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A

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.Plane
 
acquire - Variable in class loci.formats.in.ZeissLSMReader.SubBlock
 
acquiredDate - Variable in class loci.formats.in.LIFReader
 
acquiredDate - Variable in class loci.formats.in.ZeissCZIReader
 
acquiredDate - Variable in class loci.formats.in.ZeissLSMReader
 
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.
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
 
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.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
 
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.
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(int, String) - Method in class loci.formats.in.DicomReader
 
addInfo(int, int) - 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.
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.
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.
addSeriesMetaList(String, Object) - Method in class loci.formats.FormatReader
Add the given key/value pair to the current series metadata hashtable.
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.LIFReader
 
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
 
AE - Static variable in class loci.formats.in.DicomReader
 
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
 
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.NativeQTReader
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.LIFReader
 
altPlanes - Variable in class loci.formats.in.NativeQTReader
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.
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.LIFReader.ROI
 
ARTIST - Static variable in class loci.formats.tiff.IFD
 
AS - Static variable in class loci.formats.in.DicomReader
 
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
Gets the given MetadataStore object as a MetadataRetrieve.
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.
asStore(MetadataRetrieve) - Method in interface loci.formats.services.OMEXMLService
Gets the given MetadataRetrieve object as a MetadataStore.
asStore(MetadataRetrieve) - Method in class loci.formats.services.OMEXMLServiceImpl
 
ASTRONOMY_DOMAIN - Static variable in class loci.formats.FormatTools
Identifies the astronomy domain.
AT - Static variable in class loci.formats.in.DicomReader
 
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
 
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

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.NativeND2Reader
 
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.
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
 
bBox - Variable in class loci.formats.services.WlzServiceImpl
 
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_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.out.TiffWriter
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.in.DicomReader
 
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
Deprecated.
Use loci.common.RandomAccessInputStream instead
BitBuffer(byte[]) - Constructor for class loci.formats.codec.BitBuffer
Deprecated.
Default constructor.
bitDepth - Variable in class loci.formats.in.CellSensReader.Pyramid
 
BITMASK_COMPRESSION - Static variable in class loci.formats.in.FlowSightReader
 
bits - Variable in class loci.formats.in.BrukerReader
 
bits - Variable in class loci.formats.in.TargaReader
 
BITS_ALLOCATED - Static variable in class loci.formats.in.DicomReader
 
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.DicomReader
Bits per pixel.
bitsPerPixel - Variable in class loci.formats.in.NativeQTReader
Pixel depth.
bitsPerSample - Variable in class loci.formats.codec.CodecOptions
Number of bits per channel.
BitWriter - Class in loci.formats.codec
Deprecated.
Use loci.common.RandomAccessOutputStream instead
BitWriter() - Constructor for class loci.formats.codec.BitWriter
Deprecated.
Constructs a new bit writer.
BitWriter(int) - Constructor for class loci.formats.codec.BitWriter
Deprecated.
Constructs a new bit writer with the given initial buffer size.
biWriter - Variable in class loci.formats.gui.DataConverter
 
bizarreMultichannelAcquisition - Variable in class loci.formats.in.MetamorphReader
 
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
 
BRIGHT_FIELD - Static variable in class loci.formats.in.LegacyND2Reader
 
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.NativeND2Reader
 
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.
buildTypes() - Static method in class loci.formats.in.DicomReader
Assemble the data dictionary.
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.
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
 
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

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
 
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
 
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.
canDoQT() - Method in class loci.formats.gui.LegacyQTTools
Whether QuickTime is available to this JVM.
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.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.LegacyQTWriter
 
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.out.WlzWriter
 
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
 
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.
canUsePrevious - Variable in class loci.formats.in.NativeQTReader
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
 
cBegin - Variable in class loci.plugins.in.ImporterOptions
 
CCD_SENSITIVITY - Static variable in class loci.formats.in.CellSensReader
 
cChoice - Variable in class loci.formats.gui.DataConverter
 
cChoice - Variable in class loci.plugins.in.SwapDialog
 
cdata - Variable in class loci.formats.in.LeicaSCNReader.LeicaSCNHandler
 
cdata - Variable in class loci.formats.in.ZeissTIFFHandler
 
CELL_LENGTH - Static variable in class loci.formats.tiff.IFD
 
CELL_WIDTH - Static variable in class loci.formats.tiff.IFD
 
CellH5Constants() - Constructor for class loci.formats.in.CellH5Reader.CellH5Constants
 
CellH5Coordinate(String, String, String) - Constructor for class loci.formats.in.CellH5Reader.CellH5Coordinate
 
CellH5PathsToImageData - Variable in class loci.formats.in.CellH5Reader
 
CellH5PositionList - Variable in class loci.formats.in.CellH5Reader
 
CellH5Reader - Class in loci.formats.in
Reader for CellH5 (HDF) files.
CellH5Reader() - Constructor for class loci.formats.in.CellH5Reader
Constructs a new CellH5 HDF reader.
CellH5Reader.CellH5Constants - Class in loci.formats.in
 
CellH5Reader.CellH5Coordinate - Class in loci.formats.in
 
CellH5Writer - Class in loci.formats.out
CellH5Writer is the file format writer for CellH5 format.
CellH5Writer() - Constructor for class loci.formats.out.CellH5Writer
 
CellH5Writer(String, String[]) - Constructor for class loci.formats.out.CellH5Writer
 
cellObjectNames - Variable in class loci.formats.in.BDVReader
 
cellObjectNames - Variable in class loci.formats.in.CellH5Reader
 
cellomicsPattern - Variable in class loci.formats.in.CellomicsReader
 
CellomicsReader - Class in loci.formats.in
Reader for Cellomics C01 files.
CellomicsReader() - Constructor for class loci.formats.in.CellomicsReader
Constructs a new Cellomics reader.
CellomicsReader.ChannelFile - Class in loci.formats.in
 
CellSensReader - Class in loci.formats.in
CellSensReader is the file format reader for cellSens .vsi files.
CellSensReader() - Constructor for class loci.formats.in.CellSensReader
Constructs a new cellSens reader.
CellSensReader.Pyramid - Class in loci.formats.in
 
CellSensReader.TileCoordinate - Class in loci.formats.in
 
CellSensWidgets - Class in loci.plugins.config
Custom widgets for configuring Bio-Formats CellSens .vsi support.
CellSensWidgets() - Constructor for class loci.plugins.config.CellSensWidgets
 
CellVoyagerReader - Class in loci.formats.in
A bioformat reader for the Yokagawa Cellvoyager CV1000 automated microscope ( http://www.yokogawa.com/scanner/products/cv1000e.htm).
CellVoyagerReader() - Constructor for class loci.formats.in.CellVoyagerReader
 
CellVoyagerReader.AreaInfo - Class in loci.formats.in
 
CellVoyagerReader.ChannelInfo - Class in loci.formats.in
 
CellVoyagerReader.FieldInfo - Class in loci.formats.in
 
CellVoyagerReader.WellInfo - Class in loci.formats.in
 
CellWorxReader - Class in loci.formats.in
CellWorxReader is the file format reader for CellWorx .pnl files.
CellWorxReader() - Constructor for class loci.formats.in.CellWorxReader
Constructs a new CellWorx reader.
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.
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.
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
 
changedUpdate(DocumentEvent) - Method in class loci.plugins.config.FlexWidgets
 
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 - 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 - 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() - Constructor for class loci.formats.in.OIRReader.Channel
 
channel - Variable in class loci.formats.in.PrairieMetadata.PFile
channel of this <File>.
channel - Variable in class loci.formats.in.SPCReader
 
Channel() - Constructor for class loci.formats.in.ZeissCZIReader.Channel
 
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
 
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.MicromanagerReader.Position
 
channelColors - Variable in class loci.formats.in.NativeND2Reader
 
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
 
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.
channelMap - Variable in class loci.formats.in.CV7000Reader.MeasurementDataHandler
 
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.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.ZeissLSMReader.DetectionChannel
 
channelNames - Variable in class loci.formats.in.BDReader
 
channelNames - Variable in class loci.formats.in.CellSensReader.Pyramid
 
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.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
 
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.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.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.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
 
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.
checkClassDependency(Class<? extends Object>) - Method in class loci.formats.services.WlzServiceImpl
 
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.LIFReader
 
checkHeader() - Method in class loci.formats.tiff.TiffParser
Checks the TIFF header.
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.
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
 
checkQTLibrary() - Method in class loci.formats.gui.LegacyQTTools
Checks whether QTJava is available, throwing an exception if not.
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.
CHIP_SIZE_X - Static variable in class loci.formats.in.FluoviewReader
 
CHIP_SIZE_Y - Static variable in class loci.formats.in.FluoviewReader
 
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.NativeND2Reader.ChunkMapEntry
 
chunkSize - Variable in class loci.formats.in.OBFReader.State
 
chunkSizes - Variable in class loci.formats.in.NativeQTReader
Number of bytes in each plane.
CI_SERVER - Static variable in class loci.formats.UpgradeChecker
Location of the OME continuous integration server.
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
 
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
 
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.LegacyQTReader
 
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.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.NativeND2Reader
 
close(boolean) - Method in class loci.formats.in.NativeQTReader
 
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.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.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.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.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.WlzReader
 
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.ICSWriter
 
close() - Method in class loci.formats.out.JavaWriter
 
close() - Method in class loci.formats.out.LegacyQTWriter
 
close() - Method in class loci.formats.out.OMETiffWriter
 
close() - Method in class loci.formats.out.OMEXMLWriter
 
close() - Method in class loci.formats.out.PyramidOMETiffWriter
 
close() - Method in class loci.formats.out.QTWriter
 
close() - Method in class loci.formats.out.TiffWriter
 
close() - Method in class loci.formats.out.V3DrawWriter
 
close() - Method in class loci.formats.out.WlzWriter
 
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() - Method in interface loci.formats.services.WlzService
Closes the file.
close() - Method in class loci.formats.services.WlzServiceImpl
 
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
 
closeFileOnly() - Method in class loci.plugins.macro.LociFunctions
 
cm - Variable in class loci.formats.FormatWriter
Default color model.
cNames - Variable in class loci.formats.in.ImprovisionTiffReader
 
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 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.NativeND2Reader
Codec to use when decompressing pixel data.
codec - Variable in class loci.formats.in.NativeQTReader
Video codec used by this movie.
codec - Variable in class loci.formats.out.LegacyQTWriter
The codec to use.
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.
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.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.NativeND2Reader
 
colors - Variable in class loci.formats.in.ND2Handler
 
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.Plane
 
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
 
COLUMNS - Static variable in class loci.formats.in.DicomReader
 
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
 
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(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
 
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
 
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
 
constructLoader() - Static method in class loci.formats.gui.LegacyQTTools
 
constructSliceLabel(int, IFormatReader, IMetadata, int, int, int, int) - Method in class loci.plugins.in.ImagePlusReader
 
CONTAINER_TYPES - Static variable in class loci.formats.in.NativeQTReader
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
 
convert12to16(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
 
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.NativeND2Reader
 
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
Deprecated.
This method is no longer required for sub-resolution support.
coreIndexToSeries(int) - Method in class loci.formats.ImageReader
 
coreIndexToSeries(int) - Method in class loci.formats.ReaderWrapper
 
coreIndexToSeries(int) - Method in class loci.formats.SubResolutionFormatReader
 
coreIndexToSeries(int) - Method in class loci.formats.WrappedReader
 
CoreMetadata - 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 - 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.LIFReader
 
correctUnits(Double, String) - Method in class loci.formats.in.ColumbusReader
 
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
 
countImages() - Method in class loci.formats.in.BaseZeissReader
 
countImages() - Method in class loci.formats.in.ZeissTIFFReader
 
countImages() - Method in class loci.formats.in.ZeissZVIReader
 
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.
createChannelPriorities() - Static method in class loci.formats.in.LIFReader
 
createCodec(boolean) - Method in class loci.formats.in.NativeND2Reader
 
createColorModel() - Method in class loci.plugins.util.ImageProcessorReader
 
createCompatibleWritableRaster(int, int) - Method in class loci.formats.gui.Index16ColorModel
 
createCompatibleWritableRaster(int, int) - Method in class loci.formats.gui.SignedColorModel
 
createCompatibleWritableRaster(int, int) - Method in class loci.formats.gui.UnsignedIntColorModel
 
created - Variable in class loci.formats.out.QTWriter
Time the file was created.
createElectricPotential(Double, Unit<ElectricPotential>) - Static method in class loci.formats.FormatTools
 
createElectricPotential(Integer, Unit<ElectricPotential>) - Static method in class loci.formats.FormatTools
 
createElectricPotential(T, Unit<ElectricPotential>) - Static method in class loci.formats.FormatTools
 
createFileInfo() - Method in class loci.plugins.in.ImagePlusReader
 
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_TAG - Static variable in class loci.formats.in.ImaconReader
 
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 - Static variable in class loci.formats.in.DicomReader
 
CS_2C - Static variable in class loci.formats.gui.TwoChannelColorSpace
 
cScroll - Variable in class loci.plugins.util.DataBrowser
 
cSlider - Variable in class loci.formats.gui.ImageViewer
 
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
 
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
 
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.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.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.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>.
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

d(String) - Method in class loci.formats.in.PrairieMetadata
Converts the given string to a Double, or null if incompatible.
DA - Static variable in class loci.formats.in.DicomReader
 
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
 
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.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
Deprecated.
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
 
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.
decodeToMemoryGray16(short[], int, int, int, int, int, int, int, int, int, int) - Method in interface loci.formats.services.LuraWaveService
Wraps lwfDecoder.decodeToMemoryGray16(short[], int, int, int, int, int, int, int, int, int, int).
decodeToMemoryGray16(short[], int, int, int, int, int, int, int, int, int, int) - Method in class loci.formats.services.LuraWaveServiceImpl
 
decodeToMemoryGray8(byte[], int, int, int) - Method in interface loci.formats.services.LuraWaveService
Wraps lwfDecoder.decodeToMemoryGray8(byte[], int, int, int).
decodeToMemoryGray8(byte[], int, int, int) - Method in class loci.formats.services.LuraWaveServiceImpl
 
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
The CodecOptions parameter should have the following fields set: maxBytes interleaved bitsPerSample littleEndian width height
decompress(RandomAccessInputStream, CodecOptions) - Method in class loci.formats.codec.NikonCodec
The CodecOptions parameter must be an instance of NikonCodecOptions, and should have the following fields set: lossless vPredictor curve split bitsPerSample maxBytes width height
decompress(RandomAccessInputStream, CodecOptions) - Method in class loci.formats.codec.TargaRLECodec
The CodecOptions parameter should have the following fields set: maxBytes CodecOptions.bitsPerSample
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[]) - 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 value for Memoizer.minimumElapsed if none is provided in the constructor.
DEFAULT_PIXEL_TYPE - Static variable in class loci.formats.in.FakeReader
 
DEFAULT_RANGE - Static variable in class loci.formats.cache.CacheStrategy
Default cache range.
DEFAULT_RESOLUTION_SCALE - Static variable in class loci.formats.in.FakeReader
 
DEFAULT_RGB_CHANNEL_COUNT - Static variable in class loci.formats.in.FakeReader
 
DEFAULT_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
Default implementation of MetadataOptions.
DefaultMetadataOptions() - Constructor for class loci.formats.in.DefaultMetadataOptions
Construct a new DefaultMetadataOptions.
DefaultMetadataOptions(MetadataLevel) - Constructor for class loci.formats.in.DefaultMetadataOptions
Construct a new DefaultMetadataOptions.
defaultMinMax(int) - Static method in class loci.formats.FormatTools
Get the default range for the specified pixel type.
defaultValue - Variable in class loci.plugins.prefs.BooleanOption
The option's default value.
defaultValue - Variable in class loci.plugins.prefs.DoubleOption
The option's default value.
defaultValue - Variable in class loci.plugins.prefs.StringOption
The option's default value.
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
 
delegate - Variable in class loci.formats.services.LuraWaveServiceImpl
LuraWave decoder delegate.
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.
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 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
 
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.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.LIFReader
 
detectorOffset - Variable in class loci.formats.in.BaseZeissReader
 
detectorOffset - Variable in class loci.formats.in.OpenlabReader
 
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
 
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.
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(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_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
 
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_STRING - Static variable in class loci.formats.in.KodakReader
 
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.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.
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
 
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
 
documentUpdate() - Method in class loci.plugins.config.FlexWidgets
 
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.
DS - Static variable in class loci.formats.in.DicomReader
 
DT - Static variable in class loci.formats.in.DicomReader
 
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
 
duplicateRecurse(Class<? extends IFormatReader>) - Method in class loci.formats.ReaderWrapper
 
duplicateRecurse(Class<? extends IFormatWriter>) - Method in class loci.formats.WriterWrapper
 
DV_MAGIC_BYTES_1 - Static variable in class loci.formats.in.DeltavisionReader
 
DV_MAGIC_BYTES_2 - Static variable in class loci.formats.in.DeltavisionReader
 
DVExtHdrFields(RandomAccessInputStream) - Constructor for class loci.formats.in.DeltavisionReader.DVExtHdrFields
 
DWORD - Static variable in class loci.formats.in.CellSensReader
 
dyeName - Variable in class loci.formats.in.FV1000Reader.ChannelData
 
dyeName - Variable in class loci.formats.in.LeicaHandler.MultiBand
 
dyeNames - Variable in class loci.formats.in.SVSReader
 
dyes - Variable in class loci.formats.in.ND2Handler
 
DYNAMIC_PROPERTIES - Static variable in class loci.formats.in.CellSensReader
 
DynamicMetadataOptions - Class in loci.formats.in
Configuration object for readers and writers.
DynamicMetadataOptions() - Constructor for class loci.formats.in.DynamicMetadataOptions
Creates an options object with metadata level set to DynamicMetadataOptions.METADATA_LEVEL_DEFAULT and file validation set to DynamicMetadataOptions.READER_VALIDATE_DEFAULT.
DynamicMetadataOptions(MetadataLevel) - Constructor for class loci.formats.in.DynamicMetadataOptions
Creates an options object with metadata level set to the specified value and file validation set to DynamicMetadataOptions.READER_VALIDATE_DEFAULT

E

ealDE - Variable in class loci.formats.in.SDTInfo
 
ECAT7_MAGIC - Static variable in class loci.formats.in.Ecat7Reader
 
ECAT7_MAGIC_REGEX - Static variable in class loci.formats.in.Ecat7Reader
 
Ecat7Reader - Class in loci.formats.in
Ecat7Reader is the file format reader for ECAT 7 files.
Ecat7Reader() - Constructor for class loci.formats.in.Ecat7Reader
Constructs a new ECAT7 reader.
EditTiffG - Class in loci.formats.tools
Provides a GUI for editing TIFF file comments.
EditTiffG() - Constructor for class loci.formats.tools.EditTiffG
 
effectiveFieldCount - Variable in class loci.formats.in.FlexReader
 
EFI_HEIGHT_MAP - Static variable in class loci.formats.in.CellSensReader
 
EFI_SHARPNESS_MAP - Static variable in class loci.formats.in.CellSensReader
 
EFI_STACK - Static variable in class loci.formats.in.CellSensReader
 
EFI_TEXTURE_MAP - Static variable in class loci.formats.in.CellSensReader
 
el(NodeList, int) - Method in class loci.formats.in.PrairieMetadata
Gets the indexth element from the given list of nodes.
ELEMENT_STYLE_END - Static variable in class loci.formats.gui.XMLCellRenderer
 
ELEMENT_STYLE_START - Static variable in class loci.formats.gui.XMLCellRenderer
 
elementLength - Variable in class loci.formats.in.DicomReader
 
elementName - Variable in class loci.formats.in.LeicaHandler
 
elements - Variable in class loci.formats.FilePatternBlock
Elements within this block, e.g.
ELLIPSE - Static variable in class loci.formats.in.FV1000Reader
 
ELLIPSE - Static variable in class loci.formats.in.GatanReader
 
ELLIPSE - Static variable in class loci.formats.in.ZeissLSMReader
 
ellipses - Variable in class loci.formats.in.FakeReader
 
EM_DAC - Static variable in class loci.formats.in.FluoviewReader
 
EM_DOMAIN - Static variable in class loci.formats.FormatTools
Identifies the electron microscopy domain.
EM_GAIN - Static variable in class loci.formats.in.CellSensReader
 
EMBEDDED_STREAM - Static variable in class loci.formats.in.VolocityReader
 
embeddedImages - Variable in class loci.formats.in.TillVisionReader
 
embeddedOffset - Variable in class loci.formats.in.TillVisionReader
 
emFilters - Variable in class loci.formats.in.InCellReader
 
emission - Variable in class loci.formats.in.FlexReader.FilterGroup
 
emission - Variable in class loci.formats.in.OIRReader.Channel
 
emission - Variable in class loci.formats.in.ZeissCZIReader.Channel
 
emissionFilter - Variable in class loci.formats.in.FV1000Reader.ChannelData
 
emissionWavelength - Variable in class loci.formats.in.SVSReader
 
EMPTY_STRING - Static variable in class loci.formats.in.IM3Reader
 
emWave - Variable in class loci.formats.in.BDReader
 
emWave - Variable in class loci.formats.in.FV1000Reader.ChannelData
 
emWave - Variable in class loci.formats.in.ImarisHDFReader
 
emWave - Variable in class loci.formats.in.ND2Handler
 
emWave - Variable in class loci.formats.in.NikonTiffReader
 
emWavelen - Variable in class loci.formats.in.DeltavisionReader.DVExtHdrFields
Emission filter wavelength.
emWavelength - Variable in class loci.formats.in.BaseZeissReader
 
emWavelength - Variable in class loci.formats.in.ColumbusReader.Plane
 
emWavelength - Variable in class loci.formats.in.MetamorphReader
The TIFF's emWavelength
emWavelength - Variable in class loci.formats.in.OperettaReader.Plane
 
emWaves - Variable in class loci.formats.in.InCellReader
 
emWaves - Variable in class loci.formats.in.LeicaReader
 
enabledBox - Variable in class loci.plugins.config.ConfigWindow
 
encodeYUV(byte[], int) - Method in class org.libjpegturbo.turbojpeg.TJCompressor
Encode the uncompressed source image associated with this compressor instance and output a YUV planar image to the given destination buffer.
encodeYUV(int) - Method in class org.libjpegturbo.turbojpeg.TJCompressor
Encode the uncompressed source image associated with this compressor instance and return a buffer containing a YUV planar image.
encodeYUV(BufferedImage, byte[], int) - Method in class org.libjpegturbo.turbojpeg.TJCompressor
Encode the uncompressed source image stored in srcImage and output a YUV planar image to the given destination buffer.
encodeYUV(BufferedImage, int) - Method in class org.libjpegturbo.turbojpeg.TJCompressor
Encode the uncompressed source image stored in srcImage and return a buffer containing a YUV planar image.
encodeYUV(byte[], int, int, int, int, byte[], int, int) - Method in class org.libjpegturbo.turbojpeg.TJCompressor
 
encodeYUV(int[], int, int, int, int, byte[], int, int) - Method in class org.libjpegturbo.turbojpeg.TJCompressor
 
ENCODING - Static variable in class loci.formats.in.LIFReader
The encoding used in this file.
encoding - Variable in class loci.formats.in.NRRDReader
Data encoding.
end - Variable in class loci.formats.FilePatternBlock
 
END - Static variable in class loci.formats.in.GIFReader
 
end - Variable in class loci.formats.Modulo
 
endDocument() - Method in class loci.formats.in.BDVReader.BDVXMLHandler
 
endDocument() - Method in class loci.formats.in.ND2Handler
 
endDocument() - Method in class loci.formats.in.OMEXMLReader.OMEXMLHandler
 
endElement(String, String, String) - Method in class loci.formats.in.BDVReader.BDVXMLHandler
 
endElement(String, String, String) - Method in class loci.formats.in.BioRadSCNReader.SCNHandler
 
endElement(String, String, String) - Method in class loci.formats.in.ColumbusReader.MeasurementHandler
 
endElement(String, String, String) - Method in class loci.formats.in.CV7000Reader.MeasurementDataHandler
 
endElement(String, String, String) - Method in class loci.formats.in.CV7000Reader.MeasurementSettingsHandler
 
endElement(String, String, String) - Method in class loci.formats.in.FEITiffReader.FEIHandler
 
endElement(String, String, String) - Method in class loci.formats.in.FlexReader.FlexHandler
 
endElement(String, String, String) - Method in class loci.formats.in.InCellReader.InCellHandler
 
endElement(String, String, String) - Method in class loci.formats.in.InCellReader.MinimalInCellHandler
 
endElement(String, String, String) - Method in class loci.formats.in.IvisionReader.IvisionHandler
 
endElement(String, String, String) - Method in class loci.formats.in.LeicaHandler
 
endElement(String, String, String) - Method in class loci.formats.in.LeicaSCNReader.LeicaSCNHandler
 
endElement(String, String, String, Attributes) - Method in class loci.formats.in.ND2Handler
 
endElement(String, String, String) - Method in class loci.formats.in.OMEXMLReader.OMEXMLHandler
 
endElement(String, String, String) - Method in class loci.formats.in.OperettaReader.OperettaHandler
 
endElement(String, String, String) - Method in class loci.formats.in.ScanrReader.ScanrHandler
 
endElement(String, String, String) - Method in class loci.formats.in.ZeissTIFFHandler
 
endElement(String, String, String) - Method in class loci.formats.out.OMEXMLWriter.OMEHandler
 
ENDIANNESS_OFFSET - Static variable in class loci.formats.in.MRCReader
 
endIndex - Variable in class loci.formats.FilePattern
Indices into the pattern indicating the end of a numerical block.
endOfFrameFlag - Variable in class loci.formats.in.SPCReader
 
endOfFrameList - Variable in class loci.formats.in.SPCReader
 
endPointer - Variable in class loci.formats.in.LIFReader
 
endPos - Variable in class loci.formats.out.AVIWriter
 
endTime - Variable in class loci.formats.in.CV7000Reader
 
endTime - Variable in class loci.formats.in.SDTInfo
Macro time of the last photon.
endX - Variable in class loci.formats.in.SPEReader.SpeROI
 
endY - Variable in class loci.formats.in.SPEReader.SpeROI
 
energyConvFactor - Variable in class loci.formats.in.DeltavisionReader.DVExtHdrFields
Energy conversion factor.
ENHANCED_DYNAMIC_RANGE - Static variable in class loci.formats.in.CellSensReader
 
ensureNonExisting(String) - Method in class loci.formats.tools.MakeTestOmeTiff
 
entries - Variable in class loci.formats.in.ZeissCZIReader.AttachmentDirectory
 
entries - Variable in class loci.formats.in.ZeissCZIReader.Directory
 
entryName - Variable in class loci.formats.in.ZipReader
 
entryToString(Object, String) - Static method in class loci.formats.tools.AmiraParameters
 
ENV_SUFFIX - Static variable in class loci.formats.in.PrairieReader
 
envFile - Variable in class loci.formats.in.PrairieReader
The associated XML files.
EOI - Static variable in class loci.formats.services.JPEGTurboServiceImpl
 
EPSReader - Class in loci.formats.in
Reader is the file format reader for Encapsulated PostScript (EPS) files.
EPSReader() - Constructor for class loci.formats.in.EPSReader
Constructs a new EPS reader.
EPSWriter - Class in loci.formats.out
EPSWriter is the file format writer for Encapsulated PostScript (EPS) files.
EPSWriter() - Constructor for class loci.formats.out.EPSWriter
 
epxDiv - Variable in class loci.formats.in.SDTInfo
 
equal(Length, Length) - Static method in class loci.formats.in.PrairieReader
Determines whether the two Length values are equal.
equalReaders(IFormatReader, IFormatReader) - Static method in class loci.formats.FormatTools
Check if the two given readers are equal.
equals(Object) - Method in class loci.formats.in.CellSensReader.TileCoordinate
 
equals(Object) - Method in class loci.formats.in.MetamorphTiffReader.Well
 
equals(Object) - Method in class loci.formats.in.ZeissCZIReader.Coordinate
 
equals(Node, Node) - Method in class loci.formats.services.OMEXMLServiceImpl
Compares two Elements for equality.
equals(Object) - Method in class loci.formats.tiff.TiffRational
Indicates whether some other object is "equal to" this one.
equals(Object) - Method in class loci.formats.TileStitcher.TileCoordinate
 
equals(Object) - Method in class loci.plugins.config.FormatEntry
 
equals(Object) - Method in class loci.plugins.prefs.OptionsList
 
equals(TJScalingFactor) - Method in class org.libjpegturbo.turbojpeg.TJScalingFactor
Returns true or false, depending on whether this instance and other have the same numerator and denominator.
equalStrips - Variable in class loci.formats.in.MinimalTiffReader
 
equalStrips - Variable in class loci.formats.tiff.TiffParser
 
erode() - Method in class loci.plugins.util.RecordedImageProcessor
 
evalFile(String) - Method in class loci.formats.in.ZeissTIFFReader
Evaluate the metadata of a TIFF/XML file collection, and return this to the user.
excitation - Variable in class loci.formats.in.CV7000Reader.Channel
 
excitation - Variable in class loci.formats.in.FlexReader.FilterGroup
 
excitation - Variable in class loci.formats.in.OIRReader.Channel
 
excitation - Variable in class loci.formats.in.ZeissCZIReader.Channel
 
excitationFilter - Variable in class loci.formats.in.FV1000Reader.ChannelData
 
excitationWavelength - Variable in class loci.formats.in.SVSReader
 
exclude - Variable in class loci.formats.in.InCellReader
 
execute() - Method in class loci.plugins.in.ImportProcess
Performs the import preparation process, notifying status listeners at each step.
exFilters - Variable in class loci.formats.in.InCellReader
 
EXIF - Static variable in class loci.formats.tiff.IFD
 
EXIF_VERSION - Static variable in class loci.formats.tiff.IFD
 
EXIFService - Interface in loci.formats.services
 
EXIFServiceImpl - Class in loci.formats.services
 
EXIFServiceImpl() - Constructor for class loci.formats.services.EXIFServiceImpl
 
exists - Variable in class loci.formats.in.OMETiffReader.OMETiffPlane
Whether or not the file meant to contain this plane exists.
exists(String) - Method in interface loci.formats.services.JHDFService
Checks if path in HDF5 file exists.
exists(String) - Method in class loci.formats.services.JHDFServiceImpl
 
exit() - Method in class loci.formats.tools.EditTiffG
 
exp() - Method in class loci.plugins.util.RecordedImageProcessor
 
expandPixels(int, byte[], byte[], int) - Method in class loci.formats.in.PictReader
Expand an array of bytes.
EXPANSION_TABLE - Static variable in class loci.formats.in.PictReader
Table used in expanding pixels that use less than 8 bits.
expectETS - Variable in class loci.formats.in.CellSensReader
 
EXPERIMENT - Static variable in class loci.formats.in.LeicaReader
 
EXPERIMENT_FILE - Static variable in class loci.formats.in.BDReader
 
EXPERIMENT_FILE - Static variable in class loci.formats.in.ScanrReader
 
experimenterName - Variable in class loci.formats.in.ImaconReader
 
EXPIRED_QT_MSG - Static variable in class loci.formats.gui.LegacyQTTools
 
expiredQT - Variable in class loci.formats.gui.LegacyQTTools
Flag indicating QuickTime for Java has expired.
explode() - Method in class loci.formats.FilePatternBlock
 
exporter - Variable in class loci.plugins.LociExporter
 
Exporter - Class in loci.plugins.out
Core logic for the Bio-Formats Exporter ImageJ plugin.
Exporter(LociExporter, ImagePlus) - Constructor for class loci.plugins.out.Exporter
 
exposure - Variable in class loci.formats.in.BDReader
 
exposure - Variable in class loci.formats.in.InCellReader.Image
 
exposure - Variable in class loci.formats.in.InCellReader.InCellHandler
 
exposure - Variable in class loci.formats.in.ZeissCZIReader.Channel
 
EXPOSURE_BIAS_VALUE - Static variable in class loci.formats.tiff.IFD
 
EXPOSURE_INDEX - Static variable in class loci.formats.tiff.IFD
 
EXPOSURE_METERING_MODE - Static variable in class loci.formats.in.CellSensReader
 
EXPOSURE_MODE - Static variable in class loci.formats.tiff.IFD
 
EXPOSURE_PROGRAM - Static variable in class loci.formats.tiff.IFD
 
EXPOSURE_RATIO - Static variable in class loci.formats.in.NDPIReader
 
EXPOSURE_TIME - Static variable in class loci.formats.in.CellSensReader
 
EXPOSURE_TIME - Static variable in class loci.formats.in.FluoviewReader
 
EXPOSURE_TIME - Static variable in class loci.formats.in.NDPIReader
 
EXPOSURE_TIME - Static variable in class loci.formats.tiff.IFD
EXIF tags.
exposures - Variable in class loci.formats.in.MetamorphHandler
 
exposures - Variable in class loci.formats.in.ScanrReader
 
exposureScale - Variable in class loci.formats.in.SVSReader
 
exposureTime - Variable in class loci.formats.in.BaseZeissReader
 
exposureTime - Variable in class loci.formats.in.BioRadSCNReader
 
exposureTime - Variable in class loci.formats.in.CV7000Reader.Channel
 
exposureTime - Variable in class loci.formats.in.FakeReader
exposure time per plane info
exposureTime - Variable in class loci.formats.in.FluoviewReader
 
exposureTime - Variable in class loci.formats.in.IvisionReader
 
exposureTime - Variable in class loci.formats.in.LeicaReader
 
exposureTime - Variable in class loci.formats.in.LiFlimReader
 
exposureTime - Variable in class loci.formats.in.MetamorphReader
 
exposureTime - Variable in class loci.formats.in.MicroCTReader
 
exposureTime - Variable in class loci.formats.in.MicromanagerReader.Position
 
exposureTime - Variable in class loci.formats.in.NativeND2Reader
 
exposureTime - Variable in class loci.formats.in.ND2Handler
 
exposureTime - Variable in class loci.formats.in.OperettaReader.Plane
 
exposureTime - Variable in class loci.formats.in.SVSReader
 
exposureTime - Variable in class loci.formats.in.ZeissCZIReader.SubBlock
 
exposureTimes - Variable in class loci.formats.in.CellSensReader.Pyramid
 
exposureTimes - Variable in class loci.formats.in.SimplePCITiffReader
 
exposureTimes - Variable in class loci.formats.in.TillVisionReader
 
exposureTimeUnit - Variable in class loci.formats.in.LiFlimReader
 
expTime - Variable in class loci.formats.in.DeltavisionReader.DVExtHdrFields
Exposure time in seconds.
expTimes - Variable in class loci.formats.in.LIFReader
 
extCount - Variable in class loci.formats.in.PerkinElmerReader
 
EXTENSION - Static variable in class loci.formats.in.GIFReader
 
ExtensionFileFilter - Class in loci.formats.gui
A file filter based on file extensions, for use with a JFileChooser.
ExtensionFileFilter(String, String) - Constructor for class loci.formats.gui.ExtensionFileFilter
Constructs a new filter that accepts the given extension.
ExtensionFileFilter(String[], String) - Constructor for class loci.formats.gui.ExtensionFileFilter
Constructs a new filter that accepts the given extensions.
extensions - Variable in class loci.plugins.config.ConfigWindow
 
extensions - Variable in class loci.plugins.macro.MacroFunctions
 
EXTERNAL_DATA_VOLUME - Static variable in class loci.formats.in.CellSensReader
 
EXTERNAL_FILE_PROPERTIES - Static variable in class loci.formats.in.CellSensReader
 
externals - Variable in class loci.formats.FileStitcher
 
ExternalSeries(FilePattern) - Constructor for class loci.formats.FileStitcher.ExternalSeries
 
extHdrFields - Variable in class loci.formats.in.DeltavisionReader
Initialize an array of Extended Header Field structures.
extHeaderSize - Variable in class loci.formats.in.MRCReader
Size of extended header
extIndex - Variable in class loci.formats.in.PerkinElmerReader.PixelsFile
 
EXTRA_FILES - Static variable in class loci.formats.in.VectraReader
 
EXTRA_IMAGES - Static variable in class loci.formats.in.AFIReader
 
EXTRA_SAMPLES - Static variable in class loci.formats.in.CellSensReader
 
EXTRA_SAMPLES - Static variable in class loci.formats.tiff.IFD
 
EXTRA_SAMPLES_PROPERTIES - Static variable in class loci.formats.in.CellSensReader
 
EXTRA_TAG_1 - Static variable in class loci.formats.in.VentanaReader
 
EXTRA_TAG_2 - Static variable in class loci.formats.in.VentanaReader
 
extractCoreMetaData() - Method in class loci.formats.tools.AmiraParameters
 
extractTokensFromFakeSeries(String) - Method in class loci.formats.in.FakeReader
 
extraFiles - Variable in class loci.formats.in.CV7000Reader
 
extraFiles - Variable in class loci.formats.in.VolocityReader
 
extraImages - Variable in class loci.formats.in.ZeissCZIReader
 
extras - Variable in class loci.formats.in.LeicaHandler
 
exts - Variable in class loci.formats.gui.ExtensionFileFilter
List of valid extensions.
extSize - Variable in class loci.formats.in.DeltavisionReader
Size of extended header.
exWave - Variable in class loci.formats.in.BDReader
 
exWave - Variable in class loci.formats.in.FV1000Reader.ChannelData
 
exWave - Variable in class loci.formats.in.ImarisHDFReader
 
exWave - Variable in class loci.formats.in.LeicaHandler.Channel
 
exWave - Variable in class loci.formats.in.ND2Handler
 
exWave - Variable in class loci.formats.in.NikonTiffReader
 
exWavelen - Variable in class loci.formats.in.DeltavisionReader.DVExtHdrFields
Excitation filter wavelength.
exWavelength - Variable in class loci.formats.in.BaseZeissReader
 
exWavelength - Variable in class loci.formats.in.ColumbusReader.Plane
 
exWavelength - Variable in class loci.formats.in.OperettaReader.Plane
 
exWaves - Variable in class loci.formats.in.InCellReader
 
exWaves - Variable in class loci.formats.in.LeicaReader
 
exWaves - Variable in class loci.formats.in.LIFReader
 

F

F_KEY - Static variable in class loci.formats.in.LiFlimReader
 
F_NUMBER - Static variable in class loci.formats.tiff.IFD
 
factor - Variable in class loci.formats.in.ZeissTIFFHandler.Scaling.Dimension
 
factors - Variable in class loci.formats.in.FlexReader.FlexFile
 
factors - Variable in class loci.formats.in.FlexReader.FlexHandler
 
factory - Variable in class loci.formats.FormatReader
 
FAIL_ON_MISSING_DEFAULT - Static variable in class loci.formats.in.CellSensReader
 
FAIL_ON_MISSING_KEY - Static variable in class loci.formats.in.CellSensReader
 
failOnMissingETS() - Method in class loci.formats.in.CellSensReader
 
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
 
FD - Static variable in class loci.formats.in.DicomReader
 
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 - 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 - 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.NativeND2Reader
 
FieldInfo() - Constructor for class loci.formats.in.CellVoyagerReader.FieldInfo
 
fieldMap - Variable in class loci.formats.in.CellWorxReader
 
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.LIFReader
 
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.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.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
 
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.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.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.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.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.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
 
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
 
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.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.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
 
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.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
 
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
 
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(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
 
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
 
findPixelsOffset(int) - Method in class loci.formats.in.VisitechReader
 
findRootNode(Node) - Method in class loci.formats.services.OMEXMLServiceImpl
Return the absolute root node for the specified child node.
findSeriesPatterns(String) - Static method in class loci.formats.FilePattern
Works like FilePattern.findSeriesPatterns(String, String, String[]), but dir and nameList are inferred from the given file's absolute path.
findSeriesPatterns(String, String, String[]) - Static method in class loci.formats.FilePattern
Similar to FilePattern.findPattern(String, String, String[]), but this does not merge series indices into a pattern block.
findString(String) - Method in class loci.formats.in.KodakReader
 
findTIFFs() - Method in class loci.formats.in.MetamorphTiffReader
 
findXML(String) - Static method in class loci.formats.in.ColumbusReader
 
findZipEntries() - Method in class loci.formats.in.ZipReader
 
finish(ImportProcess) - Method in class loci.plugins.in.Importer
 
finishTime - Variable in class loci.formats.in.PerkinElmerReader
 
finishTiming() - Method in class loci.plugins.in.ImagePlusReader
 
FIRMWARE_VERSION - Static variable in class loci.formats.in.NDPIReader
 
FIRMWARE_VERSION - Static variable in class loci.formats.in.NikonReader
 
firstAvailable(int...) - Method in class loci.plugins.in.SwapDialog
 
firstDataStream - Variable in class loci.formats.tools.AmiraParameters
 
firstFile - Variable in class loci.formats.in.PrairieMetadata.Frame
The first actual <File> element for this <Frame>.
firstFrame - Variable in class loci.formats.in.PrairieMetadata.Sequence
The first actual <Frame> element for this <Sequence>.
firstIFD - Variable in class loci.formats.tiff.TiffParser
Cached first IFD in the current file.
firstIndex - Variable in class loci.formats.in.PerkinElmerReader.PixelsFile
 
firstSequence - Variable in class loci.formats.in.PrairieMetadata
The first actual <Sequence> element.
firstSeriesChannels - Variable in class loci.formats.in.MetamorphReader
 
firstStamp - Variable in class loci.formats.in.LeicaHandler
 
firstTimeLoop - Variable in class loci.formats.in.ND2Handler
 
firstTimepoint - Variable in class loci.formats.in.BDVReader
 
firstWellPlanes() - Method in class loci.formats.in.FlexReader
Returns the number of planes in the first well that has data.
fis - Variable in class loci.formats.Memoizer.KryoDeser
 
FitsReader - Class in loci.formats.in
FitsReader is the file format reader for Flexible Image Transport System (FITS) images.
FitsReader() - Constructor for class loci.formats.in.FitsReader
Constructs a new FitsReader.
fixed - Variable in class loci.formats.FilePatternBlock
Whether or not this is a fixed-width block.
FL - Static variable in class loci.formats.in.DicomReader
 
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
Call FormatReader.updateMetadataLists(Hashtable) on all metadata hashtables.
flattenHashtables() - Method in class loci.formats.SubResolutionFormatReader
Call FormatReader.updateMetadataLists(Hashtable) on all metadata hashtables.
flbckX - Variable in class loci.formats.in.SDTInfo
 
flbckY - Variable in class loci.formats.in.SDTInfo
 
FLEX - 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.
FlexWidgets - Class in loci.plugins.config
Custom widgets for configuring Bio-Formats Flex support.
FlexWidgets() - Constructor for class loci.plugins.config.FlexWidgets
 
FLIM_DOMAIN - Static variable in class loci.formats.FormatTools
Identifies the fluorescence-lifetime domain.
flip - Variable in class loci.formats.in.NativeQTReader
 
flipHorizontal() - Method in class loci.plugins.util.RecordedImageProcessor
 
flipVertical() - Method in class loci.plugins.util.RecordedImageProcessor
 
flipX - Variable in class loci.formats.in.LIFReader
 
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.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
 
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.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.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.NativeQTReader
 
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) - Method in class loci.formats.in.DicomReader
 
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
 
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(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
 

G

gain - Variable in class loci.formats.in.BDReader
 
gain - Variable in class loci.formats.in.BioRadReader
 
gain - Variable in class loci.formats.in.BioRadSCNReader
 
gain - Variable in class loci.formats.in.CellSensReader.Pyramid
 
gain - Variable in class loci.formats.in.FV1000Reader.ChannelData
 
gain - Variable in class loci.formats.in.ImarisHDFReader
 
gain - Variable in class loci.formats.in.InCellReader
 
gain - Variable in class loci.formats.in.IvisionReader
 
gain - Variable in class loci.formats.in.LeicaHandler.Channel
 
gain - Variable in class loci.formats.in.MetamorphHandler
 
gain - Variable in class loci.formats.in.MetamorphReader
 
gain - Variable in class loci.formats.in.MicromanagerReader.Position
 
gain - Variable in class loci.formats.in.ND2Handler
 
gain - Variable in class loci.formats.in.NikonTiffReader
 
gain - Variable in class loci.formats.in.OIRReader.Detector
 
gain - Variable in class loci.formats.in.OpenlabReader
 
gain - Variable in class loci.formats.in.ZeissCZIReader.Channel
 
gain - Variable in class loci.formats.in.ZeissCZIReader
 
gain - Variable in class loci.formats.in.ZeissLSMReader.DetectionChannel
 
GAIN_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.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.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.MIASReader
 
get16BitLookupTable() - Method in class loci.formats.in.MinimalTiffReader
 
get16BitLookupTable() - Method in class loci.formats.in.NativeND2Reader
 
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.MIASReader
 
get8BitLookupTable() - Method in class loci.formats.in.MinimalTiffReader
 
get8BitLookupTable() - Method in class loci.formats.in.NativeND2Reader
 
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
 
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
 
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
 
getAxisCount(int) - Method in class loci.formats.AxisGuesser
Gets the number of axes in the pattern of the given type.
getAxisCountC() - Method in class loci.formats.AxisGuesser
Gets the number of C axes in the pattern.
getAxisCountS() - Method in class loci.formats.AxisGuesser
Gets the number of S axes in the pattern.
getAxisCountT() - Method in class loci.formats.AxisGuesser
Gets the number of T axes in the pattern.
getAxisCountZ() - Method in class loci.formats.AxisGuesser
Gets the number of Z axes in the pattern.
getAxisGuesser() - Method in class loci.formats.FileStitcher.ExternalSeries
 
getAxisGuesser() - Method in class loci.formats.FileStitcher
Gets the axis guesser object used to guess which dimensional axes are which.
getAxisType(String) - Static method in class loci.formats.AxisGuesser
Convert the given label to an axis type.
getAxisTypes() - Method in class loci.formats.AxisGuesser
Gets the guessed axis type for each dimensional block.
getAxisTypes() - Method in class loci.formats.FileStitcher
Gets the axis type for each dimensional block.
getBackgroundValue() - Method in class loci.plugins.util.RecordedImageProcessor
 
getBaseReader() - Method in class loci.plugins.in.ImportProcess
Valid only after ImportStep.READER.
getBestIndex(Color) - Method in class loci.plugins.util.RecordedImageProcessor
 
getBGRComponents(short[]) - Method in class loci.formats.services.JPEGXRServiceImpl
 
getBinaryOnlyOMEXML(String, String, String) - Method in class loci.formats.out.OMETiffWriter
 
getBinning(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.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(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 backing byte array.
getBytes(BufferedImage) - Static method in class loci.formats.gui.AWTImageTools
Extracts pixel data as arrays of unsigned bytes, one per channel.
getBytes(WritableRaster) - Static method in class loci.formats.gui.AWTImageTools
Extracts pixel data as arrays of unsigned bytes, one per channel.
getBytes(WritableRaster, int, int, int, int) - Static method in class loci.formats.gui.AWTImageTools
Extracts pixel data as arrays of unsigned bytes, one per channel.
getBytes(BufferedImage, boolean) - Static method in class loci.formats.gui.AWTImageTools
Get the bytes from an image, merging the channels as necessary.
getBytesPerElement() - Method in enum loci.formats.tiff.IFDType
Retrieves the number of bytes per element.
getBytesPerPixel(int) - Static method in class loci.formats.FormatTools
Retrieves how many bytes per pixel the current plane or section has.
getBytesPerPixel(String) - Static method in class loci.formats.FormatTools
Retrieves the number of bytes per pixel in the current plane.
getBytesPerPixel(int) - Method in class loci.formats.in.LegacyND2Reader
 
getBytesPerSample() - Method in class loci.formats.tiff.IFD
Retrieves the image's bytes per sample (derived from tag BitsPerSample) from this IFD.
getC() - Method in class loci.formats.gui.ImageViewer
Gets the C value of the currently displayed image.
getCache() - Method in class loci.formats.gui.CacheComponent
 
getCache() - Method in class loci.plugins.util.BFVirtualStack
 
getCacheListeners() - Method in class loci.formats.cache.Cache
 
getCacheListeners() - Method in interface loci.formats.cache.CacheReporter
Gets a list of all registered status update listeners.
getCacheListeners() - Method in class loci.formats.cache.CacheStrategy
 
getCalibrationTable() - Method in class loci.plugins.util.RecordedImageProcessor
 
getCameraModel() - Method in class loci.formats.in.ND2Handler
 
getCaptureMode(int) - Method in class loci.formats.in.NDPIReader
Get the description of the given capture mode.
getCategory() - Method in class loci.formats.in.BaseZeissReader.Tag
 
getCBegin(int) - Method in class loci.plugins.in.ImporterOptions
 
getCBegin(int) - Method in class loci.plugins.in.ImportProcess
 
getCCount(int) - Method in class loci.plugins.in.ImportProcess
Valid only after ImportStep.SERIES.
getCEnd(int) - Method in class loci.plugins.in.ImporterOptions
 
getCEnd(int) - Method in class loci.plugins.in.ImportProcess
Valid only after ImportStep.STACK.
getChannel(String) - Method in class loci.formats.in.CellomicsReader
 
getChannel() - Method in class loci.formats.in.PrairieMetadata.PFile
Gets the channel associated with this File.
getChannelColor(int) - Method in class loci.formats.in.LIFReader
 
getChannelColorFromFile(String) - Method in class loci.formats.in.MIASReader
Get the color associated with the given file's channel.
getChannelColors() - Method in class loci.formats.in.ND2Handler
 
getChannelCount() - Method in class loci.formats.in.SDTReader
Gets the number of spectral channels.
getChannelDescriptionNodes(Element) - Method in class loci.formats.in.LIFReader
 
getChannelDimCount(Double[]) - Method in class loci.plugins.macro.LociFunctions
 
getChannelDimLength(Double, Double[]) - Method in class loci.plugins.macro.LociFunctions
 
getChannelDimType(Double, Double[]) - Method in class loci.plugins.macro.LociFunctions
 
getChannelFiller() - Method in class loci.plugins.in.ImportProcess
Valid only after ImportStep.STACK.
getChannelGlobalMaximum(int) - Method in class loci.formats.MinMaxCalculator
Retrieves a specified channel's global maximum.
getChannelGlobalMinimum(int) - Method in class loci.formats.MinMaxCalculator
Retrieves a specified channel's global minimum.
getChannelIndex(Element) - Method in class loci.formats.in.LIFReader
 
getChannelIndexOfCellObjectName(String) - Method in class loci.formats.in.BDVReader
 
getChannelIndexOfCellObjectName(String) - Method in class loci.formats.in.CellH5Reader
 
getChannelKnownMaximum(int) - Method in class loci.formats.MinMaxCalculator
Retrieves the specified channel's maximum based on the images that have been read.
getChannelKnownMinimum(int) - Method in class loci.formats.MinMaxCalculator
Retrieves the specified channel's minimum based on the images that have been read.
getChannelLabel(int) - Method in class loci.formats.in.TextReader
Gets the label for the given channel.
getChannelName(int, int, int, int) - Method in class loci.formats.in.LegacyND2Reader
 
getChannelName() - Method in class loci.formats.in.MetamorphHandler
 
getChannelName() - Method in class loci.formats.in.PrairieMetadata.PFile
Gets the channelName associated with this File.
getChannelNames() - Method in class loci.formats.in.MetamorphHandler
 
getChannelNames() - Method in class loci.formats.in.ND2Handler
 
getChannels(int) - Method in class loci.formats.in.LegacyND2Reader
 
getChannelSeparator() - Method in class loci.plugins.in.ImportProcess
Valid only after ImportStep.STACK.
getChar(int) - Method in class loci.formats.tools.AsciiImage
 
getCheckboxes(GenericDialog) - Static method in class loci.plugins.util.WindowTools
 
getChild(Element, String) - Static method in class loci.formats.in.CellVoyagerReader
 
getChild(Element, String[]) - Static method in class loci.formats.in.CellVoyagerReader
 
getChild() - Method in class loci.plugins.util.RecordedImageProcessor
 
getChildIndex(Integer, String) - Method in class loci.formats.in.VolocityReader
 
getChildNodes(Element) - Method in class loci.formats.in.OBFReader
 
getChildren(Element, String) - Static method in class loci.formats.in.CellVoyagerReader
 
getChildText(Element, String[]) - Static method in class loci.formats.in.CellVoyagerReader
 
getChildText(Element, String) - Static method in class loci.formats.in.CellVoyagerReader
 
getChoices(GenericDialog) - Static method in class loci.plugins.util.WindowTools
 
getClass(String) - Method in class loci.formats.in.DynamicMetadataOptions
Get the value of property name as a class.
getClass(String, Class<?>) - Method in class loci.formats.in.DynamicMetadataOptions
Get the value of property name as a class.
getClasses() - Method in class loci.formats.ClassList
Gets the list of classes as an array.
getCode() - Method in enum loci.formats.codec.CompressionType
Implemented as specified by the CodedEnum I/F.
getCode() - Method in enum loci.formats.codec.JPEG2000BoxType
Implemented as specified by the CodedEnum I/F.
getCode() - Method in enum loci.formats.codec.JPEG2000SegmentMarker
Implemented as specified by the CodedEnum I/F.
getCode() - Method in enum loci.formats.tiff.IFDType
 
getCode() - Method in enum loci.formats.tiff.PhotoInterp
 
getCode() - Method in enum loci.formats.tiff.TiffCompression
 
getCodecName(int) - Method in class loci.formats.in.AVIReader
 
getCodecName() - Method in enum loci.formats.tiff.TiffCompression
Retrieves the name of the TIFF compression codec.
getCodecOptions() - Method in class loci.formats.tiff.TiffParser
Retrieves the current set of codec options being used to decompress pixel data.
getCodestreamOffset() - Method in class loci.formats.in.JPEG2000MetadataParser
Retrieves the offset to the first contiguous codestream.
getCodestreamPixelType() - Method in class loci.formats.in.JPEG2000MetadataParser
Returns the pixel type as specified in the header.
getCodestreamSizeC() - Method in class loci.formats.in.JPEG2000MetadataParser
Returns the number of channels the image has as specified in the header.
getCodestreamSizeX() - Method in class loci.formats.in.JPEG2000MetadataParser
Returns the width of the image as specified in the header.
getCodestreamSizeY() - Method in class loci.formats.in.JPEG2000MetadataParser
Returns the height of the image as specified in the header.
getColorMap(IFD) - Method in class loci.formats.tiff.TiffParser
Retrieve the color map associated with the given IFD.
getColorMode() - Method in class loci.plugins.in.ImporterOptions
 
getColorModeInfo() - Method in class loci.plugins.in.ImporterOptions
 
getColorModel() - Method in class loci.formats.FormatWriter
 
getColorModel() - Method in interface loci.formats.IFormatWriter
Gets the color model.
getColorModel() - Method in class loci.formats.ImageWriter
 
getColorModel() - Method in class loci.formats.WriterWrapper
 
getColorModel() - Method in class loci.plugins.util.RecordedImageProcessor
 
getColorModes() - Method in class loci.plugins.in.ImporterOptions
 
getColorValue(TextField) - Method in class loci.plugins.in.ColorDialog
 
getColumn() - Method in class loci.formats.in.OMEXMLReader.BinData
 
getColumn(int, int, int[], int) - Method in class loci.plugins.util.RecordedImageProcessor
 
getColumNames(int) - Method in interface loci.formats.services.MetakitService
 
getColumNames(int) - Method in class loci.formats.services.MetakitServiceImpl
 
getColumnNames(String) - Method in interface loci.formats.services.MetakitService
 
getColumnNames(String) - Method in class loci.formats.services.MetakitServiceImpl
 
getColumnTypes(int) - Method in interface loci.formats.services.MetakitService
 
getColumnTypes(String) - Method in interface loci.formats.services.MetakitService
 
getColumnTypes(int) - Method in class loci.formats.services.MetakitServiceImpl
 
getColumnTypes(String) - Method in class loci.formats.services.MetakitServiceImpl
 
getComment(int, int) - Method in class loci.formats.in.MetamorphReader
 
getComment() - Method in class loci.formats.tiff.IFD
Convenience method for obtaining the ImageDescription from this IFD.
getComment() - Method in class loci.formats.tiff.TiffParser
Convenience method for obtaining a stream's first ImageDescription.
getComments() - Method in class loci.formats.in.JPEG2000MetadataParser
Retrieves the list of comments stored in the file.
getCompanion() - Method in class loci.formats.out.OMETiffWriter
 
getComponent(int, int) - Method in class loci.formats.gui.UnsignedIntColorModel
 
getCompressedSize() - Method in class org.libjpegturbo.turbojpeg.TJCompressor
Returns the size of the image (in bytes) generated by the most recent compress/encode operation.
getCompression() - Method in enum loci.formats.codec.CompressionType
Returns the compression.
getCompression(String) - Method in class loci.formats.FormatReader
getCompression() - Method in class loci.formats.FormatWriter
 
getCompression() - Method in interface loci.formats.IFormatWriter
Gets the current compression type.
getCompression() - Method in class loci.formats.ImageWriter
 
getCompression(int) - Method in class loci.formats.in.OBFReader
 
getCompression(String) - Static method in class loci.formats.MetadataTools
Retrieves an Compression enumeration value for the given String.
getCompression() - Method in class loci.formats.tiff.IFD
Retrieves the image's compression type (TIFF tag Compression) from this IFD.
getCompression() - Method in class loci.formats.WriterWrapper
 
getCompressionCodecOptions(IFD) - Method in enum loci.formats.tiff.TiffCompression
Creates a set of codec options for compression.
getCompressionCodecOptions(IFD, CodecOptions) - Method in enum loci.formats.tiff.TiffCompression
Creates a set of codec options for compression.
getCompressionMap() - Static method in enum loci.formats.tiff.TiffCompression
 
getCompressionTypes() - Method in class loci.formats.FormatWriter
 
getCompressionTypes() - Method in interface loci.formats.IFormatWriter
Gets the available compression types.
getCompressionTypes() - Method in class loci.formats.ImageWriter
 
getCompressionTypes() - Method in class loci.formats.WriterWrapper
 
getConcatenateInfo() - Method in class loci.plugins.in.ImporterOptions
 
getConfig(String) - Method in class loci.formats.in.PrairieMetadata
Gets the value of the given configuration key.
getConfig() - Method in class loci.formats.in.PrairieMetadata
Gets the map of configuration key/value pairs.
getConstraintsForCell(int, int, Container, int) - Static method in class loci.plugins.config.SpringUtilities
 
getContrastMethod(String) - Method in class loci.formats.FormatReader
getContrastMethod(String) - Static method in class loci.formats.MetadataTools
Retrieves an ContrastMethod enumeration value for the given String.
getCoreIndex() - Method in class loci.formats.FileStitcher
 
getCoreIndex() - Method in class loci.formats.FormatReader
 
getCoreIndex() - Method in interface loci.formats.IFormatReader
Deprecated.
This method is no longer required for sub-resolution support.
getCoreIndex() - Method in class loci.formats.ImageReader
 
getCoreIndex() - Method in class loci.formats.ReaderWrapper
 
getCoreIndex() - Method in class loci.formats.SubResolutionFormatReader
 
getCoreIndex() - Method in class loci.formats.WrappedReader
 
getCoreMetadataList() - Method in class loci.formats.DimensionSwapper
 
getCoreMetadataList() - Method in class loci.formats.FileStitcher
 
getCoreMetadataList() - Method in class loci.formats.FormatReader
 
getCoreMetadataList() - Method in interface loci.formats.IFormatReader
Deprecated.
Reader internals should not be accessed by reader users
getCoreMetadataList() - Method in class loci.formats.ImageReader
 
getCoreMetadataList() - Method in class loci.formats.in.FilePatternReader
 
getCoreMetadataList() - Method in class loci.formats.in.LeicaHandler
 
getCoreMetadataList() - Method in class loci.formats.in.ND2Handler
 
getCoreMetadataList() - Method in class loci.formats.ReaderWrapper
 
getCoreMetadataList() - Method in class loci.formats.SubResolutionFormatReader
 
getCoreMetadataList() - Method in class loci.formats.WrappedReader
 
getCorrection(String) - Method in class loci.formats.FormatReader
getCorrection() - Method in class loci.formats.in.ND2Handler
 
getCorrection(String) - Static method in class loci.formats.MetadataTools
Retrieves an Correction enumeration value for the given String.
getCount() - Method in class loci.formats.FilePattern
Gets the number of elements for each pattern block.
getCreationDate() - Method in interface loci.formats.services.EXIFService
 
getCreationDate() - Method in class loci.formats.services.EXIFServiceImpl
 
getCropInfo() - Method in class loci.plugins.in.ImporterOptions
 
getCropRegion(int) - Method in class loci.plugins.in.ImporterOptions
 
getCropRegion(int) - Method in class loci.plugins.in.ImportProcess
Valid only after ImportStep.STACK.
getCStep(int) - Method in class loci.plugins.in.ImporterOptions
 
getCStep(int) - Method in class loci.plugins.in.ImportProcess
 
getCurrentColorModel() - Method in class loci.plugins.util.RecordedImageProcessor
 
getCurrentCore() - Method in class loci.formats.FormatReader
Get the CoreMetadata corresponding to the current series and resolution
getCurrentCore() - Method in class loci.formats.SubResolutionFormatReader
Get the CoreMetadata corresponding to the current series and resolution
getCurrentFile() - Method in class loci.formats.FormatReader
 
getCurrentFile() - Method in interface loci.formats.IFormatReader
Returns the current file.
getCurrentFile() - Method in class loci.formats.ImageReader
 
getCurrentFile() - Method in class loci.formats.ReaderWrapper
 
getCurrentFile() - Method in class loci.plugins.in.ImportProcess
Valid only after ImportStep.STACK.
getCurrentFile(String[]) - Method in class loci.plugins.macro.LociFunctions
 
getCurrentPos() - Method in class loci.formats.cache.Cache
Gets the current dimensional position.
getCustomColor(int, int) - Method in class loci.plugins.in.ImporterOptions
 
getCustomColorKey(int, int) - Method in class loci.plugins.in.ImporterOptions
 
getCutIn(Double) - Static method in class loci.formats.FormatTools
 
getCutOut(Double) - Static method in class loci.formats.FormatTools
 
getCycle() - Method in class loci.formats.in.PrairieMetadata.Sequence
Gets the cycle associated with this Sequence.
getCycleCount() - Method in class loci.formats.in.PrairieMetadata
Gets the number of recorded cycles.
getCycleMax() - Method in class loci.formats.in.PrairieMetadata
Gets the maximum cycle value.
getCycleMin() - Method in class loci.formats.in.PrairieMetadata
Gets the minimum cycle value.
getCZTag(IFD) - Method in class loci.formats.in.ZeissLSMReader
 
getData() - Method in class loci.formats.gui.SignedByteBuffer
 
getData(int) - Method in class loci.formats.gui.SignedByteBuffer
 
getData() - Method in class loci.formats.gui.SignedShortBuffer
 
getData(int) - Method in class loci.formats.gui.SignedShortBuffer
 
getData() - Method in class loci.formats.gui.UnsignedIntBuffer
 
getData(int) - Method in class loci.formats.gui.UnsignedIntBuffer
 
getDataElements(int, Object) - Method in class loci.formats.gui.Index16ColorModel
 
getDataElements(int, Object) - Method in class loci.formats.gui.SignedColorModel
 
getDataElements(int, Object) - Method in class loci.formats.gui.UnsignedIntColorModel
 
getDatasetStructureDescription() - Method in class loci.formats.FormatReader
 
getDatasetStructureDescription() - Method in interface loci.formats.IFormatReader
Returns a short description of the dataset structure.
getDatasetStructureDescription() - Method in class loci.formats.ImageReader
 
getDatasetStructureDescription() - Method in class loci.formats.ReaderWrapper
 
getDatasetStructureDescription() - Method in class loci.formats.WrappedReader
 
getDate() - Method in class loci.formats.in.MetamorphHandler
 
getDate() - Method in class loci.formats.in.ND2Handler
 
getDate() - Method in class loci.formats.in.PrairieMetadata
Gets the date of the acquisition.
getDatestamp() - Method in class loci.formats.in.SVSReader
 
getDecompressedStream(String) - Method in class loci.formats.in.CellomicsReader
 
getDefault() - Method in class loci.plugins.prefs.BooleanOption
Gets the default value of the option.
getDefault() - Method in class loci.plugins.prefs.DoubleOption
Gets the default value of the option.
getDefault() - Method in class loci.plugins.prefs.StringOption
Gets the default value of the option.
getDefaultColorModel() - Method in class loci.plugins.util.RecordedImageProcessor
 
getDefaultConfiguration() - Static method in class loci.formats.gui.AWTImageTools
Gets the default graphics configuration for the environment.
getDefaultCustomColor(int) - Method in class loci.plugins.in.ImporterOptions
 
getDefaultOptions() - Static method in class loci.formats.codec.CodecOptions
Return CodecOptions with reasonable default values.
getDefaultOptions() - Static method in class loci.formats.codec.JPEG2000CodecOptions
Return JPEG2000CodecOptions with reasonable default values.
getDefaultOptions(CodecOptions) - Static method in class loci.formats.codec.JPEG2000CodecOptions
Return JPEG2000CodecOptions using the given CodecOptions as the default.
getDefaultReaderClasses() - Static method in class loci.formats.ImageReader
 
getDefaultValue(String) - Method in class loci.plugins.prefs.OptionsList
Gets the default value of the string option with the given key.
getDefaultWriterClasses() - Static method in class loci.formats.ImageWriter
 
getDenom() - Method in class org.libjpegturbo.turbojpeg.TJScalingFactor
Returns denominator
getDenominator() - Method in class loci.formats.tiff.TiffRational
Gets this number's denominator.
getDescription() - Method in class loci.formats.gui.ComboFileFilter
Returns the filter's description.
getDescription() - Method in class loci.formats.gui.ExtensionFileFilter
Gets the filter's description.
getDescription() - Method in class loci.formats.gui.FormatFileFilter
Gets the filter's description.
getDescription() - Method in class loci.formats.gui.NoExtensionFileFilter
Gets the filter's description.
getDeser() - Method in class loci.formats.Memoizer
Returns a configured Kryo instance.
getDetectorType(String) - Method in class loci.formats.FormatReader
getDetectorType(String) - Static method in class loci.formats.MetadataTools
Retrieves an DetectorType enumeration value for the given String.
getDeviceSubtype(String) - Method in class loci.formats.in.CellSensReader
 
getDimension(RandomAccessInputStream) - Method in class loci.formats.in.I2IReader
 
getDimension(String) - Method in class loci.formats.in.ZeissTIFFHandler.Scaling
Get a dimension by its index.
getDimension(String) - Method in interface loci.formats.services.NetCDFService
Retrieves the length of a dimension.
getDimension(String) - Method in class loci.formats.services.NetCDFServiceImpl
 
getDimensionDescriptionNodes(Element) - Method in class loci.formats.in.LIFReader
 
getDimensionOrder() - Method in class loci.formats.ChannelMerger
 
getDimensionOrder() - Method in class loci.formats.ChannelSeparator
 
getDimensionOrder() - Method in class loci.formats.DimensionSwapper
 
getDimensionOrder() - Method in class loci.formats.FileStitcher
 
getDimensionOrder() - Method in class loci.formats.FormatReader
 
getDimensionOrder(String) - Method in class loci.formats.FormatReader
getDimensionOrder() - Method in interface loci.formats.IFormatReader
Gets a five-character string representing the dimension order in which planes will be returned.
getDimensionOrder() - Method in class loci.formats.ImageReader
 
getDimensionOrder(String) - Static method in class loci.formats.MetadataTools
Retrieves an DimensionOrder enumeration value for the given String.
getDimensionOrder() - Method in class loci.formats.ReaderWrapper
 
getDimensionOrder() - Method in class loci.formats.WrappedReader
 
getDimensionOrder(String[]) - Method in class loci.plugins.macro.LociFunctions
 
getDimensionSwapper() - Method in class loci.plugins.in.ImportProcess
Valid only after ImportStep.STACK.
getDirectory(String) - Method in class loci.formats.services.NetCDFServiceImpl
 
getDisplayColor() - Method in class loci.formats.in.SVSReader
 
getDocument() - Method in class loci.formats.gui.XMLWindow
Gets the XML document currently being displayed within the window.
getDocumentBytes(String) - Method in interface loci.formats.services.POIService
Retrieve all of the raw bytes that correspond to the given file name.
getDocumentBytes(String, int) - Method in interface loci.formats.services.POIService
Retrieve at most 'length' bytes that correspond to the given file name.
getDocumentBytes(String) - Method in class loci.formats.services.POIServiceImpl
 
getDocumentBytes(String, int) - Method in class loci.formats.services.POIServiceImpl
 
getDocumentList() - Method in interface loci.formats.services.POIService
Retrieve a list of all files in the current POI file system.
getDocumentList() - Method in class loci.formats.services.POIServiceImpl
 
getDocumentStream(String) - Method in interface loci.formats.services.POIService
Retrieve a RandomAccessInputStream corresponding to the given file name.
getDocumentStream(String) - Method in class loci.formats.services.POIServiceImpl
 
getDomains() - Method in class loci.formats.FormatReader
 
getDomains() - Method in interface loci.formats.IFormatReader
Returns the list of domains represented by the current file.
getDomains() - Method in class loci.formats.ImageReader
 
getDomains() - Method in class loci.formats.in.CellomicsReader
 
getDomains() - Method in class loci.formats.in.ICSReader
 
getDomains() - Method in class loci.formats.in.MetamorphReader
 
getDomains() - Method in class loci.formats.in.MetamorphTiffReader
 
getDomains() - Method in class loci.formats.in.NiftiReader
 
getDomains() - Method in class loci.formats.in.OMETiffReader
 
getDomains() - Method in class loci.formats.in.OMEXMLReader
 
getDomains() - Method in class loci.formats.ReaderWrapper
 
getDomains() - Method in class loci.formats.WrappedReader
 
getDouble(String) - Method in class loci.formats.in.DynamicMetadataOptions
Get the value of property name as a Double.
getDouble(String, Double) - Method in class loci.formats.in.DynamicMetadataOptions
Get the value of property name as a Double.
getDoubles(BufferedImage) - Static method in class loci.formats.gui.AWTImageTools
Extracts pixel data as arrays of doubles, one per channel.
getDoubles(WritableRaster) - Static method in class loci.formats.gui.AWTImageTools
Extracts pixel data as arrays of doubles, one per channel.
getDoubles(WritableRaster, int, int, int, int) - Static method in class loci.formats.gui.AWTImageTools
Extracts pixel data as arrays of doubles, one per channel.
getDoubleValue(int) - Method in class loci.formats.in.ZeissLSMReader.SubBlock
 
getDT(int, int, int, int) - Method in class loci.formats.in.LegacyND2Reader
 
getDX(int, int, int, int) - Method in class loci.formats.in.LegacyND2Reader
 
getDY(int, int, int, int) - Method in class loci.formats.in.LegacyND2Reader
 
getDyeNames() - Method in class loci.formats.in.SVSReader
 
getDZ(int, int, int, int) - Method in class loci.formats.in.LegacyND2Reader
 
getEffectiveSeries(int) - Method in class loci.formats.in.ZeissLSMReader
 
getEffectiveSizeC() - Method in class loci.formats.FormatReader
 
getEffectiveSizeC() - Method in interface loci.formats.IFormatReader
Gets the effective size of the C dimension, guaranteeing that getEffectiveSizeC() * getSizeZ() * getSizeT() == getImageCount() regardless of the result of isRGB().
getEffectiveSizeC() - Method in class loci.formats.ImageReader
 
getEffectiveSizeC() - Method in class loci.formats.ReaderWrapper
 
getEffectiveSizeC() - Method in class loci.formats.WrappedReader
 
getEffectiveSizeC(Double[]) - Method in class loci.plugins.macro.LociFunctions
 
getElem(int) - Method in class loci.formats.gui.SignedByteBuffer
 
getElem(int, int) - Method in class loci.formats.gui.SignedByteBuffer
 
getElem(int, int) - Method in class loci.formats.gui.SignedShortBuffer
 
getElem(int) - Method in class loci.formats.gui.UnsignedIntBuffer
 
getElem(int, int) - Method in class loci.formats.gui.UnsignedIntBuffer
 
getElemDouble(int) - Method in class loci.formats.gui.UnsignedIntBuffer
 
getElemDouble(int, int) - Method in class loci.formats.gui.UnsignedIntBuffer
 
getElements() - Method in class loci.formats.FilePattern
Gets individual elements for each pattern block.
getElements() - Method in class loci.formats.FilePatternBlock
Gets all block elements.
getElementSize(String) - Method in interface loci.formats.services.JHDFService
Retrieves the Element Size of a dataset in Byte.
getElementSize(String) - Method in class loci.formats.services.JHDFServiceImpl
 
getElemFloat(int) - Method in class loci.formats.gui.UnsignedIntBuffer
 
getElemFloat(int, int) - Method in class loci.formats.gui.UnsignedIntBuffer
 
getEmission() - Method in class loci.formats.in.SVSReader
 
getEmissionWavelength(Double) - Static method in class loci.formats.FormatTools
 
getEmissionWavelengths() - Method in class loci.formats.in.ND2Handler
 
getEndX() - Method in class loci.formats.in.SPEReader.SpeROI
 
getEndY() - Method in class loci.formats.in.SPEReader.SpeROI
 
getEntries(IRandomAccess) - Method in class loci.formats.in.IM3Reader.FloatIM3Record
Return all entries as an array
getEntry(IRandomAccess, int) - Method in class loci.formats.in.IM3Reader.BooleanIM3Record
Get the boolean value at the given index
getEntry(IRandomAccess, int) - Method in class loci.formats.in.IM3Reader.FloatIM3Record
Get the floating-point value at the given index
getEntry(IRandomAccess, int) - Method in class loci.formats.in.IM3Reader.IntIM3Record
Get the integer value at the given index
getEnum(String, T) - Method in class loci.formats.in.DynamicMetadataOptions
Get the value of property name as an enumerated type.
getErrorMessage() - Method in class loci.formats.FilePattern
Gets the file pattern error message, if any.
getExcitation() - Method in class loci.formats.in.SVSReader
 
getExcitationWavelength(Double) - Static method in class loci.formats.FormatTools
 
getExcitationWavelengths() - Method in class loci.formats.in.ND2Handler
 
getExifIFDs() - Method in class loci.formats.tiff.TiffParser
Returns EXIF IFDs.
getExifTagName(int) - Static method in class loci.formats.in.BaseTiffReader
 
getExperimenterName() - Method in class loci.formats.in.OperettaReader.OperettaHandler
 
getExperimentType(String) - Method in class loci.formats.FormatReader
getExperimentType(String) - Static method in class loci.formats.MetadataTools
Retrieves an ExperimentType enumeration value for the given String.
getExposures() - Method in class loci.formats.in.MetamorphHandler
 
getExposureTime() - Method in class loci.formats.in.SVSReader
 
getExposureTimes() - Method in class loci.formats.in.ND2Handler
 
getExtension() - Method in class loci.formats.gui.ExtensionFileFilter
Gets the filter's first valid extension.
getExtensionFunctions() - Method in class loci.plugins.macro.MacroFunctions
 
getExtensions() - Method in class loci.formats.gui.ExtensionFileFilter
Gets the filter's valid extensions.
getExternalSeries() - Method in class loci.formats.FileStitcher
 
getExternalSeries(int) - Method in class loci.formats.FileStitcher
 
getExtraSeries(String) - Method in class loci.formats.in.ZeissLSMReader
 
getf(int) - Method in class loci.plugins.util.RecordedImageProcessor
 
getf(int, int) - Method in class loci.plugins.util.RecordedImageProcessor
 
getField(String) - Method in class loci.formats.in.CellomicsReader
 
getField(String) - Method in class loci.formats.in.FlexReader
 
getField(int) - Method in class loci.formats.in.FluoviewReader
 
getField(String) - Method in class loci.formats.in.MetamorphTiffReader
 
getFieldFromSeries(int) - Method in class loci.formats.in.InCellReader
 
getFieldIndex() - Method in class loci.formats.in.ND2Handler
 
getFieldName(int) - Static method in class loci.formats.tiff.IFD
This method uses reflection to scan the values of this class's static fields, returning the first matching field's name.
getFilamentType(String) - Method in class loci.formats.FormatReader
getFilamentType(String) - Static method in class loci.formats.MetadataTools
Retrieves an FilamentType enumeration value for the given String.
getFile(int, int) - Method in class loci.formats.in.CellWorxReader
Retrieve the .pnl file corresponding to the given series.
getFile(String) - Method in class loci.formats.in.DynamicMetadataOptions
Get the value of property name as a file object.
getFile(String, File) - Method in class loci.formats.in.DynamicMetadataOptions
Get the value of property name as a file object.
getFile(String) - Method in class loci.formats.in.FV1000Reader
 
getFile(int) - Method in class loci.formats.in.MicromanagerReader.Position
 
getFile(String, int, int, int, int, int) - Method in class loci.formats.in.MicromanagerReader.Position
 
getFile(int) - Method in class loci.formats.in.PerkinElmerReader
 
getFile(int) - Method in class loci.formats.in.PrairieMetadata.Frame
Gets the File with the given channel.
getFile(int, int, int) - Method in class loci.formats.in.PrairieMetadata
Gets the Frame at the given (cycle, index, channel).
getFile(int, int) - Method in class loci.formats.in.PrairieMetadata.Sequence
Gets the Frame at the given (cycle, index, channel).
getFile(Integer, Location) - Method in class loci.formats.in.VolocityReader
 
getFile() - Method in interface loci.formats.services.JHDFService
Retrieves the current initialized file path.
getFile() - Method in class loci.formats.services.JHDFServiceImpl
 
getFile() - Method in interface loci.formats.services.NetCDFService
Retrieves the current initialized file path.
getFile() - Method in class loci.formats.services.NetCDFServiceImpl
 
getFileHandle(String) - Method in class loci.formats.in.FlexReader
 
getFileIndex(int) - Method in class loci.formats.in.PerkinElmerReader
 
getFilename(int, int, IFormatReader, String) - Static method in class loci.formats.FormatTools
 
getFilename(int, int, IFormatReader, String, boolean) - Static method in class loci.formats.FormatTools
 
getFilename(int, int, MetadataRetrieve, String, boolean) - Static method in class loci.formats.FormatTools
 
getFilename(int, int) - Method in class loci.formats.in.BDReader
 
getFilename() - Method in class loci.formats.in.PrairieMetadata.PFile
Gets the filename associated with this File.
getFilenames(String, IFormatReader) - Static method in class loci.formats.FormatTools
 
getFilePattern() - Method in class loci.formats.AxisGuesser
Gets the file pattern.
getFilePattern() - Method in class loci.formats.FileStitcher.ExternalSeries
 
getFilePattern() - Method in class loci.formats.FileStitcher
Gets the file pattern object used to build the list of files.
getFiles() - Method in class loci.formats.FilePattern
Gets a listing of all files matching this file pattern.
getFiles() - Method in class loci.formats.FileStitcher.ExternalSeries
 
getFileSize(String) - Method in interface loci.formats.services.POIService
Retrieve the total number of bytes in the given file.
getFileSize(String) - Method in class loci.formats.services.POIServiceImpl
 
getFileStitcher() - Method in class loci.plugins.in.ImportProcess
Valid only after ImportStep.STACK.
getFileVersion(RandomAccessInputStream) - Method in class loci.formats.in.OBFReader
 
getFillRule(String) - Method in class loci.formats.FormatReader
getFillRule(String) - Static method in class loci.formats.MetadataTools
Retrieves an FillRule enumeration value for the given String.
getFilter(String) - Method in class loci.formats.in.FV1000Reader.ChannelData
 
getFilters() - Method in class loci.formats.gui.ComboFileFilter
Gets the list of file filters forming this filter combination.
getFilterType(String) - Method in class loci.formats.FormatReader
getFilterType(String) - Static method in class loci.formats.MetadataTools
Retrieves an FilterType enumeration value for the given String.
getFirst() - Method in class loci.formats.FilePattern
Gets the START element for all blocks.
getFirst() - Method in class loci.formats.FilePatternBlock
Gets the first element in a range block.
getFirstChannel(String) - Method in class loci.formats.in.SlidebookTiffReader
 
getFirstChild(Element, String) - Method in class loci.formats.in.OIRReader
 
getFirstChild(Element, String) - Method in class loci.formats.in.PrairieMetadata
Gets the first child element with the given name.
getFirstComment(int) - Method in class loci.formats.in.MetamorphReader
Returns the TIFF comment from the first IFD of the first STK file in the given series.
getFirstFile() - Method in class loci.formats.in.PrairieMetadata.Frame
Gets the first File of the Sequence.
getFirstFrame() - Method in class loci.formats.in.PrairieMetadata.Sequence
Gets the first Frame of the Sequence.
getFirstIFD(String) - Static method in class loci.formats.in.OMETiffReader
 
getFirstIFD() - Method in class loci.formats.tiff.TiffParser
Gets the first IFD within the TIFF file, or null if the input source is not a valid TIFF file.
getFirstIFDEntry(int) - Method in class loci.formats.tiff.TiffParser
Retrieve a given entry from the first IFD in the stream.
getFirstNode(Element, String) - Method in class loci.formats.in.ZeissCZIReader
 
getFirstNodeValue(Element, String) - Method in class loci.formats.in.ZeissCZIReader
 
getFirstOffset() - Method in class loci.formats.tiff.TiffParser
Gets offset to the first IFD, or -1 if stream is not TIFF.
getFirstSequence() - Method in class loci.formats.in.PrairieMetadata
Gets the first Sequence.
getFirstTimeInfo() - Method in class loci.plugins.in.ImporterOptions
 
getFixedHeader() - Method in class loci.formats.services.JPEGTurboServiceImpl
 
getFlattenedList() - Method in class loci.formats.CoreMetadataList
 
getFlexFiles() - Method in class loci.formats.in.FlexReader.MeaHandler
 
getFloat(String) - Method in class loci.formats.in.DynamicMetadataOptions
Get the value of property name as a Float.
getFloat(String, Float) - Method in class loci.formats.in.DynamicMetadataOptions
Get the value of property name as a Float.
getFloatArray() - Method in class loci.plugins.util.RecordedImageProcessor
 
getFloats(BufferedImage) - Static method in class loci.formats.gui.AWTImageTools
Extracts pixel data as arrays of floats, one per channel.
getFloats(WritableRaster) - Static method in class loci.formats.gui.AWTImageTools
Extracts pixel data as arrays of floats, one per channel.
getFloats(WritableRaster, int, int, int, int) - Static method in class loci.formats.gui.AWTImageTools
Extracts pixel data as arrays of floats, one per channel.
getFloatValue(int) - Method in class loci.formats.in.ZeissLSMReader.SubBlock
 
getFontFamily(String) - Method in class loci.formats.FormatReader
getFontFamily(String) - Static method in class loci.formats.MetadataTools
Retrieves an FontFamily enumeration value for the given String.
getFontMetrics() - Method in class loci.plugins.util.RecordedImageProcessor
 
getFontSize(Integer) - Static method in class loci.formats.FormatTools
 
getFontStyle(String) - Method in class loci.formats.FormatReader
getFontStyle(String) - Static method in class loci.formats.MetadataTools
Retrieves an FontStyle enumeration value for the given String.
getForceThumbnailsInfo() - Method in class loci.plugins.in.ImporterOptions
 
getFormat() - Method in class loci.formats.FormatHandler
 
getFormat() - Method in interface loci.formats.IFormatHandler
Gets the name of this file format.
getFormat(String) - Method in class loci.formats.ImageReader
Gets a string describing the file format for the given file.
getFormat() - Method in class loci.formats.ImageReader
 
getFormat(String) - Method in class loci.formats.ImageWriter
Gets a string describing the file format for the given file.
getFormat() - Method in class loci.formats.ImageWriter
 
getFormat() - Method in class loci.formats.ReaderWrapper
 
getFormat() - Method in class loci.formats.WriterWrapper
 
getFormat(String, String[]) - Method in class loci.plugins.macro.LociFunctions
 
getFrame(int, int) - Method in class loci.formats.in.PrairieMetadata
Gets the Frame at the given (cycle and index).
getFrame() - Method in class loci.formats.in.PrairieMetadata.PFile
Gets the <Frame> containing this <File>.
getFrame(int) - Method in class loci.formats.in.PrairieMetadata.Sequence
Gets the Frame with the given index.
getFramesPerSecond() - Method in class loci.formats.FormatWriter
 
getFramesPerSecond() - Method in interface loci.formats.IFormatWriter
Gets the frames per second to use when writing.
getFramesPerSecond() - Method in class loci.formats.ImageWriter
 
getFramesPerSecond() - Method in class loci.formats.WriterWrapper
 
getGain() - Method in class loci.formats.in.MetamorphHandler
 
getGain(int) - Method in class loci.formats.in.PrairieMetadata.Frame
Gets the cth gain for this Frame.
getGains() - Method in class loci.formats.in.ND2Handler
 
getGlobalMeta(String) - Method in class loci.formats.FormatReader
Gets a value from the global metadata table.
getGlobalMetadata() - Method in class loci.formats.FormatReader
 
getGlobalMetadata() - Method in interface loci.formats.IFormatReader
Obtains the hashtable containing the metadata field/value pairs from the current file.
getGlobalMetadata() - Method in class loci.formats.ImageReader
 
getGlobalMetadata() - Method in class loci.formats.in.LeicaHandler
 
getGlobalMetadata() - Method in class loci.formats.ReaderWrapper
 
getGlobalMetadata() - Method in class loci.formats.WrappedReader
 
getGrandchildren(Element, String) - Method in class loci.formats.in.ZeissCZIReader
 
getGrandchildren(Element, String, String) - Method in class loci.formats.in.ZeissCZIReader
 
getGreen(int) - Method in class loci.formats.gui.Index16ColorModel
 
getGreen(int) - Method in class loci.formats.gui.SignedColorModel
 
getGreen(Object) - Method in class loci.formats.gui.SignedColorModel
 
getGreen(int) - Method in class loci.formats.gui.UnsignedIntColorModel
 
getGreen(Object) - Method in class loci.formats.gui.UnsignedIntColorModel
 
getGreenOffset(int) - Static method in class org.libjpegturbo.turbojpeg.TJ
For the given pixel format, returns the number of bytes that the green component is offset from the start of the pixel.
getGreens() - Method in class loci.formats.gui.Index16ColorModel
Return the array of green color components.
getGroup(String) - Method in class loci.formats.services.NetCDFServiceImpl
Retrieves a group based on its fully qualified path.
getGroupFilesInfo() - Method in class loci.plugins.in.ImporterOptions
 
getGroupX() - Method in class loci.formats.in.SPEReader.SpeROI
 
getGroupY() - Method in class loci.formats.in.SPEReader.SpeROI
 
getHeader() - Method in class loci.formats.in.SPEReader.SpeHeader
 
getHeaderInfo(int, String) - Method in class loci.formats.in.DicomReader
 
getHeaderPixelType() - Method in class loci.formats.in.JPEG2000MetadataParser
Returns the pixel type as specified in the header.
getHeaderSize() - Method in class loci.formats.in.SPEReader.SpeHeader
 
getHeaderSizeC() - Method in class loci.formats.in.JPEG2000MetadataParser
Returns the number of channels the image has as specified in the header.
getHeaderSizeX() - Method in class loci.formats.in.JPEG2000MetadataParser
Returns the width of the image as specified in the header.
getHeaderSizeY() - Method in class loci.formats.in.JPEG2000MetadataParser
Returns the height of the image as specified in the header.
getHeight() - Method in class loci.formats.codec.JPEGTileDecoder
 
getHeight(int) - Method in class loci.formats.in.LegacyND2Reader
 
getHeight() - Method in interface loci.formats.services.LuraWaveService
Wraps lwfDecoder.getHeight()
getHeight() - Method in class loci.formats.services.LuraWaveServiceImpl
 
getHeight(IFormatReader, String, int) - Static method in class loci.plugins.util.BFVirtualStack
 
getHeight() - Method in class loci.plugins.util.BFVirtualStack
 
getHeight() - Method in class loci.plugins.util.RecordedImageProcessor
 
getHeight() - Method in class org.libjpegturbo.turbojpeg.TJDecompressor
Returns the height of the JPEG image associated with this decompressor instance.
getHelper() - Method in class loci.formats.in.FilePatternReader
 
getHelper() - Method in class loci.formats.WrappedReader
Get the helper class that reads images
getHistogram() - Method in class loci.plugins.util.RecordedImageProcessor
 
getHistogramMax() - Method in class loci.plugins.util.RecordedImageProcessor
 
getHistogramMin() - Method in class loci.plugins.util.RecordedImageProcessor
 
getHistogramSize() - Method in class loci.plugins.util.RecordedImageProcessor
 
getId(String) - Method in class loci.formats.tools.MakeTestOmeTiff
 
getId() - Method in class loci.plugins.in.ImporterOptions
 
getIdInfo() - Method in class loci.plugins.in.ImporterOptions
 
getIdLocation() - Method in class loci.plugins.in.ImportProcess
Valid only after ImportStep.READER.
getIdName() - Method in class loci.plugins.in.ImportProcess
Valid only after ImportStep.READER.
getIFD(long) - Method in class loci.formats.tiff.TiffParser
Gets the IFD stored at the given offset.
getIFDComment(int) - Method in class loci.formats.in.VectraReader
 
getIFDIndex() - Method in class loci.formats.in.CellSensReader
 
getIFDIndex(int, int) - Method in class loci.formats.in.NDPIReader
 
getIFDIndex(int, int) - Method in class loci.formats.in.SVSReader
 
getIFDIndex(int, int) - Method in class loci.formats.in.VectraReader
Returns the index of the IFD to be used for the given core index and image number.
getIFDIndex(int, int) - Method in class loci.formats.in.VentanaReader
 
getIFDIntArray(int) - Method in class loci.formats.tiff.IFD
Gets the given directory entry values in int format from this IFD, performing some error checking.
getIFDIntValue(int) - Method in class loci.formats.tiff.IFD
Gets the given directory entry value in int format from this IFD, or -1 if the given directory does not exist.
getIFDIntValue(int, int) - Method in class loci.formats.tiff.IFD
Gets the given directory entry value in int format from this IFD, performing some error checking.
getIFDLongArray(int) - Method in class loci.formats.tiff.IFD
Gets the given directory entry values in long format from this IFD, performing some error checking.
getIFDLongValue(int, long) - Method in class loci.formats.tiff.IFD
Gets the given directory entry value in long format from this IFD, performing some error checking.
getIFDOffsets() - Method in class loci.formats.tiff.TiffParser
Gets the offsets to every IFD in the file.
getIFDRationalValue(int) - Method in class loci.formats.tiff.IFD
Gets the given directory entry value in rational format from this IFD, performing some error checking.
getIFDs() - Method in class loci.formats.in.MinimalTiffReader
Gets the list of IFDs associated with the current TIFF's image planes.
getIFDs() - Method in class loci.formats.tiff.TiffParser
getIFDShortArray(int) - Method in class loci.formats.tiff.IFD
Gets the given directory entry values in short format from this IFD, performing some error checking.
getIFDStringValue(int) - Method in class loci.formats.tiff.IFD
Gets the given directory entry value as a string from this IFD, performing some error checking.
getIFDTagName(int) - Static method in class loci.formats.tiff.IFD
Gets the name of the IFD tag encoded by the given number.
getIFDTextValue(int) - Method in class loci.formats.tiff.IFD
Gets the given directory entry value as a string (regardless of type).
getIFDValue(int) - Method in class loci.formats.tiff.IFD
Gets the given directory entry value from this IFD.
getIFDValue(int, Class) - Method in class loci.formats.tiff.IFD
Gets the given directory entry value from this IFD, performing some error checking.
getIFDValue(TiffIFDEntry) - Method in class loci.formats.tiff.TiffParser
Retrieve the value corresponding to the given TiffIFDEntry.
getIlluminationType(String) - Method in class loci.formats.FormatReader
getIlluminationType(String) - Static method in class loci.formats.MetadataTools
Retrieves an IlluminationType enumeration value for the given String.
getImage() - Method in class loci.formats.gui.ImageViewer
Gets the currently displayed image.
getImage(byte[], int, int, int, int) - Method in class loci.formats.in.LegacyND2Reader
 
getImageCount() - Method in class loci.formats.ChannelMerger
 
getImageCount() - Method in class loci.formats.ChannelSeparator
 
getImageCount() - Method in class loci.formats.FileStitcher
 
getImageCount() - Method in class loci.formats.FormatReader
 
getImageCount() - Method in interface loci.formats.IFormatReader
Determines the number of image planes in the current file.
getImageCount() - Method in class loci.formats.ImageReader
 
getImageCount() - Method in class loci.formats.ReaderWrapper
 
getImageCount() - Method in class loci.formats.WrappedReader
 
getImageCount(Double[]) - Method in class loci.plugins.macro.LociFunctions
 
getImageCreationDate() - Method in class loci.formats.in.BaseTiffReader
Retrieves the image creation date.
getImageCreationDate(String[]) - Method in class loci.plugins.macro.LociFunctions
 
getImageData(int, int, int, int, int) - Method in class loci.formats.in.BDVReader
 
getImageData(int, int, int) - Method in class loci.formats.in.CellH5Reader
 
getImageData(int, int, int, int, int) - Method in class loci.formats.in.ImarisHDFReader
Retrieve an array corresponding to the specified image tile.
getImageDescription(Element) - Method in class loci.formats.in.LIFReader
 
getImageIndex() - Method in class loci.formats.gui.ImageViewer
Gets the index of the currently displayed image.
getImageIndex(int) - Method in class loci.formats.in.FluoviewReader
 
getImageIndex(String) - Method in class loci.formats.in.PCIReader
Get the image index from the image file name.
getImageLength() - Method in class loci.formats.tiff.IFD
Retrieves the image's length (TIFF tag ImageLength) from a given TIFF IFD.
getImageName() - Method in class loci.formats.in.MetamorphHandler
 
getImageName(int) - Method in class loci.formats.in.VectraReader
 
getImageNumber(String, int) - Method in class loci.formats.in.ZeissZVIReader
 
getImageReader() - Method in class loci.plugins.in.ImportProcess
Valid only after ImportStep.READER.
getImageSequence(int) - Method in class loci.formats.in.DeltavisionReader
Get the image sequence string.
getImagesPerFile() - Method in class loci.formats.FileStitcher.ExternalSeries
 
getImagesPerFile(String, IFormatReader) - Static method in class loci.formats.FormatTools
 
getImageType(int) - Method in class loci.formats.in.VectraReader
 
getImageWidth() - Method in class loci.formats.tiff.IFD
Retrieves the image's width (TIFF tag ImageWidth) from a given TIFF IFD.
getImagingDevice() - Method in class loci.formats.in.PrairieMetadata.Frame
Gets the imaging device associated with this Frame.
getImmersion(String) - Method in class loci.formats.FormatReader
getImmersion() - Method in class loci.formats.in.ND2Handler
 
getImmersion() - Method in class loci.formats.in.PrairieMetadata.Frame
Extracts the immersion from the objective lens string.
getImmersion(String) - Static method in class loci.formats.MetadataTools
Retrieves an Immersion enumeration value for the given String.
getIndex() - Method in class loci.formats.cache.CacheEvent
Gets the index relevant to the cache update, if any.
getIndex(int, int, int, int, int, int) - Method in class loci.formats.ChannelMerger
 
getIndex(int, int, int) - Method in class loci.formats.ChannelMerger
 
getIndex(int, int, int) - Method in class loci.formats.ChannelSeparator
 
getIndex(int, int, int, int, int, int) - Method in class loci.formats.ChannelSeparator
 
getIndex(int, int, int) - Method in class loci.formats.DimensionSwapper
 
getIndex(int, int, int, int, int, int) - Method in class loci.formats.DimensionSwapper
 
getIndex(int, int, int) - Method in class loci.formats.FileStitcher
 
getIndex(int, int, int, int, int, int) - Method in class loci.formats.FileStitcher
 
getIndex(int, int, int) - Method in class loci.formats.FormatReader
 
getIndex(int, int, int, int, int, int) - Method in class loci.formats.FormatReader
 
getIndex(IFormatReader, int, int, int) - Static method in class loci.formats.FormatTools
Gets the rasterized index corresponding to the given Z, C and T coordinates (real sizes).
getIndex(IFormatReader, int, int, int, int, int, int) - Static method in class loci.formats.FormatTools
Gets the rasterized index corresponding to the given Z, C, T, ModuloZ, ModuloC and ModuloT coordinates (effective sizes).
getIndex(String, int, int, int, int, int, int, int) - Static method in class loci.formats.FormatTools
Gets the rasterized index corresponding to the given Z, C and T coordinates (real sizes).
getIndex(String, int, int, int, int, int, int, int, int, int, int, int, int, int) - Static method in class loci.formats.FormatTools
Gets the rasterized index corresponding to the given Z, C, T, ModuloZ, ModuloC, ModuloT coordinates (effective sizes).
getIndex(int, int, int) - Method in interface loci.formats.IFormatReader
Gets the rasterized index corresponding to the given Z, C and T coordinates (real sizes).
getIndex(int, int, int, int, int, int) - Method in interface loci.formats.IFormatReader
Gets the rasterized index corresponding to the given Z, C, T, moduloZ, moduloC and moduloT coordinates (effective sizes).
getIndex(int, int, int) - Method in class loci.formats.ImageReader
 
getIndex(int, int, int, int, int, int) - Method in class loci.formats.ImageReader
 
getIndex() - Method in class loci.formats.in.BaseZeissReader.Tag
 
getIndex() - Method in class loci.formats.in.PrairieMetadata.Frame
Gets the index associated with this Frame.
getIndex(int, int, int) - Method in class loci.formats.ReaderWrapper
 
getIndex(int, int, int, int, int, int) - Method in class loci.formats.ReaderWrapper
 
getIndex(int, int, int) - Method in class loci.formats.WrappedReader
 
getIndex(Double, Double, Double, Double[]) - Method in class loci.plugins.macro.LociFunctions
 
getIndexCount() - Method in class loci.formats.in.PrairieMetadata.Sequence
Gets the number of recorded indices at this Sequence.
getIndexMax() - Method in class loci.formats.in.PrairieMetadata.Sequence
Gets the maximum index value.
getIndexMin() - Method in class loci.formats.in.PrairieMetadata.Sequence
Gets the minimum index value.
getInfo() - Method in class loci.formats.in.SDTReader
Gets object containing SDT header information.
getInfo() - Method in class loci.plugins.prefs.Option
Gets documentation about the option.
getInfo(String) - Method in class loci.plugins.prefs.OptionsList
Gets the documentation for the option with the given key.
getIniFile(String) - Method in class loci.formats.in.FV1000Reader
 
getInputOrder() - Method in class loci.formats.DimensionSwapper
 
getInputOrder(int) - Method in class loci.plugins.in.ImporterOptions
 
getInputStream(String) - Method in interface loci.formats.services.POIService
Retrieve an InputStream corresponding to the given file name.
getInputStream(String) - Method in class loci.formats.services.POIServiceImpl
 
getInstance(int) - Static method in class loci.formats.gui.TwoChannelColorSpace
 
getInt(SPEReader.SpeHeaderEntry) - Method in class loci.formats.in.SPEReader.SpeHeader
Method used to retrieve data values for Integer entries into the SPE header table
getInt(int) - Method in class loci.formats.in.SPEReader.SpeHeader
Private method used to retrieve an Integer value from the SPE header
getIntArray(SPEReader.SpeHeaderEntry) - Method in class loci.formats.in.SPEReader.SpeHeader
Method used to retrieve data values for Integer Array entries into the SPE header table
getIntArray() - Method in class loci.plugins.util.RecordedImageProcessor
 
getInteger(String) - Method in class loci.formats.in.DynamicMetadataOptions
Get the value of property name as an Integer.
getInteger(String, Integer) - Method in class loci.formats.in.DynamicMetadataOptions
Get the value of property name as an Integer.
getInterpolate() - Method in class loci.plugins.util.RecordedImageProcessor
 
getInterpolatedPixel(double, double) - Method in class loci.plugins.util.RecordedImageProcessor
 
getInts(BufferedImage) - Static method in class loci.formats.gui.AWTImageTools
Extracts pixel data as arrays of signed integers, one per channel.
getInts(WritableRaster) - Static method in class loci.formats.gui.AWTImageTools
Extracts pixel data as arrays of signed integers, one per channel.
getInts(WritableRaster, int, int, int, int) - Static method in class loci.formats.gui.AWTImageTools
Extracts pixel data as arrays of signed integers, one per channel.
getIntValue(int) - Method in class loci.formats.in.ZeissLSMReader.SubBlock
 
getJPEGBuf() - Method in class org.libjpegturbo.turbojpeg.TJDecompressor
Returns the JPEG image buffer associated with this decompressor instance.
getJPEGSize() - Method in class org.libjpegturbo.turbojpeg.TJDecompressor
Returns the size of the JPEG image (in bytes) associated with this decompressor instance.
getKey() - Method in class loci.formats.in.BaseZeissReader.Tag
 
getKey(int) - Method in class loci.formats.in.BaseZeissReader.Tag
Return the string corresponding to the given ID.
getKey(int) - Method in class loci.formats.in.MetamorphReader
 
getKey() - Method in class loci.formats.meta.OriginalMetadataAnnotation
 
getKey() - Method in class loci.plugins.prefs.Option
Gets the option's key name.
getKeyID() - Method in class loci.formats.in.BaseZeissReader.Tag
 
getLabel() - Method in class loci.plugins.prefs.Option
Gets label describing the option.
getLabel(String) - Method in class loci.plugins.prefs.OptionsList
Gets the label for the option with the given key.
getLabels() - Method in class loci.plugins.config.CellSensWidgets
 
getLabels() - Method in class loci.plugins.config.FlexWidgets
 
getLabels() - Method in interface loci.plugins.config.IFormatWidgets
 
getLabels() - Method in class loci.plugins.config.LIFWidgets
 
getLabels() - Method in class loci.plugins.config.ND2Widgets
 
getLabels() - Method in class loci.plugins.config.PictWidgets
 
getLabels() - Method in class loci.plugins.config.QTWidgets
 
getLabels() - Method in class loci.plugins.config.SDTWidgets
 
getLabels() - Method in class loci.plugins.config.TiffDelegateWidgets
 
getLabels() - Method in class loci.plugins.config.ZeissCZIWidgets
 
getLaserMedium(String) - Method in class loci.formats.FormatReader
getLaserMedium(String) - Static method in class loci.formats.MetadataTools
Retrieves an LaserMedium enumeration value for the given String.
getLaserPower() - Method in class loci.formats.in.PrairieMetadata
Gets the first laserPower recorded in the configuration.
getLaserType(String) - Method in class loci.formats.FormatReader
getLaserType(String) - Static method in class loci.formats.MetadataTools
Retrieves an LaserType enumeration value for the given String.
getLast() - Method in class loci.formats.FilePattern
Gets the STOP element for all blocks.
getLast() - Method in class loci.formats.FilePatternBlock
Gets the last element in a range block.
getLatestVersion() - Method in interface loci.formats.services.OMEXMLService
Retrieves the latest supported version of the OME-XML schema.
getLatestVersion() - Method in class loci.formats.services.OMEXMLServiceImpl
 
