- a - Variable in class loci.formats.in.VentanaReader.Overlap
-
- About - Class in loci.plugins
-
Displays a small information dialog about the Bio-Formats Plugins package.
- About() - Constructor for class loci.plugins.About
-
- about() - Static method in 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
-
absoluteTime attribute of this <Frame>.
- 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(String) - Method in class loci.formats.NumberFilter
-
Tests if a specified file should be included in a file list.
- accept(File) - Method in class loci.formats.NumberFilter
-
Tests if a specified file should be included in a file list.
- 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
-
- 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_CYCLE_TIME - Static variable in class loci.formats.in.FluoviewReader
-
- ACQUISITION_FILE - Static variable in class loci.formats.in.ScanrReader
-
- ACQUISITION_PROPERTIES - Static variable in class loci.formats.in.CellSensReader
-
- ACQUISITION_TIME_TAG - Static variable in class loci.formats.in.FlowSightReader
-
- 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
-
- 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_TEMPERATURE - Static variable in class loci.formats.in.FluoviewReader
-
- 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(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(int, CoreMetadata) - Method in class loci.formats.CoreMetadataList
-
Add a secondary array element to the specified primary array
- add() - Method in class loci.formats.MetadataList
-
Add a empty primary array element.
- add(int) - Method in class loci.formats.MetadataList
-
Add a empty primary array element.
- add(int, T) - Method in class loci.formats.MetadataList
-
Add a secondary array element to the specified primary array
- add(T) - Method in class loci.formats.MetadataList
-
Add a new primary element containing a single specified value.
- add(List<T>) - Method in class loci.formats.MetadataList
-
Add a new primary element containing the specified values.
- add(double) - Method in class loci.plugins.util.RecordedImageProcessor
-
- add(int) - Method in class loci.plugins.util.RecordedImageProcessor
-
- 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
-
- 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, Object) - Method in class loci.formats.FormatReader
-
Adds an entry to the global metadata table.
- 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, short) - 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, float) - 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, char) - 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
-
- addMeta(String, Object, Hashtable<String, Object>) - Method in class loci.formats.FormatReader
-
Adds an entry to the specified Hashtable.
- 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, 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) - Method in class loci.formats.services.OMEXMLServiceImpl
-
- 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.
- 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, Object) - Method in class loci.formats.FormatReader
-
Adds an entry to the metadata table for the current series.
- 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, short) - 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, float) - 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, char) - 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
-
- 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
-
- advanceBlock() - Method in class loci.formats.in.APNGReader.PNGInputStream
-
- 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.
- ALIGNMENT - Static variable in class loci.formats.in.ZeissCZIReader
-
- 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.
- altCodec - Variable in class loci.formats.in.QTReader
-
Some movies use two video codecs -- this is the second codec.
- 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.
- amplificationGain - Variable in class loci.formats.in.ZeissLSMReader.DetectionChannel
-
- 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.
- 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
-
- ANGLE - Static variable in class loci.formats.in.ZeissLSMReader
-
- angle - Variable in class loci.formats.in.ZeissTIFFHandler.Scaling.Dimension
-
- angles - Variable in class loci.formats.in.ZeissCZIReader
-
- 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_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
-
- 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(ClassList<T>) - Method in class loci.formats.ClassList
-
Appends a class list which must be assignable to the base class
- 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(ILoggingEvent) - Method in class loci.plugins.util.IJStatusEchoer
-
- 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
-
- 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
-
- 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 - 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
-
- ARTIST - Static variable in class loci.formats.tiff.IFD
-
- ascii - Variable in class loci.formats.in.AmiraReader
-
- ASCII(int, int) - Constructor for class loci.formats.in.AmiraReader.ASCII
-
- ascii - Variable in class loci.formats.tools.AmiraParameters
-
- 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
-
- 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
-
- asStore(MetadataRetrieve) - Method in interface loci.formats.services.OMEXMLService
-
- asStore(MetadataRetrieve) - Method in class loci.formats.services.OMEXMLServiceImpl
-
- ASTRONOMY_DOMAIN - Static variable in class loci.formats.FormatTools
-
Identifies the astronomy domain.
- 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(String, long) - Constructor for class loci.formats.in.ZeissCZIReader.Attachment
-
- attachment - Variable in class loci.formats.in.ZeissCZIReader.Attachment
-
- attachment - Variable in class loci.formats.in.ZeissCZIReader.Metadata
-
- 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
-
- AUTOEXPOSURE - Static variable in class loci.formats.in.CellSensReader
-
- 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.
- 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.
- 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.
- 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
-
- 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 BufferedImage form.
- 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(String) - Method in class loci.formats.in.PrairieMetadata
-
Converts the given string to a boolean.
- b - Variable in class loci.formats.in.VentanaReader.Overlap
-
- 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
-
- bandUsed - Variable in class loci.formats.in.NDPISReader
-
- bankData - Variable in class loci.formats.gui.SignedByteBuffer
-
- bankData - Variable in class loci.formats.gui.UnsignedIntBuffer
-
- barcode - Variable in class loci.formats.in.LeicaSCNReader.ImageCollection
-
- barrierFilter - Variable in class loci.formats.in.FV1000Reader.ChannelData
-
- base - Variable in class loci.formats.ClassList
-
Base class to which all classes are assignable.
- Base64Codec - Class in loci.formats.codec
-
Implements encoding (compress) and decoding (decompress) methods
for Base64.
