URL_JAVADOCS - Static variable in class loci.plugins.macro.LociFunctions
-
URL for Javadocs.
- URL_OME_TIFF - Static variable in class loci.formats.FormatTools
-
URL of OME-TIFF web page.
- URL_SOFTWARE - Static variable in class loci.plugins.About
-
URL of the Bio-Formats web page.
- urlPath - Variable in class loci.plugins.Updater
-
Path to bioformats_package.jar uber-jar.
- US - Enum constant in enum class loci.formats.dicom.DicomVR
- USE_CHUNKMAP_DEFAULT - Static variable in class loci.formats.in.ND2Reader
- USE_CHUNKMAP_KEY - Static variable in class loci.formats.in.ND2Reader
- USE_CHUNKMAP_LEGACY_KEY - Static variable in class loci.formats.in.ND2Reader
-
Deprecated.
- USE_ORIGINAL_FRAME_RATE - Static variable in class loci.formats.in.CellSensReader
- use64Bit - Variable in class loci.formats.in.MinimalTiffReader
- useChunkMap() - Method in class loci.formats.in.ND2Reader
- used - Variable in class loci.formats.in.APLReader
- used - Variable in class loci.formats.in.BioRadReader
- used - Variable in class loci.formats.in.OMETiffReader
-
List of used files.
- usedFile(String) - Method in class loci.formats.in.LeicaReader
- usedFiles - Variable in class loci.formats.in.CellSensReader
- usedFiles - Variable in class loci.formats.in.FV1000Reader
-
Used file list.
- usedSize - Variable in class loci.formats.in.ZeissCZIReader.Segment
- usedToInitialize - Variable in class loci.formats.FileInfo
-
Whether or not this file can be passed to the appropriate reader's setId(String) method.
- useLegacy - Variable in class loci.formats.DelegateReader
-
Flag indicating whether to use legacy reader by default.
- useMotor - Variable in class loci.formats.in.SDTInfo
- useND2Chunkmap() - Static method in class loci.plugins.util.LociPrefs
- useOldPhysicalSizeCalculation() - Method in class loci.formats.in.LeicaMicrosystemsMetadata.LMSFileReader
- useOldPhysicalSizeCalculation() - Method in class loci.formats.in.LIFReader
- usePatternIds - Variable in class loci.plugins.in.ImporterOptions
- USER - Static variable in class loci.formats.in.OpenlabReader
- USER_COMMENT - Static variable in class loci.formats.tiff.IFD
- userDisplayName - Variable in class loci.formats.in.ZeissCZIReader
- userEmail - Variable in class loci.formats.in.ZeissCZIReader
- userFirstName - Variable in class loci.formats.in.ZeissCZIReader
- userInstitution - Variable in class loci.formats.in.ZeissCZIReader
- userLastName - Variable in class loci.formats.in.ZeissCZIReader
- userMetadataStore - Variable in class loci.formats.Memoizer
-
MetadataStoreset by the caller. - userMiddleName - Variable in class loci.formats.in.ZeissCZIReader
- userName - Variable in class loci.formats.in.FEITiffReader
- userName - Variable in class loci.formats.in.ZeissCZIReader
- userName - Variable in class loci.formats.in.ZeissLSMReader
- users - Variable in class loci.formats.in.BrukerReader
- useTiffParser(IFD) - Method in class loci.formats.in.NDPIReader
- useZ - Variable in class loci.formats.in.ND2Reader
- USHORT - Static variable in class loci.formats.in.CellSensReader
- USHORT - Static variable in class loci.formats.in.GatanReader
- UT - Enum constant in enum class loci.formats.dicom.DicomVR
- uuid - Variable in class loci.formats.in.LeicaSCNReader.Image
- uuid - Variable in class loci.formats.in.LeicaSCNReader.ImageCollection
- UUID - Enum constant in enum class loci.formats.codec.JPEG2000BoxType
- UUID_INFO - Enum constant in enum class loci.formats.codec.JPEG2000BoxType
- UUID_LIST - Enum constant in enum class loci.formats.codec.JPEG2000BoxType
- uuids - Variable in class loci.formats.out.OMETiffWriter
- UV - Enum constant in enum class loci.formats.dicom.DicomVR
V
- V3DrawWriter - Class in loci.formats.out
-
V3DrawWriter writes images in the .v3draw format for rapid I/O in Vaa3D, an open-source 3D visualization and analysis toolkit.
- V3DrawWriter() - Constructor for class loci.formats.out.V3DrawWriter
- valid - Variable in class loci.formats.FilePattern
-
The validity of the file pattern.
- valid - Variable in class loci.formats.in.LeicaReader
- valid - Variable in class loci.formats.in.LeicaSCNReader.LeicaSCNHandler
- valid() - Method in class loci.formats.in.BaseZeissReader.Tag
-
Check if the tag is valid (key, value and category have been set).
- valid() - Method in class loci.formats.in.ZeissTIFFHandler.Tag
-
Check if the tag is valid (key, value and category have been set).
- validate - Variable in class loci.formats.in.DefaultMetadataOptions
- validate(List<DicomTag>) - Method in class loci.formats.dicom.DicomTag
-
Check this tag against a list of existing tags.
- validateOMEXML(String) - Method in interface loci.formats.services.OMEXMLService
-
Attempts to validate the given OME-XML string using Java's XML validation facility.
- validateOMEXML(String) - Method in class loci.formats.services.OMEXMLServiceImpl
- validateOMEXML(String, boolean) - Method in interface loci.formats.services.OMEXMLService
-
Attempts to validate the given OME-XML string using Java's XML validation facility.
- validateOMEXML(String, boolean) - Method in class loci.formats.services.OMEXMLServiceImpl
- validateValue() - Method in class loci.formats.dicom.DicomTag
-
Compare the value type to the VR.
- validBits - Variable in class loci.formats.FormatWriter
-
The number of valid bits per pixel.
- validBits - Variable in class loci.formats.in.FV1000Reader
- validChannel - Variable in class loci.formats.in.ScanrReader.ScanrHandler
- validLoopState - Variable in class loci.formats.in.ND2Handler
- validPixelCount - Variable in class loci.formats.out.DicomWriter
- validStream(RandomAccessInputStream, int, boolean) - Static method in class loci.formats.FormatTools
-
Returns true if the given RandomAccessInputStream conatins at least 'len' bytes.
- validZ - Variable in class loci.formats.in.MetamorphReader
- value - Variable in class loci.formats.dicom.DicomTag
- value - Variable in enum class loci.formats.in.BaseZeissReader.Charset
- value - Variable in enum class loci.formats.in.BaseZeissReader.DrawStyle
- value - Variable in enum class loci.formats.in.BaseZeissReader.FeatureType
- value - Variable in enum class loci.formats.in.BaseZeissReader.FillStyle
- value - Variable in enum class loci.formats.in.BaseZeissReader.LineEndPositions
- value - Variable in enum class loci.formats.in.BaseZeissReader.LineEndStyle
- value - Variable in enum class loci.formats.in.BaseZeissReader.PointStyle
- value - Variable in class loci.formats.in.BaseZeissReader.Tag
- value - Variable in enum class loci.formats.in.BaseZeissReader.TextAlignment
- value - Variable in class loci.formats.in.FEITiffReader.FEIHandler
- value - Variable in class loci.formats.in.ImaconReader.ImaconHandler
- value - Variable in class loci.formats.in.IvisionReader.IvisionHandler
- value - Variable in class loci.formats.in.PrairieMetadata.ValueItem
- value - Variable in class loci.formats.in.ZeissTIFFHandler.Tag
- value - Variable in class loci.formats.meta.OriginalMetadataAnnotation
- value - Variable in class loci.plugins.prefs.BooleanOption
-
The option's current value.
- value - Variable in class loci.plugins.prefs.DoubleOption
-
The option's current value.
- value - Variable in class loci.plugins.prefs.StringOption
-
The option's current value.
- value() - Method in interface loci.formats.in.PrairieMetadata.Value
- value() - Method in class loci.formats.in.PrairieMetadata.ValueItem
- value() - Method in class loci.formats.in.PrairieMetadata.ValueTable
- value(PrairieMetadata.Value) - Method in class loci.formats.in.PrairieMetadata
-
Returns
value.value(), or null ifvalueis null. - value(PrairieMetadata.Value, int) - Method in class loci.formats.in.PrairieMetadata
-
Returns
value.get(index).value(), or null ifvalueorvalue.get(index)is null. - value(PrairieMetadata.Value, String) - Method in class loci.formats.in.PrairieMetadata
-
Returns
value.get(key).value(), or null ifvalueorvalue.get(key)is null. - VALUE - Static variable in class loci.formats.in.CellSensReader
- VALUE - Static variable in class loci.formats.in.GatanReader
- valueChanged(ListSelectionEvent) - Method in class loci.plugins.config.ConfigWindow
- valueCount - Variable in class loci.formats.tiff.TiffIFDEntry
-
The number of values, Count of the indicated Type.