getLength(RandomAccessInputStream, int) - Method in class loci.formats.in.DicomReader
 
getLength(long) - Method in class loci.formats.in.OBFReader
 
getLengths() - Method in class loci.formats.cache.CacheStrategy
 
getLengths() - Method in interface loci.formats.cache.ICacheStrategy
Gets the lengths of all the axes.
getLengths(IFormatReader) - Static method in class loci.formats.tools.CacheConsole
Helper utility for constructing lengths array, used by main.
getLensNA() - Method in class loci.formats.in.MetamorphHandler
 
getLensRI() - Method in class loci.formats.in.MetamorphHandler
 
getLetter() - Method in class loci.formats.ResourceNamer
Returns a String representing a single letter (in the case where the class instance has been initialized with a resource count lower than 26) or a concatenation of two letters (if resource count is higher than 26).
getLicenseCode() - Method in interface loci.formats.services.LuraWaveService
Retrieves the current license code as a string.
getLicenseCode() - Method in class loci.formats.services.LuraWaveServiceImpl
 
getLine(double, double, double, double) - Method in class loci.plugins.util.RecordedImageProcessor
 
getLinesPerFrame() - Method in class loci.formats.in.PrairieMetadata.Frame
Gets the lines per frame for this Frame.
getLoadList(int[]) - Method in class loci.formats.cache.CacheStrategy
 
getLoadList(int[]) - Method in interface loci.formats.cache.ICacheStrategy
Gets the indices of the objects to cache, surrounding the object at the given position.
getLocation() - Method in class loci.plugins.in.ImporterOptions
 
getLocationFromResourceName(Location, String, int, String) - Method in class loci.formats.ResourceNamer
Creates a new Location instance using the provided parent path and child node name.
getLocationInfo() - Method in class loci.plugins.in.ImporterOptions
 
getLocations() - Method in class loci.plugins.in.ImporterOptions
 
getLong(String) - Method in class loci.formats.in.DynamicMetadataOptions
Get the value of property name as a Long.
getLong(String, Long) - Method in class loci.formats.in.DynamicMetadataOptions
Get the value of property name as a Long.
getLong(SPEReader.SpeHeaderEntry) - Method in class loci.formats.in.SPEReader.SpeHeader
Method used to retrieve data values for Long enteries into the SPE header table
getLong(int) - Method in class loci.formats.in.SPEReader.SpeHeader
Private method used to retrieve a Long value from the SPE header
getLongArray(SPEReader.SpeHeaderEntry) - Method in class loci.formats.in.SPEReader.SpeHeader
Method used to retrieve data values for Long Array entries into the SPE header table
getLookupTable(ColorModel) - Static method in class loci.formats.gui.AWTImageTools
Convers an Index16ColorModel to a 2D short array.
getLookupTable(Map) - Method in class loci.formats.in.AmiraReader
 
getLookupTable() - Method in class loci.formats.in.JPEG2000MetadataParser
Returns the color lookup table stored in the file, or null if a lookup table is not present.
getLookupTableComponentCount() - Method in class loci.formats.ChannelFiller
Gets the number of color components in the lookup table.
getLSMFileFromSeries(int) - Method in class loci.formats.in.ZeissLSMReader
 
getLutNames() - Method in class loci.formats.in.LeicaHandler
 
getLutUpdateMode() - Method in class loci.plugins.util.RecordedImageProcessor
 
getMagnification(int, int, int, int) - Method in class loci.formats.in.LegacyND2Reader
 
getMagnification() - Method in class loci.formats.in.ND2Handler
 
getMagnification() - Method in class loci.formats.in.PrairieMetadata.Frame
Extracts the magnification from the objective lens string.
getMagnification() - Method in class loci.formats.in.SVSReader
 
getMagnitudes() - Method in class loci.formats.in.IM3Reader.Spectrum
 
getMainIFDs() - Method in class loci.formats.tiff.TiffParser
Returns the main list of IFDs in the file.
getMap() - Method in class loci.formats.tools.AmiraParameters
 
getMarker(String) - Method in class loci.formats.FormatReader
getMarker(String) - Static method in class loci.formats.MetadataTools
Retrieves an Marker enumeration value for the given String.
getMask() - Method in class loci.plugins.util.RecordedImageProcessor
 
getMaskArray() - Method in class loci.plugins.util.RecordedImageProcessor
 
getMax() - Method in class loci.plugins.util.RecordedImageProcessor
 
getMaxFieldCount(Integer) - Static method in class loci.formats.FormatTools
 
getMaximumSize() - Method in class loci.formats.gui.CacheIndicator
 
getMaximumSize() - Method in class loci.formats.gui.DataConverter.RowPanel
 
getMaxThreshold() - Method in class loci.plugins.util.RecordedImageProcessor
 
getMCUHeight(int) - Static method in class org.libjpegturbo.turbojpeg.TJ
Returns the MCU block height for the given level of chrominance subsampling.
getMCUWidth(int) - Static method in class org.libjpegturbo.turbojpeg.TJ
Returns the MCU block width for the given level of chrominance subsampling.
getMDBFile(String) - Method in class loci.formats.in.ZeissLSMReader
 
getMeasurementID() - Method in class loci.formats.in.ColumbusReader.MeasurementHandler
 
getMeasurementID() - Method in class loci.formats.in.OperettaReader.OperettaHandler
 
getMeasurementName() - Method in class loci.formats.in.ColumbusReader.MeasurementHandler
 
getMeasurementTime() - Method in class loci.formats.in.OperettaReader.OperettaHandler
 
getMedium(String) - Method in class loci.formats.FormatReader
getMedium(String) - Static method in class loci.formats.MetadataTools
Retrieves an Medium enumeration value for the given String.
getMember(String) - Method in interface loci.formats.services.JHDFService
Retrieves the all members of a group.
getMember(String) - Method in class loci.formats.services.JHDFServiceImpl
 
getMemoFile(String) - Method in class loci.formats.Memoizer
Constructs a File object from id string.
getMemoryUsage() - Method in class loci.plugins.in.ImportProcess
Gets a projection of required memory in bytes.
getMessage() - Method in enum loci.plugins.in.ImportStep
 
getMetadata() - Method in class loci.formats.in.ND2Handler
 
getMetadataLevel() - Method in class loci.formats.in.DefaultMetadataOptions
 
getMetadataLevel() - Method in class loci.formats.in.DynamicMetadataOptions
 
getMetadataLevel() - Method in interface loci.formats.in.MetadataOptions
Get the configured metadata level.
getMetadataOptions() - Method in class loci.formats.DelegateReader
 
getMetadataOptions() - Method in class loci.formats.FormatHandler
 
getMetadataOptions() - Method in class loci.formats.ImageReader
 
getMetadataOptions() - Method in class loci.formats.ImageWriter
 
getMetadataOptions() - Method in interface loci.formats.IMetadataConfigurable
 
getMetadataOptions() - Method in class loci.formats.ReaderWrapper
 
getMetadataOptions() - Method in class loci.formats.WriterWrapper
 
getMetadataRetrieve() - Method in class loci.formats.FormatWriter
 
getMetadataRetrieve() - Method in interface loci.formats.IFormatWriter
Retrieves the current metadata retrieval object for this writer.
getMetadataRetrieve() - Method in class loci.formats.ImageWriter
 
getMetadataRetrieve() - Method in class loci.formats.WriterWrapper
 
getMetadataRoot(String) - Method in class loci.formats.in.LIFReader
 
getMetadataStore() - Method in class loci.formats.FileStitcher
 
getMetadataStore() - Method in class loci.formats.FormatReader
 
getMetadataStore() - Method in interface loci.formats.IFormatReader
Retrieves the current metadata store for this reader.
getMetadataStore() - Method in class loci.formats.ImageReader
 
getMetadataStore() - Method in class loci.formats.in.FilePatternReader
 
getMetadataStore() - Method in class loci.formats.Memoizer
 
getMetadataStore() - Method in class loci.formats.ReaderWrapper
 
getMetadataStoreForConversion() - Method in class loci.formats.in.OMETiffReader
Deprecated.
Use the general FormatReader.getMetadataStore() method.
getMetadataStoreForDisplay() - Method in class loci.formats.in.OMETiffReader
Deprecated.
Use the general FormatReader.getMetadataStore() method.
getMetadataStoreRoot() - Method in class loci.formats.FileStitcher
 
getMetadataStoreRoot() - Method in class loci.formats.FormatReader
 
getMetadataStoreRoot() - Method in interface loci.formats.IFormatReader
Retrieves the current metadata store's root object.
getMetadataStoreRoot() - Method in class loci.formats.ImageReader
 
getMetadataStoreRoot() - Method in class loci.formats.ReaderWrapper
 
getMetadataStoreRoot() - Method in class loci.formats.WrappedReader
 
getMetadataString(String) - Method in class loci.plugins.in.ImporterMetadata
Returns a string with each key/value pair on its own line.
getMetadataType() - Method in enum loci.formats.tiff.PhotoInterp
Retrieves the metadata type of the photometric interpretation.
getMetadataValue(String) - Method in class loci.formats.FormatReader
 
getMetadataValue(String) - Method in interface loci.formats.IFormatReader
Obtains the specified metadata field's value for the current file.
getMetadataValue(String) - Method in class loci.formats.ImageReader
 
getMetadataValue(String) - Method in class loci.formats.ReaderWrapper
 
getMetadataValue(String) - Method in class loci.formats.WrappedReader
 
getMetadataValue(String, String[]) - Method in class loci.plugins.macro.LociFunctions
 
getMethodStack() - Method in class loci.plugins.util.BFVirtualStack
 
getMethodStack() - Method in class loci.plugins.util.RecordedImageProcessor
 
getMicrobeamManipulationType(String) - Method in class loci.formats.FormatReader
getMicrobeamManipulationType(String) - Static method in class loci.formats.MetadataTools
Retrieves an MicrobeamManipulationType enumeration value for the given String.
getMicronsPerPixelX() - Method in class loci.formats.in.PrairieMetadata.Frame
Gets the microns per pixel along X for this Frame.
getMicronsPerPixelY() - Method in class loci.formats.in.PrairieMetadata.Frame
Gets the microns per pixel along Y for this Frame.
getMicroscopeType(String) - Method in class loci.formats.FormatReader
getMicroscopeType(String) - Static method in class loci.formats.MetadataTools
Retrieves an MicroscopeType enumeration value for the given String.
getMin() - Method in class loci.plugins.util.RecordedImageProcessor
 
getMinimumSize() - Method in class loci.formats.gui.CacheIndicator
 
getMinMaxCalculator() - Method in class loci.plugins.in.ImportProcess
Valid only after ImportStep.STACK.
getMinMaxStore() - Method in class loci.formats.MinMaxCalculator
Retrieves the current active min-max store for the calculator.
getMinThreshold() - Method in class loci.plugins.util.RecordedImageProcessor
 
getModalities() - Method in class loci.formats.in.ND2Handler
 
getModality(int, int, int, int) - Method in class loci.formats.in.LegacyND2Reader
 
getModuloAlong(OMEXMLMetadata, String, int) - Method in class loci.formats.services.OMEXMLServiceImpl
Create a Modulo corresponding to the given ModuloAlong* tag.
getModuloAlongC(OMEXMLMetadata, int) - Method in interface loci.formats.services.OMEXMLService
Retrieve the ModuloAlongC annotation in the given Image in the given OME-XML metadata object.
getModuloAlongC(OMEXMLMetadata, int) - Method in class loci.formats.services.OMEXMLServiceImpl
 
getModuloAlongT(OMEXMLMetadata, int) - Method in interface loci.formats.services.OMEXMLService
Retrieve the ModuloAlongT annotation in the given Image in the given OME-XML metadata object.
getModuloAlongT(OMEXMLMetadata, int) - Method in class loci.formats.services.OMEXMLServiceImpl
 
getModuloAlongZ(OMEXMLMetadata, int) - Method in interface loci.formats.services.OMEXMLService
Retrieve the ModuloAlongZ annotation in the given Image in the given OME-XML metadata object.
getModuloAlongZ(OMEXMLMetadata, int) - Method in class loci.formats.services.OMEXMLServiceImpl
 
getModuloC() - Method in class loci.formats.FormatReader
 
getModuloC() - Method in interface loci.formats.IFormatReader
 
getModuloC() - Method in class loci.formats.ImageReader
 
getModuloC() - Method in class loci.formats.ReaderWrapper
 
getModuloC() - Method in class loci.formats.WrappedReader
 
getModuloT() - Method in class loci.formats.FormatReader
 
getModuloT() - Method in interface loci.formats.IFormatReader
 
getModuloT() - Method in class loci.formats.ImageReader
 
getModuloT() - Method in class loci.formats.ReaderWrapper
 
getModuloT() - Method in class loci.formats.WrappedReader
 
getModuloZ() - Method in class loci.formats.FormatReader
 
getModuloZ() - Method in interface loci.formats.IFormatReader
 
getModuloZ() - Method in class loci.formats.ImageReader
 
getModuloZ() - Method in class loci.formats.ReaderWrapper
 
getModuloZ() - Method in class loci.formats.WrappedReader
 
getMontage(int) - Method in class loci.formats.in.FluoviewReader
 
getMustGroupInfo() - Method in class loci.plugins.in.ImporterOptions
 
getNA(int, int, int, int) - Method in class loci.formats.in.LegacyND2Reader
 
getName() - Method in enum loci.formats.codec.JPEG2000BoxType
Returns the name of the box type.
getName() - Method in enum loci.formats.codec.JPEG2000SegmentMarker
Returns the name of the segment marker.
getName(int) - Method in class loci.formats.gui.TwoChannelColorSpace
 
getName() - Method in enum loci.formats.in.BaseZeissReader.Charset
 
getName() - Method in class loci.formats.in.IM3Reader.Spectrum
 
getName(String) - Method in class loci.formats.services.NetCDFServiceImpl
 
getName() - Method in enum loci.formats.tiff.PhotoInterp
Retrieves the given name of the photometric interpretation.
getNamingConvention(String) - Method in class loci.formats.FormatReader
getNamingConvention(String) - Static method in class loci.formats.MetadataTools
Retrieves an NamingConvention enumeration value for the given String.
getNativeDataType() - Method in class loci.formats.ChannelFiller
 
getNativeDataType() - Method in class loci.formats.ChannelMerger
 
getNativeDataType() - Method in class loci.formats.ChannelSeparator
 
getNativeDataType() - Method in class loci.formats.FormatHandler
 
getNativeDataType() - Method in interface loci.formats.IFormatHandler
Returns the native data type of image planes for this reader, as returned by IFormatReader.openPlane(int, int, int, int, int) or IFormatWriter.savePlane(int, java.lang.Object).
getNativeDataType() - Method in class loci.formats.ImageReader
 
getNativeDataType() - Method in class loci.formats.ImageWriter
 
getNativeDataType() - Method in class loci.formats.in.BIFormatReader
 
getNativeDataType() - Method in class loci.formats.in.TextReader
 
getNativeDataType() - Method in class loci.formats.MinMaxCalculator
 
getNativeDataType() - Method in class loci.formats.out.ImageIOWriter
 
getNativeDataType() - Method in class loci.formats.out.LegacyQTWriter
 
getNativeDataType() - Method in class loci.formats.ReaderWrapper
 
getNativeDataType() - Method in class loci.formats.TileStitcher
 
getNativeDataType() - Method in class loci.formats.WrappedReader
 
getNativeDataType() - Method in class loci.formats.WriterWrapper
 
getNativeDataType() - Method in class loci.plugins.util.ImageProcessorReader
 
getNChannels() - Method in class loci.plugins.util.RecordedImageProcessor
 
getNextLine(byte[]) - Method in class loci.formats.in.MicromanagerReader
 
getNextLine(List<String>) - Method in class loci.formats.in.TextReader
 
getNextOffset(long) - Method in class loci.formats.tiff.TiffParser
Read a file offset.
getNextTag(RandomAccessInputStream) - Method in class loci.formats.in.DicomReader
 
getNextTag(RandomAccessInputStream, boolean) - Method in class loci.formats.in.DicomReader
 
getNextTag(RandomAccessInputStream) - Method in class loci.formats.in.ZeissZVIReader
 
getNodes(Element, String) - Method in class loci.formats.in.LIFReader
 
getNonThumbnailIFDs() - Method in class loci.formats.tiff.TiffParser
Returns non-thumbnail IFDs.
getNoWlzMsg() - Method in interface loci.formats.services.WlzService
Gets the text string for when Woolz has not been found.
getNoWlzMsg() - Method in class loci.formats.services.WlzServiceImpl
 
getNum() - Method in class org.libjpegturbo.turbojpeg.TJScalingFactor
Returns numerator
getNumber(String) - Method in class loci.formats.NumberFilter
Gets numbers filling the asterisk positions.
getNumBytes(int) - Method in class loci.formats.in.GatanReader
 
getNumComponents() - Method in class loci.formats.gui.TwoChannelColorSpace
 
getNumEntries(IRandomAccess) - Method in class loci.formats.in.IM3Reader.BooleanIM3Record
Get the # of boolean values in this record
getNumEntries(IRandomAccess) - Method in class loci.formats.in.IM3Reader.FloatIM3Record
Get the # of floating-point values in this record
getNumEntries(IRandomAccess) - Method in class loci.formats.in.IM3Reader.IntIM3Record
Get the # of integer values in this record
getNumerator() - Method in class loci.formats.tiff.TiffRational
Gets this number's numerator.
getNumericalAperture() - Method in class loci.formats.in.ND2Handler
 
getNumericFields(GenericDialog) - Method in class loci.plugins.in.ColorDialog
 
getNumericFields(GenericDialog) - Static method in class loci.plugins.util.WindowTools
 
getNumSeries() - Method in class loci.formats.in.LegacyND2Reader
 
getObject(int) - Method in class loci.formats.cache.ByteArraySource
 
getObject(int[]) - Method in class loci.formats.cache.Cache
Gets the cached object at the given dimensional position.
getObject(int) - Method in class loci.formats.cache.CacheSource
 
getObject(int) - Method in interface loci.formats.cache.ICacheSource
Get the object corresponding to the given index.
getObject(int) - Method in class loci.formats.gui.BufferedImageSource
 
getObject(int) - Method in class loci.plugins.util.ImageProcessorSource
 
getObjectCount() - Method in class loci.formats.cache.CacheSource
 
getObjectCount() - Method in interface loci.formats.cache.ICacheSource
Get the total number of objects that this source can retrieve.
getObjectCount() - Method in class loci.formats.gui.BufferedImageSource
 
getObjectCount() - Method in class loci.plugins.util.ImageProcessorSource
 
getObjectiveLens() - Method in class loci.formats.in.PrairieMetadata.Frame
Gets the objective lens string for this Frame.
getObjectiveLensNA() - Method in class loci.formats.in.PrairieMetadata.Frame
Gets the numerical aperture of the lens for this Frame.
getObjectiveManufacturer() - Method in class loci.formats.in.PrairieMetadata.Frame
Extracts the objective manufacturer from the objective lens string.
getObjectiveModel() - Method in class loci.formats.in.ND2Handler
 
getObjectiveName(int, int, int, int) - Method in class loci.formats.in.LegacyND2Reader
 
getOffset(int) - Method in class loci.formats.in.PrairieMetadata.Frame
Gets the cth offset for this Frame.
getOMEMetadata(MetadataRetrieve) - Method in interface loci.formats.services.OMEXMLService
Returns a OMEXMLMetadata object with the same contents as the given MetadataRetrieve, converting it if necessary.
getOMEMetadata(MetadataRetrieve) - Method in class loci.formats.services.OMEXMLServiceImpl
 
getOMEMetadata() - Method in class loci.plugins.in.ImportProcess
Valid only after ImportStep.READER.
getOMEXML(String) - Method in class loci.formats.out.OMETiffWriter
 
getOMEXML(MetadataRetrieve) - Method in interface loci.formats.services.OMEXMLService
Extracts an OME-XML metadata string from the given metadata object, by converting to an OME-XML metadata object if necessary.
getOMEXML(MetadataRetrieve) - Method in class loci.formats.services.OMEXMLServiceImpl
 
getOMEXML() - Method in class loci.plugins.in.ImportProcess
Valid only after ImportStep.READER.
getOmeXmlMetadata() - Method in class loci.formats.in.FakeReader
 
getOmeXmlService() - Method in class loci.formats.in.FakeReader
 
getOMEXMLVersion(Object) - Method in interface loci.formats.services.OMEXMLService
Gets the schema version for the given OME-XML metadata or root object (e.g., "2007-06" or "2003-FC").
getOMEXMLVersion(Object) - Method in class loci.formats.services.OMEXMLServiceImpl
 
getOnDemandStripOffsets() - Method in class loci.formats.tiff.IFD
 
getOpenAllSeriesInfo() - Method in class loci.plugins.in.ImporterOptions
 
getOpticalZoom() - Method in class loci.formats.in.PrairieMetadata.Frame
Gets the optical zoom associated with this Frame.
getOptimalTileHeight() - Method in class loci.formats.DelegateReader
 
getOptimalTileHeight() - Method in class loci.formats.FormatReader
 
getOptimalTileHeight() - Method in interface loci.formats.IFormatReader
Returns the optimal sub-image height for use with openBytes.
getOptimalTileHeight() - Method in class loci.formats.ImageReader
 
getOptimalTileHeight() - Method in class loci.formats.in.AFIReader
 
getOptimalTileHeight() - Method in class loci.formats.in.AmiraReader
 
getOptimalTileHeight() - Method in class loci.formats.in.APLReader
 
getOptimalTileHeight() - Method in class loci.formats.in.BaseZeissReader
 
getOptimalTileHeight() - Method in class loci.formats.in.BDReader
 
getOptimalTileHeight() - Method in class loci.formats.in.BioRadReader
 
getOptimalTileHeight() - Method in class loci.formats.in.CellH5Reader
 
getOptimalTileHeight() - Method in class loci.formats.in.CellSensReader
 
getOptimalTileHeight() - Method in class loci.formats.in.EPSReader
 
getOptimalTileHeight() - Method in class loci.formats.in.FlexReader
 
getOptimalTileHeight() - Method in class loci.formats.in.FV1000Reader
 
getOptimalTileHeight() - Method in class loci.formats.in.HamamatsuVMSReader
 
getOptimalTileHeight() - Method in class loci.formats.in.ImageIOReader
 
getOptimalTileHeight() - Method in class loci.formats.in.ImarisHDFReader
 
getOptimalTileHeight() - Method in class loci.formats.in.InCellReader
 
getOptimalTileHeight() - Method in class loci.formats.in.IPWReader
 
getOptimalTileHeight() - Method in class loci.formats.in.L2DReader
 
getOptimalTileHeight() - Method in class loci.formats.in.LeicaReader
 
getOptimalTileHeight() - Method in class loci.formats.in.LeicaSCNReader
 
getOptimalTileHeight() - Method in class loci.formats.in.LIFReader
 
getOptimalTileHeight() - Method in class loci.formats.in.MIASReader
 
getOptimalTileHeight() - Method in class loci.formats.in.MicromanagerReader
 
getOptimalTileHeight() - Method in class loci.formats.in.MinimalTiffReader
 
getOptimalTileHeight() - Method in class loci.formats.in.ND2Reader
 
getOptimalTileHeight() - Method in class loci.formats.in.NDPIReader
 
getOptimalTileHeight() - Method in class loci.formats.in.NDPISReader
 
getOptimalTileHeight() - Method in class loci.formats.in.NRRDReader
 
getOptimalTileHeight() - Method in class loci.formats.in.OMETiffReader
 
getOptimalTileHeight() - Method in class loci.formats.in.OpenlabReader
 
getOptimalTileHeight() - Method in class loci.formats.in.PCIReader
 
getOptimalTileHeight() - Method in class loci.formats.in.PerkinElmerReader
 
getOptimalTileHeight() - Method in class loci.formats.in.PrairieReader
 
getOptimalTileHeight() - Method in class loci.formats.in.PyramidTiffReader
 
getOptimalTileHeight() - Method in class loci.formats.in.ScanrReader
 
getOptimalTileHeight() - Method in class loci.formats.in.SVSReader
 
getOptimalTileHeight() - Method in class loci.formats.in.TrestleReader
 
getOptimalTileHeight() - Method in class loci.formats.in.VectraReader
 
getOptimalTileHeight() - Method in class loci.formats.in.VentanaReader
 
getOptimalTileHeight() - Method in class loci.formats.in.VisitechReader
 
getOptimalTileHeight() - Method in class loci.formats.in.ZeissCZIReader
 
getOptimalTileHeight() - Method in class loci.formats.in.ZeissLSMReader
 
getOptimalTileHeight() - Method in class loci.formats.ReaderWrapper
 
getOptimalTileHeight() - Method in class loci.formats.WrappedReader
 
getOptimalTileWidth() - Method in class loci.formats.DelegateReader
 
getOptimalTileWidth() - Method in class loci.formats.FormatReader
 
getOptimalTileWidth() - Method in interface loci.formats.IFormatReader
Returns the optimal sub-image width for use with openBytes.
getOptimalTileWidth() - Method in class loci.formats.ImageReader
 
getOptimalTileWidth() - Method in class loci.formats.in.AFIReader
 
getOptimalTileWidth() - Method in class loci.formats.in.APLReader
 
getOptimalTileWidth() - Method in class loci.formats.in.BDReader
 
getOptimalTileWidth() - Method in class loci.formats.in.CellSensReader
 
getOptimalTileWidth() - Method in class loci.formats.in.EPSReader
 
getOptimalTileWidth() - Method in class loci.formats.in.FlexReader
 
getOptimalTileWidth() - Method in class loci.formats.in.FV1000Reader
 
getOptimalTileWidth() - Method in class loci.formats.in.HamamatsuVMSReader
 
getOptimalTileWidth() - Method in class loci.formats.in.ImarisHDFReader
 
getOptimalTileWidth() - Method in class loci.formats.in.InCellReader
 
getOptimalTileWidth() - Method in class loci.formats.in.IPWReader
 
getOptimalTileWidth() - Method in class loci.formats.in.L2DReader
 
getOptimalTileWidth() - Method in class loci.formats.in.LeicaReader
 
getOptimalTileWidth() - Method in class loci.formats.in.LeicaSCNReader
 
getOptimalTileWidth() - Method in class loci.formats.in.MIASReader
 
getOptimalTileWidth() - Method in class loci.formats.in.MicromanagerReader
 
getOptimalTileWidth() - Method in class loci.formats.in.MinimalTiffReader
 
getOptimalTileWidth() - Method in class loci.formats.in.NDPIReader
 
getOptimalTileWidth() - Method in class loci.formats.in.NDPISReader
 
getOptimalTileWidth() - Method in class loci.formats.in.OMETiffReader
 
getOptimalTileWidth() - Method in class loci.formats.in.PCIReader
 
getOptimalTileWidth() - Method in class loci.formats.in.PerkinElmerReader
 
getOptimalTileWidth() - Method in class loci.formats.in.PrairieReader
 
getOptimalTileWidth() - Method in class loci.formats.in.PyramidTiffReader
 
getOptimalTileWidth() - Method in class loci.formats.in.ScanrReader
 
getOptimalTileWidth() - Method in class loci.formats.in.SVSReader
 
getOptimalTileWidth() - Method in class loci.formats.in.TrestleReader
 
getOptimalTileWidth() - Method in class loci.formats.in.VectraReader
 
getOptimalTileWidth() - Method in class loci.formats.in.VentanaReader
 
getOptimalTileWidth() - Method in class loci.formats.in.ZeissCZIReader
 
getOptimalTileWidth() - Method in class loci.formats.ReaderWrapper
 
getOptimalTileWidth() - Method in class loci.formats.WrappedReader
 
getOptimalWidth() - Method in class loci.formats.in.ZeissLSMReader
 
getOption(String) - Method in class loci.plugins.prefs.OptionsList
Gets the option with the given key.
getOptions() - Method in class loci.formats.ClassList
Gets the list of options as a map.
getOptions(CodecOptions) - Static method in class loci.formats.codec.WrappedCodec
 
getOptions() - Method in class loci.plugins.in.ImportProcess
 
getOrder() - Method in class loci.formats.cache.CacheStrategy
 
getOrder() - Method in interface loci.formats.cache.ICacheStrategy
Retrieves the order in which objects should be loaded along each axis.
getOrgX() - Method in interface loci.formats.services.WlzService
Gets column origin.
getOrgX() - Method in class loci.formats.services.WlzServiceImpl
 
getOrgY() - Method in interface loci.formats.services.WlzService
Gets line origin.
getOrgY() - Method in class loci.formats.services.WlzServiceImpl
 
getOrgZ() - Method in interface loci.formats.services.WlzService
Gets plane origin.
getOrgZ() - Method in class loci.formats.services.WlzServiceImpl
 
getOriginalIndex(int) - Method in class loci.formats.ChannelMerger
Returns the image number in the original dataset that corresponds to the given image number.
getOriginalIndex(int) - Method in class loci.formats.ChannelSeparator
Returns the image number in the original dataset that corresponds to the given image number.
getOriginalMetadata(OMEXMLMetadata) - Method in interface loci.formats.services.OMEXMLService
Parse any OriginalMetadata annotations from the given OME-XML metadata object and store them in a Hashtable.
getOriginalMetadata(OMEXMLMetadata) - Method in class loci.formats.services.OMEXMLServiceImpl
 
getOriginalMetadata() - Method in class loci.plugins.in.ImportProcess
Valid only after ImportStep.METADATA.
getOriginalOrder() - Method in class loci.formats.AxisGuesser
Gets the original dimension order.
getOriginalOrder() - Method in class loci.formats.FileStitcher.ExternalSeries
 
getParent(int) - Method in class loci.formats.in.LeicaSCNReader
 
getParentName(Integer) - Method in class loci.formats.in.VolocityReader
 
getPath(PrairieMetadata.PFile) - Method in class loci.formats.in.PrairieReader
Gets the absolute path to the filename of the given PrairieMetadata.PFile.
getPath() - Method in class loci.plugins.util.BFVirtualStack
 
getPattern() - Method in class loci.formats.FilePattern
Gets the file pattern string.
getPhotometricInterpretation() - Method in class loci.formats.tiff.IFD
Retrieves the image's photometric interpretation (TIFF tag PhotometricInterpretation) from this IFD.
getPhysicalSize(Double, String) - Static method in class loci.formats.FormatTools
 
getPhysicalSizes() - Method in class loci.formats.in.SVSReader
 
getPhysicalSizeX(Double) - Static method in class loci.formats.FormatTools
Formats the input value for the physical size in X into a length in microns
getPhysicalSizeX(Double, String) - Static method in class loci.formats.FormatTools
Formats the input value for the physical size in X into a length of the given unit.
getPhysicalSizeX(Double, Unit<Length>) - Static method in class loci.formats.FormatTools
Formats the input value for the physical size in X into a length of the given unit.
getPhysicalSizeY(Double) - Static method in class loci.formats.FormatTools
Formats the input value for the physical size in Y into a length in microns
getPhysicalSizeY(Double, String) - Static method in class loci.formats.FormatTools
Formats the input value for the physical size in Y into a length of the given unit.
getPhysicalSizeY(Double, Unit<Length>) - Static method in class loci.formats.FormatTools
Formats the input value for the physical size in Y into a length of the given unit.
getPhysicalSizeZ(Double) - Static method in class loci.formats.FormatTools
Formats the input value for the physical size in Z into a length in microns.
getPhysicalSizeZ(Double, String) - Static method in class loci.formats.FormatTools
Formats the input value for the physical size in Z into a length of the given unit.
getPhysicalSizeZ(Double, Unit<Length>) - Static method in class loci.formats.FormatTools
Formats the input value for the physical size in Z into a length of the given unit.
getPictDimensions(byte[]) - Method in class loci.formats.gui.LegacyQTTools
Gets width and height for the given PICT bytes.
getPinholeSize() - Method in class loci.formats.in.ND2Handler
 
getPixel(int, int) - Method in class loci.plugins.util.RecordedImageProcessor
 
getPixel(int, int, int[]) - Method in class loci.plugins.util.RecordedImageProcessor
 
getPixelBytes(BufferedImage, boolean) - Static method in class loci.formats.gui.AWTImageTools
Return a 2D array of bytes representing the image.
getPixelBytes(WritableRaster, boolean) - Static method in class loci.formats.gui.AWTImageTools
Return a 2D array of bytes representing the image.
getPixelBytes(BufferedImage, boolean, int, int, int, int) - Static method in class loci.formats.gui.AWTImageTools
Return a 2D array of bytes representing the image.
getPixelBytes(WritableRaster, boolean, int, int, int, int) - Static method in class loci.formats.gui.AWTImageTools
Return a 2D array of bytes representing the image.
getPixelCount() - Method in class loci.plugins.util.RecordedImageProcessor
 
getPixelFormat(byte[]) - Method in class loci.formats.services.JPEGXRServiceImpl
 
getPixelInterpolated(double, double) - Method in class loci.plugins.util.RecordedImageProcessor
 
getPixels(BufferedImage) - Static method in class loci.formats.gui.AWTImageTools
Gets the image's pixel data as arrays of primitives, one per channel.
getPixels(BufferedImage, int, int, int, int) - Static method in class loci.formats.gui.AWTImageTools
Gets the image's pixel data as arrays of primitives, one per channel.
getPixels(WritableRaster) - Static method in class loci.formats.gui.AWTImageTools
Gets the raster's pixel data as arrays of primitives, one per channel.
getPixels(WritableRaster, int, int, int, int) - Static method in class loci.formats.gui.AWTImageTools
Gets the raster's pixel data as arrays of primitives, one per channel.
getPixels() - Method in class loci.plugins.util.RecordedImageProcessor
 
getPixelsCopy() - Method in class loci.plugins.util.RecordedImageProcessor
 
getPixelSize(int) - Static method in class org.libjpegturbo.turbojpeg.TJ
Returns the pixel size (in bytes) of the given pixel format.
getPixelSizeX() - Method in class loci.formats.in.MetamorphHandler
 
getPixelSizeX() - Method in class loci.formats.in.ND2Handler
 
getPixelSizeY() - Method in class loci.formats.in.MetamorphHandler
 
getPixelSizeY() - Method in class loci.formats.in.ND2Handler
 
getPixelSizeZ() - Method in class loci.formats.in.ND2Handler
 
getPixelsPerLine() - Method in class loci.formats.in.PrairieMetadata.Frame
Gets the pixels per line for this Frame.
getPixelsPhysicalSizeX(Double[]) - Method in class loci.plugins.macro.LociFunctions
 
getPixelsPhysicalSizeY(Double[]) - Method in class loci.plugins.macro.LociFunctions
 
getPixelsPhysicalSizeZ(Double[]) - Method in class loci.plugins.macro.LociFunctions
 
getPixelsTimeIncrement(Double[]) - Method in class loci.plugins.macro.LociFunctions
 
getPixelString(int) - Method in class loci.formats.in.DeltavisionReader
Get a descriptive string representing the pixel type.
getPixelType() - Method in class loci.formats.FileStitcher
 
getPixelType() - Method in class loci.formats.FormatReader
 
getPixelType(String) - Method in class loci.formats.FormatReader
getPixelType(BufferedImage) - Static method in class loci.formats.gui.AWTImageTools
Gets the pixel type of the given image.
getPixelType() - Method in interface loci.formats.IFormatReader
Gets the pixel type.
getPixelType() - Method in class loci.formats.ImageReader
 
getPixelType(int) - Method in class loci.formats.in.DeltavisionReader
Get the OME pixel type from the pixel type stored in the file.
getPixelType(int) - Method in class loci.formats.in.OBFReader
 
getPixelType(String) - Static method in class loci.formats.MetadataTools
Retrieves an PixelType enumeration value for the given String.
getPixelType() - Method in class loci.formats.ReaderWrapper
 
getPixelType() - Method in interface loci.formats.services.WlzService
Gets the image pixel type.
getPixelType() - Method in class loci.formats.services.WlzServiceImpl
 
getPixelType() - Method in class loci.formats.tiff.IFD
Retrieves the image's pixel type based on the BitsPerSample tag.
getPixelType() - Method in class loci.formats.WrappedReader
 
getPixelType(String[]) - Method in class loci.plugins.macro.LociFunctions
 
getPixelTypeFromString(String) - Method in class loci.formats.in.LiFlimReader
 
getPixelTypes() - Method in class loci.formats.FormatWriter
 
getPixelTypes(String) - Method in class loci.formats.FormatWriter
 
getPixelTypes() - Method in interface loci.formats.IFormatWriter
Gets the supported pixel types.
getPixelTypes(String) - Method in interface loci.formats.IFormatWriter
Gets the supported pixel types for the given codec.
getPixelTypes() - Method in class loci.formats.ImageWriter
 
getPixelTypes(String) - Method in class loci.formats.ImageWriter
 
getPixelTypes(String) - Method in class loci.formats.out.APNGWriter
 
getPixelTypes(String) - Method in class loci.formats.out.AVIWriter
 
getPixelTypes(String) - Method in class loci.formats.out.CellH5Writer
 
getPixelTypes(String) - Method in class loci.formats.out.EPSWriter
 
getPixelTypes(String) - Method in class loci.formats.out.ICSWriter
 
getPixelTypes(String) - Method in class loci.formats.out.ImageIOWriter
 
getPixelTypes(String) - Method in class loci.formats.out.JavaWriter
 
getPixelTypes(String) - Method in class loci.formats.out.JPEG2000Writer
Overridden to return the formats supported by the writer.
getPixelTypes(String) - Method in class loci.formats.out.JPEGWriter
 
getPixelTypes(String) - Method in class loci.formats.out.OMEXMLWriter
 
getPixelTypes(String) - Method in class loci.formats.out.QTWriter
 
getPixelTypes(String) - Method in class loci.formats.out.TiffWriter
 
getPixelTypes(String) - Method in class loci.formats.out.V3DrawWriter
 
getPixelTypes(String) - Method in class loci.formats.out.WlzWriter
 
getPixelTypes() - Method in class loci.formats.WriterWrapper
 
getPixelTypes(String) - Method in class loci.formats.WriterWrapper
 
getPixelTypeString(int) - Static method in class loci.formats.FormatTools
Takes a pixel type value and gets a corresponding string representation.
getPixelValue(int, int) - Method in class loci.plugins.util.RecordedImageProcessor
 
getPlanarConfiguration() - Method in class loci.formats.tiff.IFD
Retrieves the image's planar configuration (TIFF tag PlanarConfiguration) from this IFD.
getPlane(int, int) - Method in class loci.formats.in.FV1000Reader
 
getPlane(int[]) - Method in class loci.formats.in.OpenlabReader
 
getPlaneByteOffset(int, int, int) - Method in class loci.formats.in.DeltavisionReader
Given any specific Z, W, and T of a plane, determine the absolute byte offset of the plane in the file.
getPlaneCount() - Method in class loci.formats.FormatWriter
Retrieve the total number of planes in the current series.
getPlaneCount(int) - Method in class loci.formats.FormatWriter
Retrieve the total number of planes in given series.
getPlaneCount() - Method in class loci.formats.out.CellH5Writer
 
getPlaneCount() - Method in class loci.formats.out.TiffWriter
 
getPlaneIndex(int, int) - Method in class loci.formats.in.DeltavisionReader
 
getPlaneIndex(IFormatReader, int) - Static method in class loci.plugins.macro.LociFunctions
Finds the Plane index corresponding to the given image plane number.
getPlaneMaximum(int) - Method in class loci.formats.MinMaxCalculator
Retrieves the maximum pixel value for the specified plane.
getPlaneMinimum(int) - Method in class loci.formats.MinMaxCalculator
Retrieves the minimum pixel value for the specified plane.
getPlanePositionX(Double[], Double) - Method in class loci.plugins.macro.LociFunctions
 
getPlanePositionY(Double[], Double) - Method in class loci.plugins.macro.LociFunctions
 
getPlanePositionZ(Double[], Double) - Method in class loci.plugins.macro.LociFunctions
 
getPlanes() - Method in class loci.formats.in.CV7000Reader.MeasurementDataHandler
 
getPlanes() - Method in class loci.formats.in.OperettaReader.OperettaHandler
 
getPlaneSize(IFormatReader) - Static method in class loci.formats.FormatTools
Returns the size in bytes of a single plane.
getPlaneSize(IFormatReader, int, int) - Static method in class loci.formats.FormatTools
Returns the size in bytes of a w * h tile.
getPlanesToLoad(int) - Method in class loci.plugins.in.ImagePlusReader
 
getPlaneTimingDeltaT(Double[], Double) - Method in class loci.plugins.macro.LociFunctions
 
getPlaneTimingExposureTime(Double[], Double) - Method in class loci.plugins.macro.LociFunctions
 
getPlateColumns() - Method in class loci.formats.in.ColumbusReader.MeasurementHandler
 
getPlateColumns() - Method in class loci.formats.in.CV7000Reader.WPIHandler
 
getPlateColumns() - Method in class loci.formats.in.OperettaReader.OperettaHandler
 
getPlateDescription() - Method in class loci.formats.in.CV7000Reader.WPIHandler
 
getPlateDescription() - Method in class loci.formats.in.OperettaReader.OperettaHandler
 
getPlateID() - Method in class loci.formats.in.CV7000Reader.WPIHandler
 
getPlateIdentifier() - Method in class loci.formats.in.OperettaReader.OperettaHandler
 
getPlateName(String) - Method in class loci.formats.in.CellomicsReader
 
getPlateName() - Method in class loci.formats.in.ColumbusReader.MeasurementHandler
 
getPlateName() - Method in class loci.formats.in.CV7000Reader.WPIHandler
 
getPlateName() - Method in class loci.formats.in.OperettaReader.OperettaHandler
 
getPlateRows() - Method in class loci.formats.in.ColumbusReader.MeasurementHandler
 
getPlateRows() - Method in class loci.formats.in.CV7000Reader.WPIHandler
 
getPlateRows() - Method in class loci.formats.in.OperettaReader.OperettaHandler
 
getPlateType() - Method in class loci.formats.in.ColumbusReader.MeasurementHandler
 
getPoints() - Method in enum loci.formats.in.BaseZeissReader.FeatureType
 
getPoints(int) - Method in class loci.formats.in.FakeReader
 
getPos(int) - Method in class loci.formats.in.FluoviewReader
 
getPosition(int) - Method in class loci.formats.in.ZeissLSMReader
 
getPositionFromFile(String) - Method in class loci.formats.in.MIASReader
Returns an array of length 5 that contains the well, time point, Z and channel indices corresponding to the given analysis file.
getPositionNames() - Method in class loci.formats.in.ND2Handler
 
getPositionX() - Method in class loci.formats.in.PrairieMetadata.Frame
Gets the X stage position associated with this Frame.
getPositionY() - Method in class loci.formats.in.PrairieMetadata.Frame
Gets the Y stage position associated with this Frame.
getPositionZ() - Method in class loci.formats.in.PrairieMetadata.Frame
Gets the Z stage position associated with this Frame.
getPossible(String) - Method in class loci.plugins.prefs.OptionsList
Gets the possible values for the string option with the given key.
getPossible() - Method in class loci.plugins.prefs.StringOption
Gets the list of possible values.
getPossibleDomains(String) - Method in class loci.formats.FormatReader
 
getPossibleDomains(String) - Method in interface loci.formats.IFormatReader
Returns a list of scientific domains in which this format is used.
getPossibleDomains(String) - Method in class loci.formats.ImageReader
 
getPossibleDomains(String) - Method in class loci.formats.ReaderWrapper
 
getPossibleDomains(String) - Method in class loci.formats.WrappedReader
 
getPossiblePositions() - Method in class loci.formats.cache.CacheStrategy
Gets positions to consider for possible inclusion in the cache, assuming a current position at the origin (0).
getPossiblePositions() - Method in class loci.formats.cache.CrosshairStrategy
 
getPossiblePositions() - Method in class loci.formats.cache.RectangleStrategy
 
getPowers() - Method in class loci.formats.in.ND2Handler
 
getPref(String, Class<? extends IFormatReader>, boolean) - Static method in class loci.plugins.util.LociPrefs
 
getPreferredSize() - Method in class loci.formats.gui.CacheIndicator
 
getPreferredSize() - Method in class loci.formats.gui.PreviewPane
 
getPrefix() - Method in class loci.formats.FilePattern
Gets the pattern's substring that comes before any block sections.
getPrefix(int) - Method in class loci.formats.FilePattern
Gets the pattern's substring between block i-1 (or the beginning of the pattern, if i is 0) and block i.
getPrefix(String) - Method in class loci.formats.in.ZeissTIFFReader
 
getPrefixes() - Method in class loci.formats.FilePattern
Gets all block prefixes.
getPrefixMetadataName(String) - Method in class loci.formats.in.MicromanagerReader
 
getPreviewNameIndex(String) - Method in class loci.formats.in.FV1000Reader
 
getPriorities() - Method in class loci.formats.cache.CacheStrategy
 
getPriorities() - Method in interface loci.formats.cache.ICacheStrategy
Retrieves the priority for caching each axis.
getProcessor(int) - Method in class loci.plugins.util.BFVirtualStack
 
getPulse(String) - Method in class loci.formats.FormatReader
getPulse(String) - Static method in class loci.formats.MetadataTools
Retrieves an Pulse enumeration value for the given String.
getQTVersion() - Method in class loci.formats.gui.LegacyQTTools
Gets the QuickTime for Java version number.
getQuietInfo() - Method in class loci.plugins.in.ImporterOptions
 
getRange() - Method in class loci.formats.cache.CacheStrategy
 
getRange() - Method in interface loci.formats.cache.ICacheStrategy
Retrieves the number of objects to cache along each axis.
getRasterLength(int[]) - Static method in class loci.formats.FormatTools
Computes the number of raster values for a positional array with the given lengths.
getReader(int) - Method in class loci.formats.FileStitcher.ExternalSeries
 
getReader() - Method in class loci.formats.FileStitcher
Gets the wrapped reader prototype.
getReader(int) - Method in class loci.formats.FileStitcher
Gets the reader appropriate for use with the given image plane.
getReader(int, int) - Method in class loci.formats.FileStitcher
Gets the reader that should be used with the given series and image plane.
getReader(IFormatReader, Class<? extends IFormatReader>) - Static method in class loci.formats.FormatTools
Recursively look for the first underlying reader that is an instance of the given class.
getReader() - Method in class loci.formats.gui.FormatFileFilter
Returns the filter's reader.
getReader(String) - Method in class loci.formats.ImageReader
Gets the reader used to open the given file.
getReader() - Method in class loci.formats.ImageReader
Gets the reader used to open the current file.
getReader(Class<? extends IFormatReader>) - Method in class loci.formats.ImageReader
Gets the file format reader instance matching the given class.
getReader(String, boolean) - Method in class loci.formats.in.CellWorxReader
 
getReader() - Method in class loci.formats.ReaderWrapper
Gets the wrapped reader.
getReader() - Method in class loci.formats.services.JAIIIOServiceImpl
Set up the JPEG-2000 image reader.
getReader() - Method in class loci.plugins.in.ImportProcess
Valid only after ImportStep.STACK.
getReader() - Method in class loci.plugins.util.BFVirtualStack
 
getReaders() - Method in class loci.formats.FileStitcher.ExternalSeries
 
getReaders() - Method in class loci.formats.ImageReader
Gets all constituent file format readers.
getReadOutRate() - Method in class loci.formats.in.MetamorphHandler
 
getRealSTKFile(Location) - Method in class loci.formats.in.MetamorphReader
Check that the given STK file exists.
getRecordedProcessor() - Method in class loci.plugins.util.BFVirtualStack
 
getRed(int) - Method in class loci.formats.gui.Index16ColorModel
 
getRed(int) - Method in class loci.formats.gui.SignedColorModel
 
getRed(Object) - Method in class loci.formats.gui.SignedColorModel
 
getRed(int) - Method in class loci.formats.gui.UnsignedIntColorModel
 
getRed(Object) - Method in class loci.formats.gui.UnsignedIntColorModel
 
getRedOffset(int) - Static method in class org.libjpegturbo.turbojpeg.TJ
For the given pixel format, returns the number of bytes that the red component is offset from the start of the pixel.
getReds() - Method in class loci.formats.gui.Index16ColorModel
Return the array of red color components.
getRefractiveIndex() - Method in class loci.formats.in.ND2Handler
 
getRelativeTime() - Method in class loci.formats.in.PrairieMetadata.Frame
Gets the relativeTime associated with this Frame.
getReorderedIndex(IFormatReader, String, int) - Static method in class loci.formats.FormatTools
Converts index from the given dimension order to the reader's native one.
getReorderedIndex(String, String, int, int, int, int, int) - Static method in class loci.formats.FormatTools
Converts index from one dimension order to another.
getRequiredDirectories(String[]) - Method in class loci.formats.FileStitcher
 
getRequiredDirectories(String[]) - Method in class loci.formats.FormatReader
 
getRequiredDirectories(String[]) - Static method in class loci.formats.FormatTools
Returns the maximum number of directories below the common parent of a list of file paths
getRequiredDirectories(String[]) - Method in interface loci.formats.IFormatReader
Returns the number of parent directories that are important when processing the given list of files.
getRequiredDirectories(String[]) - Method in class loci.formats.ImageReader
 
getRequiredDirectories(String[]) - Method in class loci.formats.in.BrukerReader
 
getRequiredDirectories(String[]) - Method in class loci.formats.in.CellVoyagerReader
 
getRequiredDirectories(String[]) - Method in class loci.formats.in.ColumbusReader
 
getRequiredDirectories(String[]) - Method in class loci.formats.in.CV7000Reader
 
getRequiredDirectories(String[]) - Method in class loci.formats.in.DicomReader
 
getRequiredDirectories(String[]) - Method in class loci.formats.in.MIASReader
 
getRequiredDirectories(String[]) - Method in class loci.formats.in.MicroCTReader
 
getRequiredDirectories(String[]) - Method in class loci.formats.in.OMETiffReader
 
getRequiredDirectories(String[]) - Method in class loci.formats.in.OperettaReader
 
getRequiredDirectories(String[]) - Method in class loci.formats.ReaderWrapper
 
getResolution() - Method in class loci.formats.FileStitcher
 
getResolution() - Method in class loci.formats.FormatReader
 
getResolution() - Method in class loci.formats.FormatWriter
 
getResolution() - Method in class loci.formats.ImageReader
 
getResolution() - Method in class loci.formats.ImageWriter
 
getResolution() - Method in interface loci.formats.IPyramidHandler
Get the current resolution level.
getResolution() - Method in class loci.formats.ReaderWrapper
 
getResolution() - Method in class loci.formats.SubResolutionFormatReader
 
getResolution() - Method in class loci.formats.WrappedReader
 
getResolution() - Method in class loci.formats.WriterWrapper
 
getResolutionCount() - Method in class loci.formats.FormatReader
 
getResolutionCount() - Method in class loci.formats.FormatWriter
 
getResolutionCount() - Method in class loci.formats.ImageReader
 
getResolutionCount() - Method in class loci.formats.ImageWriter
 
getResolutionCount() - Method in interface loci.formats.IPyramidHandler
Return the number of resolutions for the current series.
getResolutionCount(int) - Method in interface loci.formats.meta.IPyramidStore
Retrieve the number of pyramid resolutions defined for the given Image.
getResolutionCount(int) - Method in class loci.formats.ome.OMEPyramidStore
 
getResolutionCount() - Method in class loci.formats.ReaderWrapper
 
getResolutionCount() - Method in class loci.formats.SubResolutionFormatReader
 
getResolutionCount() - Method in class loci.formats.WrappedReader
 
getResolutionCount() - Method in class loci.formats.WriterWrapper
 
getResolutionLevels() - Method in class loci.formats.in.JPEG2000MetadataParser
Returns the number of resolution levels the file JPEG 2000 data has.
getResolutionMultiplier() - Method in class loci.formats.tiff.IFD
Retrieve the value by which to multiply the X and Y resolution so that the resolutions are in microns per pixel.
getResolutions() - Method in class loci.formats.FormatWriter
 
getResolutions() - Method in interface loci.formats.IFormatWriter
Get a list of resolution objects for the current series.
getResolutions() - Method in class loci.formats.ImageWriter
 
getResolutions() - Method in class loci.formats.WriterWrapper
 
getResolutionSizeX(int, int) - Method in interface loci.formats.meta.IPyramidStore
Retrieve the image width in pixels of the given pyramid resolution.
getResolutionSizeX(int, int) - Method in class loci.formats.ome.OMEPyramidStore
 
getResolutionSizeY(int, int) - Method in interface loci.formats.meta.IPyramidStore
Retrieve the image height in pixels of the given pyramid resolution.
getResolutionSizeY(int, int) - Method in class loci.formats.ome.OMEPyramidStore
 
getResolutionUnitFromComment(IFD) - Method in class loci.formats.in.BaseTiffReader
Extracts the resolution unit symbol from the comment field
getRestartMarkers() - Method in interface loci.formats.services.JPEGTurboService
 
getRestartMarkers() - Method in class loci.formats.services.JPEGTurboServiceImpl
 
getRevision(String[]) - Method in class loci.plugins.macro.LociFunctions
 
getRGBChannelCount() - Method in class loci.formats.FormatReader
 
getRGBChannelCount() - Method in interface loci.formats.IFormatReader
Gets the number of channels returned with each call to openBytes.
getRGBChannelCount() - Method in class loci.formats.ImageReader
 
getRGBChannelCount() - Method in class loci.formats.ReaderWrapper
 
getRGBChannelCount() - Method in class loci.formats.WrappedReader
 
getRGBChannelCount(Double[]) - Method in class loci.plugins.macro.LociFunctions
 
getRoi() - Method in class loci.plugins.util.RecordedImageProcessor
 
getROIs() - Method in class loci.formats.in.ND2Handler
 
getROIs() - Method in class loci.formats.in.SPEReader.SpeHeader
Method used to read and return meta data for upto 10 rectangular ROI's stored in the SPE header table
getROIsMode() - Method in class loci.plugins.in.ImporterOptions
 
getROIsModeInfo() - Method in class loci.plugins.in.ImporterOptions
 
getROIsModes() - Method in class loci.plugins.in.ImporterOptions
 
getRotationTransform(double) - Method in class loci.formats.FormatReader
Construct an AffineTransform corresponding to the given angle.
getRow() - Method in class loci.formats.in.OMEXMLReader.BinData
 
getRow(int, int, int[], int) - Method in class loci.plugins.util.RecordedImageProcessor
 
getRowCount(int) - Method in interface loci.formats.services.MetakitService
 
getRowCount(String) - Method in interface loci.formats.services.MetakitService
 
getRowCount(int) - Method in class loci.formats.services.MetakitServiceImpl
 
getRowCount(String) - Method in class loci.formats.services.MetakitServiceImpl
 
getRowData(String[], double[]) - Method in class loci.formats.in.TextReader
Parses numerical row data from the given tokens.
getRowData(int, String) - Method in interface loci.formats.services.MetakitService
 
getRowData(int, int) - Method in interface loci.formats.services.MetakitService
 
getRowData(int, String) - Method in class loci.formats.services.MetakitServiceImpl
 
getRowData(int, int) - Method in class loci.formats.services.MetakitServiceImpl
 
getRowsPerStrip() - Method in class loci.formats.tiff.IFD
Retrieves the number of rows per strip for image (TIFF tag RowsPerStrip) from this IFD.
getSample(BitBuffer, CodecOptions) - Method in class loci.formats.codec.HuffmanCodec
Deprecated.
getSample(RandomAccessInputStream, CodecOptions) - Method in class loci.formats.codec.HuffmanCodec
 
getSamples(IFD, byte[]) - Method in class loci.formats.tiff.TiffParser
 
getSamples(IFD, byte[], int, int, long, long) - Method in class loci.formats.tiff.TiffParser
 
getSamples(IFD, byte[], int, int, long, long, int, int) - Method in class loci.formats.tiff.TiffParser
 
getSamplesPerPixel() - Method in class loci.formats.FormatWriter
Retrieve the number of samples per pixel for the current series.
getSamplesPerPixel(int) - Method in class loci.formats.FormatWriter
Retrieve the number of samples per pixel for given series.
getSamplesPerPixel() - Method in class loci.formats.tiff.IFD
Retrieves the number of samples per pixel for the image (TIFF tag SamplesPerPixel) from this IFD.
getScale(int) - Method in class loci.formats.in.VentanaReader
 
getScaled(int) - Method in class org.libjpegturbo.turbojpeg.TJScalingFactor
Returns the scaled value of dimension.
getScaledHeight(int, int) - Method in class org.libjpegturbo.turbojpeg.TJDecompressor
Returns the height of the largest scaled down image that the TurboJPEG decompressor can generate without exceeding the desired image width and height.
getScaledWidth(int, int) - Method in class org.libjpegturbo.turbojpeg.TJDecompressor
Returns the width of the largest scaled down image that the TurboJPEG decompressor can generate without exceeding the desired image width and height.
getScalingFactors() - Static method in class org.libjpegturbo.turbojpeg.TJ
Returns a list of fractional scaling factors that the JPEG decompressor in this implementation of TurboJPEG supports.
getScanline(int) - Method in class loci.formats.codec.JPEGTileDecoder
 
getScanlinePad() - Method in class loci.formats.in.NativeND2Reader
 
getScanNames() - Method in class loci.formats.in.L2DReader
Return a list of scan names.
getScanProfileXML() - Method in class loci.formats.in.VectraReader
Returns an XML string corresponding to the ScanProfile node.
getScreenName() - Method in class loci.formats.in.ColumbusReader.MeasurementHandler
 
getSequence() - Method in class loci.formats.in.PrairieMetadata.Frame
Gets the <Sequence> containing this <Frame>.
getSequence(int) - Method in class loci.formats.in.PrairieMetadata
Gets the Sequence at the given cycle.
getSequences() - Method in class loci.formats.in.PrairieMetadata
Gets all Sequences, ordered by cycle.
getSeries() - Method in class loci.formats.FileStitcher
 
getSeries() - Method in class loci.formats.FormatReader
 
getSeries() - Method in class loci.formats.FormatWriter
 
getSeries() - Method in interface loci.formats.IFormatReader
Gets the currently active series.
getSeries() - Method in interface loci.formats.IFormatWriter
Returns the current series.
getSeries() - Method in class loci.formats.ImageReader
 
getSeries() - Method in class loci.formats.ImageWriter
 
getSeries() - Method in class loci.formats.ReaderWrapper
 
getSeries() - Method in class loci.formats.SubResolutionFormatReader
 
getSeries() - Method in class loci.formats.WrappedReader
 
getSeries() - Method in class loci.formats.WriterWrapper
 
getSeries(Double[]) - Method in class loci.plugins.macro.LociFunctions
 
getSeriesCount() - Method in class loci.formats.FileStitcher
 
getSeriesCount() - Method in class loci.formats.FormatReader
 
getSeriesCount() - Method in interface loci.formats.IFormatReader
Gets the number of series in this file.
getSeriesCount() - Method in class loci.formats.ImageReader
 
getSeriesCount() - Method in class loci.formats.in.ND2Handler
 
getSeriesCount() - Method in class loci.formats.ReaderWrapper
 
getSeriesCount() - Method in class loci.formats.SubResolutionFormatReader
 
getSeriesCount() - Method in class loci.formats.TileStitcher
 
getSeriesCount() - Method in class loci.formats.WrappedReader
 
getSeriesCount() - Method in class loci.plugins.in.ImportProcess
Valid only after ImportStep.STACK.
getSeriesCount(Double[]) - Method in class loci.plugins.macro.LociFunctions
 
getSeriesHashtable(int) - Method in class loci.formats.in.LeicaHandler
 
getSeriesIndex(int, int, int) - Method in class loci.formats.in.MetamorphTiffReader
 
getSeriesLabel(int) - Method in class loci.plugins.in.ImportProcess
Valid only after ImportStep.STACK.
getSeriesList() - Method in class loci.formats.CoreMetadataList
 
getSeriesMeta(String) - Method in class loci.formats.FormatReader
Gets an entry from the metadata table for the current series.
getSeriesMetadata() - Method in class loci.formats.FileStitcher
 
getSeriesMetadata() - Method in class loci.formats.FormatReader
 
getSeriesMetadata() - Method in interface loci.formats.IFormatReader
Obtains the hashtable containing metadata field/value pairs from the current series in the current file.
getSeriesMetadata() - Method in class loci.formats.ImageReader
 
getSeriesMetadata() - Method in class loci.formats.ReaderWrapper
 
getSeriesMetadata() - Method in class loci.formats.WrappedReader
 
getSeriesMetadataValue(String) - Method in class loci.formats.FormatReader
 
getSeriesMetadataValue(String) - Method in interface loci.formats.IFormatReader
Obtains the specified metadata field's value for the current series in the current file.
getSeriesMetadataValue(String) - Method in class loci.formats.ImageReader
 
getSeriesMetadataValue(String) - Method in class loci.formats.ReaderWrapper
 
getSeriesMetadataValue(String) - Method in class loci.formats.WrappedReader
 
getSeriesMetadataValue(String, String[]) - Method in class loci.plugins.macro.LociFunctions
 
getSeriesName(String[]) - Method in class loci.plugins.macro.LociFunctions
 
getSeriesUsedFiles(boolean) - Method in class loci.formats.DelegateReader
 
getSeriesUsedFiles() - Method in class loci.formats.FileStitcher
 
getSeriesUsedFiles(boolean) - Method in class loci.formats.FileStitcher
 
getSeriesUsedFiles() - Method in class loci.formats.FormatReader
 
getSeriesUsedFiles(boolean) - Method in class loci.formats.FormatReader
 
getSeriesUsedFiles() - Method in interface loci.formats.IFormatReader
Returns an array of filenames needed to open the current series.
getSeriesUsedFiles(boolean) - Method in interface loci.formats.IFormatReader
Returns an array of filenames needed to open the current series.
getSeriesUsedFiles() - Method in class loci.formats.ImageReader
 
getSeriesUsedFiles(boolean) - Method in class loci.formats.ImageReader
 
getSeriesUsedFiles(boolean) - Method in class loci.formats.in.AFIReader
 
getSeriesUsedFiles(boolean) - Method in class loci.formats.in.AnalyzeReader
 
getSeriesUsedFiles(boolean) - Method in class loci.formats.in.APLReader
 
getSeriesUsedFiles(boolean) - Method in class loci.formats.in.BDReader
 
getSeriesUsedFiles(boolean) - Method in class loci.formats.in.BioRadReader
 
getSeriesUsedFiles(boolean) - Method in class loci.formats.in.BrukerReader
 
getSeriesUsedFiles(boolean) - Method in class loci.formats.in.CellomicsReader
 
getSeriesUsedFiles(boolean) - Method in class loci.formats.in.CellSensReader
 
getSeriesUsedFiles(boolean) - Method in class loci.formats.in.CellVoyagerReader
 
getSeriesUsedFiles(boolean) - Method in class loci.formats.in.CellWorxReader
 
getSeriesUsedFiles(boolean) - Method in class loci.formats.in.ColumbusReader
 
getSeriesUsedFiles(boolean) - Method in class loci.formats.in.CV7000Reader
 
getSeriesUsedFiles(boolean) - Method in class loci.formats.in.DeltavisionReader
 
getSeriesUsedFiles(boolean) - Method in class loci.formats.in.DicomReader
 
getSeriesUsedFiles(boolean) - Method in class loci.formats.in.FakeReader
 
getSeriesUsedFiles(boolean) - Method in class loci.formats.in.FilePatternReader
 
getSeriesUsedFiles(boolean) - Method in class loci.formats.in.FlexReader
 
getSeriesUsedFiles(boolean) - Method in class loci.formats.in.FujiReader
 
getSeriesUsedFiles(boolean) - Method in class loci.formats.in.FV1000Reader
 
getSeriesUsedFiles(boolean) - Method in class loci.formats.in.HamamatsuVMSReader
 
getSeriesUsedFiles(boolean) - Method in class loci.formats.in.HitachiReader
 
getSeriesUsedFiles(boolean) - Method in class loci.formats.in.ICSReader
 
getSeriesUsedFiles(boolean) - Method in class loci.formats.in.ImagicReader
 
getSeriesUsedFiles(boolean) - Method in class loci.formats.in.ImprovisionTiffReader
 
getSeriesUsedFiles(boolean) - Method in class loci.formats.in.InCellReader
 
getSeriesUsedFiles(boolean) - Method in class loci.formats.in.JEOLReader
 
getSeriesUsedFiles(boolean) - Method in class loci.formats.in.JPEGReader
 
getSeriesUsedFiles(boolean) - Method in class loci.formats.in.L2DReader
 
getSeriesUsedFiles(boolean) - Method in class loci.formats.in.LeicaReader
 
getSeriesUsedFiles(boolean) - Method in class loci.formats.in.LIFReader
 
getSeriesUsedFiles(boolean) - Method in class loci.formats.in.MetamorphReader
 
getSeriesUsedFiles(boolean) - Method in class loci.formats.in.MIASReader
 
getSeriesUsedFiles(boolean) - Method in class loci.formats.in.MicroCTReader
 
getSeriesUsedFiles(boolean) - Method in class loci.formats.in.MicromanagerReader
 
getSeriesUsedFiles(boolean) - Method in class loci.formats.in.NativeQTReader
 
getSeriesUsedFiles(boolean) - Method in class loci.formats.in.NDPISReader
 
getSeriesUsedFiles(boolean) - Method in class loci.formats.in.NiftiReader
 
getSeriesUsedFiles(boolean) - Method in class loci.formats.in.NRRDReader
 
getSeriesUsedFiles(boolean) - Method in class loci.formats.in.OIRReader
 
getSeriesUsedFiles(boolean) - Method in class loci.formats.in.OMETiffReader
 
getSeriesUsedFiles(boolean) - Method in class loci.formats.in.OperettaReader
 
getSeriesUsedFiles(boolean) - Method in class loci.formats.in.PCORAWReader
 
getSeriesUsedFiles(boolean) - Method in class loci.formats.in.PDSReader
 
getSeriesUsedFiles(boolean) - Method in class loci.formats.in.PerkinElmerReader
 
getSeriesUsedFiles(boolean) - Method in class loci.formats.in.PrairieReader
 
getSeriesUsedFiles(boolean) - Method in class loci.formats.in.ScanrReader
 
getSeriesUsedFiles(boolean) - Method in class loci.formats.in.SEQReader
 
getSeriesUsedFiles(boolean) - Method in class loci.formats.in.SlidebookTiffReader
 
getSeriesUsedFiles(boolean) - Method in class loci.formats.in.SPCReader
 
getSeriesUsedFiles(boolean) - Method in class loci.formats.in.TCSReader
 
getSeriesUsedFiles(boolean) - Method in class loci.formats.in.TiffReader
 
getSeriesUsedFiles(boolean) - Method in class loci.formats.in.TillVisionReader
 
getSeriesUsedFiles(boolean) - Method in class loci.formats.in.TrestleReader
 
getSeriesUsedFiles(boolean) - Method in class loci.formats.in.VarianFDFReader
 
getSeriesUsedFiles(boolean) - Method in class loci.formats.in.VectraReader
 
getSeriesUsedFiles(boolean) - Method in class loci.formats.in.VisitechReader
 
getSeriesUsedFiles(boolean) - Method in class loci.formats.in.VolocityReader
 
getSeriesUsedFiles(boolean) - Method in class loci.formats.in.ZeissCZIReader
 
getSeriesUsedFiles(boolean) - Method in class loci.formats.in.ZeissLSMReader
 
getSeriesUsedFiles(boolean) - Method in class loci.formats.in.ZeissTIFFReader
 
getSeriesUsedFiles() - Method in class loci.formats.ReaderWrapper
 
getSeriesUsedFiles(boolean) - Method in class loci.formats.ReaderWrapper
 
getSeriesUsedFiles(boolean) - Method in class loci.formats.WrappedReader
 
getService() - Method in class loci.formats.Memoizer
 
getShape(String) - Method in interface loci.formats.services.JHDFService
Retrieves the shape of a dataset.
getShape(String) - Method in class loci.formats.services.JHDFServiceImpl
 
getShort(SPEReader.SpeHeaderEntry) - Method in class loci.formats.in.SPEReader.SpeHeader
Method used to retrieve data values for Short entries into the SPE header table
getShort(int) - Method in class loci.formats.in.SPEReader.SpeHeader
Private method used to retrieve a Short value from the SPE header
getShortArray(SPEReader.SpeHeaderEntry) - Method in class loci.formats.in.SPEReader.SpeHeader
Method used to retrieve data values for Short Array entries into the SPE header table
getShorts(BufferedImage) - Static method in class loci.formats.gui.AWTImageTools
Extracts pixel data as arrays of unsigned shorts, one per channel.
getShorts(WritableRaster) - Static method in class loci.formats.gui.AWTImageTools
Extracts pixel data as arrays of unsigned shorts, one per channel.
getShorts(WritableRaster, int, int, int, int) - Static method in class loci.formats.gui.AWTImageTools
Extracts pixel data as arrays of unsigned shorts, one per channel.
getShowMetadataInfo() - Method in class loci.plugins.in.ImporterOptions
 
getShowOMEXMLInfo() - Method in class loci.plugins.in.ImporterOptions
 
getShowROIsInfo() - Method in class loci.plugins.in.ImporterOptions
 
getSize(Image) - Static method in class loci.formats.gui.AWTImageTools
Gets the width and height of the given AWT image, waiting for it to finish loading if necessary.
getSize() - Method in class loci.plugins.util.BFVirtualStack
 
getSizeC() - Method in class loci.formats.ChannelFiller
 
getSizeC() - Method in class loci.formats.DimensionSwapper
 
getSizeC() - Method in class loci.formats.FileStitcher
 
getSizeC() - Method in class loci.formats.FormatReader
 
getSizeC() - Method in interface loci.formats.IFormatReader
Gets the size of the C dimension.
getSizeC() - Method in class loci.formats.ImageReader
 
getSizeC() - Method in class loci.formats.ReaderWrapper
 
getSizeC() - Method in interface loci.formats.services.WlzService
Gets number of channels.
getSizeC() - Method in class loci.formats.services.WlzServiceImpl
 
getSizeC() - Method in class loci.formats.WrappedReader
 
getSizeC(Double[]) - Method in class loci.plugins.macro.LociFunctions
 
getSizeT() - Method in class loci.formats.DimensionSwapper
 
getSizeT() - Method in class loci.formats.FileStitcher
 
getSizeT() - Method in class loci.formats.FormatReader
 
getSizeT() - Method in interface loci.formats.IFormatReader
Gets the size of the T dimension.
getSizeT() - Method in class loci.formats.ImageReader
 
getSizeT() - Method in class loci.formats.ReaderWrapper
 
getSizeT() - Method in interface loci.formats.services.WlzService
Gets number of time samples.
getSizeT() - Method in class loci.formats.services.WlzServiceImpl
 
getSizeT() - Method in class loci.formats.WrappedReader
 
getSizeT(Double[]) - Method in class loci.plugins.macro.LociFunctions
 
getSizeX() - Method in class loci.formats.DimensionSwapper
 
getSizeX() - Method in class loci.formats.FileStitcher
 
getSizeX() - Method in class loci.formats.FormatReader
 
getSizeX() - Method in class loci.formats.FormatWriter
 
getSizeX() - Method in interface loci.formats.IFormatReader
Gets the size of the X dimension.
getSizeX() - Method in class loci.formats.ImageReader
 
getSizeX() - Method in class loci.formats.ReaderWrapper
 
getSizeX() - Method in interface loci.formats.services.WlzService
Gets width in pixels/voxels.
getSizeX() - Method in class loci.formats.services.WlzServiceImpl
 
getSizeX() - Method in class loci.formats.TileStitcher
 
getSizeX() - Method in class loci.formats.WrappedReader
 
getSizeX(Double[]) - Method in class loci.plugins.macro.LociFunctions
 
getSizeY() - Method in class loci.formats.DimensionSwapper
 
getSizeY() - Method in class loci.formats.FileStitcher
 
getSizeY() - Method in class loci.formats.FormatReader
 
getSizeY() - Method in class loci.formats.FormatWriter
 
getSizeY() - Method in interface loci.formats.IFormatReader
Gets the size of the Y dimension.
getSizeY() - Method in class loci.formats.ImageReader
 
getSizeY() - Method in class loci.formats.ReaderWrapper
 
getSizeY() - Method in interface loci.formats.services.WlzService
Gets height in pixels/voxels.
getSizeY() - Method in class loci.formats.services.WlzServiceImpl
 
getSizeY() - Method in class loci.formats.TileStitcher
 
getSizeY() - Method in class loci.formats.WrappedReader
 
getSizeY(Double[]) - Method in class loci.plugins.macro.LociFunctions
 
getSizeZ() - Method in class loci.formats.DimensionSwapper
 
getSizeZ() - Method in class loci.formats.FileStitcher
 
getSizeZ() - Method in class loci.formats.FormatReader
 
getSizeZ() - Method in interface loci.formats.IFormatReader
Gets the size of the Z dimension.
getSizeZ() - Method in class loci.formats.ImageReader
 
getSizeZ() - Method in class loci.formats.ReaderWrapper
 
getSizeZ() - Method in interface loci.formats.services.WlzService
Gets depth (number of x-y planes) in voxels.
getSizeZ() - Method in class loci.formats.services.WlzServiceImpl
 
getSizeZ() - Method in class loci.formats.WrappedReader
 
getSizeZ(Double[]) - Method in class loci.plugins.macro.LociFunctions
 
getSliceLabelBaseIndex() - Static method in class loci.plugins.util.LociPrefs
 
getSliceLabelPattern() - Static method in class loci.plugins.util.LociPrefs
 
getSnapshotPixels() - Method in class loci.plugins.util.RecordedImageProcessor
 
getSource() - Method in class loci.formats.cache.Cache
Gets the cache's caching source.
getSource() - Method in class loci.formats.cache.CacheEvent
Gets the source of the cache update.
getSpecifyRangesInfo() - Method in class loci.plugins.in.ImporterOptions
 
getSpectra() - Method in class loci.formats.in.IM3Reader
If a Nuance file is a spectral library set (.csl) file, there is a spectral library inside that contains a profile of spectral bin magnitudes for each of several measured fluorophores (or auto fluorescence).
getSpeeds() - Method in class loci.formats.in.ND2Handler
 
getSplitChannelsInfo() - Method in class loci.plugins.in.ImporterOptions
 
getSplitFocalPlanesInfo() - Method in class loci.plugins.in.ImporterOptions
 
getSplitTimepointsInfo() - Method in class loci.plugins.in.ImporterOptions
 
getStackFormat() - Method in class loci.plugins.in.ImporterOptions
 
getStackFormatInfo() - Method in class loci.plugins.in.ImporterOptions
 
getStackFormats() - Method in class loci.plugins.in.ImporterOptions
 
getStackOrder() - Method in class loci.plugins.in.ImporterOptions
 
getStackOrder() - Method in class loci.plugins.in.ImportProcess
Valid only after ImportStep.STACK.
getStackOrderInfo() - Method in class loci.plugins.in.ImporterOptions
 
getStackOrders() - Method in class loci.plugins.in.ImporterOptions
 
getStackSize() - Method in class loci.formats.in.SPEReader.SpeHeader
Method used to determined the stack size of the SPE file.
getStackType(String) - Method in class loci.formats.in.CellSensReader
 
getStageLabel() - Method in class loci.formats.in.MetamorphHandler
 
getStagePosition(Double, Unit<Length>) - Static method in class loci.formats.FormatTools
Formats the input value for the stage position into a length of the given unit.
getStagePosition(Double, String) - Static method in class loci.formats.FormatTools
Formats the input value for the stage position into a length of the given unit.
getStagePositionX() - Method in class loci.formats.in.MetamorphHandler
 
getStagePositionY() - Method in class loci.formats.in.MetamorphHandler
 
getStart(Hashtable<String, Object>) - Method in class loci.formats.in.MINCReader
 
getStartX() - Method in class loci.formats.in.SPEReader.SpeROI
 
getStartY() - Method in class loci.formats.in.SPEReader.SpeROI
 
getStatistics(int, int, double, double) - Method in class loci.plugins.util.VirtualImagePlus
 
getStep() - Method in class loci.formats.FilePattern
Gets the STEP element for all blocks.
getStep() - Method in class loci.formats.FilePatternBlock
Gets the difference between consecutive elements in a range block.
getStep(int) - Static method in enum loci.plugins.in.ImportStep
 
getStep() - Method in enum loci.plugins.in.ImportStep
 
getStepSize(Hashtable<String, Object>) - Method in class loci.formats.in.MINCReader
 
getStitchTilesInfo() - Method in class loci.plugins.in.ImporterOptions
 
getStrategy() - Method in class loci.formats.cache.Cache
Gets the cache's caching strategy.
getStream(int) - Method in class loci.formats.in.VolocityReader
 
getStream() - Method in class loci.formats.in.ZeissCZIReader.Segment
 
getStream() - Method in class loci.formats.tiff.OnDemandLongArray
 
getStream() - Method in class loci.formats.tiff.TiffParser
Gets the stream from which TIFF data is being parsed.
getStream() - Method in class loci.formats.tiff.TiffSaver
Gets the stream from which TIFF data is being saved.
getStreams() - Method in class loci.formats.tools.AmiraParameters
 
getString(int) - Method in class loci.formats.in.LeicaReader
 
getString(boolean) - Method in class loci.formats.in.LeicaReader
 
getString(SPEReader.SpeHeaderEntry) - Method in class loci.formats.in.SPEReader.SpeHeader
Method used to retrieve data values for String entries into the SPE header table
getString(int, int) - Method in class loci.formats.in.SPEReader.SpeHeader
Private method used to retrieve a String value from the SPE header
getString(Integer) - Method in class loci.formats.in.VolocityReader
 
getStringOption(String) - Method in class loci.plugins.prefs.OptionsList
Gets the string option with the given key.
getStringValue(int) - Method in class loci.formats.in.ZeissLSMReader.SubBlock
 
getStringWidth(String) - Method in class loci.plugins.util.RecordedImageProcessor
 
getStripByteCounts() - Method in class loci.formats.tiff.IFD
Retrieves strip byte counts for the image (TIFF tag StripByteCounts) from this IFD.
getStripOffsets() - Method in class loci.formats.tiff.IFD
Retrieves the strip offsets for the image (TIFF tag StripOffsets) from this IFD.
getSubIFDs(IFD) - Method in class loci.formats.tiff.TiffParser
Returns the SUBIFDS belonging to a given IFD.
getSubimage(BufferedImage, boolean, int, int, int, int) - Static method in class loci.formats.gui.AWTImageTools
Returns a subimage of the specified image.
getSubimage(byte[], byte[], int, int, int, int, int, int, int, int, boolean) - Static method in class loci.formats.ImageTools
 
getSubsamp() - Method in class org.libjpegturbo.turbojpeg.TJDecompressor
Returns the level of chrominance subsampling used in the JPEG image associated with this decompressor instance.
getSuffix() - Method in class loci.formats.FilePattern
Gets the pattern's substring that comes after all block sections.
getSuffixes() - Method in class loci.formats.FormatHandler
 
getSuffixes() - Method in interface loci.formats.IFormatHandler
Gets the default file suffixes for this file format.
getSuffixes() - Method in class loci.formats.ImageReader
 
getSuffixes() - Method in class loci.formats.ImageWriter
 
getSuffixes() - Method in class loci.formats.ReaderWrapper
 
getSuffixes() - Method in class loci.formats.WriterWrapper
 
getSupPixelTypes() - Method in interface loci.formats.services.WlzService
Gets supported pixel types.
getSupPixelTypes() - Method in class loci.formats.services.WlzServiceImpl
 
getSupportedMetadataLevels() - Method in class loci.formats.DelegateReader
 
getSupportedMetadataLevels() - Method in class loci.formats.FormatHandler
 
getSupportedMetadataLevels() - Method in class loci.formats.ImageReader
 
getSupportedMetadataLevels() - Method in class loci.formats.ImageWriter
 
getSupportedMetadataLevels() - Method in interface loci.formats.IMetadataConfigurable
 
getSupportedMetadataLevels() - Method in class loci.formats.ReaderWrapper
 
getSupportedMetadataLevels() - Method in class loci.formats.WriterWrapper
 
getSwapDimensionsInfo() - Method in class loci.plugins.in.ImporterOptions
 
getT() - Method in class loci.formats.gui.ImageViewer
Gets the T value of the currently displayed image.
getT(String) - Method in class loci.formats.in.OIRReader
 
getTableCount() - Method in interface loci.formats.services.MetakitService
 
getTableCount() - Method in class loci.formats.services.MetakitServiceImpl
 
getTableData(String) - Method in interface loci.formats.services.MetakitService
 
getTableData(int) - Method in interface loci.formats.services.MetakitService
 
getTableData(String) - Method in class loci.formats.services.MetakitServiceImpl
 
getTableData(int) - Method in class loci.formats.services.MetakitServiceImpl
 
getTableNames() - Method in interface loci.formats.services.MetakitService
 
getTableNames() - Method in class loci.formats.services.MetakitServiceImpl
 
getTag() - Method in class loci.formats.tiff.TiffIFDEntry
Retrieves the entry's Tag value.
getTagName(int) - Method in class loci.formats.in.CellSensReader
 
getTags() - Method in interface loci.formats.services.EXIFService
 
getTags() - Method in class loci.formats.services.EXIFServiceImpl
 
getTBegin(int) - Method in class loci.plugins.in.ImporterOptions
 
getTBegin(int) - Method in class loci.plugins.in.ImportProcess
 
getTCount(int) - Method in class loci.plugins.in.ImportProcess
Valid only after ImportStep.SERIES.
getTemperature() - Method in class loci.formats.in.MetamorphHandler
 
getTemperatures() - Method in class loci.formats.in.ND2Handler
 
getTEnd(int) - Method in class loci.plugins.in.ImporterOptions
 
getTEnd(int) - Method in class loci.plugins.in.ImportProcess
Valid only after ImportStep.STACK.
getTFrames(int) - Method in class loci.formats.in.LegacyND2Reader
 
getThumbnailIFDs() - Method in class loci.formats.in.MinimalTiffReader
Gets the list of IFDs associated with the current TIFF's thumbnails.
getThumbnailIFDs() - Method in class loci.formats.tiff.TiffParser
Returns thumbnail IFDs.
getThumbSizeX() - Method in class loci.formats.FileStitcher
 
getThumbSizeX() - Method in class loci.formats.FormatReader
 
getThumbSizeX() - Method in interface loci.formats.IFormatReader
Get the size of the X dimension for the thumbnail.
getThumbSizeX() - Method in class loci.formats.ImageReader
 
getThumbSizeX() - Method in class loci.formats.in.LeicaSCNReader
 
getThumbSizeX() - Method in class loci.formats.in.MinimalTiffReader
 
getThumbSizeX() - Method in class loci.formats.in.VentanaReader
 
getThumbSizeX() - Method in class loci.formats.ReaderWrapper
 
getThumbSizeX() - Method in class loci.formats.WrappedReader
 
getThumbSizeY() - Method in class loci.formats.FileStitcher
 
getThumbSizeY() - Method in class loci.formats.FormatReader
 
getThumbSizeY() - Method in interface loci.formats.IFormatReader
Get the size of the Y dimension for the thumbnail.
getThumbSizeY() - Method in class loci.formats.ImageReader
 
getThumbSizeY() - Method in class loci.formats.in.LeicaSCNReader
 
getThumbSizeY() - Method in class loci.formats.in.MinimalTiffReader
 
getThumbSizeY() - Method in class loci.formats.in.VentanaReader
 
getThumbSizeY() - Method in class loci.formats.ReaderWrapper
 
getThumbSizeY() - Method in class loci.formats.WrappedReader
 
getTiffFiles(String, char, int, int, int, int) - Method in class loci.formats.in.CellWorxReader
 
getTIFFList() - Method in class loci.formats.in.LeicaReader
 
getTiffs() - Method in class loci.formats.in.BDReader
 
getTile(int, int, int, int, Region) - Method in class loci.formats.in.MIASReader
 
getTile(byte[], Region, Region) - Method in class loci.formats.out.TiffWriter
 
getTile(byte[], int, int, int, int) - Method in interface loci.formats.services.JPEGTurboService
 
getTile(int, int) - Method in interface loci.formats.services.JPEGTurboService
 
getTile(byte[], int, int, int, int) - Method in class loci.formats.services.JPEGTurboServiceImpl
 
getTile(int, int) - Method in class loci.formats.services.JPEGTurboServiceImpl
 
getTile(IFD, byte[], int, int) - Method in class loci.formats.tiff.TiffParser
 
getTileColumn(int, int, int) - Method in class loci.formats.in.VentanaReader
 
getTileFilename(int, int, int, String) - Static method in class loci.formats.FormatTools
 
getTileIndex(int) - Method in class loci.formats.in.LIFReader
 
getTileLength() - Method in class loci.formats.tiff.IFD
Returns the length of an image tile.
getTileSize() - Method in class loci.formats.in.CellSensReader
 
getTileSizeX() - Method in class loci.formats.FormatWriter
 
getTileSizeX() - Method in interface loci.formats.IFormatWriter
Retrieves the current tile width Defaults to 0 if not supported
getTileSizeX() - Method in class loci.formats.ImageWriter
 
getTileSizeX() - Method in class loci.formats.out.TiffWriter
 
getTileSizeX() - Method in class loci.formats.WriterWrapper
 
getTileSizeY() - Method in class loci.formats.FormatWriter
 
getTileSizeY() - Method in interface loci.formats.IFormatWriter
Retrieves the current tile height Defaults to 0 if not supported
getTileSizeY() - Method in class loci.formats.ImageWriter
 
getTileSizeY() - Method in class loci.formats.out.TiffWriter
 
getTileSizeY() - Method in class loci.formats.WriterWrapper
 
getTilesPerColumn() - Method in class loci.formats.tiff.IFD
Returns the number of image tiles per column.
getTilesPerRow() - Method in class loci.formats.tiff.IFD
Returns the number of image tiles per row.
getTileWidth() - Method in class loci.formats.tiff.IFD
Returns the width of an image tile.
getTime(Double, String) - Static method in class loci.formats.FormatTools
Formats the input value for the time into a length of the given unit.
getTimeBinCount() - Method in class loci.formats.in.SDTReader
Gets the number of bins in the lifetime histogram.
getTimepoints() - Method in class loci.formats.in.ND2Handler
 
getTimestamp(String) - Method in class loci.formats.in.BDReader
 
getTimestamp(String) - Method in class loci.formats.in.SlidebookTiffReader
 
getTimestampIndex(String) - Method in class loci.formats.in.PCIReader
 
getTimestamps() - Method in class loci.formats.in.MetamorphHandler
 
getTotalPlaneHeaderSize() - Method in class loci.formats.in.DeltavisionReader
 
getTransformedSizes() - Method in class org.libjpegturbo.turbojpeg.TJTransformer
Returns an array containing the sizes of the transformed JPEG images from the most recent call to transform().
getTreeCellRendererComponent(JTree, Object, boolean, boolean, boolean, int, boolean) - Method in class loci.formats.gui.XMLCellRenderer
 
getTStep(int) - Method in class loci.plugins.in.ImporterOptions
 
getTStep(int) - Method in class loci.plugins.in.ImportProcess
 
getType() - Method in class loci.formats.cache.CacheEvent
Gets the type of cache update.
getType() - Method in class loci.formats.gui.TwoChannelColorSpace
 
getType() - Method in class loci.formats.in.PrairieMetadata.Sequence
Gets the type associated with this Sequence.
getType() - Method in class loci.formats.tiff.TiffIFDEntry
Retrieves the entry's Type value.
getUnderlyingReaders() - Method in class loci.formats.FileStitcher
 
getUnderlyingReaders() - Method in class loci.formats.FormatReader
 
getUnderlyingReaders() - Method in interface loci.formats.IFormatReader
Retrieves all underlying readers.
getUnderlyingReaders() - Method in class loci.formats.ImageReader
 
getUnderlyingReaders() - Method in class loci.formats.ReaderWrapper
 
getUnderlyingReaders() - Method in class loci.formats.WrappedReader
 
getUngroupFilesInfo() - Method in class loci.plugins.in.ImporterOptions
 
getUniverse() - Method in class loci.formats.gui.LegacyQTTools
Gets QuickTime for Java reflected universe.
getUpgradeCheckInfo() - Method in class loci.plugins.in.ImporterOptions
 
getUsedFile(Double, String[]) - Method in class loci.plugins.macro.LociFunctions
 
getUsedFileCount(Double[]) - Method in class loci.plugins.macro.LociFunctions
 
getUsedFiles() - Method in class loci.formats.FileStitcher
 
getUsedFiles(boolean) - Method in class loci.formats.FileStitcher
 
getUsedFiles() - Method in class loci.formats.FormatReader
 
getUsedFiles(boolean) - Method in class loci.formats.FormatReader
 
getUsedFiles() - Method in interface loci.formats.IFormatReader
Returns an array of filenames needed to open this dataset.
getUsedFiles(boolean) - Method in interface loci.formats.IFormatReader
Returns an array of filenames needed to open this dataset.
getUsedFiles() - Method in class loci.formats.ImageReader
 
getUsedFiles(boolean) - Method in class loci.formats.ImageReader
 
getUsedFiles(boolean) - Method in class loci.formats.in.BDVReader
 
getUsedFiles(boolean) - Method in class loci.formats.in.CellomicsReader
 
getUsedFiles(boolean) - Method in class loci.formats.in.CellWorxReader
 
getUsedFiles(boolean) - Method in class loci.formats.in.CV7000Reader
 
getUsedFiles(boolean) - Method in class loci.formats.in.FilePatternReader
 
getUsedFiles(boolean) - Method in class loci.formats.in.InveonReader
 
getUsedFiles(boolean) - Method in class loci.formats.in.KLBReader
 
getUsedFiles(boolean) - Method in class loci.formats.in.MetamorphTiffReader
 
getUsedFiles(boolean) - Method in class loci.formats.in.OperettaReader
 
getUsedFiles(boolean) - Method in class loci.formats.in.UnisokuReader
 
getUsedFiles() - Method in class loci.formats.ReaderWrapper
 
getUsedFiles(boolean) - Method in class loci.formats.ReaderWrapper
 
getUsedFiles(boolean) - Method in class loci.formats.WrappedReader
 
getUUID(String) - Method in class loci.formats.in.ImprovisionTiffReader
 
getUUID(String) - Method in class loci.formats.out.OMETiffWriter
Gets the UUID corresponding to the given filename.
getValue() - Method in enum loci.formats.in.BaseZeissReader.Charset
 
getValue() - Method in enum loci.formats.in.BaseZeissReader.DrawStyle
 
getValue() - Method in enum loci.formats.in.BaseZeissReader.FeatureType
 
getValue() - Method in enum loci.formats.in.BaseZeissReader.FillStyle
 
getValue() - Method in enum loci.formats.in.BaseZeissReader.LineEndPositions
 
getValue() - Method in enum loci.formats.in.BaseZeissReader.LineEndStyle
 
getValue() - Method in enum loci.formats.in.BaseZeissReader.PointStyle
 
getValue() - Method in class loci.formats.in.BaseZeissReader.Tag
 
getValue() - Method in enum loci.formats.in.BaseZeissReader.TextAlignment
 
getValue(IRandomAccess) - Method in class loci.formats.in.IM3Reader.StringIM3Record
Return the string value for this record
getValue(String) - Method in class loci.formats.in.PrairieMetadata.Frame
Gets the value of the given key, beneath this Frame, inferring the value from the parent <Sequence> or grandparent <PVScan> section as needed.
getValue(String) - Method in class loci.formats.in.PrairieMetadata
Gets the value of the given key, at the top-level <PVScan> element.
getValue(String) - Method in class loci.formats.in.PrairieMetadata.Sequence
Gets the value of the given key, beneath this Sequence, inferring the value from the parent <PVScan> section as needed.
getValue() - Method in class loci.plugins.prefs.BooleanOption
Gets the current value of the option.
getValue() - Method in class loci.plugins.prefs.DoubleOption
Gets the current value of the option.
getValue(String) - Method in class loci.plugins.prefs.OptionsList
Gets the value of the string option with the given key.
getValue() - Method in class loci.plugins.prefs.StringOption
Gets the current value of the option.
getValueCount() - Method in class loci.formats.tiff.TiffIFDEntry
Retrieves the entry's ValueCount value.
getValueForKey() - Method in class loci.formats.meta.OriginalMetadataAnnotation
Return just the value (i.e.
getValueOffset() - Method in class loci.formats.tiff.TiffIFDEntry
Retrieves the entry's ValueOffset value.
getValues() - Method in class loci.formats.in.PrairieMetadata.Frame
Gets the table of Frame key/value pairs.
getValues() - Method in class loci.formats.in.PrairieMetadata
Gets the table of PVScan key/value pairs.
getValues() - Method in class loci.formats.in.PrairieMetadata.Sequence
Gets the table of Frame key/value pairs.
getVariableAttributes(String) - Method in interface loci.formats.services.NetCDFService
Retrieves all of a variable's attributes.
getVariableAttributes(String) - Method in class loci.formats.services.NetCDFServiceImpl
 
getVariableList() - Method in interface loci.formats.services.NetCDFService
Retrieves an exhaustive list of the HDF paths for all variables in the HDF document.
getVariableList() - Method in class loci.formats.services.NetCDFServiceImpl
 
getVariableValue(String) - Method in interface loci.formats.services.NetCDFService
Retrieves a variable's value.
getVariableValue(String) - Method in class loci.formats.services.NetCDFServiceImpl
 
getVersionNumber(String[]) - Method in class loci.plugins.macro.LociFunctions
 
getVirtualInfo() - Method in class loci.plugins.in.ImporterOptions
 
getVirtualReader() - Method in class loci.plugins.in.ImportProcess
Valid only after ImportStep.STACK.
getVoltage() - Method in class loci.formats.in.ND2Handler
 
getVolumeName(int) - Method in class loci.formats.in.CellSensReader
 
getVoxSzX() - Method in interface loci.formats.services.WlzService
Gets voxel width.
getVoxSzX() - Method in class loci.formats.services.WlzServiceImpl
 
getVoxSzY() - Method in interface loci.formats.services.WlzService
Gets voxel height.
getVoxSzY() - Method in class loci.formats.services.WlzServiceImpl
 
getVoxSzZ() - Method in interface loci.formats.services.WlzService
Gets voxel depth.
getVoxSzZ() - Method in class loci.formats.services.WlzServiceImpl
 
getWaitTime() - Method in class loci.formats.in.PrairieMetadata
Gets the waitTime recorded in the configuration.
getWavelength(Double, String) - Static method in class loci.formats.FormatTools
Formats the input value for the wavelength into a length of the given unit.
getWavelength(Double) - Static method in class loci.formats.FormatTools
 
getWavelength(int, int, int, int) - Method in class loci.formats.in.LegacyND2Reader
 
getWavelengthMax() - Method in class loci.formats.in.PrairieMetadata.PFile
Gets the wavelengthMax associated with this File.
getWavelengthMin() - Method in class loci.formats.in.PrairieMetadata.PFile
Gets the wavelengthMin associated with this File.
getWavelengths() - Method in class loci.formats.in.IM3Reader.Spectrum
 
getWavelengths() - Method in class loci.formats.in.MetamorphHandler
 
getWell(int) - Method in class loci.formats.in.CellWorxReader
Retrieve the well index corresponding to the given series.
getWell(String) - Method in class loci.formats.in.FlexReader
Returns a two-element array containing the well row and well column corresponding to the given file.
getWell(int) - Method in class loci.formats.in.MetamorphTiffReader
 
getWellColumn(String) - Method in class loci.formats.in.CellomicsReader
 
getWellColumn(int) - Method in class loci.formats.in.CellWorxReader
Retrieve the well column corresponding to the given series.
getWellColumn(String) - Method in class loci.formats.in.MetamorphTiffReader
 
getWellCoords(String) - Method in class loci.formats.in.MetamorphReader
 
getWellFromSeries(int) - Method in class loci.formats.in.InCellReader
 
getWellName(String) - Method in class loci.formats.in.CellomicsReader
 
getWellRow(String) - Method in class loci.formats.in.CellomicsReader
 
getWellRow(int) - Method in class loci.formats.in.CellWorxReader
Retrieve the well row corresponding to the given series.
getWellRow(String) - Method in class loci.formats.in.MetamorphTiffReader
 
getWidgets() - Method in class loci.plugins.config.CellSensWidgets
 
getWidgets() - Method in class loci.plugins.config.FlexWidgets
 
getWidgets() - Method in interface loci.plugins.config.IFormatWidgets
 
getWidgets() - Method in class loci.plugins.config.LIFWidgets
 
getWidgets() - Method in class loci.plugins.config.ND2Widgets
 
getWidgets() - Method in class loci.plugins.config.PictWidgets
 
getWidgets() - Method in class loci.plugins.config.QTWidgets
 
getWidgets() - Method in class loci.plugins.config.SDTWidgets
 
getWidgets() - Method in class loci.plugins.config.TiffDelegateWidgets
 
getWidgets() - Method in class loci.plugins.config.ZeissCZIWidgets
 
getWidth() - Method in class loci.formats.codec.JPEGTileDecoder
 
getWidth(int) - Method in class loci.formats.in.LegacyND2Reader
 
getWidth() - Method in interface loci.formats.services.LuraWaveService
Wraps lwfDecoder.getWidth()
getWidth() - Method in class loci.formats.services.LuraWaveServiceImpl
 
getWidth(IFormatReader, String, int) - Static method in class loci.plugins.util.BFVirtualStack
 
getWidth() - Method in class loci.plugins.util.BFVirtualStack
 
getWidth() - Method in class loci.plugins.util.RecordedImageProcessor
 
getWidth() - Method in class org.libjpegturbo.turbojpeg.TJDecompressor
Returns the width of the JPEG image associated with this decompressor instance.
getWindowlessInfo() - Method in class loci.plugins.in.ImporterOptions
 
getWlzOrgLabelName() - Method in interface loci.formats.services.WlzService
Gets the text string used for the Woolz origin label.
getWlzOrgLabelName() - Method in class loci.formats.services.WlzServiceImpl
 
getWrapped() - Method in class loci.formats.codec.BitBuffer
Deprecated.
 
getWrapped() - Method in class loci.formats.codec.BitWriter
Deprecated.
 
getWrapped() - Method in class loci.formats.codec.ByteVector
 
getWrapped() - Method in class loci.formats.codec.JPEGTileDecoder
 
getWriter(String) - Method in class loci.formats.ImageWriter
Gets the writer used to save the given file.
getWriter() - Method in class loci.formats.ImageWriter
Gets the writer used to save the current file.
getWriter(Class<? extends IFormatWriter>) - Method in class loci.formats.ImageWriter
Gets the file format writer instance matching the given class.
getWriter() - Method in class loci.formats.WriterWrapper
Gets the wrapped writer.
getWriters() - Method in class loci.formats.ImageWriter
Gets all constituent file format writers.
getX(int) - Method in class loci.formats.in.FakeReader
 
getX(double[]) - Method in class loci.formats.in.TextReader
 
getXFields() - Method in class loci.formats.in.ND2Handler
 
getXML() - Method in class loci.formats.tools.EditTiffG
 
getXPositions() - Method in class loci.formats.in.ND2Handler
 
getXResolution() - Method in class loci.formats.tiff.IFD
Retrieve the X resolution (TIFF tag XResolution) from this IFD.
getY(int) - Method in class loci.formats.in.FakeReader
 
getY(double[]) - Method in class loci.formats.in.TextReader
 
getYPositions() - Method in class loci.formats.in.ND2Handler
 
getYResolution() - Method in class loci.formats.tiff.IFD
Retrieve the Y resolution (TIFF tag YResolution) from this IFD.
getZ() - Method in class loci.formats.gui.ImageViewer
Gets the Z value of the currently displayed image.
getZ(String) - Method in class loci.formats.in.OIRReader
 
getZBegin(int) - Method in class loci.plugins.in.ImporterOptions
 
getZBegin(int) - Method in class loci.plugins.in.ImportProcess
 
getZCount(int) - Method in class loci.plugins.in.ImportProcess
Valid only after ImportStep.SERIES.
getZCTCoords(int) - Method in class loci.formats.ChannelMerger
 
getZCTCoords(int) - Method in class loci.formats.ChannelSeparator
 
getZCTCoords(int) - Method in class loci.formats.DimensionSwapper
 
getZCTCoords(int) - Method in class loci.formats.FileStitcher
 
getZCTCoords(int) - Method in class loci.formats.FormatReader
 
getZCTCoords(IFormatReader, int) - Static method in class loci.formats.FormatTools
Gets the Z, C and T coordinates corresponding to the given rasterized index value (real sizes).
getZCTCoords(String, int, int, int, int, int) - Static method in class loci.formats.FormatTools
Gets the Z, C and T coordinates corresponding to the given rasterized index value (real sizes).
getZCTCoords(String, int, int, int, int, int, int, int, int) - Static method in class loci.formats.FormatTools
Gets the Z, C and T coordinates corresponding to the given rasterized index value.
getZCTCoords(int) - Method in interface loci.formats.IFormatReader
Gets the Z, C and T coordinates (real sizes) corresponding to the given rasterized index value.
getZCTCoords(int) - Method in class loci.formats.ImageReader
 
getZCTCoords(int) - Method in class loci.formats.ReaderWrapper
 
getZCTCoords(int) - Method in class loci.formats.WrappedReader
 
getZCTCoords(Double, Double[], Double[], Double[]) - Method in class loci.plugins.macro.LociFunctions
 
getZCTModuloCoords(int) - Method in class loci.formats.ChannelMerger
 
getZCTModuloCoords(int) - Method in class loci.formats.ChannelSeparator
 
getZCTModuloCoords(int) - Method in class loci.formats.DimensionSwapper
 
getZCTModuloCoords(int) - Method in class loci.formats.FileStitcher
 
getZCTModuloCoords(int) - Method in class loci.formats.FormatReader
 
getZCTModuloCoords(IFormatReader, int) - Static method in class loci.formats.FormatTools
Gets the Z, C, T, ModuloZ, ModuloC and ModuloZ coordinates corresponding to the given rasterized index value (effective sizes).
getZCTModuloCoords(int) - Method in interface loci.formats.IFormatReader
Gets the Z, C, T, moduloZ, moduloC and moduloT coordinates (effective sizes) corresponding to the given rasterized index value.
getZCTModuloCoords(int) - Method in class loci.formats.ImageReader
 
getZCTModuloCoords(int) - Method in class loci.formats.ReaderWrapper
 
getZEnd(int) - Method in class loci.plugins.in.ImporterOptions
 
getZEnd(int) - Method in class loci.plugins.in.ImportProcess
Valid only after ImportStep.STACK.
getZeroOffset(ImagePlus) - Static method in class loci.plugins.in.Colorizer
 
getZoom() - Method in class loci.formats.in.MetamorphHandler
 
getZPositions() - Method in class loci.formats.in.MetamorphHandler
 
getZPositions() - Method in class loci.formats.in.ND2Handler
 
getZSections() - Method in class loci.formats.in.ND2Handler
 
getZSlices(int) - Method in class loci.formats.in.LegacyND2Reader
 
getZStep(int) - Method in class loci.plugins.in.ImporterOptions
 
getZStep(int) - Method in class loci.plugins.in.ImportProcess
 
GIF_MAGIC_STRING - Static variable in class loci.formats.in.GIFReader
 
GIFReader - Class in loci.formats.in
GIFReader is the file format reader for Graphics Interchange Format (GIF) files.
GIFReader() - Constructor for class loci.formats.in.GIFReader
Constructs a new GIF reader.
global - Variable in class loci.formats.in.BMPReader
Offset to image data.
globalMetadata - Variable in class loci.formats.in.LeicaHandler
 
gradient(int, int, int) - Method in class loci.formats.tools.MakeTestOmeTiff
 
GRADIENT_LUT - Static variable in class loci.formats.in.CellSensReader
 
GRAPHICS - Static variable in class loci.formats.in.GIFReader
 
GRAPHICS_DOMAIN - Static variable in class loci.formats.FormatTools
Identifies the graphics domain.
GRAY16 - Static variable in class loci.formats.in.ZeissCZIReader
 
GRAY32 - Static variable in class loci.formats.in.ZeissCZIReader
 
GRAY8 - Static variable in class loci.formats.in.ZeissCZIReader
Pixel type constants.
GRAY_ALPHA - Static variable in class loci.formats.in.APNGReader
 
GRAY_DOUBLE - Static variable in class loci.formats.in.ZeissCZIReader
 
GRAY_FLOAT - Static variable in class loci.formats.in.ZeissCZIReader
 
GRAY_RESPONSE_CURVE - Static variable in class loci.formats.tiff.IFD
 
GRAY_RESPONSE_UNIT - Static variable in class loci.formats.tiff.IFD
 
GRAYSCALE - Static variable in class loci.formats.in.APNGReader
Color types.
GREEN_GAIN - Static variable in class loci.formats.in.CellSensReader
 
GREEN_MULTIPLIER - Static variable in class loci.formats.in.NDPIReader
 
GREEN_OFFSET - Static variable in class loci.formats.in.CellSensReader
 
GREEN_TO_RED_MIN - Static variable in class loci.plugins.in.Colorizer
 
greenGain - Variable in class loci.formats.in.CellSensReader.Pyramid
 
greenOffset - Variable in class loci.formats.in.CellSensReader.Pyramid
 
greenOffset - Static variable in class org.libjpegturbo.turbojpeg.TJ
 
greenShort - Variable in class loci.formats.gui.Index16ColorModel
Lookup tables.
GREYSCALE_COMPRESSION - Static variable in class loci.formats.in.FlowSightReader
 
GRID - Static variable in class loci.formats.in.FV1000Reader
 
GRIDSIZE_OFFSET - Static variable in class loci.formats.in.MRCReader
 
group - Variable in class loci.formats.FileStitcher
 
group - Variable in class loci.formats.FormatReader
Whether or not to group multi-file formats.
GROUP - Static variable in class loci.formats.in.GatanReader
Tag types.
groupFiles(String[], MetadataStore) - Method in class loci.formats.in.FlexReader
 
groupFiles() - Method in class loci.formats.in.TCSReader
 
groupFilesBox - Variable in class loci.plugins.in.MainDialog
 
groupX - Variable in class loci.formats.in.SPEReader.SpeROI
 
groupY - Variable in class loci.formats.in.SPEReader.SpeROI
 
GUITools - Class in loci.formats.gui
A utility class for working with graphical user interfaces.
GUITools() - Constructor for class loci.formats.gui.GUITools
 
gz - Variable in class loci.formats.in.LiFlimReader
Stream to use for reading gzip-compressed pixel data.
gzip - Variable in class loci.formats.in.ICSReader
Whether or not the pixels are GZIP-compressed.
gzip - Variable in class loci.formats.in.LiFlimReader
True if gzip compression was used to deflate the pixels.
gzip - Variable in class loci.formats.in.NRRDReader
 
gzipStream - Variable in class loci.formats.in.ICSReader
 
gzPos - Variable in class loci.formats.in.LiFlimReader
Image number indicating position in gzip stream.
gzSeries - Variable in class loci.formats.in.LiFlimReader
Series number indicating position in gzip stream.