- Base64Codec() - Constructor for class loci.formats.codec.Base64Codec
-
- BASE_OFFSET - Static variable in class loci.formats.in.BioRadGelReader
-
- 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.OIRReader
-
- basename - Variable in class loci.formats.in.ZeissTIFFHandler.Plane
-
- 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 in loci.formats.in
-
- BaseZeissReader.Context - Enum in loci.formats.in
-
- BaseZeissReader.DrawStyle - Enum in loci.formats.in
-
Line drawing styles.
- BaseZeissReader.FeatureType - Enum in loci.formats.in
-
Feature types.
- BaseZeissReader.FillStyle - Enum 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 in loci.formats.in
-
- BaseZeissReader.LineEndStyle - Enum in loci.formats.in
-
Line ending styles.
- BaseZeissReader.PointStyle - Enum 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 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 - Variable in class loci.formats.in.CellH5Reader
-
- BBOX - Static variable in class loci.formats.in.CellH5Reader.CellH5Constants
-
- 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
-
- 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 - Static variable in class loci.formats.in.CellSensReader
-
- bgr - 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
-
- 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
-
- 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
-
- 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_PER_SAMPLE - Static variable in class loci.formats.tiff.IFD
-
- 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
-
- 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
-
- 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
-
- 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
-
- 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_GAIN - Static variable in class loci.formats.in.CellSensReader
-
- 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 - 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
-
- bold - Variable in class loci.formats.in.BaseZeissReader.Shape
-
- 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(HashMap<String, String>) - Constructor for class loci.plugins.prefs.BooleanOption
-
Constructs a boolean option with the parameters from the given map.
- BooleanOption(String, boolean, String, String, boolean) - Constructor for class loci.plugins.prefs.BooleanOption
-
Constructs a boolean option with the given parameters.
- BORDER - Static variable in class loci.plugins.shortcut.ShortcutPanel
-
Number of pixels for window border.
- bordL - Variable in class loci.formats.in.SDTInfo
-
- bordU - Variable in class loci.formats.in.SDTInfo
-
- 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
-
- 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_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(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.
- 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.
- 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.
- 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(IFormatReader) - Constructor for class loci.formats.cache.ByteArraySource
-
Constructs a byte array source from the given Bio-Formats reader.
- ByteArraySource(String) - Constructor for class loci.formats.cache.ByteArraySource
-
Constructs a byte array source that draws from the given file.
- 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 loci.formats.tiff.IFDType
-
Number of bytes per element of this type.
- 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
-
- 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(int) - Constructor for class loci.formats.codec.ByteVector
-
- ByteVector(byte[]) - Constructor for class loci.formats.codec.ByteVector
-
- C - Static variable in class loci.formats.in.CellSensReader
-
- 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.OperettaReader.Plane
-
- c - Variable in class loci.formats.tools.AmiraParameters
-
- C01_MAGIC_BYTES - Static variable in class loci.formats.in.CellomicsReader
-
- 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
-
- 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.
- 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
-
- 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 in loci.formats.cache
-
CacheException is the exception thrown when something
goes wrong performing a cache operation.
- CacheException() - Constructor for exception loci.formats.cache.CacheException
-
- CacheException(String) - Constructor for exception loci.formats.cache.CacheException
-
- CacheException(String, Throwable) - Constructor for exception loci.formats.cache.CacheException
-
- CacheException(Throwable) - Constructor for exception 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(IFormatReader) - Constructor for class loci.formats.cache.CacheSource
-
Constructs a cache source from the given Bio-Formats reader.
- CacheSource(String) - Constructor for class loci.formats.cache.CacheSource
-
Constructs a cache source that draws from the given file.
- 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.
- 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
-
- 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
-
- 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
-
- 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
-
- 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
-
- 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
-
- 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_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 - Static variable in class loci.formats.FormatTools
-
Identifies the Channel dimensional type,
representing a generic channel dimension.
- channel - Variable in class loci.formats.in.CellomicsReader.ChannelFile
-
- channel - Variable in class loci.formats.in.ColumbusReader.Plane
-
- Channel() - Constructor for class loci.formats.in.CV7000Reader.Channel
-
- Channel(CV7000Reader.Channel) - Constructor for class loci.formats.in.CV7000Reader.Channel
-
- channel - Variable in class loci.formats.in.CV7000Reader.Plane
-
- Channel() - Constructor for class loci.formats.in.LeicaHandler.Channel
-
- channel - Variable in class loci.formats.in.LeicaHandler.Detector
-
- channel - Variable in class loci.formats.in.LeicaHandler.MultiBand
-
- Channel - Class in loci.formats.in.LeicaMicrosystemsMetadata
-
This class represents image channels extracted from LMS image xmls.
- Channel(int, int, double, double, String, String, long) - Constructor for class loci.formats.in.LeicaMicrosystemsMetadata.Channel
-
- Channel() - Constructor for class loci.formats.in.OIRReader.Channel
-
- Channel() - Constructor for class loci.formats.in.OperettaReader.Channel
-
- channel - Variable in class loci.formats.in.PrairieMetadata.PFile
-
channel of this <File>.
- channel - Variable in class loci.formats.in.SPCReader
-
- Channel(String) - Constructor for class loci.formats.in.TecanReader.Channel
-
- Channel() - Constructor for class loci.formats.in.ZeissCZIReader.Channel
-
- Channel.ChannelType - Enum in loci.formats.in.LeicaMicrosystemsMetadata
-
- 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_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
-
- 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 - 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.
- channelFiller - Variable in class loci.plugins.in.ImportProcess
-
- 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
-
channelName attribute 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.ZeissCZIReader
-
- 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.