- ValueItem(String, String) - Constructor for class loci.formats.in.PrairieMetadata.ValueItem
- valueOf(String) - Static method in enum class loci.formats.codec.CompressionType
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class loci.formats.codec.JPEG2000BoxType
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class loci.formats.codec.JPEG2000SegmentMarker
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class loci.formats.dicom.DicomAttribute
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class loci.formats.dicom.DicomVR
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class loci.formats.dicom.ResolutionStrategy
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class loci.formats.in.BaseZeissReader.Charset
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class loci.formats.in.BaseZeissReader.Context
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class loci.formats.in.BaseZeissReader.DrawStyle
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class loci.formats.in.BaseZeissReader.FeatureType
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class loci.formats.in.BaseZeissReader.FillStyle
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class loci.formats.in.BaseZeissReader.LineEndPositions
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class loci.formats.in.BaseZeissReader.LineEndStyle
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class loci.formats.in.BaseZeissReader.PointStyle
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class loci.formats.in.BaseZeissReader.TextAlignment
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class loci.formats.in.LeicaMicrosystemsMetadata.Channel.ChannelType
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class loci.formats.in.LeicaMicrosystemsMetadata.Dimension.DimensionKey
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class loci.formats.in.LeicaMicrosystemsMetadata.LMSFileReader.ImageFormat
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class loci.formats.in.LeicaMicrosystemsMetadata.LMSXmlDocument.InitFrom
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class loci.formats.in.LOFReader.MetadataSource
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class loci.formats.in.MetadataLevel
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class loci.formats.in.SlideBook7Reader.EGraphicType
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class loci.formats.in.SPEReader.SpeHeaderEntry
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class loci.formats.in.SPEReader.SpeHeaderType
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class loci.formats.tiff.IFDType
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class loci.formats.tiff.PhotoInterp
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class loci.formats.tiff.TiffCompression
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class loci.plugins.in.ImportStep
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class loci.plugins.util.LibraryChecker.Library
-
Returns the enum constant of this class with the specified name.
- valueOffset - Variable in class loci.formats.tiff.TiffIFDEntry
-
The Value Offset, the file offset (in bytes) of the Value for the field.
- values() - Static method in enum class loci.formats.codec.CompressionType
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class loci.formats.codec.JPEG2000BoxType
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class loci.formats.codec.JPEG2000SegmentMarker
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class loci.formats.dicom.DicomAttribute
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class loci.formats.dicom.DicomVR
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class loci.formats.dicom.ResolutionStrategy
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class loci.formats.in.BaseZeissReader.Charset
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class loci.formats.in.BaseZeissReader.Context
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class loci.formats.in.BaseZeissReader.DrawStyle
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class loci.formats.in.BaseZeissReader.FeatureType
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class loci.formats.in.BaseZeissReader.FillStyle
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class loci.formats.in.BaseZeissReader.LineEndPositions
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class loci.formats.in.BaseZeissReader.LineEndStyle
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class loci.formats.in.BaseZeissReader.PointStyle
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class loci.formats.in.BaseZeissReader.TextAlignment
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class loci.formats.in.LeicaMicrosystemsMetadata.Channel.ChannelType
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class loci.formats.in.LeicaMicrosystemsMetadata.Dimension.DimensionKey
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class loci.formats.in.LeicaMicrosystemsMetadata.LMSFileReader.ImageFormat
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class loci.formats.in.LeicaMicrosystemsMetadata.LMSXmlDocument.InitFrom
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class loci.formats.in.LOFReader.MetadataSource
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class loci.formats.in.MetadataLevel
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class loci.formats.in.SlideBook7Reader.EGraphicType
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class loci.formats.in.SPEReader.SpeHeaderEntry
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class loci.formats.in.SPEReader.SpeHeaderType
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class loci.formats.tiff.IFDType
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class loci.formats.tiff.PhotoInterp
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class loci.formats.tiff.TiffCompression
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class loci.plugins.in.ImportStep
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class loci.plugins.util.LibraryChecker.Library
-
Returns an array containing the constants of this enum class, in the order they are declared.
- valuesByKey(Map<K, V>) - Method in class loci.formats.in.PrairieMetadata
-
Gets the values of the given map, sorted by key.
- ValueTable() - Constructor for class loci.formats.in.PrairieMetadata.ValueTable
- valueToIndex - Variable in class loci.formats.in.FakeReader
-
For indexed color, mapping from indices to values and vice versa.
- VARIABLE_FLIP_ANGLE_FLAG - Enum constant in enum class loci.formats.dicom.DicomAttribute
- VARIABLE_PIXEL_DATA - Enum constant in enum class loci.formats.dicom.DicomAttribute
- variableList - Variable in class loci.formats.services.NetCDFServiceImpl
- variableZ - Variable in class loci.formats.in.InCellReader
- VarianFDFReader - Class in loci.formats.in
-
VarianFDFReader is the file format reader for Varian FDF files.
- VarianFDFReader() - Constructor for class loci.formats.in.VarianFDFReader
-
Constructs a new Varian FDF reader.
- VCLOCK_AMPLITUDE - Static variable in class loci.formats.in.CellSensReader
- VCS_REVISION - Static variable in class loci.formats.FormatTools
-
Current VCS revision.
- VCS_SHORT_REVISION - Static variable in class loci.formats.FormatTools
-
Deprecated.Use the general
FormatTools.VCS_REVISIONfield. - vector - Variable in class loci.formats.codec.ByteVector
- VECTOR_DATA - Static variable in class loci.formats.in.CellSensReader
- VECTOR_LAYER_VOLUME - Static variable in class loci.formats.in.CellSensReader
- VectraReader - Class in loci.formats.in
-
VectraReader is the reader for PerkinElmer Vectra QPTIFF data
- VectraReader() - Constructor for class loci.formats.in.VectraReader
-
Constructs a new Vectra reader.
- VeecoReader - Class in loci.formats.in
-
VeecoReader is the file format reader for Veeco HDF files.
- VeecoReader() - Constructor for class loci.formats.in.VeecoReader
-
Constructs a new Veeco reader.
- VentanaReader - Class in loci.formats.in
-
VentanaReader is the file format reader for Ventana .bif files.
- VentanaReader() - Constructor for class loci.formats.in.VentanaReader
-
Constructs a new Ventana reader.
- VentanaReader.AreaOfInterest - Class in loci.formats.in
- VentanaReader.Overlap - Class in loci.formats.in
- VentanaReader.TIFFTile - Class in loci.formats.in
- verifyMinimumPopulated(MetadataRetrieve) - Static method in class loci.formats.MetadataTools
-
Checks whether the given metadata object has the minimum metadata populated to successfully describe an Image.
- verifyMinimumPopulated(MetadataRetrieve, int) - Static method in class loci.formats.MetadataTools
-
Checks whether the given metadata object has the minimum metadata populated to successfully describe the nth Image.
- verifyOMENamespace(String) - Method in class loci.formats.services.OMEXMLServiceImpl
-
Ensures that an xmlns:ome element exists.
- verifyOptions(Object) - Method in class loci.plugins.in.MainDialog
-
Ensures that the options dialog has no mutually exclusive options.
- version - Variable in class loci.formats.in.DCIMGReader
- version - Variable in class loci.formats.in.GatanReader
- version - Variable in class loci.formats.in.LiFlimReader
- version - Variable in class loci.formats.in.OpenlabReader
-
LIFF version (should be 2 or 5).
- version - Variable in class loci.plugins.config.ConfigWindow
- version - Variable in class loci.plugins.config.LibraryEntry
- VERSION - Enum constant in enum class loci.formats.in.SPEReader.SpeHeaderEntry
- VERSION - Static variable in class loci.formats.FormatTools
-
Version number of this release.
- VERSION - Static variable in class loci.formats.in.NDPIReader
- VERSION - Static variable in class loci.formats.Memoizer
-
Default file version.
- VERSION_KEY - Static variable in class loci.formats.in.LiFlimReader
- VERSION_NUMBER - Static variable in class loci.formats.in.CellSensReader
- VERSION_PROPERTIES - Static variable in class loci.formats.FormatTools
- versionChecking - Variable in class loci.formats.Memoizer
-
Boolean specifying whether to invalidate the memo file based upon mismatched major/minor version numbers.
- versionMismatch() - Method in class loci.formats.Memoizer
-
Returns
trueif the version of the memo file as returned byMemoizer.Deser.loadReleaseVersion()andMemoizer.Deser.loadRevision()do not match the current version as specified byFormatTools.VERSION. - versionOne - Variable in class loci.formats.in.PictReader
-
Whether or not the file is PICT v1.
- versionTwo - Variable in class loci.formats.in.ICSReader
-
Flag indicating whether current file is v2.0.
- VERT_CLOCK_SPEED - Enum constant in enum class loci.formats.in.SPEReader.SpeHeaderEntry
- VERTICAL_CLOCK_VOLTAGE - Static variable in class loci.formats.in.FluoviewReader
- VERTICAL_FLIP - Static variable in class loci.formats.in.FluoviewReader
- VERTICAL_LINE - Enum constant in enum class loci.formats.in.BaseZeissReader.FillStyle
- VERTICAL_SHIFT_SPEED - Static variable in class loci.formats.in.FluoviewReader
- VERTICES_OF_POLYGONAL_COLLIMATOR - Enum constant in enum class loci.formats.dicom.DicomAttribute
- VERTICES_OF_POLYGONAL_SHUTTER - Enum constant in enum class loci.formats.dicom.DicomAttribute
- VFF_MAGIC - Static variable in class loci.formats.in.MicroCTReader
- vffs - Variable in class loci.formats.in.MicroCTReader
- VG_MAGIC_STRING - Static variable in class loci.formats.in.VGSAMReader
- VGSAMReader - Class in loci.formats.in
-
VGSAMReader is the file format reader for VG SAM .dti files.