H

H5Constants() - Constructor for class loci.formats.in.BDVReader.H5Constants
 
H5Coordinate(String, String, String) - Constructor for class loci.formats.in.BDVReader.H5Coordinate
 
h5Id - Variable in class loci.formats.in.BDVReader
 
H5PathsToImageData - Variable in class loci.formats.in.BDVReader
 
H5PositionList - Variable in class loci.formats.in.BDVReader
 
HALFTONE_HINTS - Static variable in class loci.formats.tiff.IFD
 
HamamatsuVMSReader - Class in loci.formats.in
HamamatsuVMSReader is the file format reader for Hamamatsu VMS datasets.
HamamatsuVMSReader() - Constructor for class loci.formats.in.HamamatsuVMSReader
Constructs a new Hamamatsu VMS reader.
handle - Variable in class org.libjpegturbo.turbojpeg.TJCompressor
 
handle - Variable in class org.libjpegturbo.turbojpeg.TJDecompressor
 
handleBitmap(int) - Method in class loci.formats.in.PictReader
Extract the image data in a PICT bitmap structure.
handleExtension(String, Object[]) - Method in class loci.plugins.macro.MacroFunctions
 
handleKeyValue(String, String) - Method in class loci.formats.in.MicromanagerReader
Process a piece of metadata represented by a key/value pair.
handleMetadataStore(IFormatReader) - Method in class loci.formats.Memoizer
Return the IFormatReader instance that is passed in or null if it has been invalidated, which will include the instance being closed.
handlePixmap(int) - Method in class loci.formats.in.PictReader
Extracts the image data in a PICT pixmap structure.
handlePixmap(int, int) - Method in class loci.formats.in.PictReader
Handles the unpacking of the image data.
handler - Variable in class loci.formats.in.LeicaSCNReader
 
handler - Variable in class loci.formats.in.NikonElementsTiffReader
 
handler - Variable in class loci.formats.in.ZeissTIFFReader.TIFFInfo
 
handleSize - Variable in class loci.formats.in.BaseZeissReader.Shape
 
HARMONY_MAGIC - Static variable in class loci.formats.in.OperettaReader
 
harvestResults(GenericDialog) - Method in class loci.plugins.in.ColorDialog
 
harvestResults(GenericDialog) - Method in class loci.plugins.in.CropDialog
 
harvestResults(GenericDialog) - Method in class loci.plugins.in.FilePatternDialog
 
harvestResults(GenericDialog) - Method in class loci.plugins.in.IdDialog
 
harvestResults(GenericDialog) - Method in class loci.plugins.in.ImporterDialog
 
harvestResults(GenericDialog) - Method in class loci.plugins.in.LocationDialog
 
harvestResults(GenericDialog) - Method in class loci.plugins.in.MainDialog
 
harvestResults(GenericDialog) - Method in class loci.plugins.in.MemoryDialog
 
harvestResults(GenericDialog) - Method in class loci.plugins.in.RangeDialog
 
harvestResults(GenericDialog) - Method in class loci.plugins.in.SeriesDialog
 
harvestResults(GenericDialog) - Method in class loci.plugins.in.SwapDialog
 
harvestResults(GenericDialog) - Method in class loci.plugins.in.UpgradeDialog
 
HAS_EXTERNAL_FILE - Static variable in class loci.formats.in.CellSensReader
 
hasAbsoluteZ - Variable in class loci.formats.in.MetamorphReader
 
hasAbsoluteZValid - Variable in class loci.formats.in.MetamorphReader
 
hasChipOffsets - Variable in class loci.formats.in.MetamorphReader
 
hasCompanionFiles - Variable in class loci.formats.FormatReader
Whether this format supports multi-file datasets.
hasCompanionFiles() - Method in class loci.formats.FormatReader
 
hasCompanionFiles() - Method in interface loci.formats.IFormatReader
Returns true if this format supports multi-file datasets.
hasCompanionFiles() - Method in class loci.formats.ImageReader
 
hasCompanionFiles() - Method in class loci.formats.in.FilePatternReader
 
hasCompanionFiles() - Method in class loci.formats.ReaderWrapper
 
hasCompanionFiles() - Method in class loci.formats.WrappedReader
 
hasDetectorSettings - Variable in class loci.formats.in.ZeissCZIReader
 
hasDualCamera() - Method in class loci.formats.in.MetamorphHandler
 
hasExtendedMeasureInfo - Variable in class loci.formats.in.SDTInfo
 
hasFlattenedResolutions() - Method in class loci.formats.FormatReader
 
hasFlattenedResolutions() - Method in interface loci.formats.IFormatReader
Return whether or not resolution flattening is enabled.
hasFlattenedResolutions() - Method in class loci.formats.ImageReader
 
hasFlattenedResolutions() - Method in class loci.formats.in.FilePatternReader
 
hasFlattenedResolutions() - Method in class loci.formats.ReaderWrapper
 
hashCode() - Method in class loci.formats.in.MetamorphTiffReader.Well
 
hashCode() - Method in class loci.formats.in.ZeissCZIReader.Coordinate
 
hashCode() - Method in class loci.formats.tiff.TiffRational
Reasonable hash value for use with hashtables.
hashCode() - Method in class loci.plugins.config.FormatEntry
 
hashCode() - Method in class loci.plugins.prefs.OptionsList
 
hasInstrumentData - Variable in class loci.formats.in.ICSReader
 
hasMeasFCSInfo - Variable in class loci.formats.in.SDTInfo
 
hasMeasHISTInfo - Variable in class loci.formats.in.SDTInfo
 
hasMeasStopInfo - Variable in class loci.formats.in.SDTInfo
 
hasMeasureInfo - Variable in class loci.formats.in.SDTInfo
 
hasPaddingByte - Variable in class loci.formats.in.IvisionReader
 
hasPlaneReader - Variable in class loci.formats.in.AmiraReader
 
hasResolutions() - Method in class loci.formats.FormatWriter
 
hasSPW - Variable in class loci.formats.in.OMETiffReader
 
hasSPW - Variable in class loci.formats.in.OMEXMLReader
 
hasStagePositions - Variable in class loci.formats.in.MetamorphReader
 
HCS_DOMAIN - Static variable in class loci.formats.FormatTools
Identifies the high content screening domain.
HDF_MAGIC_STRING - Static variable in class loci.formats.in.BDVReader
 
HDF_MAGIC_STRING - Static variable in class loci.formats.in.CellH5Reader
 
HDF_MAGIC_STRING - Static variable in class loci.formats.in.ImarisHDFReader
 
hdfReader - Variable in class loci.formats.services.JHDFServiceImpl
Root of the HDF5 file.
hdfWriter - Variable in class loci.formats.services.JHDFServiceImpl
Root of the HDF5 file.
HDRI_EXPOSURE_RANGE - Static variable in class loci.formats.in.CellSensReader
 
HDRI_FRAMES - Static variable in class loci.formats.in.CellSensReader
 
HDRI_MAP_MODE - Static variable in class loci.formats.in.CellSensReader
 
HDRI_ON - Static variable in class loci.formats.in.CellSensReader
 
HEADER - Static variable in class loci.formats.in.InveonReader
 
header - Variable in class loci.formats.in.SPEReader
 
header - Variable in class loci.formats.in.SPEReader.SpeHeader
 
header - Variable in class loci.formats.services.JPEGTurboServiceImpl
 
HEADER_LENGTH - Static variable in class loci.formats.in.DeltavisionReader
 
HEADER_MARKER - Static variable in class loci.formats.in.VisitechReader
 
HEADER_SIZE - Static variable in class loci.formats.in.Ecat7Reader
 
HEADER_SIZE - Static variable in class loci.formats.in.GatanDM2Reader
 
HEADER_SIZE - Static variable in class loci.formats.in.I2IReader
 
HEADER_SIZE - Static variable in class loci.formats.in.INRReader
 
HEADER_SIZE - Static variable in class loci.formats.in.MRCReader
 
HEADER_SIZE - Static variable in class loci.formats.in.OpenlabRawReader
 
HEADER_SIZE - Static variable in class loci.formats.in.PovrayReader
 
HEADER_SIZE - Static variable in class loci.formats.in.PQBinReader
 
HEADER_SIZE - Static variable in class loci.formats.in.RHKReader
 
HEADER_SIZE - Static variable in class loci.formats.in.SBIGReader
 
HEADER_SIZE - Static variable in class loci.formats.in.SeikoReader
 
HEADER_SIZE - Static variable in class loci.formats.in.SMCameraReader
 
HEADER_SIZE - Static variable in class loci.formats.in.UBMReader
 
HEADER_SIZE - Static variable in class loci.formats.in.WATOPReader
 
HEADER_SIZE - Static variable in class loci.formats.in.ZeissCZIReader
 
headerIFDs - Variable in class loci.formats.in.LeicaReader
Array of IFD-like structures containing metadata.
headerPixelType - Variable in class loci.formats.in.JPEG2000MetadataParser
Pixel type as specified in the header.
headerSize - Variable in class loci.formats.in.FEIReader
 
headerSize - Variable in class loci.formats.in.KLBReader
 
headerSize - Variable in class loci.formats.in.MicroCTReader
 
headerSize - Variable in class loci.formats.in.OxfordInstrumentsReader
 
headerSize - Static variable in class loci.formats.in.SPEReader.SpeHeader
 
headerSize - Variable in class loci.formats.in.SpiderReader
 
headerSizeC - Variable in class loci.formats.in.JPEG2000MetadataParser
Number of channels the image has as specified in the header.
headerSizeX - Variable in class loci.formats.in.JPEG2000MetadataParser
Width of the image as specified in the header.
headerSizeY - Variable in class loci.formats.in.JPEG2000MetadataParser
Height of the image as specified in the header.
headerValid - Variable in class loci.formats.in.SDTInfo
 
headerVersion - Variable in class loci.formats.in.KLBReader
 
height - Variable in class loci.formats.codec.CodecOptions
Height, in pixels, of the image.
height - Variable in class loci.formats.in.BaseZeissReader.Shape
 
height - Variable in class loci.formats.in.CellSensReader.Pyramid
 
height - Variable in class loci.formats.in.CellVoyagerReader.AreaInfo
 
height - Variable in class loci.formats.in.CellVoyagerReader.ChannelInfo
 
height - Variable in class loci.formats.in.OpenlabReader.PlaneInfo
 
height - Variable in class loci.formats.in.SDTInfo
 
height - Variable in class loci.formats.out.LegacyQTWriter
Frame height.
height - Variable in class loci.formats.tools.AmiraParameters
 
HELIOS_TAG - Static variable in class loci.formats.in.FEITiffReader
 
HELP_MENU - Static variable in class loci.plugins.shortcut.ShortcutPanel
Name of the 'About Plugins' submenu.
helper - Variable in class loci.formats.gui.SignedColorModel
 
helper - Variable in class loci.formats.gui.SignedShortBuffer
 
helper - Variable in class loci.formats.gui.UnsignedIntColorModel
 
helper - Variable in class loci.formats.in.DicomReader
 
helper - Variable in class loci.formats.in.FilePatternReader
 
helper - Variable in class loci.formats.in.NRRDReader
Helper reader.
helperReader - Variable in class loci.formats.in.HitachiReader
 
hex2Rgb(String) - Static method in class loci.formats.in.BDVReader
 
hex2Rgb(String) - Static method in class loci.formats.in.CellH5Reader
 
HIDDEN_LAYER - Static variable in class loci.formats.in.CellSensReader
 
HIGH_PRIORITY - Static variable in interface loci.formats.cache.ICacheStrategy
 
HIS_MAGIC_STRING - Static variable in class loci.formats.in.HISReader
 
HISReader - Class in loci.formats.in
HISReader is the file format reader for Hamamatsu .his files.
HISReader() - Constructor for class loci.formats.in.HISReader
Constructs a new Hamamatsu .his reader.
HISTOLOGY_DOMAIN - Static variable in class loci.formats.FormatTools
Identifies the histology domain.
HISTORY_KEYS - Static variable in class loci.formats.in.ICSReader
 
HitachiReader - Class in loci.formats.in
HitachiReader is the file format reader for S-4800 files.
HitachiReader() - Constructor for class loci.formats.in.HitachiReader
Constructs a new Hitachi reader.
HORIZONTAL_FLIP - Static variable in class loci.formats.in.FluoviewReader
 
HOST_COMPUTER - Static variable in class loci.formats.tiff.IFD
 
hostnames - Variable in class loci.formats.in.FlexReader.MeaHandler
 
HOT_PIXEL_CORRECTION - Static variable in class loci.formats.in.CellSensReader
 
HRDGDFReader - Class in loci.formats.in
HRDGDFReader is the file format reader for the Gridded Data Format used by NOAA's Hurricane Research Division.
HRDGDFReader() - Constructor for class loci.formats.in.HRDGDFReader
Constructs a new Gridded Data Format reader.
HTM_SUFFIX - Static variable in class loci.formats.in.PerkinElmerReader
 
HTML_REGEX - Static variable in class loci.formats.in.PerkinElmerReader
 
HTML_SUFFIX - Static variable in class loci.formats.in.VisitechReader
 
HUE - Static variable in class loci.formats.in.NikonReader
 
HuffmanCodec - Class in loci.formats.codec
This class implements Huffman decoding.
HuffmanCodec() - Constructor for class loci.formats.codec.HuffmanCodec
 
HuffmanCodecOptions - Class in loci.formats.codec
Options for compressing and decompressing Huffman data.
HuffmanCodecOptions() - Constructor for class loci.formats.codec.HuffmanCodecOptions
 
humidity - Variable in class loci.formats.in.ZeissCZIReader
 
HxRLE(int, long) - Constructor for class loci.formats.in.AmiraReader.HxRLE
 
HxZip(long) - Constructor for class loci.formats.in.AmiraReader.HxZip
 

I

i(String) - Method in class loci.formats.in.PrairieMetadata
Converts the given string to an Integer, or null if incompatible.
I2IReader - Class in loci.formats.in
I2IReader is the file format reader for I2I files.
I2IReader() - Constructor for class loci.formats.in.I2IReader
Constructs a new I2I reader.
ICacheSource - Interface in loci.formats.cache
Interface for cache sources.
ICacheStrategy - Interface in loci.formats.cache
Interface for cache strategies.
ICC_ENABLED - Static variable in class loci.formats.in.CellSensReader
 
icon - Variable in class loci.formats.gui.ImageViewer
 
icon - Variable in class loci.formats.gui.PreviewPane
 
ICON_IMAGE_SEQUENCE - Static variable in class loci.formats.in.DicomReader
 
iconLabel - Variable in class loci.formats.gui.ImageViewer
 
iconLabel - Variable in class loci.formats.gui.PreviewPane
Labels containing thumbnail and dimensional information.
iconText - Variable in class loci.formats.gui.PreviewPane
 
iconTip - Variable in class loci.formats.gui.PreviewPane
 
ICSReader - Class in loci.formats.in
ICSReader is the file format reader for ICS (Image Cytometry Standard) files.
ICSReader() - Constructor for class loci.formats.in.ICSReader
Constructs a new ICSReader.
ICSWriter - Class in loci.formats.out
ICSWriter is the file format writer for ICS files.
ICSWriter() - Constructor for class loci.formats.out.ICSWriter
 
id - Variable in class loci.formats.gui.CacheComponent
File name that the cache is working with (debugging only).
id - Variable in class loci.formats.in.BaseZeissReader.Shape
 
id - Variable in class loci.formats.in.FlexReader.FilterGroup
 
id - Variable in class loci.formats.in.LeicaHandler.Laser
 
id - Variable in class loci.formats.in.LeicaReader.Detector
 
id - Variable in class loci.formats.in.OIRReader.Channel
 
id - Variable in class loci.formats.in.OIRReader.Detector
 
id - Variable in class loci.formats.in.OIRReader.Laser
 
id - Variable in class loci.formats.in.OMETiffReader.OMETiffPlane
File containing this plane.
id - Variable in class loci.formats.in.ZeissCZIReader.Segment
 
id - Variable in class loci.plugins.util.BFVirtualStack
 
idatCount - Variable in class loci.formats.in.APNGReader
 
IdDialog - Class in loci.plugins.in
Bio-Formats Importer id chooser dialog box.
IdDialog(ImportProcess) - Constructor for class loci.plugins.in.IdDialog
Creates an id chooser dialog for the Bio-Formats Importer.
IDENTIFIER - Static variable in class loci.formats.in.OIRReader
 
idLoc - Variable in class loci.plugins.in.ImportProcess
 
idName - Variable in class loci.plugins.in.ImportProcess
 
idx1Pos - Variable in class loci.formats.out.AVIWriter
 
ifd - Variable in class loci.formats.in.LeicaSCNReader.Dimension
 
ifd - Variable in class loci.formats.in.OMETiffReader.OMETiffPlane
IFD number of this plane.
ifd - Variable in class loci.formats.in.VentanaReader.TIFFTile
 
IFD - Class in loci.formats.tiff
Data structure for working with TIFF Image File Directories (IFDs).
IFD() - Constructor for class loci.formats.tiff.IFD
 
IFD(IFD) - Constructor for class loci.formats.tiff.IFD
 
ifdCounts - Variable in class loci.formats.out.OMETiffWriter
 
ifdIndex - Variable in class loci.formats.in.SVSCoreMetadata
 
IFDList - Class in loci.formats.tiff
Data structure for working with a list of TIFF IFDs.
IFDList() - Constructor for class loci.formats.tiff.IFDList
 
ifdList - Variable in class loci.formats.tiff.TiffParser
Cached list of IFDs in the current file.
IFDMap - Variable in class loci.formats.in.LeicaSCNReader.LeicaSCNHandler
 
ifdOffsets - Variable in class loci.formats.in.FlowSightReader
 
ifds - Variable in class loci.formats.in.APLReader
 
ifds - Variable in class loci.formats.in.CellSensReader
 
ifds - Variable in class loci.formats.in.EPSReader
 
ifds - Variable in class loci.formats.in.FlexReader.FlexFile
 
ifds - Variable in class loci.formats.in.FV1000Reader
 
ifds - Variable in class loci.formats.in.LeicaReader
 
ifds - Variable in class loci.formats.in.MinimalTiffReader
List of IFDs for the current TIFF.
ifdsList - Variable in class loci.formats.in.ZeissLSMReader
 
IFDType - Enum in loci.formats.tiff
An enumeration of IFD types.
IFDType(int, int) - Constructor for enum loci.formats.tiff.IFDType
Default constructor.
IFormatHandler - Interface in loci.formats
Interface for all biological file format readers and writers.
IFormatReader - Interface in loci.formats
Interface for all biological file format readers.
IFormatWidgets - Interface in loci.plugins.config
Interface for defining custom widgets for a specific file format reader.
IFormatWriter - Interface in loci.formats
Interface for all biological file format writers.
ignore - Variable in class loci.plugins.util.SearchableWindow.SearchBox
 
ignoreCase - Variable in class loci.plugins.util.SearchableWindow.SearchBox
 
ih - Variable in class loci.formats.in.GIFReader
Current image rectangle.
IJStatusEchoer - Class in loci.plugins.util
Echoes status messages to the ImageJ status bar.
IJStatusEchoer() - Constructor for class loci.plugins.util.IJStatusEchoer
 
IllegalBlockException - Exception in loci.formats
Exception thrown when FilePatternBlock encounters an invalid pattern.
IllegalBlockException() - Constructor for exception loci.formats.IllegalBlockException
 
IllegalBlockException(String) - Constructor for exception loci.formats.IllegalBlockException
 
IllegalBlockException(String, Throwable) - Constructor for exception loci.formats.IllegalBlockException
 
IllegalBlockException(Throwable) - Constructor for exception loci.formats.IllegalBlockException
 
ILLUM_CHANNEL_ACQUIRE - Static variable in class loci.formats.in.ZeissLSMReader
 
ILLUM_CHANNEL_ATTENUATION - Static variable in class loci.formats.in.ZeissLSMReader
 
ILLUM_CHANNEL_NAME - Static variable in class loci.formats.in.ZeissLSMReader
 
ILLUM_CHANNEL_WAVELENGTH - Static variable in class loci.formats.in.ZeissLSMReader
 
ILLUMINATION - Static variable in class loci.formats.FormatTools
Identifies the Illumination dimensional type, representing a dimension consisting of illuminations.
illumination - Variable in class loci.formats.in.ZeissCZIReader.Channel
 
IlluminationChannel() - Constructor for class loci.formats.in.ZeissLSMReader.IlluminationChannel
 
illuminationLabels - Variable in class loci.formats.in.ZeissCZIReader
 
illuminations - Variable in class loci.formats.in.FV1000Reader
 
illuminations - Variable in class loci.formats.in.ZeissCZIReader
 
illuminations - Variable in class loci.formats.in.ZeissLSMReader
 
illumNA - Variable in class loci.formats.in.LeicaSCNReader.Image
 
illumSource - Variable in class loci.formats.in.LeicaSCNReader.Image
 
IM3Reader - Class in loci.formats.in
 
IM3Reader() - Constructor for class loci.formats.in.IM3Reader
Construct an uninitialized reader of .im3 files.
IM3Reader.BooleanIM3Record - Class in loci.formats.in
A record containing boolean values
IM3Reader.ContainerRecord - Class in loci.formats.in
 
IM3Reader.FloatIM3Record - Class in loci.formats.in
 
IM3Reader.IM3Record - Class in loci.formats.in
 
IM3Reader.IntIM3Record - Class in loci.formats.in
 
IM3Reader.Spectrum - Class in loci.formats.in
 
IM3Reader.StringIM3Record - Class in loci.formats.in
 
IM3Record(String, int, long, int) - Constructor for class loci.formats.in.IM3Reader.IM3Record
 
ImaconHandler() - Constructor for class loci.formats.in.ImaconReader.ImaconHandler
 
ImaconReader - Class in loci.formats.in
ImaconReader is the file format reader for Imacon .fff (TIFF) files.
ImaconReader() - Constructor for class loci.formats.in.ImaconReader
Constructs a new Imacon reader.
ImaconReader.ImaconHandler - Class in loci.formats.in
 
IMAGE - Static variable in class loci.formats.in.CellH5Reader.CellH5Constants
 
Image() - Constructor for class loci.formats.in.InCellReader.Image
 
image - Variable in class loci.formats.in.LegacyQTReader
Image containing current frame.
Image(Attributes) - Constructor for class loci.formats.in.LeicaSCNReader.Image
 
image - Variable in class loci.formats.in.VeecoReader
 
IMAGE_BOUNDARY - Static variable in class loci.formats.in.CellSensReader
 
IMAGE_COLLECTION_PROPERTIES - Static variable in class loci.formats.in.CellSensReader
 
IMAGE_DESCRIPTION - Static variable in class loci.formats.tiff.IFD
 
IMAGE_FRAME_VOLUME - Static variable in class loci.formats.in.CellSensReader
 
IMAGE_LENGTH - Static variable in class loci.formats.tiff.IFD
 
IMAGE_PATH - Static variable in class loci.formats.in.CellH5Reader.CellH5Constants
 
IMAGE_PRO_TAG_1 - Static variable in class loci.formats.in.SEQReader
An array of shorts (length 12) with identical values in all of our samples; assuming this is some sort of format identifier.
IMAGE_PRO_TAG_2 - Static variable in class loci.formats.in.SEQReader
Frame rate.
IMAGE_PRO_TAG_3 - Static variable in class loci.formats.in.SEQReader
 
IMAGE_SEPARATOR - Static variable in class loci.formats.in.GIFReader
 
IMAGE_SOURCE_DATA - Static variable in class loci.formats.in.PhotoshopTiffReader
 
IMAGE_TYPE_1 - Static variable in class loci.formats.in.OpenlabReader
Tag types.
IMAGE_TYPE_2 - Static variable in class loci.formats.in.OpenlabReader
 
IMAGE_TYPES - Static variable in class loci.formats.in.DeltavisionReader
 
IMAGE_WIDTH - Static variable in class loci.formats.tiff.IFD
 
ImageCollection(Attributes) - Constructor for class loci.formats.in.LeicaSCNReader.ImageCollection
 
imageCount - Variable in class loci.formats.CoreMetadata
Total number of images.
imageCount - Variable in class loci.formats.in.ZeissCZIReader.Coordinate
 
imageCreationDate - Variable in class loci.formats.in.MetamorphReader
The TIFF's creation date
imageDepth - Variable in class loci.formats.in.FV1000Reader
 
imageDescription - Variable in class loci.formats.in.BaseZeissReader
 
imageDescription - Variable in class loci.formats.in.FEITiffReader
 
imageDescription - Variable in class loci.formats.in.MicroCTReader
 
imageDescriptions - Variable in class loci.formats.in.SlidebookReader
 
imageDimensions - Variable in class loci.formats.services.JPEGTurboServiceImpl
 
imageFile - Variable in class loci.formats.in.PCORAWReader
 
imageFiles - Variable in class loci.formats.in.BaseZeissReader
 
imageFiles - Variable in class loci.formats.in.InCellReader
 
imageFiles - Variable in class loci.formats.in.IPWReader
List of embedded image file names (one per image plane).
imageFiles - Variable in class loci.formats.in.PCIReader
 
imageFolder - Variable in class loci.formats.in.CellVoyagerReader
 
imageHeight - Variable in class loci.formats.in.InCellReader
 
imageHeight - Variable in class loci.formats.services.JPEGTurboServiceImpl
 
imageIFD(int) - Method in class loci.formats.in.LeicaSCNReader
 
ImageIOReader - Class in loci.formats.in
ImageIOReader is the superclass for file format readers that use the javax.imageio package.
ImageIOReader(String, String) - Constructor for class loci.formats.in.ImageIOReader
Constructs a new ImageIOReader.
ImageIOReader(String, String[]) - Constructor for class loci.formats.in.ImageIOReader
Constructs a new ImageIOReader.
ImageIOWriter - Class in loci.formats.out
ImageIOWriter is the superclass for file format writers that use the javax.imageio library.
ImageIOWriter(String, String, String) - Constructor for class loci.formats.out.ImageIOWriter
Constructs an ImageIO-based writer with the given name, default suffix and output type (e.g., png, jpeg).
ImageIOWriter(String, String[], String) - Constructor for class loci.formats.out.ImageIOWriter
Constructs an ImageIO-based writer with the given name, default suffixes and output type (e.g., png, jpeg).
IMAGEJ_MSG - Static variable in class loci.plugins.util.LibraryChecker
Message to be displayed if ImageJ is too old for Bio-Formats plugins.
IMAGEJ_TAG - Static variable in class loci.formats.in.TiffReader
 
IMAGEJ_VERSION - Static variable in class loci.plugins.util.LibraryChecker
Minimum version of ImageJ necessary for Bio-Formats plugins.
imageLocations - Variable in class loci.formats.out.OMETiffWriter
 
imageMap - Variable in class loci.formats.in.LeicaSCNReader.LeicaSCNHandler
 
imageName - Variable in class loci.formats.in.BioRadSCNReader
 
imageName - Variable in class loci.formats.in.FEITiffReader
 
imageName - Variable in class loci.formats.in.ImaconReader
 
imageName - Variable in class loci.formats.in.MetamorphHandler
 
imageName - Variable in class loci.formats.in.MetamorphReader
The TIFF's name
imageName - Variable in class loci.formats.in.SISReader
 
imageName - Variable in class loci.formats.in.ZeissCZIReader
 
imageNames - Variable in class loci.formats.in.BrukerReader
 
imageNames - Variable in class loci.formats.in.LIFReader
 
imageNames - Variable in class loci.formats.in.TillVisionReader
 
imageNames - Variable in class loci.formats.in.ZeissLSMReader
 
imageNumber - Variable in class loci.formats.in.APNGReader.PNGInputStream
 
imageNumEnd - Variable in class loci.formats.in.LeicaSCNReader.Image
 
imageNumStart - Variable in class loci.formats.in.LeicaSCNReader.Image
 
imageOffset - Variable in class loci.formats.in.IvisionReader
 
ImagePlusReader - Class in loci.plugins.in
A high-level reader for ImagePlus objects.
ImagePlusReader() - Constructor for class loci.plugins.in.ImagePlusReader
Constructs an ImagePlusReader with the default options.
ImagePlusReader(ImportProcess) - Constructor for class loci.plugins.in.ImagePlusReader
Constructs an ImagePlusReader with the given complete import preparation process.
ImageProcessorReader - Class in loci.plugins.util
A low-level reader for ImageProcessor objects.
ImageProcessorReader() - Constructor for class loci.plugins.util.ImageProcessorReader
Constructs an ImageProcessorReader around a new image reader.
ImageProcessorReader(IFormatReader) - Constructor for class loci.plugins.util.ImageProcessorReader
Constructs an ImageProcessorReader with the given reader.
ImageProcessorSource - Class in loci.plugins.util
Retrieves ImageJ image processors from an image reader.
ImageProcessorSource(IFormatReader) - Constructor for class loci.plugins.util.ImageProcessorSource
 
ImageReader - Class in loci.formats
ImageReader is the master file format reader for all supported formats.
ImageReader() - Constructor for class loci.formats.ImageReader
Constructs a new ImageReader with the default list of reader classes from readers.txt.
ImageReader(ClassList<IFormatReader>) - Constructor for class loci.formats.ImageReader
Constructs a new ImageReader from the given list of reader classes.
imageReader - Variable in class loci.plugins.in.ImportProcess
 
imageROIs - Variable in class loci.formats.in.LIFReader
 
imageRX - Variable in class loci.formats.in.SDTInfo
 
imageRY - Variable in class loci.formats.in.SDTInfo
 
images - Variable in class loci.formats.gui.ImageViewer
 
images - Variable in class loci.formats.in.GIFReader
 
IMAGES - Static variable in class loci.formats.in.LeicaReader
 
images - Variable in class loci.formats.in.LeicaSCNReader.ImageCollection
 
imageSequence - Variable in class loci.formats.in.DeltavisionReader
 
imagesPerFile - Variable in class loci.formats.FileStitcher.ExternalSeries
 
imagesPerFile - Variable in class loci.formats.in.DicomReader
 
imageThumbnail - Variable in class loci.formats.in.LeicaSCNReader.Image
 
ImageTools - Class in loci.formats
A utility class with convenience methods for manipulating images in primitive array form.
ImageTools() - Constructor for class loci.formats.ImageTools
 
imageType - Variable in class loci.formats.in.DicomReader
 
ImageViewer - Class in loci.formats.gui
ImageViewer is a simple viewer/converter for the Bio-Formats image formats.
ImageViewer() - Constructor for class loci.formats.gui.ImageViewer
Constructs an image viewer.
ImageViewer(boolean) - Constructor for class loci.formats.gui.ImageViewer
Constructs an image viewer.
imageWidth - Variable in class loci.formats.in.InCellReader
 
imageWidth - Variable in class loci.formats.services.JPEGTurboServiceImpl
 
ImageWriter - Class in loci.formats
ImageWriter is the master file format writer for all supported formats.
ImageWriter() - Constructor for class loci.formats.ImageWriter
Constructs a new ImageWriter with the default list of writer classes from writers.txt.
ImageWriter(ClassList<IFormatWriter>) - Constructor for class loci.formats.ImageWriter
Constructs a new ImageWriter from the given list of writer classes.
imageX - Variable in class loci.formats.in.SDTInfo
4 subsequent fields valid only for Camera mode or FIFO_IMAGE mode.
imageY - Variable in class loci.formats.in.SDTInfo
 
ImagicReader - Class in loci.formats.in
ImagicReader is the file format reader for IMAGIC files.
ImagicReader() - Constructor for class loci.formats.in.ImagicReader
Constructs a new IMAGIC reader.
IMARIS_MAGIC_BYTES - Static variable in class loci.formats.in.ImarisReader
Magic number; present in all files.
ImarisHDFReader - Class in loci.formats.in
Reader for Bitplane Imaris 5.5 (HDF) files.
ImarisHDFReader() - Constructor for class loci.formats.in.ImarisHDFReader
Constructs a new Imaris HDF reader.
ImarisReader - Class in loci.formats.in
ImarisReader is the file format reader for Bitplane Imaris files.
ImarisReader() - Constructor for class loci.formats.in.ImarisReader
Constructs a new Imaris reader.
ImarisTiffReader - Class in loci.formats.in
ImarisTiffReader is the file format reader for Bitplane Imaris 3 files (TIFF variant).
ImarisTiffReader() - Constructor for class loci.formats.in.ImarisTiffReader
Constructs a new Imaris TIFF reader.
IMetadata - Interface in loci.formats.meta
 
IMetadataConfigurable - Interface in loci.formats
 
img - Variable in class loci.formats.in.ImageIOReader
Transient reference to a BufferedImage for this FormatHandler.currentId.
img - Variable in class loci.formats.tools.AsciiImage
 
IMinMaxStore - Interface in loci.formats.meta
Interface for consumers of minima and maxima pixel intensities across a given wavelength.
immersion - Variable in class loci.formats.in.ND2Handler
 
immersion - Variable in class loci.formats.in.NikonTiffReader
 
immersion - Variable in class loci.formats.in.OIRReader.Objective
 
immersion - Variable in class loci.formats.in.SimplePCITiffReader
 
immersion - Variable in class loci.formats.in.ZeissLSMReader.Recording
 
immersions - Variable in class loci.formats.in.LIFReader
 
IMODReader - Class in loci.formats.in
Reader for IMOD binary files.
IMODReader() - Constructor for class loci.formats.in.IMODReader
Constructs a new IMOD reader.
IMODSTAMP_OFFSET - Static variable in class loci.formats.in.MRCReader
 
imp - Variable in class loci.plugins.out.Exporter
Current stack.
imp - Variable in class loci.plugins.Slicer
Current image stack.
IMPLICIT_VR - Static variable in class loci.formats.in.DicomReader
 
importData(JComponent, Transferable) - Method in class loci.plugins.shortcut.ShortcutTransferHandler
 
Importer - Class in loci.plugins.in
Core logic for the Bio-Formats Importer ImageJ plugin.
Importer(LociImporter) - Constructor for class loci.plugins.in.Importer
 
ImporterDialog - Class in loci.plugins.in
Abstract superclass of importer dialogs.
ImporterDialog(ImportProcess) - Constructor for class loci.plugins.in.ImporterDialog
 
ImporterMetadata - Class in loci.plugins.in
Helper class for storing original metadata key/value pairs.
ImporterMetadata(IFormatReader, ImportProcess, boolean) - Constructor for class loci.plugins.in.ImporterMetadata
 
ImporterOptions - Class in loci.plugins.in
Helper class for managing Bio-Formats Importer options.
ImporterOptions() - Constructor for class loci.plugins.in.ImporterOptions
 
ImporterPrompter - Class in loci.plugins.in
Helper class for presenting the user with dialog boxes for configuring importer options.
ImporterPrompter(ImportProcess) - Constructor for class loci.plugins.in.ImporterPrompter
 
ImportProcess - Class in loci.plugins.in
Manages the import preparation process.
ImportProcess() - Constructor for class loci.plugins.in.ImportProcess
 
ImportProcess(ImporterOptions) - Constructor for class loci.plugins.in.ImportProcess
 
ImportStep - Enum in loci.plugins.in
An enumeration of the steps in the import preparation process.
ImportStep(int, String) - Constructor for enum loci.plugins.in.ImportStep
 
IMPROVISION_MAGIC_STRING - Static variable in class loci.formats.in.ImprovisionTiffReader
 
ImprovisionTiffReader - Class in loci.formats.in
ImprovisionTiffReader is the file format reader for Improvision TIFF files.
ImprovisionTiffReader() - Constructor for class loci.formats.in.ImprovisionTiffReader
 
ImspectorReader - Class in loci.formats.in
ImspectorReader is the file format reader for Imspector .msr files.
ImspectorReader() - Constructor for class loci.formats.in.ImspectorReader
Constructs a new Imspector reader.
in - Variable in class loci.formats.FormatReader
Current file.
in - Variable in class loci.formats.gui.ImageViewer
 
in - Variable in class loci.formats.in.JPEG2000MetadataParser
Stream that we're parsing metadata from.
in - Variable in class loci.formats.out.TiffWriter
Input stream to use when overwriting data.
in - Variable in class loci.formats.services.JPEGTurboServiceImpl
 
in - Variable in class loci.formats.tiff.TiffParser
Input source from which to parse TIFF data.
in - Variable in class loci.formats.tools.AmiraParameters
 
inCache - Variable in class loci.formats.cache.Cache
Whether each position is currently supposed to be cached.
InCell3000Reader - Class in loci.formats.in
InCell3000Reader is the file format reader for InCell 3000.
InCell3000Reader() - Constructor for class loci.formats.in.InCell3000Reader
Constructs a new InCell 3000 reader.
INCELL_MAGIC_STRING - Static variable in class loci.formats.in.InCellReader
 
InCellHandler(MetadataStore) - Constructor for class loci.formats.in.InCellReader.InCellHandler
 
InCellReader - Class in loci.formats.in
InCellReader is the file format reader for InCell 1000/2000 datasets.
InCellReader() - Constructor for class loci.formats.in.InCellReader
Constructs a new InCell 1000/2000 reader.
InCellReader.Image - Class in loci.formats.in
 
InCellReader.InCellHandler - Class in loci.formats.in
SAX handler for parsing XML.
InCellReader.MinimalInCellHandler - Class in loci.formats.in
 
INCLUDE_ATTACHMENTS_DEFAULT - Static variable in class loci.formats.in.ZeissCZIReader
 
INCLUDE_ATTACHMENTS_KEY - Static variable in class loci.formats.in.ZeissCZIReader
 
includeC - Variable in class loci.formats.gui.DataConverter
 
includeCZIAttachments() - Static method in class loci.plugins.util.LociPrefs
 
includeT - Variable in class loci.formats.gui.DataConverter
 
includeZ - Variable in class loci.formats.gui.DataConverter
 
incr - Variable in class loci.formats.in.SDTInfo
 
index - Variable in class loci.formats.cache.CacheEvent
Relevant index to the event, if any.
index - Variable in class loci.formats.in.BaseZeissReader.Tag
 
index - Variable in class loci.formats.in.CellVoyagerReader.AreaInfo
 
index - Variable in class loci.formats.in.CellVoyagerReader.FieldInfo
 
index - Variable in class loci.formats.in.CV7000Reader.Channel
 
index - Variable in class loci.formats.in.LeicaHandler.Laser
 
index - Variable in class loci.formats.in.LeicaReader.Detector
 
Index(int[]) - Constructor for class loci.formats.in.MicromanagerReader.Index
 
index - Variable in class loci.formats.in.PrairieMetadata.Frame
index of this <Frame>.
index - Variable in class loci.formats.in.VentanaReader.AreaOfInterest
 
index - Variable in class loci.formats.in.ZeissTIFFHandler.Tag
 
index - Variable in class loci.formats.Resolution
 
index - Variable in class loci.plugins.in.ThumbLoader.SeriesInfo
 
index - Variable in class loci.plugins.util.SearchableWindow
 
Index16ColorModel - Class in loci.formats.gui
ColorModel that handles 16 bits per channel lookup tables.
Index16ColorModel(int, int, short[][], boolean) - Constructor for class loci.formats.gui.Index16ColorModel
 
indexed - Variable in class loci.formats.CoreMetadata
Indicates whether or not the images are stored as indexed color.
INDEXED - Static variable in class loci.formats.in.APNGReader
 
indexedAsRGB - Variable in class loci.formats.FormatReader
Whether or not MetadataStore sets C = 3 for indexed color images.
indexedToRGB(BufferedImage, boolean) - Static method in class loci.formats.gui.AWTImageTools
Converts an indexed color BufferedImage to an RGB BufferedImage.
indexedToRGB(byte[][], byte[]) - Static method in class loci.formats.ImageTools
Converts a LUT and an array of indices into an array of RGB tuples.
indexedToRGB(short[][], byte[], boolean) - Static method in class loci.formats.ImageTools
Converts a LUT and an array of indices into an array of RGB tuples.
indexIntoPlanes - Variable in class loci.formats.in.ZeissCZIReader
 
indexMax - Variable in class loci.formats.in.PrairieMetadata.Sequence
Maximum index value.
indexMin - Variable in class loci.formats.in.PrairieMetadata.Sequence
Minimum index value.
indexToValue - Variable in class loci.formats.in.FakeReader
For indexed color, mapping from indices to values and vice versa.
inDimensionProperties - Variable in class loci.formats.in.CellSensReader
 
INDIVIDUAL_JARS - Static variable in class loci.formats.UpgradeChecker
Names of the individual JARs.
infFile - Variable in class loci.formats.in.FujiReader
 
infFiles - Variable in class loci.formats.in.TillVisionReader
 
inflateInputBuffer - Variable in class loci.formats.in.OBFReader.State
 
inflater - Variable in class loci.formats.in.OBFReader.State
 
info - Variable in class loci.formats.in.GatanReader
 
info - Variable in class loci.formats.in.OMETiffReader
Mapping from series and plane numbers to files and IFD entries.
info - Variable in class loci.formats.in.SDTInfo
 
info - Variable in class loci.formats.in.SDTReader
Object containing SDT header information.
info - Variable in class loci.plugins.prefs.Option
Documentation about the option, in HTML.
INFO_DEFAULT - Static variable in class loci.plugins.in.MainDialog
Initial message to display in help text box.
INFO_TABLE - Static variable in class loci.formats.in.LiFlimReader
 
infoLength - Variable in class loci.formats.in.SDTInfo
Length of the info part.
infoOffs - Variable in class loci.formats.in.SDTInfo
Offset of the info part which contains general text information (Title, date, time, contents etc.).
infoPane - Variable in class loci.plugins.in.MainDialog
 
infoTable - Variable in class loci.plugins.in.MainDialog
 
ini - Variable in class loci.formats.in.LiFlimReader
Parsed configuration data.
INI_DEFAULT - Static variable in class loci.plugins.prefs.Option
INI key indicating option's default value.
INI_INFO - Static variable in class loci.plugins.prefs.Option
INI key indicating option's info.
INI_KEY - Static variable in class loci.plugins.prefs.Option
INI key indicating option's key.
INI_LABEL - Static variable in class loci.plugins.prefs.Option
INI key indicating option's label.
INI_POSSIBLE - Static variable in class loci.plugins.prefs.StringOption
INI key indicating option's possible values.
INI_SAVE - Static variable in class loci.plugins.prefs.Option
INI key indicating whether option should be saved to prefs file.
INI_TYPE - Static variable in class loci.plugins.prefs.OptionsList
INI key indicating option's type.
iniFile - Variable in class loci.formats.in.FakeReader
Properties companion file which can be associated with this fake file
init() - Method in class loci.formats.services.NetCDFServiceImpl
 
init() - Method in class org.libjpegturbo.turbojpeg.TJCompressor
 
init() - Method in class org.libjpegturbo.turbojpeg.TJDecompressor
 
init() - Method in class org.libjpegturbo.turbojpeg.TJTransformer
 
initAlternateMetadata() - Method in class loci.formats.in.FluoviewReader
 
initAlternateMetadataStore() - Method in class loci.formats.in.FluoviewReader
 
initClass() - Method in class loci.formats.gui.LegacyQTTools
Initializes the class.
initCoreMetadata(int, int) - Method in class loci.formats.in.LeicaSCNReader
 
initCoreMetadata() - Method in class loci.formats.in.LiFlimReader
 
initDecompressor() - Method in class loci.formats.in.AmiraReader.HxZip
 
initExtraMetadata() - Method in class loci.formats.in.DeltavisionReader
 
initFile(String) - Method in class loci.formats.FileStitcher
Initializes the given file or file pattern.
initFile(String) - Method in class loci.formats.FormatReader
Initializes the given file (parsing header information, etc.).
initFile(String) - Method in class loci.formats.in.AFIReader
 
initFile(String) - Method in class loci.formats.in.AIMReader
 
initFile(String) - Method in class loci.formats.in.AliconaReader
 
initFile(String) - Method in class loci.formats.in.AmiraReader
 
initFile(String) - Method in class loci.formats.in.AnalyzeReader
 
initFile(String) - Method in class loci.formats.in.APLReader
 
initFile(String) - Method in class loci.formats.in.APNGReader
 
initFile(String) - Method in class loci.formats.in.ARFReader
 
initFile(String) - Method in class loci.formats.in.AVIReader
 
initFile(String) - Method in class loci.formats.in.BaseTiffReader
 
initFile(String) - Method in class loci.formats.in.BDReader
 
initFile(String) - Method in class loci.formats.in.BDVReader
 
initFile(String) - Method in class loci.formats.in.BioRadGelReader
 
initFile(String) - Method in class loci.formats.in.BioRadReader
 
initFile(String) - Method in class loci.formats.in.BioRadSCNReader
 
initFile(String) - Method in class loci.formats.in.BMPReader
 
initFile(String) - Method in class loci.formats.in.BrukerReader
 
initFile(String) - Method in class loci.formats.in.BurleighReader
 
initFile(String) - Method in class loci.formats.in.CanonRawReader
 
initFile(String) - Method in class loci.formats.in.CellH5Reader
 
initFile(String) - Method in class loci.formats.in.CellomicsReader
 
initFile(String) - Method in class loci.formats.in.CellSensReader
 
initFile(String) - Method in class loci.formats.in.CellVoyagerReader
 
initFile(String) - Method in class loci.formats.in.CellWorxReader
 
initFile(String) - Method in class loci.formats.in.ColumbusReader
 
initFile(String) - Method in class loci.formats.in.CV7000Reader
 
initFile(String) - Method in class loci.formats.in.DeltavisionReader
 
initFile(String) - Method in class loci.formats.in.DicomReader
 
initFile(String) - Method in class loci.formats.in.DNGReader
 
initFile(String) - Method in class loci.formats.in.Ecat7Reader
 
initFile(String) - Method in class loci.formats.in.EPSReader
 
initFile(String) - Method in class loci.formats.in.FakeReader
 
initFile(String) - Method in class loci.formats.in.FEIReader
 
initFile(String) - Method in class loci.formats.in.FilePatternReader
 
initFile(String) - Method in class loci.formats.in.FitsReader
 
initFile(String) - Method in class loci.formats.in.FlexReader
 
initFile(String) - Method in class loci.formats.in.FlowSightReader
 
initFile(String) - Method in class loci.formats.in.FujiReader
 
initFile(String) - Method in class loci.formats.in.FV1000Reader
 
initFile(String) - Method in class loci.formats.in.GatanDM2Reader
 
initFile(String) - Method in class loci.formats.in.GatanReader
 
initFile(String) - Method in class loci.formats.in.GIFReader
 
initFile(String) - Method in class loci.formats.in.HamamatsuVMSReader
 
initFile(String) - Method in class loci.formats.in.HISReader
 
initFile(String) - Method in class loci.formats.in.HitachiReader
 
initFile(String) - Method in class loci.formats.in.HRDGDFReader
 
initFile(String) - Method in class loci.formats.in.I2IReader
 
initFile(String) - Method in class loci.formats.in.ICSReader
 
initFile(String) - Method in class loci.formats.in.IM3Reader
 
initFile(String) - Method in class loci.formats.in.ImageIOReader
 
initFile(String) - Method in class loci.formats.in.ImagicReader
 
initFile(String) - Method in class loci.formats.in.ImarisHDFReader
 
initFile(String) - Method in class loci.formats.in.ImarisReader
 
initFile(String) - Method in class loci.formats.in.ImarisTiffReader
 
initFile(String) - Method in class loci.formats.in.IMODReader
 
initFile(String) - Method in class loci.formats.in.ImspectorReader
 
initFile(String) - Method in class loci.formats.in.InCell3000Reader
 
initFile(String) - Method in class loci.formats.in.InCellReader
 
initFile(String) - Method in class loci.formats.in.INRReader
 
initFile(String) - Method in class loci.formats.in.InveonReader
 
initFile(String) - Method in class loci.formats.in.IPLabReader
 
initFile(String) - Method in class loci.formats.in.IPWReader
 
initFile(String) - Method in class loci.formats.in.IvisionReader
 
initFile(String) - Method in class loci.formats.in.JEOLReader
 
initFile(String) - Method in class loci.formats.in.JPEG2000Reader
 
initFile(String) - Method in class loci.formats.in.JPEGReader.DefaultJPEGReader
 
initFile(String) - Method in class loci.formats.in.JPXReader
 
initFile(String) - Method in class loci.formats.in.KhorosReader
 
initFile(String) - Method in class loci.formats.in.KLBReader
 
initFile(String) - Method in class loci.formats.in.KodakReader
 
initFile(String) - Method in class loci.formats.in.L2DReader
 
initFile(String) - Method in class loci.formats.in.LegacyND2Reader
 
initFile(String) - Method in class loci.formats.in.LegacyQTReader
 
initFile(String) - Method in class loci.formats.in.LeicaReader
 
initFile(String) - Method in class loci.formats.in.LiFlimReader
 
initFile(String) - Method in class loci.formats.in.LIFReader
 
initFile(String) - Method in class loci.formats.in.LIMReader
 
initFile(String) - Method in class loci.formats.in.MetamorphReader
 
initFile(String) - Method in class loci.formats.in.MetamorphTiffReader
 
initFile(String) - Method in class loci.formats.in.MIASReader
 
initFile(String) - Method in class loci.formats.in.MicroCTReader
 
initFile(String) - Method in class loci.formats.in.MicromanagerReader
 
initFile(String) - Method in class loci.formats.in.MINCReader
 
initFile(String) - Method in class loci.formats.in.MinimalTiffReader
 
initFile(String) - Method in class loci.formats.in.MNGReader
 
initFile(String) - Method in class loci.formats.in.MolecularImagingReader
 
initFile(String) - Method in class loci.formats.in.MRCReader
 
initFile(String) - Method in class loci.formats.in.MRWReader
 
initFile(String) - Method in class loci.formats.in.NAFReader
 
initFile(String) - Method in class loci.formats.in.NativeND2Reader
 
initFile(String) - Method in class loci.formats.in.NativeQTReader
 
initFile(String) - Method in class loci.formats.in.NDPIReader
 
initFile(String) - Method in class loci.formats.in.NDPISReader
 
initFile(String) - Method in class loci.formats.in.NiftiReader
 
initFile(String) - Method in class loci.formats.in.NikonReader
 
initFile(String) - Method in class loci.formats.in.NRRDReader
 
initFile(String) - Method in class loci.formats.in.OBFReader
 
initFile(String) - Method in class loci.formats.in.OIRReader
 
initFile(String) - Method in class loci.formats.in.OMETiffReader
 
initFile(String) - Method in class loci.formats.in.OMEXMLReader
 
initFile(String) - Method in class loci.formats.in.OpenlabRawReader
 
initFile(String) - Method in class loci.formats.in.OpenlabReader
 
initFile(String) - Method in class loci.formats.in.OperettaReader
 
initFile(String) - Method in class loci.formats.in.OxfordInstrumentsReader
 
initFile(String) - Method in class loci.formats.in.PCIReader
 
initFile(String) - Method in class loci.formats.in.PCORAWReader
 
initFile(String) - Method in class loci.formats.in.PCXReader
 
initFile(String) - Method in class loci.formats.in.PDSReader
 
initFile(String) - Method in class loci.formats.in.PerkinElmerReader
 
initFile(String) - Method in class loci.formats.in.PGMReader
 
initFile(String) - Method in class loci.formats.in.PhotoshopTiffReader
 
initFile(String) - Method in class loci.formats.in.PictReader
 
initFile(String) - Method in class loci.formats.in.PovrayReader
 
initFile(String) - Method in class loci.formats.in.PQBinReader
 
initFile(String) - Method in class loci.formats.in.PrairieReader
 
initFile(String) - Method in class loci.formats.in.PSDReader
 
initFile(String) - Method in class loci.formats.in.QuesantReader
 
initFile(String) - Method in class loci.formats.in.RHKReader
 
initFile(String) - Method in class loci.formats.in.SBIGReader
 
initFile(String) - Method in class loci.formats.in.ScanrReader
 
initFile(String) - Method in class loci.formats.in.SDTReader
 
initFile(String) - Method in class loci.formats.in.SeikoReader
 
initFile(String) - Method in class loci.formats.in.SEQReader
 
initFile(String) - Method in class loci.formats.in.SIFReader
 
initFile(String) - Method in class loci.formats.in.SlidebookReader
 
initFile(String) - Method in class loci.formats.in.SMCameraReader
 
initFile(String) - Method in class loci.formats.in.SPCReader
 
initFile(String) - Method in class loci.formats.in.SPEReader
 
initFile(String) - Method in class loci.formats.in.SpiderReader
 
initFile(String) - Method in class loci.formats.in.TargaReader
 
initFile(String) - Method in class loci.formats.in.TCSReader
 
initFile(String) - Method in class loci.formats.in.TextReader
 
initFile(String) - Method in class loci.formats.in.TiffJAIReader
 
initFile(String) - Method in class loci.formats.in.TileJPEGReader
 
initFile(String) - Method in class loci.formats.in.TillVisionReader
 
initFile(String) - Method in class loci.formats.in.TopometrixReader
 
initFile(String) - Method in class loci.formats.in.TrestleReader
 
initFile(String) - Method in class loci.formats.in.UBMReader
 
initFile(String) - Method in class loci.formats.in.UnisokuReader
 
initFile(String) - Method in class loci.formats.in.VarianFDFReader
 
initFile(String) - Method in class loci.formats.in.VeecoReader
 
initFile(String) - Method in class loci.formats.in.VGSAMReader
 
initFile(String) - Method in class loci.formats.in.VisitechReader
 
initFile(String) - Method in class loci.formats.in.VolocityClippingReader
 
initFile(String) - Method in class loci.formats.in.VolocityReader
 
initFile(String) - Method in class loci.formats.in.WATOPReader
 
initFile(String) - Method in class loci.formats.in.WlzReader
 
initFile(String) - Method in class loci.formats.in.ZeissCZIReader
 
initFile(String) - Method in class loci.formats.in.ZeissLMSReader
 
initFile(String) - Method in class loci.formats.in.ZeissLSMReader
 
initFile(String) - Method in class loci.formats.in.ZeissTIFFReader
 
initFile(String) - Method in class loci.formats.in.ZeissZVIReader
 
initFile(String) - Method in class loci.formats.in.ZipReader
 
initFile(String) - Method in class loci.formats.SubResolutionFormatReader
Initializes the given file (parsing header information, etc.).
initFileMain(String) - Method in class loci.formats.in.BaseZeissReader
 
initFlexFile(String) - Method in class loci.formats.in.FlexReader
 
initialize(String, int) - Method in class loci.formats.codec.JPEGTileDecoder
 
initialize(RandomAccessInputStream, int) - Method in class loci.formats.codec.JPEGTileDecoder
 
initialize(RandomAccessInputStream, int, int, int) - Method in class loci.formats.codec.JPEGTileDecoder
 
initialize() - Method in class loci.formats.codec.JPEGXRCodec
Initializes the JPEG-XR dependency service.
initialize(String) - Method in interface loci.formats.services.EXIFService
 
initialize(String) - Method in class loci.formats.services.EXIFServiceImpl
 
initialize(RandomAccessInputStream, int, int) - Method in interface loci.formats.services.JPEGTurboService
 
initialize(RandomAccessInputStream, int, int) - Method in class loci.formats.services.JPEGTurboServiceImpl
 
initialize(InputStream) - Method in interface loci.formats.services.LuraWaveService
Wraps lwfDecoder.lwfDecoder(InputStream, String, String).
initialize(InputStream) - Method in class loci.formats.services.LuraWaveServiceImpl
 
initialize(String) - Method in interface loci.formats.services.MDBService
Prepare the given .mdb file for reading.
initialize(String) - Method in class loci.formats.services.MDBServiceImpl
 
initialize(String) - Method in interface loci.formats.services.MetakitService
 
initialize(RandomAccessInputStream) - Method in interface loci.formats.services.MetakitService
 
initialize(String) - Method in class loci.formats.services.MetakitServiceImpl
 
initialize(RandomAccessInputStream) - Method in class loci.formats.services.MetakitServiceImpl
 
initialize(String) - Method in interface loci.formats.services.POIService
Construct a new POI filesystem around the given file.
initialize(RandomAccessInputStream) - Method in interface loci.formats.services.POIService
Construct a new POI filesystem around the given stream.
initialize(String) - Method in class loci.formats.services.POIServiceImpl
 
initialize(RandomAccessInputStream) - Method in class loci.formats.services.POIServiceImpl
 
initializeColors() - Method in class loci.plugins.in.ImportProcess
Performed following ImportStep.COLORS notification.
initializeCrop() - Method in class loci.plugins.in.ImportProcess
Performed following ImportStep.CROP notification.
initialized - Variable in class loci.formats.FormatWriter
Whether each plane in each series of the current file has been prepped for writing.
initialized - Variable in class loci.formats.gui.LegacyQTTools
Flag indicating this class has been initialized.
initializedFile - Variable in class loci.formats.in.HamamatsuVMSReader
 
initializeDimOrder() - Method in class loci.plugins.in.ImportProcess
Performed following ImportStep.DIM_ORDER notification.
initializedPlane - Variable in class loci.formats.in.HamamatsuVMSReader
 
initializedPlane - Variable in class loci.formats.in.NDPIReader
 
initializedSeries - Variable in class loci.formats.in.HamamatsuVMSReader
 
initializedSeries - Variable in class loci.formats.in.NDPIReader
 
initializeFile() - Method in class loci.plugins.in.ImportProcess
Performed following ImportStep.FILE notification.
initializeHelper - Variable in class loci.formats.in.NRRDReader
 
initializeJHDFService(String) - Method in class loci.formats.in.BDVReader
 
initializeJHDFService(String) - Method in class loci.formats.in.CellH5Reader
 
initializeMetadata() - Method in class loci.plugins.in.ImportProcess
Performed following ImportStep.METADATA notification.
initializeRange() - Method in class loci.plugins.in.ImportProcess
Performed following ImportStep.RANGE notification.
initializeReader(IFormatReader, String) - Method in class loci.formats.in.OMETiffReader
 
initializeReader() - Method in class loci.plugins.in.ImportProcess
Performed following ImportStep.READER notification.
initializeSeries() - Method in class loci.plugins.in.ImportProcess
Performed following ImportStep.SERIES notification.
initializeStack() - Method in class loci.plugins.in.ImportProcess
Performed following ImportStep.STACK notification.
initImage() - Method in class loci.formats.in.ImageIOReader
 
initIntArray(String, long[], long) - Method in interface loci.formats.services.JHDFService
Creates an HDF5 dataset in path consisting of integers specified by bytes per pixel bpp.
initIntArray(String, long[], long) - Method in class loci.formats.services.JHDFServiceImpl
 
initLicense() - Method in class loci.formats.services.LuraWaveServiceImpl
 
initLicenseCode() - Static method in class loci.plugins.util.LuraWave
Reads LuraWave license code from ImageJ preferences, if available.
initMeaFile(String) - Method in class loci.formats.in.FlexReader
Initialize the dataset from a .mea file.
initMetadata() - Method in class loci.formats.in.BaseTiffReader
Populates the metadata hashtable and metadata store.
initMetadata() - Method in class loci.formats.in.GelReader
 
initMetadata(String) - Method in class loci.formats.in.LIFReader
Parses a string of XML and puts the values in a Hashtable.
initMetadata(int) - Method in class loci.formats.in.ZeissLSMReader
 
initMetadataStore() - Method in class loci.formats.in.BaseTiffReader
Populates the metadata store using the data parsed in BaseTiffReader.initStandardMetadata() along with some further parsing done in the method itself.
initMetadataStore() - Method in class loci.formats.in.FEITiffReader
 
initMetadataStore() - Method in class loci.formats.in.FluoviewReader
 
initMetadataStore() - Method in class loci.formats.in.ImaconReader
 
initMetadataStore() - Method in class loci.formats.in.ImprovisionTiffReader
 
initMetadataStore() - Method in class loci.formats.in.IonpathMIBITiffReader
 
initMetadataStore() - Method in class loci.formats.in.JPKReader
 
initMetadataStore() - Method in class loci.formats.in.LeicaSCNReader
 
initMetadataStore() - Method in class loci.formats.in.LEOReader
 
initMetadataStore() - Method in class loci.formats.in.NDPIReader
 
initMetadataStore() - Method in class loci.formats.in.NikonElementsTiffReader
 
initMetadataStore() - Method in class loci.formats.in.NikonTiffReader
 
initMetadataStore() - Method in class loci.formats.in.PyramidTiffReader
 
initMetadataStore() - Method in class loci.formats.in.SimplePCITiffReader
 
initMetadataStore() - Method in class loci.formats.in.SISReader
 
initMetadataStore() - Method in class loci.formats.in.SlidebookTiffReader
 
initMetadataStore() - Method in class loci.formats.in.SVSReader
 
initMetadataStore() - Method in class loci.formats.in.TiffReader
 
initMetadataStore() - Method in class loci.formats.in.TrestleReader
 
initMetadataStore() - Method in class loci.formats.in.VectraReader
 
initMetadataStore() - Method in class loci.formats.in.VentanaReader
 
initMinMax() - Method in class loci.formats.MinMaxCalculator
Ensures internal min/max variables are initialized properly.
initOMEMetadata() - Method in class loci.formats.in.LiFlimReader
 
initOriginalMetadata() - Method in class loci.formats.in.LiFlimReader
 
initPixels() - Method in class loci.formats.in.DeltavisionReader
 
initPlaneReader() - Method in class loci.formats.in.AmiraReader
 
initPOIService() - Method in class loci.formats.in.FV1000Reader
 
initPOIService() - Method in class loci.formats.in.IPWReader
 
initPOIService() - Method in class loci.formats.in.PCIReader
 
initPOIService() - Method in class loci.formats.in.ZeissZVIReader
 
initReader(int, int) - Method in class loci.formats.FileStitcher
 
initResFile(String) - Method in class loci.formats.in.FlexReader
Initialize the dataset from a .res file.
initStack(long) - Method in class loci.formats.in.OBFReader
 
initStandardMetadata() - Method in class loci.formats.in.BaseTiffReader
Parses standard metadata.
initStandardMetadata() - Method in class loci.formats.in.DNGReader
 
initStandardMetadata() - Method in class loci.formats.in.FEITiffReader
 
initStandardMetadata() - Method in class loci.formats.in.FluoviewReader
 
initStandardMetadata() - Method in class loci.formats.in.ImaconReader
 
initStandardMetadata() - Method in class loci.formats.in.ImprovisionTiffReader
 
initStandardMetadata() - Method in class loci.formats.in.IonpathMIBITiffReader
 
initStandardMetadata() - Method in class loci.formats.in.JPKReader
 
initStandardMetadata() - Method in class loci.formats.in.LeicaSCNReader
 
initStandardMetadata() - Method in class loci.formats.in.LEOReader
 
initStandardMetadata() - Method in class loci.formats.in.MetamorphReader
 
initStandardMetadata() - Method in class loci.formats.in.NDPIReader
 
initStandardMetadata() - Method in class loci.formats.in.NikonElementsTiffReader
 
initStandardMetadata() - Method in class loci.formats.in.NikonReader
 
initStandardMetadata() - Method in class loci.formats.in.NikonTiffReader
 
initStandardMetadata() - Method in class loci.formats.in.PyramidTiffReader
 
initStandardMetadata() - Method in class loci.formats.in.SEQReader
 
initStandardMetadata() - Method in class loci.formats.in.SimplePCITiffReader
 
initStandardMetadata() - Method in class loci.formats.in.SISReader
 
initStandardMetadata() - Method in class loci.formats.in.SlidebookTiffReader
 
initStandardMetadata() - Method in class loci.formats.in.SVSReader
 
initStandardMetadata() - Method in class loci.formats.in.TiffReader
 
initStandardMetadata() - Method in class loci.formats.in.TrestleReader
 
initStandardMetadata() - Method in class loci.formats.in.VectraReader
 
initStandardMetadata() - Method in class loci.formats.in.VentanaReader
 
initTiffParser() - Method in class loci.formats.in.LeicaSCNReader
 
initTiffParser() - Method in class loci.formats.in.MinimalTiffReader
Reinitialize the underlying TiffParser.
initVars(String) - Method in class loci.formats.in.BaseZeissReader
 
initVars(String) - Method in class loci.formats.in.ZeissTIFFReader
 
initVars(String) - Method in class loci.formats.in.ZeissZVIReader
 
INK_NAMES - Static variable in class loci.formats.tiff.IFD
 
INK_SET - Static variable in class loci.formats.tiff.IFD
 
inPixels - Variable in class loci.formats.in.BDVReader.BDVXMLHandler
 
inPixels - Variable in class loci.formats.in.OMEXMLReader.OMEXMLHandler
 
input - Variable in class loci.formats.gui.DataConverter
 
input - Variable in class loci.formats.Memoizer.KryoDeser
 
inputOrder - Variable in class loci.formats.SwappableMetadata
Order in which dimensions are stored.
inputOrder - Variable in class loci.plugins.in.ImporterOptions
 
INR_MAGIC - Static variable in class loci.formats.in.INRReader
 
INRReader - Class in loci.formats.in
INRReader is the file format reader for INR files.
INRReader() - Constructor for class loci.formats.in.INRReader
Constructs a new INR reader.
inSequence - Variable in class loci.formats.in.DicomReader
 
insert(ImageProcessor, int, int) - Method in class loci.plugins.util.RecordedImageProcessor
 
insertResolution(OMEPyramidStore.Resolution, int, int) - Method in class loci.formats.ome.OMEPyramidStore
Store the given Resolution object at the given indices.
insertUpdate(DocumentEvent) - Method in class loci.plugins.config.FlexWidgets
 
insertWarningComment(String) - Method in class loci.formats.out.OMETiffWriter
 
install(String, String) - Method in class loci.formats.UpgradeChecker
Download and install a JAR file from the given URL.
install(String) - Static method in class loci.plugins.Updater
Install the tools bundle which can be retrieved from the specified path.
installButton - Variable in class loci.plugins.config.ConfigWindow
 
installIndividualJars(String, String) - Method in class loci.formats.UpgradeChecker
Download and install all of the individual JAR files into the given directory.
InstallWizard - Class in loci.plugins.config
A wizard for walking users through installation of third party libraries and plugins used by the Bio-Formats plugins.
InstallWizard() - Constructor for class loci.plugins.config.InstallWizard
 
institutions - Variable in class loci.formats.in.BrukerReader
 
instrumentModel - Variable in class loci.formats.in.NDPIReader
 
INT - Static variable in class loci.formats.in.CellSensReader
 
INT - Static variable in class loci.formats.in.GatanReader
 
INT16 - Static variable in class loci.formats.FormatTools
Identifies the INT16 data type used to store pixel values.
INT16 - Static variable in class loci.formats.in.SPEReader
 
INT16_TYPE - Static variable in class loci.formats.in.KLBReader
 
INT32 - Static variable in class loci.formats.FormatTools
Identifies the INT32 data type used to store pixel values.
INT32 - Static variable in class loci.formats.in.SPEReader
 
INT32_TYPE - Static variable in class loci.formats.in.KLBReader
 
INT64_TYPE - Static variable in class loci.formats.in.KLBReader
 
INT8 - Static variable in class loci.formats.FormatTools
Identifies the INT8 data type used to store pixel values.
INT8_TYPE - Static variable in class loci.formats.in.KLBReader
 
INT_2 - Static variable in class loci.formats.in.CellSensReader
 
INT_3 - Static variable in class loci.formats.in.CellSensReader
 
INT_4 - Static variable in class loci.formats.in.CellSensReader
 
INT_ARRAY_2 - Static variable in class loci.formats.in.CellSensReader
 
INT_ARRAY_3 - Static variable in class loci.formats.in.CellSensReader
 
INT_ARRAY_4 - Static variable in class loci.formats.in.CellSensReader
 
INT_ARRAY_5 - Static variable in class loci.formats.in.CellSensReader
 
INT_INTERVAL - Static variable in class loci.formats.in.CellSensReader
 
INT_RECT - Static variable in class loci.formats.in.CellSensReader
 
intenScaling - Variable in class loci.formats.in.DeltavisionReader.DVExtHdrFields
Intensity scaling factor.
intensity - Variable in class loci.formats.in.LeicaHandler.Laser
 
intensity - Variable in class loci.formats.in.SDTReader
Whether to combine lifetime bins into single intensity image planes.
interlace - Variable in class loci.formats.in.APNGReader
 
interlace - Variable in class loci.formats.in.GIFReader
Interlace flag.
interlaced - Variable in class loci.formats.codec.MJPBCodecOptions
Indicates whether or not channels are interlaced.
interlaced - Variable in class loci.formats.in.NativeQTReader
Set to true if the scanlines in a plane are interlaced (mjpb only).
interleaved - Variable in class loci.formats.codec.CodecOptions
Indicates whether or not channels are interleaved.
interleaved - Variable in class loci.formats.CoreMetadata
True if channels are stored RGBRGBRGB...; false if channels are stored RRR...GGG...BBB...
interleaved - Variable in class loci.formats.FormatWriter
Whether the channels in an RGB image are interleaved.
internalOffsets - Variable in class loci.formats.in.AmiraReader.HxRLE
 
internalStamps - Variable in class loci.formats.in.MetamorphReader
 
interpolate(short[], byte[], int[], int, int, boolean) - Static method in class loci.formats.ImageTools
 
intFormat(int, int) - Static method in class loci.formats.in.MetamorphReader
Formats an integer value with leading 0s if needed.
intFormatMax(int, int) - Static method in class loci.formats.in.MetamorphReader
Formats an integer with leading 0 using maximum sequence number.
IntIM3Record(String, int, long, int) - Constructor for class loci.formats.in.IM3Reader.IntIM3Record
 
intValue() - Method in class loci.formats.tiff.TiffRational
Returns the value of the specified number as an int.
INVALID_LICENSE_MSG - Static variable in class loci.formats.services.LuraWaveServiceImpl
Message to display if an invalid LuraWave license code is given.
INVALID_PIXELS - Static variable in class loci.formats.in.FEIReader
 
invalidAndMark(int) - Method in class loci.formats.in.SPCReader
 
invalidAndMarkInit(int) - Method in class loci.formats.in.SPCReader
 
InveonReader - Class in loci.formats.in
InveonReader is the file format reader for Inveon files.
InveonReader() - Constructor for class loci.formats.in.InveonReader
Constructs a new Inveon reader.
invert() - Method in class loci.plugins.util.RecordedImageProcessor
 
inverted - Variable in class loci.formats.in.DicomReader
 
invertLut() - Method in class loci.plugins.util.RecordedImageProcessor
 
invertX - Variable in class loci.formats.in.RHKReader
 
invertY - Variable in class loci.formats.in.BMPReader
 
invertY - Variable in class loci.formats.in.ICSReader
Whether or not the image is inverted along the Y axis.
invertY - Variable in class loci.formats.in.RHKReader
 
invokeMethod(String, String, FormatEntry, boolean) - Method in class loci.plugins.config.ConfigWindow
 
IONPATH_MIBI_SOFTWARE_PREFIX - Static variable in class loci.formats.in.IonpathMIBITiffReader
TIFF software tag prefix for Ionpath MIBI files.
IonpathMIBITiffReader - Class in loci.formats.in
IonpathMIBITiffReader is the file format reader for Ionpath MIBI TIFF files.
IonpathMIBITiffReader() - Constructor for class loci.formats.in.IonpathMIBITiffReader
Constructs a new Ionpath MIBI reader.
IPLabReader - Class in loci.formats.in
IPLabReader is the file format reader for IPLab (.IPL) files.
IPLabReader() - Constructor for class loci.formats.in.IPLabReader
Constructs a new IPLab reader.
IPW_MAGIC_BYTES - Static variable in class loci.formats.in.IPWReader
 
IPWReader - Class in loci.formats.in
IPWReader is the file format reader for Image-Pro Workspace (IPW) files.
IPWReader() - Constructor for class loci.formats.in.IPWReader
Constructs a new IPW reader.
IPyramidHandler - Interface in loci.formats
Interface for defining image pyramids.
IPyramidStore - Interface in loci.formats.meta
Interface for defining pyramid resolutions.
ir - Variable in class loci.plugins.in.ThumbLoader
 
iris - Variable in class loci.formats.in.ZeissLSMReader.Recording
 
IS - Static variable in class loci.formats.in.DicomReader
 
IS_GLITCHED - Static variable in class loci.plugins.prefs.OptionsDialog
Flag indicating whether to invoke workaround for AWT refresh bug.
IS_LITTLE - Static variable in class loci.formats.in.ImarisReader
Specifies endianness.
IS_TRANSMISSION - Static variable in class loci.formats.in.CellSensReader
 
isAutoscale() - Method in class loci.plugins.in.ImporterOptions
 
isBGR(short[]) - Method in class loci.formats.services.JPEGXRServiceImpl
 
isBigTiff - Variable in class loci.formats.out.TiffWriter
Whether or not the output file is a BigTIFF file.
isBigTiff() - Method in class loci.formats.tiff.IFD
Gets whether this is a BigTIFF IFD.
isBigTiff() - Method in class loci.formats.tiff.TiffParser
Returns whether or not the current TIFF file contains BigTIFF data.
isBigTiff() - Method in class loci.formats.tiff.TiffSaver
Returns whether or not we are writing BigTIFF data.
isBitOnByteBoundary() - Method in class loci.formats.codec.BitBuffer
Deprecated.
Checks if the current position is on a byte boundary, that is the next bit in the byte array is the first bit in a byte.
isCellsensFailOnMissing() - Static method in class loci.plugins.util.LociPrefs
 
isCertain() - Method in class loci.formats.AxisGuesser
Gets whether the guesser is confident that all axes are correct.
isColorLut() - Method in class loci.plugins.util.RecordedImageProcessor
 
isColorModeColorized() - Method in class loci.plugins.in.ImporterOptions
 
isColorModeComposite() - Method in class loci.plugins.in.ImporterOptions
 
isColorModeCustom() - Method in class loci.plugins.in.ImporterOptions
 
isColorModeDefault() - Method in class loci.plugins.in.ImporterOptions
 
isColorModeGrayscale() - Method in class loci.plugins.in.ImporterOptions
 
isCompatibleRaster(Raster) - Method in class loci.formats.gui.Index16ColorModel
 
isCompatibleRaster(Raster) - Method in class loci.formats.gui.SignedColorModel
 
isCompatibleRaster(Raster) - Method in class loci.formats.gui.UnsignedIntColorModel
 
isCompressed - Variable in class loci.formats.in.LIMReader
 
isConcatenate() - Method in class loci.plugins.in.ImporterOptions
 
isContainer(String) - Method in class loci.formats.in.NativeQTReader
Checks if the given String is a container atom type.
isCS_sRGB() - Method in class loci.formats.gui.TwoChannelColorSpace
 
isCurrentFile(String) - Method in class loci.formats.in.OIRReader
 
isDeflate - Variable in class loci.formats.in.DicomReader
 
isDimensions(String) - Method in class loci.formats.in.ND2Handler
Returns whether or not the specified key is denotes dimensions.
isEnabled - Variable in class loci.formats.in.CellVoyagerReader.ChannelInfo
 
isEqual(OMEXMLMetadata, OMEXMLMetadata) - Method in interface loci.formats.services.OMEXMLService
Determine whether or not two OMEXMLMetadata objects are equal.
isEqual(OMEXMLMetadata, OMEXMLMetadata) - Method in class loci.formats.services.OMEXMLServiceImpl
 
isFalseColor() - Method in class loci.formats.FileStitcher
 
isFalseColor() - Method in class loci.formats.FormatReader
 
isFalseColor() - Method in interface loci.formats.IFormatReader
Returns false if IFormatReader.isIndexed() is false, or if IFormatReader.isIndexed() is true and the lookup table represents "real" color data.
isFalseColor() - Method in class loci.formats.ImageReader
 
isFalseColor() - Method in class loci.formats.ReaderWrapper
 
isFalseColor() - Method in class loci.formats.WrappedReader
 
isFiji() - Static method in class loci.plugins.Updater
Returns true if the current ImageJ instance is actually a Fiji instance.
isFilled() - Method in class loci.formats.ChannelFiller
Returns true if the indices are being factored out.
isFirstTime() - Method in class loci.plugins.in.ImporterOptions
 
isFixed() - Method in class loci.formats.FilePatternBlock
Whether or not this is a fixed-width block.
isFLIM - Variable in class loci.formats.in.ImspectorReader
Whether or not this file contains FLIM data.
isFLIMLabel(String) - Method in class loci.formats.in.OBFReader
 
isFloat - Variable in class loci.formats.in.BrukerReader
 
isFloatingPoint(IFormatReader) - Static method in class loci.formats.FormatTools
Determines whether the given reader represents any floating point data.
isFloatingPoint(int) - Static method in class loci.formats.FormatTools
Determines whether the given pixel type is floating point or integer.
isForceThumbnails() - Method in class loci.plugins.in.ImporterOptions
 
isFullPlane(int, int, int, int) - Method in class loci.formats.FormatWriter
Returns true if the given rectangle coordinates correspond to a full image in the given series.
isGreaterThanEpsilon(double) - Method in class loci.formats.in.SlidebookReader
Returns true if the given double is greater than epsilon (defined here as 0.000001), i.e.
isGroupFiles() - Method in class loci.formats.FileStitcher
 
isGroupFiles() - Method in class loci.formats.FormatReader
 
isGroupFiles() - Method in interface loci.formats.IFormatReader
Returns true if we should group files in multi-file formats.
isGroupFiles() - Method in class loci.formats.ImageReader
 
isGroupFiles() - Method in class loci.formats.in.FilePatternReader
 
isGroupFiles() - Method in class loci.formats.ReaderWrapper
 
isGroupFiles() - Method in class loci.plugins.in.ImporterOptions
 
isGroupFiles(String[]) - Method in class loci.plugins.macro.LociFunctions
 
isHarmony - Variable in class loci.formats.in.OperettaReader.OperettaHandler
 
isHCS - Variable in class loci.formats.in.MetamorphReader
 
isHTTP() - Method in class loci.plugins.in.ImporterOptions
 
isInCache(int[]) - Method in class loci.formats.cache.Cache
Returns true if the object at the given dimensional position is in the cache.
isInCache(int) - Method in class loci.formats.cache.Cache
Returns true if the object at the given index is in the cache.
isIndexed() - Method in class loci.formats.ChannelFiller
 
isIndexed() - Method in class loci.formats.ChannelMerger
 
isIndexed() - Method in class loci.formats.FileStitcher
 
isIndexed() - Method in class loci.formats.FormatReader
 
isIndexed() - Method in interface loci.formats.IFormatReader
Gets whether the image planes are indexed color.
isIndexed() - Method in class loci.formats.ImageReader
 
isIndexed() - Method in class loci.formats.ReaderWrapper
 
isIndexed() - Method in class loci.formats.WrappedReader
 
isIndexed(String[]) - Method in class loci.plugins.macro.LociFunctions
 
isIntensity() - Method in class loci.formats.in.SDTReader
Gets whether the reader is combining each lifetime histogram into a summed intensity image plane.
isInterleaved() - Method in class loci.formats.ChannelMerger
 
isInterleaved() - Method in class loci.formats.FileStitcher
 
isInterleaved(int) - Method in class loci.formats.FileStitcher
 
isInterleaved() - Method in class loci.formats.FormatReader
 
isInterleaved(int) - Method in class loci.formats.FormatReader
 
isInterleaved() - Method in class loci.formats.FormatWriter
 
isInterleaved() - Method in interface loci.formats.IFormatReader
Gets whether or not the channels are interleaved.
isInterleaved(int) - Method in interface loci.formats.IFormatReader
Gets whether or not the given sub-channel is interleaved.
isInterleaved() - Method in interface loci.formats.IFormatWriter
Gets whether or not the channels in an image are interleaved.
isInterleaved() - Method in class loci.formats.ImageReader
 
isInterleaved(int) - Method in class loci.formats.ImageReader
 
isInterleaved() - Method in class loci.formats.ImageWriter
 
isInterleaved(int) - Method in class loci.formats.in.ICSReader
 
isInterleaved(int) - Method in class loci.formats.in.SDTReader
 
isInterleaved() - Method in class loci.formats.ReaderWrapper
 
isInterleaved(int) - Method in class loci.formats.ReaderWrapper
 
isInterleaved() - Method in class loci.formats.WrappedReader
 
isInterleaved(int) - Method in class loci.formats.WrappedReader
 
isInterleaved() - Method in class loci.formats.WriterWrapper
 
isInterleaved(String[]) - Method in class loci.plugins.macro.LociFunctions
 
isInterleavedSubC(Double, String[]) - Method in class loci.plugins.macro.LociFunctions
 
isInvertedLut() - Method in class loci.plugins.util.RecordedImageProcessor
 
isInvertX() - Method in class loci.formats.in.PrairieMetadata
Gets whether the stage position X coordinates are inverted (i.e., left-to-right).
isInvertY() - Method in class loci.formats.in.PrairieMetadata
Gets whether the stage position Y coordinates are inverted (i.e., bottom-to-top).
isJNG - Variable in class loci.formats.in.MNGReader
 
isJP2K - Variable in class loci.formats.in.DicomReader
 
isJPEG - Variable in class loci.formats.in.BaseZeissReader
 
isJPEG - Variable in class loci.formats.in.DicomReader
 
isJPEG - Variable in class loci.formats.in.NativeND2Reader
Whether or not the pixel data is compressed using JPEG 2000.
isJVM64Bit() - Method in class loci.formats.gui.LegacyQTTools
Whether this JVM is 64-bit.
isLegacy() - Method in class loci.formats.DelegateReader
Gets whether to use the legacy reader by default.
isLeicaLIFPhysicalSizeBackwardsCompatible() - Static method in class loci.plugins.util.LociPrefs
 
isLicenseCodeException(FormatException) - Static method in class loci.plugins.util.LuraWave
Returns true if the given exception was cause by a missing or invalid LuraWave license code.
isLittleEndian() - Method in class loci.formats.FileStitcher
 
isLittleEndian() - Method in class loci.formats.FormatReader
 
isLittleEndian() - Method in interface loci.formats.IFormatReader
Gets whether the data is in little-endian format.
isLittleEndian() - Method in class loci.formats.ImageReader
 
isLittleEndian() - Method in class loci.formats.ReaderWrapper
 
isLittleEndian() - Method in class loci.formats.tiff.IFD
Gets whether the TIFF information in this IFD is little-endian.
isLittleEndian() - Method in class loci.formats.tiff.TiffSaver
Returns whether or not we are writing little-endian data.
isLittleEndian() - Method in class loci.formats.WrappedReader
 
isLittleEndian(String[]) - Method in class loci.plugins.macro.LociFunctions
 
isLoadedFromMemo() - Method in class loci.formats.Memoizer
Returns whether the ReaderWrapper.reader instance currently active was loaded from the memo file during Memoizer.setId(String).
isLocal() - Method in class loci.plugins.in.ImporterOptions
 
isLossless - Variable in class loci.formats.in.NativeND2Reader
Whether or not the pixel data is losslessly compressed.
isLossless - Variable in class loci.formats.in.ND2Handler
 
isLossless() - Method in class loci.formats.in.ND2Handler
 
isMetadataComplete() - Method in class loci.formats.FormatReader
 
isMetadataComplete() - Method in interface loci.formats.IFormatReader
Returns true if this format's metadata is completely parsed.
isMetadataComplete() - Method in class loci.formats.ImageReader
 
isMetadataComplete() - Method in class loci.formats.ReaderWrapper
 
isMetadataComplete() - Method in class loci.formats.WrappedReader
 
isMetadataComplete(String[]) - Method in class loci.plugins.macro.LociFunctions
 
isMetadataFiltered() - Method in class loci.formats.FormatReader
 
isMetadataFiltered() - Method in interface loci.formats.IFormatReader
Returns true if ugly metadata (entries with unprintable characters, and extremely large entries) are discarded from the metadata table.
isMetadataFiltered() - Method in class loci.formats.ImageReader
 
isMetadataFiltered() - Method in class loci.formats.in.FilePatternReader
 
isMetadataFiltered() - Method in class loci.formats.ReaderWrapper
 
isMetadataFiltered(String[]) - Method in class loci.plugins.macro.LociFunctions
 
isMINC2 - Variable in class loci.formats.in.MINCReader
 
isMinimumMetadata() - Method in class loci.formats.in.PrairieReader
Gets whether to populate only the minimum required metadata.
isMinMaxPopulated() - Method in class loci.formats.MinMaxCalculator
Returns true if the values returned by getChannelGlobalMinimum/Maximum can be trusted.
isModulo - Variable in class loci.formats.tools.MakeTestOmeTiff
 
isND2Nikon() - Static method in class loci.plugins.util.LociPrefs
 
isNormalized() - Method in class loci.formats.FormatReader
 
isNormalized() - Method in interface loci.formats.IFormatReader
Returns true if we should normalize float data.
isNormalized() - Method in class loci.formats.ImageReader
 
isNormalized() - Method in class loci.formats.in.FilePatternReader
 
isNormalized() - Method in class loci.formats.ReaderWrapper
 
isNormalized(Boolean[]) - Method in class loci.plugins.macro.LociFunctions
 
isNumeric() - Method in class loci.formats.FilePatternBlock
Whether or not this is a numeric block.
ISO - Static variable in class loci.formats.in.NikonReader
 
ISO_SENSITIVITY - Static variable in class loci.formats.in.CellSensReader
 
ISO_SPEED_RATINGS - Static variable in class loci.formats.tiff.IFD
 
isOIB - Variable in class loci.formats.in.FV1000Reader
Flag indicating this is an OIB dataset.
isOMERO() - Method in class loci.plugins.in.ImporterOptions
 
isOMEXMLMetadata(Object) - Method in interface loci.formats.services.OMEXMLService
Checks whether the given object is an OME-XML metadata object.
isOMEXMLMetadata(Object) - Method in class loci.formats.services.OMEXMLServiceImpl
 
isOMEXMLRoot(Object) - Method in interface loci.formats.services.OMEXMLService
Checks whether the given object is an OME-XML root object.
isOMEXMLRoot(Object) - Method in class loci.formats.services.OMEXMLServiceImpl
 
isOne() - Method in class org.libjpegturbo.turbojpeg.TJScalingFactor
Returns true or false, depending on whether this instance is equal to 1/1.
isOrderCertain() - Method in class loci.formats.FileStitcher
 
isOrderCertain() - Method in class loci.formats.FormatReader
 
isOrderCertain() - Method in interface loci.formats.IFormatReader
Gets whether the dimension order and sizes are known, or merely guesses.
isOrderCertain() - Method in class loci.formats.ImageReader
 
isOrderCertain() - Method in class loci.formats.ReaderWrapper
 
isOrderCertain() - Method in class loci.formats.WrappedReader
 
isOrderCertain(String[]) - Method in class loci.plugins.macro.LociFunctions
 
isOriginalMetadataPopulated() - Method in class loci.formats.FormatReader
 
isOriginalMetadataPopulated() - Method in interface loci.formats.IFormatReader
Returns true if we should save proprietary metadata in the MetadataStore.
isOriginalMetadataPopulated() - Method in class loci.formats.ImageReader
 
isOriginalMetadataPopulated() - Method in class loci.formats.in.FilePatternReader
 
isOriginalMetadataPopulated() - Method in class loci.formats.ReaderWrapper
 
isOriginalMetadataPopulated(Boolean[]) - Method in class loci.plugins.macro.LociFunctions
 
isPictQTJava() - Static method in class loci.plugins.util.LociPrefs
 
isPositiveValue(Double) - Static method in class loci.formats.FormatTools
 
isPossible(String, String) - Method in class loci.plugins.prefs.OptionsList
Gets whether the specified value is a possible one for the string option with the given key.
isPreviewName(String) - Method in class loci.formats.in.FV1000Reader
 
isPseudoColorLut() - Method in class loci.plugins.util.RecordedImageProcessor
 
isQTExpired() - Method in class loci.formats.gui.LegacyQTTools
Whether QuickTime for Java has expired.
isQTQTJava() - Static method in class loci.plugins.util.LociPrefs
 
isQuiet() - Method in class loci.plugins.in.ImporterOptions
 
isRawCodestream - Variable in class loci.formats.in.JPEG2000MetadataParser
Whether or not the codestream is raw and not JP2 boxed.
isRawCodestream() - Method in class loci.formats.in.JPEG2000MetadataParser
Whether or not the codestream is raw and not JP2 boxed.
isReaderEnabled(FormatEntry) - Method in class loci.plugins.config.ConfigWindow
 
isReaderEnabled(Class<? extends IFormatReader>) - Static method in class loci.plugins.util.LociPrefs
 
isReaderPref(String, FormatEntry, boolean) - Method in class loci.plugins.config.ConfigWindow
 
isReaderWindowless(FormatEntry) - Method in class loci.plugins.config.ConfigWindow
 
isRegex - Variable in class loci.formats.FilePattern
Whether or not this FilePattern represents a regular expression.
isRegex() - Method in class loci.formats.FilePattern
Returns whether or not this pattern is a regular expression.
isRGB() - Method in class loci.formats.ChannelFiller
 
isRGB() - Method in class loci.formats.ChannelMerger
 
isRGB() - Method in class loci.formats.ChannelSeparator
 
isRGB() - Method in class loci.formats.FileStitcher
 
isRGB() - Method in class loci.formats.FormatReader
 
isRGB() - Method in interface loci.formats.IFormatReader
Checks if the image planes in the file have more than one channel per IFormatReader.openBytes(int) call.
isRGB() - Method in class loci.formats.ImageReader
 
isRGB() - Method in class loci.formats.ReaderWrapper
 
isRGB() - Method in interface loci.formats.services.WlzService
Gets boolean for whether image is colour or not.
isRGB() - Method in class loci.formats.services.WlzServiceImpl
 
isRGB() - Method in class loci.formats.WrappedReader
 
isRLE - Variable in class loci.formats.in.DicomReader
 
isSaved() - Method in class loci.plugins.prefs.Option
Gets whether option should be saved to ImageJ preferences file.
isSaved(String) - Method in class loci.plugins.prefs.OptionsList
Gets whether the option with the given key is saved to the ImageJ preferences file.
isSavedToMemo() - Method in class loci.formats.Memoizer
Returns whether the ReaderWrapper.reader instance currently active was saved to the memo file during Memoizer.setId(String).
isSDTIntensity() - Static method in class loci.plugins.util.LociPrefs
 
isSeriesOn(int) - Method in class loci.plugins.in.ImporterOptions
 
isSet(String) - Method in class loci.plugins.prefs.OptionsList
Gets the value of the boolean option with the given key.
isSetByDefault(String) - Method in class loci.plugins.prefs.OptionsList
Gets the default value of the boolean option with the given key.
isShowMetadata() - Method in class loci.plugins.in.ImporterOptions
 
isShowOMEXML() - Method in class loci.plugins.in.ImporterOptions
 
isSigned(int) - Static method in class loci.formats.FormatTools
Determines whether the given pixel type is signed or unsigned.
isSIM - Variable in class loci.formats.in.ZeissLSMReader
 
isSingleFile(String) - Method in class loci.formats.FormatReader
 
isSingleFile(String) - Method in interface loci.formats.IFormatReader
Returns true if the named file is expected to be the only file in the dataset.
isSingleFile(String) - Method in class loci.formats.ImageReader
 
isSingleFile(String) - Method in class loci.formats.in.AFIReader
 
isSingleFile(String) - Method in class loci.formats.in.AnalyzeReader
 
isSingleFile(String) - Method in class loci.formats.in.APLReader
 
isSingleFile(String) - Method in class loci.formats.in.BDReader
 
isSingleFile(String) - Method in class loci.formats.in.BioRadReader
 
isSingleFile(String) - Method in class loci.formats.in.BrukerReader
 
isSingleFile(String) - Method in class loci.formats.in.CellSensReader
 
isSingleFile(String) - Method in class loci.formats.in.CellVoyagerReader
 
isSingleFile(String) - Method in class loci.formats.in.ColumbusReader
 
isSingleFile(String) - Method in class loci.formats.in.CV7000Reader
 
isSingleFile(String) - Method in class loci.formats.in.DeltavisionReader
 
isSingleFile(String) - Method in class loci.formats.in.FakeReader
 
isSingleFile(String) - Method in class loci.formats.in.FilePatternReader
 
isSingleFile(String) - Method in class loci.formats.in.FlexReader
 
isSingleFile(String) - Method in class loci.formats.in.FujiReader
 
isSingleFile(String) - Method in class loci.formats.in.FV1000Reader
 
isSingleFile(String) - Method in class loci.formats.in.HitachiReader
 
isSingleFile(String) - Method in class loci.formats.in.ICSReader
 
isSingleFile(String) - Method in class loci.formats.in.ImagicReader
 
isSingleFile(String) - Method in class loci.formats.in.InCellReader
 
isSingleFile(String) - Method in class loci.formats.in.L2DReader
 
isSingleFile(String) - Method in class loci.formats.in.LeicaReader
 
isSingleFile(String) - Method in class loci.formats.in.MetamorphReader
 
isSingleFile(String) - Method in class loci.formats.in.MIASReader
 
isSingleFile(String) - Method in class loci.formats.in.MicroCTReader
 
isSingleFile(String) - Method in class loci.formats.in.MicromanagerReader
 
isSingleFile(String) - Method in class loci.formats.in.NDPISReader
 
isSingleFile(String) - Method in class loci.formats.in.NiftiReader
 
isSingleFile(String) - Method in class loci.formats.in.NRRDReader
 
isSingleFile(String) - Method in class loci.formats.in.OIRReader
 
isSingleFile(String) - Method in class loci.formats.in.OMETiffReader
 
isSingleFile(String) - Method in class loci.formats.in.OperettaReader
 
isSingleFile(String) - Method in class loci.formats.in.PerkinElmerReader
 
isSingleFile(String) - Method in class loci.formats.in.PrairieReader
 
isSingleFile(String) - Method in class loci.formats.in.ScanrReader
 
isSingleFile(String) - Method in class loci.formats.in.SPCReader
 
isSingleFile(String) - Method in class loci.formats.in.TCSReader
 
isSingleFile(String) - Method in class loci.formats.in.TillVisionReader
 
isSingleFile(String) - Method in class loci.formats.in.VisitechReader
 
isSingleFile(String) - Method in class loci.formats.in.ZeissLSMReader
 
isSingleFile(String) - Method in class loci.formats.in.ZeissTIFFReader
 
isSingleFile(String) - Method in class loci.formats.ReaderWrapper
 
isSingleFile(String) - Method in class loci.formats.WrappedReader
 
isSpecifyRanges() - Method in class loci.plugins.in.ImporterOptions
 
isSpectralMode() - Method in class loci.formats.in.PrairieMetadata.Sequence
 
isSplitChannels() - Method in class loci.plugins.in.ImporterOptions
 
isSplitFocalPlanes() - Method in class loci.plugins.in.ImporterOptions
 
isSplitTimepoints() - Method in class loci.plugins.in.ImporterOptions
 
isSpool - Variable in class loci.formats.in.SlidebookReader
 
isSPWStructure(String) - Method in class loci.formats.in.FakeReader
 
isSupportedType(int) - Method in class loci.formats.FormatWriter
 
isSupportedType(int) - Method in interface loci.formats.IFormatWriter
Checks if the given pixel type is supported.
isSupportedType(int) - Method in class loci.formats.ImageWriter
 
isSupportedType(int) - Method in class loci.formats.WriterWrapper
 
isSwapDimensions() - Method in class loci.plugins.in.ImporterOptions
 
isTable() - Method in interface loci.formats.in.PrairieMetadata.Value
 
isTable() - Method in class loci.formats.in.PrairieMetadata.ValueItem
 
isTable() - Method in class loci.formats.in.PrairieMetadata.ValueTable
 
isThisType(String, boolean) - Method in class loci.formats.DelegateReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.DelegateReader
 
isThisType(String) - Method in class loci.formats.FormatHandler
Checks if a file matches the type of this format handler.
isThisType(String, boolean) - Method in class loci.formats.FormatReader
Checks if a file matches the type of this format reader.
isThisType(byte[]) - Method in class loci.formats.FormatReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.FormatReader
 
isThisType(String) - Method in class loci.formats.FormatReader
 
isThisType(String) - Method in interface loci.formats.IFormatHandler
Checks if the given string is a valid filename for this file format.
isThisType(String, boolean) - Method in interface loci.formats.IFormatReader
Checks if the given file is a valid instance of this file format.
isThisType(byte[]) - Method in interface loci.formats.IFormatReader
Checks if the given block is a valid header for this file format.
isThisType(RandomAccessInputStream) - Method in interface loci.formats.IFormatReader
Checks if the given stream is a valid stream for this file format.
isThisType(String, boolean) - Method in class loci.formats.ImageReader
 
isThisType(byte[]) - Method in class loci.formats.ImageReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.ImageReader
 
isThisType(String) - Method in class loci.formats.ImageReader
 
isThisType(IFormatReader, String, boolean) - Method in class loci.formats.ImageReader
 
isThisType(IFormatReader, byte[]) - Method in class loci.formats.ImageReader
 
isThisType(IFormatReader, RandomAccessInputStream) - Method in class loci.formats.ImageReader
 
isThisType(String) - Method in class loci.formats.ImageWriter
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.AFIReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.AliconaReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.AmiraReader
 
isThisType(String, boolean) - Method in class loci.formats.in.AnalyzeReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.AnalyzeReader
 
isThisType(String, boolean) - Method in class loci.formats.in.APLReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.APNGReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.ARFReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.AVIReader
 
isThisType(String, boolean) - Method in class loci.formats.in.BDReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.BDReader
 
isThisType(String, boolean) - Method in class loci.formats.in.BDVReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.BDVReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.BioRadGelReader
 
isThisType(String, boolean) - Method in class loci.formats.in.BioRadReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.BioRadReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.BioRadSCNReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.BMPReader
 
isThisType(String, boolean) - Method in class loci.formats.in.BrukerReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.BrukerReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.BurleighReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.CanonRawReader
 
isThisType(String, boolean) - Method in class loci.formats.in.CellH5Reader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.CellH5Reader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.CellomicsReader
 
isThisType(String, boolean) - Method in class loci.formats.in.CellVoyagerReader
 
isThisType(String, boolean) - Method in class loci.formats.in.CellWorxReader
 
isThisType(String, boolean) - Method in class loci.formats.in.ColumbusReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.ColumbusReader
 
isThisType(String, boolean) - Method in class loci.formats.in.DeltavisionReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.DeltavisionReader
 
isThisType(String, boolean) - Method in class loci.formats.in.DicomReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.DicomReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.DNGReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.Ecat7Reader
 
isThisType(String, boolean) - Method in class loci.formats.in.FakeReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.FEIReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.FEITiffReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.FlowSightReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.FluoviewReader
 
isThisType(String, boolean) - Method in class loci.formats.in.FujiReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.FujiReader
 
isThisType(String, boolean) - Method in class loci.formats.in.FV1000Reader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.FV1000Reader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.GatanDM2Reader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.GatanReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.GelReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.GIFReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.HISReader
 
isThisType(String, boolean) - Method in class loci.formats.in.HitachiReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.HitachiReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.HRDGDFReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.I2IReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.IM3Reader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.ImaconReader
 
isThisType(String, boolean) - Method in class loci.formats.in.ImagicReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.ImarisHDFReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.ImarisReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.IMODReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.ImprovisionTiffReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.ImspectorReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.InCell3000Reader
 
isThisType(String, boolean) - Method in class loci.formats.in.InCellReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.InCellReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.INRReader
 
isThisType(String, boolean) - Method in class loci.formats.in.InveonReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.InveonReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.IonpathMIBITiffReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.IPLabReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.IPWReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.IvisionReader
 
isThisType(String, boolean) - Method in class loci.formats.in.JEOLReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.JEOLReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.JPEG2000Reader
 
isThisType(String, boolean) - Method in class loci.formats.in.JPEGReader.DefaultJPEGReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.JPEGReader.DefaultJPEGReader
 
isThisType(String, boolean) - Method in class loci.formats.in.JPKReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.JPXReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.KhorosReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.KodakReader
 
isThisType(String, boolean) - Method in class loci.formats.in.L2DReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.L2DReader
 
isThisType(String, boolean) - Method in class loci.formats.in.LegacyND2Reader
 
isThisType(String, boolean) - Method in class loci.formats.in.LeicaReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.LeicaReader
 
isThisType(String, boolean) - Method in class loci.formats.in.LeicaSCNReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.LEOReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.LIFReader
 
isThisType(String, boolean) - Method in class loci.formats.in.MetamorphReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.MetamorphReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.MetamorphTiffReader
 
isThisType(String, boolean) - Method in class loci.formats.in.MIASReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.MIASReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.MicroCTReader
 
isThisType(String, boolean) - Method in class loci.formats.in.MicromanagerReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.MicromanagerReader
 
isThisType(String, boolean) - Method in class loci.formats.in.MikroscanTiffReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.MinimalTiffReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.MNGReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.MolecularImagingReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.MRCReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.MRWReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.NativeND2Reader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.NativeQTReader
 
isThisType(String, boolean) - Method in class loci.formats.in.NDPIReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.NDPISReader
 
isThisType(String, boolean) - Method in class loci.formats.in.NiftiReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.NiftiReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.NikonElementsTiffReader
 
isThisType(String, boolean) - Method in class loci.formats.in.NikonReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.NikonReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.NikonTiffReader
 
isThisType(String, boolean) - Method in class loci.formats.in.NRRDReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.NRRDReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.OBFReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.OIRReader
 
isThisType(String, boolean) - Method in class loci.formats.in.OMETiffReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.OMETiffReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.OMEXMLReader
 
isThisType(String, boolean) - Method in class loci.formats.in.OMEXMLReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.OpenlabRawReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.OpenlabReader
 
isThisType(String, boolean) - Method in class loci.formats.in.OperettaReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.OperettaReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.OxfordInstrumentsReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.PCIReader
 
isThisType(String, boolean) - Method in class loci.formats.in.PCORAWReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.PCORAWReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.PCXReader
 
isThisType(String, boolean) - Method in class loci.formats.in.PDSReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.PDSReader
 
isThisType(String, boolean) - Method in class loci.formats.in.PerkinElmerReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.PGMReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.PhotoshopTiffReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.PQBinReader
 
isThisType(String, boolean) - Method in class loci.formats.in.PrairieReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.PrairieReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.PSDReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.PyramidTiffReader
 
isThisType(String, boolean) - Method in class loci.formats.in.RCPNLReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.SBIGReader
 
isThisType(String, boolean) - Method in class loci.formats.in.ScanrReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.ScanrReader
 
isThisType(String, boolean) - Method in class loci.formats.in.SEQReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.SEQReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.SIFReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.SimplePCITiffReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.SISReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.SlidebookReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.SlidebookTiffReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.SMCameraReader
 
isThisType(String, boolean) - Method in class loci.formats.in.SPCReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.SPEReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.SpiderReader
 
isThisType(String, boolean) - Method in class loci.formats.in.SVSReader
 
isThisType(String, boolean) - Method in class loci.formats.in.TCSReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.TCSReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.TextReader
 
isThisType(String, boolean) - Method in class loci.formats.in.TillVisionReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.TopometrixReader
 
isThisType(String, boolean) - Method in class loci.formats.in.TrestleReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.TrestleReader
 
isThisType(String, boolean) - Method in class loci.formats.in.UnisokuReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.UnisokuReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.VarianFDFReader
 
isThisType(String, boolean) - Method in class loci.formats.in.VectraReader
 
isThisType(String, boolean) - Method in class loci.formats.in.VentanaReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.VGSAMReader
 
isThisType(String, boolean) - Method in class loci.formats.in.VisitechReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.VolocityClippingReader
 
isThisType(String, boolean) - Method in class loci.formats.in.VolocityReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.VolocityReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.WATOPReader
 
isThisType(String, boolean) - Method in class loci.formats.in.WlzReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.ZeissCZIReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.ZeissLMSReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.ZeissLSMReader
 
isThisType(String, boolean) - Method in class loci.formats.in.ZeissTIFFReader
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.ZeissZVIReader
 
isThisType(String) - Method in class loci.formats.out.PyramidOMETiffWriter
 
isThisType(String, boolean) - Method in class loci.formats.ReaderWrapper
 
isThisType(byte[]) - Method in class loci.formats.ReaderWrapper
 
isThisType(RandomAccessInputStream) - Method in class loci.formats.ReaderWrapper
 
isThisType(String) - Method in class loci.formats.ReaderWrapper
 
isThisType(String) - Method in class loci.formats.WriterWrapper
 
isThisType(String, String[]) - Method in class loci.plugins.macro.LociFunctions
 
isThisTypeFast(String, String[]) - Method in class loci.plugins.macro.LociFunctions
 
isThumbnailSeries() - Method in class loci.formats.FileStitcher
 
isThumbnailSeries() - Method in class loci.formats.FormatReader
 
isThumbnailSeries() - Method in interface loci.formats.IFormatReader
Gets whether the current series is a lower resolution copy of a different series.
isThumbnailSeries() - Method in class loci.formats.ImageReader
 
isThumbnailSeries() - Method in class loci.formats.ReaderWrapper
 
isThumbnailSeries() - Method in class loci.formats.WrappedReader
 
isTiff - Variable in class loci.formats.in.EPSReader
 
isTiff - Variable in class loci.formats.in.InCellReader.Image
 
isTiff - Variable in class loci.formats.in.PerkinElmerReader
Flag indicating that the image data is in TIFF format.
isTiffImageIO() - Static method in class loci.plugins.util.LociPrefs
 
isTiled() - Method in class loci.formats.tiff.IFD
 
isTimeSeries() - Method in class loci.formats.in.PrairieMetadata.Sequence
Gets whether this Sequence should be considered a time series.
isUngroupFiles() - Method in class loci.plugins.in.ImporterOptions
 
isUsedFile(String) - Method in class loci.formats.FormatReader
Returns true if the given file name is in the used files list.
isUsingPatternIds() - Method in class loci.formats.FileStitcher
Gets whether the reader is using file patterns for IDs.
isUsingPatternIds() - Method in class loci.plugins.in.ImporterOptions
 
isValid() - Method in class loci.formats.FilePattern
Returns whether or not the file pattern is valid.
isValidate() - Method in class loci.formats.in.DefaultMetadataOptions
 
isValidate() - Method in class loci.formats.in.DynamicMetadataOptions
 
isValidate() - Method in interface loci.formats.in.MetadataOptions
Checks whether file validation has been set.
isValidHeader() - Method in class loci.formats.tiff.TiffParser
Tests this stream to see if it represents a TIFF file.
isValidRange(int, int, int) - Static method in class loci.formats.tools.FakeImage
 
isVersionChecking() - Method in class loci.formats.Memoizer
Returns whether or not version checking is done based upon major/minor version numbers.
isViewBrowser() - Method in class loci.plugins.in.ImporterOptions
 
isViewHyperstack() - Method in class loci.plugins.in.ImporterOptions
 
isViewImage5D() - Method in class loci.plugins.in.ImporterOptions
 
isViewNone() - Method in class loci.plugins.in.ImporterOptions
 
isViewStandard() - Method in class loci.plugins.in.ImporterOptions
 
isViewView5D() - Method in class loci.plugins.in.ImporterOptions
 
isVirtual() - Method in class loci.plugins.in.ImporterOptions
 
isWellAcquired(int, int) - Method in class loci.formats.in.CV7000Reader
 
isWhitelistedKey(String) - Method in class loci.formats.ClassList
Returns whether a given key is a whitelisted option.
isWindowless() - Method in class loci.plugins.in.ImporterOptions
 
isWindowless() - Method in class loci.plugins.in.ImportProcess
 
isWindowless(IFormatReader) - Static method in class loci.plugins.util.LociPrefs
Gets whether windowless mode should be used when opening this reader's currently initialized dataset.
isWritableDirectory(File) - Method in class loci.formats.Memoizer
Test if the given File instance is a writable directory.
isZlib - Variable in class loci.formats.in.BaseZeissReader
 
italic - Variable in class loci.formats.in.BaseZeissReader.Shape
 
ITEM - Static variable in class loci.formats.in.DicomReader
 
ITEM_DELIMINATION - Static variable in class loci.formats.in.DicomReader
 
itemStateChanged(ItemEvent) - Method in class loci.plugins.config.CellSensWidgets
 
itemStateChanged(ItemEvent) - Method in class loci.plugins.config.ConfigWindow
 
itemStateChanged(ItemEvent) - Method in class loci.plugins.config.LIFWidgets
 
itemStateChanged(ItemEvent) - Method in class loci.plugins.config.ND2Widgets
 
itemStateChanged(ItemEvent) - Method in class loci.plugins.config.PictWidgets
 
itemStateChanged(ItemEvent) - Method in class loci.plugins.config.QTWidgets
 
itemStateChanged(ItemEvent) - Method in class loci.plugins.config.SDTWidgets
 
itemStateChanged(ItemEvent) - Method in class loci.plugins.config.TiffDelegateWidgets
 
itemStateChanged(ItemEvent) - Method in class loci.plugins.config.ZeissCZIWidgets
 
itemStateChanged(ItemEvent) - Method in class loci.plugins.in.MainDialog
Handles toggling of mutually exclusive options.
itemStateChanged(ItemEvent) - Method in class loci.plugins.in.SwapDialog
 
iterateIn(RandomAccessInputStream, Long) - Method in class loci.formats.in.NativeND2Reader
Function for iterating through ND2 metaAttributes
IvisionHandler() - Constructor for class loci.formats.in.IvisionReader.IvisionHandler
 
IvisionReader - Class in loci.formats.in
IvisionReader is the file format reader for IVision (.IPM) files.
IvisionReader() - Constructor for class loci.formats.in.IvisionReader
Constructs a new Ivision reader.
IvisionReader.IvisionHandler - Class in loci.formats.in
 
iw - Variable in class loci.formats.in.GIFReader
Current image rectangle.
ix - Variable in class loci.formats.in.GIFReader
Current image rectangle.
iy - Variable in class loci.formats.in.GIFReader
Current image rectangle.

