A B C D E F G H I J K L M N O P Q R S T U V W X Y Z

## 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.Channel
acqType - Variable in class loci.formats.in.OperettaReader.Plane
acquire - Variable in class loci.formats.in.ZeissLSMReader.SubBlock
acquiredDate - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataTempBuffer
acquiredDate - Variable in class loci.formats.in.LIFReader
acquiredDate - Variable in class loci.formats.in.ZeissCZIReader
acquiredDate - Variable in class loci.formats.in.ZeissLSMReader
acquiredWells - Variable in class loci.formats.in.CV7000Reader
ACQUISITION_CYCLE_TIME - Static variable in class loci.formats.in.FluoviewReader
ACQUISITION_FILE - Static variable in class loci.formats.in.ScanrReader
ACQUISITION_PROPERTIES - Static variable in class loci.formats.in.CellSensReader
ACQUISITION_TIME_TAG - Static variable in class loci.formats.in.FlowSightReader
acquisitionDate - Variable in class loci.formats.in.BaseZeissReader
acquisitionDate - Variable in class loci.formats.in.BioRadSCNReader
acquisitionDate - Variable in class loci.formats.in.ColumbusReader
acquisitionDate - Variable in class loci.formats.in.OIRReader
acquisitionDate - Variable in class loci.formats.in.SISReader
acquisitionDates - Variable in class loci.formats.in.FlexReader
acquisitionMode - Variable in class loci.formats.in.ZeissCZIReader.Channel
acquisitions - Variable in class loci.formats.in.ZeissCZIReader
acquisitionTime - Variable in class loci.formats.in.CellSensReader.Pyramid
act - Variable in class loci.formats.in.GIFReader
  Active color table.
actionIndex - Variable in class loci.formats.in.CV7000Reader.Channel
actionIndex - Variable in class loci.formats.in.CV7000Reader.MeasurementSettingsHandler
actionIndex - Variable in class loci.formats.in.CV7000Reader.Plane
actionPerformed(ActionEvent) - Method in class loci.formats.gui.CacheComponent
  Handles combo box changes.
actionPerformed(ActionEvent) - Method in class loci.formats.gui.DataConverter
actionPerformed(ActionEvent) - Method in class loci.formats.gui.ImageViewer
  Handles menu commands.
actionPerformed(ActionEvent) - Method in class loci.formats.tools.EditTiffG
actionPerformed(ActionEvent) - Method in class loci.plugins.config.ConfigWindow
actionPerformed(ActionEvent) - Method in class loci.plugins.in.SeriesDialog
actionPerformed(ActionEvent) - Method in class loci.plugins.shortcut.ShortcutPanel
  Handles button presses.
actionPerformed(ActionEvent) - Method in class loci.plugins.util.DataBrowser
actionPerformed(ActionEvent) - Method in class loci.plugins.util.SearchableWindow
actionPerformed(ActionEvent) - Method in class loci.plugins.util.SearchableWindow.SearchBox
active - Variable in class loci.formats.in.FV1000Reader.ChannelData
active - Variable in class loci.formats.in.LeicaHandler.Detector
active - Variable in class loci.formats.in.LeicaReader.Detector
ACTIVE_CHANNEL - Static variable in class loci.formats.in.CellSensReader
ACTIVE_LAYER_INDEX_VECTOR - Static variable in class loci.formats.in.CellSensReader
ACTIVE_LAYER_VECTOR - Static variable in class loci.formats.in.CellSensReader
ACTIVE_STACK_DIMENSION - Static variable in class loci.formats.in.CellSensReader
activeChannel - Variable in class loci.formats.in.OperettaReader.OperettaHandler
activeChannelIndices - Variable in class loci.formats.in.LeicaReader
activeChannels - Variable in class loci.formats.in.PrairieMetadata
  Set of active channel indices.
activeDetector - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataTempBuffer
activeDetector - Variable in class loci.formats.in.LIFReader
activePlane - Variable in class loci.formats.in.OperettaReader.OperettaHandler
ACTUAL_TEMPERATURE - Static variable in class loci.formats.in.FluoviewReader
adcDE - Variable in class loci.formats.in.SDTInfo
  ADC sample delay (SPC-930).