- VGSAMReader() - Constructor for class loci.formats.in.VGSAMReader
-
Constructs a new VG SAM reader.
- VIDEO_IMAGE_FORMAT_ACQUIRED - Enum constant in enum class loci.formats.dicom.DicomAttribute
- VIETNAMESE_CHARSET - Enum constant in enum class loci.formats.in.BaseZeissReader.Charset
- VIEW_BROWSER - Static variable in class loci.plugins.in.ImporterOptions
- VIEW_HYPERSTACK - Static variable in class loci.plugins.in.ImporterOptions
- VIEW_IMAGE_5D - Static variable in class loci.plugins.in.ImporterOptions
- VIEW_KEYS - Static variable in class loci.formats.in.ICSReader
- VIEW_NAME - Enum constant in enum class loci.formats.dicom.DicomAttribute
- VIEW_NONE - Static variable in class loci.plugins.in.ImporterOptions
- VIEW_NUMBER - Enum constant in enum class loci.formats.dicom.DicomAttribute
- VIEW_POSITION - Enum constant in enum class loci.formats.dicom.DicomAttribute
- VIEW_STANDARD - Static variable in class loci.plugins.in.ImporterOptions
- VIEW_VIEW_5D - Static variable in class loci.plugins.in.ImporterOptions
- VIRTUAL_CHIP - Enum constant in enum class loci.formats.in.SPEReader.SpeHeaderEntry
- VIRTUAL_XDIM - Enum constant in enum class loci.formats.in.SPEReader.SpeHeaderEntry
- VIRTUAL_YDIM - Enum constant in enum class loci.formats.in.SPEReader.SpeHeaderEntry
- virtualBox - Variable in class loci.plugins.in.MainDialog
- VirtualImagePlus - Class in loci.plugins.util
-
Extension of
ImagePlusthat supports Bio-Formats-driven virtual stacks. - VirtualImagePlus(String, ImageStack) - Constructor for class loci.plugins.util.VirtualImagePlus
- virtualReader - Variable in class loci.plugins.in.ImportProcess
- VirtualReader - Class in loci.plugins.util
-
TODO
- VirtualReader(IFormatReader) - Constructor for class loci.plugins.util.VirtualReader
- VisitechReader - Class in loci.formats.in
-
VisitechReader is the file format reader for Visitech XYS files.
- VisitechReader() - Constructor for class loci.formats.in.VisitechReader
- vmid - Variable in class loci.formats.out.DicomWriter.UIDCreator
- vOffsetX - Variable in class loci.formats.in.LeicaSCNReader.Image
- vOffsetY - Variable in class loci.formats.in.LeicaSCNReader.Image
- VOI_LUT_SEQUENCE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- VolocityClippingReader - Class in loci.formats.in
-
VolocityClippingReader is the file format reader for Volocity library clipping files.
- VolocityClippingReader() - Constructor for class loci.formats.in.VolocityClippingReader
-
Constructs a new Volocity clipping reader.
- VolocityReader - Class in loci.formats.in
-
VolocityReader is the file format reader for Volocity library files.
- VolocityReader() - Constructor for class loci.formats.in.VolocityReader
-
Constructs a new Volocity reader.
- VolocityReader.Stack - Class in loci.formats.in
- voltage - Variable in class loci.formats.in.FV1000Reader.ChannelData
- voltage - Variable in class loci.formats.in.GatanReader
- voltage - Variable in class loci.formats.in.LeicaHandler.Detector
- voltage - Variable in class loci.formats.in.LeicaReader.Detector
- voltage - Variable in class loci.formats.in.MicromanagerReader.Position
- voltage - Variable in class loci.formats.in.ND2Handler
- voltage - Variable in class loci.formats.in.OIRReader.Detector
- voltage - Variable in class loci.formats.in.ZeissXRMReader
- voltages - Variable in class loci.formats.in.FluoviewReader
- VOLUME_BASED_CALCULATION_TECHNIQUE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- VOLUME_INDEX - Static variable in class loci.formats.in.CellSensReader
- VOLUMETRIC_PROPERTIES - Enum constant in enum class loci.formats.dicom.DicomAttribute
- volumeType - Variable in class loci.formats.in.OpenlabReader.PlaneInfo
- voxelC - Variable in class loci.formats.in.FluoviewReader
-
Pixel dimensions for this file.
- voxelHeight - Variable in class loci.formats.in.NiftiReader
- voxelSizes - Variable in class loci.formats.in.BDVReader.BDVXMLHandler
- voxelT - Variable in class loci.formats.in.FluoviewReader
-
Pixel dimensions for this file.
- voxelUnit - Variable in class loci.formats.in.BDVReader.BDVXMLHandler
- voxelWidth - Variable in class loci.formats.in.NiftiReader
- voxelX - Variable in class loci.formats.in.FluoviewReader
-
Pixel dimensions for this file.
- voxelX - Variable in class loci.formats.in.TCSReader
- voxelY - Variable in class loci.formats.in.FluoviewReader
-
Pixel dimensions for this file.
- voxelY - Variable in class loci.formats.in.TCSReader
- voxelZ - Variable in class loci.formats.in.FluoviewReader
-
Pixel dimensions for this file.
- voxelZ - Variable in class loci.formats.in.TCSReader
- vPredictor - Variable in class loci.formats.codec.NikonCodecOptions
- vPredictor - Variable in class loci.formats.in.NikonReader
- vr - Variable in class loci.formats.dicom.DicomTag
- vSizeX - Variable in class loci.formats.in.LeicaSCNReader.Image
- vSizeY - Variable in class loci.formats.in.LeicaSCNReader.Image
- vSpacingZ - Variable in class loci.formats.in.LeicaSCNReader.Image
W
- wait(boolean) - Method in class loci.formats.gui.ImageViewer
-
Toggles wait cursor.
- waitTime - Variable in class loci.formats.in.PrairieMetadata
-
The wait time of the acquisition.
- warn(boolean, String) - Static method in class loci.plugins.BF
- warnFile(PrairieMetadata.Sequence, int, int) - Method in class loci.formats.in.PrairieReader
-
Emits a warning about a missing
<File>. - warnFilename(PrairieMetadata.Sequence, int, int) - Method in class loci.formats.in.PrairieReader
-
Emits a warning about a
<File>'s missingfilename. - warnFrame(PrairieMetadata.Sequence, int) - Method in class loci.formats.in.PrairieReader
-
Emits a warning about a missing
<Frame>. - WARNING_COMMENT - Static variable in class loci.formats.out.OMETiffWriter
- wasCanceled() - Method in class loci.plugins.in.ImportProcess
-
Gets whether the import process was canceled.
- WAT_MAGIC_STRING - Static variable in class loci.formats.in.WATOPReader
- WATOPReader - Class in loci.formats.in
-
WATOPReader is the file format reader for WA Technology .wat files.
- WATOPReader() - Constructor for class loci.formats.in.WATOPReader
-
Constructs a new WA Technology reader.
- wave - Variable in class loci.formats.in.MetamorphReader
- WAVE_MAX - Static variable in class loci.formats.in.TissueFAXSReader
- WAVE_MIN - Static variable in class loci.formats.in.TissueFAXSReader
- wavelength - Variable in class loci.formats.in.CV7000Reader.LightSource
- wavelength - Variable in class loci.formats.in.IvisionReader
- wavelength - Variable in class loci.formats.in.LeicaHandler.Laser
- wavelength - Variable in class loci.formats.in.NikonTiffReader
- wavelength - Variable in class loci.formats.in.OIRReader.Laser
- wavelength - Variable in class loci.formats.in.OpenlabReader.PlaneInfo
- wavelength - Variable in class loci.formats.in.ZeissLSMReader.IlluminationChannel
- WAVELENGTH - Static variable in class loci.formats.in.NDPIReader
- wavelengths - Variable in class loci.formats.in.CellWorxReader
- wavelengths - Variable in class loci.formats.in.FV1000Reader
- wavelengths - Variable in class loci.formats.in.IM3Reader.Spectrum
- wavelengths - Variable in class loci.formats.in.MetamorphHandler
- waveMax - Variable in class loci.formats.in.PrairieMetadata.PFile
-
wavelengthMaxattribute of this<File>. - waveMin - Variable in class loci.formats.in.PrairieMetadata.PFile
-
wavelengthMinattribute of this<File>. - waveNames - Variable in class loci.formats.in.MetamorphReader
- WB_MODE - Static variable in class loci.formats.in.CellSensReader
- WB_PRESET_ID - Static variable in class loci.formats.in.CellSensReader
- WB_PRESET_NAME - Static variable in class loci.formats.in.CellSensReader
- wbg - Variable in class loci.formats.in.MRWReader
- wc - Variable in class loci.formats.gui.DataConverter
- wd - Variable in class loci.formats.in.OIRReader.Objective
- well - Variable in class loci.formats.in.CellH5Reader.CellH5Coordinate
- well - Variable in class loci.formats.in.FlexReader.FlexHandler
- well - Variable in class loci.formats.in.MetamorphTiffReader.Well
- well - Variable in class loci.formats.in.MIASReader.AnalysisFile
- Well(int, int, int) - Constructor for class loci.formats.in.MetamorphTiffReader.Well
- WELL - Static variable in class loci.formats.in.CellH5Reader.CellH5Constants
- WELL - Static variable in class loci.formats.ResourceNamer
- WELL_COORDS - Static variable in class loci.formats.in.MetamorphReader
- wellCol - Variable in class loci.formats.in.InCellReader.MinimalInCellHandler
- wellCols - Variable in class loci.formats.in.BDReader
- wellCols - Variable in class loci.formats.in.InCellReader
- wellColumn - Variable in class loci.formats.in.TecanReader.Image
- wellColumns - Variable in class loci.formats.in.FlexReader
- wellColumns - Variable in class loci.formats.in.MIASReader
- wellColumns - Variable in class loci.formats.in.ScanrReader
- WellContainer - Class in loci.formats.internal
-
Represents a well in a plate.