J

j2kCodecOptions - Variable in class loci.formats.in.MinimalTiffReader
Codec options to use when decoding JPEG 2000 data.
JAIIIOService - Interface in loci.formats.services
Interface defining methods for reading data using JAI Image I/O.
JAIIIOServiceImpl - Class in loci.formats.services
Implementation of JAIIIOService for reading and writing JPEG-2000 data.
JAIIIOServiceImpl() - Constructor for class loci.formats.services.JAIIIOServiceImpl
Default constructor.
JavaWriter - Class in loci.formats.out
JavaWriter is the file format writer for Java source code.
JavaWriter() - Constructor for class loci.formats.out.JavaWriter
 
JEOLReader - Class in loci.formats.in
JEOLReader is the file format reader for JEOL files.
JEOLReader() - Constructor for class loci.formats.in.JEOLReader
Constructs a new JEOL reader.
jhdf - Variable in class loci.formats.in.BDVReader
 
jhdf - Variable in class loci.formats.in.CellH5Reader
 
jhdf - Variable in class loci.formats.out.CellH5Writer
 
JHDFService - Interface in loci.formats.services
Utility class for working with NetCDF/HDF files.
JHDFServiceImpl - Class in loci.formats.services
Utility class for working with HDF files.
JHDFServiceImpl() - Constructor for class loci.formats.services.JHDFServiceImpl
Default constructor.
JPEG - Static variable in class loci.formats.in.AVIReader
 
JPEG - Static variable in class loci.formats.in.CellSensReader
 
jpeg - Variable in class loci.formats.in.CellSensReader
 
JPEG - Static variable in class loci.formats.in.ZeissCZIReader
 
JPEG2000BoxType - Enum in loci.formats.codec
An enumeration of JPEG 2000 box types.
JPEG2000BoxType(int, String) - Constructor for enum loci.formats.codec.JPEG2000BoxType
Default constructor.
JPEG2000Codec - Class in loci.formats.codec
This class implements JPEG 2000 compression and decompression.
JPEG2000Codec() - Constructor for class loci.formats.codec.JPEG2000Codec
 
JPEG2000CodecOptions - Class in loci.formats.codec
Options for compressing and decompressing JPEG-2000 data.
JPEG2000CodecOptions() - Constructor for class loci.formats.codec.JPEG2000CodecOptions
Creates a new instance.
JPEG2000CodecOptions(CodecOptions) - Constructor for class loci.formats.codec.JPEG2000CodecOptions
Creates a new instance with options.
JPEG2000MetadataParser - Class in loci.formats.in
A parser for JPEG 2000 metadata.
JPEG2000MetadataParser(RandomAccessInputStream) - Constructor for class loci.formats.in.JPEG2000MetadataParser
Constructs a new JPEG2000MetadataParser.
JPEG2000MetadataParser(RandomAccessInputStream, long) - Constructor for class loci.formats.in.JPEG2000MetadataParser
Constructs a new JPEG2000MetadataParser.
JPEG2000Reader - Class in loci.formats.in
JPEG2000Reader is the file format reader for JPEG-2000 images.
JPEG2000Reader() - Constructor for class loci.formats.in.JPEG2000Reader
Constructs a new JPEG2000Reader.
JPEG2000SegmentMarker - Enum in loci.formats.codec
An enumeration of JPEG 2000 segment markers.
JPEG2000SegmentMarker(int, String) - Constructor for enum loci.formats.codec.JPEG2000SegmentMarker
Default constructor.
JPEG2000Writer - Class in loci.formats.out
JPEG2000Writer is the file format writer for JPEG2000 files.
JPEG2000Writer() - Constructor for class loci.formats.out.JPEG2000Writer
Creates a new instance.
JPEG_2000 - Static variable in class loci.formats.in.CellSensReader
 
JPEG_AC_TABLES - Static variable in class loci.formats.tiff.IFD
 
JPEG_DC_TABLES - Static variable in class loci.formats.tiff.IFD
 
JPEG_INTERCHANGE_FORMAT - Static variable in class loci.formats.tiff.IFD
 
JPEG_INTERCHANGE_FORMAT_LENGTH - Static variable in class loci.formats.tiff.IFD
 
JPEG_LOSSLESS - Static variable in class loci.formats.in.CellSensReader
 
JPEG_LOSSLESS_PREDICTORS - Static variable in class loci.formats.tiff.IFD
 
JPEG_POINT_TRANSFORMS - Static variable in class loci.formats.tiff.IFD
 
JPEG_PROC - Static variable in class loci.formats.tiff.IFD
 
JPEG_Q_TABLES - Static variable in class loci.formats.tiff.IFD
 
JPEG_QUALITY - Static variable in class loci.formats.in.NDPIReader
 
JPEG_RESTART_INTERVAL - Static variable in class loci.formats.tiff.IFD
 
JPEG_TABLES - Static variable in class loci.formats.tiff.IFD
 
jpegBuf - Variable in class org.libjpegturbo.turbojpeg.TJDecompressor
 
jpegBufSize - Variable in class org.libjpegturbo.turbojpeg.TJDecompressor
 
JPEGCodec - Class in loci.formats.codec
This class implements JPEG compression and decompression.
JPEGCodec() - Constructor for class loci.formats.codec.JPEGCodec
 
jpegHeight - Variable in class org.libjpegturbo.turbojpeg.TJDecompressor
 
jpegOffsets - Variable in class loci.formats.in.PictReader
 
jpegQuality - Variable in class org.libjpegturbo.turbojpeg.TJCompressor
 
JPEGReader - Class in loci.formats.in
JPEGReader is the file format reader for JPEG images.
JPEGReader() - Constructor for class loci.formats.in.JPEGReader
Constructs a new JPEGReader.
JPEGReader.DefaultJPEGReader - Class in loci.formats.in
 
jpegSubsamp - Variable in class org.libjpegturbo.turbojpeg.TJDecompressor
 
JPEGTileDecoder - Class in loci.formats.codec
 
JPEGTileDecoder() - Constructor for class loci.formats.codec.JPEGTileDecoder
 
JPEGTurboService - Interface in loci.formats.services
 
JPEGTurboServiceImpl - Class in loci.formats.services
Based upon the NDPI to OME-TIFF converter by Matthias Baldauf: http://matthias-baldauf.at/software/ndpi_converter/
JPEGTurboServiceImpl() - Constructor for class loci.formats.services.JPEGTurboServiceImpl
 
jpegWidth - Variable in class org.libjpegturbo.turbojpeg.TJDecompressor
 
JPEGWriter - Class in loci.formats.out
JPEGWriter is the file format writer for JPEG files.
JPEGWriter() - Constructor for class loci.formats.out.JPEGWriter
 
JPEGXR - Static variable in class loci.formats.in.ZeissCZIReader
 
JPEGXRCodec - Class in loci.formats.codec
 
JPEGXRCodec() - Constructor for class loci.formats.codec.JPEGXRCodec
 
JPEGXRService - Interface in loci.formats.services
Interface defining methods for working with JPEG-XR data
JPEGXRServiceImpl - Class in loci.formats.services
Interface defining methods for working with JPEG-XR data
JPEGXRServiceImpl() - Constructor for class loci.formats.services.JPEGXRServiceImpl
 
JPKReader - Class in loci.formats.in
JPKReader is the file format reader for JPK Instruments files.
JPKReader() - Constructor for class loci.formats.in.JPKReader
Constructs a new JPK reader.
JPXReader - Class in loci.formats.in
JPXReader is the file format reader for JPX (3D JPEG-2000) images.
JPXReader() - Constructor for class loci.formats.in.JPXReader
Constructs a new JPX Reader.
JSON_TAG - Static variable in class loci.formats.in.MicromanagerReader
 
jvm64Bit - Variable in class loci.formats.gui.LegacyQTTools
Flag indicating 64-bit JVM (does not support QTJava).
JVM_64BIT_MSG - Static variable in class loci.formats.gui.LegacyQTTools
 

K

key - Variable in class loci.formats.in.BaseZeissReader.Layer
 
key - Variable in class loci.formats.in.BioRadSCNReader.SCNHandler
 
key - Variable in class loci.formats.in.FEITiffReader.FEIHandler
 
key - Variable in class loci.formats.in.ImaconReader.ImaconHandler
 
key - Variable in class loci.formats.in.IvisionReader.IvisionHandler
 
key - Variable in class loci.formats.in.ScanrReader.ScanrHandler
 
key - Variable in class loci.formats.in.ZeissTIFFHandler.Scaling
 
key - Variable in class loci.formats.in.ZeissTIFFHandler.Tag
 
key - Variable in class loci.formats.meta.OriginalMetadataAnnotation
 
key - Variable in class loci.plugins.prefs.Option
Key name for ImageJ preferences file.
KEY_AUTOSCALE - Static variable in class loci.plugins.in.ImporterOptions
 
KEY_COLOR_MODE - Static variable in class loci.plugins.in.ImporterOptions
 
KEY_CONCATENATE - Static variable in class loci.plugins.in.ImporterOptions
 
KEY_CROP - Static variable in class loci.plugins.in.ImporterOptions
 
KEY_FIRST - Static variable in class loci.plugins.in.ImporterOptions
 
KEY_FORCE_THUMBS - Static variable in class loci.plugins.in.ImporterOptions
 
KEY_GROUP_FILES - Static variable in class loci.plugins.in.ImporterOptions
 
KEY_ID - Static variable in class loci.plugins.in.ImporterOptions
 
KEY_LOCATION - Static variable in class loci.plugins.in.ImporterOptions
 
KEY_MUST_GROUP - Static variable in class loci.plugins.in.ImporterOptions
 
KEY_OPEN_ALL_SERIES - Static variable in class loci.plugins.in.ImporterOptions
 
KEY_PREFIX - Static variable in class loci.plugins.prefs.Option
Prefix to use for all plugins preferences.
KEY_QUIET - Static variable in class loci.plugins.in.ImporterOptions
 
KEY_ROIS_MODE - Static variable in class loci.plugins.in.ImporterOptions
 
KEY_SHOW_METADATA - Static variable in class loci.plugins.in.ImporterOptions
 
KEY_SHOW_OME_XML - Static variable in class loci.plugins.in.ImporterOptions
 
KEY_SHOW_ROIS - Static variable in class loci.plugins.in.ImporterOptions
 
KEY_SPECIFY_RANGES - Static variable in class loci.plugins.in.ImporterOptions
 
KEY_SPLIT_C - Static variable in class loci.plugins.in.ImporterOptions
 
KEY_SPLIT_T - Static variable in class loci.plugins.in.ImporterOptions
 
KEY_SPLIT_Z - Static variable in class loci.plugins.in.ImporterOptions
 
KEY_STACK_FORMAT - Static variable in class loci.plugins.in.ImporterOptions
 
KEY_STACK_ORDER - Static variable in class loci.plugins.in.ImporterOptions
 
KEY_STITCH_TILES - Static variable in class loci.plugins.in.ImporterOptions
 
KEY_SWAP_DIMS - Static variable in class loci.plugins.in.ImporterOptions
 
KEY_UNGROUP_FILES - Static variable in class loci.plugins.in.ImporterOptions
 
KEY_UPGRADE_CHECK - Static variable in class loci.plugins.in.ImporterOptions
 
KEY_VIRTUAL - Static variable in class loci.plugins.in.ImporterOptions
 
KEY_WINDOWLESS - Static variable in class loci.plugins.in.ImporterOptions
 
keyid - Variable in class loci.formats.in.BaseZeissReader.Tag
 
keyPressed(KeyEvent) - Method in class loci.formats.gui.ImageViewer
Handles key presses.
keyReleased(KeyEvent) - Method in class loci.formats.gui.ImageViewer
 
KEYS - Static variable in class loci.formats.ClassList
 
keys(Hashtable<String, Object>) - Static method in class loci.formats.MetadataTools
Gets a sorted list of keys from the given hashtable.
keyTyped(KeyEvent) - Method in class loci.formats.gui.ImageViewer
 
KHOROS_MAGIC_BYTES - Static variable in class loci.formats.in.KhorosReader
 
KhorosReader - Class in loci.formats.in
Reader for Khoros XV files.
KhorosReader() - Constructor for class loci.formats.in.KhorosReader
Constructs a new Khoros reader.
kind - Variable in class loci.formats.out.ImageIOWriter
 
KINETIC_CYCLE_TIME - Static variable in class loci.formats.in.FluoviewReader
 
KLB_DATA_DIMS - Static variable in class loci.formats.in.KLBReader
 
KLB_DEFAULT_HEADER_VERSION - Static variable in class loci.formats.in.KLBReader
 
KLB_METADATA_SIZE - Static variable in class loci.formats.in.KLBReader
 
KLBReader - Class in loci.formats.in
Reader for Keller Lab Block (KLB) files.
KLBReader() - Constructor for class loci.formats.in.KLBReader
Constructs a new BDV reader.
KNOWN_VERSIONS - Static variable in class loci.formats.in.LiFlimReader
 
KodakReader - Class in loci.formats.in
KodakReader is the file format reader for Kodak Molecular Imaging .bip files.
KodakReader() - Constructor for class loci.formats.in.KodakReader
Constructs a new Kodak reader.
kryo - Variable in class loci.formats.Memoizer.KryoDeser
 
KryoDeser() - Constructor for class loci.formats.Memoizer.KryoDeser
 

L

L2DReader - Class in loci.formats.in
L2DReader is the file format reader for Li-Cor L2D datasets.
L2DReader() - Constructor for class loci.formats.in.L2DReader
Construct a new L2D reader.
label - Variable in class loci.plugins.prefs.Option
Label describing the option, for use with ImageJ dialogs.
LABEL_OBSCURED - Static variable in class loci.formats.in.NDPIReader
 
LABEL_X - Static variable in class loci.formats.in.TextReader
 
LABEL_Y - Static variable in class loci.formats.in.TextReader
 
labels - Variable in class loci.formats.in.FakeReader
 
labels - Variable in class loci.formats.in.ICSReader
Dimensional reordering for lifetime data
labels - Variable in class loci.formats.Modulo
 
labels - Variable in class loci.plugins.config.CellSensWidgets
 
labels - Variable in class loci.plugins.config.FlexWidgets
 
labels - Variable in class loci.plugins.config.FormatEntry
 
labels - Variable in class loci.plugins.config.LIFWidgets
 
labels - Variable in class loci.plugins.config.ND2Widgets
 
labels - Variable in class loci.plugins.config.PictWidgets
 
labels - Variable in class loci.plugins.config.QTWidgets
 
labels - Variable in class loci.plugins.config.SDTWidgets
 
labels - Variable in class loci.plugins.config.TiffDelegateWidgets
 
labels - Variable in class loci.plugins.config.ZeissCZIWidgets
 
LAMBDA - Static variable in class loci.formats.in.CellSensReader
 
LAMBDA_INCREMENT - Static variable in class loci.formats.in.CellSensReader
 
LAMBDA_START - Static variable in class loci.formats.in.CellSensReader
 
LAMBDA_VALUE - Static variable in class loci.formats.in.CellSensReader
 
LAMP_AGE - Static variable in class loci.formats.in.NDPIReader
 
Laser() - Constructor for class loci.formats.in.LeicaHandler.Laser
 
Laser() - Constructor for class loci.formats.in.OIRReader.Laser
 
Laser() - Constructor for class loci.formats.in.ZeissLSMReader.Laser
 
LASER_ACQUIRE - Static variable in class loci.formats.in.ZeissLSMReader
 
LASER_NAME - Static variable in class loci.formats.in.ZeissLSMReader
 
LASER_POWER - Static variable in class loci.formats.in.ZeissLSMReader
 
LASER_SCAN_CONFOCAL - Static variable in class loci.formats.in.LegacyND2Reader
 
laserActive - Variable in class loci.formats.in.LIFReader
 
laserCount - Variable in class loci.formats.in.LeicaHandler
 
laserFrap - Variable in class loci.formats.in.LIFReader
 
laserIDs - Variable in class loci.formats.in.NikonTiffReader
 
laserIndex - Variable in class loci.formats.in.OIRReader.Channel
 
laserIntensity - Variable in class loci.formats.in.LIFReader
 
lasers - Variable in class loci.formats.in.LeicaHandler
 
lasers - Variable in class loci.formats.in.OIRReader
 
laserWavelength - Variable in class loci.formats.in.LIFReader
 
lastChannel - Variable in class loci.formats.in.BDVReader
 
lastChannel - Variable in class loci.formats.in.BioRadReader
 
lastChannel - Variable in class loci.formats.in.CellH5Reader
 
lastChannel - Variable in class loci.formats.in.FV1000Reader
 
lastChannel - Variable in class loci.formats.in.ImarisHDFReader
 
lastChannel - Variable in class loci.formats.in.LIFReader
 
lastChannel - Variable in class loci.formats.in.NativeND2Reader
 
lastChannel - Variable in class loci.formats.in.OIRReader
 
lastCodeOffset - Variable in class loci.formats.in.AmiraReader.HxRLE
 
lastDispose - Variable in class loci.formats.in.GIFReader
 
lastFile - Variable in class loci.formats.in.CellWorxReader
 
lastFile - Variable in class loci.formats.in.ImprovisionTiffReader
 
lastFile - Variable in class loci.formats.in.SlidebookTiffReader
 
lastId - Variable in class loci.formats.gui.PreviewPane
Last ID loaded.
lastIFD - Variable in class loci.formats.in.LeicaSCNReader.Pixels
 
lastImage - Variable in class loci.formats.ChannelSeparator
Last image opened.
lastImage - Variable in class loci.formats.in.APNGReader
 
lastImage - Variable in class loci.formats.in.AVIReader
 
lastImage - Variable in class loci.formats.in.InCellReader.MinimalInCellHandler
 
lastImageHeight - Variable in class loci.formats.ChannelSeparator
Height of last image opened.
lastImageIndex - Variable in class loci.formats.ChannelSeparator
Index of last image opened.
lastImageIndex - Variable in class loci.formats.in.APNGReader
 
lastImageNo - Variable in class loci.formats.in.AVIReader
 
lastImageRow - Variable in class loci.formats.in.APNGReader
 
lastImageSeries - Variable in class loci.formats.ChannelSeparator
Series of last image opened.
lastImageWidth - Variable in class loci.formats.ChannelSeparator
Width of last image opened.
lastImageX - Variable in class loci.formats.ChannelSeparator
X index of last image opened.
lastImageY - Variable in class loci.formats.ChannelSeparator
Y index of last image opened.
lastIndex - Variable in class loci.formats.in.DNGReader
 
lastIndex - Variable in class loci.formats.in.NikonReader
 
lastPlane - Variable in class loci.formats.in.BaseZeissReader
 
lastPlane - Variable in class loci.formats.in.DNGReader
 
lastPlane - Variable in class loci.formats.in.JPXReader
 
lastPlane - Variable in class loci.formats.in.LeicaReader
 
lastPlane - Variable in class loci.formats.in.MinimalTiffReader
 
lastPlane - Variable in class loci.formats.in.NikonReader
 
lastPlane - Variable in class loci.formats.in.NRRDReader
 
lastPlane - Variable in class loci.formats.in.OMETiffReader
 
lastPlane - Variable in class loci.formats.in.OpenlabReader
 
lastPlane - Variable in class loci.formats.in.TCSReader
 
lastPlane - Variable in class loci.formats.out.ICSWriter
 
lastPlane - Variable in class loci.formats.out.V3DrawWriter
 
lastReader - Variable in class loci.formats.in.CellWorxReader
 
lastSeries - Variable in class loci.formats.in.BrukerReader
 
lastSeries - Variable in class loci.formats.in.JPEG2000Reader
 
lastSeries - Variable in class loci.formats.in.JPXReader
 
lastSeriesPlane - Variable in class loci.formats.in.JPEG2000Reader
 
lastSeriesPlane - Variable in class loci.formats.in.JPXReader
 
lastTimepoint - Variable in class loci.formats.in.BDVReader
 
LATEST_VERSION - Static variable in class loci.formats.services.OMEXMLServiceImpl
Latest OME-XML version namespace.
Layer() - Constructor for class loci.formats.in.BaseZeissReader.Layer
 
layer_count - Variable in class loci.formats.in.ZeissTIFFHandler
 
LAYER_INFO_PROPERTIES - Static variable in class loci.formats.in.CellSensReader
 
LAYER_SELECTION - Static variable in class loci.formats.in.CellSensReader
 
LAYER_SELECTION_INDEX - Static variable in class loci.formats.in.CellSensReader
 
LAYER_XY_FIXED - Static variable in class loci.formats.in.CellSensReader
 
layerNames - Variable in class loci.formats.in.PhotoshopTiffReader
 
layerOffset - Variable in class loci.formats.in.PhotoshopTiffReader
 
layers - Variable in class loci.formats.in.BaseZeissReader
 
layers - Variable in class loci.formats.in.ZeissTIFFHandler
 
LAYOUT_KEYS - Static variable in class loci.formats.in.ICSReader
 
LAYOUT_TABLE - Static variable in class loci.formats.in.LiFlimReader
 
lblockNo - Variable in class loci.formats.in.SDTInfo
Long blockNo - see remarks below.
legacy - Variable in class loci.formats.in.PictReader
 
legacy - Variable in class loci.formats.out.QTWriter
Legacy QuickTime writer.
LegacyND2Reader - Class in loci.formats.in
LegacyND2Reader is a file format reader for Nikon ND2 files that uses the Nikon ND2 SDK - it is only usable on Windows machines.
LegacyND2Reader() - Constructor for class loci.formats.in.LegacyND2Reader
 
LegacyQTReader - Class in loci.formats.in
LegacyQTReader is a file format reader for QuickTime movie files.
LegacyQTReader() - Constructor for class loci.formats.in.LegacyQTReader
Constructs a new QT reader.
LegacyQTTools - Class in loci.formats.gui
Utility class for working with QuickTime for Java.
LegacyQTTools() - Constructor for class loci.formats.gui.LegacyQTTools
 
LegacyQTWriter - Class in loci.formats.out
LegacyQTWriter is a file format writer for QuickTime movies.
LegacyQTWriter() - Constructor for class loci.formats.out.LegacyQTWriter
 
legacyReader - Variable in class loci.formats.DelegateReader
Legacy reader.
legacyReaderInitialized - Variable in class loci.formats.DelegateReader
Flag indicating that the legacy reader was successfully initialized.
LEI_SUFFIX - Static variable in class loci.formats.in.LeicaReader
 
LEICA_MAGIC_TAG - Static variable in class loci.formats.in.LeicaReader
All Leica TIFFs have this tag.
LeicaHandler - Class in loci.formats.in
SAX handler for parsing XML in Leica LIF and Leica TCS files.
LeicaHandler(MetadataStore, MetadataLevel) - Constructor for class loci.formats.in.LeicaHandler
 
LeicaHandler.Channel - Class in loci.formats.in
 
LeicaHandler.Detector - Class in loci.formats.in
 
LeicaHandler.Laser - Class in loci.formats.in
 
LeicaHandler.MultiBand - Class in loci.formats.in
 
LeicaHandler.ROI - Class in loci.formats.in
 
LeicaReader - Class in loci.formats.in
LeicaReader is the file format reader for Leica files.
LeicaReader() - Constructor for class loci.formats.in.LeicaReader
Constructs a new Leica reader.
LeicaReader.Detector - Class in loci.formats.in
 
LeicaSCNHandler() - Constructor for class loci.formats.in.LeicaSCNReader.LeicaSCNHandler
 
LeicaSCNReader - Class in loci.formats.in
LeicaSCNReader is the file format reader for Leica SCN TIFF files.
LeicaSCNReader() - Constructor for class loci.formats.in.LeicaSCNReader
Constructs a new LeicaSCN reader.
LeicaSCNReader.Dimension - Class in loci.formats.in
 
LeicaSCNReader.Image - Class in loci.formats.in
 
LeicaSCNReader.ImageCollection - Class in loci.formats.in
 
LeicaSCNReader.LeicaSCNHandler - Class in loci.formats.in
SAX handler for parsing XML in Leica SCN files.
LeicaSCNReader.Pixels - Class in loci.formats.in
 
leiFilename - Variable in class loci.formats.in.LeicaReader
Name of current LEI file
len - Variable in class loci.plugins.util.BFVirtualStack
 
lenC - Variable in class loci.formats.FileStitcher
Component lengths for each axis type.
length() - Method in class loci.formats.cache.CacheStrategy
Shortcut for computing total number of positions.
length - Variable in class loci.formats.in.APNGReader.PNGBlock
 
length - Variable in class loci.formats.in.IM3Reader.IM3Record
 
length - Variable in class loci.formats.in.NativeND2Reader.ChunkMapEntry
 
length - Variable in class loci.formats.in.OBFReader.Stack
 
length - Variable in class loci.formats.in.OIRReader.PixelBlock
 
length() - Method in class loci.formats.Modulo
 
lengths - Variable in class loci.formats.cache.CacheStrategy
Length of each dimensional axis.
lengths - Variable in class loci.formats.gui.CacheComponent
Length of each dimensional axis, obtained from cache strategy.
lengths - Variable in class loci.formats.in.AVIReader
Number of bytes in each plane.
lengths - Variable in class loci.formats.in.DeltavisionReader
 
lengths - Variable in class loci.formats.in.MNGReader.SeriesInfo
 
LENS - Static variable in class loci.formats.in.NikonReader
 
lens - Variable in class loci.formats.in.PSDReader
 
LENS_TYPE - Static variable in class loci.formats.in.NikonReader
 
lensNA - Variable in class loci.formats.in.FluoviewReader
 
lensNA - Variable in class loci.formats.in.FV1000Reader
 
lensNA - Variable in class loci.formats.in.IvisionReader
 
lensNA - Variable in class loci.formats.in.LIFReader
 
lensNA - Variable in class loci.formats.in.MetamorphHandler
 
lensNA - Variable in class loci.formats.in.NikonTiffReader
 
lensNA - Variable in class loci.formats.in.OperettaReader.Plane
 
lensNA - Variable in class loci.formats.in.ZeissLSMReader.Recording
 
lensRI - Variable in class loci.formats.in.MetamorphHandler
 
lenT - Variable in class loci.formats.FileStitcher
Component lengths for each axis type.
lenZ - Variable in class loci.formats.FileStitcher
Component lengths for each axis type.
LEO_TAG - Static variable in class loci.formats.in.LEOReader
 
LEOReader - Class in loci.formats.in
LEOReader is the file format reader for LEO EM files.
LEOReader() - Constructor for class loci.formats.in.LEOReader
Constructs a new LEO reader.
letter - Variable in class loci.formats.ResourceNamer
 
level - Variable in class loci.formats.in.BioRadReader.Note
 
level - Variable in class loci.formats.in.FlexReader.FlexHandler
 
level - Variable in class loci.formats.in.LeicaHandler
 
libClass - Variable in class loci.plugins.config.LibraryEntry
 
Library() - Constructor for enum loci.plugins.util.LibraryChecker.Library
 
LibraryChecker - Class in loci.plugins.util
Utility methods for verifying that classes are present and versions are correct.
LibraryChecker() - Constructor for class loci.plugins.util.LibraryChecker
 
LibraryChecker.Library - Enum in loci.plugins.util
List of possible libraries for which to check.
LibraryEntry - Class in loci.plugins.config
A list entry for the configuration window's Libraries tab.
LibraryEntry(PrintWriter, HashMap<String, String>) - Constructor for class loci.plugins.config.LibraryEntry
 
LibraryEntry(PrintWriter, String, String, String, String, String, String, String) - Constructor for class loci.plugins.config.LibraryEntry
 
libraryFound - Static variable in class loci.formats.in.LegacyND2Reader
 
libraryLoaded - Static variable in class loci.formats.services.JPEGTurboServiceImpl
 
libsList - Variable in class loci.plugins.config.ConfigWindow
 
libsListModel - Variable in class loci.plugins.config.ConfigWindow
 
license - Variable in class loci.formats.services.LuraWaveServiceImpl
License code.
license - Variable in class loci.plugins.config.ConfigWindow
 
license - Variable in class loci.plugins.config.LibraryEntry
 
LICENSE_PROPERTY - Static variable in class loci.formats.services.LuraWaveServiceImpl
System property to check for the LuraWave license code.
licenseBox - Variable in class loci.plugins.config.FlexWidgets
 
LICOR_MAGIC_STRING - Static variable in class loci.formats.in.L2DReader
 
LIF_MAGIC_BYTE - Static variable in class loci.formats.in.LIFReader
 
LIF_MEMORY_BYTE - Static variable in class loci.formats.in.LIFReader
 
LIFETIME - Static variable in class loci.formats.FormatTools
Identifies the Lifetime dimensional type, representing a dimension consisting of a lifetime histogram.
lifetime - Variable in class loci.formats.in.ICSReader
Whether or not the channels represent lifetime histogram bins.
LIFF_MAGIC_BYTES - Static variable in class loci.formats.in.OpenlabReader
 
LiFlimReader - Class in loci.formats.in
LiFlimReader is the file format reader for LI-FLIM files.
LiFlimReader() - Constructor for class loci.formats.in.LiFlimReader
Constructs a new LI-FLIM reader.
LiFlimReader.ROI - Class in loci.formats.in
 
LIFReader - Class in loci.formats.in
LIFReader is the file format reader for Leica LIF files.
LIFReader() - Constructor for class loci.formats.in.LIFReader
Constructs a new Leica LIF reader.
LIFReader.ROI - Class in loci.formats.in
 
LIFWidgets - Class in loci.plugins.config
Custom widgets for configuring Bio-Formats Leica LIF support.
LIFWidgets() - Constructor for class loci.plugins.config.LIFWidgets
 
LIGHT_SOURCE - Static variable in class loci.formats.tiff.IFD
 
LIGHT_TYPE - Static variable in class loci.formats.in.NikonReader
 
LightSource() - Constructor for class loci.formats.in.CV7000Reader.LightSource
 
lightSourceCombinationIDs - Variable in class loci.formats.in.FlexReader
 
lightSourceCombinationRefs - Variable in class loci.formats.in.FlexReader
 
lightSourceID - Variable in class loci.formats.in.FlexReader.FlexHandler
 
lightSourceIDs - Variable in class loci.formats.in.FlexReader
 
lightSourceRefs - Variable in class loci.formats.in.CV7000Reader.Channel
 
lightSources - Variable in class loci.formats.in.CV7000Reader
 
limitHeight(JComponent) - Method in class loci.formats.gui.DataConverter
 
LIMReader - Class in loci.formats.in
LIMReader is the file format reader for Laboratory Imaging/Nikon LIM files.
LIMReader() - Constructor for class loci.formats.in.LIMReader
Constructs a new LIM reader.
LINE - Static variable in class loci.formats.in.FV1000Reader
 
line - Variable in class loci.formats.in.FV1000Reader
 
LINE - Static variable in class loci.formats.in.GatanReader
Shape types
LINE - Static variable in class loci.formats.in.LeicaHandler.ROI
 
LINE - Static variable in class loci.formats.in.LIFReader.ROI
 
LINE - Static variable in class loci.formats.in.ZeissLSMReader
 
line - Variable in class loci.formats.tools.MakeTestOmeTiff.TextLine
 
LINE_LENGTH - Static variable in class loci.formats.in.FitsReader
 
LINEAR - Static variable in class loci.formats.in.GelReader
 
linediv - Variable in class loci.formats.in.SDTInfo
Line predivider = 2 ** (linediv).
LineEndPositions(int) - Constructor for enum loci.formats.in.BaseZeissReader.LineEndPositions
 
lineEndPositions - Variable in class loci.formats.in.BaseZeissReader.Shape
 
lineEndSize - Variable in class loci.formats.in.BaseZeissReader.Shape
 
LineEndStyle(int) - Constructor for enum loci.formats.in.BaseZeissReader.LineEndStyle
 
lineEndStyle - Variable in class loci.formats.in.BaseZeissReader.Shape
 
lineMode - Variable in class loci.formats.in.SPCReader
 
lines - Variable in class loci.formats.in.FakeReader
 
lineTo(int, int) - Method in class loci.plugins.util.RecordedImageProcessor
 
lineWidth - Variable in class loci.formats.in.BaseZeissReader.Shape
 
linewidth - Variable in class loci.formats.in.LeicaHandler.ROI
 
linewidth - Variable in class loci.formats.in.LIFReader.ROI
 
linkedInstruments - Variable in class loci.formats.in.LeicaHandler
 
listeners - Variable in class loci.formats.cache.Cache
List of cache event listeners.
listeners - Variable in class loci.formats.cache.CacheStrategy
List of cache event listeners.
listeners - Variable in class loci.plugins.in.ImagePlusReader
 
listeners - Variable in class loci.plugins.in.ImportProcess
 
listFakeSeries(String) - Method in class loci.formats.in.FakeReader
Traverses a fake file folder structure indicated by traversedDirectory
listString - Variable in class loci.formats.in.AVIReader
 
LITTLE - Static variable in class loci.formats.tiff.TiffConstants
 
LITTLE_ENDIAN - Static variable in class loci.formats.in.BioRadReader
Always little endian.
LITTLE_ENDIAN - Static variable in class loci.formats.in.DeltavisionReader
 
LITTLE_ENDIAN - Static variable in class loci.formats.in.OBFReader
 
LITTLE_ENDIAN - Static variable in class loci.formats.in.TextReader
 
LITTLE_ENDIAN - Static variable in class loci.formats.tiff.IFD
 
littleEndian - Variable in class loci.formats.codec.CodecOptions
Indicates endianness of pixel data.
littleEndian - Variable in class loci.formats.CoreMetadata
Indicates whether or not each pixel's bytes are in little endian order.
littleEndian - Variable in class loci.formats.out.APNGWriter
 
littleEndian - Variable in class loci.formats.tools.AmiraParameters
 
LIVE_OVERFLOW - Static variable in class loci.formats.in.CellSensReader
 
LM_DOMAIN - Static variable in class loci.formats.FormatTools
Identifies the light microscopy domain.
LO - Static variable in class loci.formats.in.DicomReader
 
load(String, File, boolean) - Static method in class loci.formats.Memoizer
 
load() - Static method in class org.libjpegturbo.turbojpeg.TJLoader
 
loadedFromMemo - Variable in class loci.formats.Memoizer
Whether the ReaderWrapper.reader instance currently active was loaded from the memo file during Memoizer.setId(String).
LOADER - Static variable in class loci.formats.gui.LegacyQTTools
This custom class loader searches additional paths for the QTJava.zip library.
loader - Variable in class loci.formats.gui.PreviewPane
Thumbnail loading thread.
loader - Variable in class loci.plugins.in.ThumbLoader
 
loaderAlive - Variable in class loci.formats.gui.PreviewPane
Flag indicating whether loader thread should keep running.
loadId - Variable in class loci.formats.gui.PreviewPane
Current ID to load.
loadImage(Image) - Static method in class loci.formats.gui.AWTImageTools
Ensures the given AWT image is fully loaded.
loadManifest() - Static method in class loci.formats.FormatTools
 
loadMemo() - Method in class loci.formats.Memoizer
Load a memo file if possible, returning a null if not.
loadOption() - Method in class loci.plugins.prefs.BooleanOption
 
loadOption() - Method in class loci.plugins.prefs.DoubleOption
 
loadOption() - Method in class loci.plugins.prefs.Option
Loads the option's value from the ImageJ preferences file.
loadOption() - Method in class loci.plugins.prefs.StringOption
 
loadOptions() - Method in class loci.plugins.prefs.OptionsList
Loads option values from the ImageJ preferences file.
loadProperties() - Static method in class loci.formats.FormatTools
Deprecated.
This method should no longer be used. The properties are now obtained from the jar manifest.
loadReader() - Method in interface loci.formats.Memoizer.Deser
 
loadReader() - Method in class loci.formats.Memoizer.KryoDeser
 
loadReader() - Method in class loci.formats.Memoizer.RandomAccessDeser
 
loadReleaseVersion() - Method in interface loci.formats.Memoizer.Deser
 
loadReleaseVersion() - Method in class loci.formats.Memoizer.KryoDeser
 
loadReleaseVersion() - Method in class loci.formats.Memoizer.RandomAccessDeser
 
loadRevision() - Method in interface loci.formats.Memoizer.Deser
 
loadRevision() - Method in class loci.formats.Memoizer.KryoDeser
 
loadRevision() - Method in class loci.formats.Memoizer.RandomAccessDeser
 
loadStart(File) - Method in interface loci.formats.Memoizer.Deser
 
loadStart(File) - Method in class loci.formats.Memoizer.KryoDeser
 
loadStart(File) - Method in class loci.formats.Memoizer.RandomAccessDeser
 
loadStop() - Method in interface loci.formats.Memoizer.Deser
 
loadStop() - Method in class loci.formats.Memoizer.KryoDeser
 
loadStop() - Method in class loci.formats.Memoizer.RandomAccessDeser
 
loadStream - Variable in class loci.formats.Memoizer.RandomAccessDeser
 
loadThumb(BufferedImageReader, int, Panel, boolean) - Static method in class loci.plugins.in.ThumbLoader
 
loadVersion() - Method in interface loci.formats.Memoizer.Deser
 
loadVersion() - Method in class loci.formats.Memoizer.KryoDeser
 
loadVersion() - Method in class loci.formats.Memoizer.RandomAccessDeser
 
locateExperimentFile(String) - Method in class loci.formats.in.BDReader
 
locateFirstValidFile() - Method in class loci.formats.in.MetamorphReader
Locates the first valid file in the STK arrays.
location - Variable in class loci.formats.in.DicomReader
 
LOCATION_HTTP - Static variable in class loci.plugins.in.ImporterOptions
 
LOCATION_LOCAL - Static variable in class loci.plugins.in.ImporterOptions
 
LOCATION_OMERO - Static variable in class loci.plugins.in.ImporterOptions
 
LocationDialog - Class in loci.plugins.in
Bio-Formats Importer location chooser dialog box.
LocationDialog(ImportProcess) - Constructor for class loci.plugins.in.LocationDialog
Creates a location chooser dialog for the Bio-Formats Importer.
locator - Variable in class loci.formats.in.OMEXMLReader.OMEXMLHandler
 
loci.formats - package loci.formats
Bio-Formats: a library for reading and writing popular microscopy file formats.
loci.formats.cache - package loci.formats.cache
Package containing Bio-Formats caching logic, for managing subsets of large collections of image planes in memory.
loci.formats.codec - package loci.formats.codec
 
loci.formats.gui - package loci.formats.gui
Package containing Bio-Formats graphical user interface code.
loci.formats.in - package loci.formats.in
Package containing Bio-Formats file format readers.
loci.formats.meta - package loci.formats.meta
Package containing core Bio-Formats metadata interfaces for the OME data model.
loci.formats.ome - package loci.formats.ome
Package containing Bio-Formats OME-related logic for OME-XML metadata, and database import, upload and download.
loci.formats.out - package loci.formats.out
Package containing Bio-Formats file format writers.
loci.formats.services - package loci.formats.services
 
loci.formats.tiff - package loci.formats.tiff
Package containing Bio-Formats TIFF code of general utility.
loci.formats.tools - package loci.formats.tools
Package containing utility methods corresponding to the Bio-Formats command line tools.
loci.plugins - package loci.plugins
Bio-Formats Plugins: a collection of plugins for ImageJ, including the Bio-Formats Importer, Bio-Formats Exporter, Bio-Formats Macro Extensions, Data Browser and Stack Slicer.
loci.plugins.config - package loci.plugins.config
Bio-Formats Plugins Configuration plugin for ImageJ.
loci.plugins.in - package loci.plugins.in
Bio-Formats Importer plugin for ImageJ.
loci.plugins.macro - package loci.plugins.macro
Bio-Formats Macro Extensions plugin for ImageJ.
loci.plugins.out - package loci.plugins.out
Bio-Formats Exporter plugin for ImageJ.
loci.plugins.prefs - package loci.plugins.prefs
Classes for managing Bio-Formats plugins preferences.
loci.plugins.shortcut - package loci.plugins.shortcut
Bio-Formats Plugins Shortcut Window plugin for ImageJ.
loci.plugins.util - package loci.plugins.util
Utility classes and methods for the Bio-Formats plugins for ImageJ.
LociConfig - Class in loci.plugins.config
An ImageJ plugin for displaying the Bio-Formats plugins configuration dialog.
LociConfig() - Constructor for class loci.plugins.config.LociConfig
 
LociExporter - Class in loci.plugins
ImageJ plugin for writing files using the OME Bio-Formats package.
LociExporter() - Constructor for class loci.plugins.LociExporter
 
LociFunctions - Class in loci.plugins.macro
This class provides macro extensions in ImageJ for Bio-Formats.
LociFunctions() - Constructor for class loci.plugins.macro.LociFunctions
 
LociImporter - Class in loci.plugins
ImageJ plugin for reading files using the OME Bio-Formats package.
LociImporter() - Constructor for class loci.plugins.LociImporter
 
LociInstaller - Class in loci.plugins.config
An ImageJ plugin for installing and upgrading libraries related to the Bio-Formats plugins.
LociInstaller() - Constructor for class loci.plugins.config.LociInstaller
 
LociPrefs - Class in loci.plugins.util
Utility methods for ImageJ preferences for Bio-Formats plugins.
LociPrefs() - Constructor for class loci.plugins.util.LociPrefs
 
log - Variable in class loci.plugins.config.ConfigWindow
 
log() - Method in class loci.plugins.util.RecordedImageProcessor
 
logFile - Variable in class loci.formats.in.DeltavisionReader
 
logFiles - Variable in class loci.formats.in.CellWorxReader
 
LOGGER - Static variable in class loci.formats.cache.CacheUpdater
 
LOGGER - Static variable in class loci.formats.ClassList
 
LOGGER - Static variable in class loci.formats.codec.BaseCodec
 
LOGGER - Static variable in class loci.formats.FileStitcher
 
LOGGER - Static variable in class loci.formats.FormatHandler
 
LOGGER - Static variable in class loci.formats.FormatTools
 
LOGGER - Static variable in class loci.formats.gui.AWTImageTools
 
LOGGER - Static variable in class loci.formats.gui.CacheComponent
 
LOGGER - Static variable in class loci.formats.gui.DataConverter
 
LOGGER - Static variable in class loci.formats.gui.ImageViewer
 
LOGGER - Static variable in class loci.formats.gui.LegacyQTTools
 
LOGGER - Static variable in class loci.formats.gui.PreviewPane
 
LOGGER - Static variable in class loci.formats.ImageReader
 
LOGGER - Static variable in class loci.formats.ImageWriter
 
LOGGER - Static variable in class loci.formats.in.BaseTiffReader
Logger for this class.
LOGGER - Static variable in class loci.formats.in.CV7000Reader
 
LOGGER - Static variable in class loci.formats.in.DNGReader
Logger for this class.
LOGGER - Static variable in class loci.formats.in.IM3Reader
Logger for outputting summary diagnostics.
LOGGER - Static variable in class loci.formats.in.ImarisTiffReader
Logger for this class.
LOGGER - Static variable in class loci.formats.in.JPEG2000MetadataParser
Logger for this class.
LOGGER - Static variable in class loci.formats.in.JPEG2000Reader
Logger for this class.
LOGGER - Static variable in class loci.formats.in.JPXReader
Logger for this class.
LOGGER - Static variable in class loci.formats.in.LeicaHandler
Logger for this class.
LOGGER - Static variable in class loci.formats.in.LeicaReader
 
LOGGER - Static variable in class loci.formats.in.LeicaSCNReader
Logger for this class.
LOGGER - Static variable in class loci.formats.in.MetamorphReader
Logger for this class.
LOGGER - Static variable in class loci.formats.in.MikroscanTiffReader
Logger for this class.
LOGGER - Static variable in class loci.formats.in.MinimalTiffReader
Logger for this class.
LOGGER - Static variable in class loci.formats.in.ND2Handler
 
LOGGER - Static variable in class loci.formats.in.NikonReader
Logger for this class.
LOGGER - Static variable in class loci.formats.in.PyramidTiffReader
Logger for this class.
LOGGER - Static variable in class loci.formats.in.SVSReader
Logger for this class.
LOGGER - Static variable in class loci.formats.in.TiffReader
Logger for this class.
LOGGER - Static variable in class loci.formats.in.TrestleReader
Logger for this class.
LOGGER - Static variable in class loci.formats.in.VectraReader
Logger for this class.
LOGGER - Static variable in class loci.formats.in.VentanaReader
Logger for this class.
LOGGER - Static variable in class loci.formats.in.ZeissTIFFHandler
 
LOGGER - Static variable in class loci.formats.Memoizer
Default Logger for the memoizer class
LOGGER - Static variable in class loci.formats.MetadataTools
 
LOGGER - Static variable in class loci.formats.services.JPEGTurboServiceImpl
 
logger - Variable in class loci.formats.services.JPEGTurboServiceImpl
 
LOGGER - Static variable in class loci.formats.services.JPEGXRServiceImpl
 
LOGGER - Static variable in class loci.formats.services.OMEXMLServiceImpl
Logger for this class.
LOGGER - Static variable in class loci.formats.tiff.IFD
 
LOGGER - Static variable in enum loci.formats.tiff.TiffCompression
 
LOGGER - Static variable in class loci.formats.tiff.TiffParser
 
LOGGER - Static variable in class loci.formats.tiff.TiffSaver
 
LOGGER - Static variable in class loci.formats.TileStitcher
 
LOGGER - Static variable in class loci.formats.tools.EditTiffG
 
LOGGER - Static variable in class loci.formats.tools.FakeImage
 
LOGGER - Static variable in class loci.formats.UpgradeChecker
 
logIsThisTypeError(IFormatReader, Exception) - Method in class loci.formats.ImageReader
 
LOGO_FILE - Static variable in class loci.formats.in.LIFReader
 
LONG - Static variable in class loci.formats.in.CellSensReader
 
LONG_DATE_FORMAT - Static variable in class loci.formats.in.MetamorphReader
 
longValue() - Method in class loci.formats.tiff.TiffRational
Returns the value of the specified number as a long.
lookup - Static variable in enum loci.formats.codec.CompressionType
Map used to retrieve the compression type corresponding to the code.
lookup - Static variable in enum loci.formats.codec.JPEG2000BoxType
Map used to retrieve the box type corresponding to the code.
lookup - Static variable in enum loci.formats.codec.JPEG2000SegmentMarker
Map used to retrieve the segment marker corresponding to the code.
lookup - Static variable in enum loci.formats.in.BaseZeissReader.Charset
 
lookup - Static variable in enum loci.formats.in.BaseZeissReader.DrawStyle
 
lookup - Static variable in enum loci.formats.in.BaseZeissReader.FeatureType
 
lookup - Static variable in enum loci.formats.in.BaseZeissReader.FillStyle
 
lookup - Static variable in enum loci.formats.in.BaseZeissReader.LineEndPositions
 
lookup - Static variable in enum loci.formats.in.BaseZeissReader.LineEndStyle
 
lookup - Static variable in enum loci.formats.in.BaseZeissReader.PointStyle
 
lookup - Static variable in enum loci.formats.in.BaseZeissReader.TextAlignment
 
lookup - Variable in class loci.formats.in.PictReader
Color lookup table for palette color images.
lookup(String) - Method in class loci.formats.in.ZeissTIFFReader
Translate a file path from the XML file to an actual path on disk.
lookup - Static variable in enum loci.formats.tiff.IFDType
 
lookup - Static variable in enum loci.formats.tiff.PhotoInterp
 
lookup - Static variable in enum loci.formats.tiff.TiffCompression
Reverse lookup of code to TIFF compression enumerate value.
lookupDimension(int, int, int) - Method in class loci.formats.in.LeicaSCNReader.Pixels
 
lookupFile(int, int) - Method in class loci.formats.in.CellomicsReader
 
lookupFile(int, int, int) - Method in class loci.formats.in.FlexReader
 
lookupFile(int) - Method in class loci.formats.in.FlexReader
 
lookupFile(int) - Method in class loci.formats.in.PerkinElmerReader
 
lookupPlane(int, int, int, int, int) - Method in class loci.formats.in.ColumbusReader
 
lookupPlane(int, int) - Method in class loci.formats.in.CV7000Reader
 
lookupResolution(int, int) - Method in class loci.formats.ome.OMEPyramidStore
Find the Resolution object for the given indices.
lookupResolution(int, int, boolean) - Method in class loci.formats.ome.OMEPyramidStore
Find the Resolution object for the given indices.
lossless - Variable in class loci.formats.codec.CodecOptions
Used with codecs allowing lossy and lossless compression.
LOSSLESS_DECODER_CONFIGURATION_12 - Static variable in class loci.formats.codec.NikonCodec
 
LOSSLESS_DECODER_CONFIGURATION_14 - Static variable in class loci.formats.codec.NikonCodec
 
LosslessJPEGCodec - Class in loci.formats.codec
Decompresses lossless JPEG images.
LosslessJPEGCodec() - Constructor for class loci.formats.codec.LosslessJPEGCodec
 
LOSSY_DECODER_CONFIGURATION_12 - Static variable in class loci.formats.codec.NikonCodec
 
LOSSY_DECODER_CONFIGURATION_14 - Static variable in class loci.formats.codec.NikonCodec
 
lossyCompression - Variable in class loci.formats.in.NikonReader
 
LOW_PRIORITY - Static variable in interface loci.formats.cache.ICacheStrategy
 
lPad - Variable in class loci.formats.gui.CacheIndicator
 
lsmFilenames - Variable in class loci.formats.in.ZeissLSMReader
 
LT - Static variable in class loci.formats.in.DicomReader
 
LUMA_BLUE - Static variable in enum loci.formats.tiff.PhotoInterp
 
LUMA_GREEN - Static variable in enum loci.formats.tiff.PhotoInterp
 
LUMA_RED - Static variable in enum loci.formats.tiff.PhotoInterp
Default luminance values for YCbCr data.
LuraWave - Class in loci.plugins.util
Utility methods for dealing with proprietary LuraWave licensing.
LuraWave() - Constructor for class loci.plugins.util.LuraWave
 
LuraWaveCodec - Class in loci.formats.codec
This class provides LuraWave decompression, using LuraWave's Java decoding library.
LuraWaveCodec() - Constructor for class loci.formats.codec.LuraWaveCodec
 
LuraWaveService - Interface in loci.formats.services
 
LuraWaveServiceImpl - Class in loci.formats.services
 
LuraWaveServiceImpl() - Constructor for class loci.formats.services.LuraWaveServiceImpl
Default constructor.
lut - Variable in class loci.formats.in.AmiraReader
 
lut - Variable in class loci.formats.in.APNGReader
 
lut - Variable in class loci.formats.in.AVIReader
 
lut - Variable in class loci.formats.in.BioRadReader
 
lut - Variable in class loci.formats.in.DicomReader
 
lut - Variable in class loci.formats.in.FV1000Reader
 
lut - Variable in class loci.formats.in.IvisionReader
 
lut - Variable in class loci.formats.in.JPEG2000MetadataParser
Color lookup table stored in the file.
lut - Variable in class loci.formats.in.JPEG2000Reader
The color lookup table associated with this file.
lut - Variable in class loci.formats.in.JPXReader
The color lookup table associated with this file.
lut - Variable in class loci.formats.in.KhorosReader
Global lookup table.
lut - Variable in class loci.formats.in.OIRReader.Channel
 
lut - Variable in class loci.formats.in.PCXReader
 
lut - Variable in class loci.formats.in.PSDReader
Lookup table.
lut - Variable in class loci.formats.in.ZeissLMSReader
 
lut - Variable in class loci.formats.in.ZeissLSMReader
 
lut16 - Variable in class loci.formats.in.FakeReader
16-bit lookup table, if indexed color, one per channel.
lut8 - Variable in class loci.formats.in.FakeReader
8-bit lookup table, if indexed color, one per channel.
LUT_LENGTH - Static variable in class loci.formats.in.BioRadReader
 
LUT_SIZE - Static variable in class loci.formats.in.NAFReader
 
LUTDESC - Static variable in class loci.formats.in.LeicaReader
 
lutIndex - Variable in class loci.formats.in.PDSReader
 
lutLength - Variable in class loci.formats.ChannelFiller
Number of LUT components.
lutNames - Variable in class loci.formats.in.FV1000Reader
 
lutNames - Variable in class loci.formats.in.LeicaHandler
 
lutNames - Variable in class loci.formats.in.LIFReader
 
luts - Variable in class loci.formats.in.OpenlabReader
 
luts - Variable in class loci.plugins.util.VirtualImagePlus
 
LZOCodec - Class in loci.formats.codec
This class implements LZO decompression.
LZOCodec() - Constructor for class loci.formats.codec.LZOCodec
 
LZW - Static variable in class loci.formats.in.ZeissCZIReader
 
LZWCodec - Class in loci.formats.codec
This is an optimized LZW codec for use with TIFF files.
LZWCodec() - Constructor for class loci.formats.codec.LZWCodec
 

M

MAC_16_BIT_COLOR - Static variable in class loci.formats.in.OpenlabReader
 
MAC_16_COLORS - Static variable in class loci.formats.in.OpenlabReader
 
MAC_16_GREYS - Static variable in class loci.formats.in.OpenlabReader
 
MAC_1_BIT - Static variable in class loci.formats.in.OpenlabReader
Image types.
MAC_24_BIT_COLOR - Static variable in class loci.formats.in.OpenlabReader
 
MAC_256_COLORS - Static variable in class loci.formats.in.OpenlabReader
 
MAC_256_GREYS - Static variable in class loci.formats.in.OpenlabReader
 
MAC_4_GREYS - Static variable in class loci.formats.in.OpenlabReader
 
MAC_OS_X - Static variable in class loci.formats.gui.LegacyQTTools
 
MACRO_IMAGE - Static variable in class loci.formats.in.CellSensReader
 
macroFile - Variable in class loci.formats.in.HamamatsuVMSReader
 
MacroFunctions - Class in loci.plugins.macro
Convenience class that simplifies implemention of ImageJ macro extensions.
MacroFunctions() - Constructor for class loci.plugins.macro.MacroFunctions
 
mag - Variable in class loci.formats.in.FluoviewReader
 
mag - Variable in class loci.formats.in.GatanReader
 
mag - Variable in class loci.formats.in.ND2Handler
 
MAG_MULTIPLIER - Static variable in class loci.formats.in.FEITiffReader
 
MAGIC - Static variable in class loci.formats.in.AnalyzeReader
 
MAGIC - Static variable in class loci.formats.in.BioRadSCNReader
 
MAGIC - Static variable in class loci.formats.in.ColumbusReader
 
MAGIC - Static variable in class loci.formats.in.HitachiReader
 
MAGIC_BYTES - Static variable in class loci.formats.in.BioRadGelReader
 
MAGIC_NUMBER - Static variable in class loci.formats.in.OBFReader
 
MAGIC_NUMBER - Static variable in class loci.formats.tiff.TiffConstants
 
MAGIC_STRING - Static variable in class loci.formats.in.HRDGDFReader
 
MAGIC_STRING - Static variable in class loci.formats.in.IMODReader
 
MAGIC_STRING - Static variable in class loci.formats.in.ImspectorReader
The header for each file contains this string.
MAGIC_STRING - Static variable in class loci.formats.in.KodakReader
 
MAGIC_STRING - Static variable in class loci.formats.in.MolecularImagingReader
 
MAGIC_STRING - Static variable in class loci.formats.in.SIFReader
 
MAGIC_STRING - Static variable in class loci.formats.in.SimplePCITiffReader
 
MAGNIFICATION - Static variable in class loci.formats.in.CellSensReader
 
magnification - Variable in class loci.formats.in.CellSensReader.Pyramid
 
magnification - Variable in class loci.formats.in.CV7000Reader.Channel
 
magnification - Variable in class loci.formats.in.FEITiffReader
 
magnification - Variable in class loci.formats.in.FV1000Reader
 
magnification - Variable in class loci.formats.in.IvisionReader
 
magnification - Variable in class loci.formats.in.LIFReader
 
magnification - Variable in class loci.formats.in.NDPIReader
 
magnification - Variable in class loci.formats.in.NikonTiffReader
 
magnification - Variable in class loci.formats.in.OIRReader.Objective
 
magnification - Variable in class loci.formats.in.OperettaReader.Plane
 
magnification - Variable in class loci.formats.in.SimplePCITiffReader
 
magnification - Variable in class loci.formats.in.SISReader
 
magnification - Variable in class loci.formats.in.SVSReader
 
magnification - Variable in class loci.formats.in.VentanaReader
 
magnification - Variable in class loci.formats.in.VolocityReader.Stack
 
magnification - Variable in class loci.formats.in.ZeissLSMReader.Recording
 
MAGNIFICATION_TAG - Static variable in class loci.formats.in.SlidebookTiffReader
 
magnitudes - Variable in class loci.formats.in.IM3Reader.Spectrum
 
main(String[]) - Static method in class loci.formats.codec.BitBuffer
Deprecated.
Testing method.
main(String[]) - Static method in class loci.formats.codec.BitWriter
Deprecated.
Tests the BitWriter class.
main(String[]) - Static method in class loci.formats.gui.DataConverter
 
main(String[]) - Static method in class loci.formats.gui.ImageViewer
 
main(String[]) - Static method in class loci.formats.gui.XMLWindow
 
main(String[]) - Static method in class loci.formats.in.IM3Reader
Write a summary of each record to STDOUT
main(String[]) - Static method in class loci.formats.Memoizer
 
main(String[]) - Static method in class loci.formats.tools.AmiraParameters
 
main(String[]) - Static method in class loci.formats.tools.BioFormatsExtensionPrinter
 
main(String[]) - Static method in class loci.formats.tools.CacheConsole
Interactive interpreter for testing Bio-Formats caching implementation.
main(String[]) - Static method in class loci.formats.tools.EditTiffG
 
main(String[]) - Static method in class loci.formats.tools.MakeTestOmeTiff
 
main(String[]) - Static method in class loci.formats.tools.UpgradeCheck
 
main(String[]) - Static method in class loci.plugins.About
 
main(String[]) - Static method in class loci.plugins.config.LociConfig
 
main(String[]) - Static method in class loci.plugins.in.Importer
Main method, for testing.
main_tagset - Variable in class loci.formats.in.ZeissTIFFHandler
 
MainDialog - Class in loci.plugins.in
Bio-Formats Importer general options dialog box.
MainDialog(ImportProcess) - Constructor for class loci.plugins.in.MainDialog
Creates a general options dialog for the Bio-Formats Importer.
majorVersion - Variable in class loci.formats.in.ZeissCZIReader.FileHeader
 
MAKE - Static variable in class loci.formats.tiff.IFD
 
make24Bits(Object, int, int, boolean, boolean) - Static method in class loci.formats.ImageTools
Convert an arbitrary primitive type array with 3 samples per pixel to a 3 x (width * height) byte array.
make24Bits(Object, int, int, boolean, boolean, Double, Double) - Static method in class loci.formats.ImageTools
Convert an arbitrary primitive type array with 3 samples per pixel to a 3 x (width * height) byte array.
make24Bits(Object, int, int, boolean) - Static method in class loci.formats.ImageTools
Convert an arbitrary primitive type array with 3 samples per pixel to an int array, i.e.
make24Bits(Object, int, int, boolean, Double, Double) - Static method in class loci.formats.ImageTools
Convert an arbitrary primitive type array with 3 samples per pixel to an int array, i.e.
makeBitArray(int, int) - Static method in class loci.formats.gui.SignedColorModel
 
makeBitArray(int, int) - Static method in class loci.formats.gui.UnsignedIntColorModel
 
makeBuffered(Image) - Static method in class loci.formats.gui.AWTImageTools
Creates a buffered image from the given AWT image object.
makeBuffered(Image, ColorModel) - Static method in class loci.formats.gui.AWTImageTools
Creates a buffered image possessing the given color model, from the specified AWT image object.
makeBufferedImageReader(IFormatReader) - Static method in class loci.formats.gui.BufferedImageReader
Converts the given reader into a BufferedImageReader, wrapping if needed.
makeBufferedImageWriter(IFormatWriter) - Static method in class loci.formats.gui.BufferedImageWriter
Converts the given writer into a BufferedImageWriter, wrapping if needed.
makeChannelFiller(IFormatReader) - Static method in class loci.formats.ChannelFiller
Converts the given reader into a ChannelFiller, wrapping if needed.
makeChannelMerger(IFormatReader) - Static method in class loci.formats.ChannelMerger
Converts the given reader into a ChannelMerger, wrapping if needed.
makeChannelSeparator(IFormatReader) - Static method in class loci.formats.ChannelSeparator
Converts the given reader into a ChannelSeparator, wrapping if needed.
makeColorModel(int, int) - Static method in class loci.formats.gui.AWTImageTools
Gets a color model for the given number of color components.
makeColorSpace(int) - Static method in class loci.formats.gui.AWTImageTools
Gets a color space for the given number of color components.
makeComboFilter(FileFilter[]) - Static method in class loci.formats.gui.GUITools
Creates an "All supported file types" combo filter encompassing all of the given filters.
makeCompactGrid(Container, int, int, int, int, int, int) - Static method in class loci.plugins.config.SpringUtilities
Aligns the first rows * cols components of parent in a grid.
makeCompatible(BufferedImage, GraphicsConfiguration) - Static method in class loci.formats.gui.AWTImageTools
Creates a buffered image compatible with the given graphics configuration, using the given buffered image as a source.
makeDimensionSwapper(IFormatReader) - Static method in class loci.formats.DimensionSwapper
Converts the given reader into a DimensionSwapper, wrapping if needed.
makeDimensionTable() - Static method in class loci.formats.in.LeicaReader
 
makeDummySlider() - Static method in class loci.plugins.util.DataBrowser
 
makeFileList() - Method in class loci.formats.in.DicomReader
 
makeFilterMetadata() - Method in class loci.formats.FormatReader
Return a properly configured loci.formats.meta.FilterMetadata.
makeGrid(Container, int, int, int, int, int, int) - Static method in class loci.plugins.config.SpringUtilities
Aligns the first rows * cols components of parent in a grid.
makeHeavyPanel(Component) - Static method in class loci.plugins.util.DataBrowser
Makes AWT play nicely with Swing components.
makeImage(byte[], int, int, boolean) - Static method in class loci.formats.gui.AWTImageTools
Creates an image from the given single-channel byte data.
makeImage(short[], int, int, boolean) - Static method in class loci.formats.gui.AWTImageTools
Creates an image from the given single-channel short data.
makeImage(int[], int, int, boolean) - Static method in class loci.formats.gui.AWTImageTools
Creates an image from the given single-channel int data.
makeImage(float[], int, int) - Static method in class loci.formats.gui.AWTImageTools
Creates an image from the given single-channel float data.
makeImage(double[], int, int) - Static method in class loci.formats.gui.AWTImageTools
Creates an image from the given single-channel double data.
makeImage(byte[], int, int, int, boolean, boolean) - Static method in class loci.formats.gui.AWTImageTools
Creates an image from the given byte data.
makeImage(short[], int, int, int, boolean, boolean) - Static method in class loci.formats.gui.AWTImageTools
Creates an image from the given short data.
makeImage(int[], int, int, int, boolean, boolean) - Static method in class loci.formats.gui.AWTImageTools
Creates an image from the given int data.
makeImage(float[], int, int, int, boolean) - Static method in class loci.formats.gui.AWTImageTools
Creates an image from the given float data.
makeImage(double[], int, int, int, boolean) - Static method in class loci.formats.gui.AWTImageTools
Creates an image from the given double data.
makeImage(byte[][], int, int, boolean) - Static method in class loci.formats.gui.AWTImageTools
Creates an image from the given byte data.
makeImage(short[][], int, int, boolean) - Static method in class loci.formats.gui.AWTImageTools
Creates an image from the given short data.
makeImage(int[][], int, int, boolean) - Static method in class loci.formats.gui.AWTImageTools
Creates an image from the given int data.
makeImage(float[][], int, int) - Static method in class loci.formats.gui.AWTImageTools
Creates an image from the given single-precision floating point data.
makeImage(double[][], int, int) - Static method in class loci.formats.gui.AWTImageTools
Creates an image from the given double-precision floating point data.
makeImage(byte[], boolean, MetadataRetrieve, int) - Static method in class loci.formats.gui.AWTImageTools
Creates an image from the given raw byte array, obtaining the dimensional parameters from the specified metadata object.
makeImage(byte[], int, int, int, boolean, int, boolean, boolean, boolean) - Static method in class loci.formats.gui.AWTImageTools
Creates an image from the given raw byte array, performing any necessary type conversions.
makeImage(byte[][], int, int, int, boolean, boolean, boolean) - Static method in class loci.formats.gui.AWTImageTools
Creates an image from the given raw byte array, performing any necessary type conversions.
makeImage(String) - Method in class loci.formats.gui.PreviewPane
Creates a blank image with the given message painted on top (e.g., a loading or error message), matching the size of the active reader's thumbnails.
makeImageName(int) - Method in class loci.formats.in.MetamorphReader
Create an appropriate name for the given series.
makeImageProcessorReader(IFormatReader) - Static method in class loci.plugins.util.ImageProcessorReader
Converts the given reader into a ImageProcessorReader, wrapping if needed.
makeImageReader() - Static method in class loci.plugins.util.LociPrefs
Creates an image reader according to the current configuration settings, including which format readers are currently enabled, as well as format-specific configuration settings.
makeJTree(Document) - Static method in class loci.formats.gui.XMLCellRenderer
Constructs a Swing JTree that displays the given XML DOM document.
makeLabel(String, boolean) - Method in class loci.plugins.config.ConfigWindow
 
makeLabel(String, int, int) - Method in class loci.plugins.in.ColorDialog
 
makeList(DefaultListModel) - Method in class loci.plugins.config.ConfigWindow
 
makeLUT(int, int) - Method in class loci.plugins.in.Colorizer
 
makeLUT(Color) - Method in class loci.plugins.in.Colorizer
 
makeLUTs(ColorModel[], boolean) - Method in class loci.plugins.in.Colorizer
 
makeLUTs(int) - Method in class loci.plugins.in.Colorizer
 
makeMinMaxCalculator(IFormatReader) - Static method in class loci.formats.MinMaxCalculator
Converts the given reader into a MinMaxCalculator, wrapping if needed.
makeModuloElement(Document) - Method in class loci.formats.meta.ModuloAnnotation
Construct a DOM element for this annotation using the given Document as the root.
makeOmeTiff(String...) - Method in class loci.formats.tools.MakeTestOmeTiff
 
makeOmeTiff(String, CoreMetadata) - Method in class loci.formats.tools.MakeTestOmeTiff
 
makeOmeTiffExtensions(String...) - Method in class loci.formats.tools.MakeTestOmeTiff
 
makeOriginalMetadata(Document) - Method in class loci.formats.meta.OriginalMetadataAnnotation
Create a DOM element for this annotation with the given document as the parent.
makePixelTypes() - Static method in class loci.formats.FormatTools
 
MAKER_NOTE - Static variable in class loci.formats.tiff.IFD
 
MAKER_WHITE_BALANCE - Static variable in class loci.formats.in.NikonReader
 
makeRGBImage(byte[], int, int, int, boolean) - Static method in class loci.formats.gui.AWTImageTools
 
makeRGBImage(byte[][], int, int) - Static method in class loci.formats.gui.AWTImageTools
 
makerNoteOffset - Variable in class loci.formats.in.NikonReader
Offset to the Nikon Maker Note.
makeSamples() - Method in class loci.formats.tools.MakeTestOmeTiff
 
makeSaneDimensionOrder(String) - Static method in class loci.formats.MetadataTools
Adjusts the given dimension order as needed so that it contains exactly one of each of the following characters: 'X', 'Y', 'Z', 'C', 'T'.
makeSplitPane(JList, JPanel) - Method in class loci.plugins.config.ConfigWindow
 
makeStack(ImageStack) - Method in class loci.plugins.Slicer
Returns a new ImageStack using the given ImageStack as a template.
MakeTestOmeTiff - Class in loci.formats.tools
Creates sample OME-TIFF datasets according to the given parameters.
MakeTestOmeTiff() - Constructor for class loci.formats.tools.MakeTestOmeTiff
 
MakeTestOmeTiff.TextLine - Class in loci.formats.tools
 
makeTextField() - Static method in class loci.plugins.config.ConfigWindow
 
makeTileStitcher(IFormatReader) - Static method in class loci.formats.TileStitcher
Converts the given reader into a TileStitcher, wrapping if needed.
makeTreeNode(Node) - Static method in class loci.formats.gui.XMLCellRenderer
Recursively builds JTree node structure from DOM node structure.
makeUnsigned(BufferedImage) - Static method in class loci.formats.gui.AWTImageTools
Converts the given BufferedImage into an image with unsigned pixel data.
makeValidIFD(IFD, int, int) - Method in class loci.formats.tiff.TiffSaver
Makes a valid IFD.
map - Variable in class loci.formats.in.EPSReader
 
map - Variable in class loci.formats.tools.AmiraParameters
 
mapFile - Variable in class loci.formats.in.HamamatsuVMSReader
 
mapOIBFiles() - Method in class loci.formats.in.FV1000Reader
 
mappedFiles - Variable in class loci.formats.in.ZipReader
 
mapServer(String, String) - Static method in class loci.formats.in.FlexReader
Map the server named 'alias' to the path 'realName'.
mapServer(String, String[]) - Static method in class loci.formats.in.FlexReader
Map the server named 'alias' to the paths in 'realNames'.
mapServersFromConfigurationFile(String) - Static method in class loci.formats.in.FlexReader
Read a configuration file with lines of the form: <server alias>=<real server name> and call mapServer(String, String) accordingly.
MARKER - Static variable in class loci.formats.in.ZeissLMSReader
 
Marker() - Constructor for class loci.formats.in.ZeissLSMReader.Marker
 
MARKER_0 - Static variable in class loci.formats.in.TillVisionReader
 
MARKER_1 - Static variable in class loci.formats.in.TillVisionReader
 
MARKER_2 - Static variable in class loci.formats.in.TillVisionReader
 
MARKER_3 - Static variable in class loci.formats.in.TillVisionReader
 
MARKER_TAG - Static variable in class loci.formats.in.NDPIReader
 
masks - Variable in class loci.formats.in.FakeReader
 
masterClock - Variable in class loci.formats.in.SDTInfo
Use or not Master Clock (SPC140 multi-module).
matchFilename(String) - Method in class loci.formats.in.CellomicsReader
 
matchFiles(String[], NumberFilter) - Static method in class loci.formats.FilePattern
 
matrix - Variable in class loci.formats.in.ZeissTIFFHandler.Scaling
 
max - Variable in class loci.formats.gui.SignedColorModel
 
max - Variable in class loci.formats.in.InCellReader.Image
 
max(double) - Method in class loci.plugins.util.RecordedImageProcessor
 
MAX_APERTURE_VALUE - Static variable in class loci.formats.tiff.IFD
 
MAX_BLOCK_SIZE - Static variable in class loci.formats.services.POIServiceImpl
 
MAX_CHANNELS - Static variable in class loci.formats.in.DeltavisionReader
 
MAX_COMPONENTS - Static variable in class loci.plugins.in.SeriesDialog
 
MAX_HEADER_SIZE - Static variable in class loci.formats.in.QuesantReader
 
MAX_JPEG_SIZE - Static variable in class loci.formats.in.HamamatsuVMSReader
 
MAX_MAJOR_VERSION - Static variable in class loci.formats.in.MicromanagerReader
Defines maximum Micro-Manager version supported.
MAX_PRIORITY - Static variable in interface loci.formats.cache.ICacheStrategy
 
MAX_READERS - Static variable in class loci.formats.FileStitcher
 
MAX_SAMPLE_VALUE - Static variable in class loci.formats.tiff.IFD
 
MAX_SERIES_THUMBS - Static variable in class loci.plugins.in.SeriesDialog
 
MAX_SERIES_TOGGLES - Static variable in class loci.plugins.in.SeriesDialog
 
MAX_SIZE - Static variable in class loci.formats.in.HamamatsuVMSReader
 
MAX_SIZE - Static variable in class loci.formats.in.JPEGReader
 
MAX_SIZE - Static variable in class loci.formats.in.NDPIReader
 
MAX_STACK_SIZE - Static variable in class loci.formats.in.GIFReader
Maximum buffer size.
MAX_TRIES - Static variable in class loci.plugins.util.LuraWave
 
MAX_VERSION - Static variable in class loci.formats.in.MicromanagerReader
 
maxAdcRate - Variable in class loci.formats.in.SDTInfo
 
maxBytes - Variable in class loci.formats.codec.CodecOptions
If compressing, this is the maximum number of raw bytes to compress.
maxC - Variable in class loci.formats.in.CV7000Reader.MinMax
 
maxCfdRate - Variable in class loci.formats.in.SDTInfo
(-1.0 - not set).
MAXIMAL_NUMBER_OF_DIMENSIONS - Static variable in class loci.formats.in.OBFReader
 
maximumReadOffset - Variable in class loci.formats.in.JPEG2000MetadataParser
Maximum read offset within in the stream.
maxInten - Variable in class loci.formats.in.DeltavisionReader.DVExtHdrFields
Maxiumum intensity.
maxOffsetIndex - Variable in class loci.formats.in.AmiraReader.HxRLE
 
maxPixelRange - Variable in class loci.formats.in.DicomReader
 
maxResolution - Variable in class loci.formats.in.ZeissCZIReader
 
maxSyncRate - Variable in class loci.formats.in.SDTInfo
Maximum rates during the measurement.
maxT - Variable in class loci.formats.in.CV7000Reader.MinMax
 
maxTacRate - Variable in class loci.formats.in.SDTInfo
 
maxValue() - Method in class loci.plugins.util.RecordedImageProcessor
 
maxX - Variable in class loci.formats.in.ImarisHDFReader
 
maxY - Variable in class loci.formats.in.ImarisHDFReader
 
maxZ - Variable in class loci.formats.in.CV7000Reader.MinMax
 
maxZ - Variable in class loci.formats.in.ImarisHDFReader
 
mcsPoints - Variable in class loci.formats.in.SDTInfo
No of MCS values.
mcstaPoints - Variable in class loci.formats.in.SDTInfo
Number of MCS_TA points.
mcsTime - Variable in class loci.formats.in.SDTInfo
Interval time [ms] for MCS histogram.
mcuHeight - Static variable in class org.libjpegturbo.turbojpeg.TJ
 
mcuWidth - Static variable in class org.libjpegturbo.turbojpeg.TJ
 
MD_FILE_UNITS - Static variable in class loci.formats.in.GelReader
 
MD_FILETAG - Static variable in class loci.formats.in.GelReader
 
MD_LAB_NAME - Static variable in class loci.formats.in.GelReader
 
MD_PREP_DATE - Static variable in class loci.formats.in.GelReader
 
MD_PREP_TIME - Static variable in class loci.formats.in.GelReader
 
MD_SAMPLE_INFO - Static variable in class loci.formats.in.GelReader
 
MD_SCALE_PIXEL - Static variable in class loci.formats.in.GelReader
 
mdb - Variable in class loci.formats.services.MDBServiceImpl
 
MDB_SUFFIX - Static variable in class loci.formats.in.ZeissLSMReader
 
MDBService - Interface in loci.formats.services
Interface defining methods for parsing MDB database files.
MDBServiceImpl - Class in loci.formats.services
Implementation of MDBService for parsing MDB database files.
MDBServiceImpl() - Constructor for class loci.formats.services.MDBServiceImpl
Default constructor.
MEA_SUFFIX - Static variable in class loci.formats.in.FlexReader
 
MeaHandler() - Constructor for class loci.formats.in.FlexReader.MeaHandler
 
measDescBlockLength - Variable in class loci.formats.in.SDTInfo
 
measDescBlockNo - Variable in class loci.formats.in.SDTInfo
Number of the measurement description block corresponding to this data block.
measDescBlockOffs - Variable in class loci.formats.in.SDTInfo
 
measMode - Variable in class loci.formats.in.SDTInfo
 
MEASUREMENT_DETAIL - Static variable in class loci.formats.in.CV7000Reader
 
MEASUREMENT_FILE - Static variable in class loci.formats.in.CV7000Reader
 
MEASUREMENT_SUFFIXES - Static variable in class loci.formats.in.FlexReader
 
MeasurementDataHandler(String) - Constructor for class loci.formats.in.CV7000Reader.MeasurementDataHandler
 
MeasurementDetailHandler() - Constructor for class loci.formats.in.CV7000Reader.MeasurementDetailHandler
 
measurementFiles - Variable in class loci.formats.in.FlexReader
 
measurementFolder - Variable in class loci.formats.in.CellVoyagerReader
 
MeasurementHandler() - Constructor for class loci.formats.in.ColumbusReader.MeasurementHandler
 
measurementID - Variable in class loci.formats.in.ColumbusReader.MeasurementHandler
 
measurementID - Variable in class loci.formats.in.OperettaReader.OperettaHandler
 
measurementName - Variable in class loci.formats.in.ColumbusReader.MeasurementHandler
 
measurementPath - Variable in class loci.formats.in.CV7000Reader
 
measurementResultFile - Variable in class loci.formats.in.CellVoyagerReader
 
MeasurementSettingsHandler() - Constructor for class loci.formats.in.CV7000Reader.MeasurementSettingsHandler
 
measurementTime - Variable in class loci.formats.in.OperettaReader.OperettaHandler
 
medianFilter() - Method in class loci.plugins.util.RecordedImageProcessor
 
MEDICAL_DOMAIN - Static variable in class loci.formats.FormatTools
Identifies the medical imaging domain.
medium - Variable in class loci.formats.in.ZeissCZIReader
 
medium - Variable in class loci.formats.in.ZeissLSMReader.Laser
 
MEM_MODEL - Static variable in class loci.formats.in.CellSensReader
 
memBank - Variable in class loci.formats.in.SDTInfo
 
memoFile - Variable in class loci.formats.Memoizer
 
Memoizer - Class in loci.formats
ReaderWrapper implementation which caches the state of the delegate (including and other ReaderWrapper instances) after Memoizer.setId(String) has been called.
Memoizer() - Constructor for class loci.formats.Memoizer
Constructs a memoizer around a new ImageReader creating memo files under the same directory as the original file only if the call to Memoizer.setId(java.lang.String) takes longer than 100L in milliseconds.
Memoizer(long) - Constructor for class loci.formats.Memoizer
Constructs a memoizer around a new ImageReader creating memo files under the same directory as the original file only if the call to Memoizer.setId(java.lang.String) takes longer than minimumElapsed in milliseconds.
Memoizer(long, File) - Constructor for class loci.formats.Memoizer
Constructs a memoizer around a new ImageReader creating memo file files under the directory argument including the full path of the original file only if the call to Memoizer.setId(java.lang.String) takes longer than minimumElapsed in milliseconds.
Memoizer(IFormatReader) - Constructor for class loci.formats.Memoizer
Constructs a memoizer around the given IFormatReader creating memo files under the same directory as the original file only if the call to Memoizer.setId(java.lang.String) takes longer than 100L in milliseconds.
Memoizer(IFormatReader, long) - Constructor for class loci.formats.Memoizer
Constructs a memoizer around the given IFormatReader creating memo files under the same directory as the original file only if the call to Memoizer.setId(java.lang.String) takes longer than minimumElapsed in milliseconds.
Memoizer(IFormatReader, long, File) - Constructor for class loci.formats.Memoizer
Constructs a memoizer around the given IFormatReader creating memo files under the directory argument including the full path of the original file only if the call to Memoizer.setId(java.lang.String) takes longer than minimumElapsed in milliseconds.
Memoizer.Deser - Interface in loci.formats
 
Memoizer.KryoDeser - Class in loci.formats
 
Memoizer.RandomAccessDeser - Class in loci.formats
Helper implementation that can be used to implement Memoizer.Deser classes for libraries working solely with byte arrays.
MemoryDialog - Class in loci.plugins.in
Bio-Formats Importer memory usage confirmation dialog box.
MemoryDialog(ImportProcess) - Constructor for class loci.plugins.in.MemoryDialog
Creates a memory confirmation dialog for the Bio-Formats Importer.
merge(Map<String, Object>, Map<String, Object>, String) - Static method in class loci.formats.MetadataTools
Merges the given lists of metadata, prepending the specified prefix for the destination keys.
merge - Variable in class loci.plugins.util.BFVirtualStack
 
MERGE_NAMES - Static variable in class loci.formats.in.BioRadReader
List of merge types.
mergeChannels(BufferedImage[]) - Static method in class loci.formats.gui.AWTImageTools
Merges the given images into a single multi-channel image.
mergeSubIFDs - Variable in class loci.formats.in.MinimalTiffReader
Merge SubIFDs into the main IFD list.
message - Variable in enum loci.plugins.in.ImportStep
 
meta - Variable in class loci.formats.in.OMETiffReader
 
meta - Variable in class loci.formats.in.PrairieReader
Format-specific metadata.
meta - Variable in class loci.plugins.in.ImportProcess
 
META_EXT - Static variable in class loci.formats.in.BDReader
 
metadata - Variable in class loci.formats.FormatReader
Hashtable containing metadata key/value pairs.
metadata - Variable in class loci.formats.in.MetamorphHandler
 
METADATA - Static variable in class loci.formats.in.MicromanagerReader
File containing extra metadata.
metadata - Variable in class loci.formats.in.ND2Handler
 
Metadata() - Constructor for class loci.formats.in.ZeissCZIReader.Metadata
 
metadata - Variable in class loci.formats.in.ZeissCZIReader.SubBlock
 
metadata - Variable in class loci.plugins.in.ImportProcess
 
metadata - Variable in class loci.plugins.util.DataBrowser
 
METADATA_KEYS - Static variable in class loci.formats.in.ZeissLSMReader
 
METADATA_LEVEL_DEFAULT - Static variable in class loci.formats.in.DynamicMetadataOptions
 
METADATA_LEVEL_KEY - Static variable in class loci.formats.in.DynamicMetadataOptions
 
METADATA_SUFFIXES - Static variable in class loci.formats.in.APLReader
 
METADATA_SUFFIXES - Static variable in class loci.formats.in.InCellReader
 
METADATA_SUFFIXES - Static variable in class loci.formats.in.ScanrReader
 
METADATA_TAG - Static variable in class loci.formats.in.NDPIReader
 
METADATA_XML_TAG - Static variable in class loci.formats.in.FlowSightReader
 
metadataComplete - Variable in class loci.formats.CoreMetadata
Indicates whether or not we are confident that all of the metadata stored within the file has been parsed.
MetadataConverter - Class in loci.formats.meta
Deprecated.
Use ome.xml.meta.MetadataConverter.
MetadataConverter() - Constructor for class loci.formats.meta.MetadataConverter
Deprecated.
Private constructor; all methods in MetadataConverter are static, so this should not be called.
metadataFile - Variable in class loci.formats.in.MicromanagerReader.Position
 
metadataFile - Variable in class loci.formats.in.OMETiffReader
 
metadataFiles - Variable in class loci.formats.in.BDReader
 
metadataFiles - Variable in class loci.formats.in.CellomicsReader
 
metadataFiles - Variable in class loci.formats.in.ColumbusReader
 
metadataFiles - Variable in class loci.formats.in.InCellReader
 
metadataFiles - Variable in class loci.formats.in.L2DReader
List of all metadata files in the dataset.
metadataFiles - Variable in class loci.formats.in.MicroCTReader
 
metadataFiles - Variable in class loci.formats.in.OperettaReader
 
metadataFiles - Variable in class loci.formats.in.ScanrReader
 
metadataIndex - Variable in class loci.formats.in.CellSensReader
 
metadataInPlanes - Variable in class loci.formats.in.SlidebookReader
 
metadataLevel - Variable in class loci.formats.in.DefaultMetadataOptions
 
MetadataLevel - Enum in loci.formats.in
 
MetadataLevel() - Constructor for enum loci.formats.in.MetadataLevel
 
MetadataList<T> - Class in loci.formats
A container of metadata for FormatReader and other reader implementations.
MetadataList() - Constructor for class loci.formats.MetadataList
 
MetadataList(MetadataList<T>) - Constructor for class loci.formats.MetadataList
Copy a list.
MetadataList(int) - Constructor for class loci.formats.MetadataList
Construct a list containing a specified number of primary elements.
MetadataList(int, int) - Constructor for class loci.formats.MetadataList
Construct a list containing a specified number of primary elements and a fixed number of secondary elements.
MetadataList(int[]) - Constructor for class loci.formats.MetadataList
Construct a list containing a specified number of primary and secondary elements.
metadataOffsets - Variable in class loci.formats.in.SlidebookReader
 
metadataOptions - Variable in class loci.formats.FormatHandler
Metadata parsing options.
MetadataOptions - Interface in loci.formats.in
Holds metadata-related options.
metadataPosition - Variable in class loci.formats.in.ZeissCZIReader.FileHeader
 
metadataRetrieve - Variable in class loci.formats.FormatWriter
Current metadata retrieval object.
MetadataRetrieve - Interface in loci.formats.meta
 
metadataSize - Variable in class loci.formats.in.ZeissCZIReader.SubBlock
 
metadataStore - Variable in class loci.formats.FormatReader
Current metadata store.
MetadataStore - Interface in loci.formats.meta
 
MetadataTools - Class in loci.formats
A utility class for working with metadata objects, including MetadataStore, MetadataRetrieve, and OME-XML strings.
MetadataTools() - Constructor for class loci.formats.MetadataTools
 
metadataType - Variable in enum loci.formats.tiff.PhotoInterp
Metadata type of the photometric interpretation.
metaFile - Variable in class loci.formats.in.OMETiffReader
 
MetakitService - Interface in loci.formats.services
Interface defining methods for interacting with the OME Metakit library.
MetakitServiceImpl - Class in loci.formats.services
Implementation of MetakitService for interacting with the OME Metakit library.
MetakitServiceImpl() - Constructor for class loci.formats.services.MetakitServiceImpl
 
METAMORPH_ID - Static variable in class loci.formats.in.MetamorphReader
 
MetamorphHandler - Class in loci.formats.in
MetamorphTiffReader is the file format reader for TIFF files produced by Metamorph software version 7.5 and above.
MetamorphHandler() - Constructor for class loci.formats.in.MetamorphHandler
 
MetamorphHandler(Hashtable) - Constructor for class loci.formats.in.MetamorphHandler
 
MetamorphReader - Class in loci.formats.in
Reader is the file format reader for Metamorph STK files.
MetamorphReader() - Constructor for class loci.formats.in.MetamorphReader
Constructs a new Metamorph reader.
MetamorphTiffReader - Class in loci.formats.in
MetamorphTiffReader is the file format reader for TIFF files produced by Metamorph software version 7.5 and above.
MetamorphTiffReader() - Constructor for class loci.formats.in.MetamorphTiffReader
Constructs a new Metamorph TIFF reader.
MetamorphTiffReader.NumericComparator - Class in loci.formats.in
 
MetamorphTiffReader.Well - Class in loci.formats.in
 
metaWindow - Variable in class loci.plugins.util.DataBrowser
 
METER_MULTIPLY - Static variable in class loci.formats.in.LIFReader
 
METERING_MODE - Static variable in class loci.formats.tiff.IFD
 
method - Variable in class loci.plugins.util.RecordedImageProcessor.MethodEntry
 
MethodEntry() - Constructor for class loci.plugins.util.RecordedImageProcessor.MethodEntry
 
methodStack - Variable in class loci.plugins.util.RecordedImageProcessor
 
methodStacks - Variable in class loci.plugins.util.BFVirtualStack
 
MIASReader - Class in loci.formats.in
MIASReader is the file format reader for Maia Scientific MIAS-2 datasets.
MIASReader() - Constructor for class loci.formats.in.MIASReader
Constructs a new MIAS reader.
MIASReader.AnalysisFile - Class in loci.formats.in
 
MicroCTReader - Class in loci.formats.in
MicroCTReader is the file format reader for VFF files from a GE MicroCT scanner.
MicroCTReader() - Constructor for class loci.formats.in.MicroCTReader
Constructs a new MicroCT reader.
MicromanagerHandler() - Constructor for class loci.formats.in.MicromanagerReader.MicromanagerHandler
 
MicromanagerReader - Class in loci.formats.in
MicromanagerReader is the file format reader for Micro-Manager files.
MicromanagerReader() - Constructor for class loci.formats.in.MicromanagerReader
Constructs a new Micromanager reader.
MicromanagerReader.Index - Class in loci.formats.in
 
MicromanagerReader.MicromanagerHandler - Class in loci.formats.in
SAX handler for parsing Acqusition.xml.
MicromanagerReader.Position - Class in loci.formats.in
 
microscopeModel - Variable in class loci.formats.in.FEITiffReader
 
microscopeModels - Variable in class loci.formats.in.LIFReader
 
microscopyMode - Variable in class loci.formats.in.ImarisHDFReader
 
microSecPerFrame - Variable in class loci.formats.out.AVIWriter
 
MIKROSCAN_IMAGE_DESCRIPTION_PREFIX - Static variable in class loci.formats.in.MikroscanTiffReader
TIFF image description prefix for Mikroscan TIF files.
MikroscanTiffReader - Class in loci.formats.in
MikroscanTiffReader is the file format reader for Mikroscan TIFF files.
MikroscanTiffReader() - Constructor for class loci.formats.in.MikroscanTiffReader
Constructs a new Mikroscan TIF reader.
min - Variable in class loci.formats.in.InCellReader.Image
 
min(double) - Method in class loci.plugins.util.RecordedImageProcessor
 
MIN_BROWSER_WIDTH - Static variable in class loci.plugins.util.DataBrowser
 
MIN_PRIORITY - Static variable in interface loci.formats.cache.ICacheStrategy
 
MIN_SAMPLE_VALUE - Static variable in class loci.formats.tiff.IFD
 
minAdcRate - Variable in class loci.formats.in.SDTInfo
 
minC - Variable in class loci.formats.in.CV7000Reader.MinMax
 
minCfdRate - Variable in class loci.formats.in.SDTInfo
(-1.0 - not set).
MINCReader - Class in loci.formats.in
MINCReader is the file format reader for MINC MRI files.
MINCReader() - Constructor for class loci.formats.in.MINCReader
Constructs a new MINC reader.
MINIMAL_TAGS - Static variable in class loci.formats.in.FlowSightReader
The tags that must be present for this reader to function properly
MinimalInCellHandler() - Constructor for class loci.formats.in.InCellReader.MinimalInCellHandler
 
MinimalTiffReader - Class in loci.formats.in
MinimalTiffReader is the superclass for file format readers compatible with or derived from the TIFF 6.0 file format.
MinimalTiffReader() - Constructor for class loci.formats.in.MinimalTiffReader
Constructs a new MinimalTiffReader.
MinimalTiffReader(String, String) - Constructor for class loci.formats.in.MinimalTiffReader
Constructs a new MinimalTiffReader.
MinimalTiffReader(String, String[]) - Constructor for class loci.formats.in.MinimalTiffReader
Constructs a new MinimalTiffReader.
MINIMUM_MEMORY_PADDING - Static variable in class loci.plugins.in.MemoryDialog
Minimum amount of wiggle room for available memory, in bytes.
minimumElapsed - Variable in class loci.formats.Memoizer
Minimum number of milliseconds which must elapse during the call to Memoizer.setId(java.lang.String) before a memo file will be created.
minInten - Variable in class loci.formats.in.DeltavisionReader.DVExtHdrFields
Minimum intensity
MinMax() - Constructor for class loci.formats.in.CV7000Reader.MinMax
 
MinMaxCalculator - Class in loci.formats
Logic to compute minimum and maximum values for each channel.
MinMaxCalculator() - Constructor for class loci.formats.MinMaxCalculator
Constructs a MinMaxCalculator around a new image reader.
MinMaxCalculator(IFormatReader) - Constructor for class loci.formats.MinMaxCalculator
Constructs a MinMaxCalculator with the given reader.
minMaxCalculator - Variable in class loci.plugins.in.ImportProcess
 
minMaxDone - Variable in class loci.formats.MinMaxCalculator
Number of planes for which min/max computations have been completed.
minMaxStore - Variable in class loci.formats.MinMaxCalculator
Consumer of channel global minima and maxima
minorVersion - Variable in class loci.formats.in.ZeissCZIReader.FileHeader
 
minSyncRate - Variable in class loci.formats.in.SDTInfo
Minimum rates during the measurement.
minT - Variable in class loci.formats.in.CV7000Reader.MinMax
 
minT - Variable in class loci.formats.in.OIRReader
 
minTacRate - Variable in class loci.formats.in.SDTInfo
 
minValue() - Method in class loci.plugins.util.RecordedImageProcessor
 
minX - Variable in class loci.formats.in.ImarisHDFReader
 
minY - Variable in class loci.formats.in.ImarisHDFReader
 
minZ - Variable in class loci.formats.in.CV7000Reader.MinMax
 
minZ - Variable in class loci.formats.in.ImarisHDFReader
 
minZ - Variable in class loci.formats.in.OIRReader
 
mipmapLevel - Variable in class loci.formats.in.BDVReader.H5Coordinate
 
MIRROR_H - Static variable in class loci.formats.in.CellSensReader
 
MIRROR_V - Static variable in class loci.formats.in.CellSensReader
 
MISSING - Static variable in class loci.plugins.config.LibraryEntry
HTML markup for missing library.
MISSING_VERSION_CODE - Static variable in class loci.plugins.config.LibraryEntry
Version code to indicate a missing library.
MissingLibraryException - Exception in loci.formats
MissingLibraryException is the exception thrown when a particular data stream or filename requires a library that is not present on the system.
MissingLibraryException() - Constructor for exception loci.formats.MissingLibraryException
 
MissingLibraryException(String) - Constructor for exception loci.formats.MissingLibraryException
 
MissingLibraryException(String, Throwable) - Constructor for exception loci.formats.MissingLibraryException
 
MissingLibraryException(Throwable) - Constructor for exception loci.formats.MissingLibraryException
 
MJPBCodec - Class in loci.formats.codec
Methods for compressing and decompressing QuickTime Motion JPEG-B data.
MJPBCodec() - Constructor for class loci.formats.codec.MJPBCodec
 
MJPBCodecOptions - Class in loci.formats.codec
Options for compressing and decompressing MJPB data.
MJPBCodecOptions() - Constructor for class loci.formats.codec.MJPBCodecOptions
 
MJPEG_HUFFMAN_TABLE - Static variable in class loci.formats.in.AVIReader
Huffman table for MJPEG data.
MM_JSON_TAG - Static variable in class loci.formats.in.MicromanagerReader
 
MMHEADER - Static variable in class loci.formats.in.FluoviewReader
Private TIFF tags
mmPlanes - Variable in class loci.formats.in.MetamorphReader
 
MMSTAMP - Static variable in class loci.formats.in.FluoviewReader
 
MNG_MAGIC_BYTES - Static variable in class loci.formats.in.MNGReader
 
MNGReader - Class in loci.formats.in
MNGReader is the file format reader for Multiple-image Network Graphics (MNG) files.
MNGReader() - Constructor for class loci.formats.in.MNGReader
Constructs a new MNG reader.
MNGReader.SeriesInfo - Class in loci.formats.in
 
mod - Variable in class loci.formats.in.SDTInfo
Module number.
modality - Variable in class loci.formats.in.ND2Handler
 
model - Variable in class loci.formats.in.BioRadSCNReader
 
MODEL - Static variable in class loci.formats.in.FluoviewReader
 
model - Variable in class loci.formats.in.FluoviewReader
 
model - Variable in class loci.formats.in.LeicaHandler.Detector
 
model - Variable in class loci.formats.in.ZeissLSMReader.Laser
 
MODEL - Static variable in class loci.formats.tiff.IFD
 
modFpgaVer - Variable in class loci.formats.in.SDTInfo
New in v.8.4.
modSerNo - Variable in class loci.formats.in.SDTInfo
Serial number of the module.
modType - Variable in class loci.formats.in.SDTInfo
Module type.
modTypeCode - Variable in class loci.formats.in.SDTInfo
 
modulo - Variable in class loci.formats.meta.ModuloAnnotation
 
Modulo - Class in loci.formats
Represents a subdimension of Z, C, or T as needed for supporting Modulo annotations.
Modulo(String) - Constructor for class loci.formats.Modulo
 
Modulo(Modulo) - Constructor for class loci.formats.Modulo
 
MODULO_NS - Static variable in class loci.formats.meta.ModuloAnnotation
 
ModuloAnnotation - Class in loci.formats.meta
 
ModuloAnnotation() - Constructor for class loci.formats.meta.ModuloAnnotation
 
moduloC - Variable in class loci.formats.CoreMetadata
 
moduloT - Variable in class loci.formats.CoreMetadata
 
moduloZ - Variable in class loci.formats.CoreMetadata
 
MolecularImagingReader - Class in loci.formats.in
MolecularImagingReader is the file format reader for Molecular Imaging files.
MolecularImagingReader() - Constructor for class loci.formats.in.MolecularImagingReader
Constructs a new Molecular Imaging reader.
montageIndex - Variable in class loci.formats.in.FluoviewReader
 
montageOffsets - Variable in class loci.formats.in.FluoviewReader
 
mosaics - Variable in class loci.formats.in.ZeissCZIReader
 
mouseClicked(MouseEvent) - Method in class loci.plugins.in.MainDialog
 
mouseDragged(MouseEvent) - Method in class loci.formats.gui.ImageViewer
Handles cursor probes.
mouseEntered(MouseEvent) - Method in class loci.plugins.in.MainDialog
Focuses the component upon mouseover.
mouseExited(MouseEvent) - Method in class loci.plugins.in.MainDialog
 
mouseMoved(MouseEvent) - Method in class loci.formats.gui.ImageViewer
Handles cursor probes.
mousePressed(MouseEvent) - Method in class loci.plugins.in.MainDialog
 
mouseReleased(MouseEvent) - Method in class loci.plugins.in.MainDialog
 
mouseWheelMoved(MouseWheelEvent) - Method in class loci.plugins.util.DataBrowser
 
moveTo(int, int) - Method in class loci.plugins.util.RecordedImageProcessor
 
MRC_SUFFIXES - Static variable in class loci.formats.in.MRCReader
 
MRCReader - Class in loci.formats.in
MRCReader is the file format reader for MRC files.
MRCReader() - Constructor for class loci.formats.in.MRCReader
Constructs a new MRC reader.
mReserved1 - Variable in class loci.formats.in.SDTInfo
 
mReserved2 - Variable in class loci.formats.in.SDTInfo
 
MRW_MAGIC_STRING - Static variable in class loci.formats.in.MRWReader
 
MRWReader - Class in loci.formats.in
MRWReader is the file format reader for Minolta MRW files.
MRWReader() - Constructor for class loci.formats.in.MRWReader
Constructs a new MRW reader.
MS_VIDEO - Static variable in class loci.formats.in.AVIReader
 
msg - Variable in class loci.formats.FilePattern
Error message generated during file pattern construction.
msg(String) - Method in class loci.formats.gui.DataConverter
 
MSRLE - Static variable in class loci.formats.in.AVIReader
Supported compression types.
MSRLECodec - Class in loci.formats.codec
Methods for compressing and decompressing data using Microsoft RLE.
MSRLECodec() - Constructor for class loci.formats.codec.MSRLECodec
 
MSVideoCodec - Class in loci.formats.codec
Methods for compressing and decompressing data using Microsoft Video 1.
MSVideoCodec() - Constructor for class loci.formats.codec.MSVideoCodec
 
mtResol - Variable in class loci.formats.in.SDTInfo
Macro time clock in 0.1 ns units.
MULTI_PHOTON - Static variable in class loci.formats.in.LegacyND2Reader
 
MultiBand() - Constructor for class loci.formats.in.LeicaHandler.MultiBand
 
multiBands - Variable in class loci.formats.in.LeicaHandler
 
MULTIDIM_IMAGE_VOLUME - Static variable in class loci.formats.in.CellSensReader
 
MULTIDIM_STACK_PROPERTIES - Static variable in class loci.formats.in.CellSensReader
 
multifile - Variable in class loci.formats.in.ZeissTIFFReader.TIFFInfo
 
multiply(double) - Method in class loci.plugins.util.RecordedImageProcessor
 
MUST_GROUP - Static variable in class loci.formats.FormatTools
File grouping options.
MUST_GROUP - Static variable in interface loci.formats.IFormatReader
File grouping options.
myReader - Variable in class loci.formats.gui.ImageViewer
Current format reader.
myWriter - Variable in class loci.formats.gui.ImageViewer
Current format writer.