adcRE - Variable in class loci.formats.in.SDTInfo
adcResShift - Variable in class loci.formats.in.SPCReader
adcZoom - Variable in class loci.formats.in.SDTInfo
add(byte) - Method in class loci.formats.codec.ByteVector
add(byte[]) - Method in class loci.formats.codec.ByteVector
add(byte[], int, int) - Method in class loci.formats.codec.ByteVector
add(int, CoreMetadata) - Method in class loci.formats.CoreMetadataList
  Add a secondary array element to the specified primary array
add() - Method in class loci.formats.MetadataList
  Add a empty primary array element.
add(int) - Method in class loci.formats.MetadataList
  Add a empty primary array element.
add(int, T) - Method in class loci.formats.MetadataList
  Add a secondary array element to the specified primary array
add(T) - Method in class loci.formats.MetadataList
  Add a new primary element containing a single specified value.
add(List<T>) - Method in class loci.formats.MetadataList
  Add a new primary element containing the specified values.
add(double) - Method in class loci.plugins.util.RecordedImageProcessor
add(int) - Method in class loci.plugins.util.RecordedImageProcessor
addAnnotation(MetadataStore, SlideBook7Reader.CAnnotation70, int, int, int) - Method in class loci.formats.in.SlideBook7Reader
addCacheListener(CacheListener) - Method in class loci.formats.cache.Cache
addCacheListener(CacheListener) - Method in interface loci.formats.cache.CacheReporter
  Adds a listener for status update events.
addCacheListener(CacheListener) - Method in class loci.formats.cache.CacheStrategy
addChannelDimension(int) - Method in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataTempBuffer
  Adds channel dimension
addCheckbox(GenericDialog, String) - Method in class loci.plugins.prefs.OptionsDialog
  Adds a checkbox to the given dialog object corresponding to the boolean option identified by the specified key.
addChoice(GenericDialog, String) - Method in class loci.plugins.prefs.OptionsDialog
  Adds a choice to the given dialog object corresponding to the string option identified by the specified key.
addClass(int, Class<? extends T>) - Method in class loci.formats.ClassList
  Adds the given class, which must be assignable to the base class, to the list.
addClass(Class<? extends T>) - Method in class loci.formats.ClassList
  Adds the given class, which must be assignable to the base class, to the list.
addDimension(int, Dimension) - Method in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataTempBuffer
  Inserts dimension to buffer and optionally adapts other dimension-dependent values
addDirectory(String, int) - Method in class loci.formats.in.L2DReader
  Recursively add all of the files in the given directory to the used file list.
addEntry(Comparable<Object>, DefaultListModel) - Static method in class loci.plugins.config.ConfigWindow
addFile(String, int, int) - Method in class loci.formats.in.JDCEReader.JDCEWell
  Add file for the given field and plane indexes.
addFile(String) - Method in class loci.formats.internal.WellContainer
addFileToList(String) - Method in class loci.formats.in.DCIMGReader
addFileToList(String, boolean) - Method in class loci.formats.in.DicomReader
  Determine if the given file belongs in the same dataset as this file.
addGlobalMeta(String, Object) - Method in class loci.formats.FormatReader
  Adds an entry to the global metadata table.
addGlobalMeta(String, boolean) - Method in class loci.formats.FormatReader
  Adds an entry to the global metadata table.
addGlobalMeta(String, byte) - Method in class loci.formats.FormatReader
  Adds an entry to the global metadata table.
addGlobalMeta(String, short) - Method in class loci.formats.FormatReader
  Adds an entry to the global metadata table.
addGlobalMeta(String, int) - Method in class loci.formats.FormatReader
  Adds an entry to the global metadata table.
addGlobalMeta(String, long) - Method in class loci.formats.FormatReader
  Adds an entry to the global metadata table.
addGlobalMeta(String, float) - Method in class loci.formats.FormatReader
  Adds an entry to the global metadata table.
addGlobalMeta(String, double) - Method in class loci.formats.FormatReader
  Adds an entry to the global metadata table.
addGlobalMeta(String, char) - Method in class loci.formats.FormatReader
  Adds an entry to the global metadata table.
addGlobalMetaList(String, Object) - Method in class loci.formats.FormatReader
  Add the given key/value pair to the global metadata hashtable.