- WellContainer() - Constructor for class loci.formats.internal.WellContainer
- WellContainer(int, int, int, int) - Constructor for class loci.formats.internal.WellContainer
- wellCoordinates - Variable in class loci.formats.in.InCellReader
- wellCount - Variable in class loci.formats.in.CellWorxReader
- wellCount - Variable in class loci.formats.in.FlexReader
- wellCount - Variable in class loci.formats.in.MetamorphTiffReader
- wellCount - Variable in class loci.formats.in.ScanrReader
- wellFiles - Variable in class loci.formats.in.CellWorxReader
- wellIndex - Variable in class loci.formats.in.ScanrReader.ScanrHandler
- wellIndex - Variable in class loci.formats.internal.WellContainer
- WellInfo() - Constructor for class loci.formats.in.CellVoyagerReader.WellInfo
- wellLabels - Variable in class loci.formats.in.BDReader
- wellLabels - Variable in class loci.formats.in.ScanrReader
- wellList - Variable in class loci.formats.in.BDReader
- wellNumber - Variable in class loci.formats.in.FlexReader
-
Specifies the row and column index into 'flexFiles' for a given well.
- wellNumber - Variable in class loci.formats.in.MIASReader
- wellNumbers - Variable in class loci.formats.in.ScanrReader
- wellRow - Variable in class loci.formats.in.InCellReader.MinimalInCellHandler
- wellRow - Variable in class loci.formats.in.TecanReader.Image
- wellRows - Variable in class loci.formats.in.BDReader
- wellRows - Variable in class loci.formats.in.FlexReader
- wellRows - Variable in class loci.formats.in.InCellReader
- wellRows - Variable in class loci.formats.in.ScanrReader
- wells - Variable in class loci.formats.in.CellVoyagerReader
- wells - Variable in class loci.formats.in.JDCEReader
- WHITE_BALANCE - Static variable in class loci.formats.tiff.IFD
- WHITE_BALANCE_FINE - Static variable in class loci.formats.in.NikonReader
- WHITE_BALANCE_RGB_COEFFS - Static variable in class loci.formats.in.DNGReader
- WHITE_BALANCE_RGB_COEFFS - Static variable in class loci.formats.in.NikonReader
- WHITE_IS_ZERO - Enum constant in enum class loci.formats.tiff.PhotoInterp
- WHITE_POINT - Static variable in class loci.formats.tiff.IFD
- whiteBalance - Variable in class loci.formats.in.DNGReader
- whiteBalance - Variable in class loci.formats.in.NikonReader
- WHOLE_BODY_TECHNIQUE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- WHOLE_SLIDE_FRAME_TYPE_SEQUENCE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- wholeStackBuffer - Variable in class loci.formats.in.OBFReader.State
- WIDER - Static variable in class loci.formats.in.CellSensReader
- WIDER_ENABLED - Static variable in class loci.formats.in.CellSensReader
- widgets - Variable in class loci.plugins.config.CellSensWidgets
- widgets - Variable in class loci.plugins.config.FormatEntry
- widgets - Variable in class loci.plugins.config.LIFWidgets
- widgets - Variable in class loci.plugins.config.ND2Widgets
- widgets - Variable in class loci.plugins.config.SDTWidgets
- widgets - Variable in class loci.plugins.config.TiffDelegateWidgets
- widgets - Variable in class loci.plugins.config.ZeissCZIWidgets
- width - Variable in class loci.formats.codec.CodecOptions
-
Width, in pixels, of the image.
- width - Variable in enum class loci.formats.dicom.DicomVR
- width - Variable in class loci.formats.in.BaseZeissReader.Shape
- width - Variable in class loci.formats.in.CellSensReader.Pyramid
- width - Variable in class loci.formats.in.CellVoyagerReader.AreaInfo
- width - Variable in class loci.formats.in.CellVoyagerReader.ChannelInfo
- width - Variable in class loci.formats.in.OpenlabReader.PlaneInfo
- width - Variable in class loci.formats.in.SDTInfo
- width - Variable in class loci.formats.tools.AmiraParameters
- WIDTH - Enum constant in enum class loci.formats.in.SPEReader.SpeHeaderEntry
- WINDOW_CENTER - Enum constant in enum class loci.formats.dicom.DicomAttribute
- WINDOW_CENTER_AND_WIDTH_EXPLANATION - Enum constant in enum class loci.formats.dicom.DicomAttribute
- WINDOW_SIZE - Enum constant in enum class loci.formats.in.SPEReader.SpeHeaderEntry
- WINDOW_WIDTH - Enum constant in enum class loci.formats.dicom.DicomAttribute
- windowActivated(WindowEvent) - Method in class loci.formats.gui.ImageViewer
- windowClosed(WindowEvent) - Method in class loci.formats.gui.ImageViewer
- windowClosing(WindowEvent) - Method in class loci.formats.gui.ImageViewer
- windowDeactivated(WindowEvent) - Method in class loci.formats.gui.ImageViewer
- windowDeiconified(WindowEvent) - Method in class loci.formats.gui.ImageViewer
- windowIconified(WindowEvent) - Method in class loci.formats.gui.ImageViewer
- windowlessBox - Variable in class loci.plugins.config.ConfigWindow
- windowOpened(WindowEvent) - Method in class loci.formats.gui.ImageViewer
- WindowTools - Class in loci.plugins.util
-
Utility methods for managing ImageJ dialogs and windows.
- WindowTools() - Constructor for class loci.plugins.util.WindowTools
- WINVIEW_ID - Enum constant in enum class loci.formats.in.SPEReader.SpeHeaderEntry
- with(int) - Static method in enum class loci.formats.in.LeicaMicrosystemsMetadata.Dimension.DimensionKey
- withinPixels(long) - Method in class loci.formats.in.SlidebookReader
- WORKING_DISTANCE - Static variable in class loci.formats.in.CellSensReader
- workingDistance - Variable in class loci.formats.in.CellSensReader.Pyramid
- workingDistance - Variable in class loci.formats.in.FV1000Reader
- workingDistance - Variable in class loci.formats.in.LEOReader
- workingDistance - Variable in class loci.formats.in.NikonTiffReader
- WPIHandler() - Constructor for class loci.formats.in.CV7000Reader.WPIHandler
- wppPath - Variable in class loci.formats.in.CV7000Reader
- WrappedCodec - Class in loci.formats.codec
-
Generic wrapper for codecs from ome-codecs.
- WrappedCodec(Codec) - Constructor for class loci.formats.codec.WrappedCodec
-
Construct with a codec implementation to wrap.
- WrappedReader - Class in loci.formats
-
Helper class for readers which wrap other readers.
- WrappedReader(String, String[]) - Constructor for class loci.formats.WrappedReader
-
Constructs a new wrapped reader with the given name and suffixes.
- write(char[], int, int) - Method in class loci.plugins.config.TextAreaWriter
-
Writes the given characters to the associated text area component.
- write(int, int) - Method in class loci.formats.codec.BitWriter
-
Deprecated.Writes the given value using the given number of bits.
- write(Kryo, Output) - Method in class loci.formats.services.NetCDFServiceImpl
- write(String) - Method in class loci.formats.codec.BitWriter
-
Deprecated.Writes the bits represented by a bit string to the buffer.
- WRITE_TIME - Static variable in class loci.formats.in.NDPIReader
- writeArraySlice(String, MDByteArray, long[]) - Method in interface loci.formats.services.JHDFService
-
Writes an array as sub-slice into an existing HDF5 dataset
- writeArraySlice(String, MDByteArray, long[]) - Method in class loci.formats.services.JHDFServiceImpl
- writeArraySlice(String, MDIntArray, long[]) - Method in interface loci.formats.services.JHDFService
-
Writes an array as sub-slice into an existing HDF5 dataset
- writeArraySlice(String, MDIntArray, long[]) - Method in class loci.formats.services.JHDFServiceImpl
- writeArraySlice(String, MDShortArray, long[]) - Method in interface loci.formats.services.JHDFService
-
Writes an array as sub-slice into an existing HDF5 dataset
- writeArraySlice(String, MDShortArray, long[]) - Method in class loci.formats.services.JHDFServiceImpl
- writeAtom(int, String) - Method in class loci.formats.out.QTWriter
-
Write the atom length and type.
- writeBox - Variable in class loci.formats.codec.JPEG2000CodecOptions
-
Whether or not to write a boxed stream, i.e.
- writeData(String, CoreMetadata, String, OMETiffWriter) - Method in class loci.formats.tools.MakeTestOmeTiff
- writeDualPersonality() - Method in class loci.formats.out.DicomWriter
-
Checks the writer's associated MetadataOptions to see if dual personality writing has been explicitly enabled or disabled.
- writeFCTL(int, int) - Method in class loci.formats.out.APNGWriter
- writeFooter() - Method in class loci.formats.out.APNGWriter
- writeFooter() - Method in class loci.formats.out.JavaWriter
- writeFooter() - Method in class loci.formats.out.QTWriter
- writeHeader() - Method in class loci.formats.out.DicomWriter
-
Write the preamble, prefix, and file meta elements.