N

N_ACCUMULATIONS - Static variable in class loci.formats.in.FluoviewReader
 
N_FRAMES - Static variable in class loci.formats.in.FluoviewReader
 
na - Variable in class loci.formats.in.ND2Handler
 
na - Variable in class loci.formats.in.OIRReader.Objective
 
NAFReader - Class in loci.formats.in
NAFReader is the file format reader for Hamamatsu Aquacosmos NAF files.
NAFReader() - Constructor for class loci.formats.in.NAFReader
Constructs a new NAF reader.
name - Variable in enum loci.formats.codec.JPEG2000BoxType
The name of the box type.
name - Variable in enum loci.formats.codec.JPEG2000SegmentMarker
The name of the segment marker.
name - Variable in enum loci.formats.in.BaseZeissReader.Charset
 
name - Variable in class loci.formats.in.BaseZeissReader.Layer
 
name - Variable in class loci.formats.in.BaseZeissReader.Shape
 
name - Variable in class loci.formats.in.CellSensReader.Pyramid
 
name - Variable in class loci.formats.in.CellVoyagerReader.ChannelInfo
 
name - Variable in class loci.formats.in.CV7000Reader.LightSource
 
name - Variable in class loci.formats.in.CV7000Reader.WPIHandler
 
name - Variable in class loci.formats.in.FV1000Reader.ChannelData
 
name - Variable in class loci.formats.in.IM3Reader.IM3Record
 
name - Variable in class loci.formats.in.IM3Reader.Spectrum
 
name - Variable in class loci.formats.in.LeicaHandler.Channel
 
name - Variable in class loci.formats.in.LeicaHandler.ROI
 
name - Variable in class loci.formats.in.LeicaReader.Detector
 
name - Variable in class loci.formats.in.LeicaSCNReader.Image
 
name - Variable in class loci.formats.in.LeicaSCNReader.ImageCollection
 
name - Variable in class loci.formats.in.LiFlimReader.ROI
 
name - Variable in class loci.formats.in.LIFReader.ROI
 
name - Variable in class loci.formats.in.MicromanagerReader.Position
 
name - Variable in class loci.formats.in.NativeND2Reader.ChunkMapEntry
 
name - Variable in class loci.formats.in.OIRReader.Channel
 
name - Variable in class loci.formats.in.OIRReader.Laser
 
name - Variable in class loci.formats.in.OIRReader.Objective
 
name - Variable in class loci.formats.in.ZeissCZIReader.AttachmentEntry
 
name - Variable in class loci.formats.in.ZeissCZIReader.Channel
 
name - Variable in class loci.formats.in.ZeissLSMReader.DataChannel
 
name - Variable in class loci.formats.in.ZeissLSMReader.IlluminationChannel
 
name - Variable in class loci.formats.in.ZeissLSMReader.Recording
 
name - Variable in enum loci.formats.tiff.PhotoInterp
Given name of the photometric interpretation.
name - Variable in class loci.plugins.config.LibraryEntry
 
name - Variable in class loci.plugins.in.IdDialog
 
name - Variable in class loci.plugins.util.RecordedImageProcessor.MethodEntry
 
nameLength - Variable in class loci.formats.in.LeicaReader
 
names - Variable in class loci.formats.in.FlexReader.FlexHandler
 
names - Static variable in class loci.plugins.shortcut.ShortcutPanel
Details for installed plugins.
NAMESPACE - Static variable in class loci.formats.ome.OMEPyramidStore
 
nameStack - Variable in class loci.formats.in.LeicaHandler
 
nameStack - Variable in class loci.formats.in.LeicaSCNReader.LeicaSCNHandler
 
nameStack - Variable in class loci.formats.in.ZeissTIFFHandler
 
NATIVE_LIB_CLASS - Static variable in class loci.formats.services.JPEGTurboServiceImpl
 
NativeND2Reader - Class in loci.formats.in
NativeND2Reader is the file format reader for Nikon ND2 files.
NativeND2Reader() - Constructor for class loci.formats.in.NativeND2Reader
Constructs a new ND2 reader.
NativeND2Reader.ChunkMapEntry - Class in loci.formats.in
 
NativeQTReader - Class in loci.formats.in
NativeQTReader is the file format reader for QuickTime movie files.
NativeQTReader() - Constructor for class loci.formats.in.NativeQTReader
Constructs a new QuickTime reader.
nativeReader - Variable in class loci.formats.DelegateReader
Native reader.
nativeReaderInitialized - Variable in class loci.formats.DelegateReader
Flag indicating that the native reader was successfully initialized.
nBuffers - Variable in class loci.formats.in.SPCReader
 
nChannels - Variable in class loci.formats.gui.SignedColorModel
 
nChannels - Variable in class loci.formats.gui.UnsignedIntColorModel
 
nChannels - Variable in class loci.formats.in.InCellReader.MinimalInCellHandler
 
nChannels - Variable in class loci.formats.in.SPCReader
Number of spectral nChannels.
nColorPlanes - Variable in class loci.formats.in.PCXReader
 
nCols - Variable in class loci.formats.in.FlexReader
 
nCols - Variable in class loci.formats.in.HamamatsuVMSReader
 
ncx - Variable in class loci.formats.in.SDTInfo
 
ncy - Variable in class loci.formats.in.SDTInfo
 
ND2_MAGIC_BYTES_1 - Static variable in class loci.formats.in.NativeND2Reader
 
ND2_MAGIC_BYTES_2 - Static variable in class loci.formats.in.NativeND2Reader
 
ND2Handler - Class in loci.formats.in
DefaultHandler implementation for handling XML produced by Nikon Elements.
ND2Handler(CoreMetadataList, int) - Constructor for class loci.formats.in.ND2Handler
 
ND2Handler(CoreMetadataList, boolean, int) - Constructor for class loci.formats.in.ND2Handler
 
ND2Reader - Class in loci.formats.in
ND2Reader is the file format reader for Nikon ND2 files.
ND2Reader() - Constructor for class loci.formats.in.ND2Reader
Constructs a new ND2 reader.
ND2Widgets - Class in loci.plugins.config
Custom widgets for configuring Bio-Formats ND2 support.
ND2Widgets() - Constructor for class loci.plugins.config.ND2Widgets
 
ND_SUFFIX - Static variable in class loci.formats.in.MetamorphReader
 
ndFilename - Variable in class loci.formats.in.MetamorphReader
 
ndFilter - Variable in class loci.formats.in.DeltavisionReader.DVExtHdrFields
Neutral density value.
ndFilters - Variable in class loci.formats.in.DeltavisionReader
 
ndFilters - Variable in class loci.formats.in.SlidebookReader
 
nDimensions - Variable in class loci.formats.in.CellSensReader
 
nDimensions - Variable in class loci.formats.in.NiftiReader
 
ndpiFiles - Variable in class loci.formats.in.NDPISReader
 
NDPIReader - Class in loci.formats.in
NDPIReader is the file format reader for Hamamatsu .ndpi files.
NDPIReader() - Constructor for class loci.formats.in.NDPIReader
Constructs a new NDPI reader.
NDPISReader - Class in loci.formats.in
NDPISReader is the file format reader for Hamamatsu .ndpis files.
NDPISReader() - Constructor for class loci.formats.in.NDPISReader
Constructs a new NDPIS reader.
needLegacy - Variable in class loci.formats.out.QTWriter
Whether we need the legacy writer.
needMem - Variable in class loci.plugins.in.MemoryDialog
Required memory for the dataset, in bytes.
needPrompt() - Method in class loci.plugins.in.ColorDialog
 
needPrompt() - Method in class loci.plugins.in.CropDialog
 
needPrompt() - Method in class loci.plugins.in.FilePatternDialog
 
needPrompt() - Method in class loci.plugins.in.IdDialog
 
needPrompt() - Method in class loci.plugins.in.ImporterDialog
 
needPrompt() - Method in class loci.plugins.in.LocationDialog
 
needPrompt() - Method in class loci.plugins.in.MainDialog
 
needPrompt() - Method in class loci.plugins.in.MemoryDialog
 
needPrompt() - Method in class loci.plugins.in.RangeDialog
 
needPrompt() - Method in class loci.plugins.in.SeriesDialog
 
needPrompt() - Method in class loci.plugins.in.SwapDialog
 
needPrompt() - Method in class loci.plugins.in.UpgradeDialog
 
NEF_SUFFIX - Static variable in class loci.formats.in.NikonReader
 
netcdf - Variable in class loci.formats.in.ImarisHDFReader
 
netcdf - Variable in class loci.formats.in.MINCReader
 
netcdf - Variable in class loci.formats.in.VeecoReader
 
netCDFFile - Variable in class loci.formats.services.NetCDFServiceImpl
NetCDF file instance.
NetCDFService - Interface in loci.formats.services
Utility class for working with NetCDF/HDF files.
NetCDFServiceImpl - Class in loci.formats.services
Utility class for working with NetCDF/HDF files.
NetCDFServiceImpl() - Constructor for class loci.formats.services.NetCDFServiceImpl
Default constructor.
NEW_MDIM_VOLUME_HEADER - Static variable in class loci.formats.in.CellSensReader
 
NEW_SUBFILE_TYPE - Static variable in class loci.formats.tiff.IFD
 
NEW_TYPE - Static variable in class loci.formats.in.DeltavisionReader
 
NEW_VOLUME_HEADER - Static variable in class loci.formats.in.CellSensReader
 
newFileType - Variable in class loci.formats.in.DeltavisionReader
 
newOrder - Variable in class loci.formats.AxisGuesser
Adjusted ordering of internal dimensional axes.
newVersionAvailable(String) - Method in class loci.formats.UpgradeChecker
Contact the OME registry and return true if a new version is available.
newVersionAvailable(String, String) - Method in class loci.formats.UpgradeChecker
Contact the OME registry and return true if a new version is available.
nextBlockOffs - Variable in class loci.formats.in.SDTInfo
Offset to the data block header of the next data block.
nextCamera - Variable in class loci.formats.in.FlexReader.FlexHandler
 
nextChannel - Variable in class loci.formats.in.LeicaHandler
 
nextChannel - Variable in class loci.formats.in.LeicaReader
 
nextChName - Variable in class loci.formats.in.BaseZeissReader
 
nextDetectChannel - Variable in class loci.formats.in.ZeissLSMReader
 
nextDetector - Variable in class loci.formats.in.LeicaReader
 
nextDetector - Variable in class loci.formats.in.ZeissLSMReader
 
nextDichroic - Variable in class loci.formats.in.FlexReader.FlexHandler
 
nextDichroic - Variable in class loci.formats.in.ZeissLSMReader
 
nextDichroicChannel - Variable in class loci.formats.in.ZeissLSMReader
 
nextEmWave - Variable in class loci.formats.in.BaseZeissReader
 
nextExWave - Variable in class loci.formats.in.BaseZeissReader
 
nextFilter - Variable in class loci.formats.in.FlexReader.FlexHandler
 
nextFilter - Variable in class loci.formats.in.LeicaHandler
 
nextFilter - Variable in class loci.formats.in.ZeissLSMReader
 
nextFilterSet - Variable in class loci.formats.in.FlexReader.FlexHandler
 
nextIllumChannel - Variable in class loci.formats.in.ZeissLSMReader
 
nextImage - Variable in class loci.formats.in.FlexReader.FlexHandler
 
nextLaser - Variable in class loci.formats.in.FlexReader.FlexHandler
 
nextLaser - Variable in class loci.formats.in.ZeissLSMReader
 
nextLetter() - Method in class loci.formats.ResourceNamer
Increments the internal alphabet pointer to the next element of the alphabet.
nextObjective - Variable in class loci.formats.in.FlexReader.FlexHandler
 
nextPlate - Variable in class loci.formats.in.FlexReader.FlexHandler
 
nextPlate - Variable in class loci.formats.in.InCellReader.InCellHandler
 
nextReadPosition - Variable in class loci.formats.in.OBFReader.State
 
nextROI - Variable in class loci.formats.in.LeicaHandler
 
nextSequenceNumber - Variable in class loci.formats.out.APNGWriter
 
nextSliderRef - Variable in class loci.formats.in.FlexReader.FlexHandler
 
nextTag - Variable in class loci.formats.in.OpenlabReader
 
nextXPos - Variable in class loci.formats.in.ScanrReader.ScanrHandler
 
nextYPos - Variable in class loci.formats.in.ScanrReader.ScanrHandler
 
nFields - Variable in class loci.formats.in.ColumbusReader
 
nFiles - Variable in class loci.formats.in.FlexReader
 
nFrames - Variable in class loci.formats.in.SPCReader
 
ni - Variable in class loci.formats.in.BrukerReader
 
NiftiReader - Class in loci.formats.in
NiftiReader is the file format reader for NIfTI files.
NiftiReader() - Constructor for class loci.formats.in.NiftiReader
Constructs a new NIfTI reader.
NIKON_XML_TAG - Static variable in class loci.formats.in.NikonElementsTiffReader
 
NIKON_XML_TAG_2 - Static variable in class loci.formats.in.NikonElementsTiffReader
 
NikonCodec - Class in loci.formats.codec
This class implements Nikon decompression.
NikonCodec() - Constructor for class loci.formats.codec.NikonCodec
 
NikonCodecOptions - Class in loci.formats.codec
Options for compressing and decompressing Nikon NEF data.
NikonCodecOptions() - Constructor for class loci.formats.codec.NikonCodecOptions
 
NikonElementsTiffReader - Class in loci.formats.in
NikonElementsTiffReader is the file format reader for TIFF files produced by Nikon Elements.
NikonElementsTiffReader() - Constructor for class loci.formats.in.NikonElementsTiffReader
 
NikonReader - Class in loci.formats.in
NikonReader is the file format reader for Nikon NEF (TIFF) files.
NikonReader() - Constructor for class loci.formats.in.NikonReader
Constructs a new Nikon reader.
NikonTiffReader - Class in loci.formats.in
NikonTiffReader is the file format reader for Nikon TIFF files.
NikonTiffReader() - Constructor for class loci.formats.in.NikonTiffReader
 
nImages - Variable in class loci.formats.in.ND2Handler
 
NL - Static variable in class loci.formats.in.ICSReader
Newline characters.
NL - Static variable in class loci.formats.tools.AsciiImage
 
nLines - Variable in class loci.formats.in.SPCReader
 
no - Variable in class loci.formats.in.CV7000Reader.Plane
 
NO_ASSOC_ERROR - Static variable in class org.libjpegturbo.turbojpeg.TJCompressor
 
NO_ASSOC_ERROR - Static variable in class org.libjpegturbo.turbojpeg.TJDecompressor
 
NO_J2K_MSG - Static variable in class loci.formats.services.JAIIIOServiceImpl
 
NO_JAI_MSG - Static variable in class loci.formats.in.TiffJAIReader
 
NO_JHDF_MSG - Static variable in class loci.formats.services.JHDFServiceImpl
 
NO_LICENSE_MSG - Static variable in class loci.formats.services.LuraWaveServiceImpl
Message to display if no LuraWave license code is given.
NO_LURAWAVE_MSG - Static variable in class loci.formats.services.LuraWaveServiceImpl
Message displayed if the LuraWave LWF decoder library is not found.
NO_NETCDF_MSG - Static variable in class loci.formats.services.NetCDFServiceImpl
 
NO_NIKON_MSG - Static variable in class loci.formats.in.LegacyND2Reader
 
NO_OME_XML_MSG - Static variable in class loci.formats.services.OMEXMLServiceImpl
 
NO_QT_MSG - Static variable in class loci.formats.gui.LegacyQTTools
 
NO_WLZ_MSG - Static variable in class loci.formats.in.WlzReader
 
NO_WLZ_MSG - Static variable in class loci.formats.out.WlzWriter
 
NO_WLZ_MSG - Static variable in class loci.formats.services.WlzServiceImpl
 
node - Variable in class loci.formats.gui.XMLCellRenderer.XMLItem
 
NoExtensionFileFilter - Class in loci.formats.gui
A file filter that selects files with no extension, for use with a JFileChooser.
NoExtensionFileFilter() - Constructor for class loci.formats.gui.NoExtensionFileFilter
 
noise(double) - Method in class loci.plugins.util.RecordedImageProcessor
 
NOISE_REDUCTION - Static variable in class loci.formats.in.CellSensReader
 
NON_GRAPHICS_DOMAINS - Static variable in class loci.formats.FormatTools
List of non-graphics domains.
NON_HCS_DOMAINS - Static variable in class loci.formats.FormatTools
List of non-HCS domains.
NON_SPECIAL_DOMAINS - Static variable in class loci.formats.FormatTools
List of domains that do not require special handling.
NONE - Static variable in class loci.formats.in.APNGReader
Filter types.
noOfDataBlocks - Variable in class loci.formats.in.SDTInfo
no_of_data_blocks valid only when in 0 ..
noOfMeasDescBlocks - Variable in class loci.formats.in.SDTInfo
 
noQT - Variable in class loci.formats.gui.LegacyQTTools
Flag indicating QuickTime for Java is not installed.
NORMAL_MENU - Static variable in class loci.plugins.shortcut.ShortcutPanel
Name of the 'Bio-Formats' submenu.
NORMAL_PRIORITY - Static variable in interface loci.formats.cache.ICacheStrategy
 
normalize() - Method in class loci.formats.in.LeicaHandler.ROI
Vertices and transformation values are not stored in pixel coordinates.
normalize() - Method in class loci.formats.in.LIFReader.ROI
Vertices and transformation values are not stored in pixel coordinates.
normalized - Variable in class loci.formats.in.LeicaHandler.ROI
 
normalized - Variable in class loci.formats.in.LIFReader.ROI
 
normalizeData - Variable in class loci.formats.FormatReader
Whether or not to normalize float data.
normalizeFilename(String, String) - Method in class loci.formats.in.OMETiffReader
 
noStitch - Variable in class loci.formats.FileStitcher
 
noSubresolutions - Variable in class loci.formats.in.MinimalTiffReader
 
Note() - Constructor for class loci.formats.in.BioRadReader.Note
 
NOTE_NAMES - Static variable in class loci.formats.in.BioRadReader
List of note types.
NOTE_TYPE_4D_SERIES - Static variable in class loci.formats.in.BioRadReader
 
NOTE_TYPE_ARROW - Static variable in class loci.formats.in.BioRadReader
 
NOTE_TYPE_COLLECT - Static variable in class loci.formats.in.BioRadReader
 
NOTE_TYPE_FILE1 - Static variable in class loci.formats.in.BioRadReader
 
NOTE_TYPE_FILE2 - Static variable in class loci.formats.in.BioRadReader
 
NOTE_TYPE_LINE - Static variable in class loci.formats.in.BioRadReader
 
NOTE_TYPE_LIVE - Static variable in class loci.formats.in.BioRadReader
 
NOTE_TYPE_MERGE - Static variable in class loci.formats.in.BioRadReader
 
NOTE_TYPE_NUMBER - Static variable in class loci.formats.in.BioRadReader
 
NOTE_TYPE_SCALEBAR - Static variable in class loci.formats.in.BioRadReader
 
NOTE_TYPE_STRUCTURE - Static variable in class loci.formats.in.BioRadReader
 
NOTE_TYPE_THRUVIEW - Static variable in class loci.formats.in.BioRadReader
 
NOTE_TYPE_USER - Static variable in class loci.formats.in.BioRadReader
 
NOTE_TYPE_VARIABLE - Static variable in class loci.formats.in.BioRadReader
 
notes - Variable in class loci.plugins.config.ConfigWindow
 
notes - Variable in class loci.plugins.config.LibraryEntry
 
noteStrings - Variable in class loci.formats.in.BioRadReader
 
notifyListeners(CacheEvent) - Method in class loci.formats.cache.Cache
Informs listeners of a cache update.
notifyListeners(CacheEvent) - Method in class loci.formats.cache.CacheStrategy
Informs listeners of a cache update.
notifyListeners(StatusEvent) - Method in class loci.plugins.in.ImagePlusReader
 
notifyListeners(StatusEvent) - Method in class loci.plugins.in.ImportProcess
 
nPixels - Variable in class loci.formats.in.SPCReader
 
nr - Variable in class loci.formats.in.BrukerReader
 
nRows - Variable in class loci.formats.in.FlexReader
 
nRows - Variable in class loci.formats.in.HamamatsuVMSReader
 
NRRD_MAGIC_STRING - Static variable in class loci.formats.in.NRRDReader
 
NRRDReader - Class in loci.formats.in
File format reader for NRRD files; see http://teem.sourceforge.net/nrrd.
NRRDReader() - Constructor for class loci.formats.in.NRRDReader
Constructs a new NRRD reader.
ns - Variable in class loci.formats.in.BrukerReader
 
nSlider - Variable in class loci.formats.gui.ImageViewer
 
nStreams - Variable in class loci.formats.tools.AmiraParameters
 
nTimebins - Variable in class loci.formats.in.SPCReader
Number of time bins in lifetime histogram.
num - Variable in class loci.formats.in.BioRadReader.Note
 
num - Variable in class org.libjpegturbo.turbojpeg.TJScalingFactor
Numerator
NUM_COMPONENTS - Static variable in class loci.formats.gui.TwoChannelColorSpace
 
NUM_DIMENSIONS - Static variable in class loci.formats.in.FV1000Reader
 
number - Variable in class loci.formats.in.CellVoyagerReader.WellInfo
 
NUMBER_OF_FRAMES - Static variable in class loci.formats.in.DicomReader
 
NUMBER_OF_INKS - Static variable in class loci.formats.tiff.IFD
 
numberBuffer - Variable in class loci.formats.in.AmiraReader.ASCII
 
NumberFilter - Class in loci.formats
NumberFilter is a helper filter for FilePattern.findPattern().
NumberFilter(String, String) - Constructor for class loci.formats.NumberFilter
Creates a filter for files containing a numerical block, sandwiched between the given strings.
numBlocks - Variable in class loci.formats.in.KLBReader
 
numBytes - Variable in class loci.formats.in.AliconaReader
Number of bytes per pixel (either 1 or 2).
numBytes - Variable in class loci.formats.out.QTWriter
Total number of pixel bytes.
numChannels - Variable in class loci.formats.in.LeicaHandler
 
numDatasets - Variable in class loci.formats.in.LeicaHandler
 
numDecompositionLevels - Variable in class loci.formats.codec.JPEG2000CodecOptions
The number of decomposition levels as would be provided to: J2KImageWriteParam.setNumDecompositionLevels(int) (WRITE).
numer - Variable in class loci.formats.tiff.TiffRational
Components of the rational's fractional representation.
numeric - Variable in class loci.formats.FilePatternBlock
Whether or not this is a numeric block.
NUMERICAL_APERTURE - Static variable in class loci.formats.in.CellSensReader
 
numericalAperture - Variable in class loci.formats.in.CellSensReader.Pyramid
 
NumericComparator() - Constructor for class loci.formats.in.MetamorphTiffReader.NumericComparator
 
numFloatsPerSection - Variable in class loci.formats.in.DeltavisionReader
 
numFrames - Variable in class loci.formats.out.APNGWriter
 
numFramesPointer - Variable in class loci.formats.out.APNGWriter
 
numIntsPerSection - Variable in class loci.formats.in.DeltavisionReader
The number of ints in each extended header section.
NUMOP - Static variable in class org.libjpegturbo.turbojpeg.TJTransform
The number of lossless transform operations
NUMPF - Static variable in class org.libjpegturbo.turbojpeg.TJ
The number of pixel formats
numPixelBytes - Variable in class loci.formats.in.GatanReader
 
numRegions - Variable in class loci.formats.in.LiFlimReader
 
NUMSAMP - Static variable in class org.libjpegturbo.turbojpeg.TJ
The number of chrominance subsampling options
numSeries - Variable in class loci.formats.in.LeicaReader
Number of series in the file.
numSeries - Variable in class loci.formats.in.ND2Handler
 
numWritten - Variable in class loci.formats.out.LegacyQTWriter
Number of frames written.
numWritten - Variable in class loci.formats.out.QTWriter
 
nXFields - Variable in class loci.formats.in.NativeND2Reader
 
nXFields - Variable in class loci.formats.in.ND2Handler
 
nYFields - Variable in class loci.formats.in.ND2Handler
 

O

OB - Static variable in class loci.formats.in.DicomReader
 
OBFReader - Class in loci.formats.in
OBFReader is the file format reader for Imspector OBF files.
OBFReader() - Constructor for class loci.formats.in.OBFReader
 
OBFReader.Stack - Class in loci.formats.in
 
OBFReader.State - Class in loci.formats.in
 
OBJECT - Static variable in class loci.formats.in.BDVReader.H5Constants
 
OBJECT - Static variable in class loci.formats.in.CellH5Reader.CellH5Constants
 
OBJECT_DROPPED - Static variable in class loci.formats.cache.CacheEvent
Event type indicating an object has been removed from the cache.
OBJECT_LOADED - Static variable in class loci.formats.cache.CacheEvent
Event type indicating an object has been added to the cache.
objective - Variable in class loci.formats.in.BDReader
 
objective - Variable in class loci.formats.in.CV7000Reader.Channel
 
Objective() - Constructor for class loci.formats.in.OIRReader.Objective
 
OBJECTIVE_MAG - Static variable in class loci.formats.in.CellSensReader
 
OBJECTIVE_NAME - Static variable in class loci.formats.in.CellSensReader
 
OBJECTIVE_TYPE - Static variable in class loci.formats.in.CellSensReader
 
objectiveID - Variable in class loci.formats.in.CV7000Reader.Channel
 
objectiveIDs - Variable in class loci.formats.in.FlexReader
 
objectiveManufacturer - Variable in class loci.formats.in.FluoviewReader
 
objectiveModel - Variable in class loci.formats.in.ND2Handler
 
objectiveModels - Variable in class loci.formats.in.LIFReader
 
objectiveName - Variable in class loci.formats.in.CellSensReader.Pyramid
 
objectiveName - Variable in class loci.formats.in.FV1000Reader
 
objectiveNames - Variable in class loci.formats.in.CellSensReader.Pyramid
 
objectiveRefs - Variable in class loci.formats.in.FlexReader
 
objectives - Variable in class loci.formats.in.OIRReader
 
objectiveSettingsID - Variable in class loci.formats.in.ZeissCZIReader
 
objectiveTypes - Variable in class loci.formats.in.CellSensReader.Pyramid
 
objGType - Variable in class loci.formats.services.WlzServiceImpl
 
objMag - Variable in class loci.formats.in.LeicaSCNReader.Image
 
objType - Variable in class loci.formats.services.WlzServiceImpl
 
OBS - Static variable in class loci.formats.gui.AWTImageTools
ImageObserver for working with AWT images.
ocr - Variable in class loci.formats.in.LeicaSCNReader.ImageCollection
 
od - Variable in class loci.plugins.in.IdDialog
 
oddLocations - Variable in class loci.formats.in.DicomReader
 
OECF - Static variable in class loci.formats.tiff.IFD
 
offset - Variable in class loci.formats.in.APNGReader.PNGBlock
 
offset - Variable in class loci.formats.in.BDReader
 
offset - Variable in class loci.formats.in.BioRadGelReader
 
offset - Variable in class loci.formats.in.BioRadReader
 
offset - Variable in class loci.formats.in.CellSensReader.Pyramid
 
offset - Variable in class loci.formats.in.ICSReader
Offset to pixel data.
offset - Variable in class loci.formats.in.IM3Reader.IM3Record
 
offset - Variable in class loci.formats.in.IvisionReader
 
offset - Variable in class loci.formats.in.KhorosReader
Image offset.
offset - Variable in class loci.formats.in.LeicaHandler.Detector
 
offset - Variable in class loci.formats.in.LeicaReader.Detector
 
offset - Variable in class loci.formats.in.MRWReader
Offset to image data.
offset - Variable in class loci.formats.in.NRRDReader
Offset to pixel data.
offset - Variable in class loci.formats.in.OIRReader.Detector
 
offset - Variable in class loci.formats.in.OIRReader.PixelBlock
 
offset - Variable in class loci.formats.in.PCXReader
Offset to pixel data.
offset - Variable in class loci.formats.in.PGMReader
Offset to pixel data.
offset - Variable in class loci.formats.in.PSDReader
Offset to pixel data.
offset - Variable in class loci.formats.in.SDTInfo
 
offset - Variable in enum loci.formats.in.SPEReader.SpeHeaderEntry
 
offset - Variable in class loci.formats.in.TargaReader
 
offset - Variable in class loci.formats.in.VentanaReader.TIFFTile
 
offset - Variable in class loci.formats.services.JPEGTurboServiceImpl
 
OFFSET_HIGH_BYTES - Static variable in class loci.formats.in.NDPIReader
 
offsetFilePointer - Variable in class loci.formats.in.KLBReader
 
offsetOfFirstStream - Variable in class loci.formats.in.AmiraReader
 
offsetOfStream - Variable in class loci.formats.in.AmiraReader.HxZip
 
offsetPointCounter - Variable in class loci.formats.in.InCellReader
 
offsets - Variable in class loci.formats.in.AmiraReader.ASCII
 
offsets - Variable in class loci.formats.in.AmiraReader.HxRLE
 
offsets - Variable in class loci.formats.in.AVIReader
Offset to each plane.
offsets - Variable in class loci.formats.in.BaseZeissReader
 
offsets - Variable in class loci.formats.in.DicomReader
 
offsets - Variable in class loci.formats.in.FlexReader.FlexFile
 
offsets - Variable in class loci.formats.in.FluoviewReader
 
offsets - Variable in class loci.formats.in.ImarisReader
Offsets to each image.
offsets - Variable in class loci.formats.in.LIFReader
Offsets to memory blocks, paired with their corresponding description.
offsets - Variable in class loci.formats.in.MNGReader.SeriesInfo
 
offsets - Variable in class loci.formats.in.NAFReader
 
offsets - Variable in class loci.formats.in.NativeND2Reader
Array of image offsets.
offsets - Variable in class loci.formats.in.NativeQTReader
Offsets to each plane's pixel data.
offsets - Variable in class loci.formats.in.OpenlabRawReader
Offset to each image's pixel data.
offsets - Variable in class loci.formats.in.ZeissLMSReader
 
offsets - Variable in class loci.formats.out.QTWriter
Vector of plane offsets.
OIB_SUFFIX - Static variable in class loci.formats.in.FV1000Reader
 
oibMapping - Variable in class loci.formats.in.FV1000Reader
File mappings for OIB file.
OIF_SUFFIX - Static variable in class loci.formats.in.FV1000Reader
 
OIRReader - Class in loci.formats.in
OIRReader is the file format reader for Olympus .oir files.
OIRReader() - Constructor for class loci.formats.in.OIRReader
Constructs a new OIR reader.
OIRReader.Channel - Class in loci.formats.in
 
OIRReader.Detector - Class in loci.formats.in
 
OIRReader.Laser - Class in loci.formats.in
 
OIRReader.Objective - Class in loci.formats.in
 
OIRReader.PixelBlock - Class in loci.formats.in
 
OLD_PHYSICAL_SIZE_DEFAULT - Static variable in class loci.formats.in.LIFReader
 
OLD_PHYSICAL_SIZE_KEY - Static variable in class loci.formats.in.LIFReader
 
OLD_TOOLS - Static variable in class loci.formats.UpgradeChecker
Name of the previous versions' tools JAR.
ome_meta_data - Variable in class loci.formats.in.OBFReader
 
OME_TIFF_SUFFIXES - Static variable in class loci.formats.in.OMETiffReader
 
OME_TOOLS - Static variable in class loci.formats.UpgradeChecker
Name of the OME tools JAR.
OMEHandler() - Constructor for class loci.formats.out.OMEXMLWriter.OMEHandler
 
omeMeasurementFile - Variable in class loci.formats.in.CellVoyagerReader
 
omeMeta - Variable in class loci.formats.gui.ImageViewer
Attached OME metadata store, if available.
omeMeta - Variable in class loci.formats.out.OMETiffWriter
 
OMEPyramidStore - Class in loci.formats.ome
Extension of OMEXMLMetadataImpl that allows for pyramid resolution storage and retrieval.
OMEPyramidStore() - Constructor for class loci.formats.ome.OMEPyramidStore
 
OMEPyramidStore.Resolution - Class in loci.formats.ome
 
OMETiffCoreMetadata() - Constructor for class loci.formats.in.OMETiffReader.OMETiffCoreMetadata
 
OMETiffCoreMetadata(OMETiffReader.OMETiffCoreMetadata) - Constructor for class loci.formats.in.OMETiffReader.OMETiffCoreMetadata
 
OMETiffCoreMetadata(CoreMetadata) - Constructor for class loci.formats.in.OMETiffReader.OMETiffCoreMetadata
 
OMETiffPlane() - Constructor for class loci.formats.in.OMETiffReader.OMETiffPlane
 
OMETiffReader - Class in loci.formats.in
OMETiffReader is the file format reader for OME-TIFF files.
OMETiffReader() - Constructor for class loci.formats.in.OMETiffReader
Constructs a new OME-TIFF reader.
OMETiffReader.OMETiffCoreMetadata - Class in loci.formats.in
 
OMETiffReader.OMETiffPlane - Class in loci.formats.in
Structure containing details on where to find a particular image plane.
OMETiffWriter - Class in loci.formats.out
OMETiffWriter is the file format writer for OME-TIFF files.
OMETiffWriter() - Constructor for class loci.formats.out.OMETiffWriter
 
omexml - Variable in class loci.formats.in.OMEXMLReader
 
omeXML - Variable in class loci.plugins.in.ImportProcess
 
OMEXMLHandler() - Constructor for class loci.formats.in.OMEXMLReader.OMEXMLHandler
 
omeXmlMetadata - Variable in class loci.formats.in.FakeReader
 
OMEXMLMetadata - Interface in loci.formats.ome
 
OMEXMLMetadataImpl - Class in loci.formats.ome
 
OMEXMLMetadataImpl() - Constructor for class loci.formats.ome.OMEXMLMetadataImpl
 
OMEXMLReader - Class in loci.formats.in
OMEXMLReader is the file format reader for OME-XML files.
OMEXMLReader() - Constructor for class loci.formats.in.OMEXMLReader
Constructs a new OME-XML reader.
OMEXMLReader.BinData - Class in loci.formats.in
 
OMEXMLReader.OMEXMLHandler - Class in loci.formats.in
 
omexmlService - Variable in class loci.formats.gui.ImageViewer
Service for working with OME-XML metadata.
omeXmlService - Variable in class loci.formats.in.FakeReader
 
OMEXMLService - Interface in loci.formats.services
 
OMEXMLServiceImpl - Class in loci.formats.services
 
OMEXMLServiceImpl() - Constructor for class loci.formats.services.OMEXMLServiceImpl
Default constructor.
OMEXMLWriter - Class in loci.formats.out
OMEXMLWriter is the file format writer for OME-XML files.
OMEXMLWriter() - Constructor for class loci.formats.out.OMEXMLWriter
 
OMEXMLWriter.OMEHandler - Class in loci.formats.out
 
OnDemandLongArray - Class in loci.formats.tiff
 
OnDemandLongArray(RandomAccessInputStream) - Constructor for class loci.formats.tiff.OnDemandLongArray
 
ONE - Static variable in class loci.formats.AxisGuesser
 
oneHeaderPerSlice - Variable in class loci.formats.in.SpiderReader
 
oneTimepointPerSeries - Variable in class loci.formats.in.InCellReader
 
op - Variable in class org.libjpegturbo.turbojpeg.TJTransform
Transform operation (one of OP_*)
OP_HFLIP - Static variable in class org.libjpegturbo.turbojpeg.TJTransform
Flip (mirror) image horizontally.
OP_NONE - Static variable in class org.libjpegturbo.turbojpeg.TJTransform
Do not transform the position of the image pixels.
OP_ROT180 - Static variable in class org.libjpegturbo.turbojpeg.TJTransform
Rotate image 180 degrees.
OP_ROT270 - Static variable in class org.libjpegturbo.turbojpeg.TJTransform
Rotate image counter-clockwise by 90 degrees.
OP_ROT90 - Static variable in class org.libjpegturbo.turbojpeg.TJTransform
Rotate image clockwise by 90 degrees.
OP_TRANSPOSE - Static variable in class org.libjpegturbo.turbojpeg.TJTransform
Transpose image (flip/mirror along upper left to lower right axis).
OP_TRANSVERSE - Static variable in class org.libjpegturbo.turbojpeg.TJTransform
Transverse transpose image (flip/mirror along upper right to lower left axis).
OP_VFLIP - Static variable in class org.libjpegturbo.turbojpeg.TJTransform
Flip (mirror) image vertically.
open(String) - Method in class loci.formats.gui.ImageViewer
Opens the given data source using the current format reader.
open(String, IFormatReader) - Method in class loci.formats.gui.ImageViewer
Opens from the given data source using the specified reader in a separate thread.
open(String, String) - Method in interface loci.formats.services.WlzService
Initializes the service for the given file path.
open(String, String) - Method in class loci.formats.services.WlzServiceImpl
 
open() - Method in class loci.formats.tools.EditTiffG
 
open(String) - Static method in class loci.formats.tools.EditTiffG
 
open(String) - Method in class loci.plugins.shortcut.ShortcutPanel
Opens the given location (e.g., file) with the Bio-Formats Importer plugin.
OPEN_ARROW - Static variable in class loci.formats.in.ZeissLSMReader
 
OPEN_BEZIER - Static variable in class loci.formats.in.ZeissLSMReader
 
OPEN_POLYLINE - Static variable in class loci.formats.in.ZeissLSMReader
 
openAllSeries() - Method in class loci.plugins.in.ImporterOptions
 
openAllSeriesBox - Variable in class loci.plugins.in.MainDialog
 
openBitmaskBytes(IFD, int, int) - Method in class loci.formats.in.FlowSightReader
Decode the whole IFD plane using bitmask compression
openBufferedImage(int) - Method in class loci.formats.in.TiffJAIReader
Obtains a BufferedImage from the given data source using JAI.
openBytes(int) - Method in class loci.formats.ChannelFiller
 
openBytes(int, byte[]) - Method in class loci.formats.ChannelFiller
 
openBytes(int, int, int, int, int) - Method in class loci.formats.ChannelFiller
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.ChannelFiller
 
openBytes(int) - Method in class loci.formats.ChannelMerger
 
openBytes(int, byte[]) - Method in class loci.formats.ChannelMerger
 
openBytes(int, int, int, int, int) - Method in class loci.formats.ChannelMerger
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.ChannelMerger
 
openBytes(int) - Method in class loci.formats.ChannelSeparator
 
openBytes(int, byte[]) - Method in class loci.formats.ChannelSeparator
 
openBytes(int, int, int, int, int) - Method in class loci.formats.ChannelSeparator
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.ChannelSeparator
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.DelegateReader
 
openBytes(int) - Method in class loci.formats.DimensionSwapper
 
openBytes(int, int, int, int, int) - Method in class loci.formats.DimensionSwapper
 
openBytes(int, byte[]) - Method in class loci.formats.DimensionSwapper
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.DimensionSwapper
 
openBytes(int) - Method in class loci.formats.FileStitcher
 
openBytes(int, byte[]) - Method in class loci.formats.FileStitcher
 
openBytes(int, int, int, int, int) - Method in class loci.formats.FileStitcher
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.FileStitcher
 
openBytes(int) - Method in class loci.formats.FormatReader
 
openBytes(int, byte[]) - Method in class loci.formats.FormatReader
 
openBytes(int, int, int, int, int) - Method in class loci.formats.FormatReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.FormatReader
 
openBytes(int) - Method in interface loci.formats.IFormatReader
Obtains the specified image plane from the current file as a byte array.
openBytes(int, int, int, int, int) - Method in interface loci.formats.IFormatReader
Obtains a sub-image of the specified image plane, whose upper-left corner is given by (x, y).
openBytes(int, byte[]) - Method in interface loci.formats.IFormatReader
Obtains the specified image plane from the current file into a pre-allocated byte array of (sizeX * sizeY * bytesPerPixel * RGB channel count).
openBytes(int, byte[], int, int, int, int) - Method in interface loci.formats.IFormatReader
Obtains a sub-image of the specified image plane into a pre-allocated byte array.
openBytes(int) - Method in class loci.formats.ImageReader
 
openBytes(int, int, int, int, int) - Method in class loci.formats.ImageReader
 
openBytes(int, byte[]) - Method in class loci.formats.ImageReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.ImageReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.AFIReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.AIMReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.AliconaReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.AmiraReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.AnalyzeReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.APLReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.APNGReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.ARFReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.AVIReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.BDReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.BDVReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.BIFormatReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.BioRadGelReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.BioRadReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.BioRadSCNReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.BMPReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.BrukerReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.BurleighReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.CanonRawReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.CellH5Reader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.CellomicsReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.CellSensReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.CellVoyagerReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.CellWorxReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.ColumbusReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.CV7000Reader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.DeltavisionReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.DicomReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.DNGReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.Ecat7Reader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.EPSReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.FakeReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.FEIReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.FitsReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.FlexReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.FlowSightReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.FluoviewReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.FujiReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.FV1000Reader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.GatanDM2Reader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.GatanReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.GelReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.GIFReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.HamamatsuVMSReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.HISReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.HitachiReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.HRDGDFReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.I2IReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.ICSReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.IM3Reader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.ImaconReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.ImagicReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.ImarisHDFReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.ImarisReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.IMODReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.ImprovisionTiffReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.ImspectorReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.InCell3000Reader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.InCellReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.INRReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.InveonReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.IonpathMIBITiffReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.IPLabReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.IPWReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.IvisionReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.JEOLReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.JPEG2000Reader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.JPKReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.JPXReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.KhorosReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.KLBReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.KodakReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.L2DReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.LegacyND2Reader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.LeicaReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.LeicaSCNReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.LiFlimReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.LIFReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.LIMReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.MetamorphReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.MetamorphTiffReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.MIASReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.MicroCTReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.MicromanagerReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.MINCReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.MinimalTiffReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.MolecularImagingReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.MRCReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.MRWReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.NAFReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.NativeND2Reader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.NativeQTReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.NDPIReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.NDPISReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.NiftiReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.NikonReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.NRRDReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.OBFReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.OIRReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.OMETiffReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.OMEXMLReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.OpenlabRawReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.OpenlabReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.OperettaReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.OxfordInstrumentsReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.PCIReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.PCORAWReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.PCXReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.PDSReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.PerkinElmerReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.PGMReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.PhotoshopTiffReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.PictReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.PovrayReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.PQBinReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.PrairieReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.PSDReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.PyramidTiffReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.QuesantReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.RHKReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.SBIGReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.ScanrReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.SDTReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.SeikoReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.SEQReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.SIFReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.SimplePCITiffReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.SlidebookReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.SlidebookTiffReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.SMCameraReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.SPCReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.SPEReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.SpiderReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.SVSReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.TargaReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.TCSReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.TextReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.TiffDelegateReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.TileJPEGReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.TillVisionReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.TopometrixReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.TrestleReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.UBMReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.UnisokuReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.VarianFDFReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.VectraReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.VeecoReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.VentanaReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.VGSAMReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.VisitechReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.VolocityClippingReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.VolocityReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.WATOPReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.WlzReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.ZeissCZIReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.ZeissLMSReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.ZeissLSMReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.ZeissTIFFReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.ZeissZVIReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.ZipReader
 
openBytes(int) - Method in class loci.formats.MinMaxCalculator
 
openBytes(int, byte[]) - Method in class loci.formats.MinMaxCalculator
 
openBytes(int, int, int, int, int) - Method in class loci.formats.MinMaxCalculator
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.MinMaxCalculator
 
openBytes(int) - Method in class loci.formats.ReaderWrapper
 
openBytes(int, int, int, int, int) - Method in class loci.formats.ReaderWrapper
 
openBytes(int, byte[]) - Method in class loci.formats.ReaderWrapper
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.ReaderWrapper
 
openBytes(int) - Method in class loci.formats.TileStitcher
 
openBytes(int, byte[]) - Method in class loci.formats.TileStitcher
 
openBytes(int, int, int, int, int) - Method in class loci.formats.TileStitcher
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.TileStitcher
 
openBytes(int) - Method in class loci.formats.WrappedReader
 
openBytes(int, int, int, int, int) - Method in class loci.formats.WrappedReader
 
openBytes(int, byte[]) - Method in class loci.formats.WrappedReader
 
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.WrappedReader
 
OPENER_PLUGIN - Static variable in class loci.plugins.shortcut.ShortcutPanel
Name of plugin to use for opening dropped files.
openerIndex - Static variable in class loci.plugins.shortcut.ShortcutPanel
Index of plugin to use to open dropped files.
openFile(String) - Method in class loci.formats.in.LegacyND2Reader
 
openFile(File) - Method in class loci.formats.tools.EditTiffG
 
openFile(File, RandomAccessInputStream) - Method in class loci.formats.tools.EditTiffG
 
openFile(String) - Static method in class loci.formats.tools.EditTiffG
Deprecated.
openFiles - Variable in class loci.formats.in.MetamorphReader
 
openGreyscaleBytes(IFD, int, int) - Method in class loci.formats.in.FlowSightReader
Decode the whole IFD plane using greyscale compression
openImage(byte[], IFormatReader, int, int) - Static method in class loci.formats.gui.AWTImageTools
Creates an image from the given byte array, using the given IFormatReader to retrieve additional information.
openImage(byte[], IFormatReader, int, int, boolean) - Static method in class loci.formats.gui.AWTImageTools
Creates an image from the given byte array, using the given IFormatReader to retrieve additional information.
openImage(int) - Method in class loci.formats.gui.BufferedImageReader
Obtains the specified image from the current file.
openImage(int, int, int, int, int) - Method in class loci.formats.gui.BufferedImageReader
Obtains a sub-image of the specified image, whose upper-left corner is given by (x, y).
openImage - Variable in class loci.formats.in.InCellReader.InCellHandler
 
openImage(String, Double) - Method in class loci.plugins.macro.LociFunctions
 
openImagePlus(String) - Static method in class loci.plugins.BF
 
openImagePlus(ImporterOptions) - Static method in class loci.plugins.BF
 
openImagePlus() - Method in class loci.plugins.in.ImagePlusReader
Opens one or more ImagePlus objects corresponding to the reader's associated options.
openImagePlus(String) - Method in class loci.plugins.macro.LociFunctions
 
OPENLAB_RAW_MAGIC_STRING - Static variable in class loci.formats.in.OpenlabRawReader
 
OpenlabRawReader - Class in loci.formats.in
OpenlabRawReader is the file format reader for Openlab RAW files.
OpenlabRawReader() - Constructor for class loci.formats.in.OpenlabRawReader
Constructs a new RAW reader.
OpenlabReader - Class in loci.formats.in
OpenlabReader is the file format reader for Openlab LIFF files.
OpenlabReader() - Constructor for class loci.formats.in.OpenlabReader
Constructs a new OpenlabReader.
OpenlabReader.PlaneInfo - Class in loci.formats.in
Helper class for storing plane info.
openPlane(int, int, int, int, int) - Method in class loci.formats.FileStitcher
 
openPlane(int, int, int, int, int) - Method in class loci.formats.FormatReader
 
openPlane(int, int, int, int, int) - Method in interface loci.formats.IFormatReader
Obtains the specified image plane (or sub-image thereof) in the reader's native data structure.
openPlane(int, int, int, int, int) - Method in class loci.formats.ImageReader
 
openPlane(int, int, int, int, int) - Method in class loci.formats.in.ImageIOReader
 
openPlane(int, int, int, int, int) - Method in class loci.formats.in.LegacyQTReader
 
openPlane(int, int, int, int, int) - Method in class loci.formats.in.MNGReader
 
openPlane(int, int, int, int, int) - Method in class loci.formats.in.TextReader
 
openPlane(int, int, int, int, int) - Method in class loci.formats.in.TiffJAIReader
 
openPlane(int, int, int, int, int) - Method in class loci.formats.ReaderWrapper
 
openPlane(int, int, int, int, int) - Method in class loci.formats.WrappedReader
 
openPlane(int, int, int, int, int) - Method in class loci.plugins.util.ImageProcessorReader
 
openProcessors(int) - Method in class loci.plugins.util.ImageProcessorReader
Creates an ImageJ image processor object for the image plane at the given position.
openProcessors(int, int, int, int, int) - Method in class loci.plugins.util.ImageProcessorReader
Returns an array of ImageProcessors that represent the given slice.
openRaw() - Method in class loci.formats.in.IM3Reader
Open the current series in raw-mode, returning the interleaved image bytes.
openRead(String) - Method in class loci.formats.services.WlzServiceImpl
 
openROIs(IMetadata, ImagePlus[]) - Static method in class loci.plugins.util.ROIHandler
Look for ROIs in the given OMEXMLMetadata; if any are present, apply them to the given images and display them in the ROI manager.
openROIs(IMetadata, ImagePlus[], boolean) - Static method in class loci.plugins.util.ROIHandler
Opens the rois and converts them into ImageJ Rois.
openROIs(IMetadata, ImagePlus[], boolean, String) - Static method in class loci.plugins.util.ROIHandler
Opens the rois and converts them into ImageJ Rois.
openSubImage(String, Double, Double, Double, Double, Double) - Method in class loci.plugins.macro.LociFunctions
 
openThumbBytes(int) - Method in class loci.formats.ChannelSeparator
 
openThumbBytes(int) - Method in class loci.formats.DimensionSwapper
 
openThumbBytes(int) - Method in class loci.formats.FileStitcher
 
openThumbBytes(int) - Method in class loci.formats.FormatReader
 
openThumbBytes(IFormatReader, int) - Static method in class loci.formats.FormatTools
Default implementation for IFormatReader.openThumbBytes(int).
openThumbBytes(int) - Method in interface loci.formats.IFormatReader
Obtains a thumbnail for the specified image plane from the current file, as a byte array.
openThumbBytes(int) - Method in class loci.formats.ImageReader
 
openThumbBytes(int) - Method in class loci.formats.in.AFIReader
 
openThumbBytes(int) - Method in class loci.formats.in.CellSensReader
 
openThumbBytes(int) - Method in class loci.formats.in.LeicaSCNReader
 
openThumbBytes(int) - Method in class loci.formats.in.MinimalTiffReader
 
openThumbBytes(int) - Method in class loci.formats.in.NDPIReader
 
openThumbBytes(int) - Method in class loci.formats.in.SVSReader
 
openThumbBytes(int) - Method in class loci.formats.in.VectraReader
 
openThumbBytes(int) - Method in class loci.formats.in.VentanaReader
 
openThumbBytes(int) - Method in class loci.formats.ReaderWrapper
 
openThumbBytes(int) - Method in class loci.formats.WrappedReader
 
openThumbImage(int) - Method in class loci.formats.gui.BufferedImageReader
Obtains a thumbnail for the specified image from the current file.
openThumbImage(String, Double) - Method in class loci.plugins.macro.LociFunctions
 
openThumbImagePlus(String) - Static method in class loci.plugins.BF
 
openThumbImagePlus(ImporterOptions) - Static method in class loci.plugins.BF
 
openThumbImagePlus() - Method in class loci.plugins.in.ImagePlusReader
 
openThumbImagePlus(String) - Method in class loci.plugins.macro.LociFunctions
 
openThumbProcessors(int) - Method in class loci.plugins.util.ImageProcessorReader
 
openWrite(String) - Method in class loci.formats.services.WlzServiceImpl
 
OPERETTA_MAGIC - Static variable in class loci.formats.in.OperettaReader
 
OperettaHandler() - Constructor for class loci.formats.in.OperettaReader.OperettaHandler
 
OperettaReader - Class in loci.formats.in
OperettaReader is the file format reader for PerkinElmer Operetta data.
OperettaReader() - Constructor for class loci.formats.in.OperettaReader
Constructs a new Operetta reader.
OperettaReader.OperettaHandler - Class in loci.formats.in
 
OperettaReader.Plane - Class in loci.formats.in
 
OPT_CROP - Static variable in class org.libjpegturbo.turbojpeg.TJTransform
This option will enable lossless cropping.
OPT_GRAY - Static variable in class org.libjpegturbo.turbojpeg.TJTransform
This option will discard the color data in the input image and produce a grayscale output image.
OPT_NOOUTPUT - Static variable in class org.libjpegturbo.turbojpeg.TJTransform
This option will prevent TJTransformer.transform() from outputting a JPEG image for this particular transform.
OPT_PERFECT - Static variable in class org.libjpegturbo.turbojpeg.TJTransform
This option will cause TJTransformer.transform() to throw an exception if the transform is not perfect.
OPT_TRIM - Static variable in class org.libjpegturbo.turbojpeg.TJTransform
This option will discard any partial MCU blocks that cannot be transformed.
OPTICAL_PATH - Static variable in class loci.formats.in.CellSensReader
 
Option - Class in loci.plugins.prefs
Base class for an option for one of the plugins.
Option(String, boolean, String, String) - Constructor for class loci.plugins.prefs.Option
Constructs an option with the given parameters.
options - Variable in class loci.formats.ClassList
List of options.
options - Variable in class loci.formats.FormatWriter
The options if required.
options - Variable in class loci.formats.tiff.TiffSaver
The codec options if set.
options - Variable in class loci.plugins.in.DisplayHandler
 
options - Variable in class loci.plugins.in.ImporterDialog
 
options - Variable in class loci.plugins.in.ImportProcess
Associated importer options.
options - Variable in class loci.plugins.prefs.OptionsList
Table of options defining this set of preferences.
options - Variable in class loci.plugins.util.DataBrowser
 
options - Variable in class org.libjpegturbo.turbojpeg.TJTransform
Transform options (bitwise OR of one or more of OPT_*)
OptionsDialog - Class in loci.plugins.prefs
Base class for options dialogs.
OptionsDialog(OptionsList) - Constructor for class loci.plugins.prefs.OptionsDialog
Creates a new options dialog with the given associated options.
optionsList - Variable in class loci.plugins.prefs.OptionsDialog
Options list associated with the dialog.
OptionsList - Class in loci.plugins.prefs
Base class for ImageJ preferences for plugins.
OptionsList(String, Class<?>) - Constructor for class loci.plugins.prefs.OptionsList
 
OptionsList(IniList) - Constructor for class loci.plugins.prefs.OptionsList
 
optionsWindow - Variable in class loci.plugins.util.DataBrowser
 
or(int) - Method in class loci.plugins.util.RecordedImageProcessor
 
order - Variable in class loci.formats.cache.CacheStrategy
The order in which planes should be loaded along each axis.
order - Variable in class loci.formats.gui.CacheComponent
Combo boxes for choosing planar ordering.
ORDER - Static variable in class loci.plugins.out.Exporter
 
ORDER_CHANGED - Static variable in class loci.formats.cache.CacheEvent
Event type indicating new planar ordering.
ORDER_DEFAULT - Static variable in class loci.plugins.in.ImporterOptions
 
ORDER_VALUES - Static variable in class loci.formats.gui.CacheComponent
 
ORDER_XYCTZ - Static variable in class loci.plugins.in.ImporterOptions
 
ORDER_XYCZT - Static variable in class loci.plugins.in.ImporterOptions
 
ORDER_XYTCZ - Static variable in class loci.plugins.in.ImporterOptions
 
ORDER_XYTZC - Static variable in class loci.plugins.in.ImporterOptions
 
ORDER_XYZCT - Static variable in class loci.plugins.in.ImporterOptions
 
ORDER_XYZTC - Static variable in class loci.plugins.in.ImporterOptions
 
orderCertain - Variable in class loci.formats.CoreMetadata
Indicates whether or not we are confident that the dimension order is correct.
orderIndex(int) - Method in class loci.formats.gui.CacheComponent
Converts enumerated order value to order chooser index.
ordering - Variable in class loci.formats.in.BrukerReader
 
ORDERS - Static variable in class loci.formats.gui.CacheComponent
 
orderValue(int) - Method in class loci.formats.gui.CacheComponent
Converts order chooser index to enumerated order value.
org.libjpegturbo.turbojpeg - package org.libjpegturbo.turbojpeg
 
orientation - Variable in class loci.formats.in.TargaReader
 
ORIENTATION - Static variable in class loci.formats.tiff.IFD
 
orientationMatrix - Variable in class loci.formats.in.OperettaReader.Plane
 
origin - Variable in class loci.formats.in.ZeissTIFFHandler.Scaling.Dimension
 
original - Variable in class loci.formats.in.DNGReader
The original IFD.
original - Variable in class loci.formats.in.NikonReader
The original IFD.
ORIGINAL_FRAME_RATE - Static variable in class loci.formats.in.CellSensReader
 
ORIGINAL_METADATA_NS - Static variable in class loci.formats.meta.OriginalMetadataAnnotation
 
originalDate - Variable in class loci.formats.in.DicomReader
 
originalID - Variable in class loci.plugins.in.FilePatternDialog
 
originalInstance - Variable in class loci.formats.in.DicomReader
 
originalMetadata - Variable in class loci.formats.in.CellSensReader.Pyramid
 
OriginalMetadataAnnotation - Class in loci.formats.meta
 
OriginalMetadataAnnotation() - Constructor for class loci.formats.meta.OriginalMetadataAnnotation
 
originalOrder - Variable in class loci.formats.FileStitcher.ExternalSeries
 
originalSeries - Variable in class loci.formats.in.DicomReader
 
originalTime - Variable in class loci.formats.in.DicomReader
 
originalX - Variable in class loci.formats.in.DicomReader
 
originalY - Variable in class loci.formats.in.DicomReader
 
originX - Variable in class loci.formats.in.CellSensReader.Pyramid
 
originX - Variable in class loci.formats.in.PerkinElmerReader
 
originX - Variable in class loci.formats.in.VarianFDFReader
 
originX - Variable in class loci.formats.in.ZeissLSMReader
 
originY - Variable in class loci.formats.in.CellSensReader.Pyramid
 
originY - Variable in class loci.formats.in.PerkinElmerReader
 
originY - Variable in class loci.formats.in.VarianFDFReader
 
originY - Variable in class loci.formats.in.ZeissLSMReader
 
originZ - Variable in class loci.formats.in.PerkinElmerReader
 
originZ - Variable in class loci.formats.in.VarianFDFReader
 
originZ - Variable in class loci.formats.in.ZeissLSMReader
 
origname - Variable in class loci.formats.in.ZeissTIFFReader.TIFFInfo
 
OTHER_KEYS - Static variable in class loci.formats.in.ICSReader
 
otherChannels - Variable in class loci.plugins.util.RecordedImageProcessor
 
out - Variable in class loci.formats.FormatWriter
Current file.
out - Variable in class loci.formats.tiff.TiffSaver
Output stream to use when saving TIFF data.
output - Variable in class loci.formats.gui.DataConverter
 
output - Variable in class loci.formats.Memoizer.KryoDeser
 
outputOrder - Variable in class loci.formats.out.ICSWriter
 
outputOrder - Variable in class loci.formats.out.V3DrawWriter
 
outputOrder - Variable in class loci.formats.out.WlzWriter
 
outputPath - Variable in class loci.formats.out.CellH5Writer
 
overfl - Variable in class loci.formats.in.SDTInfo
 
overflowCorrFactor - Variable in class loci.formats.in.SDTInfo
 
Overlap() - Constructor for class loci.formats.in.VentanaReader.Overlap
 
overlaps - Variable in class loci.formats.in.TrestleReader
 
overlaps - Variable in class loci.formats.in.VentanaReader.AreaOfInterest
 
overlayFiles - Variable in class loci.formats.in.MIASReader
 
overlayPlanes - Variable in class loci.formats.in.MIASReader
 
overruns - Variable in class loci.formats.in.SDTInfo
No of Fifo overruns when > 0 fcs curve & endTime are not valid.
OVERVIEW_IMAGE - Static variable in class loci.formats.in.CellSensReader
 
overwriteComment(RandomAccessInputStream, Object) - Method in class loci.formats.tiff.TiffSaver
Convenience method for overwriting a file's first ImageDescription.
overwriteDimensions(MetadataRetrieve) - Method in class loci.formats.out.ICSWriter
 
overwriteIFDOffset(RandomAccessInputStream, long, long) - Method in class loci.formats.tiff.TiffSaver
 
overwriteIFDValue(RandomAccessInputStream, int, int, Object) - Method in class loci.formats.tiff.TiffSaver
Surgically overwrites an existing IFD value with the given one.
overwriteIFDValue(RandomAccessInputStream, long, int, Object) - Method in class loci.formats.tiff.TiffSaver
Surgically overwrites an existing IFD value with the given one.
overwriteIFDValue(RandomAccessInputStream, long, int, Object, boolean) - Method in class loci.formats.tiff.TiffSaver
Surgically overwrites an existing IFD value with the given one.
overwriteLastIFDOffset(RandomAccessInputStream) - Method in class loci.formats.tiff.TiffSaver
 
OW - Static variable in class loci.formats.in.DicomReader
 
OXFORD_MAGIC_STRING - Static variable in class loci.formats.in.OxfordInstrumentsReader
 
OxfordInstrumentsReader - Class in loci.formats.in
OxfordInstrumentsReader is the file format reader for Oxford Instruments .top files.
OxfordInstrumentsReader() - Constructor for class loci.formats.in.OxfordInstrumentsReader
Constructs a new Oxford Instruments reader.

P

p - Variable in class loci.formats.in.BioRadReader.Note
 
p - Variable in class loci.plugins.in.SeriesDialog
 
p - Variable in class loci.plugins.in.ThumbLoader
 
P_KEY - Static variable in class loci.formats.in.LiFlimReader
 
pack() - Method in class loci.plugins.util.DataBrowser
Overridden pack method to allow us to delay initial window sizing.
PACKBITS - Static variable in class loci.formats.in.PhotoshopTiffReader
 
PackbitsCodec - Class in loci.formats.codec
This class implements packbits decompression.
PackbitsCodec() - Constructor for class loci.formats.codec.PackbitsCodec
 
pad - Variable in class loci.formats.out.QTWriter
Number of padding bytes in each row.
PAD - Static variable in class loci.plugins.config.ConfigWindow
 
padding - Variable in class loci.formats.in.UBMReader
 
PADDING_BYTES - Static variable in class loci.formats.out.AVIWriter
 
paddingZeros - Variable in class loci.plugins.in.FilePatternDialog
 
padImage(BufferedImage, int, int) - Static method in class loci.formats.gui.AWTImageTools
Pads (or crops) the image to the given width and height.
padImage(byte[], boolean, int, int, int, int) - Static method in class loci.formats.ImageTools
Pads (or crops) the byte array to the given width and height.
padImage(short[], boolean, int, int, int, int) - Static method in class loci.formats.ImageTools
Pads (or crops) the short array to the given width and height.
padImage(int[], boolean, int, int, int, int) - Static method in class loci.formats.ImageTools
Pads (or crops) the int array to the given width and height.
padImage(float[], boolean, int, int, int, int) - Static method in class loci.formats.ImageTools
Pads (or crops) the float array to the given width and height.
padImage(double[], boolean, int, int, int, int) - Static method in class loci.formats.ImageTools
Pads (or crops) the double array to the given width and height.
PAETH - Static variable in class loci.formats.in.APNGReader
 
page - Variable in class loci.formats.in.SDTInfo
 
PAGE_NAME - Static variable in class loci.formats.tiff.IFD
 
PAGE_NUMBER - Static variable in class loci.formats.tiff.IFD
 
paintComponent(Graphics) - Method in class loci.formats.gui.CacheIndicator
 
palette - Variable in class loci.formats.in.BMPReader
The palette for indexed color images.
PALETTE - Static variable in class loci.formats.in.ZeissLSMReader
 
pane - Variable in class loci.formats.gui.ImageViewer
 
panel - Variable in class loci.plugins.util.SearchableWindow
 
panelSize - Variable in class loci.formats.in.DeltavisionReader
 
PARAMETER_KEYS - Static variable in class loci.formats.in.ICSReader
 
parameterFile - Variable in class loci.formats.in.JEOLReader
 
paramFile - Variable in class loci.formats.in.PCORAWReader
 
PARAMS - Static variable in class loci.plugins.config.ConfigWindow
 
parent - Variable in class loci.formats.in.CV7000Reader
 
parentDimension - Variable in class loci.formats.Modulo
 
parentDir - Variable in class loci.formats.in.CV7000Reader.MeasurementDataHandler
 
parentNames - Variable in class loci.formats.in.FEITiffReader.FEIHandler
 
parentQName - Variable in class loci.formats.in.FlexReader.FlexHandler
 
parentType - Variable in class loci.formats.Modulo
 
parse(int, long, long) - Method in class loci.formats.in.NativeQTReader
Parse all of the atoms in the file.
parse(Element) - Method in class loci.formats.in.PrairieMetadata.Frame
Parses metadata from the given Frame element.
parse(Element) - Method in class loci.formats.in.PrairieMetadata.PFile
Parses metadata from the given File element.
parse(Element) - Method in class loci.formats.in.PrairieMetadata.Sequence
Parses metadata from the given Sequence element.
parseApplicationTags() - Method in class loci.formats.in.ZeissLSMReader
 
parseArg(String) - Method in class loci.plugins.in.ImporterOptions
Parses the plugin argument for parameter values.
parseArray(String) - Method in class loci.formats.in.VarianFDFReader
Split a String that represents an array into individual elements.
parseAttributes() - Method in class loci.formats.in.ImarisHDFReader
 
parseAttributesAndVariables(List<Group>) - Method in class loci.formats.services.NetCDFServiceImpl
Recursively parses attribute and variable paths, filling attributeList and variableList.
parseAxis(Element) - Method in class loci.formats.in.OIRReader
 
parseBoxes() - Method in class loci.formats.in.JPEG2000MetadataParser
Parses the JPEG 2000 JP2 metadata boxes.
parseCellObjects() - Method in class loci.formats.in.CellH5Reader
 
parseCFG(Document) - Method in class loci.formats.in.PrairieMetadata
Parses metadata from Prairie CFG file.
parseChannel(Element, boolean) - Method in class loci.formats.in.OIRReader
 
parseChannelData(Location) - Method in class loci.formats.in.BDReader
 
parseChannels() - Method in class loci.formats.in.PrairieMetadata
Parses details of the activated channels into the PrairieMetadata.activeChannels data structure from the "channel" entry of the configuration.
parseChannelTag() - Method in class loci.formats.in.LeicaReader
 
parseChunks(IRandomAccess) - Method in class loci.formats.in.IM3Reader.ContainerRecord
Parse and return the sub-records for the record container
parseColor(byte, byte, byte) - Static method in class loci.formats.in.BaseZeissReader
 
parseColor(String) - Method in class loci.formats.in.FakeReader
 
parseColor(byte, byte, byte) - Static method in class loci.formats.in.ZeissTIFFHandler
 
parseComment() - Method in class loci.formats.in.FluoviewReader
 
parseCommentGeneric(String) - Method in class loci.formats.in.TiffReader
 
parseCommentImageJ(String) - Method in class loci.formats.in.TiffReader
 
parseCommentMetamorph(String) - Method in class loci.formats.in.TiffReader
 
parseContiguousCodestream(long) - Method in class loci.formats.in.JPEG2000MetadataParser
Parses the JPEG 2000 codestream metadata.
parseCSVFile(String) - Method in class loci.formats.in.PerkinElmerReader
 
parseDatabase() - Method in interface loci.formats.services.MDBService
Read all tables from a pre-initialized .mdb files.
parseDatabase() - Method in class loci.formats.services.MDBServiceImpl
 
parseDeconvolutionLog(RandomAccessInputStream, MetadataStore) - Method in class loci.formats.in.DeltavisionReader
Parse deconvolution output, if it exists.
parseDimension(String) - Method in class loci.formats.in.APLReader
Parse an integer from the given dimension String.
parseDimensionSizes(String[], String[]) - Method in class loci.formats.in.NikonTiffReader
 
parseDimensionTag(int) - Method in class loci.formats.in.LeicaReader
 
parseDOM(Location) - Method in class loci.formats.in.PrairieReader
Parses a Document from the data in the given file.
parseDouble(String) - Method in class loci.formats.in.LeicaHandler
 
parseDouble(String) - Method in class loci.formats.in.TiffReader
 
parseDouble(String) - Static method in class loci.formats.in.ZeissTIFFHandler
Parse a Double from a String.
parseENV(Document) - Method in class loci.formats.in.PrairieMetadata
Parses metadata from Prairie ENV file.
parseETSFile(RandomAccessInputStream, String, int) - Method in class loci.formats.in.CellSensReader
 
parseExperimentTag() - Method in class loci.formats.in.LeicaReader
 
parseExtraTags() - Method in class loci.formats.in.GatanDM2Reader
 
parseFDF(String) - Method in class loci.formats.in.VarianFDFReader
 
parseFile(String, Class<?>) - Method in class loci.formats.ClassList
Parses a list of classes from a configuration file.
parseFile(String, MetamorphHandler) - Method in class loci.formats.in.MetamorphTiffReader
 
parseFile(DirectoryEntry) - Method in class loci.formats.services.POIServiceImpl
 
parseFileHeader(List<String>) - Method in class loci.formats.in.TextReader
Parses the file looking for the file header.
parseFilename(String[], int, int) - Method in class loci.formats.in.APLReader
 
parseFilenames(int) - Method in class loci.formats.in.LeicaReader
 
parseFlexFile(int, int, int, int, boolean, MetadataStore) - Method in class loci.formats.in.FlexReader
Parses XML metadata from the Flex file corresponding to the given well.
parseFrameProperties(Element) - Method in class loci.formats.in.OIRReader
 
parseHeader() - Method in class loci.formats.in.LiFlimReader
 
parseHeaderRow(String[]) - Method in class loci.formats.in.TextReader
Populates rowLength, xIndex, yIndex, and channels.
parseImageNames(int) - Method in class loci.formats.in.OpenlabReader
 
parseImageProperties(Element) - Method in class loci.formats.in.OIRReader
 
parseImageTag(int) - Method in class loci.formats.in.LeicaReader
 
parseImageXML(String, int) - Method in class loci.formats.in.ColumbusReader
 
parseInstrumentData(MetadataStore, int) - Method in class loci.formats.in.LeicaReader
 
parseInt(String) - Static method in class loci.formats.in.BaseZeissReader
Parse an Integer from a String.
parseInt(String, int) - Static method in class loci.formats.in.BaseZeissReader
Parse an Integer from a String.
parseInt(String) - Method in class loci.formats.in.TiffReader
 
parseIntegerString(String) - Method in class loci.formats.in.BDVReader.BDVXMLHandler
 
parseKeyAndValue(String, String, int, int, int) - Method in class loci.formats.in.MicromanagerReader
 
parseKeyAndValue(String, String, String) - Method in class loci.formats.in.ND2Handler
 
parseKeys(Element, PrairieMetadata.ValueTable) - Method in class loci.formats.in.PrairieMetadata
Parses <Key> elements beneath the given element, into the specified table.
parseKeyValue(String, String) - Method in class loci.formats.in.LEOReader
 
parseKeyValue(String, String) - Method in class loci.formats.in.PerkinElmerReader
 
parseLength(String) - Static method in class loci.formats.FormatTools
Parse a length composed of a value and an optional unit
parseLength(String, String) - Static method in class loci.formats.FormatTools
Parse a length composed of a value and an optional unit
parseLine(String) - Method in class loci.formats.ClassList
Parses a class from a string including options and comments.
parseLines(String[]) - Method in class loci.formats.in.BrukerReader
 
parseList(String) - Static method in class loci.plugins.prefs.StringOption
Parses a string of comma-separated values into a list of tokens.
parseLogFile(MetadataStore) - Method in class loci.formats.in.DeltavisionReader
Extract metadata from associated log file, if it exists.
parseLUT(int) - Method in class loci.formats.in.LeicaReader
 
parseLUT(Element, String) - Method in class loci.formats.in.OIRReader
 
parseMainTags(int, MetadataStore, ArrayList<BaseZeissReader.Tag>) - Method in class loci.formats.in.BaseZeissReader
 
parseMasks - Variable in class loci.formats.in.MIASReader
Whether or not mask pixel data should be parsed in setId.
parseMasks(MetadataStore) - Method in class loci.formats.in.MIASReader
Parse masks into a separate overlay-specific MetadataStore.
parseMasks(MetadataStore, int, int, String) - Method in class loci.formats.in.MIASReader
Parse Mask ROIs from the given TIFF and place them in the given MetadataStore.
parseMDB(String) - Method in class loci.formats.in.ZeissLSMReader
Parse a .mdb file and return a list of referenced .lsm files.
parseMetadata() - Method in class loci.formats.in.ZeissCZIReader.SubBlock
 
parseNotes(MetadataStore) - Method in class loci.formats.in.BioRadReader
 
parseObjectives(NodeList) - Method in class loci.formats.in.ZeissCZIReader
 
parseOption(String) - Method in class loci.plugins.prefs.BooleanOption
 
parseOption(String) - Method in class loci.plugins.prefs.DoubleOption
 
parseOption(String) - Method in class loci.plugins.prefs.Option
Parses the option's value from the given argument string.
parseOption(String) - Method in class loci.plugins.prefs.StringOption
 
parseOptions(String) - Method in class loci.formats.ClassList
Parses one or more options from a string.
parseOptions(String) - Method in class loci.plugins.in.Importer
Parses core options.
parseOptions(String) - Method in class loci.plugins.prefs.OptionsList
Parses option values from the given argument string.
parseOriginalMetadata(Node) - Method in class loci.formats.in.OIRReader
 
parseOverlays(int, long, String, MetadataStore) - Method in class loci.formats.in.ZeissLSMReader
Parses overlay-related fields.
parsePageName() - Method in class loci.formats.in.FluoviewReader
 
parsePhysicalSize(String, String) - Method in class loci.formats.in.FakeReader
 
parsePixelSize(int) - Method in class loci.formats.in.NRRDReader
 
parsePixelsSizeZFromKey(String) - Method in class loci.formats.in.ND2Handler
Parses the physical size from a key.
parsePoints(String) - Static method in class loci.plugins.util.ROIHandler
Parse (x, y) coordinates from a String returned by MetadataRetrieve.getPolygonpoints(...) or MetadataRetrieve.getPolylinepoints(...)
parsePosition(String, int, int, IniTable) - Method in class loci.formats.in.FakeReader
 
parsePosition(int) - Method in class loci.formats.in.MicromanagerReader
 
parsePosition(String, int) - Method in class loci.formats.in.MicromanagerReader
 
parsePrairieMetadata() - Method in class loci.formats.in.PrairieReader
This step parses the Prairie metadata files into the Prairie-specific metadata structure, PrairieReader.meta.
parsePVStateShard(Element, PrairieMetadata.ValueTable) - Method in class loci.formats.in.PrairieMetadata
Parses the <PVStateShard> element beneath the given element, into the specified table.
parser - Variable in class loci.formats.in.APLReader
 
parser - Variable in class loci.formats.in.CellSensReader
 
parser - Variable in class loci.formats.in.FV1000Reader
 
parser - Variable in class loci.formats.in.ZeissCZIReader
 
parseRecord(IRandomAccess) - Static method in class loci.formats.in.IM3Reader
Parse an IM3 record at the current file pointer location
parseResFile(String) - Method in class loci.formats.in.FlexReader
 
parseROIFile(String, MetadataStore, int, int) - Method in class loci.formats.in.FV1000Reader
 
parseROIs(MetadataStore) - Method in class loci.formats.in.BDReader
 
parseROIs(int) - Method in class loci.formats.in.BDVReader
 
parseROIs(int) - Method in class loci.formats.in.CellH5Reader
 
parseROIs(MetadataStore) - Method in class loci.formats.in.TrestleReader
 
parseROIs(RandomAccessInputStream, int, String, MetadataStore) - Method in class loci.formats.in.ZeissZVIReader
Parse ROI data from the given RandomAccessInputStream and store it in the given MetadataStore.
parseROIString(RandomAccessInputStream) - Method in class loci.formats.in.ZeissZVIReader
 
parseSeriesTable(IniTable, MetadataStore, int) - Method in class loci.formats.in.FakeReader
Translate key/value pairs from the INI table for the specified series.
parseSeriesTag() - Method in class loci.formats.in.LeicaReader
 
parseSetup(String, String) - Method in class loci.formats.in.SPCReader
 
parseSpectrumRecord(IRandomAccess, IM3Reader.ContainerRecord) - Method in class loci.formats.in.IM3Reader.Spectrum
Parse the spectrum record
parseString(IRandomAccess) - Static method in class loci.formats.in.IM3Reader
Parse a string from the IM3 file at the current file pointer loc
parseStructure() - Method in class loci.formats.in.BDVReader
 
parseStructure() - Method in class loci.formats.in.CellH5Reader
 
parseTableData(List<String>, int) - Method in class loci.formats.in.TextReader
Reads the tabular data into the data array.
parseTags(int, String, String) - Method in class loci.formats.in.GatanReader
Parses Gatan DM3 tags.
parseTags(MetadataStore) - Method in class loci.formats.in.IPLabReader
 
parseTags(int, String, MetadataStore) - Method in class loci.formats.in.ZeissZVIReader
Parse all of the tags in a stream.
parseTemplateFile(MetadataStore) - Method in class loci.formats.in.MIASReader
Parse metadata from the Nugenesistemplate.txt file.
parseText(String, int, boolean) - Method in class loci.formats.in.NativeND2Reader
 
parseTimestamp(String) - Method in class loci.formats.in.BaseZeissReader
Parse timestamp from string.
parseTimeTag(int) - Method in class loci.formats.in.LeicaReader
 
parseTimFile(String) - Method in class loci.formats.in.PerkinElmerReader
 
parseUIC1Tags(long, int) - Method in class loci.formats.in.MetamorphReader
UIC1 entry parser
parseUIC2Tags(long) - Method in class loci.formats.in.MetamorphReader
Populates metadata fields with some contained in MetaMorph UIC2 Tag.
parseUIC4Tags(long) - Method in class loci.formats.in.MetamorphReader
UIC4 metadata parser UIC4 Table contains per-plane blocks of metadata stage X/Y positions, camera chip offsets, stage labels...
parseWellLogFile(int, MetadataStore) - Method in class loci.formats.in.CellWorxReader
Parse metadata from a well log file.
parseXML(RandomAccessInputStream, String, long) - Method in class loci.formats.in.OIRReader
 
parseXML(Document) - Method in class loci.formats.in.PrairieMetadata
Parses metadata from Prairie XML file.
parseXML(String) - Method in class loci.formats.in.VentanaReader
 
parseXMLFile() - Method in class loci.formats.in.MicromanagerReader
Parse metadata values from the Acqusition.xml file.
parseZpoFile(String) - Method in class loci.formats.in.PerkinElmerReader
 
parsingAttributes - Variable in class loci.formats.in.BDVReader.BDVXMLHandler
 
parsingId - Variable in class loci.formats.in.BDVReader.BDVXMLHandler
 
parsingTimepoints - Variable in class loci.formats.in.BDVReader.BDVXMLHandler
 
parsingViewSetups - Variable in class loci.formats.in.BDVReader.BDVXMLHandler
 
parsingVoxelSizes - Variable in class loci.formats.in.BDVReader.BDVXMLHandler
 
PASS_HEIGHTS - Static variable in class loci.formats.in.APNGReader
 
PASS_WIDTHS - Static variable in class loci.formats.in.APNGReader
Interlacing pass dimensions.
PassthroughCodec - Class in loci.formats.codec
A codec which just returns the exact data it was given, performing no compression or decompression.
PassthroughCodec() - Constructor for class loci.formats.codec.PassthroughCodec
 
path - Variable in class loci.formats.in.PerkinElmerReader.PixelsFile
 
path - Variable in class loci.plugins.config.ConfigWindow
 
path - Variable in class loci.plugins.config.LibraryEntry
 
pathToImageData - Variable in class loci.formats.in.BDVReader.H5Coordinate
 
pathToImageData - Variable in class loci.formats.in.CellH5Reader.CellH5Coordinate
 
pathToPosition - Variable in class loci.formats.in.BDVReader.H5Coordinate
 
pathToPosition - Variable in class loci.formats.in.CellH5Reader.CellH5Coordinate
 
pathToSegmentationData - Variable in class loci.formats.in.CellH5Reader.CellH5Coordinate
 
pattern - Variable in class loci.formats.FilePattern
The file pattern string.
pattern - Variable in class loci.formats.FileStitcher.ExternalSeries
 
PATTERN_D - Static variable in class loci.formats.in.CellomicsReader
 
PATTERN_O - Static variable in class loci.formats.in.CellomicsReader
 
patternIds - Variable in class loci.formats.FileStitcher
Whether string ids given should be treated as file patterns rather than single file paths.
PBGRA_32 - Static variable in class loci.formats.services.JPEGXRServiceImpl
 
PCI_MAGIC_BYTES - Static variable in class loci.formats.in.PCIReader
 
PCIReader - Class in loci.formats.in
PCIReader is the file format reader for SimplePCI (Compix) .cxd files.
PCIReader() - Constructor for class loci.formats.in.PCIReader
Constructs a new SimplePCI reader.
PCORAWReader - Class in loci.formats.in
PCORAWReader is the file format reader for PCORAW files.
PCORAWReader() - Constructor for class loci.formats.in.PCORAWReader
Constructs a new PCORAW reader.
PCX_MAGIC_BYTE - Static variable in class loci.formats.in.PCXReader
 
PCXReader - Class in loci.formats.in
PCXReader is the file format reader for PCX files (originally used by PC Paintbrush; now used in Zeiss' LSM Image Browser).
PCXReader() - Constructor for class loci.formats.in.PCXReader
Constructs a new PCX reader.
PDS_MAGIC_STRING - Static variable in class loci.formats.in.PDSReader
 
PDSReader - Class in loci.formats.in
PDSReader is the file format reader for Perkin Elmer densitometer files.
PDSReader() - Constructor for class loci.formats.in.PDSReader
Constructs a new PDS reader.
PerkinElmerReader - Class in loci.formats.in
PerkinElmerReader is the file format reader for PerkinElmer files.
PerkinElmerReader() - Constructor for class loci.formats.in.PerkinElmerReader
Constructs a new PerkinElmer reader.
PerkinElmerReader.PixelsFile - Class in loci.formats.in
 
pf(Double, String) - Method in class loci.formats.in.PrairieReader
Converts the given double to a PositiveFloat, or null if incompatible.
PF_ABGR - Static variable in class org.libjpegturbo.turbojpeg.TJ
ABGR pixel format.
PF_ARGB - Static variable in class org.libjpegturbo.turbojpeg.TJ
ARGB pixel format.
PF_BGR - Static variable in class org.libjpegturbo.turbojpeg.TJ
BGR pixel format.
PF_BGRA - Static variable in class org.libjpegturbo.turbojpeg.TJ
BGRA pixel format.
PF_BGRX - Static variable in class org.libjpegturbo.turbojpeg.TJ
BGRX pixel format.
PF_GRAY - Static variable in class org.libjpegturbo.turbojpeg.TJ
Grayscale pixel format.
PF_RGB - Static variable in class org.libjpegturbo.turbojpeg.TJ
RGB pixel format.
PF_RGBA - Static variable in class org.libjpegturbo.turbojpeg.TJ
RGBA pixel format.
PF_RGBX - Static variable in class org.libjpegturbo.turbojpeg.TJ
RGBX pixel format.
PF_XBGR - Static variable in class org.libjpegturbo.turbojpeg.TJ
XBGR pixel format.
PF_XRGB - Static variable in class org.libjpegturbo.turbojpeg.TJ
XRGB pixel format.
PFile(PrairieMetadata.Frame, Element) - Constructor for class loci.formats.in.PrairieMetadata.PFile
Creates a new file by parsing the given <File> element.
pfsOffset - Variable in class loci.formats.in.NativeND2Reader
 
pfsStateOffset - Variable in class loci.formats.in.NativeND2Reader
 
PGM_MAGIC_CHAR - Static variable in class loci.formats.in.PGMReader
 
PGMReader - Class in loci.formats.in
PGMReader is the file format reader for Portable Gray Map (PGM) images.
PGMReader() - Constructor for class loci.formats.in.PGMReader
Constructs a new PGMReader.
PHASE - Static variable in class loci.formats.FormatTools
Identifies the Phase dimensional type, representing a dimension consisting of phases.
PHASE - Static variable in class loci.formats.in.CellSensReader
 
phaseLabels - Variable in class loci.formats.in.ZeissCZIReader
 
phases - Variable in class loci.formats.in.LiFlimReader
 
phases - Variable in class loci.formats.in.ZeissCZIReader
 
phases - Variable in class loci.formats.in.ZeissLSMReader
 
PHOTOBLEACHING - Static variable in class loci.formats.in.CellSensReader
 
PhotoInterp - Enum in loci.formats.tiff
Utility class for working with TIFF photometric interpretations.
PhotoInterp(int, String, String) - Constructor for enum loci.formats.tiff.PhotoInterp
Default constructor.
PHOTOMETRIC_INTERPRETATION - Static variable in class loci.formats.in.DicomReader
 
PHOTOMETRIC_INTERPRETATION - Static variable in class loci.formats.tiff.IFD
 
photon(int) - Method in class loci.formats.in.SPCReader
 
PHOTON_IMAGING_MODE - Static variable in class loci.formats.in.CellSensReader
 
photosensorReading - Variable in class loci.formats.in.DeltavisionReader.DVExtHdrFields
Photosensor reading.
PhotoshopTiffReader - Class in loci.formats.in
PhotoshopTiffReader is the file format reader for Adobe Photoshop TIFF files.
PhotoshopTiffReader() - Constructor for class loci.formats.in.PhotoshopTiffReader
Constructs a new Photoshop TIFF reader.
PHYSICAL_SIZE_TAG - Static variable in class loci.formats.in.SlidebookTiffReader
 
physicalPixelSize - Variable in class loci.formats.in.VentanaReader
 
physicalSizes - Variable in class loci.formats.in.LeicaReader
 
physicalSizeX - Variable in class loci.formats.in.BaseZeissReader
 
physicalSizeX - Variable in class loci.formats.in.BioRadSCNReader
 
physicalSizeX - Variable in class loci.formats.in.CellSensReader.Pyramid
 
physicalSizeX - Variable in class loci.formats.in.FakeReader
 
physicalSizeX - Variable in class loci.formats.in.LeicaHandler
 
physicalSizeX - Variable in class loci.formats.in.NikonTiffReader
 
physicalSizeX - Variable in class loci.formats.in.OIRReader
 
physicalSizeX - Variable in class loci.formats.in.SISReader
 
physicalSizeXs - Variable in class loci.formats.in.LIFReader
 
physicalSizeY - Variable in class loci.formats.in.BaseZeissReader
 
physicalSizeY - Variable in class loci.formats.in.BioRadSCNReader
 
physicalSizeY - Variable in class loci.formats.in.CellSensReader.Pyramid
 
physicalSizeY - Variable in class loci.formats.in.FakeReader
 
physicalSizeY - Variable in class loci.formats.in.LeicaHandler
 
physicalSizeY - Variable in class loci.formats.in.NikonTiffReader
 
physicalSizeY - Variable in class loci.formats.in.OIRReader
 
physicalSizeY - Variable in class loci.formats.in.SISReader
 
physicalSizeYs - Variable in class loci.formats.in.LIFReader
 
physicalSizeZ - Variable in class loci.formats.in.BaseZeissReader
 
physicalSizeZ - Variable in class loci.formats.in.FakeReader
 
physicalSizeZ - Variable in class loci.formats.in.NikonTiffReader
 
physicalSizeZ - Variable in class loci.formats.in.OIRReader
 
physicalSizeZ - Variable in class loci.formats.in.TiffReader
 
physicalX - Variable in class loci.formats.in.VolocityReader.Stack
 
physicalY - Variable in class loci.formats.in.VolocityReader.Stack
 
physicalZ - Variable in class loci.formats.in.VolocityReader.Stack
 
PIC_FILE_ID - Static variable in class loci.formats.in.BioRadReader
Numerical ID of a valid Bio-Rad PIC file.
PIC_SUFFIX - Static variable in class loci.formats.in.BioRadReader
 
picFiles - Variable in class loci.formats.in.BioRadReader
 
pict - Variable in class loci.formats.in.OpenlabReader
Helper reader to read PICT data.
pict - Variable in class loci.formats.in.OpenlabReader.PlaneInfo
 
PICT_9A - Static variable in class loci.formats.in.PictReader
 
PICT_BITSRECT - Static variable in class loci.formats.in.PictReader
 
PICT_BITSRGN - Static variable in class loci.formats.in.PictReader
 
PICT_CLIP_RGN - Static variable in class loci.formats.in.PictReader
 
PICT_END - Static variable in class loci.formats.in.PictReader
 
PICT_JPEG - Static variable in class loci.formats.in.PictReader
 
PICT_LONGCOMMENT - Static variable in class loci.formats.in.PictReader
 
PICT_PACKBITSRECT - Static variable in class loci.formats.in.PictReader
 
PICT_PACKBITSRGN - Static variable in class loci.formats.in.PictReader
 
PICT_TYPE_1 - Static variable in class loci.formats.in.PictReader
 
PICT_TYPE_2 - Static variable in class loci.formats.in.PictReader
 
PictReader - Class in loci.formats.in
PictReader is the file format reader for Apple PICT files.
PictReader() - Constructor for class loci.formats.in.PictReader
Constructs a new PICT reader.
pictToImage(byte[]) - Method in class loci.formats.gui.LegacyQTTools
Converts the given byte array in PICT format to a Java image.
PictWidgets - Class in loci.plugins.config
Custom widgets for configuring Bio-Formats PICT support.
PictWidgets() - Constructor for class loci.plugins.config.PictWidgets
 
pinhole - Variable in class loci.formats.in.ImarisHDFReader
 
pinhole - Variable in class loci.formats.in.LeicaHandler
 
pinhole - Variable in class loci.formats.in.LeicaReader
 
pinhole - Variable in class loci.formats.in.OIRReader.Channel
 
pinhole - Variable in class loci.formats.in.ZeissCZIReader.Channel
 
pinhole - Variable in class loci.formats.in.ZeissLSMReader.DetectionChannel
 
pinholes - Variable in class loci.formats.in.LIFReader
 
pinholeSize - Variable in class loci.formats.in.FV1000Reader
 
pinholeSize - Variable in class loci.formats.in.ND2Handler
 
pinholeSize - Variable in class loci.formats.in.NikonTiffReader
 
pix - Variable in class loci.formats.in.CanonRawReader
 
pixClk - Variable in class loci.formats.in.SDTInfo
 
PIXEL_CLOCK - Static variable in class loci.formats.in.CellSensReader
 
PIXEL_DATA - Static variable in class loci.formats.in.DicomReader
 
PIXEL_FORMAT_TAG - Static variable in class loci.formats.services.JPEGXRServiceImpl
 