- channelSeparator - Variable in class loci.plugins.in.ImportProcess
-
- 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() - Constructor for enum loci.formats.in.LeicaMicrosystemsMetadata.Channel.ChannelType
-
- channelType - Variable in class loci.formats.in.OperettaReader.Channel
-
- channelType - Variable in class loci.formats.in.OperettaReader.Plane
-
- 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(int, String) - Constructor for enum loci.formats.in.BaseZeissReader.Charset
-
- charset - Variable in class loci.formats.in.BaseZeissReader.Shape
-
- 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(LibraryChecker.Library, HashSet<String>) - Static method in class loci.plugins.util.LibraryChecker
-
Checks for a required library.
- 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).
- 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(int, byte[], int, int, int, int) - Method in class loci.formats.FormatWriter
-
Ensure that the arguments that are being passed to saveBytes(...) are
valid.
- checkParams - Variable in class loci.formats.out.TiffWriter
-
Whether or not to check the parameters passed to saveBytes.
- 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 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
-
- 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.
- 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
-
- 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
-
- ClassList<T> - Class in loci.formats
-
ClassList is a list of classes for use with
ImageReader or
ImageWriter, 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.
- classList - Variable in class loci.formats.FileStitcher
-
- 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
-
- 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
-
- CLOCKWISE - Static variable in class loci.formats.in.FluoviewReader
-
- clone() - Method in class loci.formats.CoreMetadata
-
- clone(IFormatReader, int) - Method in class loci.formats.CoreMetadata
-
- clone() - Method in class loci.formats.SwappableMetadata
-
- clone(IFormatReader, int) - Method in class loci.formats.SwappableMetadata
-
- close(boolean) - Method in class loci.formats.ChannelSeparator
-
- close() - Method in class loci.formats.codec.JPEGTileDecoder
-
- close(boolean) - Method in class loci.formats.DelegateReader
-
- close() - Method in class loci.formats.FileStitcher
-
- close(boolean) - Method in class loci.formats.FileStitcher
-
- close() - Method in class loci.formats.FileStitcher.ExternalSeries
-
- close(boolean) - Method in class loci.formats.FileStitcher.ExternalSeries
-
- close(boolean) - Method in class loci.formats.FormatReader
-
- 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(boolean) - Method in interface loci.formats.IFormatReader
-
Closes the currently open file.
- close(boolean) - Method in class loci.formats.ImageReader
-
- close() - Method in class loci.formats.ImageReader
-
- close() - Method in class loci.formats.ImageWriter
-
- 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.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.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.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() - Method in class loci.formats.in.ZeissCZIReader.Segment
-
- 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.ZeissZVIReader
-
- close(boolean) - Method in class loci.formats.in.ZipReader
-
- close() - Method in class loci.formats.Memoizer
-
- close(boolean) - Method in class loci.formats.Memoizer
-
- close() - Method in interface loci.formats.Memoizer.Deser
-
- close() - Method in class loci.formats.Memoizer.KryoDeser
-
- close(boolean) - Method in class loci.formats.MinMaxCalculator
-
- 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(boolean) - Method in class loci.formats.ReaderWrapper
-
- 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
-
- 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(boolean) - Method in class loci.formats.SubResolutionFormatReader
-
- 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(boolean) - Method in class loci.formats.WrappedReader
-
- 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.
- 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
-
- 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
-
- code - Variable in enum loci.formats.codec.CompressionType
-
Code for the compression.
- code - Variable in enum loci.formats.codec.JPEG2000BoxType
-
Code for the box type.
- code - Variable in enum loci.formats.codec.JPEG2000SegmentMarker
-
Code for the segment marker.
- code - Variable in enum loci.formats.dicom.DicomVR
-
- code - Variable in class loci.formats.in.FV1000Reader
-
- code - Variable in enum loci.formats.tiff.IFDType
-
Code for the IFD type in the actual TIFF file.
- code - Variable in enum loci.formats.tiff.PhotoInterp
-
Code for the IFD type in the actual TIFF file.
- code - Variable in enum loci.formats.tiff.TiffCompression
-
Code for the TIFF compression in the actual TIFF file.
- 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 - Interface in loci.formats.codec
-
This class is an interface for any kind of compression or decompression.
- 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 loci.formats.tiff.TiffCompression
-
TIFF compression codec.
- 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 loci.formats.tiff.TiffCompression
-
Name of the TIFF compression codec.
- 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.
- codecOptions - Variable in class loci.formats.tiff.TiffParser
-
Codec options to be used when decoding compressed pixel data.
- 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.
- 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
-
- 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.ZeissCZIReader.Channel
-
- color16 - Variable in class loci.formats.in.IvisionReader
-
- 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 - Static variable in class loci.formats.in.CellSensReader
-
- COLOR_SPACE - Static variable in class loci.formats.tiff.IFD
-
- 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.BDVReader
-
- COLORS - Variable in class loci.formats.in.CellH5Reader
-
- 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
-
- COLORSPACE - Static variable in class loci.formats.in.CellSensReader
-
- colorTables - Variable in class loci.formats.in.GIFReader
-
- 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
-
- COLUMNS - Static variable in class loci.formats.gui.DataConverter
-
- 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
-
- 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.DicomReader
-
- comparator - Static variable in class loci.formats.CoreMetadataList
-
- 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
-
- compare(File, File) - Method in class loci.formats.in.XLEFReader.PathComparator
-
- compareTo(DicomFileInfo) - Method in class loci.formats.dicom.DicomFileInfo
-
- compareTo(DicomTag) - Method in class loci.formats.dicom.DicomTag
-
- 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(OlympusTileReader.Tile) - Method in class loci.formats.in.OlympusTileReader.Tile
-
- compareTo(VentanaReader.Overlap) - Method in class loci.formats.in.VentanaReader.Overlap
-
- compareTo(Object) - Method in class loci.formats.tiff.TiffIFDEntry
-
- compareTo(TiffRational) - Method in class loci.formats.tiff.TiffRational
-
Compares this object with the specified object for order.