- writeHeader() - Method in class loci.formats.out.EPSWriter
- writeHeader() - Method in class loci.formats.out.JavaWriter
- writeHeader() - Method in class loci.formats.tiff.TiffSaver
-
Writes the TIFF file header.
- writeIFD(IFD, long) - Method in class loci.formats.tiff.TiffSaver
-
Write the given IFD to the open stream.
- writeIFD(IFD, long, boolean) - Method in class loci.formats.tiff.TiffSaver
-
Write the given IFD to the open stream.
- writeIFDs(int) - Method in class loci.formats.out.DicomWriter
- writeIFDStrips(IFD, int, byte[][], int, boolean, int, int, long) - Method in class loci.formats.tiff.TiffSaver
- writeIFDValue(RandomAccessOutputStream, long, int, Object) - Method in class loci.formats.tiff.TiffSaver
-
Writes the given IFD value to the given output object.
- writeImage(byte[][], IFDList, int) - Method in class loci.formats.tiff.TiffSaver
- writeImage(byte[], IFD, int, int, boolean) - Method in class loci.formats.tiff.TiffSaver
- writeImage(byte[], IFD, int, int, int, int, int, int, boolean) - Method in class loci.formats.tiff.TiffSaver
-
Writes to any rectangle from the passed block.
- writeImage(byte[], IFD, int, int, int, int, int, int, boolean, Integer, boolean) - Method in class loci.formats.tiff.TiffSaver
- writeImage(OutputStream, BufferedImage, JPEG2000CodecOptions) - Method in interface loci.formats.services.JAIIIOService
-
Writes an image using JAI Image I/O using the JPEG 2000 codec.
- writeImage(OutputStream, BufferedImage, JPEG2000CodecOptions) - Method in class loci.formats.services.JAIIIOServiceImpl
- writeImageIFD(IFD, int, byte[][], int, boolean, int, int) - Method in class loci.formats.tiff.TiffSaver
-
Performs the actual work of dealing with IFD data and writing it to the TIFF for a given image or sub-image.
- writeIntValue(RandomAccessOutputStream, long) - Method in class loci.formats.tiff.TiffSaver
-
Write the given value to the given RandomAccessOutputStream.
- writePixels(String, byte[], int, int, int, int) - Method in class loci.formats.out.APNGWriter
- writePlane(String, byte[], int, int) - Method in class loci.formats.out.JavaWriter
- writePlane(String, double[], int, int) - Method in class loci.formats.out.JavaWriter
- writePlane(String, float[], int, int) - Method in class loci.formats.out.JavaWriter
- writePlane(String, int[], int, int) - Method in class loci.formats.out.JavaWriter
- writePlane(String, long[], int, int) - Method in class loci.formats.out.JavaWriter
- writePlane(String, short[], int, int) - Method in class loci.formats.out.JavaWriter
- writePLTE() - Method in class loci.formats.out.APNGWriter
- writer - Variable in class loci.formats.codec.BitWriter
-
Deprecated.
- writer - Variable in class loci.formats.gui.DataConverter
- writer - Variable in class loci.formats.WriterWrapper
-
FormatWriter used to write the file.
- writeRotationMatrix() - Method in class loci.formats.out.QTWriter
-
Write the 3x3 matrix that describes how to rotate the image.
- writers - Variable in class loci.formats.ImageWriter
-
List of supported file format writers.
- WriterWrapper - Class in loci.formats
-
Abstract superclass of writer logic that wraps other writers.
- WriterWrapper() - Constructor for class loci.formats.WriterWrapper
-
Constructs a writer wrapper around a new image writer.
- WriterWrapper(IFormatWriter) - Constructor for class loci.formats.WriterWrapper
-
Constructs a writer wrapper around the given writer.
- writeSummary() - Method in class loci.formats.in.IM3Reader
-
Write a summary of each field in the IM3 file to the writer
- writeSummary(IRandomAccess, String) - Method in class loci.formats.in.IM3Reader.ContainerRecord
- writeSummary(IRandomAccess, String) - Method in class loci.formats.in.IM3Reader.FloatIM3Record
- writeSummary(IRandomAccess, String) - Method in class loci.formats.in.IM3Reader.IM3Record
-
Write a summary of the contents of the record
- writeSummary(IRandomAccess, String) - Method in class loci.formats.in.IM3Reader.IntIM3Record
- writeSummary(IRandomAccess, String) - Method in class loci.formats.in.IM3Reader.StringIM3Record
- writeTag(DicomTag) - Method in class loci.formats.out.DicomWriter
- writeTag(DicomTag, RandomAccessOutputStream) - Method in class loci.formats.out.DicomWriter
- written - Variable in class loci.formats.ome.OMEPyramidStore
- written - Variable in class loci.formats.out.DicomWriter.PlaneOffset
- wsi - Variable in class loci.formats.in.DicomReader
- wSize - Variable in class loci.formats.in.DeltavisionReader
-
Size of one wave in the extended header.
X
- x - Variable in class loci.formats.in.BioRadReader.Note
- x - Variable in class loci.formats.in.CellVoyagerReader.FieldInfo
- x - Variable in class loci.formats.in.InCellReader
- x - Variable in class loci.formats.in.LeicaHandler.ROI
- x - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.ROI
- x - Variable in class loci.formats.in.LIFReader.ROI
- x - Variable in class loci.formats.in.OperettaReader.Channel
- x - Variable in class loci.formats.in.OperettaReader.Plane
- x - Variable in class loci.formats.in.VentanaReader.Overlap
- x - Variable in class loci.formats.in.ZeissCZIReader.SubBlock
- x - Variable in class loci.formats.ome.OMEPyramidStore.Resolution
- x - Variable in class loci.formats.TileStitcher.TileCoordinate
- X - Enum constant in enum class loci.formats.in.LeicaMicrosystemsMetadata.Dimension.DimensionKey
- X_BINNING - Static variable in class loci.formats.in.CellSensReader
- X_CALIB_COUNT - Enum constant in enum class loci.formats.in.SPEReader.SpeHeaderEntry
- X_CALIB_FLAG - Enum constant in enum class loci.formats.in.SPEReader.SpeHeaderEntry
- X_CALIB_LABEL - Enum constant in enum class loci.formats.in.SPEReader.SpeHeaderEntry
- X_CALIB_VALID - Enum constant in enum class loci.formats.in.SPEReader.SpeHeaderEntry
- X_CALIB_VALUE - Enum constant in enum class loci.formats.in.SPEReader.SpeHeaderEntry
- X_DIMENSION - Enum constant in enum class loci.formats.in.SPEReader.SpeHeaderEntry
- X_EXPANSION - Enum constant in enum class loci.formats.in.SPEReader.SpeHeaderEntry
- X_FOCUS_CENTER - Enum constant in enum class loci.formats.dicom.DicomAttribute
- X_IMG_STRING - Static variable in class loci.formats.in.SDTInfo
- X_INPUT_UNIT - Enum constant in enum class loci.formats.in.SPEReader.SpeHeaderEntry
- X_KEY - Static variable in class loci.formats.in.LiFlimReader
- X_LABEL - Enum constant in enum class loci.formats.in.SPEReader.SpeHeaderEntry
- X_LASER_POS - Enum constant in enum class loci.formats.in.SPEReader.SpeHeaderEntry
- X_OFFSET_IN_SLIDE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- X_PIXEL_POSITION - Enum constant in enum class loci.formats.in.SPEReader.SpeHeaderEntry
- X_POLYNUM_COEFF - Enum constant in enum class loci.formats.in.SPEReader.SpeHeaderEntry
- X_POLYNUM_ORDER - Enum constant in enum class loci.formats.in.SPEReader.SpeHeaderEntry
- X_POLYNUM_UNIT - Enum constant in enum class loci.formats.in.SPEReader.SpeHeaderEntry
- X_POS_TAG - Static variable in class loci.formats.in.SlidebookTiffReader
- X_POSITION - Static variable in class loci.formats.in.NDPIReader
- X_POSITION - Static variable in class loci.formats.tiff.IFD
- X_POST_PIXELS - Enum constant in enum class loci.formats.in.SPEReader.SpeHeaderEntry
- X_PRE_PIXELS - Enum constant in enum class loci.formats.in.SPEReader.SpeHeaderEntry
- X_RESERVED - Enum constant in enum class loci.formats.in.SPEReader.SpeHeaderEntry
- X_RESERVED2 - Enum constant in enum class loci.formats.in.SPEReader.SpeHeaderEntry
- X_RESERVED3 - Enum constant in enum class loci.formats.in.SPEReader.SpeHeaderEntry
- X_RESOLUTION - Static variable in class loci.formats.tiff.IFD
- X_SCALING_FACTOR - Enum constant in enum class loci.formats.in.SPEReader.SpeHeaderEntry
- X_SCALING_OFFSET - Enum constant in enum class loci.formats.in.SPEReader.SpeHeaderEntry
- X_SCALING_UNIT - Enum constant in enum class loci.formats.in.SPEReader.SpeHeaderEntry
- X_SPECIAL_STRING - Enum constant in enum class loci.formats.in.SPEReader.SpeHeaderEntry
- X_STRING - Static variable in class loci.formats.in.SDTInfo
- x0 - Variable in class loci.formats.tools.AmiraParameters
- x1 - Variable in class loci.formats.in.BaseZeissReader.Shape
- x1 - Variable in class loci.formats.in.GatanReader.ROIShape
- x1 - Variable in class loci.formats.tools.AmiraParameters
- x2 - Variable in class loci.formats.in.BaseZeissReader.Shape
- x2 - Variable in class loci.formats.in.GatanReader.ROIShape
- xAxis - Variable in class loci.formats.in.SDTInfo
-
X axis representation (SPC-930).