PIXEL_INFO_TYPE - Static variable in class loci.formats.in.CellSensReader
 
PIXEL_OFFSET - Static variable in class loci.formats.in.BioRadGelReader
 
PIXEL_OFFSET - Static variable in class loci.formats.in.VGSAMReader
 
PIXEL_REPRESENTATION - Static variable in class loci.formats.in.DicomReader
 
PIXEL_SIGN - Static variable in class loci.formats.in.DicomReader
 
PIXEL_SPACING - Static variable in class loci.formats.in.DicomReader
 
PIXEL_X_DIMENSION - Static variable in class loci.formats.tiff.IFD
 
PIXEL_Y_DIMENSION - Static variable in class loci.formats.tiff.IFD
 
pixelBits - Variable in class loci.formats.gui.SignedColorModel
 
PixelBlock() - Constructor for class loci.formats.in.OIRReader.PixelBlock
 
pixelBlocks - Variable in class loci.formats.in.OIRReader
 
pixelBytes - Variable in class loci.formats.in.NativeQTReader
Total number of bytes of pixel data.
pixelData - Variable in class loci.formats.in.MINCReader
 
pixelFile - Variable in class loci.formats.in.AnalyzeReader
File containing the pixel data.
pixelFile - Variable in class loci.formats.in.NiftiReader
File containing the pixel data.
pixelLengths - Variable in class loci.formats.in.SlidebookReader
 
pixelOffset - Variable in class loci.formats.in.AIMReader
 
pixelOffset - Variable in class loci.formats.in.AnalyzeReader
Offset to the pixel data in the .img file.
pixelOffset - Variable in class loci.formats.in.FitsReader
 
pixelOffset - Variable in class loci.formats.in.GatanReader
Offset to pixel data.
pixelOffset - Variable in class loci.formats.in.HISReader
Offsets to pixel data for each series.
pixelOffset - Variable in class loci.formats.in.JEOLReader
 
pixelOffset - Variable in class loci.formats.in.KodakReader
 
pixelOffset - Variable in class loci.formats.in.MolecularImagingReader
 
pixelOffset - Variable in class loci.formats.in.NativeQTReader
Offset to start of pixel data.
pixelOffset - Variable in class loci.formats.in.NiftiReader
Offset to the pixel data in the .img file.
pixelOffset - Variable in class loci.formats.in.RHKReader
 
pixelOffset - Variable in class loci.formats.in.SIFReader
 
pixelOffset - Variable in class loci.formats.in.TopometrixReader
 
pixelOffset - Variable in class loci.formats.in.VolocityClippingReader
 
pixelOffset - Variable in class loci.formats.out.ICSWriter
 
pixelOffset - Variable in class loci.formats.out.V3DrawWriter
 
pixelOffsets - Variable in class loci.formats.in.JPXReader
 
pixelOffsets - Variable in class loci.formats.in.SlidebookReader
 
pixelOffsets - Variable in class loci.formats.in.VarianFDFReader
 
pixelOffsets - Variable in class loci.formats.in.VisitechReader
 
pixels - Variable in class loci.formats.in.AFIReader
 
pixels - Variable in class loci.formats.in.GIFReader
 
pixels - Variable in class loci.formats.in.ImagicReader
 
pixels - Variable in class loci.formats.in.LeicaSCNReader.Image
 
Pixels(Attributes) - Constructor for class loci.formats.in.LeicaSCNReader.Pixels
 
pixels - Variable in class loci.formats.in.ZeissCZIReader
 
pixels - Variable in class loci.formats.out.ICSWriter
 
pixels - Variable in class loci.formats.out.V3DrawWriter
 
pixels2 - Variable in class loci.formats.out.LegacyQTWriter
 
PIXELS_MARKER - Static variable in class loci.formats.in.VisitechReader
 
PIXELS_OFFSET - Static variable in class loci.formats.in.ARFReader
 
PIXELS_OFFSET - Static variable in class loci.formats.in.LIMReader
 
PIXELS_STRING - Static variable in class loci.formats.in.KodakReader
 
PIXELS_SUFFIXES - Static variable in class loci.formats.in.InCellReader
 
PIXELS_TAG - Static variable in class loci.formats.in.ImaconReader
 
pixelsFile - Variable in class loci.formats.in.FujiReader
 
pixelsFile - Variable in class loci.formats.in.ImagicReader
 
pixelsFile - Variable in class loci.formats.in.PDSReader
 
PixelsFile() - Constructor for class loci.formats.in.PerkinElmerReader.PixelsFile
 
pixelsFilename - Variable in class loci.formats.in.AnalyzeReader
 
pixelsFilename - Variable in class loci.formats.in.NiftiReader
 
pixelsFiles - Variable in class loci.formats.in.BrukerReader
 
pixelsFiles - Variable in class loci.formats.in.TillVisionReader
 
pixelsFiles - Variable in class loci.formats.in.VolocityReader.Stack
 
pixelSize - Variable in class loci.formats.in.FV1000Reader
 
pixelSize - Variable in class loci.formats.in.IPLabReader
 
pixelSize - Variable in class loci.formats.in.MicromanagerReader.Position
 
pixelSize - Variable in class loci.formats.in.ScanrReader
 
pixelSize - Variable in class loci.formats.in.SVSCoreMetadata
 
pixelSize - Static variable in class org.libjpegturbo.turbojpeg.TJ
 
pixelSizes - Variable in class loci.formats.in.GatanReader
List of pixel sizes.
pixelSizes - Variable in class loci.formats.in.NRRDReader
 
pixelSizeT - Variable in class loci.formats.in.FV1000Reader
 
pixelSizeT - Variable in class loci.formats.in.ImprovisionTiffReader
 
pixelSizeUnits - Variable in class loci.formats.in.GatanDM2Reader
 
pixelSizeX - Variable in class loci.formats.in.DicomReader
 
pixelSizeX - Variable in class loci.formats.in.FV1000Reader
 
pixelSizeX - Variable in class loci.formats.in.GatanDM2Reader
 
pixelSizeX - Variable in class loci.formats.in.ImarisHDFReader
 
pixelSizeX - Variable in class loci.formats.in.ImprovisionTiffReader
 
pixelSizeX - Variable in class loci.formats.in.MetamorphHandler
 
pixelSizeX - Variable in class loci.formats.in.ND2Handler
 
pixelSizeX - Variable in class loci.formats.in.PerkinElmerReader
 
pixelSizeX - Variable in class loci.formats.in.VarianFDFReader
 
pixelSizeX - Variable in class loci.formats.in.ZeissLSMReader
 
pixelSizeY - Variable in class loci.formats.in.DicomReader
 
pixelSizeY - Variable in class loci.formats.in.FV1000Reader
 
pixelSizeY - Variable in class loci.formats.in.GatanDM2Reader
 
pixelSizeY - Variable in class loci.formats.in.ImarisHDFReader
 
pixelSizeY - Variable in class loci.formats.in.ImprovisionTiffReader
 
pixelSizeY - Variable in class loci.formats.in.MetamorphHandler
 
pixelSizeY - Variable in class loci.formats.in.ND2Handler
 
pixelSizeY - Variable in class loci.formats.in.PerkinElmerReader
 
pixelSizeY - Variable in class loci.formats.in.VarianFDFReader
 
pixelSizeY - Variable in class loci.formats.in.ZeissLSMReader
 
pixelSizeZ - Variable in class loci.formats.in.DicomReader
 
pixelSizeZ - Variable in class loci.formats.in.FV1000Reader
 
pixelSizeZ - Variable in class loci.formats.in.ImarisHDFReader
 
pixelSizeZ - Variable in class loci.formats.in.ImprovisionTiffReader
 
pixelSizeZ - Variable in class loci.formats.in.ND2Handler
 
pixelSizeZ - Variable in class loci.formats.in.VarianFDFReader
 
pixelSizeZ - Variable in class loci.formats.in.ZeissLSMReader
 
pixelsOffset - Variable in class loci.formats.in.BioRadSCNReader
 
pixelsOffset - Variable in class loci.formats.in.BurleighReader
 
pixelsOffset - Variable in class loci.formats.in.InCell3000Reader
 
pixelsOffset - Variable in class loci.formats.in.JPEG2000Reader
 
pixelsOffset - Variable in class loci.formats.in.QuesantReader
 
pixelsOffsets - Variable in class loci.formats.in.ImspectorReader
List of offsets to each block of pixel data.
pixelsPerPlane - Variable in class loci.formats.in.AmiraReader.ASCII
 
pixelsStream - Variable in class loci.formats.in.TillVisionReader
 
pixelStack - Variable in class loci.formats.in.GIFReader
 
pixelType - Variable in class loci.formats.CoreMetadata
Describes the number of bytes per pixel.
pixelType - Variable in class loci.formats.in.AmiraReader.ASCII
 
pixelType - Variable in class loci.formats.in.ZeissCZIReader.DirectoryEntry
 
pixelType - Variable in class loci.formats.services.WlzServiceImpl
 
pixelTypeFromBytes(int, boolean, boolean) - Static method in class loci.formats.FormatTools
Returns an appropriate pixel type given the number of bytes per pixel.
pixelTypeFromString(String) - Static method in class loci.formats.FormatTools
Takes a string value and maps it to one of the pixel type enumerations.
pixelTypeIndex - Variable in class loci.formats.in.ZeissCZIReader.SubBlock
 
pixelTypes - Static variable in class loci.formats.FormatTools
Human readable pixel type.
pixelUIDs - Variable in class loci.formats.in.OIRReader
 
pixTime - Variable in class loci.formats.in.SDTInfo
 
placeWindow(Window) - Static method in class loci.plugins.util.WindowTools
Places the given window at a nice location on screen, either centered below the ImageJ window if there is one, or else centered on screen.
PLANAR_CONFIGURATION - Static variable in class loci.formats.in.DicomReader
 
PLANAR_CONFIGURATION - Static variable in class loci.formats.tiff.IFD
 
plane - Variable in class loci.formats.in.CanonRawReader
 
Plane() - Constructor for class loci.formats.in.ColumbusReader.Plane
 
Plane() - Constructor for class loci.formats.in.CV7000Reader.Plane
 
Plane() - Constructor for class loci.formats.in.OperettaReader.Plane
 
plane - Variable in class loci.formats.in.ZeissCZIReader.Coordinate
 
Plane(String, ZeissTIFFHandler.TagSet) - Constructor for class loci.formats.in.ZeissTIFFHandler.Plane
Constructor
Plane() - Constructor for class loci.formats.in.ZeissTIFFReader.Plane
 
PLANE_ORIGIN_RWC - Static variable in class loci.formats.in.CellSensReader
 
PLANE_SCALE_RWC - Static variable in class loci.formats.in.CellSensReader
 
PLANE_UNIT - Static variable in class loci.formats.in.CellSensReader
 
planeCount() - Method in class loci.formats.out.OMETiffWriter
 
planeData - Variable in class loci.formats.in.CV7000Reader
 
PlaneData() - Constructor for class loci.formats.in.FV1000Reader.PlaneData
 
planeDeltaT - Variable in class loci.formats.in.FlexReader
 
planeExposureTime - Variable in class loci.formats.in.FlexReader
 
planeIndex - Variable in class loci.formats.in.ZeissCZIReader.SubBlock
 
planeIndexes - Variable in class loci.plugins.util.BFVirtualStack
 
PlaneInfo() - Constructor for class loci.formats.in.OpenlabReader.PlaneInfo
 
planeMax - Variable in class loci.formats.MinMaxCalculator
Max values for each plane.
planeMin - Variable in class loci.formats.MinMaxCalculator
Min values for each plane.
planeName - Variable in class loci.formats.in.OpenlabReader.PlaneInfo
 
planeNames - Variable in class loci.formats.in.ZeissTIFFHandler
 
planeOffset - Variable in class loci.formats.in.OpenlabReader.PlaneInfo
 
planeOffset - Variable in class loci.formats.in.SlidebookReader
 
planeOffset - Variable in class loci.formats.out.EPSWriter
 
planeOffsets - Variable in class loci.formats.in.OpenlabReader
 
planePadding - Variable in class loci.formats.in.VolocityReader.Stack
 
planePositionX - Variable in class loci.formats.in.FlexReader
 
planePositionY - Variable in class loci.formats.in.FlexReader
 
planePositionZ - Variable in class loci.formats.in.FlexReader
 
planeReader - Variable in class loci.formats.in.AmiraReader
 
planes - Variable in class loci.formats.in.ColumbusReader
 
planes - Variable in class loci.formats.in.CV7000Reader.MeasurementDataHandler
 
planes - Variable in class loci.formats.in.FV1000Reader
 
planes - Variable in class loci.formats.in.OpenlabReader
 
planes - Variable in class loci.formats.in.OperettaReader.OperettaHandler
 
planes - Variable in class loci.formats.in.OperettaReader
 
planes - Variable in class loci.formats.in.ZeissCZIReader
 
planes - Variable in class loci.formats.in.ZeissTIFFHandler
 
planes - Variable in class loci.formats.in.ZeissTIFFReader
Image planes
planeSize - Variable in class loci.formats.in.AmiraReader.HxRLE
 
planeSize - Variable in class loci.formats.in.AmiraReader.HxZip
 
planesPerBlock - Variable in class loci.formats.in.ImspectorReader
Number of planes in each block of pixel data.
planesRead - Variable in class loci.formats.in.GIFReader
 
planesWritten - Variable in class loci.formats.out.AVIWriter
 
PLATE - Static variable in class loci.formats.in.CellH5Reader.CellH5Constants
 
plate - Variable in class loci.formats.in.CellH5Reader.CellH5Coordinate
 
plate - Variable in class loci.formats.in.MIASReader.AnalysisFile
 
PLATE - Static variable in class loci.formats.ResourceNamer
 
plateAcqs - Variable in class loci.formats.in.FakeReader
 
plateAcqStartTime - Variable in class loci.formats.in.FlexReader
 
plateBarcode - Variable in class loci.formats.in.FlexReader
 
plateCols - Variable in class loci.formats.in.FakeReader
 
plateCols - Variable in class loci.formats.in.OperettaReader.OperettaHandler
 
plateColumns - Variable in class loci.formats.in.ColumbusReader.MeasurementHandler
 
plateColumns - Variable in class loci.formats.in.CV7000Reader.WPIHandler
 
plateCount - Variable in class loci.formats.in.FlexReader
 
plateDescription - Variable in class loci.formats.in.BDReader
 
plateDescription - Variable in class loci.formats.in.OperettaReader.OperettaHandler
 
plateID - Variable in class loci.formats.in.CV7000Reader.WPIHandler
 
plateID - Variable in class loci.formats.in.OperettaReader.OperettaHandler
 
plateLogFile - Variable in class loci.formats.in.CellWorxReader
 
plateMap - Variable in class loci.formats.in.InCellReader
 
plateName - Variable in class loci.formats.in.BDReader
 
plateName - Variable in class loci.formats.in.ColumbusReader.MeasurementHandler
 
plateName - Variable in class loci.formats.in.FlexReader
 
plateName - Variable in class loci.formats.in.OperettaReader.OperettaHandler
 
plateName - Variable in class loci.formats.in.ScanrReader
 
plateRows - Variable in class loci.formats.in.ColumbusReader.MeasurementHandler
 
plateRows - Variable in class loci.formats.in.CV7000Reader.WPIHandler
 
plateRows - Variable in class loci.formats.in.FakeReader
 
plateRows - Variable in class loci.formats.in.OperettaReader.OperettaHandler
 
plates - Variable in class loci.formats.in.FakeReader
 
plateType - Variable in class loci.formats.in.ColumbusReader.MeasurementHandler
 
plugin - Variable in class loci.plugins.in.Importer
A handle to the plugin wrapper, for toggling the canceled and success flags.
plugin - Variable in class loci.plugins.out.Exporter
 
plugins - Static variable in class loci.plugins.shortcut.ShortcutPanel
Details for installed plugins.
PN - Static variable in class loci.formats.in.DicomReader
 
PNG - Static variable in class loci.formats.in.CellSensReader
 
PNG_SIG - Static variable in class loci.formats.out.APNGWriter
 
PNGBlock() - Constructor for class loci.formats.in.APNGReader.PNGBlock
 
PNGInputStream(String) - Constructor for class loci.formats.in.APNGReader.PNGInputStream
 
PNGInputStream(String, int) - Constructor for class loci.formats.in.APNGReader.PNGInputStream
 
poi - Variable in class loci.formats.in.FV1000Reader
 
poi - Variable in class loci.formats.in.IPWReader
Helper reader - parses embedded files from the OLE document.
poi - Variable in class loci.formats.in.PCIReader
 
poi - Variable in class loci.formats.in.ZeissZVIReader
 
POINT - Static variable in class loci.formats.in.FV1000Reader
ROI types.
pointCount - Variable in class loci.formats.in.BaseZeissReader.Shape
 
points - Variable in enum loci.formats.in.BaseZeissReader.FeatureType
 
points - Variable in class loci.formats.in.BaseZeissReader.Shape
 
points - Variable in class loci.formats.in.FakeReader
 
points - Variable in class loci.formats.in.IMODReader
 
points - Variable in class loci.formats.in.LiFlimReader.ROI
 
pointsToString() - Method in class loci.formats.in.LiFlimReader.ROI
 
PointStyle(int) - Constructor for enum loci.formats.in.BaseZeissReader.PointStyle
 
pointStyle - Variable in class loci.formats.in.BaseZeissReader.Shape
 
POIService - Interface in loci.formats.services
Interface defining methods for reading Microsoft OLE2 documents using OME's fork of Apache POI.
POIServiceImpl - Class in loci.formats.services
 
POIServiceImpl() - Constructor for class loci.formats.services.POIServiceImpl
Default constructor.
polarityF - Variable in class loci.formats.in.SDTInfo
 
polarityL - Variable in class loci.formats.in.SDTInfo
2 = disabled line markers.
polarityP - Variable in class loci.formats.in.SDTInfo
 
POLARIZATION - Static variable in class loci.formats.FormatTools
Identifies the Polarization dimensional type, representing a dimension consisting of polarization states.
POLYGON - Static variable in class loci.formats.in.FV1000Reader
 
POLYGON - Static variable in class loci.formats.in.LeicaHandler.ROI
 
POLYGON - Static variable in class loci.formats.in.LIFReader.ROI
 
polygons - Variable in class loci.formats.in.FakeReader
 
POLYLINE - Static variable in class loci.formats.in.FV1000Reader
 
POLYLINE_ARROW - Static variable in class loci.formats.in.ZeissLSMReader
 
polylines - Variable in class loci.formats.in.FakeReader
 
populateCircles(NodeList, int, int) - Method in class loci.formats.in.ZeissCZIReader
 
populateCore - Variable in class loci.formats.in.FlexReader.FlexHandler
 
populateCoreMetadata(int, int, int, List<String>) - Method in class loci.formats.in.FlexReader
Populate core metadata using the given list of image names.
populateCoreMetadata() - Method in class loci.formats.in.PrairieReader
This step populates the CoreMetadata by extracting relevant values from the parsed PrairieReader.meta structure.
populateCoreMetadata(int, int, int, int, int) - Method in class loci.formats.in.TextReader
Populates the CoreMetadata values.
populateExtendedMetadata() - Method in class loci.formats.in.NiftiReader
 
populateGlobalMetaData() - Method in class loci.formats.in.SPEReader
This function is used to populate values not contained in Core Meta Data to the Global Meta Data
populateImage(OMEXMLMetadata, int) - Method in class loci.formats.out.OMETiffWriter
 
populateLines(NodeList, int, int) - Method in class loci.formats.in.ZeissCZIReader
 
populateMaskPixels(int, int, int, MetadataStore) - Method in class loci.formats.in.MIASReader
Populate the MaskPixels.BinData attribute for the Mask identified by the given Image index, ROI index, and Shape index.
populateMetadata() - Method in class loci.formats.in.MicromanagerReader
 
populateMetadata(MetadataStore, int, String, CoreMetadata) - Static method in class loci.formats.MetadataTools
Populates the given MetadataStore, for the specified series, using the values from the provided CoreMetadata.
populateMetadata(MetadataStore, int, String, boolean, String, String, int, int, int, int, int, int) - Static method in class loci.formats.MetadataTools
Populates the given MetadataStore, for the specified series, using the provided values.
populateMetadata(MetadataStore, String, int, String, boolean, String, String, int, int, int, int, int, int) - Static method in class loci.formats.MetadataTools
Populates the given MetadataStore, for the specified series, using the provided values.
populateMetadataStore(MetadataStore) - Method in class loci.formats.in.FlexReader
 
populateMetadataStore(MetadataStore, String) - Method in class loci.formats.in.FV1000Reader
 
populateMetadataStore(String[]) - Method in class loci.formats.in.MicromanagerReader
 
populateMetadataStore(ND2Handler) - Method in class loci.formats.in.NativeND2Reader
 
populateMetadataStore() - Method in class loci.formats.in.TillVisionReader
 
populateMetadataStore(ZeissLSMReader.SubBlock, MetadataStore, int) - Method in class loci.formats.in.ZeissLSMReader
 
populateMetadataStoreImageJ(MetadataStore) - Method in class loci.formats.in.TiffReader
Checks the original metadata table for ImageJ-specific information to propagate into the metadata store.
populateObjective(MetadataStore, int) - Method in class loci.formats.in.DeltavisionReader
Populate an Objective based upon the lens ID.
populateObjective(MetadataStore, int) - Method in class loci.formats.in.RCPNLReader
 
populateOMEMetadata(IniTable, MetadataStore) - Method in class loci.formats.in.HitachiReader
 
populateOMEMetadata() - Method in class loci.formats.in.PrairieReader
This step populates the OME MetadataStore by extracting relevant values from the parsed PrairieReader.meta structure.
populateOriginalMetadata(Element, Deque<String>) - Method in class loci.formats.in.LIFReader
 
populateOriginalMetadata() - Method in class loci.formats.in.PrairieReader
This steps populates the original metadata table (the tables returned by FormatReader.getGlobalMetadata() and FormatReader.getSeriesMetadata()).
populateOriginalMetadata(Element, Deque<String>) - Method in class loci.formats.in.ZeissCZIReader
 
populateOriginalMetadata(OMEXMLMetadata, Hashtable<String, Object>) - Method in interface loci.formats.services.OMEXMLService
Adds the key/value pairs in the specified Hashtable as new OriginalMetadata annotations in the given OME-XML metadata object.
populateOriginalMetadata(OMEXMLMetadata, String, String) - Method in interface loci.formats.services.OMEXMLService
Adds the specified key/value pair as a new OriginalMetadata node to the given OME-XML metadata object.
populateOriginalMetadata(OMEXMLMetadata, Hashtable<String, Object>) - Method in class loci.formats.services.OMEXMLServiceImpl
 
populateOriginalMetadata(OMEXMLMetadata, String, String) - Method in class loci.formats.services.OMEXMLServiceImpl
 
populatePixels(MetadataStore, IFormatReader) - Static method in class loci.formats.MetadataTools
Populates the Pixels element of the given metadata store, using core metadata from the given reader.
populatePixels(MetadataStore, IFormatReader, boolean) - Static method in class loci.formats.MetadataTools
Populates the Pixels element of the given metadata store, using core metadata from the given reader.
populatePixels(MetadataStore, IFormatReader, boolean, boolean) - Static method in class loci.formats.MetadataTools
Populates the Pixels element of the given metadata store, using core metadata from the given reader.
populatePixelsOnly(MetadataStore, IFormatReader) - Static method in class loci.formats.MetadataTools
 
populatePixelsOnly(MetadataStore, int, boolean, String, String, int, int, int, int, int, int) - Static method in class loci.formats.MetadataTools
 
populatePixelType(int) - Method in class loci.formats.in.NiftiReader
 
populatePolylines(NodeList, int, int, boolean) - Method in class loci.formats.in.ZeissCZIReader
 
populateRectangles(NodeList, int, int) - Method in class loci.formats.in.ZeissCZIReader
 
populateROI(List<String>, String[], int, int, int, int, MetadataStore) - Method in class loci.formats.in.MIASReader
 
populateRoiMetaData(MetadataStore) - Method in class loci.formats.in.SPEReader
Reads and populates ROI Meta Data values.
populateROIs(MetadataStore) - Method in class loci.formats.in.ND2Handler
 
populateSPW(MetadataStore, int, int, int, int, int, int, boolean) - Method in class loci.formats.in.FakeReader
 
populateTiffData(OMEXMLMetadata, int[], int, int, int) - Method in class loci.formats.out.OMETiffWriter
 
populateXY - Variable in class loci.formats.in.ND2Handler
 
pos(int) - Method in class loci.formats.cache.CacheStrategy
Shortcut for converting rasterized position to N-D position.
pos(int, int[]) - Method in class loci.formats.cache.CacheStrategy
Shortcut for converting rasterized position to N-D position, using the given array instead of allocating a new one.
pos - Variable in class loci.formats.in.AVIReader
 
position - Variable in class loci.formats.in.MicromanagerReader.Index
 
Position() - Constructor for class loci.formats.in.MicromanagerReader.Position
 
position - Variable in class loci.formats.in.NativeND2Reader.ChunkMapEntry
 
position - Variable in class loci.formats.in.OBFReader.Stack
 
POSITION_CHANGED - Static variable in class loci.formats.cache.CacheEvent
Event type indicating an updated current dimensional position.
positionCount - Variable in class loci.formats.in.NativeND2Reader
 
positionInT - Variable in class loci.formats.in.DeltavisionReader
 
positions - Variable in class loci.formats.cache.CacheStrategy
The list of dimensional positions to consider caching, in order of preference based on strategy, axis priority and planar ordering.
positions - Variable in class loci.formats.in.MicromanagerReader.Position
 
positions - Variable in class loci.formats.in.MicromanagerReader
 
positions - Variable in class loci.formats.in.ZeissCZIReader
 
positionsMatch(int, int) - Method in class loci.formats.in.PrairieReader
Verifies that stage coordinates match for all (P, Z) across time.
positionsX - Variable in class loci.formats.in.ZeissCZIReader
 
positionsY - Variable in class loci.formats.in.ZeissCZIReader
 
positionsZ - Variable in class loci.formats.in.ZeissCZIReader
 
positionToRaster(int[], int[]) - Static method in class loci.formats.FormatTools
Computes a unique 1-D index corresponding to the given multidimensional position.
positionX - Variable in class loci.formats.in.ColumbusReader.Plane
 
positionX - Variable in class loci.formats.in.DicomReader
 
positionX - Variable in class loci.formats.in.FV1000Reader.PlaneData
 
positionX - Variable in class loci.formats.in.MetamorphHandler
 
positionX - Variable in class loci.formats.in.OperettaReader.Plane
 
positionY - Variable in class loci.formats.in.ColumbusReader.Plane
 
positionY - Variable in class loci.formats.in.DicomReader
 
positionY - Variable in class loci.formats.in.FV1000Reader.PlaneData
 
positionY - Variable in class loci.formats.in.MetamorphHandler
 
positionY - Variable in class loci.formats.in.OperettaReader.Plane
 
positionZ - Variable in class loci.formats.in.ColumbusReader.Plane
 
positionZ - Variable in class loci.formats.in.DicomReader
 
positionZ - Variable in class loci.formats.in.FV1000Reader.PlaneData
 
positionZ - Variable in class loci.formats.in.OperettaReader.Plane
 
posNames - Variable in class loci.formats.in.ND2Handler
 
possibleValues - Variable in class loci.plugins.prefs.StringOption
List of possible values.
post - Variable in class loci.formats.NumberFilter
String appearing after the numerical block.
POST_PROCESS - Static variable in class loci.formats.in.CV7000Reader
 
posX - Variable in class loci.formats.in.GatanReader
 
posX - Variable in class loci.formats.in.InCellReader
 
posX - Variable in class loci.formats.in.LIFReader
 
posX - Variable in class loci.formats.in.NativeND2Reader
 
posX - Variable in class loci.formats.in.ND2Handler
 
posY - Variable in class loci.formats.in.GatanReader
 
posY - Variable in class loci.formats.in.InCellReader
 
posY - Variable in class loci.formats.in.LIFReader
 
posY - Variable in class loci.formats.in.NativeND2Reader
 
posY - Variable in class loci.formats.in.ND2Handler
 
posZ - Variable in class loci.formats.in.GatanReader
 
posZ - Variable in class loci.formats.in.LIFReader
 
posZ - Variable in class loci.formats.in.NativeND2Reader
 
posZ - Variable in class loci.formats.in.ND2Handler
 
PovrayReader - Class in loci.formats.in
PovrayReader is the file format reader for POV-Ray .df3 files.
PovrayReader() - Constructor for class loci.formats.in.PovrayReader
Constructs a new POV-Ray reader.
power - Variable in class loci.formats.in.CV7000Reader.LightSource
 
power - Variable in class loci.formats.in.ND2Handler
 
power - Variable in class loci.formats.in.OIRReader.Laser
 
power - Variable in class loci.formats.in.ZeissLSMReader.Laser
 
PQBinReader - Class in loci.formats.in
PQBinReader is the file format reader for PicoQuant .bin files.
PQBinReader() - Constructor for class loci.formats.in.PQBinReader
Constructs a new PQBin reader.
PRAIRIE_SUFFIXES - Static variable in class loci.formats.in.PrairieReader
 
PRAIRIE_TAG_1 - Static variable in class loci.formats.in.PrairieReader
 
PRAIRIE_TAG_2 - Static variable in class loci.formats.in.PrairieReader
 
PRAIRIE_TAG_3 - Static variable in class loci.formats.in.PrairieReader
 
PrairieMetadata - Class in loci.formats.in
Metadata structure for Prairie Technologies' TIFF-based format.
PrairieMetadata(Document, Document, Document) - Constructor for class loci.formats.in.PrairieMetadata
Creates a new Prairie metadata by parsing the given XML, CFG and/or ENV documents.
PrairieMetadata.Frame - Class in loci.formats.in
A Prairie <Frame>, beneath a <Sequence>.
PrairieMetadata.PFile - Class in loci.formats.in
A Prairie <File> beneath a <Frame>.
PrairieMetadata.Sequence - Class in loci.formats.in
A Prairie <Sequence>.
PrairieMetadata.Value - Interface in loci.formats.in
A value in a Prairie metadata dictionary.
PrairieMetadata.ValueItem - Class in loci.formats.in
A leaf value with an actual PrairieMetadata.ValueItem.value() as well as an optional PrairieMetadata.ValueItem.description().
PrairieMetadata.ValueTable - Class in loci.formats.in
A table of values.
PrairieReader - Class in loci.formats.in
PrairieReader is the file format reader for Prairie Technologies' TIFF variant.
PrairieReader() - Constructor for class loci.formats.in.PrairieReader
Constructs a new Prairie TIFF reader.
pre - Variable in class loci.formats.NumberFilter
String appearing before the numerical block.
PRE_AMP_SETTING - Static variable in class loci.formats.in.FluoviewReader
 
PREAMP_GAIN_VALUE - Static variable in class loci.formats.in.CellSensReader
 
PREDICTED_CLASS_LABELS - Static variable in class loci.formats.in.BDVReader.H5Constants
 
PREDICTED_CLASS_LABELS - Static variable in class loci.formats.in.CellH5Reader.CellH5Constants
 
PREDICTOR - Static variable in class loci.formats.tiff.IFD
 
PREF_CELLSENS_FAIL - Static variable in class loci.plugins.util.LociPrefs
 
PREF_CZI_ATTACHMENT - Static variable in class loci.plugins.util.LociPrefs
 
PREF_CZI_AUTOSTITCH - Static variable in class loci.plugins.util.LociPrefs
 
PREF_LEICA_LIF_PHYSICAL_SIZE - Static variable in class loci.plugins.util.LociPrefs
 
PREF_ND2_CHUNKMAP - Static variable in class loci.plugins.util.LociPrefs
 
PREF_ND2_NIKON - Static variable in class loci.plugins.util.LociPrefs
 
PREF_PICT_QTJAVA - Static variable in class loci.plugins.util.LociPrefs
 
PREF_QT_QTJAVA - Static variable in class loci.plugins.util.LociPrefs
 
PREF_READER_ENABLED - Static variable in class loci.plugins.util.LociPrefs
 
PREF_READER_WINDOWLESS - Static variable in class loci.plugins.util.LociPrefs
 
PREF_SDT_INTENSITY - Static variable in class loci.plugins.util.LociPrefs
 
PREF_SLICE_LABEL_BASE_INDEX - Static variable in class loci.plugins.util.LociPrefs
 
PREF_SLICE_LABEL_PATTERN - Static variable in class loci.plugins.util.LociPrefs
 
PREF_TIFF_IMAGEIO - Static variable in class loci.plugins.util.LociPrefs
 
prefix - Variable in class loci.formats.in.GIFReader
 
prefix - Variable in class loci.formats.in.ND2Handler
 
PREFIX - Static variable in class loci.formats.in.TCSReader
 
prefix - Variable in class loci.formats.in.ZeissTIFFReader.TIFFInfo
 
PREFIX_PATH - Static variable in class loci.formats.in.CellH5Reader.CellH5Constants
 
preLoad - Variable in class loci.formats.in.SDTReader
Whether to pre-load all lifetime bins for faster loading.
prepareGZipStream(int) - Method in class loci.formats.in.LiFlimReader
 
prepareToWriteImage(int, byte[], IFD, int, int, int, int) - Method in class loci.formats.out.TiffWriter
Performs the preparation for work prior to the usage of the TIFF saver.
prepareUINT12Stream(int) - Method in class loci.formats.in.LiFlimReader
Similar to Gzip, make a DataInputstream for UINT12 data
prepend(ClassList<T>) - Method in class loci.formats.ClassList
Prepends a class list which must be assignable to the base class
prepend(List<Class<? extends T>>) - Method in class loci.formats.ClassList
Prepends a list of classes which must be assignable to the base class
preprocess(RandomAccessInputStream) - Method in class loci.formats.codec.JPEGTileDecoder
Pre-process the stream to make sure that the image width and height are non-zero.
PRESCANS - Static variable in class loci.formats.in.FluoviewReader
 
PRESENT - Static variable in class loci.plugins.config.LibraryEntry
HTML markup for installed library.
prestitched - Variable in class loci.formats.in.ZeissCZIReader
 
prevBuf - Variable in class loci.formats.in.ZeissLSMReader
 
prevChannel - Variable in class loci.formats.in.ZeissLSMReader
 
prevElement - Variable in class loci.formats.in.ND2Handler
 
PREVIEWNAME_PREFIXES - Static variable in class loci.formats.in.FV1000Reader
 
previewNames - Variable in class loci.formats.in.FV1000Reader
 
PreviewPane - Class in loci.formats.gui
PreviewPane is a panel for use as a JFileChooser accessory, displaying a thumbnail for the selected image, loaded in a separate thread.
PreviewPane(JFileChooser) - Constructor for class loci.formats.gui.PreviewPane
Constructs a preview pane for the given file chooser.
prevImage - Variable in class loci.formats.in.ICSReader
 
previousChannel - Variable in class loci.formats.in.ZeissCZIReader
 
previousImage - Variable in class loci.formats.codec.CodecOptions
Pixels for preceding image (READ/WRITE).
previousTag - Variable in class loci.formats.in.CellSensReader
 
prevPixels - Variable in class loci.formats.in.NativeQTReader
Pixel data for the previous image plane.
prevPlane - Variable in class loci.formats.in.NativeQTReader
Previous plane number.
prevPlane - Variable in class loci.formats.in.ZeissLSMReader
 
prevRegion - Variable in class loci.formats.in.ZeissLSMReader
 
prevRuntype - Variable in class loci.formats.in.ND2Handler
 
PRIMARY_CHROMATICITIES - Static variable in class loci.formats.tiff.IFD
 
primaryFileGUID - Variable in class loci.formats.in.ZeissCZIReader.FileHeader
 
print(int, long, String) - Method in class loci.formats.in.NativeQTReader
Debugging method; prints information on an atom.
printArray(String, int[]) - Static method in class loci.formats.tools.CacheConsole
Helper utility for outputing contents of an int array, used by main.
printIFD() - Method in class loci.formats.tiff.IFD
Prints the contents of this IFD.
printOrder(String, Cache) - Static method in class loci.formats.tools.CacheConsole
Helper utility for outputing cache strategy's order, used by main.
printSizes(Component) - Static method in class loci.plugins.config.SpringUtilities
A debugging utility that prints to stdout the component's minimum, preferred, and maximum sizes.
printSource(String, Cache) - Static method in class loci.formats.tools.CacheConsole
Helper utility for outputing cache's associated source, used by main.
printStrategy(String, Cache) - Static method in class loci.formats.tools.CacheConsole
Helper utility for outputing cache's associated strategy, used by main.
priorities - Variable in class loci.formats.cache.CacheStrategy
Priority for caching each axis.
PRIORITIES - Static variable in class loci.formats.gui.CacheComponent
 
PRIORITIES_CHANGED - Static variable in class loci.formats.cache.CacheEvent
Event type indicating new axis priorities.
priority - Variable in class loci.formats.gui.CacheComponent
Combo boxes for choosing axis priority.
PRIORITY_VALUES - Static variable in class loci.formats.gui.CacheComponent
 
priorityIndex(int) - Method in class loci.formats.gui.CacheComponent
Converts enumerated priority value to priority chooser index.
priorityValue(int) - Method in class loci.formats.gui.CacheComponent
Converts priority chooser index to enumerated priority value.
probeLabel - Variable in class loci.formats.gui.ImageViewer
 
proc - Variable in class loci.plugins.util.RecordedImageProcessor
 
process - Variable in class loci.plugins.in.Calibrator
 
process - Variable in class loci.plugins.in.Colorizer
 
process - Variable in class loci.plugins.in.DisplayHandler
 
process - Variable in class loci.plugins.in.ImagePlusReader
Import preparation process managing Bio-Formats readers and other state.
process - Variable in class loci.plugins.in.ImporterDialog
 
process - Variable in class loci.plugins.in.ImporterPrompter
 
processBuffer(int) - Method in class loci.formats.in.SPCReader
 
processElement(String) - Method in class loci.formats.in.FEITiffReader.FEIHandler
 
processKey(String, String) - Method in class loci.formats.in.MicroCTReader
Takes a key/value pair from disparate metadata files, and attempts to stores it in the original metadata table and/or MetadataStore as appropriate.
profileXML - Variable in class loci.formats.in.VectraReader
 
progress - Variable in class loci.formats.gui.DataConverter
 
progress(boolean, int, int) - Static method in class loci.plugins.BF
 
PROJECTION_PREFIX - Static variable in class loci.formats.in.KLBReader
 
PROJECTION_SUFFIX - Static variable in class loci.formats.in.KLBReader
 
promptColors() - Method in class loci.plugins.in.ImporterPrompter
Prompts for color details, if necessary.
promptCrop() - Method in class loci.plugins.in.ImporterPrompter
Prompts for cropping details, if necessary.
promptFilePattern() - Method in class loci.plugins.in.ImporterPrompter
Prompts for the file pattern, if necessary.
promptId() - Method in class loci.plugins.in.ImporterPrompter
 
promptLicenseCode(String, boolean) - Static method in class loci.plugins.util.LuraWave
Prompts the user to enter their LuraWave license code in an ImageJ dialog window.
promptLocation() - Method in class loci.plugins.in.ImporterPrompter
 
promptMain() - Method in class loci.plugins.in.ImporterPrompter
 
promptMemory() - Method in class loci.plugins.in.ImporterPrompter
Prompts for confirmation of memory usage, if necessary.
promptRange() - Method in class loci.plugins.in.ImporterPrompter
Prompts for the range of planes to import, if necessary.
promptSeries() - Method in class loci.plugins.in.ImporterPrompter
Prompts for which series to import, if necessary.
promptSwap() - Method in class loci.plugins.in.ImporterPrompter
Prompts for dimension swapping parameters, if necessary.
promptUpgrade() - Method in class loci.plugins.in.ImporterPrompter
 
PROP_LUT - Static variable in class loci.plugins.in.ImagePlusReader
Special property prefix for storing planar LUTs.
PROP_SERIES - Static variable in class loci.plugins.in.ImagePlusReader
Special property for storing series number associated with the image.
PROPERTY_FILE - Static variable in class loci.formats.FormatTools
Deprecated.
The property file is no longer used.
PROPERTY_SET_VOLUME - Static variable in class loci.formats.in.CellSensReader
 
propertyChange(PropertyChangeEvent) - Method in class loci.formats.gui.PreviewPane
Property change event, to listen for when a new file is selected, or the file chooser closes.
props - Variable in class loci.formats.in.DynamicMetadataOptions
 
PSD_MAGIC_STRING - Static variable in class loci.formats.in.PSDReader
 
PSDReader - Class in loci.formats.in
PSDReader is the file format reader for Photoshop PSD files.
PSDReader() - Constructor for class loci.formats.in.PSDReader
Constructs a new PSD reader.
ptyEnd - Variable in class loci.formats.in.FV1000Reader
 
ptyPattern - Variable in class loci.formats.in.FV1000Reader
 
ptyStart - Variable in class loci.formats.in.FV1000Reader
 
put(String, Object) - Method in class loci.formats.in.BaseTiffReader
 
put(String, int) - Method in class loci.formats.in.BaseTiffReader
 
put(String, boolean) - Method in class loci.formats.in.BaseTiffReader
 
put(String, byte) - Method in class loci.formats.in.BaseTiffReader
 
put(String, char) - Method in class loci.formats.in.BaseTiffReader
 
put(String, double) - Method in class loci.formats.in.BaseTiffReader
 
put(String, float) - Method in class loci.formats.in.BaseTiffReader
 
put(String, long) - Method in class loci.formats.in.BaseTiffReader
 
put(String, short) - Method in class loci.formats.in.BaseTiffReader
 
put(String, IFD, int) - Method in class loci.formats.in.BaseTiffReader
 
putColumn(int, int, int[], int) - Method in class loci.plugins.util.RecordedImageProcessor
 
putDouble(String, IFD, int) - Method in class loci.formats.in.BaseTiffReader
 
putIFDValue(int, Object) - Method in class loci.formats.tiff.IFD
Adds a directory entry to this IFD.
putIFDValue(int, short) - Method in class loci.formats.tiff.IFD
Adds a directory entry of type BYTE to this IFD.
putIFDValue(int, int) - Method in class loci.formats.tiff.IFD
Adds a directory entry of type SHORT to this IFD.
putIFDValue(int, long) - Method in class loci.formats.tiff.IFD
Adds a directory entry of type LONG to this IFD.
putInt(String, IFD, int) - Method in class loci.formats.in.BaseTiffReader
 
putPixel(int, int, int) - Method in class loci.plugins.util.RecordedImageProcessor
 
putPixel(int, int, int[]) - Method in class loci.plugins.util.RecordedImageProcessor
 
putPixelValue(int, int, double) - Method in class loci.plugins.util.RecordedImageProcessor
 
putRow(int, int, int[], int) - Method in class loci.plugins.util.RecordedImageProcessor
 
putString(String, IFD, int) - Method in class loci.formats.in.BaseTiffReader
 
Pyramid() - Constructor for class loci.formats.in.CellSensReader.Pyramid
 
pyramidDepth - Variable in class loci.formats.in.VectraReader
 
pyramidHeight - Variable in class loci.formats.in.NDPIReader
 
PyramidOMETiffWriter - Class in loci.formats.out
PyramidOMETiffWriter is the file format writer for pyramid OME-TIFF files.
PyramidOMETiffWriter() - Constructor for class loci.formats.out.PyramidOMETiffWriter
 
pyramids - Variable in class loci.formats.in.CellSensReader
 
PyramidTiffReader - Class in loci.formats.in
PyramidTiffReader is the file format reader for pyramid TIFFs.
PyramidTiffReader() - Constructor for class loci.formats.in.PyramidTiffReader
Constructs a new pyramid TIFF reader.
pyramidType - Variable in class loci.formats.in.ZeissCZIReader.DirectoryEntry
 

Q

qName - Variable in class loci.formats.in.ImaconReader.ImaconHandler
 
qName - Variable in class loci.formats.in.ScanrReader.ScanrHandler
 
QQ - Static variable in class loci.formats.in.DicomReader
 
qtJava - Variable in class loci.formats.gui.DataConverter
 
QTReader - Class in loci.formats.in
QTReader is the file format reader for QuickTime movie files.
QTReader() - Constructor for class loci.formats.in.QTReader
Constructs a new QuickTime reader.
QTRLECodec - Class in loci.formats.codec
Methods for compressing and decompressing data using QuickTime RLE.
QTRLECodec() - Constructor for class loci.formats.codec.QTRLECodec
 
qtTools - Variable in class loci.formats.in.PictReader
Helper reader in case this one fails.
QTWidgets - Class in loci.plugins.config
Custom widgets for configuring Bio-Formats QuickTime support.
QTWidgets() - Constructor for class loci.plugins.config.QTWidgets
 
QTWriter - Class in loci.formats.out
QTWriter is the file format writer for uncompressed QuickTime movie files.
QTWriter() - Constructor for class loci.formats.out.QTWriter
 
quality - Variable in class loci.formats.codec.CodecOptions
Compression quality level as it would be provided to: ImageWriteParam.compressionQuality (WRITE).
QUALITY - Static variable in class loci.formats.in.NikonReader
 
quality - Variable in class loci.formats.out.LegacyQTWriter
The quality to use.
quality - Variable in class loci.formats.out.QTWriter
The quality to use.
QUALITY_HIGH - Static variable in class loci.formats.out.QTWriter
Value indicating High quality.
QUALITY_LOW - Static variable in class loci.formats.out.QTWriter
Value indicating Low quality.
QUALITY_MAXIMUM - Static variable in class loci.formats.out.QTWriter
Value indicating Maximum quality.
QUALITY_NORMAL - Static variable in class loci.formats.out.QTWriter
Value indicating Normal quality.
QuesantReader - Class in loci.formats.in
QuesantReader is the file format reader for Quesant .afm files.
QuesantReader() - Constructor for class loci.formats.in.QuesantReader
Constructs a new Quesant reader.
quit - Variable in class loci.formats.cache.CacheUpdater
 
quit() - Method in class loci.formats.cache.CacheUpdater
 

R

r - Variable in class loci.formats.gui.LegacyQTTools
Reflection tool for QuickTime for Java calls.
r - Variable in class loci.formats.in.LegacyQTReader
Reflection tool for QuickTime for Java calls.
r - Variable in class loci.formats.in.LeicaSCNReader.Dimension
 
r - Variable in class loci.formats.in.TiffJAIReader
Reflection tool for JAI calls.
r - Variable in class loci.formats.out.LegacyQTWriter
Reflection tool for QuickTime for Java calls.
r - Variable in class loci.plugins.macro.LociFunctions
 
r - Variable in class loci.plugins.util.VirtualImagePlus
 
raisedException - Static variable in class loci.formats.ImageReader
 
RandomAccessDeser() - Constructor for class loci.formats.Memoizer.RandomAccessDeser
 
range - Variable in class loci.formats.cache.CacheStrategy
Number of planes to cache along each axis.
range - Variable in class loci.formats.gui.CacheComponent
Spinners for choosing range of slices to cache.
RANGE_CHANGED - Static variable in class loci.formats.cache.CacheEvent
Event type indicating new planar ordering.
RangeDialog - Class in loci.plugins.in
Bio-Formats Importer range chooser dialog box.
RangeDialog(ImportProcess) - Constructor for class loci.plugins.in.RangeDialog
Creates a range chooser dialog for the Bio-Formats Importer.
raster(int[]) - Method in class loci.formats.cache.CacheStrategy
Shortcut for converting N-D position to rasterized position.
rasterToPosition(int[], int) - Static method in class loci.formats.FormatTools
Computes a unique N-D position corresponding to the given rasterized index value.
rasterToPosition(int[], int, int[]) - Static method in class loci.formats.FormatTools
Computes a unique N-D position corresponding to the given rasterized index value.
RAW - Static variable in class loci.formats.in.BMPReader
Compression types.
RAW - Static variable in class loci.formats.in.CellSensReader
 
rawBits - Variable in class loci.formats.in.PGMReader
 
rawBuf - Variable in class loci.formats.in.SPCReader
 
rawCount - Variable in class loci.formats.in.BaseZeissReader
 
rawSize - Variable in class loci.formats.in.NativeQTReader
Raw plane size, in bytes.
rc - Variable in class loci.formats.gui.DataConverter
 
RCPNLReader - Class in loci.formats.in
 
RCPNLReader() - Constructor for class loci.formats.in.RCPNLReader
 
read(int, byte[]) - Method in class loci.formats.in.AmiraReader.ASCII
 
read(byte[], int) - Method in class loci.formats.in.AmiraReader.HxRLE
 
read(int, byte[]) - Method in class loci.formats.in.AmiraReader.HxRLE
 
read(int, byte[]) - Method in class loci.formats.in.AmiraReader.HxZip
 
read(int, byte[]) - Method in interface loci.formats.in.AmiraReader.PlaneReader
 
read() - Method in class loci.formats.in.APNGReader.PNGInputStream
 
read(byte[], int, int) - Method in class loci.formats.in.APNGReader.PNGInputStream
 
read() - Method in class loci.formats.in.ZeissLSMReader.BeamSplitter
 
read() - Method in class loci.formats.in.ZeissLSMReader.DataChannel
 
read() - Method in class loci.formats.in.ZeissLSMReader.DetectionChannel
 
read() - Method in class loci.formats.in.ZeissLSMReader.IlluminationChannel
 
read() - Method in class loci.formats.in.ZeissLSMReader.Laser
 
read() - Method in class loci.formats.in.ZeissLSMReader.Recording
 
read() - Method in class loci.formats.in.ZeissLSMReader.SubBlock
 
read() - Method in class loci.formats.in.ZeissLSMReader.Track
 
read(Kryo, Input) - Method in class loci.formats.services.NetCDFServiceImpl
 
readAbsoluteZValid() - Method in class loci.formats.in.MetamorphReader
 
readArea(Element, int, double, double, int, int) - Method in class loci.formats.in.CellVoyagerReader
 
readAttachments() - Method in class loci.formats.in.ZeissCZIReader
 
readBlock() - Method in class loci.formats.in.GIFReader
Reads the next variable length block.
readByte() - Method in class loci.formats.in.APNGReader.PNGInputStream
 
readByte() - Method in class loci.formats.tools.AmiraParameters
 
readByteArray(String) - Method in interface loci.formats.services.JHDFService
Reads a multi-dimensional byte array from path.
readByteArray(String) - Method in class loci.formats.services.JHDFServiceImpl
 
readByteBlockArray(String, int[], int[]) - Method in interface loci.formats.services.JHDFService
Reads a multi-dimensional sub-block byte array from path.
readByteBlockArray(String, int[], int[]) - Method in class loci.formats.services.JHDFServiceImpl
 
readBytes(int, byte[], int, int, int, int) - Method in interface loci.formats.services.WlzService
Reads a rectangle of bytes in an x-y plane from the opened Woolz object.
readBytes(int, byte[], int, int, int, int) - Method in class loci.formats.services.WlzServiceImpl
 
readBytes2DDomObj(byte[], int, int, int, int) - Method in class loci.formats.services.WlzServiceImpl
 
readBytes3DDomObj(byte[], int, int, int, int, int) - Method in class loci.formats.services.WlzServiceImpl
 
readChannel(Element) - Method in class loci.formats.in.CellVoyagerReader
 
readChunk() - Method in class loci.formats.in.AVIReader
 
readChunkHeader() - Method in class loci.formats.in.AVIReader
 
readCompoundArrayDataMap(String) - Method in interface loci.formats.services.JHDFService
Reads Compound array of any type
readCompoundArrayDataMap(String) - Method in class loci.formats.services.JHDFServiceImpl
 
readCString(RandomAccessInputStream, int) - Static method in class loci.formats.in.MetamorphReader
Read a null-terminated string.
readCString() - Method in class loci.formats.in.OpenlabReader
 
readCString() - Method in class loci.formats.in.SlidebookReader
 
readDate() - Method in class loci.formats.in.OxfordInstrumentsReader
 
readDoubleArray(int) - Method in class loci.formats.tools.AmiraParameters
 
readEntry() - Method in class loci.formats.in.ZeissLSMReader
 
reader - Variable in class loci.formats.cache.CacheSource
Reader from which to draw image planes.
reader - Variable in class loci.formats.FileInfo
IFormatReader implementation that would be used to read this file.
reader - Variable in class loci.formats.gui.BufferedImageSource
Image reader from which to draw BufferedImages.
reader - Variable in class loci.formats.gui.DataConverter
 
reader - Variable in class loci.formats.gui.FormatFileFilter
Associated file format reader.
reader - Variable in class loci.formats.gui.PreviewPane
Reader for use when loading thumbnails.
reader - Variable in class loci.formats.in.AFIReader
 
reader - Variable in class loci.formats.in.BDReader
 
reader - Variable in class loci.formats.in.ColumbusReader
 
reader - Variable in class loci.formats.in.CV7000Reader
 
reader - Variable in class loci.formats.in.L2DReader
 
reader - Variable in class loci.formats.in.OMETiffReader.OMETiffPlane
Reader to use for accessing this plane.
reader - Variable in class loci.formats.in.OperettaReader
 
reader - Variable in class loci.formats.in.PCORAWReader
 
reader - Variable in class loci.formats.in.ScanrReader
 
reader - Variable in class loci.formats.in.ZeissTIFFHandler
 
reader - Variable in class loci.formats.in.ZipReader
 
reader - Variable in class loci.formats.ReaderWrapper
FormatReader used to read the file.
reader - Variable in class loci.formats.services.MetakitServiceImpl
 
reader - Variable in class loci.plugins.config.FormatEntry
 
reader - Variable in class loci.plugins.in.ImportProcess
 
reader - Variable in class loci.plugins.util.BFVirtualStack
 
reader - Variable in class loci.plugins.util.ImageProcessorSource
Image reader from which to draw ImageProcessors.
READER_VALIDATE_DEFAULT - Static variable in class loci.formats.in.DynamicMetadataOptions
 
READER_VALIDATE_KEY - Static variable in class loci.formats.in.DynamicMetadataOptions
 
readerFromBytes(Class<IFormatReader>, byte[]) - Method in class loci.formats.Memoizer.RandomAccessDeser
 
readerName - Variable in class loci.plugins.config.FormatEntry
 
readers - Variable in class loci.formats.FileStitcher.ExternalSeries
 
readers - Variable in class loci.formats.ImageReader
List of supported file format readers.
readers - Variable in class loci.formats.in.ImprovisionTiffReader
 
readers - Variable in class loci.formats.in.MIASReader
Delegate readers.
readers - Variable in class loci.formats.in.NDPISReader
 
readers - Variable in class loci.formats.in.SlidebookTiffReader
 
ReaderWrapper - Class in loci.formats
Abstract superclass of reader logic that wraps other readers.
ReaderWrapper() - Constructor for class loci.formats.ReaderWrapper
Constructs a reader wrapper around a new image reader.
ReaderWrapper(IFormatReader) - Constructor for class loci.formats.ReaderWrapper
Constructs a reader wrapper around the given reader.
readExtraMetadata(MetadataStore) - Method in class loci.formats.in.KodakReader
 
readField(Element) - Method in class loci.formats.in.CellVoyagerReader
 
readFile(String) - Method in class loci.formats.in.TextReader
 
readFile(String) - Method in class loci.formats.tools.AmiraParameters
 
readFile(RandomAccessInputStream) - Method in class loci.formats.tools.AmiraParameters
 
readFileInfoMetadata(MetadataStore) - Method in class loci.formats.in.KodakReader
 
readFlimFrame(OBFReader.Stack, int, byte[], int, int, int, int) - Method in class loci.formats.in.OBFReader
 
readFloat32() - Method in class loci.formats.in.KLBReader
 
readFrameInterval(Document) - Method in class loci.formats.in.CellVoyagerReader
 
readFromOverlays() - Static method in class loci.plugins.util.ROIHandler
Returns rois if any from the overlay.
readFromRoiManager() - Static method in class loci.plugins.util.ROIHandler
Returns the rois if any stored in the ROI manager.
readFromStack(OBFReader.Stack, byte[], int, int) - Method in class loci.formats.in.OBFReader
 
readFromStackRaw(OBFReader.Stack, byte[], int, int) - Method in class loci.formats.in.OBFReader
 
readGZIPPlane(String, int, byte[], int, int, int, int) - Method in class loci.formats.in.NRRDReader
Read a tile in the specified plane from a GZIP-compressed file.
readHeader(CoreMetadata) - Method in class loci.formats.in.KLBReader
 
readImage(long) - Method in class loci.formats.in.MNGReader
 
readImage(InputStream, JPEG2000CodecOptions) - Method in interface loci.formats.services.JAIIIOService
Reads an image using JAI Image I/O using the JPEG 2000 codec.
readImage(InputStream) - Method in interface loci.formats.services.JAIIIOService
Reads an image using JAI Image I/O using the JPEG 2000 codec.
readImage(InputStream, JPEG2000CodecOptions) - Method in class loci.formats.services.JAIIIOServiceImpl
 
readImage(InputStream) - Method in class loci.formats.services.JAIIIOServiceImpl
 
readImage(int, boolean) - Method in class loci.plugins.in.ImagePlusReader
 
readImageBlock() - Method in class loci.formats.in.GIFReader
 
readImageHeader(int) - Method in class loci.formats.in.PictReader
 
readImages() - Method in class loci.plugins.in.ImagePlusReader
 
readImages(boolean) - Method in class loci.plugins.in.ImagePlusReader
 
readInfo(Document, Document) - Method in class loci.formats.in.CellVoyagerReader
 
readIntArray(String) - Method in interface loci.formats.services.JHDFService
Reads a multi-dimensional int array from path.
readIntArray(String) - Method in class loci.formats.services.JHDFServiceImpl
 
readIntArray() - Method in class loci.formats.tools.AmiraParameters
 
readIntArray(int) - Method in class loci.formats.tools.AmiraParameters
 
readIntBlockArray(String, int[], int[]) - Method in interface loci.formats.services.JHDFService
Reads a multi-dimensional sub-block int array from path.
readIntBlockArray(String, int[], int[]) - Method in class loci.formats.services.JHDFServiceImpl
 
readKey() - Method in class loci.formats.tools.AmiraParameters
 
readLine() - Method in class loci.formats.in.EPSReader
 
readLookupTables(RandomAccessInputStream) - Method in class loci.formats.in.BioRadReader
Read all lookup tables from the given file into the 'lut' variable.
readLut(int) - Method in class loci.formats.in.GIFReader
Read a color lookup table of the specified size.
readMap() - Method in class loci.formats.tools.AmiraParameters
 
readMetaData(String) - Method in class loci.formats.in.BDReader
 
readMetadataFile() - Method in class loci.formats.in.OMETiffReader
Extracts the OME-XML from the current OMETiffReader.metadataFile.
readNotes(RandomAccessInputStream, boolean) - Method in class loci.formats.in.BioRadReader
Read all of the note strings from the given file.
readNumber() - Method in class loci.formats.tools.AmiraParameters
 
readNumberArray() - Method in class loci.formats.tools.AmiraParameters
 
readNumberString() - Method in class loci.formats.in.AmiraReader.ASCII
 
READOUT_TIME - Static variable in class loci.formats.in.FluoviewReader
 
readOutRate - Variable in class loci.formats.in.MetamorphHandler
 
readoutTime - Variable in class loci.formats.in.FluoviewReader
 
readPixelBlock(RandomAccessInputStream, long) - Method in class loci.formats.in.OIRReader
 
readPixelData() - Method in class loci.formats.in.ZeissCZIReader.SubBlock
 
readPixelData(RandomAccessInputStream) - Method in class loci.formats.in.ZeissCZIReader.SubBlock
 
readPixelData(RandomAccessInputStream, Region, byte[]) - Method in class loci.formats.in.ZeissCZIReader.SubBlock
 
readPixels(byte[], RandomAccessInputStream, ZipInputStream, long) - Method in class loci.formats.in.SDTReader
 
readPixels(ImagePlusReader, ImporterOptions, DisplayHandler) - Method in class loci.plugins.in.Importer
 
readPixelsFile(String, RandomAccessInputStream) - Method in class loci.formats.in.OIRReader
 
readPlane(RandomAccessInputStream, int, int, int, int, byte[]) - Method in class loci.formats.FormatReader
Reads a raw plane from disk.
readPlane(RandomAccessInputStream, int, int, int, int, int, byte[]) - Method in class loci.formats.FormatReader
Reads a raw plane from disk.
readPlaneData() - Method in class loci.formats.in.MetamorphReader
 
readPlanes(ImportProcess, int, List<LUT>, boolean) - Method in class loci.plugins.in.ImagePlusReader
 
readProcessors(ImportProcess, int, Region, boolean) - Method in class loci.plugins.in.ImagePlusReader
HACK: This method mainly exists to prompt the user for a missing LuraWave license code, in the case of LWF-compressed Flex.
readQuotedString() - Method in class loci.formats.tools.AmiraParameters
 
readRaster(InputStream, JPEG2000CodecOptions) - Method in interface loci.formats.services.JAIIIOService
Reads an image into a raster using JAI Image I/O using the JPEG 2000 codec.
readRaster(InputStream) - Method in interface loci.formats.services.JAIIIOService
Reads an image into a raster using JAI Image I/O using the JPEG 2000 codec.
readRaster(InputStream, JPEG2000CodecOptions) - Method in class loci.formats.services.JAIIIOServiceImpl
 
readRaster(InputStream) - Method in class loci.formats.services.JAIIIOServiceImpl
 
readRational(RandomAccessInputStream) - Method in class loci.formats.in.MetamorphReader
 
readRational(RandomAccessInputStream, long) - Method in class loci.formats.in.MetamorphReader
 
readRationals(String[]) - Method in class loci.formats.in.MetamorphReader
 
readSanitizedXML(String) - Method in class loci.formats.in.CV7000Reader
 
readSegment(String) - Method in class loci.formats.in.ZeissCZIReader
 
readSegments(String) - Method in class loci.formats.in.ZeissCZIReader
 
readShortBlockArray(String, int[], int[]) - Method in interface loci.formats.services.JHDFService
Reads a multi-dimensional sub-block short array from path.
readShortBlockArray(String, int[], int[]) - Method in class loci.formats.services.JHDFServiceImpl
 
readSpecialPixels(byte[]) - Static method in class loci.formats.in.FakeReader
Read byte-encoded metadata from the given plane.
readSpecialPixels(byte[], int, boolean) - Static method in class loci.formats.in.FakeReader
Read byte-encoded metadata from the given plane.
readSpecialPixels(byte[], int, boolean, int, boolean) - Static method in class loci.formats.in.FakeReader
Read byte-encoded metadata from the given plane.
readStackFrame(OBFReader.Stack, long, byte[], int, int, int) - Method in class loci.formats.in.OBFReader
 
readStackHeader() - Method in class loci.formats.in.ImspectorReader
Read the header for an image stack.
readStageLabels() - Method in class loci.formats.in.MetamorphReader
 
readStagePositions() - Method in class loci.formats.in.MetamorphReader
 
readStamps() - Method in class loci.formats.in.FluoviewReader
 
readString() - Method in class loci.formats.in.OBFReader
 
readStringArray(String) - Method in interface loci.formats.services.JHDFService
Reads String array array from path.
readStringArray(String) - Method in class loci.formats.services.JHDFServiceImpl
 
readTagHeader() - Method in class loci.formats.in.OpenlabReader
Read the next tag.
readTags(RandomAccessInputStream, boolean, String) - Method in class loci.formats.in.CellSensReader
 
readThumbImages() - Method in class loci.plugins.in.ImagePlusReader
 
readTiffIFDEntry() - Method in class loci.formats.tiff.TiffParser
 
readTimePoints(Document) - Method in class loci.formats.in.CellVoyagerReader
 
readTopLevel() - Method in class loci.formats.tools.AmiraParameters
 
readTypeAndSize() - Method in class loci.formats.in.AVIReader
 
readUInt32() - Method in class loci.formats.in.KLBReader
 
readUInt64() - Method in class loci.formats.in.KLBReader
 
readUnsignedLong(RandomAccessInputStream) - Method in class loci.formats.in.SDTInfo
 
readValue(int) - Method in class loci.formats.in.GatanReader
 
readValue() - Method in class loci.formats.in.ZeissLSMReader
 
readVariable() - Method in class loci.formats.in.OpenlabReader
 
readVariable() - Method in class loci.formats.in.QuesantReader
 
readWavelength(int, MetadataStore) - Method in class loci.formats.in.DeltavisionReader
 
readWellInfo(Element, double, double, int, int) - Method in class loci.formats.in.CellVoyagerReader
 
readXMLBlock(String, RandomAccessInputStream) - Method in class loci.formats.in.OIRReader
 
realChannel - Variable in class loci.formats.in.LIFReader
 
realColors - Variable in class loci.formats.in.ND2Handler
 
realFile - Variable in class loci.formats.Memoizer
 
realHeight - Variable in class loci.formats.in.BaseZeissReader
 
realWidth - Variable in class loci.formats.in.BaseZeissReader
 
realX - Variable in class loci.formats.in.VentanaReader.TIFFTile
 
realY - Variable in class loci.formats.in.VentanaReader.TIFFTile
 
rebuild(GenericDialog) - Method in class loci.plugins.in.FilePatternDialog
 
rebuildDialog(GenericDialog) - Method in class loci.plugins.in.MainDialog
Fancies up the importer dialog to look much nicer.
rebuildDialog(GenericDialog, int) - Method in class loci.plugins.in.SeriesDialog
 
REC_BOOLEAN - Static variable in class loci.formats.in.IM3Reader
 
REC_CONTAINER - Static variable in class loci.formats.in.IM3Reader
A record that is a container of other records.
REC_FLOAT - Static variable in class loci.formats.in.IM3Reader
 
REC_IMAGE - Static variable in class loci.formats.in.IM3Reader
Image format int: pixel type? 3 = RGBA int: width int: height int: depth data bytes follow
REC_INT - Static variable in class loci.formats.in.IM3Reader
32-bit integer values
REC_NESTED - Static variable in class loci.formats.in.IM3Reader
A nested record of records
REC_STRING - Static variable in class loci.formats.in.IM3Reader
A string int: ? int: length 8-byte characters follow
REC_SUFFIX - Static variable in class loci.formats.in.PerkinElmerReader
 
recache(int) - Method in class loci.formats.cache.Cache
Updates the given plane.
recache() - Method in class loci.formats.cache.Cache
Updates all planes on the load list.
reCalculateBlockOffsets(int) - Method in class loci.formats.in.KLBReader
 
record - Variable in class loci.plugins.util.BFVirtualStack
 
record(String) - Method in class loci.plugins.util.RecordedImageProcessor
 
record(String, Object, Class<?>) - Method in class loci.plugins.util.RecordedImageProcessor
 
record(String, Object[], Class<?>[]) - Method in class loci.plugins.util.RecordedImageProcessor
 
RecordedImageProcessor - Class in loci.plugins.util
Image processor extension that records commands executed upon it.
RecordedImageProcessor(ImageProcessor) - Constructor for class loci.plugins.util.RecordedImageProcessor
 
RecordedImageProcessor(ImageProcessor, int, ImageProcessor[]) - Constructor for class loci.plugins.util.RecordedImageProcessor
 
RecordedImageProcessor.MethodEntry - Class in loci.plugins.util
 
Recording() - Constructor for class loci.formats.in.ZeissLSMReader.Recording
 
RECORDING_CAMERA_BINNING - Static variable in class loci.formats.in.ZeissLSMReader
 
RECORDING_DESCRIPTION - Static variable in class loci.formats.in.ZeissLSMReader
 
RECORDING_NAME - Static variable in class loci.formats.in.ZeissLSMReader
Data types.
RECORDING_OBJECTIVE - Static variable in class loci.formats.in.ZeissLSMReader
 
RECORDING_SAMPLE_0TIME - Static variable in class loci.formats.in.ZeissLSMReader
 
RECORDING_ZOOM - Static variable in class loci.formats.in.ZeissLSMReader
 
records - Variable in class loci.formats.in.IM3Reader
 
recordWidth - Variable in class loci.formats.in.PDSReader
 
RECTANGLE - Static variable in class loci.formats.in.FV1000Reader
 
RECTANGLE - Static variable in class loci.formats.in.GatanReader
 
RECTANGLE - Static variable in class loci.formats.in.LeicaHandler.ROI
 
RECTANGLE - Static variable in class loci.formats.in.LIFReader.ROI
 
RECTANGLE - Static variable in class loci.formats.in.ZeissLSMReader
 
rectangles - Variable in class loci.formats.in.FakeReader
 
RectangleStrategy - Class in loci.formats.cache
A rectangle strategy caches planes extending from the the current dimensional position along each axis and combination of axes.
RectangleStrategy(int[]) - Constructor for class loci.formats.cache.RectangleStrategy
Constructs a rectangle strategy.
RED_GAIN - Static variable in class loci.formats.in.CellSensReader
 
RED_MAX - Static variable in class loci.plugins.in.Colorizer
 
RED_MULTIPLIER - Static variable in class loci.formats.in.NDPIReader
 
RED_OFFSET - Static variable in class loci.formats.in.CellSensReader
 
redGain - Variable in class loci.formats.in.CellSensReader.Pyramid
 
redOffset - Variable in class loci.formats.in.CellSensReader.Pyramid
 
redOffset - Static variable in class org.libjpegturbo.turbojpeg.TJ
 
redShort - Variable in class loci.formats.gui.Index16ColorModel
Lookup tables.
reduce() - Method in class loci.formats.tiff.TiffRational
Reduces this rational's fraction to lowest terms.
refCount - Variable in class loci.plugins.util.VirtualReader
 
REFERENCE - Static variable in class loci.formats.in.NDPIReader
 
REFERENCE_BLACK_WHITE - Static variable in class loci.formats.tiff.IFD
 
REFOCUS_INTERVAL - Static variable in class loci.formats.in.NDPIReader
 
refractive - Variable in class loci.formats.in.InCellReader
 
REFRACTIVE_INDEX - Static variable in class loci.formats.in.CellSensReader
 
refractiveIndex - Variable in class loci.formats.in.CellSensReader.Pyramid
 
refractiveIndex - Variable in class loci.formats.in.IvisionReader
 
refractiveIndex - Variable in class loci.formats.in.LIFReader
 
refractiveIndex - Variable in class loci.formats.in.NativeND2Reader
 
refractiveIndex - Variable in class loci.formats.in.ND2Handler
 
refractiveIndex - Variable in class loci.formats.in.ZeissCZIReader
 
refresher - Variable in class loci.formats.gui.PreviewPane
Method for syncing the view to the model.
registerServiceProviders() - Static method in class loci.formats.services.JAIIIOServiceImpl
Register the JPEG-2000 readers with the reader service.
REGISTRY - Static variable in class loci.formats.UpgradeChecker
Location of the OME registry.
REGISTRY_IMAGEJ - Static variable in class loci.formats.UpgradeChecker
Registry ID identifying usage of Bio-Formats in ImageJ.
REGISTRY_LIBRARY - Static variable in class loci.formats.UpgradeChecker
Registry ID identifying usage of Bio-Formats as a library in general.
REGISTRY_PROPERTIES - Static variable in class loci.formats.UpgradeChecker
Properties that are sent to the OME registry.
RELATED_SOUND_FILE - Static variable in class loci.formats.tiff.IFD
 
relativeTime - Variable in class loci.formats.in.PrairieMetadata.Frame
relativeTime attribute of this <Frame>.
remainingBytesInChunk(OBFReader.Stack) - Method in class loci.formats.in.OBFReader
 
removeBinData(OMEXMLMetadata) - Method in interface loci.formats.services.OMEXMLService
Remove all of the BinData elements from the given OME-XML metadata object.
removeBinData(OMEXMLMetadata) - Method in class loci.formats.services.OMEXMLServiceImpl
 
removeCacheListener(CacheListener) - Method in class loci.formats.cache.Cache
 
removeCacheListener(CacheListener) - Method in interface loci.formats.cache.CacheReporter
Removes a listener for status update events.
removeCacheListener(CacheListener) - Method in class loci.formats.cache.CacheStrategy
 
removeChannels(OMEXMLMetadata, int, int) - Method in interface loci.formats.services.OMEXMLService
Remove all but the first sizeC valid Channel elements from the given OME-XML metadata object.
removeChannels(OMEXMLMetadata, int, int) - Method in class loci.formats.services.OMEXMLServiceImpl
 
removeClass(Class<? extends T>) - Method in class loci.formats.ClassList
Removes the given class from the list.
removeExtension(String) - Method in class loci.plugins.out.Exporter
Removes the extension of the specified name.
removeGST(String) - Method in class loci.formats.in.FV1000Reader
 
removeIFDComments(IFormatReader) - Method in class loci.formats.in.OMETiffReader
 
removePossible(String) - Method in class loci.plugins.prefs.StringOption
Removes a possible value from the list.
removeStatusListener(StatusListener) - Method in class loci.plugins.in.ImagePlusReader
 
removeStatusListener(StatusListener) - Method in class loci.plugins.in.ImportProcess
 
removeTiffData(OMEXMLMetadata) - Method in interface loci.formats.services.OMEXMLService
Remove all of the TiffData elements from the given OME-XML metadata object.
removeTiffData(OMEXMLMetadata) - Method in class loci.formats.services.OMEXMLServiceImpl
 
removeUpdate(DocumentEvent) - Method in class loci.plugins.config.FlexWidgets
 
RENDER_OPERATION_ID - Static variable in class loci.formats.in.CellSensReader
 
reopenFile() - Method in class loci.formats.DelegateReader
 
reopenFile() - Method in class loci.formats.FileStitcher
 
reopenFile() - Method in class loci.formats.FormatReader
 
reopenFile() - Method in interface loci.formats.IFormatReader
Reopen any files that were closed, and which are expected to be open while the reader is open.
reopenFile() - Method in class loci.formats.ImageReader
 
reopenFile() - Method in class loci.formats.in.AnalyzeReader
 
reopenFile() - Method in class loci.formats.in.BDVReader
 
reopenFile() - Method in class loci.formats.in.CellH5Reader
 
reopenFile() - Method in class loci.formats.in.CellSensReader
 
reopenFile() - Method in class loci.formats.in.FakeReader
 
reopenFile() - Method in class loci.formats.in.FlowSightReader
 
reopenFile() - Method in class loci.formats.in.HitachiReader
 
reopenFile() - Method in class loci.formats.in.ICSReader
 
reopenFile() - Method in class loci.formats.in.ImagicReader
 
reopenFile() - Method in class loci.formats.in.MinimalTiffReader
 
reopenFile() - Method in class loci.formats.in.NiftiReader
 
reopenFile() - Method in class loci.formats.in.OMETiffReader
 
reopenFile() - Method in class loci.formats.in.SPCReader
 
reopenFile() - Method in class loci.formats.in.TileJPEGReader
 
reopenFile() - Method in class loci.formats.in.ZipReader
 
reopenFile() - Method in class loci.formats.ReaderWrapper
 
reopenFile() - Method in class loci.formats.WrappedReader
 
reorder() - Method in class loci.formats.CoreMetadataList
 
reorder(int) - Method in class loci.formats.DimensionSwapper
 
reorder(ImagePlus, String, String) - Static method in class loci.plugins.Slicer
Reorder the given ImagePlus's stack.
reorderXSLT - Static variable in class loci.formats.services.OMEXMLServiceImpl
Reordering stylesheet.
replaceExtension(String, String, String) - Method in class loci.formats.in.FV1000Reader
 
replacementMetadataStore - Variable in class loci.formats.Memoizer
MetadataStore created internally.
reportException(Throwable) - Static method in class loci.plugins.util.WindowTools
Reports the given exception with stack trace in an ImageJ error dialog.
reportException(Throwable, boolean) - Static method in class loci.plugins.util.WindowTools
Reports the given exception with stack trace in an ImageJ error dialog.
reportException(Throwable, boolean, String) - Static method in class loci.plugins.util.WindowTools
Reports the given exception with stack trace in an ImageJ error dialog.
REPRESENTATION_KEYS - Static variable in class loci.formats.in.ICSReader
 
repT - Variable in class loci.formats.in.SDTInfo
 
RES_SUFFIX - Static variable in class loci.formats.in.FlexReader
 
rescale(int, int) - Method in class loci.formats.gui.SignedColorModel
 
rescale(int) - Method in class loci.formats.gui.SignedColorModel
 
RESCALE_INTERCEPT - Static variable in class loci.formats.in.DicomReader
 
RESCALE_SLOPE - Static variable in class loci.formats.in.DicomReader
 
rescaleIntercept - Variable in class loci.formats.in.DicomReader
 
rescaleSlope - Variable in class loci.formats.in.DicomReader
 
reserved1 - Variable in class loci.formats.in.SDTInfo
 
reserved2 - Variable in class loci.formats.in.SDTInfo
 
reset() - Method in class loci.formats.cache.Cache
Reallocates the cache.
reset() - Method in class loci.plugins.util.RecordedImageProcessor
 
reset(ImageProcessor) - Method in class loci.plugins.util.RecordedImageProcessor
 
resetBinaryThreshold() - Method in class loci.plugins.util.RecordedImageProcessor
 
resetMinAndMax() - Method in class loci.plugins.util.RecordedImageProcessor
 
resetRoi() - Method in class loci.plugins.util.RecordedImageProcessor
 
resetSliceLabelButton - Variable in class loci.plugins.config.ConfigWindow
 
resetThreshold() - Method in class loci.plugins.util.RecordedImageProcessor
 
ResHandler() - Constructor for class loci.formats.in.FlexReader.ResHandler
 
resize(int) - Method in class loci.plugins.util.RecordedImageProcessor
 
resize(int, int) - Method in class loci.plugins.util.RecordedImageProcessor
 
resLabel - Variable in class loci.formats.gui.PreviewPane
Labels containing thumbnail and dimensional information.
reslice(ImagePlus, boolean, boolean, boolean, String) - Method in class loci.plugins.Slicer
 
resolution - Variable in class loci.formats.codec.JPEG2000CodecOptions
The resolution level as would be provided to: J2KImageReadParam.setResolution(int) (READ).
resolution - Variable in class loci.formats.FormatReader
The number of the current resolution.
resolution - Variable in class loci.formats.FormatWriter
Current pyramid resolution.
Resolution() - Constructor for class loci.formats.ome.OMEPyramidStore.Resolution
 
Resolution(String) - Constructor for class loci.formats.ome.OMEPyramidStore.Resolution
 
Resolution - Class in loci.formats
Represents a single subresolution in a pyramid.
Resolution(int, int, int) - Constructor for class loci.formats.Resolution
 
Resolution(int, int, int, int) - Constructor for class loci.formats.Resolution
 
RESOLUTION_UNIT - Static variable in class loci.formats.tiff.IFD
 
resolutionCount - Variable in class loci.formats.CoreMetadata
 
resolutionCount - Variable in class loci.formats.in.LeicaSCNReader.LeicaSCNHandler
 
resolutionData - Variable in class loci.formats.FormatWriter
 
resolutionIndex - Variable in class loci.formats.in.ZeissCZIReader.SubBlock
 
resolutionLevels - Variable in class loci.formats.in.JPEG2000MetadataParser
Number of JPEG 2000 resolution levels the file has.
resolutionLevels - Variable in class loci.formats.in.JPEG2000Reader
The number of JPEG 2000 resolution levels the file has.
resolutionLevels - Variable in class loci.formats.in.JPXReader
The number of JPEG 2000 resolution levels the file has.
resolutionLevels - Variable in class loci.formats.in.MinimalTiffReader
Number of JPEG 2000 resolution levels.
resolutions - Variable in class loci.formats.in.VentanaReader
 
resolutions - Variable in class loci.formats.ome.OMEPyramidStore
 
resolutionX - Variable in class loci.formats.in.OperettaReader.Plane
 
resolutionY - Variable in class loci.formats.in.OperettaReader.Plane
 
resourceCount - Variable in class loci.formats.ResourceNamer
 
ResourceNamer - Class in loci.formats
Utility class helping with generating human-readable resource names based on alphanumeric indexing.
ResourceNamer(int) - Constructor for class loci.formats.ResourceNamer
 
resourceNamer - Variable in class loci.formats.tools.FakeImage
 
restartAlphabet() - Method in class loci.formats.ResourceNamer
Resets the internal state of the class so that it starts alphabet generation from the first letter (ASCII A).
restartInterval - Variable in class loci.formats.services.JPEGTurboServiceImpl
 
restartMarkers - Variable in class loci.formats.in.HamamatsuVMSReader
 
restartMarkers - Variable in class loci.formats.services.JPEGTurboServiceImpl
 
resText - Variable in class loci.formats.gui.PreviewPane
 
resTip - Variable in class loci.formats.gui.PreviewPane
 
resultFile - Variable in class loci.formats.in.MIASReader
Path to file containing analysis results for all plates.
REUSE - Static variable in class loci.formats.tiff.IFD
 
reverseFileMapping - Variable in class loci.formats.in.FlexReader
 
reversePlaneLookup - Variable in class loci.formats.in.CV7000Reader
 
reverseX - Variable in class loci.formats.in.PDSReader
 
reverseY - Variable in class loci.formats.in.PDSReader
 
revision - Variable in class loci.formats.in.SDTInfo
Software revision number (lower 4 bits >= 10(decimal)).
rgb - Variable in class loci.formats.CoreMetadata
Indicates whether or not the images are stored as RGB (multiple channels per plane).
RGB - Static variable in class loci.formats.in.CellSensReader
 
RGB_MASK - Static variable in class loci.formats.in.BMPReader
 
RHKReader - Class in loci.formats.in
RHKReader is the file format reader for RHK Technologies files.
RHKReader() - Constructor for class loci.formats.in.RHKReader
Constructs a new RHK reader.
ri - Variable in class loci.formats.in.OIRReader.Objective
 
RLE_4 - Static variable in class loci.formats.in.BMPReader
 
RLE_8 - Static variable in class loci.formats.in.BMPReader
 
roi - Variable in class loci.formats.in.LeicaHandler
 
ROI() - Constructor for class loci.formats.in.LeicaHandler.ROI
 
ROI() - Constructor for class loci.formats.in.LiFlimReader.ROI
 
ROI() - Constructor for class loci.formats.in.LIFReader.ROI
 
ROI_PREFIX - Static variable in class loci.formats.in.FakeReader
 
ROI_SIGNATURE - Static variable in class loci.formats.in.ZeissZVIReader
 
ROI_SPACING - Static variable in class loci.formats.in.FakeReader
 
roiCount - Variable in class loci.formats.in.FakeReader
 
roiDrawFile - Variable in class loci.formats.in.TrestleReader
 
roiFile - Variable in class loci.formats.in.BDReader
 
roiFile - Variable in class loci.formats.in.TrestleReader
 
roiFilenames - Variable in class loci.formats.in.FV1000Reader
 
roiFiles - Variable in class loci.formats.in.MIASReader
 
ROIHandler - Class in loci.plugins.util
Utility class for managing regions of interest within ImageJ.
ROIHandler() - Constructor for class loci.plugins.util.ROIHandler
 
roiIDs - Variable in class loci.formats.in.BaseZeissReader
 
rois - Variable in class loci.formats.in.LiFlimReader
 
rois - Variable in class loci.formats.in.ND2Handler
 
ROIS_MODE_MANAGER - Static variable in class loci.plugins.in.ImporterOptions
 
ROIS_MODE_OVERLAY - Static variable in class loci.plugins.in.ImporterOptions
 
ROIShape() - Constructor for class loci.formats.in.GatanReader.ROIShape
 
roisModeChoice - Variable in class loci.plugins.in.MainDialog
 
root - Variable in class loci.formats.services.NetCDFServiceImpl
Root of the NetCDF file.
root - Variable in class loci.formats.services.POIServiceImpl
 
rootList - Variable in class loci.formats.in.BDReader
 
rotate(double) - Method in class loci.plugins.util.RecordedImageProcessor
 
rotateLeft() - Method in class loci.plugins.util.RecordedImageProcessor
 
rotateRight() - Method in class loci.plugins.util.RecordedImageProcessor
 
ROTATION - Static variable in class loci.formats.FormatTools
Identifies the Rotation dimensional type, representing a dimension consisting of rotations.
ROTATION - Static variable in class loci.formats.in.FV1000Reader
 
rotation - Variable in class loci.formats.in.LeicaHandler.ROI
 
rotation - Variable in class loci.formats.in.LIFReader.ROI
 
rotationLabels - Variable in class loci.formats.in.ZeissCZIReader
 
rotations - Variable in class loci.formats.in.ZeissCZIReader
 
rotations - Variable in class loci.formats.in.ZeissLSMReader
 
row - Variable in class loci.formats.in.CellomicsReader.ChannelFile
 
row - Variable in class loci.formats.in.CellVoyagerReader.WellInfo
 
row - Variable in class loci.formats.in.ColumbusReader.Plane
 
row - Variable in class loci.formats.in.CV7000Reader.Plane
 
row - Variable in class loci.formats.in.FlexReader.FlexFile
 
row - Variable in class loci.formats.in.OMEXMLReader.BinData
 
row - Variable in class loci.formats.in.OperettaReader.Plane
 
row - Variable in class loci.formats.in.TextReader
Current row number.
row - Variable in class loci.formats.in.ZeissCZIReader.SubBlock
 
row - Variable in class loci.formats.tools.AmiraParameters
 
rowBytes - Variable in class loci.formats.in.PictReader
Number of bytes in a row of pixel data (variable).
rowCount - Variable in class loci.formats.in.BaseZeissReader
 
rowLength - Variable in class loci.formats.in.TextReader
Number of tokens per row.
rowName - Variable in class loci.formats.in.InCellReader
 
RowPanel() - Constructor for class loci.formats.gui.DataConverter.RowPanel
 
rows - Variable in class loci.formats.in.CellSensReader
 
ROWS - Static variable in class loci.formats.in.DicomReader
 
ROWS_PER_STRIP - Static variable in class loci.formats.tiff.IFD
 
rPad - Variable in class loci.formats.gui.CacheIndicator
 
RPZACodec - Class in loci.formats.codec
Implements encoding and decoding methods for Apple RPZA.
RPZACodec() - Constructor for class loci.formats.codec.RPZACodec
 
RST0 - Static variable in class loci.formats.services.JPEGTurboServiceImpl
 
RST7 - Static variable in class loci.formats.services.JPEGTurboServiceImpl
 
run() - Method in class loci.formats.cache.CacheUpdater
 
run() - Method in class loci.formats.gui.DataConverter
 
run() - Method in class loci.formats.gui.ImageViewer
Handles animation.
run() - Method in class loci.formats.gui.PreviewPane
Thumbnail loading routine.
RUN - Static variable in class loci.formats.ResourceNamer
 
run(String) - Method in class loci.plugins.About
 
run() - Method in class loci.plugins.config.ConfigWindow
Populate configuration information in a separate thread.
run(String) - Method in class loci.plugins.config.LociConfig
Executes the plugin.
run(String) - Method in class loci.plugins.config.LociInstaller
Executes the plugin.
run(String) - Method in class loci.plugins.in.Importer
Executes the plugin.
run() - Method in class loci.plugins.in.ThumbLoader
Does the work of loading the thumbnails.
run(ImageProcessor) - Method in class loci.plugins.LociExporter
Executes the plugin.
run(String) - Method in class loci.plugins.LociImporter
Executes the plugin.
run(String) - Method in class loci.plugins.macro.LociFunctions
 
run(String) - Method in class loci.plugins.macro.MacroFunctions
 
run() - Method in class loci.plugins.out.Exporter
Executes the plugin.
run(String) - Method in class loci.plugins.shortcut.ShortcutPanel
Executes the plugin.
run(ImageProcessor) - Method in class loci.plugins.Slicer
 
run(String) - Method in class loci.plugins.Updater
 
runPlugIn(String, String) - Static method in class loci.plugins.shortcut.ShortcutPanel
Executes the given plugin, in a separate thread.
RWC_FRAME_ORIGIN - Static variable in class loci.formats.in.CellSensReader
 
RWC_FRAME_SCALE - Static variable in class loci.formats.in.CellSensReader
 
RWC_FRAME_UNIT - Static variable in class loci.formats.in.CellSensReader
 

S

S_AXIS - Static variable in class loci.formats.AxisGuesser
Axis type for series.
S_MAX_SAMPLE_VALUE - Static variable in class loci.formats.tiff.IFD
 
S_MIN_SAMPLE_VALUE - Static variable in class loci.formats.tiff.IFD
 
S_PREFIXES - Static variable in class loci.formats.AxisGuesser
Prefixes indicating series dimension.
safeSkip(InputStream, long) - Method in class loci.formats.in.NRRDReader
Skip a specified number of bytes in a stream.
SAMP_420 - Static variable in class org.libjpegturbo.turbojpeg.TJ
4:2:0 chrominance subsampling.
SAMP_422 - Static variable in class org.libjpegturbo.turbojpeg.TJ
4:2:2 chrominance subsampling.
SAMP_440 - Static variable in class org.libjpegturbo.turbojpeg.TJ
4:4:0 chrominance subsampling.
SAMP_444 - Static variable in class org.libjpegturbo.turbojpeg.TJ
4:4:4 chrominance subsampling (no chrominance subsampling).
SAMP_GRAY - Static variable in class org.libjpegturbo.turbojpeg.TJ
Grayscale.
SAMPLE_FLAGS_LIST - Static variable in class loci.formats.in.CellSensReader
 
SAMPLE_FORMAT - Static variable in class loci.formats.tiff.IFD
 
SAMPLE_ID_LIST - Static variable in class loci.formats.in.CellSensReader
 
SAMPLE_MASK - Static variable in class loci.formats.in.CellSensReader
 
SAMPLES_PER_PIXEL - Static variable in class loci.formats.in.DicomReader
 
SAMPLES_PER_PIXEL - Static variable in class loci.formats.tiff.IFD
 
samplesWritten - Variable in class loci.formats.in.OBFReader.Stack
 
sampleTable - Variable in class loci.formats.in.VolocityReader
 
sampleTime - Variable in class loci.formats.in.GatanReader
 
sanitize(String, boolean) - Method in class loci.formats.gui.XMLCellRenderer.XMLItem
Sanitizes strings to appear correctly in HTML.
sanitizeControl(String) - Static method in class loci.formats.in.NativeND2Reader
Remove control and invalid characters from the given string.
sanitizeFile(String, String) - Method in class loci.formats.in.FV1000Reader
 
sanitizeValue(String) - Method in class loci.formats.in.FV1000Reader
 
SATURATION - Static variable in class loci.formats.in.CellSensReader
 
SATURATION - Static variable in class loci.formats.tiff.IFD
 
save(String) - Method in class loci.formats.gui.ImageViewer
Saves the current images to the given destination using the current format writer.
save(String, IFormatWriter) - Method in class loci.formats.gui.ImageViewer
Saves to the given data destination using the specified writer in a separate thread.
save() - Method in class loci.formats.tools.EditTiffG
 
save - Variable in class loci.plugins.prefs.Option
Whether option state should be saved to ImageJ preferences file.
SAVE_FILE_SIZE - Static variable in class loci.formats.out.AVIWriter
 
SAVE_JUNK_SIG - Static variable in class loci.formats.out.AVIWriter
 
SAVE_LIST1_SIZE - Static variable in class loci.formats.out.AVIWriter
 
SAVE_LIST1_SUBSIZE - Static variable in class loci.formats.out.AVIWriter
 
SAVE_LIST2_SIZE - Static variable in class loci.formats.out.AVIWriter
 
SAVE_MOVI - Static variable in class loci.formats.out.AVIWriter
 
SAVE_STRF_SIZE - Static variable in class loci.formats.out.AVIWriter
 
SAVE_STRN_POS - Static variable in class loci.formats.out.AVIWriter
 
saveBytes(int, byte[]) - Method in class loci.formats.FormatWriter
 
saveBytes(int, byte[], Region) - Method in class loci.formats.FormatWriter
 
saveBytes(int, byte[]) - Method in interface loci.formats.IFormatWriter
Saves the given image to the current series in the current file.
saveBytes(int, byte[], int, int, int, int) - Method in interface loci.formats.IFormatWriter
Saves the given image tile to the current series in the current file.
saveBytes(int, byte[], Region) - Method in interface loci.formats.IFormatWriter
Saves the given image tile to the current series in the current file.
saveBytes(int, byte[]) - Method in class loci.formats.ImageWriter
 
saveBytes(int, byte[], int, int, int, int) - Method in class loci.formats.ImageWriter
 
saveBytes(int, byte[], Region) - Method in class loci.formats.ImageWriter
 
saveBytes(int, byte[], int, int, int, int) - Method in class loci.formats.out.APNGWriter
 
saveBytes(int, byte[], int, int, int, int) - Method in class loci.formats.out.AVIWriter
 
saveBytes(int, byte[]) - Method in class loci.formats.out.CellH5Writer
Saves the given image to the specified (possibly already open) file.
saveBytes(int, byte[], int, int, int, int) - Method in class loci.formats.out.CellH5Writer
 
saveBytes(int, byte[], int, int, int, int) - Method in class loci.formats.out.EPSWriter
 
saveBytes(int, byte[], int, int, int, int) - Method in class loci.formats.out.ICSWriter
 
saveBytes(int, byte[], int, int, int, int) - Method in class loci.formats.out.ImageIOWriter
 
saveBytes(int, byte[], int, int, int, int) - Method in class loci.formats.out.JavaWriter
 
saveBytes(int, byte[], int, int, int, int) - Method in class loci.formats.out.JPEG2000Writer
 
saveBytes(int, byte[], int, int, int, int) - Method in class loci.formats.out.LegacyQTWriter
 
saveBytes(int, byte[], int, int, int, int) - Method in class loci.formats.out.OMETiffWriter
 
saveBytes(int, byte[], IFD, int, int, int, int) - Method in class loci.formats.out.OMETiffWriter
 
saveBytes(int, byte[], int, int, int, int) - Method in class loci.formats.out.OMEXMLWriter
 
saveBytes(int, byte[], IFD, int, int, int, int) - Method in class loci.formats.out.PyramidOMETiffWriter
 
saveBytes(int, byte[], int, int, int, int) - Method in class loci.formats.out.QTWriter
 
saveBytes(int, byte[], IFD) - Method in class loci.formats.out.TiffWriter
Saves the given image to the specified (possibly already open) file.
saveBytes(int, byte[], IFD, int, int, int, int) - Method in class loci.formats.out.TiffWriter
Saves the given image to the specified series in the current file.
saveBytes(int, byte[], int, int, int, int) - Method in class loci.formats.out.TiffWriter
 
saveBytes(int, byte[], int, int, int, int) - Method in class loci.formats.out.V3DrawWriter
 
saveBytes(int, byte[], int, int, int, int) - Method in class loci.formats.out.WlzWriter
 
saveBytes(int, byte[], int, int, int, int) - Method in interface loci.formats.services.WlzService
Adds a rectangle of bytes in an x-y plane to the opened Woolz object.
saveBytes(int, byte[], int, int, int, int) - Method in class loci.formats.services.WlzServiceImpl
 
saveBytes(int, byte[]) - Method in class loci.formats.WriterWrapper
 
saveBytes(int, byte[], int, int, int, int) - Method in class loci.formats.WriterWrapper
 
saveBytes(int, byte[], Region) - Method in class loci.formats.WriterWrapper
 
saveComment(String, String) - Method in class loci.formats.out.OMETiffWriter
 
savedbLength - Variable in class loci.formats.out.AVIWriter
 
saveDefaults() - Method in class loci.plugins.in.ImportProcess
Performed following ImportStep.FILE notification.
savedToMemo - Variable in class loci.formats.Memoizer
Whether the ReaderWrapper.reader instance was saved to a memo file on Memoizer.setId(String).
saveFile(File) - Method in class loci.formats.tools.EditTiffG
 
saveidx1Length - Variable in class loci.formats.out.AVIWriter
 
saveImage(int, BufferedImage) - Method in class loci.formats.gui.BufferedImageWriter
Saves the given BufferedImage to the current file.
saveImage(int, BufferedImage, int, int, int, int) - Method in class loci.formats.gui.BufferedImageWriter
Saves the given BufferedImage to the current file.
saveLUTs(ImagePlus, List<LUT>) - Static method in class loci.plugins.in.ImagePlusReader
 
saveMemo() - Method in class loci.formats.Memoizer
Save a reader including all reader wrappers inside a memo file.
saveOption() - Method in class loci.plugins.prefs.BooleanOption
 
saveOption() - Method in class loci.plugins.prefs.DoubleOption
 
saveOption() - Method in class loci.plugins.prefs.Option
Saves the option's value to the ImageJ preferences file.
saveOption() - Method in class loci.plugins.prefs.StringOption
 
saveOptions() - Method in class loci.plugins.prefs.OptionsList
Saves option values to the ImageJ preferences file.
saveOriginalMetadata - Variable in class loci.formats.FormatReader
Whether or not to save proprietary metadata in the MetadataStore.
savePlane(int, Object) - Method in class loci.formats.FormatWriter
 
savePlane(int, Object, int, int, int, int) - Method in class loci.formats.FormatWriter
 
savePlane(int, Object, Region) - Method in class loci.formats.FormatWriter
 
savePlane(int, Object) - Method in interface loci.formats.IFormatWriter
Saves the given image plane to the current series in the current file.
savePlane(int, Object, int, int, int, int) - Method in interface loci.formats.IFormatWriter
Saves the given image plane to the current series in the current file.
savePlane(int, Object, Region) - Method in interface loci.formats.IFormatWriter
Saves the given image plane to the current series in the current file.
savePlane(int, Object) - Method in class loci.formats.ImageWriter
 
savePlane(int, Object, int, int, int, int) - Method in class loci.formats.ImageWriter
 
savePlane(int, Object, Region) - Method in class loci.formats.ImageWriter
 
savePlane(int, Object, int, int, int, int) - Method in class loci.formats.out.ImageIOWriter
 
savePlane(int, Object, int, int, int, int) - Method in class loci.formats.out.LegacyQTWriter
 
savePlane(int, Object) - Method in class loci.formats.WriterWrapper
 
savePlane(int, Object, int, int, int, int) - Method in class loci.formats.WriterWrapper
 
savePlane(int, Object, Region) - Method in class loci.formats.WriterWrapper
 
saveReader(IFormatReader) - Method in interface loci.formats.Memoizer.Deser
 
saveReader(IFormatReader) - Method in class loci.formats.Memoizer.KryoDeser
 
saveReader(IFormatReader) - Method in class loci.formats.Memoizer.RandomAccessDeser
 
saveReleaseVersion(String) - Method in interface loci.formats.Memoizer.Deser
 
saveReleaseVersion(String) - Method in class loci.formats.Memoizer.KryoDeser
 
saveReleaseVersion(String) - Method in class loci.formats.Memoizer.RandomAccessDeser
 
saveRevision(String) - Method in interface loci.formats.Memoizer.Deser
 
saveRevision(String) - Method in class loci.formats.Memoizer.KryoDeser
 
saveRevision(String) - Method in class loci.formats.Memoizer.RandomAccessDeser
 
saveROIs(MetadataStore) - Static method in class loci.plugins.util.ROIHandler
Save ROIs in the ROI manager to the given MetadataStore.
saveStart(File) - Method in interface loci.formats.Memoizer.Deser
 
saveStart(File) - Method in class loci.formats.Memoizer.KryoDeser
 
saveStart(File) - Method in class loci.formats.Memoizer.RandomAccessDeser
 
saveStop() - Method in interface loci.formats.Memoizer.Deser
 
saveStop() - Method in class loci.formats.Memoizer.KryoDeser
 
saveStop() - Method in class loci.formats.Memoizer.RandomAccessDeser
 
saveStream - Variable in class loci.formats.Memoizer.RandomAccessDeser
 
saveVersion(Integer) - Method in interface loci.formats.Memoizer.Deser
 
saveVersion(Integer) - Method in class loci.formats.Memoizer.KryoDeser
 
saveVersion(Integer) - Method in class loci.formats.Memoizer.RandomAccessDeser
 
sb - Variable in class loci.formats.gui.ImageViewer
 
sb - Variable in class loci.formats.in.FEITiffReader.FEIHandler
 
SBIGReader - Class in loci.formats.in
SBIGReader is the file format reader for SBIG files.
SBIGReader() - Constructor for class loci.formats.in.SBIGReader
Constructs a new SBIG reader.
scale(BufferedImage, int, int, boolean) - Static method in class loci.formats.gui.AWTImageTools
Scales the image using the most appropriate API, with the resultant image having the same color model as the original image.
SCALE - Static variable in class loci.formats.in.FV1000Reader
 
scale - Variable in class loci.formats.in.NativeQTReader
Amount to subtract from each offset.
scale(double, double) - Method in class loci.plugins.util.RecordedImageProcessor
 
scale2D(BufferedImage, int, int, Object, GraphicsConfiguration) - Static method in class loci.formats.gui.AWTImageTools
Scales the image using the Java2D API, with the resultant image optimized for the given graphics configuration.
scale2D(BufferedImage, int, int, Object, ColorModel) - Static method in class loci.formats.gui.AWTImageTools
Scales the image using the Java2D API, with the resultant image having the given color model.
SCALE_BAR - Static variable in class loci.formats.in.LeicaHandler.ROI
 
SCALE_BAR - Static variable in class loci.formats.in.LIFReader.ROI
 
SCALE_BAR - Static variable in class loci.formats.in.ZeissLSMReader
 
scaleAWT(BufferedImage, int, int, int) - Static method in class loci.formats.gui.AWTImageTools
Scales the image using the AWT Image API.
scaleCoordinate(int, int) - Method in class loci.formats.in.VentanaReader
 
scaleFactor - Variable in class loci.formats.in.FakeReader
Scale factor for gradient, if any.
scaleFactor - Variable in class loci.formats.in.ZeissCZIReader
 
scaleX - Variable in class loci.formats.in.LeicaHandler.ROI
 
scaleX - Variable in class loci.formats.in.LIFReader.ROI
 
scaleY - Variable in class loci.formats.in.LeicaHandler.ROI
 
scaleY - Variable in class loci.formats.in.LIFReader.ROI
 
scaling - Variable in class loci.formats.in.SimplePCITiffReader
 
Scaling() - Constructor for class loci.formats.in.ZeissTIFFHandler.Scaling
 
scalings - Variable in class loci.formats.in.ZeissTIFFHandler
 
SCAN_TIME - Static variable in class loci.formats.in.NDPIReader
 
scanData(byte[], int, boolean) - Static method in class loci.formats.ImageTools
Scan a plane for the channel min and max values.
scanDim - Variable in class loci.formats.in.ZeissCZIReader
 
scanDirectory(Location, boolean) - Method in class loci.formats.in.DicomReader
Scan the given directory for files that belong to this dataset.
scanFormat(String, String) - Static method in class loci.formats.in.FV1000Reader
 
SCANNERSET - Static variable in class loci.formats.in.LeicaReader
 
ScanrHandler() - Constructor for class loci.formats.in.ScanrReader.ScanrHandler
 
ScanrReader - Class in loci.formats.in
ScanrReader is the file format reader for Olympus ScanR datasets.
ScanrReader() - Constructor for class loci.formats.in.ScanrReader
Constructs a new ScanR reader.
ScanrReader.ScanrHandler - Class in loci.formats.in
 
scanRX - Variable in class loci.formats.in.SDTInfo
 
scanRY - Variable in class loci.formats.in.SDTInfo
 
scanValues - Variable in class loci.formats.in.PrairieMetadata
Table of key/value pairs at the top level.
scanX - Variable in class loci.formats.in.SDTInfo
 
scanY - Variable in class loci.formats.in.SDTInfo
 
SCENE_CAPTURE_TYPE - Static variable in class loci.formats.tiff.IFD
 
SCENE_TYPE - Static variable in class loci.formats.tiff.IFD
 
SCHEMA_2010_03 - Static variable in class loci.formats.in.LeicaSCNReader
 
SCHEMA_2010_10 - Static variable in class loci.formats.in.LeicaSCNReader
 
SCHEMA_CLASSPATH_READER - Static variable in class loci.formats.services.OMEXMLServiceImpl
Finds OME-XML schema definitions in specifications.jar.
SCHEMA_PATH - Static variable in class loci.formats.services.OMEXMLServiceImpl
 
SCHEMA_URL_PATTERN - Static variable in class loci.formats.services.OMEXMLServiceImpl
The pattern of system ID URLs for OME-XML schema definitions.
schemaType - Variable in class loci.formats.in.ZeissCZIReader.AttachmentEntry
 
schemaType - Variable in class loci.formats.in.ZeissCZIReader.DirectoryEntry
 
SCNHandler() - Constructor for class loci.formats.in.BioRadSCNReader.SCNHandler
 
SCREENING - Static variable in class loci.formats.in.FlexReader
 
screenName - Variable in class loci.formats.in.ColumbusReader.MeasurementHandler
 
screens - Variable in class loci.formats.in.FakeReader
 
SDTInfo - Class in loci.formats.in
SDTInfo encapsulates the header information for Becker & Hickl SPC-Image SDT files.
SDTInfo(RandomAccessInputStream, Hashtable) - Constructor for class loci.formats.in.SDTInfo
Constructs a new SDT header by reading values from the given input source, populating the given metadata table.
SDTReader - Class in loci.formats.in
SDTReader is the file format reader for Becker & Hickl SPC-Image SDT files.
SDTReader() - Constructor for class loci.formats.in.SDTReader
Constructs a new SDT reader.
SDTWidgets - Class in loci.plugins.config
Custom widgets for configuring Bio-Formats SDT support.
SDTWidgets() - Constructor for class loci.plugins.config.SDTWidgets
 
SearchableWindow - Class in loci.plugins.util
Text panel with search capabilities.
SearchableWindow(String, String, String, int, int) - Constructor for class loci.plugins.util.SearchableWindow
 
SearchableWindow.SearchBox - Class in loci.plugins.util
 
SearchBox(SearchableWindow) - Constructor for class loci.plugins.util.SearchableWindow.SearchBox
 
searchBox - Variable in class loci.plugins.util.SearchableWindow.SearchBox
 
searchPane - Variable in class loci.plugins.util.SearchableWindow.SearchBox
 
SEED - Static variable in class loci.formats.in.FakeReader
 
seekStartOfPlane(int, long, long) - Method in class loci.formats.in.LIFReader
 
seekToFrameStart(OBFReader.Stack, long) - Method in class loci.formats.in.OBFReader
 
seekToNextMarker() - Method in class loci.formats.in.ZeissLMSReader
 
seekToPlaneOffset(long, int, int) - Method in class loci.formats.FormatWriter
Seek to the given (x, y) coordinate of the image that starts at the given offset.
Segment() - Constructor for class loci.formats.in.ZeissCZIReader.Segment
 
Segment(String) - Constructor for class loci.formats.in.ZeissCZIReader.Segment
 
Segment(ZeissCZIReader.Segment) - Constructor for class loci.formats.in.ZeissCZIReader.Segment
 
SEGMENTATION_PATH - Static variable in class loci.formats.in.BDVReader.H5Constants
 
SEGMENTATION_PATH - Static variable in class loci.formats.in.CellH5Reader.CellH5Constants
 
segments - Variable in class loci.formats.in.ZeissCZIReader
 
SeikoReader - Class in loci.formats.in
SeikoReader is the file format reader for Seiko .xqd/.xqf files.
SeikoReader() - Constructor for class loci.formats.in.SeikoReader
Constructs a new Seiko reader.
SELECTED_CHANNELS - Static variable in class loci.formats.in.CellSensReader
 
SELECTED_FRAMES - Static variable in class loci.formats.in.CellSensReader
 
selectLine(int) - Method in class loci.plugins.util.SearchableWindow
 
SEM_DOMAIN - Static variable in class loci.formats.FormatTools
Identifies the scanning electron microscopy domain.
SENSING_METHOD - Static variable in class loci.formats.tiff.IFD
 