addInfo(DicomTag) - Method in class loci.formats.in.DicomReader
addMeta(String, Object, Hashtable<String, Object>) - Method in class loci.formats.FormatReader
  Adds an entry to the specified Hashtable.
addMetadataList(double[], String) - Method in class loci.formats.in.ZeissXRMReader
  Add each double value in an array to the original metadata table, using the given key.
addMetadataList(double[], String, boolean) - Method in class loci.formats.in.ZeissXRMReader
  Add each double value in an array to the original metadata table, using the given key.
addMetadataOnly(OMEXMLMetadata, int) - Method in interface loci.formats.services.OMEXMLService
  Insert a MetadataOnly element under the Image specified by 'index' in the given OME-XML metadata object.
addMetadataOnly(OMEXMLMetadata, int, boolean) - Method in interface loci.formats.services.OMEXMLService
  Insert a MetadataOnly element under the Image specified by 'index' in the given OME-XML metadata object.
addMetadataOnly(OMEXMLMetadata, int) - Method in class loci.formats.services.OMEXMLServiceImpl
addMetadataOnly(OMEXMLMetadata, int, boolean) - Method in class loci.formats.services.OMEXMLServiceImpl
addMetaList(String, Object, Hashtable<String, Object>) - Method in class loci.formats.FormatReader
  Add the given key/value pair to the given hashtable.
addMissingDimensions(int) - Method in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataTempBuffer
  Adds Z, T and S dimension if they haven't been added already
addModuloAlong(OMEXMLMetadata, CoreMetadata, int) - Method in interface loci.formats.services.OMEXMLService
  Adds ModuloAlong* annotations to the given OME-XML metadata object, using the given CoreMetadata object to determine modulo dimensions.
addModuloAlong(OMEXMLMetadata, CoreMetadata, int) - Method in class loci.formats.services.OMEXMLServiceImpl
addOption(String, String) - Method in class loci.formats.ClassList
  Add a key/value pair to the list of options.
addOriginalMetadata(String, DicomTag) - Method in class loci.formats.in.DicomReader
  Store the given tag's value (if present) in the original metadata hashtable using the provided key.
addPlaneMetadata(JDCEReader.PlaneMetadata, int[]) - Method in class loci.formats.in.JDCEReader.JDCEWell
addPossible(String) - Method in class loci.plugins.prefs.StringOption
  Adds a possible value to the list.
addProp(HashMap<String, String>, String, String, HashMap<String, String>) - Method in class loci.plugins.config.ConfigWindow
addPtyFiles() - Method in class loci.formats.in.FV1000Reader
addScrollBars(Container) - Static method in class loci.plugins.util.WindowTools
  Adds AWT scroll bars to the given container.
addSeriesMeta(String, Object) - Method in class loci.formats.FormatReader
  Adds an entry to the metadata table for the current series.
addSeriesMeta(String, boolean) - Method in class loci.formats.FormatReader
  Adds an entry to the metadata table for the current series.
addSeriesMeta(String, byte) - Method in class loci.formats.FormatReader
  Adds an entry to the metadata table for the current series.
addSeriesMeta(String, short) - Method in class loci.formats.FormatReader
  Adds an entry to the metadata table for the current series.
addSeriesMeta(String, int) - Method in class loci.formats.FormatReader
  Adds an entry to the metadata table for the current series.
addSeriesMeta(String, long) - Method in class loci.formats.FormatReader
  Adds an entry to the metadata table for the current series.
addSeriesMeta(String, float) - Method in class loci.formats.FormatReader
  Adds an entry to the metadata table for the current series.
addSeriesMeta(String, double) - Method in class loci.formats.FormatReader
  Adds an entry to the metadata table for the current series.
addSeriesMeta(String, char) - Method in class loci.formats.FormatReader
  Adds an entry to the metadata table for the current series.
addSeriesMeta(String, Object) - Method in class loci.formats.in.LeicaMicrosystemsMetadata.LMSFileReader
addSeriesMetaList(String, Object) - Method in class loci.formats.FormatReader
  Add the given key/value pair to the current series metadata hashtable.