- xcal - Variable in class loci.formats.in.OpenlabReader
- xCoordinates - Variable in class loci.formats.in.ZeissLSMReader
- xDim - Variable in class loci.formats.out.AVIWriter
- xIndex - Variable in class loci.formats.in.TextReader
-
Column index for X coordinate.
- XlcfDocument - Class in loci.formats.in.LeicaMicrosystemsMetadata
-
This class loads and represents a Leica Microsystems XLCF xml document
- XlcfDocument(String, LMSCollectionXmlDocument) - Constructor for class loci.formats.in.LeicaMicrosystemsMetadata.XlcfDocument
- XlefDocument - Class in loci.formats.in.LeicaMicrosystemsMetadata
-
This class represents a Leica Microsystems XLEF xml document, a project file which references xlifs and optionally xlcfs
- XlefDocument(String) - Constructor for class loci.formats.in.LeicaMicrosystemsMetadata.XlefDocument
- XLEFReader - Class in loci.formats.in
-
XLEFReader is the file format reader for Leica Microsystems' XLEF files.
- XLEFReader() - Constructor for class loci.formats.in.XLEFReader
-
Constructs a new Leica XLEF reader.
- XLEFReader.PathComparator - Class in loci.formats.in
-
Helper class to sort file paths by name and depth
- xLen - Variable in class loci.formats.in.LiFlimReader
- XLIF - Enum constant in enum class loci.formats.in.LOFReader.MetadataSource
- XlifDocument - Class in loci.formats.in.LeicaMicrosystemsMetadata
-
This class loads and represents a Leica Microsystems XLIF xml document
- XlifDocument(String, LMSCollectionXmlDocument) - Constructor for class loci.formats.in.LeicaMicrosystemsMetadata.XlifDocument
- xLocation - Variable in class loci.formats.in.VolocityReader.Stack
- xml - Variable in class loci.formats.in.ZeissCZIReader.Metadata
- xml - Variable in class loci.plugins.util.DataBrowser
- XML - Enum constant in enum class loci.formats.codec.JPEG2000BoxType
- XML - Enum constant in enum class loci.formats.in.LeicaMicrosystemsMetadata.LMSXmlDocument.InitFrom
- XML - Static variable in class loci.formats.in.MicromanagerReader
-
Optional file containing additional acquisition parameters.
- XML_FILE - Static variable in class loci.formats.in.ColumbusReader
- XML_FILE - Static variable in class loci.formats.in.ScanrReader
- XML_FILES - Static variable in class loci.formats.in.OperettaReader
- XML_NAME - Static variable in class loci.formats.in.ZeissTIFFReader
- XML_OFFSET - Enum constant in enum class loci.formats.in.SPEReader.SpeHeaderEntry
- XML_SUFFIX - Static variable in class loci.formats.in.PrairieReader
- XML_SUFFIX - Static variable in class loci.formats.in.TCSReader
- XML_TAG - Static variable in class loci.formats.in.ImaconReader
- XML_TAG - Static variable in class loci.formats.in.OperettaReader
- XML_TAG - Static variable in class loci.formats.in.VentanaReader
- xmlBuffer - Variable in class loci.formats.in.BDVReader.BDVXMLHandler
- xmlBuffer - Variable in class loci.formats.in.OMEXMLReader.OMEXMLHandler
- XMLCellRenderer - Class in loci.formats.gui
-
A tree cell renderer for displaying syntax highlighted XML in a JTree.
- XMLCellRenderer() - Constructor for class loci.formats.gui.XMLCellRenderer
- XMLCellRenderer.XMLItem - Class in loci.formats.gui
-
Cell renderer item for use as DefaultMutableTreeNode user object.
- xmlFile - Variable in class loci.formats.in.MicromanagerReader.Position
- xmlFile - Variable in class loci.formats.in.PrairieReader
-
The associated XML files.
- xmlFile - Variable in class loci.formats.in.TCSReader
- xmlFiles - Variable in class loci.formats.in.APLReader
- xmlFragments - Variable in class loci.formats.out.OMEXMLWriter
- XMLItem(Node) - Constructor for class loci.formats.gui.XMLCellRenderer.XMLItem
- xmlname - Variable in class loci.formats.in.ZeissTIFFReader.TIFFInfo
- xmlWindow - Variable in class loci.plugins.in.DisplayHandler
- XMLWindow - Class in loci.formats.gui
-
A window containing syntax highlighted XML as a tree.
- XMLWindow() - Constructor for class loci.formats.gui.XMLWindow
- XMLWindow(String) - Constructor for class loci.formats.gui.XMLWindow
- xoff - Variable in class loci.formats.in.FakeReader.TextLine
- xoff - Variable in class loci.formats.tools.MakeTestOmeTiff.TextLine
- xOffset - Variable in class loci.formats.in.ND2Reader
- xOffset - Variable in class loci.formats.out.DicomWriter.PlaneOffset
- xOffsetReal - Variable in class loci.formats.out.DicomWriter.PlaneOffset
- xOffsetSize - Variable in class loci.formats.out.DicomWriter.PlaneOffset
- xor(int) - Method in class loci.plugins.util.RecordedImageProcessor
- xOrigin - Variable in class loci.formats.in.TiffReader
- xOrigin - Variable in class loci.formats.in.VentanaReader.AreaOfInterest
- xPad - Variable in class loci.formats.out.AVIWriter
- xPath - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.LMSXmlDocument
- xPath(String) - Method in class loci.formats.in.LeicaMicrosystemsMetadata.LMSXmlDocument
-
Searches the XML document for expressions using xPath.
- xPath(Node, String) - Method in class loci.formats.in.LeicaMicrosystemsMetadata.LMSXmlDocument
-
Searches a node for expressions using xPath.
- xpixels - Variable in class loci.formats.in.CellVoyagerReader.FieldInfo
- xpos - Variable in class loci.formats.in.CV7000Reader.Plane
- xPos - Variable in class loci.formats.in.LeicaHandler
- xPos - Variable in class loci.formats.in.OpenlabReader
- xPos - Variable in class loci.formats.in.ZeissXRMReader
- xPositions - Variable in class loci.formats.in.FlexReader
- XRAY_TUBE_CURRENT - Enum constant in enum class loci.formats.dicom.DicomAttribute
- xSize - Variable in class loci.formats.in.CV7000Reader.Channel
- xSize - Variable in class loci.formats.in.LEOReader
- xSize - Variable in class loci.formats.in.QuesantReader
- xSizes - Variable in class loci.formats.in.FlexReader
- XSLT_2003FC - Static variable in class loci.formats.services.OMEXMLServiceImpl
- XSLT_200706 - Static variable in class loci.formats.services.OMEXMLServiceImpl
- XSLT_200802 - Static variable in class loci.formats.services.OMEXMLServiceImpl
- XSLT_200809 - Static variable in class loci.formats.services.OMEXMLServiceImpl
- XSLT_200909 - Static variable in class loci.formats.services.OMEXMLServiceImpl
- XSLT_201004 - Static variable in class loci.formats.services.OMEXMLServiceImpl
- XSLT_201006 - Static variable in class loci.formats.services.OMEXMLServiceImpl
- XSLT_201106 - Static variable in class loci.formats.services.OMEXMLServiceImpl
- XSLT_201206 - Static variable in class loci.formats.services.OMEXMLServiceImpl
- XSLT_201306 - Static variable in class loci.formats.services.OMEXMLServiceImpl
- XSLT_201501 - Static variable in class loci.formats.services.OMEXMLServiceImpl
- XSLT_PATH - Static variable in class loci.formats.services.OMEXMLServiceImpl
- xTiles - Variable in class loci.formats.in.DeltavisionReader
-
Number of tiles in X direction.
- xTiles - Variable in class loci.formats.services.JPEGTurboServiceImpl
- xyGain - Variable in class loci.formats.in.SDTInfo
-
Gain for XY ADCs (SPC930).
- xyw(CellConstraints, int, int, int) - Method in class loci.plugins.in.MainDialog
-
Convenience method for creating a left-aligned, vertically centered cell constraints object.