- compareTo(Object) - Method in class loci.plugins.config.FormatEntry
-
- compareTo(Object) - Method in class loci.plugins.config.LibraryEntry
-
- compareTo(ThumbLoader.SeriesInfo) - Method in class loci.plugins.in.ThumbLoader.SeriesInfo
-
- compareTokens(String[], int, String[], int) - Method in class loci.formats.in.ICSReader
-
- 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
-
- COMPONENT_HEIGHT - Static variable in class loci.formats.gui.CacheIndicator
-
- COMPONENT_WIDTH - Static variable in class loci.formats.gui.CacheIndicator
-
- COMPONENTS_CONFIGURATION - Static variable in class loci.formats.tiff.IFD
-
- 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 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 class loci.formats.codec.WrappedCodec
-
- compress(byte[]) - Method in class loci.formats.out.OMEXMLWriter
-
Compress the given byte array using the current codec.
- compress(byte[], CodecOptions) - Method in enum loci.formats.tiff.TiffCompression
-
Encodes a strip of data.
- 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(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(BufferedImage, byte[], int) - Method in class org.libjpegturbo.turbojpeg.TJCompressor
-
Compress the uncompressed source image stored in srcImage
and 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 srcImage
and return a buffer containing a JPEG image.
- compress(byte[], int, int, int, int, byte[], int, int, int) - Method in class org.libjpegturbo.turbojpeg.TJCompressor
-
- compress(int[], int, int, int, int, byte[], int, int, int) - Method in class org.libjpegturbo.turbojpeg.TJCompressor
-
- 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 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_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 - Enum in loci.formats.codec
-
An enumeration of compression types.
- CompressionType(int, String) - Constructor for enum loci.formats.codec.CompressionType
-
Default constructor.
- compressionType - Variable in class loci.formats.in.CellSensReader
-
- compressionType - Variable in class loci.formats.in.KLBReader
-
- 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
-
- 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
-
- 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
-
- 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
-
- contentFileType - Variable in class loci.formats.in.ZeissCZIReader.AttachmentEntry
-
- contentGUID - Variable in class loci.formats.in.ZeissCZIReader.AttachmentEntry
-
- Context() - Constructor for enum loci.formats.in.BaseZeissReader.Context
-
- context - Variable in class loci.formats.in.BaseZeissReader.Tag
-
- CONTRAST - Static variable in class loci.formats.in.CellSensReader
-
- CONTRAST - Static variable in class loci.formats.tiff.IFD
-
- CONTRAST_BRIGHTNESS - Static variable in class loci.formats.in.CellSensReader
-
- CONTRAST_TARGET - Static variable in class loci.formats.in.CellSensReader
-
- 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.
- convert - Variable in class loci.formats.gui.DataConverter
-
- convert12to16LSB(byte[]) - Static method in class loci.formats.in.LiFlimReader
-
- convert12to16MSB(byte[]) - Static method in class loci.formats.in.LiFlimReader
-
- 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).
- convertMetadata(String, MetadataStore) - Method in interface loci.formats.services.OMEXMLService
-
Converts information from an OME-XML string (source)
into a metadata store (destination).
- convertMetadata(MetadataRetrieve, MetadataStore) - Method in interface loci.formats.services.OMEXMLService
-
Copies information from a metadata retrieval object
(source) into a metadata store (destination).
- convertMetadata(String, MetadataStore) - Method in class loci.formats.services.OMEXMLServiceImpl
-
- convertMetadata(MetadataRetrieve, MetadataStore) - Method in class loci.formats.services.OMEXMLServiceImpl
-
- convertPixelType(int) - Method in class loci.formats.in.CellSensReader
-
- convertPixelType(int) - Method in class loci.formats.in.JPEG2000MetadataParser
-
- convertPixelType(CoreMetadata, int) - Method in class loci.formats.in.KLBReader
-
- 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.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
-
- convertToRGB() - Method in class loci.plugins.util.RecordedImageProcessor
-
- convertToShort(boolean) - Method in class loci.plugins.util.RecordedImageProcessor
-
- convertUnits(String) - Method in class loci.formats.in.GatanReader
-
- convertUnits(int) - Method in class loci.formats.in.IMODReader
-
- 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
-
- copyOptions(CodecOptions, CodecOptions) - Static method in class loci.formats.codec.WrappedCodec
-
- copyPixels(int, int, int, int, int, int, byte[], byte[], boolean) - Method in class loci.formats.in.ND2Reader
-
- 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.
- 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
CoreMetadata objects 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
-
- 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 - Class in loci.formats
-
Encompasses core metadata values.
- CoreMetadata() - Constructor for class loci.formats.CoreMetadata
-
- CoreMetadata(IFormatReader, int) - Constructor for class loci.formats.CoreMetadata
-
- CoreMetadata(CoreMetadata) - Constructor for class loci.formats.CoreMetadata
-
- coreMetadata - Variable in class loci.formats.dicom.DicomFileInfo
-
- coreMetaData - Static variable in class loci.formats.in.SPEReader
-
- CoreMetadataList - Class in loci.formats
-
- CoreMetadataList() - Constructor for class loci.formats.CoreMetadataList
-
- CoreMetadataList(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, 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(int[]) - Constructor for class loci.formats.CoreMetadataList
-
Construct a list containing a specified number of primary and secondary elements.