SENSOR_KEYS - Static variable in class loci.formats.in.ICSReader
 
sensorHeight - Variable in class loci.formats.in.MRWReader
 
sensorWidth - Variable in class loci.formats.in.MRWReader
 
separatedFork - Variable in class loci.formats.in.NativeQTReader
Flag indicating whether the resource and data fork are separated.
SEQ_FILTERSET - Static variable in class loci.formats.in.LeicaReader
 
SEQ_FILTERSET_END - Static variable in class loci.formats.in.LeicaReader
 
SEQ_SCANNERSET - Static variable in class loci.formats.in.LeicaReader
 
SEQ_SCANNERSET_END - Static variable in class loci.formats.in.LeicaReader
 
SEQReader - Class in loci.formats.in
SEQReader is the file format reader for Image-Pro Sequence files.
SEQReader() - Constructor for class loci.formats.in.SEQReader
Constructs a new Image-Pro SEQ reader.
sequence - Variable in class loci.formats.in.PrairieMetadata.Frame
The <Sequence> containing this <Frame>.
Sequence(Element) - Constructor for class loci.formats.in.PrairieMetadata.Sequence
Creates a new sequence by parsing the given <Sequence> element.
sequence(int) - Method in class loci.formats.in.PrairieReader
Gets the first sequence associated with the given series.
sequence(int, int) - Method in class loci.formats.in.PrairieReader
Gets the sequence associated with the given series and time point.
sequence(int, int, int) - Method in class loci.formats.in.PrairieReader
Gets the sequence associated with the given time point and stage position.
SEQUENCE_DELIMINATION - Static variable in class loci.formats.in.DicomReader
 
sequences - Variable in class loci.formats.in.PrairieMetadata
<Sequence> elements, keyed on each sequence's cycle.
sequences - Variable in class loci.formats.in.PrairieReader
List of Prairie metadata Sequences, ordered by cycle.
sequenceValues - Variable in class loci.formats.in.PrairieMetadata.Sequence
Table of key/value pairs for this <Sequence>.
sequential - Variable in class loci.formats.FormatWriter
Whether or not we are writing planes sequentially.
sequential - Variable in class loci.formats.in.LeicaReader
 
SEQUENTIALSET - Static variable in class loci.formats.in.LeicaReader
 
sequentialTileFilePointer - Variable in class loci.formats.tiff.TiffSaver
 
sequentialTileOffsets - Variable in class loci.formats.tiff.TiffSaver
Store tile offsets and original file pointer when writing sequentially.
sequentialWrite - Variable in class loci.formats.tiff.TiffSaver
 
ser - Variable in class loci.formats.Memoizer
 
SERIAL_NUMBER - Static variable in class loci.formats.in.NDPIReader
 
SERIALIZED_MASK - Static variable in class loci.formats.in.CellSensReader
 
serialNumber - Variable in class loci.formats.in.BioRadSCNReader
 
serialNumber - Variable in class loci.formats.in.LIFReader
 
serialNumber - Variable in class loci.formats.in.NDPIReader
 
serialVersionUID - Static variable in class org.libjpegturbo.turbojpeg.TJTransform
 
series - Variable in class loci.formats.FileStitcher
The number of the current series (non flat).
series - Variable in class loci.formats.FormatReader
The number of the current series (non flat).
series - Variable in class loci.formats.FormatWriter
Current series.
series - Variable in class loci.formats.gui.DataConverter
 
series - Variable in class loci.formats.in.CellomicsReader.ChannelFile
 
series - Variable in class loci.formats.in.ColumbusReader.Plane
 
series - Variable in class loci.formats.in.CV7000Reader.Plane
 
SERIES - Static variable in class loci.formats.in.LeicaReader
IFD tags.
series - Variable in class loci.formats.in.OBFReader.State
 
series - Variable in class loci.formats.in.OpenlabReader.PlaneInfo
 
series - Variable in class loci.formats.in.ZeissCZIReader.Coordinate
 
series - Variable in class loci.plugins.macro.LociFunctions
 
series - Variable in class loci.plugins.util.BFVirtualStack
 
SERIES_NAME - Static variable in class loci.formats.FormatTools
 
SERIES_NUM - Static variable in class loci.formats.FormatTools
Patterns to be used when constructing a pattern for output filenames.
SERIES_PREFIXES - Static variable in class loci.formats.in.KLBReader
 
seriesCount - Variable in class loci.formats.in.BDVReader
 
seriesCount - Variable in class loci.formats.in.CellH5Reader
 
seriesCount - Variable in class loci.formats.in.ImarisHDFReader
 
seriesCounts - Variable in class loci.formats.in.ZeissLSMReader
 
seriesDescriptions - Variable in class loci.formats.in.LeicaReader
 
SeriesDialog - Class in loci.plugins.in
Bio-Formats Importer series chooser dialog box.
SeriesDialog(ImportProcess) - Constructor for class loci.plugins.in.SeriesDialog
Creates a series chooser dialog for the Bio-Formats Importer.
seriesFiles - Variable in class loci.formats.in.ScanrReader
 
seriesIFDs - Variable in class loci.formats.in.IonpathMIBITiffReader
 
seriesIndex - Variable in class loci.formats.in.LeicaSCNReader.LeicaSCNHandler
 
seriesInfo - Variable in class loci.formats.in.MNGReader
 
SeriesInfo() - Constructor for class loci.formats.in.MNGReader.SeriesInfo
 
SeriesInfo(int, int) - Constructor for class loci.plugins.in.ThumbLoader.SeriesInfo
 
seriesLabels - Variable in class loci.plugins.in.ImportProcess
A descriptive label for each series.
seriesMetadata - Variable in class loci.formats.CoreMetadata
Non-core metadata associated with this series.
seriesNames - Variable in class loci.formats.in.LeicaReader
 
seriesOn - Variable in class loci.plugins.in.ImporterOptions
 
seriesRow - Variable in class loci.formats.gui.DataConverter
 
seriesStream - Variable in class loci.formats.in.BrukerReader
 
seriesToCoreIndex(int) - Method in class loci.formats.FileStitcher
 
seriesToCoreIndex(int) - Method in class loci.formats.FormatReader
 
seriesToCoreIndex(int) - Method in interface loci.formats.IFormatReader
Deprecated.
This method is no longer required for sub-resolution support.
seriesToCoreIndex(int) - Method in class loci.formats.ImageReader
 
seriesToCoreIndex(int) - Method in class loci.formats.ReaderWrapper
 
seriesToCoreIndex(int) - Method in class loci.formats.SubResolutionFormatReader
 
seriesToCoreIndex(int) - Method in class loci.formats.WrappedReader
 
seriesToIFD - Variable in class loci.formats.in.MinimalTiffReader
 
seriesToWellArea(int) - Method in class loci.formats.in.CellVoyagerReader
Returns the well index (in the field CellVoyagerReader.wells) and the area index (in the field CellVoyagerReader.WellInfo.areas corresponding to the specified series.
seriesTypes - Variable in class loci.formats.in.IonpathMIBITiffReader
 
serverMap - Static variable in class loci.formats.in.FlexReader
Mapping from server names stored in the .mea file to actual server names.
service - Variable in class loci.formats.codec.JPEGXRCodec
 
service - Variable in class loci.formats.FormatReader
 
service - Variable in class loci.formats.in.CellWorxReader
 
service - Variable in class loci.formats.in.HamamatsuVMSReader
 
service - Variable in class loci.formats.in.NDPIReader
 
service - Variable in class loci.formats.in.OMETiffReader
 
service - Variable in class loci.formats.in.TileJPEGReader
 
service - Variable in class loci.formats.Memoizer
 
service - Variable in class loci.formats.out.OMETiffWriter
 
service - Variable in class loci.formats.out.OMEXMLWriter
 
serviceRegistry - Variable in class loci.formats.services.JAIIIOServiceImpl
 
set(String, String) - Method in class loci.formats.in.DynamicMetadataOptions
Set property name to value.
set(int, int, T) - Method in class loci.formats.MetadataList
Set the array element for the specified indexes.
set(List<T>, int, T, T) - Method in class loci.plugins.in.ImporterOptions
 
set(int, int) - Method in class loci.plugins.util.RecordedImageProcessor
 
set(int, int, int) - Method in class loci.plugins.util.RecordedImageProcessor
 
setAllowOpenFiles(boolean) - Method in class loci.formats.ImageReader
Toggles whether or not file system access is allowed when doing type detection.
setAntialiasedText(boolean) - Method in class loci.plugins.util.RecordedImageProcessor
 
setAssumeEqualStrips(boolean) - Method in class loci.formats.tiff.TiffParser
Sets whether or not to assume that strips are of equal size.
setAutomaticallyParseMasks(boolean) - Method in class loci.formats.in.MIASReader
Toggle whether or not Mask pixel data should be parsed in setId.
setAutoscale(boolean) - Method in class loci.plugins.in.ImporterOptions
 
setAutoThreshold(int, int) - Method in class loci.plugins.util.RecordedImageProcessor
 
setAxisTypes(int[]) - Method in class loci.formats.AxisGuesser
Sets the axis type for each dimensional block.
setAxisTypes(int[]) - Method in class loci.formats.FileStitcher
Sets the axis type for each dimensional block.
setBackgroundValue(double) - Method in class loci.plugins.util.RecordedImageProcessor
 
setBigTiff(boolean) - Method in class loci.formats.out.TiffWriter
Sets whether or not BigTIFF files should be written.
setBigTiff(boolean) - Method in class loci.formats.tiff.TiffSaver
Sets whether or not BigTIFF data should be written.
setBoolean(String, Boolean) - Method in class loci.formats.in.DynamicMetadataOptions
Set property name to Boolean value.
setByte(int, int) - Method in class loci.formats.in.SPEReader.SpeHeader
Private method used to set a Byte value in the SPE header
setCalibrationTable(float[]) - Method in class loci.plugins.util.RecordedImageProcessor
 
setCanChangePattern(boolean) - Method in class loci.formats.FileStitcher
 
setCanDetectBigTiff(boolean) - Method in class loci.formats.out.TiffWriter
Sets whether or not BigTIFF can be used automatically based upon the input data size (true by default).
setCanDoUpgradeCheck(boolean) - Method in class loci.formats.UpgradeChecker
Set whether or not we are ever allowed to perform an upgrade check.
setCanLookForND(boolean) - Method in class loci.formats.in.MetamorphReader
 
setCategory(int) - Method in class loci.formats.in.BaseZeissReader.Tag
 
setCBegin(int, int) - Method in class loci.plugins.in.ImporterOptions
 
setCEnd(int, int) - Method in class loci.plugins.in.ImporterOptions
 
setChannelGlobalMinMax(int, double, double, int) - Method in interface loci.formats.meta.IMinMaxStore
Populates the channel global minimum and maximum.
setClass(String, Class<?>) - Method in class loci.formats.in.DynamicMetadataOptions
Set property name to Class value.
setClipRect(Rectangle) - Method in class loci.plugins.util.RecordedImageProcessor
 
setCodec(int) - Method in class loci.formats.out.LegacyQTWriter
Sets the encoded movie's codec.
setCodec(int) - Method in class loci.formats.out.QTWriter
Sets the encoded movie's codec.
setCodec() - Method in class loci.formats.out.QTWriter
 
setCodecOptions(CodecOptions) - Method in class loci.formats.FormatWriter
 
setCodecOptions(CodecOptions) - Method in interface loci.formats.IFormatWriter
Sets the codec options.
setCodecOptions(CodecOptions) - Method in class loci.formats.ImageWriter
 
setCodecOptions(CodecOptions) - Method in class loci.formats.tiff.TiffParser
Sets the codec options to be used when decompressing pixel data.
setCodecOptions(CodecOptions) - Method in class loci.formats.tiff.TiffSaver
Sets the codec options.
setCodecOptions(CodecOptions) - Method in class loci.formats.WriterWrapper
 
setColor(Color) - Method in class loci.plugins.util.RecordedImageProcessor
 
setColor(int) - Method in class loci.plugins.util.RecordedImageProcessor
 
setColorMode(String) - Method in class loci.plugins.in.ImporterOptions
 
setColorModel(ColorModel) - Method in class loci.formats.FormatWriter
 
setColorModel(ColorModel) - Method in interface loci.formats.IFormatWriter
Sets the color model.
setColorModel(ColorModel) - Method in class loci.formats.ImageWriter
 
setColorModel(ColorModel) - Method in class loci.formats.WriterWrapper
 
setColorModel(ColorModel) - Method in class loci.plugins.util.RecordedImageProcessor
 
setCompression(String) - Method in class loci.formats.FormatWriter
 
setCompression(String) - Method in interface loci.formats.IFormatWriter
Sets the current compression type.
setCompression(String) - Method in class loci.formats.ImageWriter
 
setCompression(String) - Method in class loci.formats.WriterWrapper
 
setConcatenate(boolean) - Method in class loci.plugins.in.ImporterOptions
 
setCoreIndex(int) - Method in class loci.formats.DelegateReader
 
setCoreIndex(int) - Method in class loci.formats.FileStitcher
 
setCoreIndex(int) - Method in class loci.formats.FormatReader
 
setCoreIndex(int) - Method in interface loci.formats.IFormatReader
Deprecated.
This method is no longer required for sub-resolution support.
setCoreIndex(int) - Method in class loci.formats.ImageReader
 
setCoreIndex(int) - Method in class loci.formats.ReaderWrapper
 
setCoreIndex(int) - Method in class loci.formats.SubResolutionFormatReader
 
setCoreIndex(int) - Method in class loci.formats.WrappedReader
 
setCrop(boolean) - Method in class loci.plugins.in.ImporterOptions
 
setCropRegion(int, Region) - Method in class loci.plugins.in.ImporterOptions
 
setCStep(int, int) - Method in class loci.plugins.in.ImporterOptions
 
setCurrentPos(int[]) - Method in class loci.formats.cache.Cache
Sets the current dimensional position.
setCustomColor(int, int, Color) - Method in class loci.plugins.in.ImporterOptions
 
setDataType(String) - Method in class loci.formats.in.InveonReader
 
setDefaultCreationDate(MetadataStore, String, int) - Static method in class loci.formats.MetadataTools
Sets a default creation date.
setDefaultDateEnabled(boolean) - Static method in class loci.formats.MetadataTools
Disables the setting of a default creation date.
setDoCaching(boolean) - Method in class loci.formats.tiff.TiffParser
Sets whether or not IFD entries should be cached.
setDocument(Document) - Method in class loci.formats.gui.XMLWindow
Displays XML from the given document.
setDocumentLocator(Locator) - Method in class loci.formats.in.OMEXMLReader.OMEXMLHandler
 
setDoRecording(boolean) - Method in class loci.plugins.util.RecordedImageProcessor
 
setDouble(String, Double) - Method in class loci.formats.in.DynamicMetadataOptions
Set property name to Double value.
setElem(int, int) - Method in class loci.formats.gui.SignedByteBuffer
 
setElem(int, int, int) - Method in class loci.formats.gui.SignedByteBuffer
 
setElem(int, int, int) - Method in class loci.formats.gui.SignedShortBuffer
 
setElem(int, int) - Method in class loci.formats.gui.UnsignedIntBuffer
 
setElem(int, int, int) - Method in class loci.formats.gui.UnsignedIntBuffer
 
setElemDouble(int, double) - Method in class loci.formats.gui.UnsignedIntBuffer
 
setElemDouble(int, int, double) - Method in class loci.formats.gui.UnsignedIntBuffer
 
setElemFloat(int, float) - Method in class loci.formats.gui.UnsignedIntBuffer
 
setElemFloat(int, int, float) - Method in class loci.formats.gui.UnsignedIntBuffer
 
setEnum(String, T) - Method in class loci.formats.in.DynamicMetadataOptions
Set property name to enumerated type value.
setf(int, float) - Method in class loci.plugins.util.RecordedImageProcessor
 
setf(int, int, float) - Method in class loci.plugins.util.RecordedImageProcessor
 
setFile(String, File) - Method in class loci.formats.in.DynamicMetadataOptions
Set property name to file object value.
setFile(String) - Method in interface loci.formats.services.JHDFService
Initializes the service on a given file path.
setFile(String) - Method in class loci.formats.services.JHDFServiceImpl
 
setFile(String) - Method in interface loci.formats.services.NetCDFService
Initializes the service on a given file path.
setFile(String) - Method in class loci.formats.services.NetCDFServiceImpl
 
setFileForWrite(String) - Method in interface loci.formats.services.JHDFService
Initializes the service on a given file path.
setFileForWrite(String) - Method in class loci.formats.services.JHDFServiceImpl
 
setFilled(boolean) - Method in class loci.formats.ChannelFiller
Toggles whether the indices should be factored out.
setFirstTime(boolean) - Method in class loci.plugins.in.ImporterOptions
 
setFixed() - Method in class loci.formats.FilePatternBlock
 
setFlattenedList(List<CoreMetadata>) - Method in class loci.formats.CoreMetadataList
 
setFlattenedResolutions(boolean) - Method in class loci.formats.DelegateReader
 
setFlattenedResolutions(boolean) - Method in class loci.formats.FileStitcher
 
setFlattenedResolutions(boolean) - Method in class loci.formats.FormatReader
 
setFlattenedResolutions(boolean) - Method in interface loci.formats.IFormatReader
Set whether or not to flatten resolutions into individual series.
setFlattenedResolutions(boolean) - Method in class loci.formats.ImageReader
 
setFlattenedResolutions(boolean) - Method in class loci.formats.in.FilePatternReader
 
setFlattenedResolutions(boolean) - Method in class loci.formats.ReaderWrapper
 
setFloat(String, Float) - Method in class loci.formats.in.DynamicMetadataOptions
Set property name to Float value.
setFloatArray(float[][]) - Method in class loci.plugins.util.RecordedImageProcessor
 
setFont(Font) - Method in class loci.plugins.util.RecordedImageProcessor
 
setForceThumbnails(boolean) - Method in class loci.plugins.in.ImporterOptions
 
setFramesPerSecond(int) - Method in class loci.formats.FormatWriter
 
setFramesPerSecond(int) - Method in interface loci.formats.IFormatWriter
Sets the frames per second to use when writing.
setFramesPerSecond(int) - Method in class loci.formats.ImageWriter
 
setFramesPerSecond(int) - Method in class loci.formats.WriterWrapper
 
setGroupFiles(boolean) - Method in class loci.formats.DelegateReader
 
setGroupFiles(boolean) - Method in class loci.formats.FileStitcher
 
setGroupFiles(boolean) - Method in class loci.formats.FormatReader
 
setGroupFiles(boolean) - Method in interface loci.formats.IFormatReader
Specifies whether or not to force grouping in multi-file formats.
setGroupFiles(boolean) - Method in class loci.formats.ImageReader
 
setGroupFiles(boolean) - Method in class loci.formats.in.FilePatternReader
 
setGroupFiles(boolean) - Method in class loci.formats.in.ZipReader
 
setGroupFiles(boolean) - Method in class loci.formats.ReaderWrapper
 
setGroupFiles(boolean) - Method in class loci.plugins.in.ImporterOptions
 
setGroupFiles(String) - Method in class loci.plugins.macro.LociFunctions
 
setHeader(byte[]) - Method in class loci.formats.in.SPEReader.SpeHeader
 
setHistogramRange(double, double) - Method in class loci.plugins.util.RecordedImageProcessor
 
setHistogramSize(int) - Method in class loci.plugins.util.RecordedImageProcessor
 
setId(String) - Method in class loci.formats.ChannelFiller
 
setId(String) - Method in class loci.formats.ChannelSeparator
 
setId(String) - Method in class loci.formats.DelegateReader
 
setId(String) - Method in class loci.formats.DimensionSwapper
 
setId(String) - Method in class loci.formats.FileStitcher
 
setId(String) - Method in class loci.formats.FormatReader
Initialize a reader from the input file name.
setId(String) - Method in class loci.formats.FormatWriter
Initializes a writer from the input file name.
setId(String) - Method in interface loci.formats.IFormatHandler
Sets the current file name.
setId(String) - Method in class loci.formats.ImageReader
 
setId(String) - Method in class loci.formats.ImageWriter
 
setId(String) - Method in class loci.formats.in.JPEGReader
 
setId(String) - Method in class loci.formats.in.TiffDelegateReader
 
setId(String) - Method in class loci.formats.Memoizer
 
setId(String) - Method in class loci.formats.out.APNGWriter
 
setId(String) - Method in class loci.formats.out.AVIWriter
 
setId(String) - Method in class loci.formats.out.CellH5Writer
 
setId(String) - Method in class loci.formats.out.ICSWriter
 
setId(String) - Method in class loci.formats.out.JavaWriter
 
setId(String) - Method in class loci.formats.out.OMETiffWriter
 
setId(String) - Method in class loci.formats.out.OMEXMLWriter
 
setId(String) - Method in class loci.formats.out.QTWriter
 
setId(String) - Method in class loci.formats.out.TiffWriter
 
setId(String) - Method in class loci.formats.out.V3DrawWriter
 
setId(String) - Method in class loci.formats.out.WlzWriter
 
setId(String) - Method in class loci.formats.ReaderWrapper
 
setId(String) - Method in class loci.formats.TileStitcher
 
setId(String) - Method in class loci.formats.WriterWrapper
 
setId(String) - Method in class loci.plugins.in.ImporterOptions
 
setId() - Method in class loci.plugins.in.ImportProcess
HACK: This method mainly exists to prompt the user for a missing LuraWave license code, in the case of LWF-compressed Flex.
setId(String) - Method in class loci.plugins.macro.LociFunctions
 
setImages(BufferedImage[]) - Method in class loci.formats.gui.ImageViewer
Sets the viewer to display the given images.
setImages(IFormatReader, BufferedImage[]) - Method in class loci.formats.gui.ImageViewer
Sets the viewer to display the given images, obtaining corresponding core metadata from the specified format reader.
setIndex(int) - Method in class loci.formats.in.BaseZeissReader.Tag
 
setInputOrder(int, String) - Method in class loci.plugins.in.ImporterOptions
 
setInt(int, int) - Method in class loci.formats.in.SPEReader.SpeHeader
Private method used to set an Integer value in the SPE header
setIntArray(int[][]) - Method in class loci.plugins.util.RecordedImageProcessor
 
setInteger(String, Integer) - Method in class loci.formats.in.DynamicMetadataOptions
Set property name to Integer value.
setIntensity(boolean) - Method in class loci.formats.in.SDTReader
Toggles whether the reader should return intensity data only (the sum of each lifetime histogram).
setInterleaved(boolean) - Method in class loci.formats.FormatWriter
 
setInterleaved(boolean) - Method in interface loci.formats.IFormatWriter
Sets whether or not the channels in an image are interleaved.
setInterleaved(boolean) - Method in class loci.formats.ImageWriter
 
setInterleaved(boolean) - Method in class loci.formats.WriterWrapper
 
setInterpolate(boolean) - Method in class loci.plugins.util.RecordedImageProcessor
 
setJPEGImage(byte[], int) - Method in class org.libjpegturbo.turbojpeg.TJDecompressor
Associate the JPEG image of length imageSize bytes stored in jpegImage with this decompressor instance.
setJPEGQuality(int) - Method in class org.libjpegturbo.turbojpeg.TJCompressor
Set the JPEG image quality level for subsequent compress operations.
setJustification(int) - Method in class loci.plugins.util.RecordedImageProcessor
 
setKey(int) - Method in class loci.formats.in.BaseZeissReader.Tag
 
setKeyValue(String, String) - Method in class loci.formats.meta.OriginalMetadataAnnotation
Set the key/value metadata pair for this annotation.
setLegacy(boolean) - Method in class loci.formats.DelegateReader
Sets whether to use the legacy reader by default.
setLegacy(boolean) - Method in class loci.formats.in.PictReader
Control whether or not legacy reader (QT Java) is used.
setLicenseCode(String) - Method in interface loci.formats.services.LuraWaveService
Overrides the license code to use when initializing the LuraWave decoder.
setLicenseCode(String) - Method in class loci.formats.services.LuraWaveServiceImpl
 
setLineWidth(int) - Method in class loci.plugins.util.RecordedImageProcessor
 
setLittleEndian(RandomAccessInputStream) - Method in class loci.formats.in.MRCReader
Detect the correct endianness and set the stream accordingly.
setLittleEndian(boolean) - Method in class loci.formats.tiff.TiffSaver
Sets whether or not little-endian data should be written.
setLocation(String) - Method in class loci.plugins.in.ImporterOptions
 
setLong(String, Long) - Method in class loci.formats.in.DynamicMetadataOptions
Set property name to Long value.
setLong(int, int) - Method in class loci.formats.in.SPEReader.SpeHeader
Private method used to set a Long value in the SPE header
setLutAnimation(boolean) - Method in class loci.plugins.util.RecordedImageProcessor
 
setLUTs(LUT[]) - Method in class loci.plugins.util.VirtualImagePlus
 
setMask(ImageProcessor) - Method in class loci.plugins.util.RecordedImageProcessor
 
setMetadataFiltered(boolean) - Method in class loci.formats.DelegateReader
 
setMetadataFiltered(boolean) - Method in class loci.formats.FormatReader
 
setMetadataFiltered(boolean) - Method in interface loci.formats.IFormatReader
Specifies whether ugly metadata (entries with unprintable characters, and extremely large entries) should be discarded from the metadata table.
setMetadataFiltered(boolean) - Method in class loci.formats.ImageReader
 
setMetadataFiltered(boolean) - Method in class loci.formats.in.FilePatternReader
 
setMetadataFiltered(boolean) - Method in class loci.formats.ReaderWrapper
 
setMetadataFiltered(String) - Method in class loci.plugins.macro.LociFunctions
 
setMetadataLevel(MetadataLevel) - Method in class loci.formats.in.DefaultMetadataOptions
 
setMetadataLevel(MetadataLevel) - Method in class loci.formats.in.DynamicMetadataOptions
 
setMetadataLevel(MetadataLevel) - Method in interface loci.formats.in.MetadataOptions
Set the metadata level.
setMetadataOptions(MetadataOptions) - Method in class loci.formats.DelegateReader
 
setMetadataOptions(MetadataOptions) - Method in class loci.formats.FileStitcher
 
setMetadataOptions(MetadataOptions) - Method in class loci.formats.FormatHandler
 
setMetadataOptions(MetadataOptions) - Method in class loci.formats.ImageReader
 
setMetadataOptions(MetadataOptions) - Method in class loci.formats.ImageWriter
 
setMetadataOptions(MetadataOptions) - Method in interface loci.formats.IMetadataConfigurable
 
setMetadataOptions(MetadataOptions) - Method in class loci.formats.ReaderWrapper
 
setMetadataOptions(MetadataOptions) - Method in class loci.formats.WriterWrapper
 
setMetadataRetrieve(MetadataRetrieve) - Method in class loci.formats.FormatWriter
 
setMetadataRetrieve(MetadataRetrieve) - Method in interface loci.formats.IFormatWriter
Sets the metadata retrieval object from which to retrieve standardized metadata.
setMetadataRetrieve(MetadataRetrieve) - Method in class loci.formats.ImageWriter
 
setMetadataRetrieve(MetadataRetrieve) - Method in class loci.formats.WriterWrapper
 
setMetadataStore(MetadataStore) - Method in class loci.formats.DelegateReader
 
setMetadataStore(MetadataStore) - Method in class loci.formats.FileStitcher
 
setMetadataStore(MetadataStore) - Method in class loci.formats.FormatReader
 
setMetadataStore(MetadataStore) - Method in interface loci.formats.IFormatReader
Sets the default metadata store for this reader.
setMetadataStore(MetadataStore) - Method in class loci.formats.ImageReader
 
setMetadataStore(MetadataStore) - Method in class loci.formats.in.FilePatternReader
 
setMetadataStore(MetadataStore) - Method in class loci.formats.Memoizer
 
setMetadataStore(MetadataStore) - Method in class loci.formats.ReaderWrapper
 
setMinAndMax(double, double) - Method in class loci.plugins.util.RecordedImageProcessor
 
setMinMaxStore(IMinMaxStore) - Method in class loci.formats.MinMaxCalculator
Sets the active min-max store for the calculator.
setModulo(OMEXMLMetadata, Modulo) - Method in class loci.formats.meta.ModuloAnnotation
Set the value of this annotation using the given Modulo object
setMustGroup(boolean) - Method in class loci.plugins.in.ImporterOptions
 
setNormalized(boolean) - Method in class loci.formats.DelegateReader
 
setNormalized(boolean) - Method in class loci.formats.FileStitcher
 
setNormalized(boolean) - Method in class loci.formats.FormatReader
 
setNormalized(boolean) - Method in interface loci.formats.IFormatReader
Specifies whether or not to normalize float data.
setNormalized(boolean) - Method in class loci.formats.ImageReader
 
setNormalized(boolean) - Method in class loci.formats.in.FilePatternReader
 
setNormalized(boolean) - Method in class loci.formats.ReaderWrapper
 
setNormalized(Boolean) - Method in class loci.plugins.macro.LociFunctions
 
setNumeric() - Method in class loci.formats.FilePatternBlock
 
setOffsetInfo(int, int, int, int) - Method in class loci.formats.in.DeltavisionReader
This method calculates the size of a w, t, z section depending on which sequence is being used
setOpenAllSeries(boolean) - Method in class loci.plugins.in.ImporterOptions
 
setOrder(int, int) - Method in class loci.formats.cache.CacheStrategy
 
setOrder(int, int) - Method in interface loci.formats.cache.ICacheStrategy
Sets the order in which objects should be loaded along each axis.
setOriginalMetadataPopulated(boolean) - Method in class loci.formats.DelegateReader
 
setOriginalMetadataPopulated(boolean) - Method in class loci.formats.FileStitcher
 
setOriginalMetadataPopulated(boolean) - Method in class loci.formats.FormatReader
 
setOriginalMetadataPopulated(boolean) - Method in interface loci.formats.IFormatReader
Specifies whether or not to save proprietary metadata in the MetadataStore.
setOriginalMetadataPopulated(boolean) - Method in class loci.formats.ImageReader
 
setOriginalMetadataPopulated(boolean) - Method in class loci.formats.in.FilePatternReader
 
setOriginalMetadataPopulated(boolean) - Method in class loci.formats.ReaderWrapper
 
setOriginalMetadataPopulated(Boolean) - Method in class loci.plugins.macro.LociFunctions
 
setOutputOrder(String) - Method in class loci.formats.DimensionSwapper
Sets the output dimension order according to the given string (e.g., "XYZCT").
setOutputOrder(String) - Method in class loci.formats.out.ICSWriter
Set the order in which dimensions should be written to the file.
setOutputOrder(String) - Method in class loci.formats.out.V3DrawWriter
Set the order in which dimensions should be written to the file.
setOutputOrder(String) - Method in class loci.formats.out.WlzWriter
Set the order in which dimensions should be written to the file.
setPixels() - Method in class loci.formats.in.GIFReader
 
setPixels(int, FloatProcessor) - Method in class loci.plugins.util.RecordedImageProcessor
 
setPixels(Object) - Method in class loci.plugins.util.RecordedImageProcessor
 
setPlaneIndexes(int[]) - Method in class loci.plugins.util.BFVirtualStack
 
setPreLoad(boolean) - Method in class loci.formats.in.SDTReader
Toggles whether the reader should pre-load data for increased performance.
setPriority(int, int) - Method in class loci.formats.cache.CacheStrategy
 
setPriority(int, int) - Method in interface loci.formats.cache.ICacheStrategy
Sets the priority for caching the given axis.
setProgressBar(ProgressBar) - Method in class loci.plugins.util.RecordedImageProcessor
 
setQuality(int) - Method in class loci.formats.out.LegacyQTWriter
Sets the quality of the encoded movie.
setQuality(int) - Method in class loci.formats.out.QTWriter
Sets the quality of the encoded movie.
setQuiet(boolean) - Method in class loci.plugins.in.ImporterOptions
 
setRange(int, int) - Method in class loci.formats.cache.CacheStrategy
 
setRange(int, int) - Method in interface loci.formats.cache.ICacheStrategy
Sets the number of objects to cache along the given axis.
setReader(IFormatReader) - Method in class loci.plugins.util.VirtualImagePlus
 
setReaderClassList(ClassList<IFormatReader>) - Method in class loci.formats.FileStitcher
Set the ClassList object to use when constructing any helper readers.
setReaderEnabled(FormatEntry, boolean) - Method in class loci.plugins.config.ConfigWindow
 
setReaderPref(String, FormatEntry, boolean) - Method in class loci.plugins.config.ConfigWindow
 
setReaderWindowless(FormatEntry, boolean) - Method in class loci.plugins.config.ConfigWindow
 
setRefCount(int) - Method in class loci.plugins.util.VirtualReader
 
setResolution(int) - Method in class loci.formats.DelegateReader
 
setResolution(int) - Method in class loci.formats.FileStitcher
 
setResolution(int) - Method in class loci.formats.FormatReader
 
setResolution(int) - Method in class loci.formats.FormatWriter
 
setResolution(int) - Method in class loci.formats.ImageReader
 
setResolution(int) - Method in class loci.formats.ImageWriter
 
setResolution(int) - Method in interface loci.formats.IPyramidHandler
Set the resolution level.
setResolution(int) - Method in class loci.formats.ReaderWrapper
 
setResolution(int) - Method in class loci.formats.SubResolutionFormatReader
 
setResolution(int) - Method in class loci.formats.WrappedReader
 
setResolution(int) - Method in class loci.formats.WriterWrapper
 
setResolutionLevel(IFD) - Method in class loci.formats.in.MinimalTiffReader
Sets the resolution level when we have JPEG 2000 compressed data.
setResolutions(List<Resolution>) - Method in class loci.formats.FormatWriter
 
setResolutions(List<Resolution>) - Method in interface loci.formats.IFormatWriter
Specify a list of resolution objects for the current series.
setResolutions(List<Resolution>) - Method in class loci.formats.ImageWriter
 
setResolutions(List<Resolution>) - Method in class loci.formats.WriterWrapper
 
setResolutionSizeX(PositiveInteger, int, int) - Method in interface loci.formats.meta.IPyramidStore
Define the image width in pixels of the given pyramid resolution.
setResolutionSizeX(PositiveInteger, int, int) - Method in class loci.formats.ome.OMEPyramidStore
 
setResolutionSizeY(PositiveInteger, int, int) - Method in interface loci.formats.meta.IPyramidStore
Define the image height in pixels of the given pyramid resolution.
setResolutionSizeY(PositiveInteger, int, int) - Method in class loci.formats.ome.OMEPyramidStore
 
setRestartMarkers(long[]) - Method in interface loci.formats.services.JPEGTurboService
 
setRestartMarkers(long[]) - Method in class loci.formats.services.JPEGTurboServiceImpl
 
setRoi(int, int, int, int) - Method in class loci.plugins.util.RecordedImageProcessor
 
setRoi(Polygon) - Method in class loci.plugins.util.RecordedImageProcessor
 
setRoi(Rectangle) - Method in class loci.plugins.util.RecordedImageProcessor
 
setRoi(Roi) - Method in class loci.plugins.util.RecordedImageProcessor
 
setROIsMode(String) - Method in class loci.plugins.in.ImporterOptions
 
setRoot(MetadataRoot) - Method in class loci.formats.ome.OMEPyramidStore
 
setSeries(int) - Method in class loci.formats.DelegateReader
 
setSeries(int) - Method in class loci.formats.FileStitcher
 
setSeries(int) - Method in class loci.formats.FormatReader
 
setSeries(int) - Method in class loci.formats.FormatWriter
 
setSeries(int) - Method in interface loci.formats.IFormatReader
Activates the specified series.
setSeries(int) - Method in interface loci.formats.IFormatWriter
Sets the current series.
setSeries(int) - Method in class loci.formats.ImageReader
 
setSeries(int) - Method in class loci.formats.ImageWriter
 
setSeries(int) - Method in class loci.formats.in.IM3Reader
 
setSeries(int) - Method in class loci.formats.in.ZeissLSMReader
 
setSeries(int) - Method in class loci.formats.ReaderWrapper
 
setSeries(int) - Method in class loci.formats.SubResolutionFormatReader
 
setSeries(int) - Method in class loci.formats.WrappedReader
 
setSeries(int) - Method in class loci.formats.WriterWrapper
 
setSeries(Double) - Method in class loci.plugins.macro.LociFunctions
 
setSeriesList(String) - Method in class loci.plugins.in.ImportProcess
 
setSeriesOn(int, boolean) - Method in class loci.plugins.in.ImporterOptions
 
setShort(int, int) - Method in class loci.formats.in.SPEReader.SpeHeader
Private method used to set a Short value in the SPE header
setShowMetadata(boolean) - Method in class loci.plugins.in.ImporterOptions
 
setShowOMEXML(boolean) - Method in class loci.plugins.in.ImporterOptions
 
setShowROIs(boolean) - Method in class loci.plugins.in.ImporterOptions
 
setSize(int) - Method in class loci.formats.tiff.OnDemandLongArray
 
setSlice(int) - Method in class loci.plugins.util.VirtualImagePlus
 
setSliceLabelButton - Variable in class loci.plugins.config.ConfigWindow
 
setSnapshotCopyMode(boolean) - Method in class loci.plugins.util.RecordedImageProcessor
 
setSnapshotPixels(Object) - Method in class loci.plugins.util.RecordedImageProcessor
 
setSource(ICacheSource) - Method in class loci.formats.cache.Cache
Sets the cache's caching source.
setSourceImage(byte[], int, int, int, int) - Method in class org.libjpegturbo.turbojpeg.TJCompressor
Associate an uncompressed source image with this compressor instance.
setSpecifyRanges(boolean) - Method in class loci.plugins.in.ImporterOptions
 
setSplitChannels(boolean) - Method in class loci.plugins.in.ImporterOptions
 
setSplitFocalPlanes(boolean) - Method in class loci.plugins.in.ImporterOptions
 
setSplitTimepoints(boolean) - Method in class loci.plugins.in.ImporterOptions
 
setStackFormat(String) - Method in class loci.plugins.in.ImporterOptions
 
setStackOrder(String) - Method in class loci.plugins.in.ImporterOptions
 
setStitchTiles(boolean) - Method in class loci.plugins.in.ImporterOptions
 
setStrategy(ICacheStrategy) - Method in class loci.formats.cache.Cache
Sets the cache's caching strategy.
setStream(RandomAccessInputStream) - Method in class loci.formats.tiff.OnDemandLongArray
 
setString(int, String) - Method in class loci.formats.in.SPEReader.SpeHeader
Private method used to set a String value in the SPE header
setSubsamp(int) - Method in class org.libjpegturbo.turbojpeg.TJCompressor
Set the level of chrominance subsampling for subsequent compress/encode operations.
setSwapDimensions(boolean) - Method in class loci.plugins.in.ImporterOptions
 
setTBegin(int, int) - Method in class loci.plugins.in.ImporterOptions
 
setTEnd(int, int) - Method in class loci.plugins.in.ImporterOptions
 
setThreshold(double, double, int) - Method in class loci.plugins.util.RecordedImageProcessor
 
setTileSizeX(int) - Method in class loci.formats.FormatWriter
 
setTileSizeX(int) - Method in interface loci.formats.IFormatWriter
Will attempt to set the tile width to the desired value and return the actual value which will be used
setTileSizeX(int) - Method in class loci.formats.ImageWriter
 
setTileSizeX(int) - Method in class loci.formats.out.TiffWriter
 
setTileSizeX(int) - Method in class loci.formats.WriterWrapper
 
setTileSizeY(int) - Method in class loci.formats.FormatWriter
 
setTileSizeY(int) - Method in interface loci.formats.IFormatWriter
Will attempt to set the tile height to the desired value and return the actual value which will be used
setTileSizeY(int) - Method in class loci.formats.ImageWriter
 
setTileSizeY(int) - Method in class loci.formats.out.TiffWriter
 
setTileSizeY(int) - Method in class loci.formats.WriterWrapper
 
settingsPath - Variable in class loci.formats.in.CV7000Reader
 
setTruncatedFileFlag(boolean) - Method in class loci.formats.in.DeltavisionReader
This flag indicates if the file is known to be truncated.
setTStep(int, int) - Method in class loci.plugins.in.ImporterOptions
 
setUngroupFiles(boolean) - Method in class loci.plugins.in.ImporterOptions
 
setup - Variable in class loci.formats.in.BDVReader.H5Coordinate
 
setup - Variable in class loci.formats.in.SDTInfo
 
setup(String, ImagePlus) - Method in class loci.plugins.LociExporter
Sets up the writer.
setup(String, ImagePlus) - Method in class loci.plugins.Slicer
 
SETUP_IDENTIFIER - Static variable in class loci.formats.in.SDTInfo
For .set files (setup only).
setupAttributeList - Variable in class loci.formats.in.BDVReader
 
setUpgradeCheck(boolean) - Method in class loci.plugins.in.ImporterOptions
 
setupLength - Variable in class loci.formats.in.SDTInfo
Length of the setup data.
setupOffs - Variable in class loci.formats.in.SDTInfo
Offset of the setup text data (system parameters, display parameters, trace parameters etc.).
setupReader() - Method in class loci.formats.in.MicromanagerReader
Initialize the TIFF reader with the first non-null file in the current series.
setupResolutionCounts - Variable in class loci.formats.in.BDVReader
 
setupService() - Method in class loci.formats.FormatReader
Initialize the OMEXMLService needed by FormatReader.setId(String)
setupService() - Method in class loci.formats.in.OMETiffReader
 
setupServiceAndMetadata() - Method in class loci.formats.out.OMETiffWriter
 
setupTiffSaver() - Method in class loci.formats.out.TiffWriter
 
setupVoxelSizes - Variable in class loci.formats.in.BDVReader
 
setupWrite(int, int, int, int, int, int, int, int, double, double, double, int) - Method in interface loci.formats.services.WlzService
Sets up the service, which must have already been opened for writing.
setupWrite(int, int, int, int, int, int, int, int, double, double, double, int) - Method in class loci.formats.services.WlzServiceImpl
 
setUse64BitOffsets(boolean) - Method in class loci.formats.tiff.TiffParser
Sets whether or not 64-bit offsets are used for non-BigTIFF files.
setUsingPatternIds(boolean) - Method in class loci.formats.FileStitcher
Sets whether the reader is using file patterns for IDs.
setUsingPatternIds(boolean) - Method in class loci.plugins.in.ImporterOptions
 
setValidate(boolean) - Method in class loci.formats.in.DefaultMetadataOptions
 
setValidate(boolean) - Method in class loci.formats.in.DynamicMetadataOptions
 
setValidate(boolean) - Method in interface loci.formats.in.MetadataOptions
Specifies whether or not to validate files when reading.
setValidBitsPerPixel(int) - Method in class loci.formats.FormatWriter
 
setValidBitsPerPixel(int) - Method in interface loci.formats.IFormatWriter
Sets the number of valid bits per pixel.
setValidBitsPerPixel(int) - Method in class loci.formats.ImageWriter
 
setValidBitsPerPixel(int) - Method in class loci.formats.WriterWrapper
 
setValue(String) - Method in class loci.formats.in.BaseZeissReader.Tag
 
setValue(boolean) - Method in class loci.plugins.prefs.BooleanOption
Sets the current value of the option.
setValue(double) - Method in class loci.plugins.prefs.DoubleOption
Sets the current value of the option.
setValue(String, boolean) - Method in class loci.plugins.prefs.OptionsList
Sets the value of the boolean option with the given key.
setValue(String, String) - Method in class loci.plugins.prefs.OptionsList
Sets the value of the string option with the given key.
setValue(String) - Method in class loci.plugins.prefs.StringOption
Sets the current value of the option.
setValue(double) - Method in class loci.plugins.util.RecordedImageProcessor
 
setVersionChecking(boolean) - Method in class loci.formats.Memoizer
Set whether version checking is done based upon major/minor version numbers.
setView(Attributes) - Method in class loci.formats.in.LeicaSCNReader.Image
 
setVirtual(boolean) - Method in class loci.plugins.in.ImporterOptions
 
setVisible(boolean) - Method in class loci.formats.gui.ImageViewer
 
setVisible(boolean) - Method in class loci.plugins.util.DataBrowser
Overridden show method to allow us to delay initial window display.
setWindowless(boolean) - Method in class loci.plugins.in.ImporterOptions
 
setWriteSequentially(boolean) - Method in class loci.formats.FormatWriter
 
setWriteSequentially(boolean) - Method in interface loci.formats.IFormatWriter
Sets whether or not we know that planes will be written sequentially.
setWriteSequentially(boolean) - Method in class loci.formats.ImageWriter
 
setWriteSequentially(boolean) - Method in class loci.formats.WriterWrapper
 
setWritingSequentially(boolean) - Method in class loci.formats.tiff.TiffSaver
Sets whether or not we know that the planes will be written sequentially.
setXML(String) - Method in class loci.formats.gui.XMLWindow
Displays XML from the given string.
setXML(File) - Method in class loci.formats.gui.XMLWindow
Displays XML from the given file.
setXML(String) - Method in class loci.formats.tools.EditTiffG
 
setXML(String) - Method in class loci.plugins.util.DataBrowser
Sets XML block associated with this window.
setYCbCrCorrection(boolean) - Method in class loci.formats.tiff.TiffParser
Sets whether or not YCbCr color correction is allowed.
setZBegin(int, int) - Method in class loci.plugins.in.ImporterOptions
 
setZEnd(int, int) - Method in class loci.plugins.in.ImporterOptions
 
setZStep(int, int) - Method in class loci.plugins.in.ImporterOptions
 
SFEG_TAG - Static variable in class loci.formats.in.FEITiffReader
 
SH - Static variable in class loci.formats.in.DicomReader
 
SHADING_MUL - Static variable in class loci.formats.in.CellSensReader
 
SHADING_SUB - Static variable in class loci.formats.in.CellSensReader
 
Shape() - Constructor for class loci.formats.in.BaseZeissReader.Shape
 
shape_count - Variable in class loci.formats.in.ZeissTIFFHandler
 
SHAPE_PREFIX - Static variable in class loci.formats.in.FakeReader
 
shapes - Variable in class loci.formats.in.BaseZeissReader.Layer
 
shapes - Variable in class loci.formats.in.GatanReader
 
sharpen() - Method in class loci.plugins.util.RecordedImageProcessor
 
SHARPENING - Static variable in class loci.formats.in.NikonReader
 
SHARPNESS - Static variable in class loci.formats.in.CellSensReader
 
SHARPNESS - Static variable in class loci.formats.tiff.IFD
 
SHORT - Static variable in class loci.formats.in.CellSensReader
 
SHORT - Static variable in class loci.formats.in.GatanReader
 
SHORT_DATE_FORMAT - Static variable in class loci.formats.in.MetamorphReader
 
shortArrayToBytes(short[]) - Method in class loci.formats.in.FluoviewReader
 
SHORTCUT_PLUGIN - Static variable in class loci.plugins.shortcut.ShortcutPanel
Name of this plugin, ignored when parsing the plugins list.
ShortcutPanel - Class in loci.plugins.shortcut
A plugin that displays a small window containing shortcuts to the plugins, including the Bio-Formats Importer, Bio-Formats Exporter, Stack Colorizer and Stack Slicer.
ShortcutPanel() - Constructor for class loci.plugins.shortcut.ShortcutPanel
Constructs a shortcut panel.
shortcutPanel - Variable in class loci.plugins.shortcut.ShortcutTransferHandler
Associated shortcut panel.
ShortcutTransferHandler - Class in loci.plugins.shortcut
Drag and drop transfer handler for Bio-Formats Plugins Shortcut Window.
ShortcutTransferHandler(ShortcutPanel) - Constructor for class loci.plugins.shortcut.ShortcutTransferHandler
Constructs a new shortcut panel drag and drop transfer handler.
shortLut - Variable in class loci.formats.in.DicomReader
 
shortValue() - Method in class loci.formats.tiff.TiffRational
Returns the value of the specified number as a short.
showDialog() - Method in class loci.plugins.in.ImporterDialog
 
showDialog() - Method in class loci.plugins.prefs.OptionsDialog
Displays the options dialog, returning the status of the operation.
showDialogs(ImportProcess) - Method in class loci.plugins.in.Importer
 
showError(Throwable) - Method in class loci.formats.tools.EditTiffG
 
showMetadataBox - Variable in class loci.plugins.in.MainDialog
 
showMetadataWindow() - Method in class loci.plugins.util.DataBrowser
Displays the OME-XML metadata window onscreen.
showOMEXMLBox - Variable in class loci.plugins.in.MainDialog
 
showOptionsWindow() - Method in class loci.plugins.util.DataBrowser
Displays the caching options window onscreen.
showROIs() - Method in class loci.plugins.in.ImporterOptions
 
showROIsBox - Variable in class loci.plugins.in.MainDialog
 
shuffle(int, int[]) - Static method in class loci.formats.in.FakeReader
Fisher-Yates shuffle with constant seeds to ensure reproducibility.
shuffleAllTypesToFront(FileFilter[]) - Static method in class loci.formats.gui.GUITools
Looks for an "All supported file types" combo filter and shuffles it to the front of the list.
shutdown - Variable in class loci.formats.gui.DataConverter
 
SHUTTER_SPEED_VALUE - Static variable in class loci.formats.tiff.IFD
 
SIFReader - Class in loci.formats.in
SIFReader is the file format reader for Andor SIF files.
SIFReader() - Constructor for class loci.formats.in.SIFReader
Constructs a new SIF reader.
SIGNAL_OUTPUT - Static variable in class loci.formats.in.CellSensReader
 
SIGNATURE_SIZE - Static variable in class loci.formats.in.VolocityReader
 
signed - Variable in class loci.formats.codec.CodecOptions
Indicates whether or not the pixel data is signed.
signed - Variable in class loci.formats.in.BrukerReader
 
signed - Variable in class loci.formats.in.GatanReader
 
SignedByteBuffer - Class in loci.formats.gui
DataBuffer that stores signed bytes.
SignedByteBuffer(byte[], int) - Constructor for class loci.formats.gui.SignedByteBuffer
Construct a new buffer of signed bytes using the given byte array.
SignedByteBuffer(byte[][], int) - Constructor for class loci.formats.gui.SignedByteBuffer
Construct a new buffer of signed bytes using the given 2D byte array.
SignedColorModel - Class in loci.formats.gui
ColorModel that handles 8, 16 and 32 bits per channel signed data.
SignedColorModel(int, int, int) - Constructor for class loci.formats.gui.SignedColorModel
 
SignedShortBuffer - Class in loci.formats.gui
DataBuffer that stores signed shorts.
SignedShortBuffer(int) - Constructor for class loci.formats.gui.SignedShortBuffer
 
SignedShortBuffer(int, int) - Constructor for class loci.formats.gui.SignedShortBuffer
 
SignedShortBuffer(short[], int) - Constructor for class loci.formats.gui.SignedShortBuffer
 
SignedShortBuffer(short[], int, int) - Constructor for class loci.formats.gui.SignedShortBuffer
 
SignedShortBuffer(short[][], int) - Constructor for class loci.formats.gui.SignedShortBuffer
 
SignedShortBuffer(short[][], int, int[]) - Constructor for class loci.formats.gui.SignedShortBuffer
 
SimplePCITiffReader - Class in loci.formats.in
SimplePCITiffReader is the file format reader for TIFF files produced by SimplePCI software.
SimplePCITiffReader() - Constructor for class loci.formats.in.SimplePCITiffReader
 
simsDescription - Variable in class loci.formats.in.IonpathMIBITiffReader
 
SINGLE_TIFF_PATH_BUILDER - Static variable in class loci.formats.in.CellVoyagerReader
 
singleTiffMode - Variable in class loci.formats.in.PrairieReader
Flag indicating that the reader is operating in a mode where grouping of files is disallowed.
SIS_INI_TAG - Static variable in class loci.formats.in.SISReader
 
SIS_TAG - Static variable in class loci.formats.in.SISReader
 
SIS_TAG_2 - Static variable in class loci.formats.in.SISReader
 
SISReader - Class in loci.formats.in
SISReader is the file format reader for Olympus Soft Imaging Solutions TIFF files.
SISReader() - Constructor for class loci.formats.in.SISReader
 
SITE - Static variable in class loci.formats.in.CellH5Reader.CellH5Constants
 
site - Variable in class loci.formats.in.CellH5Reader.CellH5Coordinate
 
site - Variable in class loci.formats.in.ZeissTIFFReader.Plane
 
size() - Method in class loci.formats.codec.ByteVector
 
size - Variable in class loci.formats.in.AVIReader
 
size - Variable in class loci.formats.in.FV1000Reader
 
size - Variable in class loci.formats.in.ZeissCZIReader.DimensionEntry
 
size() - Method in class loci.formats.MetadataList
Get the size of the array (number of primary array elements).
size(int) - Method in class loci.formats.MetadataList
Get the size of the specified primary array element (number of secondary array elements).
size - Variable in class loci.formats.tiff.OnDemandLongArray
 
size() - Method in class loci.formats.tiff.OnDemandLongArray
 
size - Variable in class loci.plugins.in.ThumbLoader.SeriesInfo
 
sizeC - Variable in class loci.formats.CoreMetadata
Number of channels.
sizeC - Variable in class loci.formats.FileStitcher
Dimensional axis lengths per file.
sizeC - Variable in class loci.formats.gui.ImageViewer
 
sizeC - Variable in class loci.formats.in.BDVReader
 
sizeC - Variable in class loci.formats.in.FakeReader
 
sizeC - Variable in class loci.formats.in.LeicaSCNReader.Pixels
 
sizeCsub - Variable in class loci.formats.tools.MakeTestOmeTiff
 
sizeR - Variable in class loci.formats.in.LeicaSCNReader.Pixels
 
sizes - Variable in class loci.formats.in.BrukerReader
 
sizes() - Method in class loci.formats.MetadataList
Get the sizes of all primary array elements.
sizeT - Variable in class loci.formats.CoreMetadata
Number of timepoints.
sizeT - Variable in class loci.formats.FileStitcher
Dimensional axis lengths per file.
sizeT - Variable in class loci.formats.gui.ImageViewer
 
sizeT - Variable in class loci.formats.in.FakeReader
 
sizeTsub - Variable in class loci.formats.tools.MakeTestOmeTiff
 
sizeX - Variable in class loci.formats.CoreMetadata
Width (in pixels) of images in this series.
sizeX - Variable in class loci.formats.in.ColumbusReader.Plane
 
sizeX - Variable in class loci.formats.in.FakeReader
 
sizeX - Variable in class loci.formats.in.FEITiffReader
 
sizeX - Variable in class loci.formats.in.LeicaSCNReader.Dimension
 
sizeX - Variable in class loci.formats.in.LeicaSCNReader.ImageCollection
 
sizeX - Variable in class loci.formats.in.LeicaSCNReader.Pixels
 
sizeX - Variable in class loci.formats.in.MetamorphReader
 
sizeX - Variable in class loci.formats.in.TextReader
Image width.
sizeX - Variable in class loci.formats.Resolution
 
sizeY - Variable in class loci.formats.CoreMetadata
Height (in pixels) of images in this series.
sizeY - Variable in class loci.formats.in.ColumbusReader.Plane
 
sizeY - Variable in class loci.formats.in.FakeReader
 
sizeY - Variable in class loci.formats.in.FEITiffReader
 
sizeY - Variable in class loci.formats.in.LeicaSCNReader.Dimension
 
sizeY - Variable in class loci.formats.in.LeicaSCNReader.ImageCollection
 
sizeY - Variable in class loci.formats.in.LeicaSCNReader.Pixels
 
sizeY - Variable in class loci.formats.in.MetamorphReader
 
sizeY - Variable in class loci.formats.in.TextReader
Image height.
sizeY - Variable in class loci.formats.Resolution
 
sizeZ - Variable in class loci.formats.CoreMetadata
Number of Z sections.
sizeZ - Variable in class loci.formats.FileStitcher
Dimensional axis lengths per file.
sizeZ - Variable in class loci.formats.gui.ImageViewer
 
sizeZ - Variable in class loci.formats.in.FakeReader
 
sizeZ - Variable in class loci.formats.in.LeicaSCNReader.Pixels
 
sizeZ - Variable in class loci.formats.in.NDPIReader
 
sizeZsub - Variable in class loci.formats.tools.MakeTestOmeTiff
 
skip(InputStream, long) - Method in class loci.formats.in.LiFlimReader
 
skipBits(long) - Method in class loci.formats.codec.BitBuffer
Deprecated.
Skips a number of bits in the BitBuffer.
skipBlocks() - Method in class loci.formats.in.GIFReader
 
skipBuffer - Variable in class loci.formats.in.OBFReader
 
skipBytes(OBFReader.Stack, long) - Method in class loci.formats.in.OBFReader
 
skipComment() - Method in class loci.formats.tools.AmiraParameters
 
skipData() - Method in class loci.formats.in.ZeissCZIReader.Metadata
 
skipHeader(RandomAccessInputStream) - Method in class loci.formats.in.MicroCTReader
Skip the VFF header, which consists of a variable number of LF-terminated lines.
skipLoad - Variable in class loci.formats.Memoizer
 
skipPadding() - Method in class loci.formats.in.GatanReader
 
skipPixelBlock(String, RandomAccessInputStream, boolean) - Method in class loci.formats.in.OIRReader
 
skipSave - Variable in class loci.formats.Memoizer
 
skipSave(boolean) - Method in class loci.formats.Memoizer
Set whether a memo file should be saved if a valid file is not present.
skipTagBlock() - Method in class loci.formats.in.ImspectorReader
Skip an unknown tag.
skipTags(int) - Method in class loci.formats.in.ImspectorReader
Skip a block of unknown string values.
skipWhiteSpace() - Method in class loci.formats.in.AmiraReader.ASCII
 
skipWhiteSpace() - Method in class loci.formats.tools.AmiraParameters
 
SL - Static variable in class loci.formats.in.DicomReader
 
SLD_MAGIC_BYTES_1_0 - Static variable in class loci.formats.in.SlidebookReader
 
SLD_MAGIC_BYTES_1_1 - Static variable in class loci.formats.in.SlidebookReader
 
SLD_MAGIC_BYTES_1_2 - Static variable in class loci.formats.in.SlidebookReader
 
SLD_MAGIC_BYTES_2_0 - Static variable in class loci.formats.in.SlidebookReader
 
SLD_MAGIC_BYTES_2_1 - Static variable in class loci.formats.in.SlidebookReader
 
SLD_MAGIC_BYTES_3 - Static variable in class loci.formats.in.SlidebookReader
 
sleep(String, int) - Static method in class loci.formats.in.FakeReader
 
sleep(long) - Method in class loci.plugins.prefs.OptionsDialog
Blocks the current thread for the specified number of milliseconds.
sleepInitFile - Variable in class loci.formats.in.FakeReader
 
sleepOpenBytes - Variable in class loci.formats.in.FakeReader
 
SLICE_SPACING - Static variable in class loci.formats.in.DicomReader
 
sliceLabel - Variable in class loci.plugins.config.ConfigWindow
 
Slicer - Class in loci.plugins
A plugin for splitting an image stack into separate channels, focal planes and/or time points.
Slicer() - Constructor for class loci.plugins.Slicer
 
sliceSpace - Variable in class loci.formats.in.PerkinElmerReader
 
sliceThickness - Variable in class loci.formats.in.MicromanagerReader.Position
 
sliceThickness - Variable in class loci.formats.in.NiftiReader
 
SLIDE_INFO - Static variable in class loci.formats.in.CellSensReader
 
SLIDE_NAME - Static variable in class loci.formats.in.CellSensReader
 
SLIDE_PREPARATION - Static variable in class loci.formats.in.CellSensReader
 
SLIDE_PROPERTIES - Static variable in class loci.formats.in.CellSensReader
 
SLIDE_SPECIMEN - Static variable in class loci.formats.in.CellSensReader
 
SLIDE_STAINING - Static variable in class loci.formats.in.CellSensReader
 
SLIDE_TISSUE - Static variable in class loci.formats.in.CellSensReader
 
SLIDEBOOK_MAGIC_STRING - Static variable in class loci.formats.in.SlidebookTiffReader
 
SlidebookReader - Class in loci.formats.in
SlidebookReader is the file format reader for 3I Slidebook files.
SlidebookReader() - Constructor for class loci.formats.in.SlidebookReader
Constructs a new Slidebook reader.
SlidebookTiffReader - Class in loci.formats.in
 
SlidebookTiffReader() - Constructor for class loci.formats.in.SlidebookTiffReader
 
sliderName - Variable in class loci.formats.in.FlexReader.FlexHandler
 
sliderPanel - Variable in class loci.formats.gui.ImageViewer
 
SMC_MAGIC - Static variable in class loci.formats.in.SMCameraReader
 
SMCameraReader - Class in loci.formats.in
SMCameraReader is the file format reader for SM camera files.
SMCameraReader() - Constructor for class loci.formats.in.SMCameraReader
Constructs a new SM camera reader.
smooth() - Method in class loci.plugins.util.RecordedImageProcessor
 
snapshot() - Method in class loci.plugins.util.RecordedImageProcessor
 
SOF0 - Static variable in class loci.formats.services.JPEGTurboServiceImpl
 
SOFTWARE - Static variable in class loci.formats.tiff.IFD
 
SOFTWARE_CHECK - Static variable in class loci.formats.in.VectraReader
TIFF image description prefix for PerkinElmer Vectra/QPTIFF files.
sortFilters(FileFilter[]) - Static method in class loci.formats.gui.ComboFileFilter
Sorts the given list of file filters, and combines filters with identical descriptions into a combination filter that accepts anything any of its constituant filters do.
sortFilters(Vector) - Static method in class loci.formats.gui.ComboFileFilter
Sorts the given list of file filters, and combines filters with identical descriptions into a combination filter that accepts anything any of its constituant filters do.
sortFilters(FileFilter[]) - Static method in class loci.formats.gui.GUITools
Sorts the given list of file filters, keeping the "All supported file types" combo filter (if any) at the front of the list.
sortFilters(Vector) - Static method in class loci.formats.gui.GUITools
Sorts the given list of file filters, keeping the "All supported file types" combo filter (if any) at the front of the list.
SOS - Static variable in class loci.formats.services.JPEGTurboServiceImpl
 
sos - Variable in class loci.formats.services.JPEGTurboServiceImpl
 
source - Variable in class loci.formats.cache.Cache
Current cache source.
source - Variable in class loci.formats.cache.CacheEvent
Source of the cache update.
SOURCE_CHANGED - Static variable in class loci.formats.cache.CacheEvent
Event type indicating a new cache source.
SOURCE_LENS - Static variable in class loci.formats.in.NDPIReader
 
SOURCE_PARAMS - Static variable in class loci.formats.gui.CacheComponent
 
SOURCE_VALUES - Static variable in class loci.formats.gui.CacheComponent
 
sourceChooser - Variable in class loci.formats.gui.CacheComponent
Combo box for choosing cache source.
sourceIndex(ICacheSource) - Method in class loci.formats.gui.CacheComponent
Converts cache source to source chooser index.
SOURCES - Static variable in class loci.formats.gui.CacheComponent
 
sourceValue(int) - Method in class loci.formats.gui.CacheComponent
Generates a new cache source matching the source chooser index.
SPATIAL_FREQUENCY_RESPONSE - Static variable in class loci.formats.tiff.IFD
 
spatialUnit - Variable in class loci.formats.in.NiftiReader
 
spcId - Variable in class loci.formats.in.SPCReader
 
SPCReader - Class in loci.formats.in
SPCReader is the file format reader for Becker & Hickl SPC-Image SPC FIFO files.
SPCReader() - Constructor for class loci.formats.in.SPCReader
Constructs a new SPC reader.
specialPlateNames - Variable in class loci.formats.in.OpenlabReader
 
specifyRangesBox - Variable in class loci.plugins.in.MainDialog
 
SPECTRA - Static variable in class loci.formats.FormatTools
Identifies the Spectra dimensional type, representing a dimension consisting of spectral channels.
spectra - Variable in class loci.formats.in.IM3Reader
 
SPECTRAL_SENSITIVITY - Static variable in class loci.formats.tiff.IFD
 
spectralMode - Variable in class loci.formats.in.PrairieMetadata.Sequence
SpectralMode of this <Sequence>.
Spectrum(IRandomAccess, IM3Reader.ContainerRecord) - Constructor for class loci.formats.in.IM3Reader.Spectrum
Construct a spectrum by parsing a Spectrum record
speed - Variable in class loci.formats.in.ND2Handler
 
SpeHeader(byte[]) - Constructor for class loci.formats.in.SPEReader.SpeHeader
Constructor for SpeHeader
SpeHeaderEntry(int, SPEReader.SpeHeaderType) - Constructor for enum loci.formats.in.SPEReader.SpeHeaderEntry
Constructor for SpeHeaderEntry
SpeHeaderType() - Constructor for enum loci.formats.in.SPEReader.SpeHeaderType
 
SPEReader - Class in loci.formats.in
SPEReader is the file format reader for Princeton Instruments SPE .spe files.
SPEReader() - Constructor for class loci.formats.in.SPEReader
Constructs a new SPE reader.
SPEReader.SpeHeader - Class in loci.formats.in
SpeHeader holds a byte array containing the SPE binary data header along with associated methods for reading SPE Header Entry values in various formats
SPEReader.SpeHeaderEntry - Enum in loci.formats.in
SpeHeaderEntry is an Enum which provides a list of all available SPE header entries along with the offset value from the top of the header in bytes and their associated data type
SPEReader.SpeHeaderType - Enum in loci.formats.in
SpeHeaderType is an Enum representing the available data types stored in the SPE header
SPEReader.SpeROI - Class in loci.formats.in
Private class to represent the data for a single ROI in the SPE format
SpeROI(int, int, int, int, int, int) - Constructor for class loci.formats.in.SPEReader.SpeROI
Constructor for SpeROI objects
SpiderReader - Class in loci.formats.in
SpiderReader is the file format reader for SPIDER files.
SpiderReader() - Constructor for class loci.formats.in.SpiderReader
Constructs a new SPIDER reader.
spim - Variable in class loci.formats.in.MicromanagerReader
 
SPIN_DISK_CONFOCAL - Static variable in class loci.formats.in.LegacyND2Reader
 
split - Variable in class loci.formats.codec.NikonCodecOptions
 
split - Variable in class loci.formats.in.NativeND2Reader
 
split - Variable in class loci.formats.in.NikonReader
 
SPLIT_LOSSY_DECODER_CONFIGURATION_12 - Static variable in class loci.formats.codec.NikonCodec
 
SPLIT_LOSSY_DECODER_CONFIGURATION_14 - Static variable in class loci.formats.codec.NikonCodec
 
SPLIT_TILES_DEFAULT - Static variable in class loci.formats.in.VentanaReader
SPLIT_TILES_KEY - Static variable in class loci.formats.in.VentanaReader
MetadataOptions key for determining whether to report each tile as a separate series.
splitCBox - Variable in class loci.plugins.in.MainDialog
 
splitChannels(BufferedImage) - Static method in class loci.formats.gui.AWTImageTools
Splits the given multi-channel image into single-channel images.
splitChannels(byte[], int, int, int, boolean, boolean) - Static method in class loci.formats.ImageTools
Splits the given multi-channel array into a 2D array.
splitChannels(byte[], byte[], int, int, int, boolean, boolean, int) - Static method in class loci.formats.ImageTools
Splits the given multi-channel array into a 2D array.
splitDims(List<ImagePlus>) - Method in class loci.plugins.in.ImagePlusReader
 
splitDoubles(String) - Method in class loci.formats.in.ICSReader
Splits the given string into a list of Doubles.
splitPlanes - Variable in class loci.formats.in.ZeissLSMReader
 
splitTBox - Variable in class loci.plugins.in.MainDialog
 
splitTiles() - Method in class loci.formats.in.VentanaReader
 
splitZBox - Variable in class loci.plugins.in.MainDialog
 
SPM_DOMAIN - Static variable in class loci.formats.FormatTools
Identifies the scanning probe microscopy domain.
SpringUtilities - Class in loci.plugins.config
A 1.4 file that provides utility methods for creating form- or grid-style layouts with SpringLayout.
SpringUtilities() - Constructor for class loci.plugins.config.SpringUtilities
 
SPURIOUS_NOISE_REMOVAL - Static variable in class loci.formats.in.CellSensReader
 
SQ - Static variable in class loci.formats.in.DicomReader
 
sqr() - Method in class loci.plugins.util.RecordedImageProcessor
 
sqrt() - Method in class loci.plugins.util.RecordedImageProcessor
 
SQUARE_ROOT - Static variable in class loci.formats.in.GelReader
 
squareRoot - Variable in class loci.formats.in.IvisionReader
 
srcBuf - Variable in class org.libjpegturbo.turbojpeg.TJCompressor
 
srcHeight - Variable in class org.libjpegturbo.turbojpeg.TJCompressor
 
srcPitch - Variable in class org.libjpegturbo.turbojpeg.TJCompressor
 
srcPixelFormat - Variable in class org.libjpegturbo.turbojpeg.TJCompressor
 
srcWidth - Variable in class org.libjpegturbo.turbojpeg.TJCompressor
 
SS - Static variable in class loci.formats.in.DicomReader
 
ST - Static variable in class loci.formats.in.DicomReader
 
STABLE - Static variable in class loci.plugins.Updater
 
STABLE_BUILD - Static variable in class loci.formats.UpgradeChecker
Location of the JAR artifacts for the stable releases.
STABLE_VERSION - Static variable in class loci.formats.UpgradeChecker
Version number of the latest stable release.
Stack() - Constructor for class loci.formats.in.OBFReader.Stack
 
Stack() - Constructor for class loci.formats.in.VolocityReader.Stack
 
STACK_DISPLAY_LUT - Static variable in class loci.formats.in.CellSensReader
 
STACK_MAGIC_STRING - Static variable in class loci.formats.in.OBFReader
 
STACK_NAME - Static variable in class loci.formats.in.CellSensReader
 
STACK_TYPE - Static variable in class loci.formats.in.CellSensReader
 
stackFormatChoice - Variable in class loci.plugins.in.MainDialog
 
stackOrderChoice - Variable in class loci.plugins.in.MainDialog
 
stacks - Variable in class loci.formats.in.OBFReader
 
stacks - Variable in class loci.formats.in.VolocityReader
 
stageLabel - Variable in class loci.formats.in.MetamorphHandler
 
stageLabels - Variable in class loci.formats.in.MetamorphReader
 
stageNames - Variable in class loci.formats.in.MetamorphReader
 
stageX - Variable in class loci.formats.in.BaseZeissReader
 
stageX - Variable in class loci.formats.in.FEITiffReader
 
stageX - Variable in class loci.formats.in.GatanReader
 
stageX - Variable in class loci.formats.in.MetamorphReader
 
stageX - Variable in class loci.formats.in.ZeissCZIReader.SubBlock
 
stageXCoord - Variable in class loci.formats.in.DeltavisionReader.DVExtHdrFields
X stage coordinates.
stageY - Variable in class loci.formats.in.BaseZeissReader
 
stageY - Variable in class loci.formats.in.FEITiffReader
 
stageY - Variable in class loci.formats.in.GatanReader
 
stageY - Variable in class loci.formats.in.MetamorphReader
 
stageY - Variable in class loci.formats.in.ZeissCZIReader.SubBlock
 
stageYCoord - Variable in class loci.formats.in.DeltavisionReader.DVExtHdrFields
Y stage coordinates.
stageZ - Variable in class loci.formats.in.FEITiffReader
 
stageZ - Variable in class loci.formats.in.GatanReader
 
stageZ - Variable in class loci.formats.in.ZeissCZIReader.SubBlock
 
stageZCoord - Variable in class loci.formats.in.DeltavisionReader.DVExtHdrFields
Z stage coordinates.
stamps - Variable in class loci.formats.in.FluoviewReader
Timestamps for each plane, in seconds.
stampValues - Variable in class loci.formats.in.LiFlimReader
 
start - Variable in class loci.formats.in.EPSReader
Starting line of pixel data.
start - Variable in class loci.formats.in.MicromanagerReader
 
start - Variable in class loci.formats.in.ZeissCZIReader.DimensionEntry
 
start - Variable in class loci.formats.Modulo
 
start - Variable in class loci.formats.tiff.OnDemandLongArray
 
START_OFFSET - Static variable in class loci.formats.in.BioRadGelReader
 
START_TIME - Static variable in class loci.formats.in.ZeissLSMReader
 
startCoordinate - Variable in class loci.formats.in.ZeissCZIReader.DimensionEntry
 
startElement(String, String, String, Attributes) - Method in class loci.formats.in.AFIReader.AFIHandler
 
startElement(String, String, String, Attributes) - Method in class loci.formats.in.BDVReader.BDVXMLHandler
 
startElement(String, String, String, Attributes) - Method in class loci.formats.in.BioRadReader.BioRadHandler
 
startElement(String, String, String, Attributes) - Method in class loci.formats.in.BioRadSCNReader.SCNHandler
 
startElement(String, String, String, Attributes) - Method in class loci.formats.in.ColumbusReader.MeasurementHandler
 
startElement(String, String, String, Attributes) - Method in class loci.formats.in.CV7000Reader.MeasurementDataHandler
 
startElement(String, String, String, Attributes) - Method in class loci.formats.in.CV7000Reader.MeasurementDetailHandler
 
startElement(String, String, String, Attributes) - Method in class loci.formats.in.CV7000Reader.MeasurementSettingsHandler
 
startElement(String, String, String, Attributes) - Method in class loci.formats.in.CV7000Reader.WPIHandler
 
startElement(String, String, String, Attributes) - Method in class loci.formats.in.FEITiffReader.FEIHandler
 
startElement(String, String, String, Attributes) - Method in class loci.formats.in.FlexReader.FlexHandler
 
startElement(String, String, String, Attributes) - Method in class loci.formats.in.FlexReader.MeaHandler
 
startElement(String, String, String, Attributes) - Method in class loci.formats.in.FlexReader.ResHandler
 
startElement(String, String, String, Attributes) - Method in class loci.formats.in.ImaconReader.ImaconHandler
 
startElement(String, String, String, Attributes) - Method in class loci.formats.in.InCellReader.InCellHandler
 
startElement(String, String, String, Attributes) - Method in class loci.formats.in.InCellReader.MinimalInCellHandler
 
startElement(String, String, String, Attributes) - Method in class loci.formats.in.IvisionReader.IvisionHandler
 
startElement(String, String, String, Attributes) - Method in class loci.formats.in.LeicaHandler
 
startElement(String, String, String, Attributes) - Method in class loci.formats.in.LeicaSCNReader.LeicaSCNHandler
 
startElement(String, String, String, Attributes) - Method in class loci.formats.in.MetamorphHandler
 
startElement(String, String, String, Attributes) - Method in class loci.formats.in.MicromanagerReader.MicromanagerHandler
 
startElement(String, String, String, Attributes) - Method in class loci.formats.in.ND2Handler
 
startElement(String, String, String, Attributes) - Method in class loci.formats.in.OMEXMLReader.OMEXMLHandler
 
startElement(String, String, String, Attributes) - Method in class loci.formats.in.OperettaReader.OperettaHandler
 
startElement(String, String, String, Attributes) - Method in class loci.formats.in.ScanrReader.ScanrHandler
 
startElement(String, String, String, Attributes) - Method in class loci.formats.in.ZeissTIFFHandler
 
startElement(String, String, String, Attributes) - Method in class loci.formats.out.OMEXMLWriter.OMEHandler
 
startIndex - Variable in class loci.formats.FilePattern
Indices into the pattern indicating the start of a numerical block.
startingPosition - Variable in class loci.formats.in.ZeissCZIReader.Segment
 
startTime - Variable in class loci.formats.in.CV7000Reader
 
startTime - Variable in class loci.formats.in.PerkinElmerReader
 
startTime - Variable in class loci.formats.in.ZeissLSMReader.Recording
 
startTime - Variable in class loci.plugins.in.ImagePlusReader
 
startTiming() - Method in class loci.plugins.in.ImagePlusReader
 
startX - Variable in class loci.formats.in.SPEReader.SpeROI
 
startY - Variable in class loci.formats.in.SPEReader.SpeROI
 
state - Variable in class loci.formats.in.OBFReader
 
State(int) - Constructor for class loci.formats.in.OBFReader.State
 
state - Variable in class loci.formats.services.WlzServiceImpl
 
stateChanged(ChangeEvent) - Method in class loci.formats.gui.CacheComponent
Handles range spinner changes.
stateChanged(ChangeEvent) - Method in class loci.formats.gui.DataConverter
 
stateChanged(ChangeEvent) - Method in class loci.formats.gui.ImageViewer
Handles slider events.
stateChanged(ChangeEvent) - Method in class loci.plugins.util.SearchableWindow.SearchBox
 
status - Variable in class loci.formats.in.BioRadReader.Note
 
status - Variable in class loci.formats.in.SDTInfo
Last SPC_test_state return value (status).
status(boolean, String) - Static method in class loci.plugins.BF
 
status - Variable in class loci.plugins.config.ConfigWindow
 
status - Variable in class loci.plugins.config.LibraryEntry
 
STATUS_CANCELED - Static variable in class loci.plugins.prefs.OptionsDialog
 
STATUS_FINISHED - Static variable in class loci.plugins.prefs.OptionsDialog
 
STATUS_OK - Static variable in class loci.plugins.prefs.OptionsDialog
 
statusUpdated(StatusEvent) - Method in class loci.plugins.in.DisplayHandler
Reports status updates via ImageJ's status bar mechanism.
statusUpdated(StatusEvent) - Method in class loci.plugins.in.ImporterPrompter
 
step - Variable in class loci.formats.FilePatternBlock
 
step - Variable in class loci.formats.Modulo
 
step - Variable in class loci.plugins.in.ImportProcess
Current step in the import preparation process.
step(ImportStep) - Method in class loci.plugins.in.ImportProcess
 
step - Variable in enum loci.plugins.in.ImportStep
 
STEP_TABLE - Static variable in enum loci.plugins.in.ImportStep
 
steps - Variable in class loci.formats.in.SDTInfo
 
stepSize - Variable in class loci.formats.in.MetamorphReader
 
stitchTilesBox - Variable in class loci.plugins.in.MainDialog
 
STK_SUFFIX - Static variable in class loci.formats.in.MetamorphReader
 
stkReaders - Variable in class loci.formats.in.MetamorphReader
 
stks - Variable in class loci.formats.in.MetamorphReader
List of STK files in the dataset.
stop - Variable in class loci.plugins.in.ThumbLoader
 
stop() - Method in class loci.plugins.in.ThumbLoader
Instructs the thumbnail loader to stop loading thumbnails.
stopt - Variable in class loci.formats.in.SDTInfo
 
stopTime - Variable in class loci.formats.in.SDTInfo
Time from start to - disarm (simple measurement) - or to the end of the cycle (for complex measurement).
stopWatch() - Method in class loci.formats.Memoizer
 
storageMethod - Variable in class loci.formats.in.MRWReader
 
store - Variable in class loci.formats.FileStitcher
 
store - Variable in class loci.formats.in.BDVReader
 
store - Variable in class loci.formats.in.CellH5Reader
 
store - Variable in class loci.formats.in.FlexReader.FlexHandler
 
store - Variable in class loci.formats.in.InCellReader.InCellHandler
 
store - Variable in class loci.formats.in.KLBReader
 
store - Variable in class loci.formats.in.LeicaHandler
 
store - Variable in class loci.formats.in.ZeissCZIReader
 
storedChannel - Variable in class loci.formats.in.SDTReader
 
storedChannel - Variable in class loci.formats.in.SPCReader
 
storedRGB - Variable in class loci.formats.in.ICSReader
 
storedSeries - Variable in class loci.formats.in.SDTReader
 
storedSize - Variable in class loci.formats.in.ZeissCZIReader.DimensionEntry
 
storedT - Variable in class loci.formats.in.SPCReader
 
storeKeyValue(Hashtable, String, String) - Method in class loci.formats.in.LeicaHandler
 
storeLine(Line, MetadataStore, int, int, int, int, int) - Static method in class loci.plugins.util.ROIHandler
Stores the Line ROI into the specified metadata store.
storeOval(OvalRoi, MetadataStore, int, int, int, int, int) - Static method in class loci.plugins.util.ROIHandler
Stores the Oval ROI into the specified metadata store.
storePoint(PointRoi, MetadataStore, int, int, int, int, int) - Static method in class loci.plugins.util.ROIHandler
Stores the Point ROI into the specified metadata store.
storePolygon(PolygonRoi, MetadataStore, int, int, int, int, int) - Static method in class loci.plugins.util.ROIHandler
Stores the Polygon ROI into the specified metadata store.
storeRectangle(Roi, MetadataStore, int, int, int, int, int) - Static method in class loci.plugins.util.ROIHandler
Stores the Rectangle ROI into the specified metadata store.
storeROI(MetadataStore, int, int) - Method in class loci.formats.in.LeicaHandler.ROI
 
storeROI(MetadataStore, int, int, int) - Method in class loci.formats.in.LIFReader.ROI
 
storeROIs(MetadataStore) - Method in class loci.formats.in.BaseZeissReader
Store basic dimensions in model
storeSeriesHashtable(int, Hashtable) - Method in class loci.formats.in.LeicaHandler
 
storeText(TextRoi, MetadataStore, int, int, int, int, int) - Static method in class loci.plugins.util.ROIHandler
Stores the text ROI into the metadata stored.
STRATEGIES - Static variable in class loci.formats.gui.CacheComponent
 
strategy - Variable in class loci.formats.cache.Cache
Current cache strategy.
STRATEGY_CHANGED - Static variable in class loci.formats.cache.CacheEvent
Event type indicating a new cache strategy.
STRATEGY_PARAMS - Static variable in class loci.formats.gui.CacheComponent
 
STRATEGY_VALUES - Static variable in class loci.formats.gui.CacheComponent
 
strategyChooser - Variable in class loci.formats.gui.CacheComponent
Combo box for choosing cache strategy.
strategyIndex(ICacheStrategy) - Method in class loci.formats.gui.CacheComponent
Converts cache strategy to strategy chooser index.
strategyValue(int) - Method in class loci.formats.gui.CacheComponent
Generates a new cache strategy matching the strategy chooser index.
stream - Variable in class loci.formats.in.ZeissCZIReader.Segment
 
stream - Variable in class loci.formats.services.POIServiceImpl
 
stream - Variable in class loci.formats.tiff.OnDemandLongArray
 
streamNames - Variable in class loci.formats.tools.AmiraParameters
 
streams - Variable in class loci.formats.tools.AmiraParameters
 
streamTypes - Variable in class loci.formats.tools.AmiraParameters
 
strikeout - Variable in class loci.formats.in.BaseZeissReader.Shape
 
StringIM3Record(String, int, long, int) - Constructor for class loci.formats.in.IM3Reader.StringIM3Record
 
StringOption - Class in loci.plugins.prefs
A string option for one of the plugins.
StringOption(HashMap<String, String>) - Constructor for class loci.plugins.prefs.StringOption
Constructs a string option with the parameters from the given map.
StringOption(String, boolean, String, String, String, Vector<String>) - Constructor for class loci.plugins.prefs.StringOption
Constructs a string option with the given parameters.
stringTable - Variable in class loci.formats.in.VolocityReader
 
STRIP_BYTE_COUNTS - Static variable in class loci.formats.tiff.IFD
 
STRIP_OFFSETS - Static variable in class loci.formats.tiff.IFD
 
stripHeader() - Method in class loci.formats.in.NativeQTReader
Cut off header bytes from a resource fork file.
strips - Variable in class loci.formats.in.PictReader
Vector of byte arrays representing individual rows.
strokeColor - Variable in class loci.formats.in.GatanReader.ROIShape
 
STRUCTURE_LABELS_1 - Static variable in class loci.formats.in.BioRadReader
Structure labels.
STRUCTURE_LABELS_2 - Static variable in class loci.formats.in.BioRadReader
 
STRUCTURE_LABELS_3 - Static variable in class loci.formats.in.BioRadReader
 
STRUCTURE_LABELS_4 - Static variable in class loci.formats.in.BioRadReader
 
STRUCTURE_LABELS_5 - Static variable in class loci.formats.in.BioRadReader
 
STRUCTURE_LABELS_6 - Static variable in class loci.formats.in.BioRadReader
 
STUB_FIELD - Static variable in class loci.formats.services.LuraWaveServiceImpl
Identifying field in stub class.
STYLESHEET_FILE - Static variable in class loci.formats.in.LIFReader
 
SUB - Static variable in class loci.formats.in.APNGReader
 
SUB_IFD - Static variable in class loci.formats.tiff.IFD
 
SUB_SEC_TIME - Static variable in class loci.formats.tiff.IFD
 
SUB_SEC_TIME_DIGITIZED - Static variable in class loci.formats.tiff.IFD
 
SUB_SEC_TIME_ORIGINAL - Static variable in class loci.formats.tiff.IFD
 
SubBlock() - Constructor for class loci.formats.in.ZeissCZIReader.SubBlock
 
SubBlock(ZeissCZIReader.SubBlock) - Constructor for class loci.formats.in.ZeissCZIReader.SubBlock
 
SubBlock() - Constructor for class loci.formats.in.ZeissLSMReader.SubBlock
 
SUBBLOCK_BEAM_SPLITTER - Static variable in class loci.formats.in.ZeissLSMReader
 
SUBBLOCK_DATA_CHANNEL - Static variable in class loci.formats.in.ZeissLSMReader
 
SUBBLOCK_DETECTION_CHANNEL - Static variable in class loci.formats.in.ZeissLSMReader
 
SUBBLOCK_END - Static variable in class loci.formats.in.ZeissLSMReader
 
SUBBLOCK_ILLUMINATION_CHANNEL - Static variable in class loci.formats.in.ZeissLSMReader
 
SUBBLOCK_LASER - Static variable in class loci.formats.in.ZeissLSMReader
 
SUBBLOCK_MARKER - Static variable in class loci.formats.in.ZeissLSMReader
 
SUBBLOCK_RECORDING - Static variable in class loci.formats.in.ZeissLSMReader
Subblock types.
SUBBLOCK_TIMER - Static variable in class loci.formats.in.ZeissLSMReader
 
SUBBLOCK_TRACK - Static variable in class loci.formats.in.ZeissLSMReader
 
subdirectories - Variable in class loci.formats.in.CellWorxReader
 
SUBFILE_TYPE - Static variable in class loci.formats.tiff.IFD
 
SUBJECT_DISTANCE - Static variable in class loci.formats.tiff.IFD
 
SUBJECT_DISTANCE_RANGE - Static variable in class loci.formats.tiff.IFD
 
SUBJECT_LOCATION - Static variable in class loci.formats.tiff.IFD
 
SubResolutionFormatReader - Class in loci.formats
Abstract superclass of all biological file format readers that can handle image pyramids.
SubResolutionFormatReader(String, String) - Constructor for class loci.formats.SubResolutionFormatReader
Constructs a format reader with the given name and default suffix.
SubResolutionFormatReader(String, String[]) - Constructor for class loci.formats.SubResolutionFormatReader
Constructs a format reader with the given name and default suffixes.
subResolutionIFDs - Variable in class loci.formats.in.MinimalTiffReader
List of sub-resolution IFDs for each IFD in the current TIFF with the same order as ifds.
subresolutionOffset - Variable in class loci.formats.in.OMETiffReader.OMETiffCoreMetadata
SubIFD offset for sub-resolution level; -1 if the main IFD.
subsamp - Variable in class org.libjpegturbo.turbojpeg.TJCompressor
 
substringsBetween(String, String, String) - Static method in class loci.plugins.in.ImagePlusReader
 
subTag - Variable in class loci.formats.in.OpenlabReader
 
success - Variable in class loci.plugins.LociImporter
Flag indicating whether last operation was successful.
suffix - Variable in class loci.formats.in.GIFReader
 
SUFFIX - Static variable in class loci.formats.in.TCSReader
 
suffixes - Variable in class loci.formats.FormatHandler
Valid suffixes for this file format.
SUFFIXES - Static variable in class loci.formats.gui.LegacyQTTools
 
suffixes - Variable in class loci.formats.ImageReader
Valid suffixes for this file format.
suffixes - Variable in class loci.formats.ImageWriter
Valid suffixes for all file format writers.
SUFFIXES - Static variable in class loci.formats.in.FlexReader
 
suffixes - Variable in class loci.plugins.config.FormatEntry
 
suffixNecessary - Variable in class loci.formats.FormatReader
Whether the file extension matching one of the reader's suffixes is necessary to identify the file as an instance of this format.
suffixSufficient - Variable in class loci.formats.FormatReader
Whether the file extension matching one of the reader's suffixes is sufficient to identify the file as an instance of this format.
surfaceWind - Variable in class loci.formats.in.HRDGDFReader
 
SVSCoreMetadata - Class in loci.formats.in
 
SVSCoreMetadata() - Constructor for class loci.formats.in.SVSCoreMetadata
 
SVSReader - Class in loci.formats.in
SVSReader is the file format reader for Aperio SVS TIFF files.
SVSReader() - Constructor for class loci.formats.in.SVSReader
Constructs a new SVS reader.
SVSReader(String, String[]) - Constructor for class loci.formats.in.SVSReader
 
swap - Variable in class loci.formats.gui.DataConverter
 
SwapDialog - Class in loci.plugins.in
Bio-Formats Importer dimension swapper dialog box.
SwapDialog(ImportProcess) - Constructor for class loci.plugins.in.SwapDialog
Creates a dimension swapper dialog for the Bio-Formats Importer.
swapDimensions(String) - Method in class loci.formats.DimensionSwapper
Sets the input dimension order according to the given string (e.g., "XYZCT").
swapDimsBox - Variable in class loci.plugins.in.MainDialog
 
SwappableMetadata - Class in loci.formats
Extends CoreMetadata to include the notion of an "input order" for planes: the input order being the order planes are stored on disk.
SwappableMetadata() - Constructor for class loci.formats.SwappableMetadata
 
SwappableMetadata(IFormatReader, int) - Constructor for class loci.formats.SwappableMetadata
 
SwappableMetadata(SwappableMetadata) - Constructor for class loci.formats.SwappableMetadata
 
swapPixelArrays() - Method in class loci.plugins.util.RecordedImageProcessor
 
swapXY - Variable in class loci.formats.in.LIFReader
 
SWATCH_SIZE - Static variable in class loci.plugins.in.ColorDialog
 
SWEPT_FIELD_CONFOCAL - Static variable in class loci.formats.in.LegacyND2Reader
 
switchChunk(OBFReader.Stack, int) - Method in class loci.formats.in.OBFReader
 
syncPlane() - Method in class loci.plugins.util.DataBrowser
Updates the ImagePlus's displayed plane to match the slider values.
syncSliders() - Method in class loci.plugins.util.DataBrowser
Updates the slider values to match the ImagePlus's displayed plane.
synFD - Variable in class loci.formats.in.SDTInfo
 
synHF - Variable in class loci.formats.in.SDTInfo
 
syntaxError(String) - Method in class loci.formats.tools.AmiraParameters
 
synTH - Variable in class loci.formats.in.SDTInfo
 
synZC - Variable in class loci.formats.in.SDTInfo
 

T

T - Static variable in class loci.formats.in.CellSensReader
 
t - Variable in class loci.formats.in.MicromanagerReader.Index
 
t - Variable in class loci.formats.in.OperettaReader.Plane
 
T4_OPTIONS - Static variable in class loci.formats.tiff.IFD
 
T6_OPTIONS - Static variable in class loci.formats.tiff.IFD
 
T_AXIS - Static variable in class loci.formats.AxisGuesser
Axis type for time points.
T_KEY - Static variable in class loci.formats.in.LiFlimReader
 
T_NUM - Static variable in class loci.formats.FormatTools
 
T_PREFIXES - Static variable in class loci.formats.AxisGuesser
Prefixes indicating time dimension.
T_STRING - Static variable in class loci.formats.in.SDTInfo
 
table - Variable in class loci.formats.codec.HuffmanCodecOptions
 
TAC_GAIN - Static variable in class loci.formats.in.SPCReader
 
TAC_RANGE - Static variable in class loci.formats.in.SPCReader
 
tacG - Variable in class loci.formats.in.SDTInfo
 
tacLH - Variable in class loci.formats.in.SDTInfo
 
tacLL - Variable in class loci.formats.in.SDTInfo
 
tacOF - Variable in class loci.formats.in.SDTInfo
 
tacR - Variable in class loci.formats.in.SDTInfo
 
Tag(int, BaseZeissReader.Context) - Constructor for class loci.formats.in.BaseZeissReader.Tag
Constructor.
Tag(int, String, BaseZeissReader.Context) - Constructor for class loci.formats.in.BaseZeissReader.Tag
Constructor.
tag - Variable in class loci.formats.in.OpenlabReader
 
tag - Variable in class loci.formats.in.PhotoshopTiffReader
 
Tag(int) - Constructor for class loci.formats.in.ZeissTIFFHandler.Tag
Constructor.
tag - Variable in class loci.formats.tiff.TiffIFDEntry
The Tag that identifies the field.
TAG_CHANNEL - Static variable in class loci.formats.in.NDPISReader
 
tag_count - Variable in class loci.formats.in.ZeissTIFFHandler
 
TAG_EMISSION_WAVELENGTH - Static variable in class loci.formats.in.NDPISReader
 
tagID - Variable in class loci.formats.in.BaseZeissReader.Shape
 
taglist - Variable in class loci.formats.in.ZeissTIFFReader.Plane
 
tags - Variable in class loci.formats.in.ZeissTIFFHandler.TagSet
 
tags - Variable in class loci.formats.in.ZeissTIFFReader.Plane
 
tagset - Variable in class loci.formats.in.ZeissTIFFHandler.Plane
 
tagset - Variable in class loci.formats.in.ZeissTIFFHandler.Scaling
 
TagSet() - Constructor for class loci.formats.in.ZeissTIFFHandler.TagSet
 
tagsToParse - Variable in class loci.formats.in.BaseZeissReader
 
TargaReader - Class in loci.formats.in
File format reader for Truevision Targa files.
TargaReader() - Constructor for class loci.formats.in.TargaReader
Constructs a new Targa reader.
TargaRLECodec - Class in loci.formats.codec
This class implements Targa RLE decompression.
TargaRLECodec() - Constructor for class loci.formats.codec.TargaRLECodec
 
TARGET_PRINTER - Static variable in class loci.formats.tiff.IFD
 
tBegin - Variable in class loci.plugins.in.ImporterOptions
 
TCHAR - Static variable in class loci.formats.in.CellSensReader
 
tChoice - Variable in class loci.formats.gui.DataConverter
 
tChoice - Variable in class loci.plugins.in.SwapDialog
 
TCSReader - Class in loci.formats.in
TCSReader is the file format reader for Leica TCS TIFF files and their companion XML file.
TCSReader() - Constructor for class loci.formats.in.TCSReader
 
tDim - Variable in class loci.formats.out.AVIWriter
 
TEMPERATURE - Static variable in class loci.formats.in.FluoviewReader
 
temperature - Variable in class loci.formats.in.FluoviewReader
 
temperature - Variable in class loci.formats.in.InCellReader
 
temperature - Variable in class loci.formats.in.MetamorphHandler
 
temperature - Variable in class loci.formats.in.MicromanagerReader.Position
 
temperature - Variable in class loci.formats.in.ND2Handler
 
temperature - Variable in class loci.formats.in.ZeissCZIReader
 
TEMPERATURE_TARGET - Static variable in class loci.formats.in.CellSensReader
 
tempFile - Variable in class loci.formats.Memoizer
 
templateFile - Variable in class loci.formats.in.MIASReader
 
tempZ - Variable in class loci.formats.in.MetamorphReader
 
tEnd - Variable in class loci.plugins.in.ImporterOptions
 
test() - Method in class loci.formats.codec.BaseCodec
Main testing method default implementation.
text - Variable in class loci.formats.in.BaseZeissReader.Shape
 
text - Variable in class loci.formats.in.GatanReader.ROIShape
 
TEXT - Static variable in class loci.formats.in.GatanReader
 
TEXT - Static variable in class loci.formats.in.LeicaHandler.ROI
 
text - Variable in class loci.formats.in.LeicaHandler.ROI
 
TEXT - Static variable in class loci.formats.in.LIFReader.ROI
 
text - Variable in class loci.formats.in.LIFReader.ROI
 
TEXT - Static variable in class loci.formats.in.ZeissLSMReader
Drawing element types.
textAlignment - Variable in class loci.formats.in.BaseZeissReader.Shape
 
TextAlignment(int) - Constructor for enum loci.formats.in.BaseZeissReader.TextAlignment
 
textArea - Variable in class loci.formats.tools.EditTiffG
 
textArea - Variable in class loci.plugins.config.TextAreaWriter
Text area component to which output should be written.
TextAreaWriter - Class in loci.plugins.config
Writer implementation that writes to a JTextArea document.
TextAreaWriter(JTextArea) - Constructor for class loci.plugins.config.TextAreaWriter
Constructs a new TextAreaWriter around the given text area component.
textChannelNames - Variable in class loci.formats.in.NativeND2Reader
 
textColour - Variable in class loci.formats.in.BaseZeissReader.Shape
 
textData - Variable in class loci.formats.in.NativeND2Reader
 
textEmissionWavelengths - Variable in class loci.formats.in.NativeND2Reader
 
TextLine(String, Font, int, int) - Constructor for class loci.formats.tools.MakeTestOmeTiff.TextLine
 
TextReader - Class in loci.formats.in
Reader for text files containing tables of data.
TextReader() - Constructor for class loci.formats.in.TextReader
Constructs a new text reader.
textureOffset - Variable in class loci.formats.in.AliconaReader
Image offset.
THIRD_ID - Static variable in class loci.formats.in.CellSensReader
 
thisField - Variable in class loci.formats.in.FlexReader.FlexHandler
 
THREE - Static variable in class loci.formats.AxisGuesser
 
THRESHHOLDING - Static variable in class loci.formats.tiff.IFD
 
threshold(int) - Method in class loci.plugins.util.RecordedImageProcessor
 
throwBadBlock(String) - Method in class loci.formats.FilePatternBlock
 
throwBadBlock(String, Throwable) - Method in class loci.formats.FilePatternBlock
 
THUMB_TAG_2 - Static variable in class loci.formats.in.NDPIReader
 
thumbId - Variable in class loci.formats.in.FV1000Reader
Name of thumbnail file.
ThumbLoader - Class in loci.plugins.in
Loads thumbnails for Bio-Formats Importer series chooser in a separate thread.
ThumbLoader(IFormatReader, Panel[], Dialog) - Constructor for class loci.plugins.in.ThumbLoader
Constructs a new thumbnail loader.
ThumbLoader.SeriesInfo - Class in loci.plugins.in
Helper class for sorting series by image plane size.
thumbnail - Variable in class loci.formats.CoreMetadata
Indicates whether or not this series is a lower-resolution copy of another series.
THUMBNAIL_DIMENSION - Static variable in class loci.formats.FormatReader
Default thumbnail width and height.
thumbnailFile - Variable in class loci.formats.in.InCellReader.Image
 
thumbnailIFDs - Variable in class loci.formats.in.MinimalTiffReader
List of thumbnail IFDs for the current TIFF.
thumbReader - Variable in class loci.formats.in.FV1000Reader
Helper reader for thumbnail.
thumbReader - Variable in class loci.plugins.in.SeriesDialog
 
thumbSizeX - Variable in class loci.formats.CoreMetadata
Width (in pixels) of thumbnail images in this series.
thumbSizeX - Variable in class loci.formats.in.LeicaSCNReader.Image
 
thumbSizeY - Variable in class loci.formats.CoreMetadata
Height (in pixels) of thumbnail images in this series.
tiff - Variable in class loci.formats.in.LeicaReader
Helper readers.
tiff - Variable in class loci.formats.in.PerkinElmerReader
Helper reader.
tiff - Variable in class loci.formats.in.PrairieReader
Helper reader for opening images.
TIFF_EPS_STANDARD - Static variable in class loci.formats.in.DNGReader
 
TIFF_EPS_STANDARD - Static variable in class loci.formats.in.NikonReader
 
TIFF_IFD - Static variable in class loci.formats.in.CellSensReader
 
TIFF_SUFFIXES - Static variable in class loci.formats.in.TiffReader
 
TIFF_SUFFIXES - Static variable in class loci.formats.in.ZeissTIFFReader
 
TiffCompression - Enum in loci.formats.tiff
Utility class for performing compression operations with a TIFF file.
TiffCompression(int, Codec, String) - Constructor for enum loci.formats.tiff.TiffCompression
Default constructor.
TiffConstants - Class in loci.formats.tiff
Generally useful TIFF-related constants.
TiffConstants() - Constructor for class loci.formats.tiff.TiffConstants
 
TiffDelegateReader - Class in loci.formats.in
TiffDelegateReader is a file format reader for TIFF files.
TiffDelegateReader() - Constructor for class loci.formats.in.TiffDelegateReader
Constructs a new TIFF reader.
TiffDelegateWidgets - Class in loci.plugins.config
Custom widgets for configuring Bio-Formats TIFF support.
TiffDelegateWidgets() - Constructor for class loci.plugins.config.TiffDelegateWidgets
 
tiffFiles - Variable in class loci.formats.in.APLReader
 
TiffIFDEntry - Class in loci.formats.tiff
This class represents a single raw TIFF IFD entry.
TiffIFDEntry(int, IFDType, int, long) - Constructor for class loci.formats.tiff.TiffIFDEntry
 
tiffInfo - Variable in class loci.formats.in.ZeissTIFFReader
 
TIFFInfo() - Constructor for class loci.formats.in.ZeissTIFFReader.TIFFInfo
 
TiffJAIReader - Class in loci.formats.in
TiffJAIReader is a file format reader for TIFF images.
TiffJAIReader() - Constructor for class loci.formats.in.TiffJAIReader
Constructs a new TIFF reader that uses Java Image I/O.
tiffParser - Variable in class loci.formats.in.FlowSightReader
 
tiffParser - Variable in class loci.formats.in.MinimalTiffReader
 
tiffParser - Variable in class loci.formats.in.TCSReader
 
tiffParser - Variable in class loci.formats.in.ZeissLSMReader
 
TiffParser - Class in loci.formats.tiff
Parses TIFF data from an input source.
TiffParser(String) - Constructor for class loci.formats.tiff.TiffParser
Constructs a new TIFF parser from the given file name.
TiffParser(RandomAccessInputStream) - Constructor for class loci.formats.tiff.TiffParser
Constructs a new TIFF parser from the given input source.
TiffRational - Class in loci.formats.tiff
A rational number (numerator over denominator).
TiffRational(long, long) - Constructor for class loci.formats.tiff.TiffRational
Constructs a rational number.
tiffReader - Variable in class loci.formats.in.InCellReader
 
tiffReader - Variable in class loci.formats.in.MicromanagerReader
Helper reader for TIFF files.
TiffReader - Class in loci.formats.in
TiffReader is the file format reader for regular TIFF files, not of any specific TIFF variant.
TiffReader() - Constructor for class loci.formats.in.TiffReader
Constructs a new Tiff reader.
tiffReader - Variable in class loci.formats.in.ZeissTIFFReader
Helper reader for TIFF files.
tiffReaders - Variable in class loci.formats.in.TCSReader
Helper readers.
tiffs - Variable in class loci.formats.in.BDReader
 
tiffs - Variable in class loci.formats.in.FV1000Reader
Names of every TIFF file to open.
tiffs - Variable in class loci.formats.in.L2DReader
List of constituent TIFF files.
tiffs - Variable in class loci.formats.in.MIASReader
TIFF files - indexed by well and file.
tiffs - Variable in class loci.formats.in.MicromanagerReader.Position
 
tiffs - Variable in class loci.formats.in.ScanrReader
 
tiffs - Variable in class loci.formats.in.TCSReader
List of TIFF files.
tiffSaver - Variable in class loci.formats.out.TiffWriter
The TiffSaver that will do most of the writing.
TiffSaver - Class in loci.formats.tiff
Parses TIFF data from an input source.
TiffSaver(String) - Constructor for class loci.formats.tiff.TiffSaver
Constructs a new TIFF saver from the given filename.
TiffSaver(RandomAccessOutputStream, String) - Constructor for class loci.formats.tiff.TiffSaver
Constructs a new TIFF saver from the given output source.
TiffSaver(RandomAccessOutputStream, ByteArrayHandle) - Constructor for class loci.formats.tiff.TiffSaver
Constructs a new TIFF saver from the given output source.
TIFFTile() - Constructor for class loci.formats.in.VentanaReader.TIFFTile
 