addSeriesMetaList(String, Object) - Method in class loci.formats.in.LeicaMicrosystemsMetadata.LMSFileReader
addStatusListener(StatusListener) - Method in class loci.plugins.in.ImagePlusReader
addStatusListener(StatusListener) - Method in class loci.plugins.in.ImportProcess
addSubResolutions() - Method in class loci.formats.in.OMETiffReader
addToHashtable() - Method in class loci.formats.in.ZeissLSMReader.SubBlock
addUsedFile(String, String) - Method in class loci.formats.in.PerkinElmerReader
  Add the given file to the used files list.
addUserCommentMeta(Element, int) - Method in class loci.formats.in.LeicaMicrosystemsMetadata.LMSMetadataExtractor
  Extracts user comments and adds them to the reader's `CoreMetadata`
addUserCommentMeta(Element, int) - Method in class loci.formats.in.LIFReader
addValue(List, Object, int) - Method in class loci.formats.in.ImarisHDFReader
adjust - Variable in class loci.formats.in.SlidebookReader
adjustEndianness - Variable in class loci.formats.in.GatanReader
adjustForWhiteBalance(short, int) - Method in class loci.formats.in.DNGReader
adjustForWhiteBalance(short, int) - Method in class loci.formats.in.NikonReader
adjustmentValueChanged(AdjustmentEvent) - Method in class loci.plugins.util.DataBrowser
adjustWellDimensions() - Method in class loci.formats.in.ScanrReader
advanceBlock() - Method in class loci.formats.in.APNGReader.PNGInputStream
AFIHandler() - Constructor for class loci.formats.in.AFIReader.AFIHandler
AFIReader - Class in loci.formats.in
  AFIReader is the file format reader for Aperio AFI files.
AFIReader() - Constructor for class loci.formats.in.AFIReader
  Constructs a new AFI reader.
AFIReader.AFIHandler - Class in loci.formats.in
ag - Variable in class loci.formats.FileStitcher.ExternalSeries
AIMReader - Class in loci.formats.in
  AIMReader is the file format reader for .aim files.
AIMReader() - Constructor for class loci.formats.in.AIMReader
  Constructs a new AIM reader.
airPressure - Variable in class loci.formats.in.ZeissCZIReader
AISF - Static variable in class loci.formats.in.VolocityClippingReader
AL3D_MAGIC_STRING - Static variable in class loci.formats.in.AliconaReader
AliconaReader - Class in loci.formats.in
  AliconaReader is the file format reader for Alicona AL3D files.
AliconaReader() - Constructor for class loci.formats.in.AliconaReader
  Constructs a new Alicona reader.
ALIGNMENT - Static variable in class loci.formats.in.ZeissCZIReader
ALL_DOMAINS - Static variable in class loci.formats.FormatTools
  List of all supported domains.
ALL_TYPES - Static variable in class loci.formats.gui.GUITools
  String to use for "all types" combination filter.
allBlockLengths - Variable in class loci.formats.in.SDTInfo
allBlockOffsets - Variable in class loci.formats.in.SDTInfo
allFiles - Variable in class loci.formats.in.BrukerReader
allFiles - Variable in class loci.formats.in.CV7000Reader
allFiles - Variable in class loci.formats.in.PerkinElmerReader
  List of all files to open
allFiles - Variable in class loci.formats.in.SPCReader
  List of all files to open
allFiles - Variable in class loci.formats.in.VectraReader
allocatedSize - Variable in class loci.formats.in.ZeissCZIReader.Segment
ALLOW_AUTOSTITCHING_DEFAULT - Static variable in class loci.formats.in.ZeissCZIReader
ALLOW_AUTOSTITCHING_KEY - Static variable in class loci.formats.in.ZeissCZIReader
allowAutostitching() - Method in class loci.formats.in.ZeissCZIReader
allowCZIAutostitch() - Static method in class loci.plugins.util.LociPrefs
allowOpen - Variable in class loci.formats.gui.FormatFileFilter
  Whether it is ok to open a file to determine its type.
allowOpen - Variable in class loci.formats.ImageReader
allowShow - Variable in class loci.plugins.util.DataBrowser
allPixelsFiles - Variable in class loci.formats.in.OlympusTileReader
ALPHABET_LENGTH - Static variable in class loci.formats.ResourceNamer
alphabeticIndexCount(String) - Static method in class loci.formats.ResourceNamer
alphaShort - Variable in class loci.formats.gui.Index16ColorModel
  Lookup tables.