- CoreMetadataList(List<CoreMetadata>) - Constructor for class loci.formats.CoreMetadataList
-
- 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
-
- 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].
- count - Variable in class loci.formats.in.LeicaHandler
-
- count() - Method in class loci.formats.in.LeicaSCNReader.LeicaSCNHandler
-
- count - Variable in class loci.formats.in.ZeissTIFFHandler.TagSet
-
- 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
-
- 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
-
- 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
IFormatReader
according 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(String) - Method in class loci.formats.in.DicomReader
-
Construct a DicomFileInfo for the given file.
- createFileInfo() - Method in class loci.plugins.in.ImagePlusReader
-
- 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(String, List<ImageProcessor>) - Static method in class loci.plugins.in.ImagePlusReader
-
Creates an ImagePlus from the given image processors.
- createImage(String, ImageStack, List<LUT>) - Static method in class loci.plugins.in.ImagePlusReader
-
Creates an ImagePlus from the given image stack.
- createImage() - Method in class loci.plugins.util.RecordedImageProcessor
-
- 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.ome package.
- 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.ome package.
- 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.ome package,
wrapping a DOM representation of the given OME-XML string.
- 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.ome package,
wrapping a DOM representation of the given OME-XML string.
- createOMEXMLMetadata() - Method in class loci.formats.services.OMEXMLServiceImpl
-
- createOMEXMLMetadata(String) - Method in class loci.formats.services.OMEXMLServiceImpl
-
- 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_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
-
- 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
-
- crop() - Method in class loci.plugins.util.RecordedImageProcessor
-
- 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
-
- crossChan - Variable in class loci.formats.in.SDTInfo
-
Cross FCS routing channel number
when chan = crossChan and mod == crossMod - Auto FCS
otherwise - Cross FCS.
- 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_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_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
-
- currentThumbnail - Variable in class loci.formats.in.InCellReader.MinimalInCellHandler
-
- 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 - Static variable in class loci.formats.in.NikonReader
-
- curve - Variable in class loci.formats.in.NikonReader
-
- 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
-
cycle of 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
-
- d(String) - Method in class loci.formats.in.PrairieMetadata
-
Converts the given string to a Double, or null if
incompatible.
- 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
-
- 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_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_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.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
-
- 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.LeicaMicrosystemsMetadata.Channel
-
- datatype - Variable in class loci.formats.in.LiFlimReader
-
- 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 - Static variable in class loci.formats.FormatTools
-
Date on which this release was built.
- DATE - Static variable in class loci.formats.in.CellSensReader
-
- 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_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
-
- 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_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
-
- datFile - Variable in class loci.formats.in.InveonReader
-
- datFile - Variable in class loci.formats.in.UnisokuReader
-
- dBlock - Variable in class loci.formats.in.GIFReader
-
Current data block.
- deadTimeComp - Variable in class loci.formats.in.SDTInfo
-
- debug(String) - Static method in class loci.plugins.BF
-
- decode(APNGReader.PNGInputStream) - Method in class loci.formats.in.APNGReader
-
- decode(APNGReader.PNGInputStream, int, int) - Method in class loci.formats.in.APNGReader
-
- 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) - 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.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 class loci.formats.codec.BaseCodec
-
- decompress(byte[], CodecOptions) - Method in class loci.formats.codec.BaseCodec
-
- decompress(RandomAccessInputStream, CodecOptions) - Method in class loci.formats.codec.BaseCodec
-
- 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 interface loci.formats.codec.Codec
-
Decompresses a block of data.
- decompress(byte[]) - Method in interface loci.formats.codec.Codec
-
Decompresses a block of data.
- decompress(byte[][]) - Method in interface loci.formats.codec.Codec
-
Decompresses a block of data.
- 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(byte[], CodecOptions) - Method in class loci.formats.codec.JPEGXRCodec
-
- decompress(RandomAccessInputStream, CodecOptions) - Method in class loci.formats.codec.NikonCodec
-
- decompress(RandomAccessInputStream, CodecOptions) - Method in class loci.formats.codec.TargaRLECodec
-
- decompress(byte[], CodecOptions) - Method in class loci.formats.codec.WrappedCodec
-
- decompress(byte[][], CodecOptions) - Method in class loci.formats.codec.WrappedCodec
-
- decompress(byte[]) - Method in class loci.formats.codec.WrappedCodec
-
- decompress(byte[][]) - Method in class loci.formats.codec.WrappedCodec
-
- decompress(RandomAccessInputStream, CodecOptions) - Method in class loci.formats.codec.WrappedCodec
-
- decompress(byte[], int, int) - Method in class loci.formats.codec.ZstdCodec
-
- 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[], CodecOptions) - Method in enum loci.formats.tiff.TiffCompression
-
Decodes a strip of data.
- 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(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
BufferedImage instance.
- 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 BufferedImage instance containing the
decompressed image.
- decompress(byte[], int, byte[], int, int, int, int, int) - Method in class org.libjpegturbo.turbojpeg.TJDecompressor
-
- decompress(byte[], int, int[], int, int, int, int, int) - Method in class org.libjpegturbo.turbojpeg.TJDecompressor
-
- decompressHeader(byte[], int) - Method in class org.libjpegturbo.turbojpeg.TJDecompressor
-
- 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(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.
- decompressToYUV(byte[], int, byte[], int) - Method in class org.libjpegturbo.turbojpeg.TJDecompressor
-
- 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_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_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
-
- 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
-
- 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 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
-
- 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.