TiffWriter - Class in loci.formats.out
TiffWriter is the file format writer for TIFF files.
TiffWriter() - Constructor for class loci.formats.out.TiffWriter
 
TiffWriter(String, String[]) - Constructor for class loci.formats.out.TiffWriter
 
TILE_BYTE_COUNTS - Static variable in class loci.formats.tiff.IFD
 
TILE_GRANULARITY - Static variable in class loci.formats.out.TiffWriter
TIFF tiles must be of a height and width divisible by 16.
TILE_LENGTH - Static variable in class loci.formats.tiff.IFD
 
TILE_NUM - Static variable in class loci.formats.FormatTools
 
TILE_OFFSETS - Static variable in class loci.formats.tiff.IFD
 
TILE_ORIGIN - Static variable in class loci.formats.in.CellSensReader
 
TILE_SYSTEM - Static variable in class loci.formats.in.CellSensReader
 
TILE_WIDTH - Static variable in class loci.formats.tiff.IFD
 
TILE_X - Static variable in class loci.formats.FormatTools
 
TILE_Y - Static variable in class loci.formats.FormatTools
 
tileBytesInc - Variable in class loci.formats.in.LIFReader
 
tileCols - Variable in class loci.formats.in.MIASReader
 
tileColumns - Variable in class loci.formats.in.VentanaReader.AreaOfInterest
 
TileCoordinate(int) - Constructor for class loci.formats.in.CellSensReader.TileCoordinate
 
TileCoordinate() - Constructor for class loci.formats.TileStitcher.TileCoordinate
 
tileCount - Variable in class loci.formats.in.ImspectorReader
The number of mosaic tiles stored in the file.
tileCount - Variable in class loci.formats.in.LIFReader
 
tileDim - Variable in class loci.formats.services.JPEGTurboServiceImpl
 
tileFiles - Variable in class loci.formats.in.HamamatsuVMSReader
 
tileGridXOffset - Variable in class loci.formats.codec.CodecOptions
Horizontal offset of the tile grid as it would be provided to: ImageWriteParam.setTiling(int, int, int, int) (WRITE).
tileGridYOffset - Variable in class loci.formats.codec.CodecOptions
Vertical offset of the tile grid as it would be provided to: ImageWriteParam.setTiling(int, int, int, int) (WRITE).
tileHeight - Variable in class loci.formats.codec.CodecOptions
Tile height as it would be provided to: ImageWriteParam.setTiling(int, int, int, int) (WRITE).
tileHeight - Variable in class loci.formats.in.CellVoyagerReader.ChannelInfo
 
tileHeight - Variable in class loci.formats.in.L2DReader
 
tileHeight - Variable in class loci.formats.in.LeicaReader
 
tileHeight - Variable in class loci.formats.in.MIASReader
 
tileHeight - Variable in class loci.formats.in.OMETiffReader.OMETiffCoreMetadata
Tile size Y.
tileHeight - Variable in class loci.formats.in.ScanrReader
 
tileHeight - Variable in class loci.formats.in.VentanaReader
 
tileHeight - Variable in class loci.formats.in.ZeissCZIReader
 
tileIndices - Variable in class loci.formats.in.BaseZeissReader
 
TileJPEGReader - Class in loci.formats.in
Reader for decoding JPEG images using java.awt.Toolkit and TurboJPEG.
TileJPEGReader() - Constructor for class loci.formats.in.TileJPEGReader
 
tileMap - Variable in class loci.formats.in.CellSensReader
 
tileMap - Variable in class loci.formats.TileStitcher
 
tileOffsets - Variable in class loci.formats.in.CellSensReader
 
tileRows - Variable in class loci.formats.in.MIASReader
 
tileRows - Variable in class loci.formats.in.VentanaReader.AreaOfInterest
 
tiles - Variable in class loci.formats.in.BaseZeissReader
 
tiles - Variable in class loci.formats.in.VentanaReader
 
tileSizeX - Variable in class loci.formats.out.TiffWriter
The tile width which will be used for writing.
tileSizeY - Variable in class loci.formats.out.TiffWriter
The tile height which will be used for writing.
TileStitcher - Class in loci.formats
 
TileStitcher() - Constructor for class loci.formats.TileStitcher
Constructs a TileStitcher around a new image reader.
TileStitcher(IFormatReader) - Constructor for class loci.formats.TileStitcher
Constructs a TileStitcher with the given reader.
tileStitcher - Variable in class loci.plugins.in.ImportProcess
 
TileStitcher.TileCoordinate - Class in loci.formats
 
tileWidth - Variable in class loci.formats.codec.CodecOptions
Tile width as it would be provided to: ImageWriteParam.setTiling(int, int, int, int) (WRITE).
tileWidth - Variable in class loci.formats.in.CellVoyagerReader.ChannelInfo
 
tileWidth - Variable in class loci.formats.in.L2DReader
 
tileWidth - Variable in class loci.formats.in.LeicaReader
 
tileWidth - Variable in class loci.formats.in.MIASReader
 
tileWidth - Variable in class loci.formats.in.OMETiffReader.OMETiffCoreMetadata
Tile size X.
tileWidth - Variable in class loci.formats.in.ScanrReader
 
tileWidth - Variable in class loci.formats.in.VentanaReader
 
tileWidth - Variable in class loci.formats.in.ZeissCZIReader
 
tileX - Variable in class loci.formats.in.CellSensReader
 
tileX - Variable in class loci.formats.TileStitcher
 
tileY - Variable in class loci.formats.in.CellSensReader
 
tileY - Variable in class loci.formats.TileStitcher
 
TillVisionReader - Class in loci.formats.in
TillVisionReader is the file format reader for TillVision files.
TillVisionReader() - Constructor for class loci.formats.in.TillVisionReader
Constructs a new TillVision reader.
TIM_SUFFIX - Static variable in class loci.formats.in.PerkinElmerReader
 
time - Variable in class loci.formats.in.DicomReader
 
time - Variable in class loci.formats.in.LEOReader
 
time - Variable in class loci.formats.in.MicroCTReader
 
time - Variable in class loci.formats.in.MicromanagerReader.Position
 
time - Variable in class loci.formats.in.SDTInfo
Time of creation.
time - Variable in class loci.formats.in.SVSReader
 
time - Variable in class loci.plugins.in.ImagePlusReader
 
TIME_FORMAT - Static variable in class loci.formats.in.GelReader
 
TIME_INCREMENT - Static variable in class loci.formats.in.CellSensReader
 
TIME_OFFSET - Static variable in class loci.formats.in.TextReader
How often to report progress during initialization, in milliseconds.
TIME_PREFIX - Static variable in class loci.formats.in.KLBReader
 
TIME_SCALE - Static variable in class loci.formats.out.LegacyQTWriter
Time scale.
TIME_START - Static variable in class loci.formats.in.CellSensReader
 
TIME_SUFFIX - Static variable in class loci.formats.in.KLBReader
 
TIME_VALUE - Static variable in class loci.formats.in.CellSensReader
 
timeBins - Variable in class loci.formats.in.PQBinReader
 
timeBins - Variable in class loci.formats.in.SDTInfo
 
timeBins - Variable in class loci.formats.in.SDTReader
Number of time bins in lifetime histogram.
timeIncrement - Variable in class loci.formats.in.FEITiffReader
 
timeIncrement - Variable in class loci.formats.in.IPLabReader
 
timeIncrement - Variable in class loci.formats.in.TiffReader
 
timeIncrement - Variable in class loci.formats.in.ZeissCZIReader
 
timeIncrement - Variable in class loci.formats.in.ZeissLSMReader.Track
 
timeIndex - Variable in class loci.formats.in.FluoviewReader
 
TIMEINFO - Static variable in class loci.formats.in.LeicaReader
 
timepoint - Variable in class loci.formats.in.BaseZeissReader
 
timepoint - Variable in class loci.formats.in.BDVReader.H5Coordinate
 
timepoint - Variable in class loci.formats.in.ColumbusReader.Plane
 
timepoint - Variable in class loci.formats.in.CV7000Reader.Plane
 
timepoint - Variable in class loci.formats.in.OpenlabReader.PlaneInfo
 
timepointIncrement - Variable in class loci.formats.in.BDVReader
 
timepointIndices - Variable in class loci.formats.in.BaseZeissReader
 
timePoints - Variable in class loci.formats.in.CellVoyagerReader
 
timepoints - Variable in class loci.formats.in.SDTInfo
 
timepointUsePattern - Variable in class loci.formats.in.BDVReader
 
Timer() - Constructor for class loci.formats.in.ZeissLSMReader.Timer
 
times - Variable in class loci.formats.in.BDVReader
 
times - Variable in class loci.formats.in.CellH5Reader
 
times - Variable in class loci.formats.in.LegacyQTReader
Time offset for each frame.
TIMESTAMP - Static variable in class loci.formats.FormatTools
 
TIMESTAMP - Static variable in class loci.formats.in.CellSensReader
 
timestamp - Variable in class loci.formats.in.CV7000Reader.Plane
 
timestamp - Variable in class loci.formats.in.GatanReader
 
timestamp - Variable in class loci.formats.in.InCellReader.InCellHandler
 
timestamp - Variable in class loci.formats.in.OpenlabReader.PlaneInfo
 
timestamp - Variable in class loci.formats.in.ZeissCZIReader.SubBlock
 
TIMESTAMP_KEY - Static variable in class loci.formats.in.LiFlimReader
 
timestampFile - Variable in class loci.formats.in.VolocityReader.Stack
 
timestamps - Variable in class loci.formats.in.BaseZeissReader
 
timestamps - Variable in class loci.formats.in.BrukerReader
 
timestamps - Variable in class loci.formats.in.CellWorxReader
 
timestamps - Variable in class loci.formats.in.LeicaReader
 
timestamps - Variable in class loci.formats.in.LiFlimReader
 
timestamps - Variable in class loci.formats.in.LIFReader
 
timestamps - Variable in class loci.formats.in.MetamorphHandler
 
timestamps - Variable in class loci.formats.in.MicromanagerReader.Position
 
timestamps - Variable in class loci.formats.in.PCIReader
 
timestamps - Variable in class loci.formats.in.VolocityReader
 
timestamps - Variable in class loci.formats.in.ZeissCZIReader
 
timestamps - Variable in class loci.formats.in.ZeissLSMReader
 
timeStampSeconds - Variable in class loci.formats.in.DeltavisionReader.DVExtHdrFields
Time stamp in seconds since the experiment began.
timeUnit - Variable in class loci.formats.in.NiftiReader
 
TISSUE_INDEX - Static variable in class loci.formats.in.NDPIReader
 
TITAN_TAG - Static variable in class loci.formats.in.FEITiffReader
 
TITLE - Static variable in class loci.formats.gui.DataConverter
 
TITLE - Static variable in class loci.formats.gui.ImageViewer
 
TITLE - Static variable in class loci.formats.tools.EditTiffG
 
TJ - Class in org.libjpegturbo.turbojpeg
TurboJPEG utility class (cannot be instantiated)
TJ() - Constructor for class org.libjpegturbo.turbojpeg.TJ
 
TJCompressor - Class in org.libjpegturbo.turbojpeg
TurboJPEG compressor
TJCompressor() - Constructor for class org.libjpegturbo.turbojpeg.TJCompressor
Create a TurboJPEG compressor instance.
TJCompressor(byte[], int, int, int, int) - Constructor for class org.libjpegturbo.turbojpeg.TJCompressor
Create a TurboJPEG compressor instance and associate the uncompressed source image stored in srcImage with the newly-created instance.
TJCustomFilter - Interface in org.libjpegturbo.turbojpeg
Custom filter callback interface
TJDecompressor - Class in org.libjpegturbo.turbojpeg
TurboJPEG decompressor
TJDecompressor() - Constructor for class org.libjpegturbo.turbojpeg.TJDecompressor
Create a TurboJPEG decompresssor instance.
TJDecompressor(byte[]) - Constructor for class org.libjpegturbo.turbojpeg.TJDecompressor
Create a TurboJPEG decompressor instance and associate the JPEG image stored in jpegImage with the newly-created instance.
TJDecompressor(byte[], int) - Constructor for class org.libjpegturbo.turbojpeg.TJDecompressor
Create a TurboJPEG decompressor instance and associate the JPEG image of length imageSize bytes stored in jpegImage with the newly-created instance.
TJLoader - Class in org.libjpegturbo.turbojpeg
 
TJLoader() - Constructor for class org.libjpegturbo.turbojpeg.TJLoader
 
TJScalingFactor - Class in org.libjpegturbo.turbojpeg
Fractional scaling factor
TJScalingFactor(int, int) - Constructor for class org.libjpegturbo.turbojpeg.TJScalingFactor
 
TJTransform - Class in org.libjpegturbo.turbojpeg
Lossless transform parameters
TJTransform() - Constructor for class org.libjpegturbo.turbojpeg.TJTransform
Create a new lossless transform instance.
TJTransform(int, int, int, int, int, int, TJCustomFilter) - Constructor for class org.libjpegturbo.turbojpeg.TJTransform
Create a new lossless transform instance with the given parameters.
TJTransform(Rectangle, int, int, TJCustomFilter) - Constructor for class org.libjpegturbo.turbojpeg.TJTransform
Create a new lossless transform instance with the given parameters.
TJTransformer - Class in org.libjpegturbo.turbojpeg
TurboJPEG lossless transformer
TJTransformer() - Constructor for class org.libjpegturbo.turbojpeg.TJTransformer
Create a TurboJPEG lossless transformer instance.
TJTransformer(byte[]) - Constructor for class org.libjpegturbo.turbojpeg.TJTransformer
Create a TurboJPEG lossless transformer instance and associate the JPEG image stored in jpegImage with the newly-created instance.
TJTransformer(byte[], int) - Constructor for class org.libjpegturbo.turbojpeg.TJTransformer
Create a TurboJPEG lossless transformer instance and associate the JPEG image of length imageSize bytes stored in jpegImage with the newly-created instance.
tLabel - Variable in class loci.formats.gui.DataConverter
 
TM - Static variable in class loci.formats.in.DicomReader
 
tmpLetter - Variable in class loci.formats.ResourceNamer
 
toArray() - Method in class loci.formats.tiff.OnDemandLongArray
 
toByteArray() - Method in class loci.formats.codec.BitWriter
Deprecated.
Gets an array containing all bits written thus far.
toByteArray() - Method in class loci.formats.codec.ByteVector
 
toBytes(BufferedImage, IFormatWriter) - Static method in class loci.formats.gui.BufferedImageWriter
 
toCIEXYZ(float[]) - Method in class loci.formats.gui.TwoChannelColorSpace
 
toFloat(int, FloatProcessor) - Method in class loci.plugins.util.RecordedImageProcessor
 
toggleAnimation() - Method in class loci.plugins.util.DataBrowser
Toggles whether the data browser is animating.
token(String, String, int) - Method in class loci.formats.in.PrairieMetadata
Gets the ith token of the given string, split according to the specific regular expression.
TOKEN_SEPARATOR - Static variable in class loci.formats.in.FakeReader
 
tokenize(String) - Method in class loci.formats.in.ICSReader
 
toLength(Double, boolean) - Method in class loci.formats.in.PrairieMetadata.Frame
Convert a position number to a length in the microscope reference frame.
TONE_COMPENSATION - Static variable in class loci.formats.in.NikonReader
 
TOO_MANY_TRIES - Static variable in class loci.plugins.util.LuraWave
 
tools - Variable in class loci.formats.in.LegacyQTReader
Instance of LegacyQTTools to handle QuickTime for Java detection.
tools - Variable in class loci.formats.out.LegacyQTWriter
Instance of LegacyQTTools to handle QuickTime for Java detection.
TOOLS - Static variable in class loci.formats.UpgradeChecker
Name of the ueber tools JAR.
toOMExmlColor(Color) - Static method in class loci.plugins.util.ROIHandler
Converts the Java Color into an OME-XML Color.
TOP_LEVEL_KEYS - Static variable in class loci.formats.in.NikonTiffReader
 
TopometrixReader - Class in loci.formats.in
TopometrixReader is the file format reader for TopoMetrix .tfr, .ffr, .zfr, .zfp, and .2fl files.
TopometrixReader() - Constructor for class loci.formats.in.TopometrixReader
Constructs a new TopoMetrix reader.
toPrimitiveArray(List<Long>) - Method in class loci.formats.tiff.TiffSaver
Coverts a list to a primitive array.
toRGB(float[]) - Method in class loci.formats.gui.TwoChannelColorSpace
 
toSPWCoordinates(int) - Method in class loci.formats.in.FakeReader
Convert the given series (Image) index to a WellSample, Well, and Plate index.
toString() - Method in class loci.formats.cache.CacheEvent
 
toString() - Method in class loci.formats.CoreMetadata
 
toString() - Method in class loci.formats.FileInfo
 
toString() - Method in class loci.formats.gui.ComboFileFilter
Gets a string representation of this file filter.
toString() - Method in class loci.formats.gui.ExtensionFileFilter
Gets a string representation of this file filter.
toString() - Method in class loci.formats.gui.FormatFileFilter
Gets a string representation of this file filter.
toString() - Method in class loci.formats.gui.NoExtensionFileFilter
Gets a string representation of this file filter.
toString(boolean) - Method in class loci.formats.gui.XMLCellRenderer.XMLItem
 
toString() - Method in class loci.formats.gui.XMLCellRenderer.XMLItem
Allows copy and paste from tree component.
toString() - Method in class loci.formats.in.BaseZeissReader.Layer
 
toString() - Method in class loci.formats.in.BaseZeissReader.Shape
 
toString() - Method in class loci.formats.in.BaseZeissReader.Tag
 
toString() - Method in class loci.formats.in.BDVReader.H5Coordinate
 
toString() - Method in class loci.formats.in.BioRadReader.Note
 
toString() - Method in class loci.formats.in.CellH5Reader.CellH5Coordinate
 
toString() - Method in class loci.formats.in.CellSensReader.TileCoordinate
 
toString() - Method in class loci.formats.in.CellVoyagerReader.AreaInfo
 
toString() - Method in class loci.formats.in.CellVoyagerReader.ChannelInfo
 
toString() - Method in class loci.formats.in.CellVoyagerReader.FieldInfo
 
toString() - Method in class loci.formats.in.CellVoyagerReader.WellInfo
 
toString() - Method in class loci.formats.in.DeltavisionReader.DVExtHdrFields
Helper function which overrides toString, printing out the values in the header section.
toString() - Method in class loci.formats.in.IM3Reader.IM3Record
 
toString() - Method in class loci.formats.in.MicromanagerReader.Index
 
toString() - Method in class loci.formats.in.NativeND2Reader.ChunkMapEntry
 
toString() - Method in class loci.formats.in.PrairieMetadata.ValueItem
 
toString() - Method in class loci.formats.in.VentanaReader.AreaOfInterest
 
toString() - Method in class loci.formats.in.VentanaReader.Overlap
 
toString() - Method in class loci.formats.in.ZeissCZIReader.AttachmentEntry
 
toString() - Method in class loci.formats.in.ZeissCZIReader.Coordinate
 
toString() - Method in class loci.formats.in.ZeissCZIReader.DimensionEntry
 
toString() - Method in class loci.formats.in.ZeissCZIReader.DirectoryEntry
 
toString() - Method in class loci.formats.in.ZeissCZIReader.SubBlock
 
toString() - Method in class loci.formats.in.ZeissTIFFHandler.Plane
 
toString() - Method in class loci.formats.in.ZeissTIFFHandler.Scaling
 
toString() - Method in class loci.formats.in.ZeissTIFFHandler.Tag
 
toString() - Method in class loci.formats.in.ZeissTIFFHandler.TagSet
 
toString() - Method in class loci.formats.in.ZeissTIFFHandler
 
toString() - Method in class loci.formats.in.ZeissTIFFReader.Plane
 
toString() - Method in class loci.formats.ome.OMEPyramidStore.Resolution
 
toString() - Method in class loci.formats.tiff.TiffIFDEntry
 
toString() - Method in class loci.formats.tiff.TiffRational
Returns a string representation of the object.
toString() - Method in class loci.formats.tools.AmiraParameters
 
toString(Map, String) - Static method in class loci.formats.tools.AmiraParameters
 
toString() - Method in class loci.formats.tools.AsciiImage
 
toString() - Method in class loci.plugins.config.FormatEntry
 
toString() - Method in class loci.plugins.config.LibraryEntry
 
toString() - Method in class loci.plugins.in.ImporterMetadata
 
toString() - Method in class loci.plugins.util.RecordedImageProcessor
 
totalChannels - Variable in class loci.formats.in.InCellReader
 
totalImages - Variable in class loci.formats.in.InCellReader
 
totalROIs - Variable in class loci.formats.in.ZeissLSMReader
 
toXMLAnnotation() - Method in class loci.formats.Modulo
 
Track() - Constructor for class loci.formats.in.ZeissLSMReader.Track
 
TRACK_ACQUIRE - Static variable in class loci.formats.in.ZeissLSMReader
 
TRACK_TIME_BETWEEN_STACKS - Static variable in class loci.formats.in.ZeissLSMReader
 
TRANSFER_FUNCTION - Static variable in class loci.formats.tiff.IFD
 
TRANSFER_RANGE - Static variable in class loci.formats.tiff.IFD
 
TRANSFER_SYNTAX_UID - Static variable in class loci.formats.in.DicomReader
 
transform(byte[][], TJTransform[], int) - Method in class org.libjpegturbo.turbojpeg.TJTransformer
Losslessly transform the JPEG image associated with this transformer instance into one or more JPEG images stored in the given destination buffers.
transform(TJTransform[], int) - Method in class org.libjpegturbo.turbojpeg.TJTransformer
Losslessly transform the JPEG image associated with this transformer instance and return an array of TJDecompressor instances, each of which has a transformed JPEG image associated with it.
transform(byte[], int, byte[][], TJTransform[], int) - Method in class org.libjpegturbo.turbojpeg.TJTransformer
 
transformAcquisitionMode(String) - Method in class loci.formats.in.InveonReader
 
transformBedControl(String) - Method in class loci.formats.in.InveonReader
 
transformBedMotion(String) - Method in class loci.formats.in.InveonReader
 
transformCTProjectionInterpolation(String) - Method in class loci.formats.in.InveonReader
 
transformCTWarping(String) - Method in class loci.formats.in.InveonReader
 
transformedSizes - Variable in class org.libjpegturbo.turbojpeg.TJTransformer
 
transformEventType(String) - Method in class loci.formats.in.InveonReader
 
transformFileType(String) - Method in class loci.formats.in.InveonReader
 
transformFilter(String) - Method in class loci.formats.in.InveonReader
 
transformGantryRotation(String) - Method in class loci.formats.in.InveonReader
 
transformModality(String) - Method in class loci.formats.in.InveonReader
 
transformModalityConfiguration(String) - Method in class loci.formats.in.InveonReader
 
transformModel(String) - Method in class loci.formats.in.InveonReader
 
transformNormalizationApplied(String) - Method in class loci.formats.in.InveonReader
 
transformReconAlgorithm(String) - Method in class loci.formats.in.InveonReader
 
transformRegistrationAvailable(String) - Method in class loci.formats.in.InveonReader
 
transformRotationDirection(String) - Method in class loci.formats.in.InveonReader
 
transformSubjectLengthUnits(String) - Method in class loci.formats.in.InveonReader
 
transformSubjectOrientation(String) - Method in class loci.formats.in.InveonReader
 
transformSubjectWeightUnits(String) - Method in class loci.formats.in.InveonReader
 
transformToLatestVersion(String) - Method in interface loci.formats.services.OMEXMLService
Transforms the given OME-XML string to the latest supported version of of the OME-XML schema.
transformToLatestVersion(String) - Method in class loci.formats.services.OMEXMLServiceImpl
 
transIndex - Variable in class loci.formats.in.GIFReader
Transparent color index.
translate(int, int) - Method in class loci.plugins.util.RecordedImageProcessor
 
translateAttachmentNodes(Element, int) - Method in class loci.formats.in.LIFReader
 
translateDetectors(Element, int) - Method in class loci.formats.in.LIFReader
 
translateDisplaySettings(Element) - Method in class loci.formats.in.ZeissCZIReader
 
translateExperiment(Element) - Method in class loci.formats.in.ZeissCZIReader
 
translateFilterSettings(Element, int) - Method in class loci.formats.in.LIFReader
 
translateHardwareSettings(Element) - Method in class loci.formats.in.ZeissCZIReader
 
translateImageNames(Element, int) - Method in class loci.formats.in.LIFReader
 
translateImageNodes(Element, int) - Method in class loci.formats.in.LIFReader
 
translateInformation(Element) - Method in class loci.formats.in.ZeissCZIReader
 
translateLaserLines(Element, int) - Method in class loci.formats.in.LIFReader
 
translateLayers(Element) - Method in class loci.formats.in.ZeissCZIReader
 
translateMetadata(Element) - Method in class loci.formats.in.LIFReader
 
translateMetadata(String) - Method in class loci.formats.in.ZeissCZIReader
 
translateROIs(Element, int) - Method in class loci.formats.in.LIFReader
 
translateScaling(Element) - Method in class loci.formats.in.ZeissCZIReader
 
translateScannerSettings(Element, int) - Method in class loci.formats.in.LIFReader
 
translateSingleROIs(Element, int) - Method in class loci.formats.in.LIFReader
 
translateSingleTimestamp(String) - Method in class loci.formats.in.LIFReader
 
translateSingleTimestamp(Element) - Method in class loci.formats.in.LIFReader
 
translateTimestamps(Element, int) - Method in class loci.formats.in.LIFReader
 
transmissivity - Variable in class loci.formats.in.OIRReader.Laser
 
transparency - Variable in class loci.formats.in.GIFReader
Use transparent color.
TRANSPARENCY_ID - Static variable in class loci.formats.in.CellSensReader
 
TRANSPARENCY_VALUE - Static variable in class loci.formats.in.CellSensReader
 
transX - Variable in class loci.formats.in.LeicaHandler.ROI
 
transX - Variable in class loci.formats.in.LIFReader.ROI
 
transY - Variable in class loci.formats.in.LeicaHandler.ROI
 
transY - Variable in class loci.formats.in.LIFReader.ROI
 
TrestleReader - Class in loci.formats.in
TrestleReader is the file format reader for Trestle slide datasets.
TrestleReader() - Constructor for class loci.formats.in.TrestleReader
Constructs a new Trestle reader.
trigger - Variable in class loci.formats.in.SDTInfo
 
TRUE_ALPHA - Static variable in class loci.formats.in.APNGReader
 
TRUE_COLOR - Static variable in class loci.formats.in.APNGReader
 
trueSizeX - Variable in class loci.formats.in.NativeND2Reader
 
trueSizeY - Variable in class loci.formats.in.NativeND2Reader
 
trueSizeZ - Variable in class loci.formats.in.NativeND2Reader
 
truncatedFileFlag - Variable in class loci.formats.in.DeltavisionReader
 
TRUNK - Static variable in class loci.plugins.Updater
 
TRUNK_BUILD - Static variable in class loci.formats.UpgradeChecker
Location of the JAR artifacts for Bio-Formats' trunk build.
ts - Variable in class loci.formats.in.ND2Handler
 
tScroll - Variable in class loci.plugins.util.DataBrowser
 
tSize - Variable in class loci.formats.in.DeltavisionReader
Size of one time element in the extended header.
tSlider - Variable in class loci.formats.gui.ImageViewer
 
tsT - Variable in class loci.formats.in.NativeND2Reader
 
tStep - Variable in class loci.plugins.in.ImporterOptions
 
tSteps - Variable in class loci.formats.in.LIFReader
 
Tstore - Variable in class loci.formats.in.SPCReader
 
tstoreb - Variable in class loci.formats.in.SPCReader
 
TWO - Static variable in class loci.formats.AxisGuesser
 
TwoChannelColorSpace - Class in loci.formats.gui
ColorSpace for 2-channel images.
TwoChannelColorSpace(int, int) - Constructor for class loci.formats.gui.TwoChannelColorSpace
 
type - Variable in class loci.formats.cache.CacheEvent
Type of cache event.
type - Variable in class loci.formats.in.APNGReader.PNGBlock
 
type - Variable in class loci.formats.in.AVIReader
 
type - Variable in class loci.formats.in.BaseZeissReader.Shape
 
type - Variable in class loci.formats.in.BioRadReader.Note
 
type - Variable in class loci.formats.in.CV7000Reader.LightSource
 
type - Variable in class loci.formats.in.GatanReader.ROIShape
 
type - Variable in class loci.formats.in.IM3Reader.IM3Record
 
type - Variable in class loci.formats.in.LeicaHandler.Detector
 
type - Variable in class loci.formats.in.LeicaHandler.ROI
 
type - Variable in class loci.formats.in.LIFReader.ROI
 
type - Variable in class loci.formats.in.PrairieMetadata.Sequence
type attribute of this <Sequence>.
type - Variable in enum loci.formats.in.SPEReader.SpeHeaderEntry
 
type - Variable in class loci.formats.in.ZeissLSMReader.Laser
 
type - Variable in class loci.formats.in.ZeissTIFFHandler.Scaling.Dimension
 
type - Variable in class loci.formats.Modulo
 
type - Variable in class loci.formats.tiff.TiffIFDEntry
The field Type.
type - Variable in class loci.plugins.config.ConfigWindow
 
type - Variable in class loci.plugins.config.LibraryEntry
 
TYPE_ASCII - Static variable in class loci.formats.in.ZeissLSMReader
 
TYPE_BOOLEAN - Static variable in class loci.formats.in.ZeissLSMReader
 
TYPE_BOOLEAN - Static variable in class loci.plugins.prefs.OptionsList
String indicating option is of type boolean.
TYPE_DATE - Static variable in class loci.formats.in.ZeissLSMReader
 
TYPE_LONG - Static variable in class loci.formats.in.ZeissLSMReader
 
TYPE_RATIONAL - Static variable in class loci.formats.in.ZeissLSMReader
 
TYPE_STRING - Static variable in class loci.plugins.prefs.OptionsList
String indicating option is of type string.
TYPE_SUBBLOCK - Static variable in class loci.formats.in.ZeissLSMReader
Data types.
typeDescription - Variable in class loci.formats.Modulo
 
typeLabel - Variable in class loci.formats.gui.PreviewPane
Labels containing thumbnail and dimensional information.
TYPES - Static variable in class loci.formats.in.DicomReader
 
TYPES - Static variable in class loci.formats.in.MRCReader
 
types - Variable in class loci.formats.in.TillVisionReader
 
typeText - Variable in class loci.formats.gui.PreviewPane
 
typeTip - Variable in class loci.formats.gui.PreviewPane
 
TypeUINT12 - Variable in class loci.formats.in.LiFlimReader
if DataType is UINT12, data is compressed in 12 bits.

U

UBMReader - Class in loci.formats.in
UBMReader is the file format reader for UBM .pr3 files.
UBMReader() - Constructor for class loci.formats.in.UBMReader
Constructs a new UBM reader.
UBYTE - Static variable in class loci.formats.in.GatanReader
 
UCHAR - Static variable in class loci.formats.in.CellSensReader
 
UI - Static variable in class loci.formats.in.DicomReader
 
UIC1TAG - Static variable in class loci.formats.in.MetamorphReader
 
UIC2TAG - Static variable in class loci.formats.in.MetamorphReader
 
UIC3TAG - Static variable in class loci.formats.in.MetamorphReader
 
UIC4TAG - Static variable in class loci.formats.in.MetamorphReader
 
UID - Variable in class loci.formats.in.CellVoyagerReader.AreaInfo
 
UID - Variable in class loci.formats.in.CellVoyagerReader.WellInfo
 
UINT - Static variable in class loci.formats.in.CellSensReader
 
UINT - Static variable in class loci.formats.in.GatanReader
 
UINT12stream - Variable in class loci.formats.in.LiFlimReader
 
UINT12streamPos - Variable in class loci.formats.in.LiFlimReader
 
UINT12streamSeries - Variable in class loci.formats.in.LiFlimReader
 
UINT16 - Static variable in class loci.formats.FormatTools
Identifies the UINT16 data type used to store pixel values.
UINT16_TYPE - Static variable in class loci.formats.in.KLBReader
 
UINT32 - Static variable in class loci.formats.FormatTools
Identifies the UINT32 data type used to store pixel values.
UINT32_TYPE - Static variable in class loci.formats.in.KLBReader
 
UINT64_TYPE - Static variable in class loci.formats.in.KLBReader
 
UINT8 - Static variable in class loci.formats.FormatTools
Identifies the UINT8 data type used to store pixel values.
UINT8_TYPE - Static variable in class loci.formats.in.KLBReader
 
UL - Static variable in class loci.formats.in.DicomReader
 
ULONG - Static variable in class loci.formats.in.CellSensReader
 
UN - Static variable in class loci.formats.in.DicomReader
 
uncompress(int, byte[]) - Method in class loci.formats.in.AVIReader
 
uncompress(byte[], String) - Method in class loci.formats.in.NativeQTReader
Uncompresses an image plane according to the the codec identifier.
UNCOMPRESSED - Static variable in class loci.formats.in.ZeissCZIReader
Compression constants.
underline - Variable in class loci.formats.in.BaseZeissReader.Shape
 
undifference(byte[], IFD) - Static method in enum loci.formats.tiff.TiffCompression
Undoes in-place differencing according to the given predictor value.
unfilter(byte[], byte[], int, int) - Method in class loci.formats.in.APNGReader
See http://www.w3.org/TR/PNG/#9Filters.
ungroupFilesBox - Variable in class loci.plugins.in.MainDialog
 
UNICODE_TCHAR - Static variable in class loci.formats.in.CellSensReader
 
UNINT16 - Static variable in class loci.formats.in.SPEReader
 
UNINT32 - Static variable in class loci.formats.in.SPEReader
 
uniqueFiles - Variable in class loci.formats.out.ICSWriter
 
uniquePMTs - Variable in class loci.formats.in.ImspectorReader
List of PMTs active during acquisition.
uniqueZ - Variable in class loci.formats.in.PCIReader
 
UNISOKU_MAGIC_STRING - Static variable in class loci.formats.in.UnisokuReader
 
UnisokuReader - Class in loci.formats.in
UnisokuReader is the file format reader for Unisoku STM files.
UnisokuReader() - Constructor for class loci.formats.in.UnisokuReader
Constructs a new Unisoku reader.
unit - Variable in class loci.formats.in.ZeissTIFFHandler.Scaling.Dimension
 
unit - Variable in class loci.formats.Modulo
 
units - Variable in class loci.formats.in.GatanReader
 
units - Variable in class loci.formats.in.VarianFDFReader
 
UNITS_METER - Static variable in class loci.formats.in.NiftiReader
Code for meters.
UNITS_MM - Static variable in class loci.formats.in.NiftiReader
Code for millimeters.
UNITS_MSEC - Static variable in class loci.formats.in.NiftiReader
Code for milliseconds.
UNITS_USEC - Static variable in class loci.formats.in.NiftiReader
Code for microseconds.
UNKNOWN - Static variable in class loci.formats.in.CellSensReader
 
UNKNOWN - Static variable in class loci.formats.in.GatanReader
 
unknown1 - Variable in class loci.formats.in.BaseZeissReader.Shape
 
unknown10 - Variable in class loci.formats.in.BaseZeissReader.Shape
 
unknown11 - Variable in class loci.formats.in.BaseZeissReader.Shape
 
unknown12 - Variable in class loci.formats.in.BaseZeissReader.Shape
 
unknown13 - Variable in class loci.formats.in.BaseZeissReader.Shape
 
unknown14 - Variable in class loci.formats.in.BaseZeissReader.Shape
 
unknown15 - Variable in class loci.formats.in.BaseZeissReader.Shape
 
unknown16 - Variable in class loci.formats.in.BaseZeissReader.Shape
 
unknown17 - Variable in class loci.formats.in.BaseZeissReader.Shape
 
unknown18 - Variable in class loci.formats.in.BaseZeissReader.Shape
 
unknown19 - Variable in class loci.formats.in.BaseZeissReader.Shape
 
unknown2 - Variable in class loci.formats.in.BaseZeissReader.Shape
 
UNKNOWN2 - Static variable in class loci.formats.in.GatanReader
 
unknown3 - Variable in class loci.formats.in.BaseZeissReader.Shape
 
unknown4 - Variable in class loci.formats.in.BaseZeissReader.Shape
 
unknown5 - Variable in class loci.formats.in.BaseZeissReader.Shape
 
unknown6 - Variable in class loci.formats.in.BaseZeissReader.Shape
 
unknown7 - Variable in class loci.formats.in.BaseZeissReader.Shape
 
unknown8 - Variable in class loci.formats.in.BaseZeissReader.Shape
 
UNKNOWN_AXIS - Static variable in class loci.formats.AxisGuesser
Axis type for unclassified axes.
UNKNOWN_BLOBS_VOLUME - Static variable in class loci.formats.in.CellSensReader
 
UNKNOWN_DOMAIN - Static variable in class loci.formats.FormatTools
Identifies an unknown domain.
UnknownFormatException - Exception in loci.formats
UnknownFormatException is the exception thrown when the format of a particular data stream or filename cannot be recognized or is unsupported.
UnknownFormatException() - Constructor for exception loci.formats.UnknownFormatException
 
UnknownFormatException(String) - Constructor for exception loci.formats.UnknownFormatException
 
UnknownFormatException(String, Throwable) - Constructor for exception loci.formats.UnknownFormatException
 
UnknownFormatException(Throwable) - Constructor for exception loci.formats.UnknownFormatException
 
unmagnifiedPixelHeight - Variable in class loci.formats.in.CellVoyagerReader.ChannelInfo
 
unmagnifiedPixelWidth - Variable in class loci.formats.in.CellVoyagerReader.ChannelInfo
 
unpackBits(byte[], int[]) - Method in class loci.formats.in.PictReader
PackBits variant that outputs an int array.
unpackBytes(byte[], int, byte[], IFD) - Static method in class loci.formats.tiff.TiffParser
Extracts pixel information from the given byte array according to the bits per sample, photometric interpretation and color map IFD directory entry values, and the specified byte ordering.
unpackEndian - Variable in class loci.formats.in.VeecoReader
 
UnsignedIntBuffer - Class in loci.formats.gui
DataBuffer that stores unsigned ints.
UnsignedIntBuffer(int[], int) - Constructor for class loci.formats.gui.UnsignedIntBuffer
Construct a new buffer of unsigned ints using the given int array.
UnsignedIntBuffer(int[][], int) - Constructor for class loci.formats.gui.UnsignedIntBuffer
Construct a new buffer of unsigned ints using the given 2D int array.
UnsignedIntColorModel - Class in loci.formats.gui
ColorModel that handles unsigned 32 bit data.
UnsignedIntColorModel(int, int, int) - Constructor for class loci.formats.gui.UnsignedIntColorModel
 
UnsupportedCompressionException - Exception in loci.formats
UnsupportedCompressionException is the exception thrown when the compression scheme used in a particular file or stream is unsupported.
UnsupportedCompressionException() - Constructor for exception loci.formats.UnsupportedCompressionException
 
UnsupportedCompressionException(String) - Constructor for exception loci.formats.UnsupportedCompressionException
 
UnsupportedCompressionException(String, Throwable) - Constructor for exception loci.formats.UnsupportedCompressionException
 
UnsupportedCompressionException(Throwable) - Constructor for exception loci.formats.UnsupportedCompressionException
 
unwrap() - Method in class loci.formats.ReaderWrapper
Unwraps nested wrapped readers until the core reader (i.e., not a ReaderWrapper or ImageReader) is found.
unwrap(String) - Method in class loci.formats.ReaderWrapper
Unwraps nested wrapped readers until the core reader (i.e., not a ReaderWrapper or ImageReader) is found.
unwrap(Class<? extends IFormatReader>, String) - Method in class loci.formats.ReaderWrapper
Unwraps nested wrapped readers until the given reader class is found.
unwrap() - Method in class loci.formats.WriterWrapper
Unwraps nested wrapped writers until the core writer (i.e., not a WriterWrapper or ImageWriter) is found.
unwrap(String) - Method in class loci.formats.WriterWrapper
Unwraps nested wrapped writers until the core writer (i.e., not a WriterWrapper or ImageWriter) is found.
unwrap(Class<? extends IFormatWriter>, String) - Method in class loci.formats.WriterWrapper
Unwraps nested wrapped writers until the given writer class is found.
unwrap(int) - Static method in class loci.plugins.util.ROIHandler
Wraps the specified integer into a Non negative integer.
unwrapCodecException(CodecException) - Static method in class loci.formats.codec.WrappedCodec
 
UP - Static variable in class loci.formats.in.APNGReader
 
update2003FC - Static variable in class loci.formats.services.OMEXMLServiceImpl
Stylesheets for updating from previous schema releases.
update200706 - Static variable in class loci.formats.services.OMEXMLServiceImpl
 
update200802 - Static variable in class loci.formats.services.OMEXMLServiceImpl
 
update200809 - Static variable in class loci.formats.services.OMEXMLServiceImpl
 
update200909 - Static variable in class loci.formats.services.OMEXMLServiceImpl
 
update201004 - Static variable in class loci.formats.services.OMEXMLServiceImpl
 
update201006 - Static variable in class loci.formats.services.OMEXMLServiceImpl
 
update201106 - Static variable in class loci.formats.services.OMEXMLServiceImpl
 
update201206 - Static variable in class loci.formats.services.OMEXMLServiceImpl
 
update201306 - Static variable in class loci.formats.services.OMEXMLServiceImpl
 
update201501 - Static variable in class loci.formats.services.OMEXMLServiceImpl
 
updateComposite(int[], int) - Method in class loci.plugins.util.RecordedImageProcessor
 
updateIfGlitched() - Method in class loci.plugins.in.SeriesDialog
 
updateLabel(int, int) - Method in class loci.formats.gui.ImageViewer
Updates cursor probe label.
updateLabels(String) - Method in class loci.formats.gui.DataConverter
 
updateMetadataLists(Hashtable<String, Object>) - Method in class loci.formats.FormatReader
For the given metadata hashtable, replace any value that is a list with one key/value pair per list entry.
updateMinMax(int, byte[], int) - Method in class loci.formats.MinMaxCalculator
Updates min/max values based on the given byte array.
updateOrder(int) - Method in class loci.formats.gui.CacheComponent
Updates cache order to match the state of the GUI.
updatePending - Variable in class loci.formats.in.ZeissCZIReader.FileHeader
 
updatePriority(int) - Method in class loci.formats.gui.CacheComponent
Updates cache priority to match the state of the GUI.
Updater - Class in loci.plugins
A plugin for updating the Bio-Formats plugins.
Updater() - Constructor for class loci.plugins.Updater
 
updateRange(int) - Method in class loci.formats.gui.CacheComponent
Updates cache range to match the state of the GUI.
updateSource() - Method in class loci.formats.gui.CacheComponent
Updates cache source to match the state of the GUI.
updateStrategy() - Method in class loci.formats.gui.CacheComponent
Updates cache strategy to match the state of the GUI.
updateTiming(int, int, int, int) - Method in class loci.plugins.in.ImagePlusReader
 
UPGRADE_CHECK_ALLOWED_PROPERTY - Static variable in class loci.formats.UpgradeChecker
System property indicating whether the upgrade check is ever allowed.
UPGRADE_CHECK_KEY - Static variable in class loci.plugins.config.ConfigWindow
 
UPGRADE_CHECK_PROPERTY - Static variable in class loci.formats.UpgradeChecker
System property to set once the upgrade check is performed.
upgradeBox - Variable in class loci.plugins.config.ConfigWindow
 
UpgradeCheck - Class in loci.formats.tools
Utility that checks for a new stable version, and optionally installs a new version of Bio-Formats ueber tools.
UpgradeCheck() - Constructor for class loci.formats.tools.UpgradeCheck
 
UpgradeChecker - Class in loci.formats
Class that allows checking for new versions of Bio-Formats, as well as updating to the latest stable, daily, or trunk version.
UpgradeChecker() - Constructor for class loci.formats.UpgradeChecker
 
UpgradeDialog - Class in loci.plugins.in
Bio-Formats Importer upgrade checker dialog box.
UpgradeDialog(ImportProcess) - Constructor for class loci.plugins.in.UpgradeDialog
Creates an upgrade checker dialog for the Bio-Formats Importer.
url - Variable in class loci.plugins.config.ConfigWindow
 
url - Variable in class loci.plugins.config.LibraryEntry
 
URL_BF_SOFTWARE - Static variable in class loci.plugins.util.LibraryChecker
URL for Bio-Formats web page.
URL_BIO_FORMATS - Static variable in class loci.formats.FormatTools
URL of Bio-Formats web page.
URL_BIO_FORMATS_IMAGEJ - Static variable in class loci.plugins.About
URL of Bio-Formats ImageJ web page.
URL_BIO_FORMATS_LIBRARIES - Static variable in class loci.formats.FormatTools
URL of 'Bio-Formats as a Java Library' web page.
URL_DATA_BROWSER - Static variable in class loci.plugins.About
URL of Data Browser web page.
URL_JAVADOCS - Static variable in class loci.plugins.macro.LociFunctions
URL for Javadocs.
URL_NIKON_ND2 - Static variable in class loci.formats.in.LegacyND2Reader
 
URL_OME_TIFF - Static variable in class loci.formats.FormatTools
URL of OME-TIFF web page.
URL_SOFTWARE - Static variable in class loci.plugins.About
URL of the Bio-Formats web page.
urlPath - Variable in class loci.plugins.Updater
Path to ueber-jar whether bioformats_package.jar or loci_tools.jar.
US - Static variable in class loci.formats.in.DicomReader
 
use64Bit - Variable in class loci.formats.in.MinimalTiffReader
 
USE_CHUNKMAP_DEFAULT - Static variable in class loci.formats.in.NativeND2Reader
 
USE_CHUNKMAP_KEY - Static variable in class loci.formats.in.NativeND2Reader
 
USE_ORIGINAL_FRAME_RATE - Static variable in class loci.formats.in.CellSensReader
 
useChunkMap() - Method in class loci.formats.in.NativeND2Reader
 
used - Variable in class loci.formats.in.APLReader
 
used - Variable in class loci.formats.in.BioRadReader
 
used - Variable in class loci.formats.in.OMETiffReader
List of used files.
usedFile(String) - Method in class loci.formats.in.LeicaReader
 
usedFiles - Variable in class loci.formats.in.CellSensReader
 
usedFiles - Variable in class loci.formats.in.FV1000Reader
Used file list.
usedSize - Variable in class loci.formats.in.ZeissCZIReader.Segment
 
usedToInitialize - Variable in class loci.formats.FileInfo
Whether or not this file can be passed to the appropriate reader's setId(String) method.
useLegacy - Variable in class loci.formats.DelegateReader
Flag indicating whether to use legacy reader by default.
useMotor - Variable in class loci.formats.in.SDTInfo
 
useND2Chunkmap() - Static method in class loci.plugins.util.LociPrefs
 
useOldPhysicalSizeCalculation() - Method in class loci.formats.in.LIFReader
 
usePatternIds - Variable in class loci.plugins.in.ImporterOptions
 
USER - Static variable in class loci.formats.in.OpenlabReader
 
USER_COMMENT - Static variable in class loci.formats.tiff.IFD
 
userDisplayName - Variable in class loci.formats.in.ZeissCZIReader
 
userEmail - Variable in class loci.formats.in.ZeissCZIReader
 
userFirstName - Variable in class loci.formats.in.ZeissCZIReader
 
userInstitution - Variable in class loci.formats.in.ZeissCZIReader
 
userLastName - Variable in class loci.formats.in.ZeissCZIReader
 
userMetadataStore - Variable in class loci.formats.Memoizer
MetadataStore set by the caller.
userMiddleName - Variable in class loci.formats.in.ZeissCZIReader
 
userName - Variable in class loci.formats.in.FEITiffReader
 
userName - Variable in class loci.formats.in.ZeissCZIReader
 
userName - Variable in class loci.formats.in.ZeissLSMReader
 
users - Variable in class loci.formats.in.BrukerReader
 
useTiffParser(IFD) - Method in class loci.formats.in.NDPIReader
 
useZ - Variable in class loci.formats.in.NativeND2Reader
 
USHORT - Static variable in class loci.formats.in.CellSensReader
 
USHORT - Static variable in class loci.formats.in.GatanReader
 
UT - Static variable in class loci.formats.in.DicomReader
 
uuid - Variable in class loci.formats.in.LeicaSCNReader.Image
 
uuid - Variable in class loci.formats.in.LeicaSCNReader.ImageCollection
 
uuids - Variable in class loci.formats.out.OMETiffWriter
 

V

V3DrawWriter - Class in loci.formats.out
V3DrawWriter writes images in the .v3draw format for rapid I/O in Vaa3D, an open-source 3D visualization and analysis toolkit.
V3DrawWriter() - Constructor for class loci.formats.out.V3DrawWriter
 
valid - Variable in class loci.formats.FilePattern
The validity of the file pattern.
valid() - Method in class loci.formats.in.BaseZeissReader.Tag
Check if the tag is valid (key, value and category have been set).
valid - Variable in class loci.formats.in.LeicaReader
 
valid - Variable in class loci.formats.in.LeicaSCNReader.LeicaSCNHandler
 
valid() - Method in class loci.formats.in.ZeissTIFFHandler.Tag
Check if the tag is valid (key, value and category have been set).
validate - Variable in class loci.formats.in.DefaultMetadataOptions
 
validateOMEXML(String) - Method in interface loci.formats.services.OMEXMLService
Attempts to validate the given OME-XML string using Java's XML validation facility.
validateOMEXML(String, boolean) - Method in interface loci.formats.services.OMEXMLService
Attempts to validate the given OME-XML string using Java's XML validation facility.
validateOMEXML(String) - Method in class loci.formats.services.OMEXMLServiceImpl
 
validateOMEXML(String, boolean) - Method in class loci.formats.services.OMEXMLServiceImpl
 
validBits - Variable in class loci.formats.FormatWriter
The number of valid bits per pixel.
validBits - Variable in class loci.formats.in.FV1000Reader
 
validChannel - Variable in class loci.formats.in.ScanrReader.ScanrHandler
 
validLoopState - Variable in class loci.formats.in.ND2Handler
 
validStream(RandomAccessInputStream, int, boolean) - Static method in class loci.formats.FormatTools
Returns true if the given RandomAccessInputStream conatins at least 'len' bytes.
validZ - Variable in class loci.formats.in.MetamorphReader
 
value - Variable in enum loci.formats.in.BaseZeissReader.Charset
 
value - Variable in enum loci.formats.in.BaseZeissReader.DrawStyle
 
value - Variable in enum loci.formats.in.BaseZeissReader.FeatureType
 
value - Variable in enum loci.formats.in.BaseZeissReader.FillStyle
 
value - Variable in enum loci.formats.in.BaseZeissReader.LineEndPositions
 
value - Variable in enum loci.formats.in.BaseZeissReader.LineEndStyle
 
value - Variable in enum loci.formats.in.BaseZeissReader.PointStyle
 
value - Variable in class loci.formats.in.BaseZeissReader.Tag
 
value - Variable in enum loci.formats.in.BaseZeissReader.TextAlignment
 
VALUE - Static variable in class loci.formats.in.CellSensReader
 
value - Variable in class loci.formats.in.FEITiffReader.FEIHandler
 
VALUE - Static variable in class loci.formats.in.GatanReader
 
value - Variable in class loci.formats.in.ImaconReader.ImaconHandler
 
value - Variable in class loci.formats.in.IvisionReader.IvisionHandler
 
value(PrairieMetadata.Value) - Method in class loci.formats.in.PrairieMetadata
Returns value.value(), or null if value is null.
value(PrairieMetadata.Value, String) - Method in class loci.formats.in.PrairieMetadata
Returns value.get(key).value(), or null if value or value.get(key) is null.
value(PrairieMetadata.Value, int) - Method in class loci.formats.in.PrairieMetadata
Returns value.get(index).value(), or null if value or value.get(index) is null.
value() - Method in interface loci.formats.in.PrairieMetadata.Value
 
value - Variable in class loci.formats.in.PrairieMetadata.ValueItem
 
value() - Method in class loci.formats.in.PrairieMetadata.ValueItem
 
value() - Method in class loci.formats.in.PrairieMetadata.ValueTable
 
value - Variable in class loci.formats.in.ZeissTIFFHandler.Tag
 
value - Variable in class loci.formats.meta.OriginalMetadataAnnotation
 
value - Variable in class loci.plugins.prefs.BooleanOption
The option's current value.
value - Variable in class loci.plugins.prefs.DoubleOption
The option's current value.
value - Variable in class loci.plugins.prefs.StringOption
The option's current value.
valueChanged(ListSelectionEvent) - Method in class loci.plugins.config.ConfigWindow
 
valueCount - Variable in class loci.formats.tiff.TiffIFDEntry
The number of values, Count of the indicated Type.
ValueItem(String, String) - Constructor for class loci.formats.in.PrairieMetadata.ValueItem
 
valueOf(String) - Static method in enum loci.formats.codec.CompressionType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum loci.formats.codec.JPEG2000BoxType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum loci.formats.codec.JPEG2000SegmentMarker
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum loci.formats.in.BaseZeissReader.Charset
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum loci.formats.in.BaseZeissReader.Context
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum loci.formats.in.BaseZeissReader.DrawStyle
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum loci.formats.in.BaseZeissReader.FeatureType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum loci.formats.in.BaseZeissReader.FillStyle
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum loci.formats.in.BaseZeissReader.LineEndPositions
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum loci.formats.in.BaseZeissReader.LineEndStyle
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum loci.formats.in.BaseZeissReader.PointStyle
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum loci.formats.in.BaseZeissReader.TextAlignment
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum loci.formats.in.MetadataLevel
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum loci.formats.in.SPEReader.SpeHeaderEntry
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum loci.formats.in.SPEReader.SpeHeaderType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum loci.formats.tiff.IFDType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum loci.formats.tiff.PhotoInterp
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum loci.formats.tiff.TiffCompression
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum loci.plugins.in.ImportStep
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum loci.plugins.util.LibraryChecker.Library
Returns the enum constant of this type with the specified name.
valueOffset - Variable in class loci.formats.tiff.TiffIFDEntry
The Value Offset, the file offset (in bytes) of the Value for the field.
values() - Static method in enum loci.formats.codec.CompressionType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum loci.formats.codec.JPEG2000BoxType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum loci.formats.codec.JPEG2000SegmentMarker
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum loci.formats.in.BaseZeissReader.Charset
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum loci.formats.in.BaseZeissReader.Context
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum loci.formats.in.BaseZeissReader.DrawStyle
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum loci.formats.in.BaseZeissReader.FeatureType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum loci.formats.in.BaseZeissReader.FillStyle
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum loci.formats.in.BaseZeissReader.LineEndPositions
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum loci.formats.in.BaseZeissReader.LineEndStyle
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum loci.formats.in.BaseZeissReader.PointStyle
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum loci.formats.in.BaseZeissReader.TextAlignment
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum loci.formats.in.MetadataLevel
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum loci.formats.in.SPEReader.SpeHeaderEntry
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum loci.formats.in.SPEReader.SpeHeaderType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum loci.formats.tiff.IFDType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum loci.formats.tiff.PhotoInterp
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum loci.formats.tiff.TiffCompression
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum loci.plugins.in.ImportStep
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum loci.plugins.util.LibraryChecker.Library
Returns an array containing the constants of this enum type, in the order they are declared.
valuesByKey(Map<K, V>) - Method in class loci.formats.in.PrairieMetadata
Gets the values of the given map, sorted by key.
ValueTable() - Constructor for class loci.formats.in.PrairieMetadata.ValueTable
 
valueToIndex - Variable in class loci.formats.in.FakeReader
For indexed color, mapping from indices to values and vice versa.
variableList - Variable in class loci.formats.services.NetCDFServiceImpl
 
VarianFDFReader - Class in loci.formats.in
VarianFDFReader is the file format reader for Varian FDF files.
VarianFDFReader() - Constructor for class loci.formats.in.VarianFDFReader
Constructs a new Varian FDF reader.
VCLOCK_AMPLITUDE - Static variable in class loci.formats.in.CellSensReader
 
VCS_REVISION - Static variable in class loci.formats.FormatTools
Current VCS revision.
VCS_SHORT_REVISION - Static variable in class loci.formats.FormatTools
Deprecated.
Use the general FormatTools.VCS_REVISION field.
vector - Variable in class loci.formats.codec.ByteVector
 
VECTOR_DATA - Static variable in class loci.formats.in.CellSensReader
 
VECTOR_LAYER_VOLUME - Static variable in class loci.formats.in.CellSensReader
 
VectraReader - Class in loci.formats.in
VectraReader is the reader for PerkinElmer Vectra QPTIFF data
VectraReader() - Constructor for class loci.formats.in.VectraReader
Constructs a new Vectra reader.
VeecoReader - Class in loci.formats.in
VeecoReader is the file format reader for Veeco HDF files.
VeecoReader() - Constructor for class loci.formats.in.VeecoReader
Constructs a new Veeco reader.
VentanaReader - Class in loci.formats.in
VentanaReader is the file format reader for Ventana .bif files.
VentanaReader() - Constructor for class loci.formats.in.VentanaReader
Constructs a new Ventana reader.
VentanaReader.AreaOfInterest - Class in loci.formats.in
 
VentanaReader.Overlap - Class in loci.formats.in
 
VentanaReader.TIFFTile - Class in loci.formats.in
 
verifyMinimumPopulated(MetadataRetrieve) - Static method in class loci.formats.MetadataTools
Checks whether the given metadata object has the minimum metadata populated to successfully describe an Image.
verifyMinimumPopulated(MetadataRetrieve, int) - Static method in class loci.formats.MetadataTools
Checks whether the given metadata object has the minimum metadata populated to successfully describe the nth Image.
verifyOMENamespace(String) - Method in class loci.formats.services.OMEXMLServiceImpl
Ensures that an xmlns:ome element exists.
verifyOptions(Object) - Method in class loci.plugins.in.MainDialog
Ensures that the options dialog has no mutually exclusive options.
VERSION - Static variable in class loci.formats.FormatTools
Version number of this release.
version - Variable in class loci.formats.in.GatanReader
 
version - Variable in class loci.formats.in.LiFlimReader
 
VERSION - Static variable in class loci.formats.in.NDPIReader
 
version - Variable in class loci.formats.in.OpenlabReader
LIFF version (should be 2 or 5).
VERSION - Static variable in class loci.formats.Memoizer
Default file version.
version - Variable in class loci.plugins.config.ConfigWindow
 
version - Variable in class loci.plugins.config.LibraryEntry
 
VERSION_KEY - Static variable in class loci.formats.in.LiFlimReader
 
VERSION_NUMBER - Static variable in class loci.formats.in.CellSensReader
 
VERSION_PROPERTIES - Static variable in class loci.formats.FormatTools
 
versionChecking - Variable in class loci.formats.Memoizer
Boolean specifying whether to invalidate the memo file based upon mismatched major/minor version numbers.
versionMismatch() - Method in class loci.formats.Memoizer
Returns true if the version of the memo file as returned by Memoizer.Deser.loadReleaseVersion() and Memoizer.Deser.loadRevision() do not match the current version as specified by FormatTools.VERSION.
versionOne - Variable in class loci.formats.in.PictReader
Whether or not the file is PICT v1.
versionTwo - Variable in class loci.formats.in.ICSReader
Flag indicating whether current file is v2.0.
VERTICAL_CLOCK_VOLTAGE - Static variable in class loci.formats.in.FluoviewReader
 
VERTICAL_FLIP - Static variable in class loci.formats.in.FluoviewReader
 
VERTICAL_SHIFT_SPEED - Static variable in class loci.formats.in.FluoviewReader
 
VFF_MAGIC - Static variable in class loci.formats.in.MicroCTReader
 
vffs - Variable in class loci.formats.in.MicroCTReader
 
VG_MAGIC_STRING - Static variable in class loci.formats.in.VGSAMReader
 
VGSAMReader - Class in loci.formats.in
VGSAMReader is the file format reader for VG SAM .dti files.
VGSAMReader() - Constructor for class loci.formats.in.VGSAMReader
Constructs a new VG SAM reader.
VIEW_BROWSER - Static variable in class loci.plugins.in.ImporterOptions
 
VIEW_HYPERSTACK - Static variable in class loci.plugins.in.ImporterOptions
 
VIEW_IMAGE_5D - Static variable in class loci.plugins.in.ImporterOptions
 
VIEW_KEYS - Static variable in class loci.formats.in.ICSReader
 
VIEW_NONE - Static variable in class loci.plugins.in.ImporterOptions
 
VIEW_STANDARD - Static variable in class loci.plugins.in.ImporterOptions
 
VIEW_VIEW_5D - Static variable in class loci.plugins.in.ImporterOptions
 
virtualBox - Variable in class loci.plugins.in.MainDialog
 
VirtualImagePlus - Class in loci.plugins.util
Extension of ImagePlus that supports Bio-Formats-driven virtual stacks.
VirtualImagePlus(String, ImageStack) - Constructor for class loci.plugins.util.VirtualImagePlus
 
virtualReader - Variable in class loci.plugins.in.ImportProcess
 
VirtualReader - Class in loci.plugins.util
TODO
VirtualReader(IFormatReader) - Constructor for class loci.plugins.util.VirtualReader
 
VisitechReader - Class in loci.formats.in
VisitechReader is the file format reader for Visitech XYS files.
VisitechReader() - Constructor for class loci.formats.in.VisitechReader
 
vOffsetX - Variable in class loci.formats.in.LeicaSCNReader.Image
 
vOffsetY - Variable in class loci.formats.in.LeicaSCNReader.Image
 
VolocityClippingReader - Class in loci.formats.in
VolocityClippingReader is the file format reader for Volocity library clipping files.
VolocityClippingReader() - Constructor for class loci.formats.in.VolocityClippingReader
Constructs a new Volocity clipping reader.
VolocityReader - Class in loci.formats.in
VolocityReader is the file format reader for Volocity library files.
VolocityReader() - Constructor for class loci.formats.in.VolocityReader
Constructs a new Volocity reader.
VolocityReader.Stack - Class in loci.formats.in
 
voltage - Variable in class loci.formats.in.FV1000Reader.ChannelData
 
voltage - Variable in class loci.formats.in.GatanReader
 
voltage - Variable in class loci.formats.in.LeicaHandler.Detector
 
voltage - Variable in class loci.formats.in.LeicaReader.Detector
 
voltage - Variable in class loci.formats.in.MicromanagerReader.Position
 
voltage - Variable in class loci.formats.in.ND2Handler
 
voltage - Variable in class loci.formats.in.OIRReader.Detector
 
voltages - Variable in class loci.formats.in.FluoviewReader
 
VOLUME_INDEX - Static variable in class loci.formats.in.CellSensReader
 
volumeType - Variable in class loci.formats.in.OpenlabReader.PlaneInfo
 
voxelC - Variable in class loci.formats.in.FluoviewReader
Pixel dimensions for this file.
voxelHeight - Variable in class loci.formats.in.NiftiReader
 
voxelSizes - Variable in class loci.formats.in.BDVReader.BDVXMLHandler
 
voxelT - Variable in class loci.formats.in.FluoviewReader
Pixel dimensions for this file.
voxelUnit - Variable in class loci.formats.in.BDVReader.BDVXMLHandler
 
voxelWidth - Variable in class loci.formats.in.NiftiReader
 
voxelX - Variable in class loci.formats.in.FluoviewReader
Pixel dimensions for this file.
voxelX - Variable in class loci.formats.in.TCSReader
 
voxelY - Variable in class loci.formats.in.FluoviewReader
Pixel dimensions for this file.
voxelY - Variable in class loci.formats.in.TCSReader
 
voxelZ - Variable in class loci.formats.in.FluoviewReader
Pixel dimensions for this file.
voxelZ - Variable in class loci.formats.in.TCSReader
 
voxSz - Variable in class loci.formats.services.WlzServiceImpl
 
vPredictor - Variable in class loci.formats.codec.NikonCodecOptions
 
vPredictor - Variable in class loci.formats.in.NikonReader
 
vr - Variable in class loci.formats.in.DicomReader
 
vSizeX - Variable in class loci.formats.in.LeicaSCNReader.Image
 
vSizeY - Variable in class loci.formats.in.LeicaSCNReader.Image
 
vSpacingZ - Variable in class loci.formats.in.LeicaSCNReader.Image
 

W

wait(boolean) - Method in class loci.formats.gui.ImageViewer
Toggles wait cursor.
waitTime - Variable in class loci.formats.in.PrairieMetadata
The wait time of the acquisition.
warn(boolean, String) - Static method in class loci.plugins.BF
 
warnFile(PrairieMetadata.Sequence, int, int) - Method in class loci.formats.in.PrairieReader
Emits a warning about a missing <File>.
warnFilename(PrairieMetadata.Sequence, int, int) - Method in class loci.formats.in.PrairieReader
Emits a warning about a <File>'s missing filename.
warnFrame(PrairieMetadata.Sequence, int) - Method in class loci.formats.in.PrairieReader
Emits a warning about a missing <Frame>.
WARNING_COMMENT - Static variable in class loci.formats.out.OMETiffWriter
 
wasCanceled() - Method in class loci.plugins.in.ImportProcess
Gets whether the import process was canceled.
WAT_MAGIC_STRING - Static variable in class loci.formats.in.WATOPReader
 
WATOPReader - Class in loci.formats.in
WATOPReader is the file format reader for WA Technology .wat files.
WATOPReader() - Constructor for class loci.formats.in.WATOPReader
Constructs a new WA Technology reader.
wave - Variable in class loci.formats.in.MetamorphReader
 
wavelength - Variable in class loci.formats.in.CV7000Reader.LightSource
 
wavelength - Variable in class loci.formats.in.IvisionReader
 
wavelength - Variable in class loci.formats.in.LeicaHandler.Laser
 
WAVELENGTH - Static variable in class loci.formats.in.NDPIReader
 
wavelength - Variable in class loci.formats.in.NikonTiffReader
 
wavelength - Variable in class loci.formats.in.OIRReader.Laser
 
wavelength - Variable in class loci.formats.in.OpenlabReader.PlaneInfo
 
wavelength - Variable in class loci.formats.in.ZeissLSMReader.IlluminationChannel
 
wavelengths - Variable in class loci.formats.in.FV1000Reader
 
wavelengths - Variable in class loci.formats.in.IM3Reader.Spectrum
 
wavelengths - Variable in class loci.formats.in.MetamorphHandler
 
waveMax - Variable in class loci.formats.in.PrairieMetadata.PFile
wavelengthMax attribute of this <File>.
waveMin - Variable in class loci.formats.in.PrairieMetadata.PFile
wavelengthMin attribute of this <File>.
waveNames - Variable in class loci.formats.in.MetamorphReader
 
WB_MODE - Static variable in class loci.formats.in.CellSensReader
 
WB_PRESET_ID - Static variable in class loci.formats.in.CellSensReader
 
WB_PRESET_NAME - Static variable in class loci.formats.in.CellSensReader
 
wbg - Variable in class loci.formats.in.MRWReader
 
wc - Variable in class loci.formats.gui.DataConverter
 
wd - Variable in class loci.formats.in.OIRReader.Objective
 
WELL - Static variable in class loci.formats.in.CellH5Reader.CellH5Constants
 
well - Variable in class loci.formats.in.CellH5Reader.CellH5Coordinate
 
well - Variable in class loci.formats.in.FlexReader.FlexHandler
 
Well(int, int, int) - Constructor for class loci.formats.in.MetamorphTiffReader.Well
 
well - Variable in class loci.formats.in.MetamorphTiffReader.Well
 
well - Variable in class loci.formats.in.MIASReader.AnalysisFile
 
WELL - Static variable in class loci.formats.ResourceNamer
 
WELL_COORDS - Static variable in class loci.formats.in.MetamorphReader
 
wellCol - Variable in class loci.formats.in.InCellReader.MinimalInCellHandler
 
wellCols - Variable in class loci.formats.in.BDReader
 
wellCols - Variable in class loci.formats.in.InCellReader
 
wellColumns - Variable in class loci.formats.in.FlexReader
 
wellColumns - Variable in class loci.formats.in.MIASReader
 
wellColumns - Variable in class loci.formats.in.ScanrReader
 
wellCoordinates - Variable in class loci.formats.in.InCellReader
 
wellCount - Variable in class loci.formats.in.FlexReader
 
wellCount - Variable in class loci.formats.in.MetamorphTiffReader
 
wellCount - Variable in class loci.formats.in.ScanrReader
 
wellFiles - Variable in class loci.formats.in.CellWorxReader
 
wellIndex - Variable in class loci.formats.in.ScanrReader.ScanrHandler
 
WellInfo() - Constructor for class loci.formats.in.CellVoyagerReader.WellInfo
 
wellLabels - Variable in class loci.formats.in.BDReader
 
wellLabels - Variable in class loci.formats.in.ScanrReader
 
wellList - Variable in class loci.formats.in.BDReader
 
wellNumber - Variable in class loci.formats.in.FlexReader
Specifies the row and column index into 'flexFiles' for a given well.
wellNumber - Variable in class loci.formats.in.MIASReader
 
wellNumbers - Variable in class loci.formats.in.ScanrReader
 
wellRow - Variable in class loci.formats.in.InCellReader.MinimalInCellHandler
 
wellRows - Variable in class loci.formats.in.BDReader
 
wellRows - Variable in class loci.formats.in.FlexReader
 
wellRows - Variable in class loci.formats.in.InCellReader
 
wellRows - Variable in class loci.formats.in.ScanrReader
 
wells - Variable in class loci.formats.in.CellVoyagerReader
 
WHITE_BALANCE - Static variable in class loci.formats.tiff.IFD
 
WHITE_BALANCE_FINE - Static variable in class loci.formats.in.NikonReader
 
WHITE_BALANCE_RGB_COEFFS - Static variable in class loci.formats.in.DNGReader
 
WHITE_BALANCE_RGB_COEFFS - Static variable in class loci.formats.in.NikonReader
 
WHITE_POINT - Static variable in class loci.formats.tiff.IFD
 
whiteBalance - Variable in class loci.formats.in.DNGReader
 
whiteBalance - Variable in class loci.formats.in.NikonReader
 
wholeStackBuffer - Variable in class loci.formats.in.OBFReader.State
 
WIDE_FIELD - Static variable in class loci.formats.in.LegacyND2Reader
Modality types.
WIDER - Static variable in class loci.formats.in.CellSensReader
 
WIDER_ENABLED - Static variable in class loci.formats.in.CellSensReader
 
widgets - Variable in class loci.plugins.config.CellSensWidgets
 
widgets - Variable in class loci.plugins.config.FlexWidgets
 
widgets - Variable in class loci.plugins.config.FormatEntry
 
widgets - Variable in class loci.plugins.config.LIFWidgets
 
widgets - Variable in class loci.plugins.config.ND2Widgets
 
widgets - Variable in class loci.plugins.config.PictWidgets
 
widgets - Variable in class loci.plugins.config.QTWidgets
 
widgets - Variable in class loci.plugins.config.SDTWidgets
 
widgets - Variable in class loci.plugins.config.TiffDelegateWidgets
 
widgets - Variable in class loci.plugins.config.ZeissCZIWidgets
 
width - Variable in class loci.formats.codec.CodecOptions
Width, in pixels, of the image.
width - Variable in class loci.formats.in.BaseZeissReader.Shape
 
width - Variable in class loci.formats.in.CellSensReader.Pyramid
 
width - Variable in class loci.formats.in.CellVoyagerReader.AreaInfo
 
width - Variable in class loci.formats.in.CellVoyagerReader.ChannelInfo
 
width - Variable in class loci.formats.in.OpenlabReader.PlaneInfo
 
width - Variable in class loci.formats.in.SDTInfo
 
width - Variable in class loci.formats.out.LegacyQTWriter
Frame width.
width - Variable in class loci.formats.tools.AmiraParameters
 
WINDOW_CENTER - Static variable in class loci.formats.in.DicomReader
 
WINDOW_WIDTH - Static variable in class loci.formats.in.DicomReader
 
windowActivated(WindowEvent) - Method in class loci.formats.gui.ImageViewer
 
windowClosed(WindowEvent) - Method in class loci.formats.gui.ImageViewer
 
windowClosing(WindowEvent) - Method in class loci.formats.gui.ImageViewer
 
windowDeactivated(WindowEvent) - Method in class loci.formats.gui.ImageViewer
 
windowDeiconified(WindowEvent) - Method in class loci.formats.gui.ImageViewer
 
windowIconified(WindowEvent) - Method in class loci.formats.gui.ImageViewer
 
windowlessBox - Variable in class loci.plugins.config.ConfigWindow
 
windowOpened(WindowEvent) - Method in class loci.formats.gui.ImageViewer
 
WindowTools - Class in loci.plugins.util
Utility methods for managing ImageJ dialogs and windows.
WindowTools() - Constructor for class loci.plugins.util.WindowTools
 
withinPixels(long) - Method in class loci.formats.in.SlidebookReader
 
wlz - Variable in class loci.formats.in.WlzReader
 
wlz - Variable in class loci.formats.out.WlzWriter
 
WLZ_ORG_LABEL - Static variable in class loci.formats.services.WlzServiceImpl
 
WLZ_SERVICE_READ - Static variable in class loci.formats.services.WlzServiceImpl
 
WLZ_SERVICE_UNKNOWN - Static variable in class loci.formats.services.WlzServiceImpl
 
WLZ_SERVICE_WRITE - Static variable in class loci.formats.services.WlzServiceImpl
 
wlzFP - Variable in class loci.formats.services.WlzServiceImpl
 
wlzObj - Variable in class loci.formats.services.WlzServiceImpl
 
WlzReader - Class in loci.formats.in
WlzReader is a file format reader for Woolz files.
WlzReader() - Constructor for class loci.formats.in.WlzReader
 
WlzService - Interface in loci.formats.services
 
WlzServiceImpl - Class in loci.formats.services
 
WlzServiceImpl() - Constructor for class loci.formats.services.WlzServiceImpl
 
wlzVersion - Variable in class loci.formats.services.WlzServiceImpl
 
WlzWriter - Class in loci.formats.out
WlzWriter is the file format writer for Woolz files.
WlzWriter() - Constructor for class loci.formats.out.WlzWriter
 
WORKING_DISTANCE - Static variable in class loci.formats.in.CellSensReader
 
workingDistance - Variable in class loci.formats.in.CellSensReader.Pyramid
 
workingDistance - Variable in class loci.formats.in.FV1000Reader
 
workingDistance - Variable in class loci.formats.in.LEOReader
 
workingDistance - Variable in class loci.formats.in.NikonTiffReader
 
WPIHandler() - Constructor for class loci.formats.in.CV7000Reader.WPIHandler
 
wppPath - Variable in class loci.formats.in.CV7000Reader
 
WrappedCodec - Class in loci.formats.codec
Generic wrapper for codecs from ome-codecs.
WrappedCodec(Codec) - Constructor for class loci.formats.codec.WrappedCodec
Construct with a codec implementation to wrap.
WrappedReader - Class in loci.formats
Helper class for readers which wrap other readers.
WrappedReader(String, String[]) - Constructor for class loci.formats.WrappedReader
Constructs a new wrapped reader with the given name and suffixes.
write(int, int) - Method in class loci.formats.codec.BitWriter
Deprecated.
Writes the given value using the given number of bits.
write(String) - Method in class loci.formats.codec.BitWriter
Deprecated.
Writes the bits represented by a bit string to the buffer.
write(Kryo, Output) - Method in class loci.formats.services.NetCDFServiceImpl
 
write(char[], int, int) - Method in class loci.plugins.config.TextAreaWriter
Writes the given characters to the associated text area component.
WRITE_TIME - Static variable in class loci.formats.in.NDPIReader
 
writeArraySlice(String, MDByteArray, long[]) - Method in interface loci.formats.services.JHDFService
Writes an array as sub-slice into an existing HDF5 dataset
writeArraySlice(String, MDShortArray, long[]) - Method in interface loci.formats.services.JHDFService
Writes an array as sub-slice into an existing HDF5 dataset
writeArraySlice(String, MDIntArray, long[]) - Method in interface loci.formats.services.JHDFService
Writes an array as sub-slice into an existing HDF5 dataset
writeArraySlice(String, MDByteArray, long[]) - Method in class loci.formats.services.JHDFServiceImpl
 
writeArraySlice(String, MDShortArray, long[]) - Method in class loci.formats.services.JHDFServiceImpl
 
writeArraySlice(String, MDIntArray, long[]) - Method in class loci.formats.services.JHDFServiceImpl
 
writeAtom(int, String) - Method in class loci.formats.out.QTWriter
Write the atom length and type.
writeBox - Variable in class loci.formats.codec.JPEG2000CodecOptions
Whether or not to write a boxed stream, i.e.
writeData(String, CoreMetadata, String, OMETiffWriter) - Method in class loci.formats.tools.MakeTestOmeTiff
 
writeFCTL(int, int) - Method in class loci.formats.out.APNGWriter
 
writeFooter() - Method in class loci.formats.out.APNGWriter
 
writeFooter() - Method in class loci.formats.out.JavaWriter
 
writeFooter() - Method in class loci.formats.out.QTWriter
 
writeHeader() - Method in class loci.formats.out.EPSWriter
 
writeHeader() - Method in class loci.formats.out.JavaWriter
 
writeHeader() - Method in class loci.formats.tiff.TiffSaver
Writes the TIFF file header.
writeIFD(IFD, long) - Method in class loci.formats.tiff.TiffSaver
 
writeIFDStrips(IFD, int, byte[][], int, boolean, int, int, long) - Method in class loci.formats.tiff.TiffSaver
 
writeIFDValue(RandomAccessOutputStream, long, int, Object) - Method in class loci.formats.tiff.TiffSaver
Writes the given IFD value to the given output object.
writeImage(OutputStream, BufferedImage, JPEG2000CodecOptions) - Method in interface loci.formats.services.JAIIIOService
Writes an image using JAI Image I/O using the JPEG 2000 codec.
writeImage(OutputStream, BufferedImage, JPEG2000CodecOptions) - Method in class loci.formats.services.JAIIIOServiceImpl
 
writeImage(byte[][], IFDList, int) - Method in class loci.formats.tiff.TiffSaver
 
writeImage(byte[], IFD, int, int, boolean) - Method in class loci.formats.tiff.TiffSaver
 
writeImage(byte[], IFD, int, int, int, int, int, int, boolean) - Method in class loci.formats.tiff.TiffSaver
Writes to any rectangle from the passed block.
writeImage(byte[], IFD, int, int, int, int, int, int, boolean, Integer, boolean) - Method in class loci.formats.tiff.TiffSaver
 
writeImageIFD(IFD, int, byte[][], int, boolean, int, int) - Method in class loci.formats.tiff.TiffSaver
Performs the actual work of dealing with IFD data and writing it to the TIFF for a given image or sub-image.
writeIntValue(RandomAccessOutputStream, long) - Method in class loci.formats.tiff.TiffSaver
Write the given value to the given RandomAccessOutputStream.
writePixels(String, byte[], int, int, int, int) - Method in class loci.formats.out.APNGWriter
 
writePlane(String, byte[], int, int) - Method in class loci.formats.out.JavaWriter
 
writePlane(String, short[], int, int) - Method in class loci.formats.out.JavaWriter
 
writePlane(String, int[], int, int) - Method in class loci.formats.out.JavaWriter
 
writePlane(String, long[], int, int) - Method in class loci.formats.out.JavaWriter
 
writePlane(String, float[], int, int) - Method in class loci.formats.out.JavaWriter
 
writePlane(String, double[], int, int) - Method in class loci.formats.out.JavaWriter
 
writePLTE() - Method in class loci.formats.out.APNGWriter
 
writer - Variable in class loci.formats.codec.BitWriter
Deprecated.
 
writer - Variable in class loci.formats.gui.DataConverter
 
writer - Variable in class loci.formats.WriterWrapper
FormatWriter used to write the file.
writeRotationMatrix() - Method in class loci.formats.out.QTWriter
Write the 3x3 matrix that describes how to rotate the image.
writers - Variable in class loci.formats.ImageWriter
List of supported file format writers.
WriterWrapper - Class in loci.formats
Abstract superclass of writer logic that wraps other writers.
WriterWrapper() - Constructor for class loci.formats.WriterWrapper
Constructs a writer wrapper around a new image writer.
WriterWrapper(IFormatWriter) - Constructor for class loci.formats.WriterWrapper
Constructs a writer wrapper around the given writer.
writeSummary(IRandomAccess, String) - Method in class loci.formats.in.IM3Reader.ContainerRecord
 
writeSummary(IRandomAccess, String) - Method in class loci.formats.in.IM3Reader.FloatIM3Record
 
writeSummary(IRandomAccess, String) - Method in class loci.formats.in.IM3Reader.IM3Record
Write a summary of the contents of the record
writeSummary(IRandomAccess, String) - Method in class loci.formats.in.IM3Reader.IntIM3Record
 
writeSummary(IRandomAccess, String) - Method in class loci.formats.in.IM3Reader.StringIM3Record
 
writeSummary() - Method in class loci.formats.in.IM3Reader
Write a summary of each field in the IM3 file to the writer
written - Variable in class loci.formats.ome.OMEPyramidStore
 
wSize - Variable in class loci.formats.in.DeltavisionReader
Size of one wave in the extended header.

X

x - Variable in class loci.formats.in.BioRadReader.Note
 
x - Variable in class loci.formats.in.CellVoyagerReader.FieldInfo
 
x - Variable in class loci.formats.in.InCellReader
 
x - Variable in class loci.formats.in.LeicaHandler.ROI
 
x - Variable in class loci.formats.in.LIFReader.ROI
 
x - Variable in class loci.formats.in.OperettaReader.Plane
 
x - Variable in class loci.formats.in.VentanaReader.Overlap
 
x - Variable in class loci.formats.in.ZeissCZIReader.SubBlock
 
x - Variable in class loci.formats.ome.OMEPyramidStore.Resolution
 
x - Variable in class loci.formats.TileStitcher.TileCoordinate
 
x0 - Variable in class loci.formats.tools.AmiraParameters
 
x1 - Variable in class loci.formats.in.BaseZeissReader.Shape
 
x1 - Variable in class loci.formats.in.GatanReader.ROIShape
 
x1 - Variable in class loci.formats.tools.AmiraParameters
 
x2 - Variable in class loci.formats.in.BaseZeissReader.Shape
 
x2 - Variable in class loci.formats.in.GatanReader.ROIShape
 
X_BINNING - Static variable in class loci.formats.in.CellSensReader
 
X_IMG_STRING - Static variable in class loci.formats.in.SDTInfo
 
X_KEY - Static variable in class loci.formats.in.LiFlimReader
 
X_POS_TAG - Static variable in class loci.formats.in.SlidebookTiffReader
 
X_POSITION - Static variable in class loci.formats.in.NDPIReader
 
X_POSITION - Static variable in class loci.formats.tiff.IFD
 
X_RESOLUTION - Static variable in class loci.formats.tiff.IFD
 
X_STRING - Static variable in class loci.formats.in.SDTInfo
 
xAxis - Variable in class loci.formats.in.SDTInfo
X axis representation (SPC-930).
xcal - Variable in class loci.formats.in.OpenlabReader
 
xCoordinates - Variable in class loci.formats.in.ZeissLSMReader
 
xDim - Variable in class loci.formats.out.AVIWriter
 
xIndex - Variable in class loci.formats.in.TextReader
Column index for X coordinate.
xLen - Variable in class loci.formats.in.LiFlimReader
 
xLocation - Variable in class loci.formats.in.VolocityReader.Stack
 
XML - Static variable in class loci.formats.in.MicromanagerReader
Optional file containing additional acquisition parameters.
xml - Variable in class loci.formats.in.ZeissCZIReader.Metadata
 
xml - Variable in class loci.plugins.util.DataBrowser
 
XML_FILE - Static variable in class loci.formats.in.ColumbusReader
 
XML_FILE - Static variable in class loci.formats.in.ScanrReader
 
XML_FILES - Static variable in class loci.formats.in.OperettaReader
 
XML_NAME - Static variable in class loci.formats.in.ZeissTIFFReader
 
XML_SUFFIX - Static variable in class loci.formats.in.PrairieReader
 
XML_SUFFIX - Static variable in class loci.formats.in.TCSReader
 
XML_TAG - Static variable in class loci.formats.in.ImaconReader
 
XML_TAG - Static variable in class loci.formats.in.OperettaReader
 
XML_TAG - Static variable in class loci.formats.in.VentanaReader
 
xmlBuffer - Variable in class loci.formats.in.BDVReader.BDVXMLHandler
 
xmlBuffer - Variable in class loci.formats.in.OMEXMLReader.OMEXMLHandler
 
XMLCellRenderer - Class in loci.formats.gui
A tree cell renderer for displaying syntax highlighted XML in a JTree.
XMLCellRenderer() - Constructor for class loci.formats.gui.XMLCellRenderer
 
XMLCellRenderer.XMLItem - Class in loci.formats.gui
Cell renderer item for use as DefaultMutableTreeNode user object.
xmlFile - Variable in class loci.formats.in.MicromanagerReader.Position
 
xmlFile - Variable in class loci.formats.in.PrairieReader
The associated XML files.
xmlFile - Variable in class loci.formats.in.TCSReader
 
xmlFiles - Variable in class loci.formats.in.APLReader
 
xmlFragments - Variable in class loci.formats.out.OMEXMLWriter
 
XMLItem(Node) - Constructor for class loci.formats.gui.XMLCellRenderer.XMLItem
 
xmlname - Variable in class loci.formats.in.ZeissTIFFReader.TIFFInfo
 
XMLWindow - Class in loci.formats.gui
A window containing syntax highlighted XML as a tree.
XMLWindow() - Constructor for class loci.formats.gui.XMLWindow
 
XMLWindow(String) - Constructor for class loci.formats.gui.XMLWindow
 
xmlWindow - Variable in class loci.plugins.in.DisplayHandler
 
xoff - Variable in class loci.formats.tools.MakeTestOmeTiff.TextLine
 
xOffset - Variable in class loci.formats.in.NativeND2Reader
 
xor(int) - Method in class loci.plugins.util.RecordedImageProcessor
 
xOrigin - Variable in class loci.formats.in.TiffReader
 
xOrigin - Variable in class loci.formats.in.VentanaReader.AreaOfInterest
 
xPad - Variable in class loci.formats.out.AVIWriter
 
xpixels - Variable in class loci.formats.in.CellVoyagerReader.FieldInfo
 
xpos - Variable in class loci.formats.in.CV7000Reader.Plane
 
xPos - Variable in class loci.formats.in.LeicaHandler
 
xPos - Variable in class loci.formats.in.OpenlabReader
 
xPositions - Variable in class loci.formats.in.FlexReader
 
xSize - Variable in class loci.formats.in.CV7000Reader.Channel
 
xSize - Variable in class loci.formats.in.LEOReader
 
xSize - Variable in class loci.formats.in.QuesantReader
 
xSizes - Variable in class loci.formats.in.FlexReader
 
XSLT_2003FC - Static variable in class loci.formats.services.OMEXMLServiceImpl
 
XSLT_200706 - Static variable in class loci.formats.services.OMEXMLServiceImpl
 
XSLT_200802 - Static variable in class loci.formats.services.OMEXMLServiceImpl
 
XSLT_200809 - Static variable in class loci.formats.services.OMEXMLServiceImpl
 
XSLT_200909 - Static variable in class loci.formats.services.OMEXMLServiceImpl
 
XSLT_201004 - Static variable in class loci.formats.services.OMEXMLServiceImpl
 
XSLT_201006 - Static variable in class loci.formats.services.OMEXMLServiceImpl
 
XSLT_201106 - Static variable in class loci.formats.services.OMEXMLServiceImpl
 
XSLT_201206 - Static variable in class loci.formats.services.OMEXMLServiceImpl
 
XSLT_201306 - Static variable in class loci.formats.services.OMEXMLServiceImpl
 
XSLT_201501 - Static variable in class loci.formats.services.OMEXMLServiceImpl
 
XSLT_PATH - Static variable in class loci.formats.services.OMEXMLServiceImpl
 
xTiles - Variable in class loci.formats.in.DeltavisionReader
Number of tiles in X direction.
xTiles - Variable in class loci.formats.services.JPEGTurboServiceImpl
 
xyGain - Variable in class loci.formats.in.SDTInfo
Gain for XY ADCs (SPC930).
xyw(CellConstraints, int, int, int) - Method in class loci.plugins.in.MainDialog
Convenience method for creating a left-aligned, vertically centered cell constraints object.

Y

y - Variable in class loci.formats.in.BioRadReader.Note
 
y - Variable in class loci.formats.in.CellVoyagerReader.FieldInfo
 
y - Variable in class loci.formats.in.InCellReader
 
y - Variable in class loci.formats.in.LeicaHandler.ROI
 
y - Variable in class loci.formats.in.LIFReader.ROI
 
y - Variable in class loci.formats.in.OperettaReader.Plane
 
y - Variable in class loci.formats.in.VentanaReader.Overlap
 
y - Variable in class loci.formats.in.ZeissCZIReader.SubBlock
 
y - Variable in class loci.formats.ome.OMEPyramidStore.Resolution
 
y - Variable in class loci.formats.TileStitcher.TileCoordinate
 
y0 - Variable in class loci.formats.tools.AmiraParameters
 
y1 - Variable in class loci.formats.in.BaseZeissReader.Shape
 
y1 - Variable in class loci.formats.in.GatanReader.ROIShape
 
y1 - Variable in class loci.formats.tools.AmiraParameters
 
y2 - Variable in class loci.formats.in.BaseZeissReader.Shape
 
y2 - Variable in class loci.formats.in.GatanReader.ROIShape
 
Y8 - Static variable in class loci.formats.in.AVIReader
 
Y_BINNING - Static variable in class loci.formats.in.CellSensReader
 
Y_CB_CR_COEFFICIENTS - Static variable in class loci.formats.tiff.IFD
 
Y_CB_CR_POSITIONING - Static variable in class loci.formats.tiff.IFD
 
Y_CB_CR_SUB_SAMPLING - Static variable in class loci.formats.tiff.IFD
 
Y_DIMENSION_UNIT - Static variable in class loci.formats.in.CellSensReader
 
Y_IMG_STRING - Static variable in class loci.formats.in.SDTInfo
 
Y_KEY - Static variable in class loci.formats.in.LiFlimReader
 
Y_PLANE_DIMENSION_UNIT - Static variable in class loci.formats.in.CellSensReader
 
Y_POS_TAG - Static variable in class loci.formats.in.SlidebookTiffReader
 
Y_POSITION - Static variable in class loci.formats.in.NDPIReader
 
Y_POSITION - Static variable in class loci.formats.tiff.IFD
 
Y_RESOLUTION - Static variable in class loci.formats.tiff.IFD
 
Y_STRING - Static variable in class loci.formats.in.SDTInfo
 
ycal - Variable in class loci.formats.in.OpenlabReader
 
ycbcr - Variable in class loci.formats.codec.CodecOptions
Whether or not the decompressed data will be stored as YCbCr.
ycbcrCorrection - Variable in class loci.formats.tiff.TiffParser
 
yCoordinates - Variable in class loci.formats.in.ZeissLSMReader
 
yDim - Variable in class loci.formats.out.AVIWriter
 
YEAR - Static variable in class loci.formats.FormatTools
Year in which this release was built.
yIndex - Variable in class loci.formats.in.TextReader
Column index for Y coordinate.
yLen - Variable in class loci.formats.in.LiFlimReader
 
yLocation - Variable in class loci.formats.in.VolocityReader.Stack
 
yOffset - Variable in class loci.formats.in.NativeND2Reader
 
yOrigin - Variable in class loci.formats.in.TiffReader
 
yOrigin - Variable in class loci.formats.in.VentanaReader.AreaOfInterest
 
ypad - Variable in class loci.formats.tools.MakeTestOmeTiff.TextLine
 
ypixels - Variable in class loci.formats.in.CellVoyagerReader.FieldInfo
 
ypos - Variable in class loci.formats.in.CV7000Reader.Plane
 
yPos - Variable in class loci.formats.in.LeicaHandler
 
yPos - Variable in class loci.formats.in.OpenlabReader
 
yPositions - Variable in class loci.formats.in.FlexReader
 
ySize - Variable in class loci.formats.in.CV7000Reader.Channel
 
ySizes - Variable in class loci.formats.in.FlexReader
 
yTiles - Variable in class loci.formats.in.DeltavisionReader
Number of tiles in Y direction.
yTiles - Variable in class loci.formats.services.JPEGTurboServiceImpl
 

Z

Z - Static variable in class loci.formats.in.CellSensReader
 
z - Variable in class loci.formats.in.CV7000Reader.Plane
 
z - Variable in class loci.formats.in.LeicaSCNReader.Dimension
 
z - Variable in class loci.formats.in.MicromanagerReader.Index
 
z - Variable in class loci.formats.in.OperettaReader.Plane
 
z0 - Variable in class loci.formats.tools.AmiraParameters
 
z1 - Variable in class loci.formats.tools.AmiraParameters
 
Z_AXIS - Static variable in class loci.formats.AxisGuesser
Axis type for focal planes.
Z_INCREMENT - Static variable in class loci.formats.in.CellSensReader
 
Z_KEY - Static variable in class loci.formats.in.LiFlimReader
 
Z_NUM - Static variable in class loci.formats.FormatTools
 
Z_POS_TAG - Static variable in class loci.formats.in.SlidebookTiffReader
 
Z_POSITION - Static variable in class loci.formats.in.NDPIReader
 
Z_PREFIXES - Static variable in class loci.formats.AxisGuesser
Prefixes indicating space dimension.
Z_START - Static variable in class loci.formats.in.CellSensReader
 
Z_VALUE - Static variable in class loci.formats.in.CellSensReader
 
zBegin - Variable in class loci.plugins.in.ImporterOptions
 
zChoice - Variable in class loci.formats.gui.DataConverter
 
zChoice - Variable in class loci.plugins.in.SwapDialog
 
zCoordinates - Variable in class loci.formats.in.ZeissLSMReader
 
zCount - Variable in class loci.formats.in.CellSensReader
 
zctLabel - Variable in class loci.formats.gui.PreviewPane
Labels containing thumbnail and dimensional information.
zctText - Variable in class loci.formats.gui.PreviewPane
 
zctTip - Variable in class loci.formats.gui.PreviewPane
 
zDim - Variable in class loci.formats.out.AVIWriter
 
zDistances - Variable in class loci.formats.in.MetamorphReader
 
ZEISS_ID - Static variable in class loci.formats.in.ZeissLSMReader
Tag identifying a Zeiss LSM file.
ZeissCZIReader - Class in loci.formats.in
ZeissCZIReader is the file format reader for Zeiss .czi files.
ZeissCZIReader() - Constructor for class loci.formats.in.ZeissCZIReader
Constructs a new Zeiss .czi reader.
ZeissCZIReader.Attachment - Class in loci.formats.in
Segment with ID "ZISRAWATTACH".
ZeissCZIReader.AttachmentDirectory - Class in loci.formats.in
Segment with ID "ZISRAWATTDIR".
ZeissCZIReader.AttachmentEntry - Class in loci.formats.in
 
ZeissCZIReader.Channel - Class in loci.formats.in
 
ZeissCZIReader.Coordinate - Class in loci.formats.in
 
ZeissCZIReader.DimensionEntry - Class in loci.formats.in
 
ZeissCZIReader.Directory - Class in loci.formats.in
Segment with ID "ZISRAWDIRECTORY".
ZeissCZIReader.DirectoryEntry - Class in loci.formats.in
 
ZeissCZIReader.FileHeader - Class in loci.formats.in
Segment with ID "ZISRAWFILE".
ZeissCZIReader.Metadata - Class in loci.formats.in
Segment with ID "ZISRAWMETADATA".
ZeissCZIReader.Segment - Class in loci.formats.in
Top-level class that implements logic common to all types of Segment.
ZeissCZIReader.SubBlock - Class in loci.formats.in
Segment with ID "ZISRAWSUBBLOCK".
ZeissCZIWidgets - Class in loci.plugins.config
Custom widgets for configuring Bio-Formats Zeiss CZI support.
ZeissCZIWidgets() - Constructor for class loci.plugins.config.ZeissCZIWidgets
 
ZeissLMSReader - Class in loci.formats.in
Zeiss LMS reader for data from Zeiss CSM 700 systems.
ZeissLMSReader() - Constructor for class loci.formats.in.ZeissLMSReader
Constructs a new LMS reader.
ZeissLSMReader - Class in loci.formats.in
ZeissLSMReader is the file format reader for Zeiss LSM files.
ZeissLSMReader() - Constructor for class loci.formats.in.ZeissLSMReader
Constructs a new Zeiss LSM reader.
ZeissLSMReader.BeamSplitter - Class in loci.formats.in
 
ZeissLSMReader.DataChannel - Class in loci.formats.in
 
ZeissLSMReader.DetectionChannel - Class in loci.formats.in
 
ZeissLSMReader.IlluminationChannel - Class in loci.formats.in
 
ZeissLSMReader.Laser - Class in loci.formats.in
 
ZeissLSMReader.Marker - Class in loci.formats.in
 
ZeissLSMReader.Recording - Class in loci.formats.in
 
ZeissLSMReader.SubBlock - Class in loci.formats.in
 
ZeissLSMReader.Timer - Class in loci.formats.in
 
ZeissLSMReader.Track - Class in loci.formats.in
 
ZeissTIFFHandler - Class in loci.formats.in
SAX handler for parsing XML in Zeiss TIFF files.
ZeissTIFFHandler(ZeissTIFFReader) - Constructor for class loci.formats.in.ZeissTIFFHandler
 
ZeissTIFFHandler.Plane - Class in loci.formats.in
Metadata for a single image plane.
ZeissTIFFHandler.Scaling - Class in loci.formats.in
Scaling metadata.
ZeissTIFFHandler.Scaling.Dimension - Class in loci.formats.in
Scaling information for a single dimension.
ZeissTIFFHandler.Tag - Class in loci.formats.in
Content of a single tag from a Tags block.
ZeissTIFFHandler.TagSet - Class in loci.formats.in
A collection of tags from a single Tags block.
ZeissTIFFReader - Class in loci.formats.in
ZeissTIFFReader is the file format reader for Zeiss AxioVision TIFF files and their companion XML file.
ZeissTIFFReader() - Constructor for class loci.formats.in.ZeissTIFFReader
 
ZeissTIFFReader.Plane - Class in loci.formats.in
 
ZeissTIFFReader.TIFFInfo - Class in loci.formats.in
 
ZeissZVIReader - Class in loci.formats.in
ZeissZVIReader is the file format reader for Zeiss ZVI files.
ZeissZVIReader() - Constructor for class loci.formats.in.ZeissZVIReader
Constructs a new ZeissZVI reader.
zEnd - Variable in class loci.plugins.in.ImporterOptions
 
zeroes - Variable in class loci.formats.FilePatternBlock
The number of leading zeroes.
zIncrement - Variable in class loci.formats.in.CellSensReader.Pyramid
 
zIndices - Variable in class loci.formats.in.BaseZeissReader
 
ZIP - Static variable in class loci.formats.in.PhotoshopTiffReader
 
ZipReader - Class in loci.formats.in
Reader for Zip files.
ZipReader() - Constructor for class loci.formats.in.ZipReader
 
zLabel - Variable in class loci.formats.gui.DataConverter
 
zLen - Variable in class loci.formats.in.LiFlimReader
 
ZlibCodec - Class in loci.formats.codec
This class implements ZLIB decompression.
ZlibCodec() - Constructor for class loci.formats.codec.ZlibCodec
 
zLocation - Variable in class loci.formats.in.VolocityReader.Stack
 
zMapFile - Variable in class loci.formats.in.CellWorxReader
 
zOffset - Variable in class loci.formats.in.NativeND2Reader
 
zoom - Variable in class loci.formats.in.LeicaHandler.Detector
 
zoom - Variable in class loci.formats.in.LeicaHandler
 
zoom - Variable in class loci.formats.in.MetamorphHandler
 
zoom - Variable in class loci.formats.in.MetamorphReader
 
zoom - Variable in class loci.formats.in.ZeissCZIReader
 
zoom - Variable in class loci.formats.in.ZeissLSMReader
 
zooms - Variable in class loci.formats.in.LIFReader
 
ZPO_SUFFIX - Static variable in class loci.formats.in.PerkinElmerReader
 
zpos - Variable in class loci.formats.in.CV7000Reader.Plane
 
zPos - Variable in class loci.formats.in.LeicaHandler
 
zPos - Variable in class loci.formats.in.OpenlabReader
 
zPosition - Variable in class loci.formats.in.InCellReader.Image
 
zPosition - Variable in class loci.formats.in.InCellReader.InCellHandler
 
zPosition - Variable in class loci.formats.in.OpenlabReader.PlaneInfo
 
zPosition - Variable in class loci.formats.in.SVSReader
 
zPositions - Variable in class loci.formats.in.FluoviewReader
 
zPositions - Variable in class loci.formats.in.MetamorphHandler
 
zs - Variable in class loci.formats.in.ND2Handler
 
zScroll - Variable in class loci.plugins.util.DataBrowser
 
zSize - Variable in class loci.formats.in.DeltavisionReader
Size of one z section in the extended header.
zSlider - Variable in class loci.formats.gui.ImageViewer
 
zStart - Variable in class loci.formats.in.CellSensReader.Pyramid
 
zStart - Variable in class loci.formats.in.MetamorphReader
 
zStep - Variable in class loci.formats.in.ZeissCZIReader
 
zStep - Variable in class loci.plugins.in.ImporterOptions
 
zSteps - Variable in class loci.formats.in.LIFReader
 
zValues - Variable in class loci.formats.in.CellSensReader.Pyramid
 
ZVI_MAGIC_BYTES - Static variable in class loci.formats.in.ZeissZVIReader
 
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