alreadyChecked() - Method in class loci.formats.UpgradeChecker
  Return true if an upgrade check has already been performed in this JVM session.
altCodec - Variable in class loci.formats.in.QTReader
  Some movies use two video codecs -- this is the second codec.
alternateCenter - Variable in class loci.formats.in.LeicaHandler
alternateCenter - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataTempBuffer
alternateCenter - Variable in class loci.formats.in.LIFReader
altPlanes - Variable in class loci.formats.in.QTReader
  Number of frames that use the alternate codec.
AmiraParameters - Class in loci.formats.tools
  AmiraParameters handles parsing and writing of AmiraMesh headers.
AmiraParameters(String) - Constructor for class loci.formats.tools.AmiraParameters
AmiraParameters(RandomAccessInputStream) - Constructor for class loci.formats.tools.AmiraParameters
AmiraReader - Class in loci.formats.in
  This is a file format reader for AmiraMesh data.
AmiraReader() - Constructor for class loci.formats.in.AmiraReader
AmiraReader.ASCII - Class in loci.formats.in
  This class provides a not-quite-efficient, but simple reader for planes stored in ASCII-encoded numbers.
AmiraReader.HxRLE - Class in loci.formats.in
  This is the reader for RLE-compressed AmiraMeshes.
AmiraReader.HxZip - Class in loci.formats.in
  This is the reader for GZip-compressed AmiraMeshes.
AmiraReader.PlaneReader - Interface in loci.formats.in
  This is the common interface for all formats, compressed or not.
amplificationGain - Variable in class loci.formats.in.ZeissLSMReader.DetectionChannel
AnalysisFile() - Constructor for class loci.formats.in.MIASReader.AnalysisFile
analysisFiles - Variable in class loci.formats.in.MIASReader
AnalyzeReader - Class in loci.formats.in
  AnalyzeReader is the file format reader for Analyze 7.5 files.
AnalyzeReader() - Constructor for class loci.formats.in.AnalyzeReader
  Constructs a new Analyze reader.
and(int) - Method in class loci.plugins.util.RecordedImageProcessor
ANDOR_MAGIC_STRING - Static variable in class loci.formats.in.FluoviewReader
ANDOR_SHIFT_SPEED - Static variable in class loci.formats.in.CellSensReader
ANGLE - Static variable in class loci.formats.in.ZeissLSMReader
angle - Variable in class loci.formats.in.ZeissTIFFHandler.Scaling.Dimension
angles - Variable in class loci.formats.in.ZeissCZIReader
anim - Variable in class loci.formats.gui.ImageViewer
anim - Variable in class loci.plugins.util.DataBrowser
animate - Variable in class loci.plugins.util.DataBrowser
ANIMATION_KEY - Static variable in class loci.formats.gui.ImageViewer
ANN_BOOLEAN_VALUE - Static variable in class loci.formats.in.FakeReader
ANN_COMMENT_VALUE - Static variable in class loci.formats.in.FakeReader
ANN_DOUBLE_VALUE - Static variable in class loci.formats.in.FakeReader
ANN_LONG_VALUE - Static variable in class loci.formats.in.FakeReader
ANN_TAG_VALUE - Static variable in class loci.formats.in.FakeReader
ANN_TERM_VALUE - Static variable in class loci.formats.in.FakeReader
ANN_TIME_VALUE - Static variable in class loci.formats.in.FakeReader
ANN_XML_VALUE_END - Static variable in class loci.formats.in.FakeReader
ANN_XML_VALUE_START - Static variable in class loci.formats.in.FakeReader
annBool - Variable in class loci.formats.in.FakeReader
annComment - Variable in class loci.formats.in.FakeReader
annDouble - Variable in class loci.formats.in.FakeReader
annLong - Variable in class loci.formats.in.FakeReader
annMap - Variable in class loci.formats.in.FakeReader
ANNOTATION_NAMESPACE - Static variable in class loci.formats.in.FakeReader
ANNOTATION_PREFIX - Static variable in class loci.formats.in.FakeReader
ANNOTATION_SUFFIX - Static variable in class loci.formats.in.VectraReader
annotationBoolCount - Variable in class loci.formats.in.FakeReader
annotationCommentCount - Variable in class loci.formats.in.FakeReader