Y
- y - Variable in class loci.formats.in.BioRadReader.Note
- y - Variable in class loci.formats.in.CellVoyagerReader.FieldInfo
- y - Variable in class loci.formats.in.InCellReader
- y - Variable in class loci.formats.in.LeicaHandler.ROI
- y - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.ROI
- y - Variable in class loci.formats.in.LIFReader.ROI
- y - Variable in class loci.formats.in.OperettaReader.Channel
- y - Variable in class loci.formats.in.OperettaReader.Plane
- y - Variable in class loci.formats.in.VentanaReader.Overlap
- y - Variable in class loci.formats.in.ZeissCZIReader.SubBlock
- y - Variable in class loci.formats.ome.OMEPyramidStore.Resolution
- y - Variable in class loci.formats.TileStitcher.TileCoordinate
- Y - Enum constant in enum class loci.formats.in.LeicaMicrosystemsMetadata.Dimension.DimensionKey
- Y_BINNING - Static variable in class loci.formats.in.CellSensReader
- Y_CALIB_COUNT - Enum constant in enum class loci.formats.in.SPEReader.SpeHeaderEntry
- Y_CALIB_FLAG - Enum constant in enum class loci.formats.in.SPEReader.SpeHeaderEntry
- Y_CALIB_LABEL - Enum constant in enum class loci.formats.in.SPEReader.SpeHeaderEntry
- Y_CALIB_VALID - Enum constant in enum class loci.formats.in.SPEReader.SpeHeaderEntry
- Y_CALIB_VALUE - Enum constant in enum class loci.formats.in.SPEReader.SpeHeaderEntry
- Y_CB_CR - Enum constant in enum class loci.formats.tiff.PhotoInterp
- Y_CB_CR_COEFFICIENTS - Static variable in class loci.formats.tiff.IFD
- Y_CB_CR_POSITIONING - Static variable in class loci.formats.tiff.IFD
- Y_CB_CR_SUB_SAMPLING - Static variable in class loci.formats.tiff.IFD
- Y_DIMENSION - Enum constant in enum class loci.formats.in.SPEReader.SpeHeaderEntry
- Y_DIMENSION_UNIT - Static variable in class loci.formats.in.CellSensReader
- Y_EXPANSION - Enum constant in enum class loci.formats.in.SPEReader.SpeHeaderEntry
- Y_FOCUS_CENTER - Enum constant in enum class loci.formats.dicom.DicomAttribute
- Y_IMG_STRING - Static variable in class loci.formats.in.SDTInfo
- Y_INPUT_UNIT - Enum constant in enum class loci.formats.in.SPEReader.SpeHeaderEntry
- Y_KEY - Static variable in class loci.formats.in.LiFlimReader
- Y_LABEL - Enum constant in enum class loci.formats.in.SPEReader.SpeHeaderEntry
- Y_LASER_POS - Enum constant in enum class loci.formats.in.SPEReader.SpeHeaderEntry
- Y_OFFSET_IN_SLIDE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- Y_PIXEL_POSITION - Enum constant in enum class loci.formats.in.SPEReader.SpeHeaderEntry
- Y_PLANE_DIMENSION_UNIT - Static variable in class loci.formats.in.CellSensReader
- Y_POLYNUM_COEFF - Enum constant in enum class loci.formats.in.SPEReader.SpeHeaderEntry
- Y_POLYNUM_ORDER - Enum constant in enum class loci.formats.in.SPEReader.SpeHeaderEntry
- Y_POLYNUM_UNIT - Enum constant in enum class loci.formats.in.SPEReader.SpeHeaderEntry
- Y_POS_TAG - Static variable in class loci.formats.in.SlidebookTiffReader
- Y_POSITION - Static variable in class loci.formats.in.NDPIReader
- Y_POSITION - Static variable in class loci.formats.tiff.IFD
- Y_POST_PIXELS - Enum constant in enum class loci.formats.in.SPEReader.SpeHeaderEntry
- Y_PRE_PIXELS - Enum constant in enum class loci.formats.in.SPEReader.SpeHeaderEntry
- Y_RESERVED - Enum constant in enum class loci.formats.in.SPEReader.SpeHeaderEntry
- Y_RESERVED2 - Enum constant in enum class loci.formats.in.SPEReader.SpeHeaderEntry
- Y_RESERVED3 - Enum constant in enum class loci.formats.in.SPEReader.SpeHeaderEntry
- Y_RESOLUTION - Static variable in class loci.formats.tiff.IFD
- Y_SCALING_FACTOR - Enum constant in enum class loci.formats.in.SPEReader.SpeHeaderEntry
- Y_SCALING_OFFSET - Enum constant in enum class loci.formats.in.SPEReader.SpeHeaderEntry
- Y_SCALING_UNIT - Enum constant in enum class loci.formats.in.SPEReader.SpeHeaderEntry
- Y_SPECIAL_STRING - Enum constant in enum class loci.formats.in.SPEReader.SpeHeaderEntry
- Y_STRING - Static variable in class loci.formats.in.SDTInfo
- y0 - Variable in class loci.formats.tools.AmiraParameters
- y1 - Variable in class loci.formats.in.BaseZeissReader.Shape
- y1 - Variable in class loci.formats.in.GatanReader.ROIShape
- y1 - Variable in class loci.formats.tools.AmiraParameters
- y2 - Variable in class loci.formats.in.BaseZeissReader.Shape
- y2 - Variable in class loci.formats.in.GatanReader.ROIShape
- Y8 - Static variable in class loci.formats.in.AVIReader
- ycal - Variable in class loci.formats.in.OpenlabReader
- ycbcr - Variable in class loci.formats.codec.CodecOptions
-
Whether or not the decompressed data will be stored as YCbCr.
- ycbcrCorrection - Variable in class loci.formats.tiff.TiffParser
- yCoordinates - Variable in class loci.formats.in.ZeissLSMReader
- yDim - Variable in class loci.formats.out.AVIWriter
- YEAR - Static variable in class loci.formats.FormatTools
-
Year in which this release was built.
- yEnd - Variable in class loci.formats.in.OIRReader.PixelBlock
- yIndex - Variable in class loci.formats.in.TextReader
-
Column index for Y coordinate.
- yLen - Variable in class loci.formats.in.LiFlimReader
- yLocation - Variable in class loci.formats.in.VolocityReader.Stack
- yOffset - Variable in class loci.formats.in.ND2Reader
- yOffset - Variable in class loci.formats.out.DicomWriter.PlaneOffset
- yOffsetReal - Variable in class loci.formats.out.DicomWriter.PlaneOffset
- yOffsetSize - Variable in class loci.formats.out.DicomWriter.PlaneOffset
- yOrigin - Variable in class loci.formats.in.TiffReader
- yOrigin - Variable in class loci.formats.in.VentanaReader.AreaOfInterest
- ypad - Variable in class loci.formats.in.FakeReader.TextLine
- ypad - Variable in class loci.formats.tools.MakeTestOmeTiff.TextLine
- ypixels - Variable in class loci.formats.in.CellVoyagerReader.FieldInfo
- ypos - Variable in class loci.formats.in.CV7000Reader.Plane
- yPos - Variable in class loci.formats.in.LeicaHandler
- yPos - Variable in class loci.formats.in.OpenlabReader
- yPos - Variable in class loci.formats.in.ZeissXRMReader
- yPositions - Variable in class loci.formats.in.FlexReader
- ySize - Variable in class loci.formats.in.CV7000Reader.Channel
- ySizes - Variable in class loci.formats.in.FlexReader
- yStart - Variable in class loci.formats.in.OIRReader.PixelBlock
- YT_FLAG - Enum constant in enum class loci.formats.in.SPEReader.SpeHeaderEntry
- YT_INFO - Enum constant in enum class loci.formats.in.SPEReader.SpeHeaderEntry
- yTiles - Variable in class loci.formats.in.DeltavisionReader
-
Number of tiles in Y direction.
- yTiles - Variable in class loci.formats.services.JPEGTurboServiceImpl
Z
- z - Variable in class loci.formats.in.ColumbusReader.Plane
- z - Variable in class loci.formats.in.CV7000Reader.Plane
- z - Variable in class loci.formats.in.LeicaSCNReader.Dimension
- z - Variable in class loci.formats.in.MicromanagerReader.Index
- z - Variable in class loci.formats.in.OIRReader.CZTKey
- z - Variable in class loci.formats.in.OperettaReader.Plane
- Z - Enum constant in enum class loci.formats.in.LeicaMicrosystemsMetadata.Dimension.DimensionKey
- Z - Static variable in class loci.formats.in.CellSensReader
- Z_AXIS - Static variable in class loci.formats.AxisGuesser
-
Axis type for focal planes.
- Z_INCREMENT - Static variable in class loci.formats.in.CellSensReader
- Z_KEY - Static variable in class loci.formats.in.LiFlimReader
- Z_NUM - Static variable in class loci.formats.FormatTools
- Z_OFFSET_IN_SLIDE - Enum constant in enum class loci.formats.dicom.DicomAttribute
- Z_POS_TAG - Static variable in class loci.formats.in.SlidebookTiffReader
- Z_POSITION - Static variable in class loci.formats.in.NDPIReader
- Z_PREFIXES - Static variable in class loci.formats.AxisGuesser
-
Prefixes indicating space dimension.
- Z_START - Static variable in class loci.formats.in.CellSensReader
- Z_TAG - Static variable in class loci.formats.in.VentanaReader
- Z_VALUE - Static variable in class loci.formats.in.CellSensReader
- z0 - Variable in class loci.formats.tools.AmiraParameters
- z1 - Variable in class loci.formats.tools.AmiraParameters
- zBegin - Variable in class loci.plugins.in.ImporterOptions
- zChoice - Variable in class loci.formats.gui.DataConverter
- zChoice - Variable in class loci.plugins.in.SwapDialog
- zCoordinates - Variable in class loci.formats.in.ZeissLSMReader
- zCount - Variable in class loci.formats.in.CellSensReader
- zctLabel - Variable in class loci.formats.gui.PreviewPane
-
Labels containing thumbnail and dimensional information.
- zctText - Variable in class loci.formats.gui.PreviewPane
- zctTip - Variable in class loci.formats.gui.PreviewPane
- zDim - Variable in class loci.formats.out.AVIWriter
- zDistances - Variable in class loci.formats.in.MetamorphReader
- ZEISS_ID - Static variable in class loci.formats.in.ZeissLSMReader
-
Tag identifying a Zeiss LSM file.