- 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.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
-
- 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 loci.formats.dicom.DicomAttribute
-
- description - Variable in class loci.formats.in.CV7000Reader.WPIHandler
-
- description - Variable in class loci.formats.in.NiftiReader
-
- description() - Method in interface loci.formats.in.PrairieMetadata.Value
-
- description - Variable in class loci.formats.in.PrairieMetadata.ValueItem
-
- description() - Method in class loci.formats.in.PrairieMetadata.ValueItem
-
- description() - Method in class loci.formats.in.PrairieMetadata.ValueTable
-
- 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_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() - 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 - Variable in class loci.formats.in.VolocityReader.Stack
-
- 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
-
- detectorIndexes - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataTempBuffer
-
- detectorIndexes - Variable in class loci.formats.in.LIFReader
-
- detectorIndices - Variable in class loci.formats.in.LeicaHandler
-
- 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_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
-
- dialog - Variable in class loci.plugins.in.ThumbLoader
-
- 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 in loci.formats.dicom
-
Describes a DICOM attribute (integer tag, associated description, and expected VR).
- DicomAttribute(int) - Constructor for enum 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(DicomAttribute) - Constructor for class loci.formats.dicom.DicomTag
-
- DicomTag(DicomAttribute, DicomVR) - Constructor for class loci.formats.dicom.DicomTag
-
- 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.
- DicomTile - Class in loci.formats.dicom
-
Represents a tile stored in a DICOM file.
- DicomTile() - Constructor for class loci.formats.dicom.DicomTile
-
- DicomVR - Enum in loci.formats.dicom
-
Enumeration of valid DICOM value representations (VRs).
- DicomVR(int, int) - Constructor for enum 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 loci.formats.dicom.DicomAttribute
-
- diff - Variable in class loci.formats.in.BioRadGelReader
-
- difference(byte[], IFD) - Static method in enum loci.formats.tiff.TiffCompression
-
Performs in-place differencing according to the given predictor value.
- DIGITAL_ZOOM_RATIO - Static variable in class loci.formats.tiff.IFD
-
- 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
-
- DIMDESCR - Static variable in class loci.formats.in.LeicaReader
-
- Dimension - Class in loci.formats.in.LeicaMicrosystemsMetadata
-
This class represents image dimensions extracted from LMS image xmls.
- Dimension(Dimension.DimensionKey, int, long, String, Double, boolean) - Constructor for class loci.formats.in.LeicaMicrosystemsMetadata.Dimension
-
- Dimension() - Constructor for class loci.formats.in.LeicaMicrosystemsMetadata.Dimension
-
- Dimension(Attributes) - Constructor for class loci.formats.in.LeicaSCNReader.Dimension
-
- dimension - Variable in class loci.formats.in.ZeissCZIReader.DimensionEntry
-
- Dimension(Integer) - Constructor for class loci.formats.in.ZeissTIFFHandler.Scaling.Dimension
-
Constructor.
- dimension - Variable in class loci.formats.in.ZeissTIFFHandler.Scaling.Dimension
-
- Dimension.DimensionKey - Enum in loci.formats.in.LeicaMicrosystemsMetadata
-
- DIMENSION_DESCRIPTION_VOLUME - Static variable in class loci.formats.in.CellSensReader
-
- DIMENSION_INCREMENT_ID - Static variable in class loci.formats.in.CellSensReader
-
- 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_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
-
- 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 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 - 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.
- dimensionSwapper - Variable in class loci.plugins.in.ImportProcess
-
- 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() - Constructor for class loci.formats.in.ZeissCZIReader.Directory
-
- directory - Variable in class loci.formats.Memoizer
-
Directory where all memo files should be created.
- directory - Variable in class loci.formats.services.EXIFServiceImpl
-
- directoryCache - Variable in class loci.formats.in.ZeissTIFFReader
-
- DirectoryEntry(RandomAccessInputStream) - Constructor for class loci.formats.in.ZeissCZIReader.DirectoryEntry
-
- directoryEntry - Variable in class loci.formats.in.ZeissCZIReader.SubBlock
-
- 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
-
- 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() - Method in class loci.formats.gui.CacheComponent
-
- dispose - Variable in class loci.formats.in.GIFReader
-
- 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.
- 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
-
- 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 - Static variable in class loci.formats.ResourceNamer
-
- DOT_RANGE - Static variable in class loci.formats.tiff.IFD
-
- 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_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(HashMap<String, String>) - Constructor for class loci.plugins.prefs.DoubleOption
-
Constructs a double option with the parameters from the given map.
- DoubleOption(String, boolean, String, String, double) - Constructor for class loci.plugins.prefs.DoubleOption
-
Constructs a double option with the given parameters.
- 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
-
- 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(int) - Constructor for enum loci.formats.in.BaseZeissReader.DrawStyle
-
- drawStyle - Variable in class loci.formats.in.BaseZeissReader.Shape
-
- 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.
- 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(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() - Method in class loci.plugins.util.RecordedImageProcessor
-
- DUPLICATE_PLANES_DEFAULT - Static variable in class loci.formats.in.CV7000Reader
-
- DUPLICATE_PLANES_KEY - Static variable in class loci.formats.in.CV7000Reader
-
- duplicatePlanes() - Method in class loci.formats.in.CV7000Reader
-
- 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
-
- DynamicMetadataOptions(MetadataLevel) - Constructor for class loci.formats.in.DynamicMetadataOptions
-
- 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
-
- failOnMissingETS() - Method in class loci.formats.in.CellSensReader
-
- failOnMissingTIFF() - Method in class loci.formats.in.OMETiffReader
-
- 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.