annotationCount - Variable in class loci.formats.in.FakeReader
annotationDoubleCount - Variable in class loci.formats.in.FakeReader
annotationLongCount - Variable in class loci.formats.in.FakeReader
annotationMapCount - Variable in class loci.formats.in.FakeReader
annotationTagCount - Variable in class loci.formats.in.FakeReader
annotationTermCount - Variable in class loci.formats.in.FakeReader
annotationTimeCount - Variable in class loci.formats.in.FakeReader
annotationXmlCount - Variable in class loci.formats.in.FakeReader
annTag - Variable in class loci.formats.in.FakeReader
annTerm - Variable in class loci.formats.in.FakeReader
annTime - Variable in class loci.formats.in.FakeReader
annXml - Variable in class loci.formats.in.FakeReader
ANO_SUFFIX - Static variable in class loci.formats.in.PerkinElmerReader
APERIO_IMAGE_DESCRIPTION_PREFIX - Static variable in class loci.formats.in.SVSReader
  TIFF image description prefix for Aperio SVS files.
APERTURE_VALUE - Static variable in class loci.formats.tiff.IFD
APLReader - Class in loci.formats.in
  APLReader is the file format reader for Olympus APL files.
APLReader() - Constructor for class loci.formats.in.APLReader
  Constructs a new APL reader.
APNGReader - Class in loci.formats.in
  APNGReader is the file format reader for Animated Portable Network Graphics (APNG) images.
APNGReader() - Constructor for class loci.formats.in.APNGReader
  Constructs a new APNGReader.
APNGReader.PNGBlock - Class in loci.formats.in
APNGReader.PNGInputStream - Class in loci.formats.in
  InputStream implementation that stitches together IDAT blocks into a seamless zlib stream.
APNGWriter - Class in loci.formats.out
  APNGWriter is the file format writer for PNG and APNG files.
APNGWriter() - Constructor for class loci.formats.out.APNGWriter
append(ClassList<T>) - Method in class loci.formats.ClassList
  Appends a class list which must be assignable to the base class
append(List<Class<? extends T>>) - Method in class loci.formats.ClassList
  Appends a list of classes which must be assignable to the base class
append(ILoggingEvent) - Method in class loci.plugins.util.IJStatusEchoer
appendHexValue(StringBuilder, String, int) - Method in class loci.formats.in.BaseZeissReader.Shape
appendServerMap(String, String) - Static method in class loci.formats.in.FlexReader
  Add the path 'realName' to the mapping for the server named 'alias'.
appendValue(StringBuilder, String, Object) - Method in class loci.formats.in.BaseZeissReader.Shape
applyCalibration(ImagePlus) - Method in class loci.plugins.in.Calibrator
  Applies spatial calibrations to an image stack.
applyColors(List<ImagePlus>) - Method in class loci.plugins.in.Colorizer
applyColors(List<ImagePlus>) - Method in class loci.plugins.in.ImagePlusReader
applyDisplayRanges(ImagePlus, int) - Method in class loci.plugins.in.Colorizer
applyMatrix() - Method in class loci.formats.in.OperettaReader.Plane
  Applies the orientationMatrix to positionX, positionY, and positionZ.
applyMethodStack(List<RecordedImageProcessor.MethodEntry>) - Method in class loci.plugins.util.RecordedImageProcessor
applyTable(int[]) - Method in class loci.plugins.util.RecordedImageProcessor
applyTransformation(byte[], int, int, int, int, int, int) - Method in class loci.formats.in.TissueFAXSReader
  Extension point for doing something to an FOV immediately after decompression, before any stitching or cropping.
ARCHIVE - Static variable in class loci.formats.in.FlexReader
AreaInfo() - Constructor for class loci.formats.in.CellVoyagerReader.AreaInfo
AreaOfInterest() - Constructor for class loci.formats.in.VentanaReader.AreaOfInterest
areas - Variable in class loci.formats.in.CellVoyagerReader.WellInfo
areas - Variable in class loci.formats.in.VentanaReader
ARFReader - Class in loci.formats.in
  ARFReader is the file format reader for Axon Raw Format (ARF) files, produced by INDEC BioSystems's Imaging Workbench software.