- ZeissCZIReader - Class in loci.formats.in
-
ZeissCZIReader is the file format reader for Zeiss .czi files.
- ZeissCZIReader() - Constructor for class loci.formats.in.ZeissCZIReader
-
Constructs a new Zeiss .czi reader.
- ZeissCZIReader.Attachment - Class in loci.formats.in
-
Segment with ID "ZISRAWATTACH".
- ZeissCZIReader.AttachmentDirectory - Class in loci.formats.in
-
Segment with ID "ZISRAWATTDIR".
- ZeissCZIReader.AttachmentEntry - Class in loci.formats.in
- ZeissCZIReader.Channel - Class in loci.formats.in
- ZeissCZIReader.Coordinate - Class in loci.formats.in
- ZeissCZIReader.DimensionEntry - Class in loci.formats.in
- ZeissCZIReader.Directory - Class in loci.formats.in
-
Segment with ID "ZISRAWDIRECTORY".
- ZeissCZIReader.DirectoryEntry - Class in loci.formats.in
- ZeissCZIReader.FileHeader - Class in loci.formats.in
-
Segment with ID "ZISRAWFILE".
- ZeissCZIReader.Metadata - Class in loci.formats.in
-
Segment with ID "ZISRAWMETADATA".
- ZeissCZIReader.Segment - Class in loci.formats.in
-
Top-level class that implements logic common to all types of Segment.
- ZeissCZIReader.SubBlock - Class in loci.formats.in
-
Segment with ID "ZISRAWSUBBLOCK".
- ZeissCZIWidgets - Class in loci.plugins.config
-
Custom widgets for configuring Bio-Formats Zeiss CZI support.
- ZeissCZIWidgets() - Constructor for class loci.plugins.config.ZeissCZIWidgets
- ZeissLMSReader - Class in loci.formats.in
-
Zeiss LMS reader for data from Zeiss CSM 700 systems.
- ZeissLMSReader() - Constructor for class loci.formats.in.ZeissLMSReader
-
Constructs a new LMS reader.
- ZeissLSMReader - Class in loci.formats.in
-
ZeissLSMReader is the file format reader for Zeiss LSM files.
- ZeissLSMReader() - Constructor for class loci.formats.in.ZeissLSMReader
-
Constructs a new Zeiss LSM reader.
- ZeissLSMReader.BeamSplitter - Class in loci.formats.in
- ZeissLSMReader.DataChannel - Class in loci.formats.in
- ZeissLSMReader.DetectionChannel - Class in loci.formats.in
- ZeissLSMReader.IlluminationChannel - Class in loci.formats.in
- ZeissLSMReader.Laser - Class in loci.formats.in
- ZeissLSMReader.Marker - Class in loci.formats.in
- ZeissLSMReader.Recording - Class in loci.formats.in
- ZeissLSMReader.SubBlock - Class in loci.formats.in
- ZeissLSMReader.Timer - Class in loci.formats.in
- ZeissLSMReader.Track - Class in loci.formats.in
- ZeissTIFFHandler - Class in loci.formats.in
-
SAX handler for parsing XML in Zeiss TIFF files.
- ZeissTIFFHandler(ZeissTIFFReader) - Constructor for class loci.formats.in.ZeissTIFFHandler
- ZeissTIFFHandler.Plane - Class in loci.formats.in
-
Metadata for a single image plane.
- ZeissTIFFHandler.Scaling - Class in loci.formats.in
-
Scaling metadata.
- ZeissTIFFHandler.Scaling.Dimension - Class in loci.formats.in
-
Scaling information for a single dimension.
- ZeissTIFFHandler.Tag - Class in loci.formats.in
-
Content of a single tag from a Tags block.
- ZeissTIFFHandler.TagSet - Class in loci.formats.in
-
A collection of tags from a single Tags block.
- ZeissTIFFReader - Class in loci.formats.in
-
ZeissTIFFReader is the file format reader for Zeiss AxioVision TIFF files and their companion XML file.
- ZeissTIFFReader() - Constructor for class loci.formats.in.ZeissTIFFReader
- ZeissTIFFReader.Plane - Class in loci.formats.in
- ZeissTIFFReader.TIFFInfo - Class in loci.formats.in
- ZeissXRMReader - Class in loci.formats.in
-
ZeissXRMReader is the file format reader for Zeiss X-Ray Microscopy .txm and .txrm files.
- ZeissXRMReader() - Constructor for class loci.formats.in.ZeissXRMReader
-
Constructs a new Zeiss XRM reader.
- ZeissZVIReader - Class in loci.formats.in
-
ZeissZVIReader is the file format reader for Zeiss ZVI files.
- ZeissZVIReader() - Constructor for class loci.formats.in.ZeissZVIReader
-
Constructs a new ZeissZVI reader.
- zEnd - Variable in class loci.plugins.in.ImporterOptions
- zeroes - Variable in class loci.formats.FilePatternBlock
-
The number of leading zeroes.
- zIncrement - Variable in class loci.formats.in.CellSensReader.Pyramid
- zIndices - Variable in class loci.formats.in.BaseZeissReader
- ZIP - Static variable in class loci.formats.in.PhotoshopTiffReader
- ZipReader - Class in loci.formats.in
-
Reader for Zip files.
- ZipReader() - Constructor for class loci.formats.in.ZipReader
- zLabel - Variable in class loci.formats.gui.DataConverter
- zLen - Variable in class loci.formats.in.LiFlimReader
- ZLIB - Enum constant in enum class loci.formats.codec.CompressionType
- ZlibCodec - Class in loci.formats.codec
-
This class implements ZLIB decompression.
- ZlibCodec() - Constructor for class loci.formats.codec.ZlibCodec
- zLocation - Variable in class loci.formats.in.VolocityReader.Stack
- zMapFile - Variable in class loci.formats.in.CellWorxReader
- zOffset - Variable in class loci.formats.dicom.DicomTile
- zOffset - Variable in class loci.formats.in.ND2Reader
- zOffset - Variable in class loci.formats.out.DicomWriter.PlaneOffset
- zOffsets - Variable in class loci.formats.dicom.DicomFileInfo
- zOffsets - Variable in class loci.formats.in.DicomReader
- zOffsetSize - Variable in class loci.formats.out.DicomWriter.PlaneOffset
- zoom - Variable in class loci.formats.in.LeicaHandler.Detector
- zoom - Variable in class loci.formats.in.LeicaHandler
- zoom - Variable in class loci.formats.in.MetamorphHandler
- zoom - Variable in class loci.formats.in.MetamorphReader
- zoom - Variable in class loci.formats.in.ZeissCZIReader
- zoom - Variable in class loci.formats.in.ZeissLSMReader
- ZOOM_CENTER - Enum constant in enum class loci.formats.dicom.DicomAttribute
- ZOOM_FACTOR - Enum constant in enum class loci.formats.dicom.DicomAttribute
- zooms - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataTempBuffer
- zooms - Variable in class loci.formats.in.LIFReader
- ZPO_SUFFIX - Static variable in class loci.formats.in.PerkinElmerReader
- zpos - Variable in class loci.formats.in.CV7000Reader.Plane
- zPos - Variable in class loci.formats.in.LeicaHandler
- zPos - Variable in class loci.formats.in.OpenlabReader
- zPos - Variable in class loci.formats.in.ZeissXRMReader
- zPosition - Variable in class loci.formats.in.InCellReader.Image
- zPosition - Variable in class loci.formats.in.InCellReader.InCellHandler
- zPosition - Variable in class loci.formats.in.OpenlabReader.PlaneInfo
- zPosition - Variable in class loci.formats.in.SVSReader
- zPositions - Variable in class loci.formats.in.FluoviewReader
- zPositions - Variable in class loci.formats.in.MetamorphHandler
- zs - Variable in class loci.formats.in.ND2Handler
- zScroll - Variable in class loci.plugins.util.DataBrowser
- zSize - Variable in class loci.formats.in.DeltavisionReader
-
Size of one z section in the extended header.
- zSlider - Variable in class loci.formats.gui.ImageViewer
- zStart - Variable in class loci.formats.in.CellSensReader.Pyramid
- zStart - Variable in class loci.formats.in.MetamorphReader
- zStart - Variable in class loci.formats.in.OIRReader
- ZSTD - Enum constant in enum class loci.formats.tiff.TiffCompression
- ZSTD_0 - Static variable in class loci.formats.in.ZeissCZIReader
- ZSTD_1 - Static variable in class loci.formats.in.ZeissCZIReader
- ZstdCodec - Class in loci.formats.codec
- ZstdCodec() - Constructor for class loci.formats.codec.ZstdCodec
- zStep - Variable in class loci.formats.in.OIRReader
- zStep - Variable in class loci.formats.in.ZeissCZIReader
- zStep - Variable in class loci.plugins.in.ImporterOptions
- zSteps - Variable in class loci.formats.in.CellWorxReader
- zSteps - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataTempBuffer
- zSteps - Variable in class loci.formats.in.LIFReader
- zSteps - Variable in class loci.formats.in.TissueFAXSReader.ScanRegion
- zValues - Variable in class loci.formats.in.CellSensReader.Pyramid
- ZVI_MAGIC_BYTES - Static variable in class loci.formats.in.ZeissZVIReader
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