- 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
-
- 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 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() - Constructor for class loci.formats.in.CV7000Reader.Field
-
- 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 - 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
-
- 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.tools.EditTiffG
-
- FILE_LENGTH - Static variable in class loci.formats.in.CanonRawReader
-
- FILE_MAGIC_STRING - Static variable in class loci.formats.in.OBFReader
-
- 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.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.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.DicomReader
-
- filelist - Variable in class loci.formats.in.KLBReader
-
- 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
-
filename attribute 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
-
- 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
-
- FilePattern - Class in loci.formats
-
Represents a collection of files meant to be part of the same
data series.
- FilePattern(Location) - Constructor for class loci.formats.FilePattern
-
Creates a pattern object using the given file as a template.
- FilePattern(String, String) - Constructor for class loci.formats.FilePattern
-
Creates a pattern object using the given
filename and directory path as a template.
- FilePattern(String) - Constructor for class loci.formats.FilePattern
-
Creates a pattern object for files with the given pattern string.
- 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's channel.
- 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.services.POIServiceImpl
-
- fileSave - Variable in class loci.formats.gui.ImageViewer
-
- fileSizes - Variable in class loci.formats.services.POIServiceImpl
-
- 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 - Variable in class loci.plugins.in.ImportProcess
-
- 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
-
- fillColor - Variable in class loci.formats.FormatReader
-
Fill value for undefined pixels.
- fillColour - Variable in class loci.formats.in.BaseZeissReader.Shape
-
- filled - Variable in class loci.formats.ChannelFiller
-
Whether to fill in the indices.
- 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.
- 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
- 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(int) - Constructor for enum loci.formats.in.BaseZeissReader.FillStyle
-
- fillStyle - Variable in class loci.formats.in.BaseZeissReader.Shape
-
- 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_SET_NAME - Static variable in class loci.formats.in.NDPIReader
-
- 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 - Static variable in class loci.formats.in.LeicaReader
-
- filterSet - Variable in class loci.formats.in.ZeissLSMReader.BeamSplitter
-
- filterSet - Variable in class loci.formats.in.ZeissLSMReader.DetectionChannel
-
- 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
-
- findChildWithID(Node, String, String) - Method in class loci.formats.services.OMEXMLServiceImpl
-
Return the child node with specified value for the "ID" attribute.
- 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
-
- 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(String) - Static method in class loci.formats.FilePattern
-
Identifies the group pattern from a given file within that group.
- findPattern(Location) - Static method in class loci.formats.FilePattern
-
Identifies the group pattern from a given file within that group.
- findPattern(File) - Static method in class loci.formats.FilePattern
-
Identifies the group pattern from a given file within that group.
- findPattern(String, String) - Static method in class loci.formats.FilePattern
-
Identifies the group pattern from a given filename and directory.
- 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(String[]) - Static method in class loci.formats.FilePattern
-
Generate a pattern from a list of file names.
- findPattern(String, String[], int, int, String) - Static method in class loci.formats.FilePattern
-
- findPattern(String) - Method in class loci.formats.FileStitcher
-
- 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
-
- findSeriesPatterns(String, String, String[]) - Static method in class loci.formats.FilePattern
-
- 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.
- 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
-
- 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
-
- flattenHashtables() - Method in class loci.formats.SubResolutionFormatReader
-
- flbckX - Variable in class loci.formats.in.SDTInfo
-
- flbckY - Variable in class loci.formats.in.SDTInfo
-
- FLEX - Static variable in class loci.formats.in.FlexReader
-
Custom IFD entry for Flex XML.
- flex - Variable in class loci.formats.in.FlexReader.MeaHandler
-
- 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
-
- 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 - 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
-
- 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_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
-
- FOCUS_IMAGE - Static variable in class loci.formats.in.CellSensReader
-
- 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.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.
- 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 in loci.formats
-
FormatException is the exception thrown when something
goes wrong performing a file format operation.
- FormatException() - Constructor for exception loci.formats.FormatException
-
- FormatException(String) - Constructor for exception loci.formats.FormatException
-
- FormatException(String, Throwable) - Constructor for exception loci.formats.FormatException
-
- FormatException(Throwable) - Constructor for exception 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.
- 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 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.
- 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
-
- 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(PrairieMetadata.Sequence, Element) - Constructor for class loci.formats.in.PrairieMetadata.Frame
-
Creates a new frame by parsing the given <Frame> element.
- frame - Variable in class loci.formats.in.PrairieMetadata.PFile
-
The <Frame> containing this <File>.
- 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_PROPERTIES - Static variable in class loci.formats.in.CellSensReader
-
- FRAME_SCALE - Static variable in class loci.formats.in.CellSensReader
-
- FRAME_SIZE - Static variable in class loci.formats.in.CellSensReader
-
- FRAME_TRANSFER - Static variable in class loci.formats.in.CellSensReader
-
- FRAME_TYPE - Static variable in class loci.formats.in.CellSensReader
-
- frameClockList - Variable in class loci.formats.in.SPCReader
-
- frameCoordinates - Variable in class loci.formats.in.APNGReader
-
- 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's index.
- 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>.
- 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
-
- FULLY_AUTO_FOCUS - Static variable in class loci.formats.in.NDPIReader
-
- 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
-
- 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_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
-
- 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
-
- 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.
- 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.
- get(int) - Method in class loci.formats.codec.ByteVector
-
- get(int) - Static method in enum loci.formats.codec.CompressionType
-
Retrieves the compression by reverse lookup of its "code".
- get(int) - Static method in enum loci.formats.codec.JPEG2000BoxType
-
Retrieves the box type by reverse lookup of its "code".
- get(int) - Static method in enum loci.formats.codec.JPEG2000SegmentMarker
-
Retrieves the segment marker by reverse lookup of its "code".
- get(int) - Static method in enum loci.formats.dicom.DicomAttribute
-
Lookup the attribute for the given tag.
- get(int) - Static method in enum loci.formats.dicom.DicomVR
-
- get(int) - Static method in enum loci.formats.in.BaseZeissReader.Charset
-
- get(int) - Static method in enum loci.formats.in.BaseZeissReader.DrawStyle
-
- get(int) - Static method in enum loci.formats.in.BaseZeissReader.FeatureType
-
- get(int) - Static method in enum loci.formats.in.BaseZeissReader.FillStyle
-
- get(int) - Static method in enum loci.formats.in.BaseZeissReader.LineEndPositions
-
- get(int) - Static method in enum loci.formats.in.BaseZeissReader.LineEndStyle
-
- get(int) - Static method in enum loci.formats.in.BaseZeissReader.PointStyle
-
- get(int) - Static method in enum loci.formats.in.BaseZeissReader.TextAlignment
-
- 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(Object) - Method in interface loci.formats.in.PrairieMetadata.Value
-
- get(int) - Method in interface loci.formats.in.PrairieMetadata.Value
-
- get(Object) - Method in class loci.formats.in.PrairieMetadata.ValueItem
-
- get(int) - Method in class loci.formats.in.PrairieMetadata.ValueItem
-
- get(int) - Method in class loci.formats.in.PrairieMetadata.ValueTable
-
- get(int, int) - Method in class loci.formats.MetadataList
-
Get the array element for the specified indexes.
- get(int) - Static method in enum 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 loci.formats.tiff.PhotoInterp
-
Retrieves a photometric interpretation by reverse lookup of its "code".
- get(int) - Static method in enum loci.formats.tiff.TiffCompression
-
Retrieves a TIFF compression instance by code.
- get(List<T>, int, T) - Method in class loci.plugins.in.ImporterOptions
-
- get(int) - Method in class loci.plugins.util.RecordedImageProcessor
-
- get(int, int) - Method in class loci.plugins.util.RecordedImageProcessor
-
- 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(ColorModel) - Static method in class loci.formats.gui.AWTImageTools
-
Converts an IndexColorModel to a 2D byte array.
- 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
-
- getAbsoluteTime() - Method in class loci.formats.in.PrairieMetadata.Frame
-
Gets the absoluteTime associated with this Frame.
- getAcquisitionMode(String) - Method in class loci.formats.FormatReader
-
- getAcquisitionMode(String) - Method in class loci.formats.in.OperettaReader
-
Deprecated.
- getAcquisitionMode(String) - Static method in class loci.formats.MetadataTools
-
Retrieves an AcquisitionMode enumeration
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(String) - Method in class loci.formats.FilePattern
-
- getAlpha(int) - Method in class loci.formats.gui.Index16ColorModel
-
- getAlpha(int) - Method in class loci.formats.gui.SignedColorModel
-
- getAlpha(Object) - Method in class loci.formats.gui.SignedColorModel
-
- getAlpha(int) - Method in class loci.formats.gui.UnsignedIntColorModel
-
- 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
-
- getArcType(String) - Static method in class loci.formats.MetadataTools
-
Retrieves an ArcType enumeration
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.GatanReader
-
- 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.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
-
- 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(String) - Method in class loci.formats.FormatReader
-
- getBinning() - Method in class loci.formats.in.MetamorphHandler
-
- getBinning(String) - Static method in class loci.formats.MetadataTools
-
Retrieves an Binning enumeration
value for the given String.
- getBinnings() - Method in class loci.formats.in.ND2Handler
-
- getBitDepth() - Method in class loci.formats.in.PrairieMetadata
-
Gets the bitDepth recorded 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(int) - Method in class loci.formats.in.OBFReader
-
- getBitsPerPixel() - Method in class loci.formats.ReaderWrapper
-
- getBitsPerPixel() - Method in class loci.formats.WrappedReader
-
- getBitsPerSample(int) - Method in class loci.formats.in.NDPIReader
-
Get the number of bits per sample associated with the given capture mode.
- getBitsPerSample() - Method in class loci.formats.tiff.IFD
-
Retrieves the image's bits per sample (TIFF tag BitsPerSample) from a given
TIFF IFD.
- getBlankThumbBytes() - Method in class loci.formats.FileStitcher.ExternalSeries
-
- getBlock(int) - Method in class loci.formats.FilePattern
-
Gets the specified file pattern block (e.g., <0-9>).
- getBlock() - Method in class loci.formats.FilePatternBlock
-
Gets the block string.
- getBlock(String) - Method in class loci.formats.in.OIRReader
-
- getBlock(int, String) - Method in class loci.formats.in.ScanrReader
-
- 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(Object) - Method in class loci.formats.gui.SignedColorModel
-
- getBlue(int) - Method in class loci.formats.gui.UnsignedIntColorModel
-
- 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 name as a Boolean.
- getBoolean(String, Boolean) - Method in class loci.formats.in.DynamicMetadataOptions
-
Get the value of property name as 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(SPEReader.SpeHeaderEntry) - Method in class loci.formats.in.SPEReader.SpeHeader
-
Method used to retrieve data values for Byte entries into the SPE header table
- getByte(int) - Method in class loci.formats.in.SPEReader.SpeHeader
-
Private method used to retrieve a Byte value from the SPE header
- getByteBuffer() - Method in class loci.formats.codec.BitBuffer
-
Deprecated.
Return the backin