ARFReader() - Constructor for class loci.formats.in.ARFReader
  Constructs a new ARF reader.
arg - Variable in class loci.plugins.LociExporter
  Argument passed to setup method.
arg - Variable in class loci.plugins.Slicer
  Plugin options.
args - Static variable in class loci.plugins.shortcut.ShortcutPanel
  Details for installed plugins.
args - Variable in class loci.plugins.util.RecordedImageProcessor.MethodEntry
ARRAY - Static variable in class loci.formats.in.GatanReader
  Data types.
ArrayListOfArrayLists(int, Class<T>) - Method in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataTempBuffer
ArrayListOfHashMaps(int, Class<T>, Class<S>) - Method in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataTempBuffer
arrayToString(Array) - Method in class loci.formats.services.NetCDFServiceImpl
ARROW - Static variable in class loci.formats.in.FV1000Reader
ARROW - Static variable in class loci.formats.in.LeicaHandler.ROI
ARROW - Static variable in class loci.formats.in.LeicaMicrosystemsMetadata.ROI
ARROW - Static variable in class loci.formats.in.LIFReader.ROI
ARTIST - Static variable in class loci.formats.tiff.IFD
ascii - Variable in class loci.formats.in.AmiraReader
ASCII(int, int) - Constructor for class loci.formats.in.AmiraReader.ASCII
ascii - Variable in class loci.formats.tools.AmiraParameters
AsciiImage - Class in loci.formats.tools
  A utility class for outputting a BufferedImage as ASCII text.
AsciiImage(BufferedImage) - Constructor for class loci.formats.tools.AsciiImage
asMap() - Method in class loci.formats.in.DeltavisionReader.DVExtHdrFields
asRetrieve(MetadataStore) - Method in interface loci.formats.services.OMEXMLService
  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.
associatedXmlDoc - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.LMSFileReader
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.
attachCompanionFiles() - Method in class loci.formats.in.DicomReader
  DICOM datasets produced by: http://www.ct-imaging.de/index.php/en/ct-systeme-e/mikro-ct-e.html contain a bunch of extra metadata and log files.
attachListeners(List<TextField>, List<Panel>) - Method in class loci.plugins.in.ColorDialog
Attachment(String, long) - Constructor for class loci.formats.in.ZeissCZIReader.Attachment
attachment - Variable in class loci.formats.in.ZeissCZIReader.Attachment
attachment - Variable in class loci.formats.in.ZeissCZIReader.Metadata
attachmentData - Variable in class loci.formats.in.ZeissCZIReader.Attachment
AttachmentDirectory() - Constructor for class loci.formats.in.ZeissCZIReader.AttachmentDirectory
attachmentDirectoryPosition - Variable in class loci.formats.in.ZeissCZIReader.FileHeader
AttachmentEntry(RandomAccessInputStream) - Constructor for class loci.formats.in.ZeissCZIReader.AttachmentEntry
attachmentSize - Variable in class loci.formats.in.ZeissCZIReader.SubBlock
attenuation - Variable in class loci.formats.in.ZeissLSMReader.IlluminationChannel
attr(Element, String) - Method in class loci.formats.in.PrairieMetadata
  Gets the attribute value with the given name, or null if not defined.
ATTR_NAME_STYLE_END - Static variable in class loci.formats.gui.XMLCellRenderer
ATTR_NAME_STYLE_START - Static variable in class loci.formats.gui.XMLCellRenderer
ATTR_VALUE_STYLE_END - Static variable in class loci.formats.gui.XMLCellRenderer
ATTR_VALUE_STYLE_START - Static variable in class loci.formats.gui.XMLCellRenderer
attribute - Variable in class loci.formats.dicom.DicomTag
attributeList - Variable in class loci.formats.services.NetCDFServiceImpl
AUTOEXPOSURE - Static variable in class loci.formats.in.CellSensReader
AUTORECON_PATH - Static variable in class loci.formats.in.ZeissXRMReader
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.ND2Reader
BACKWARD_ORDER - Static variable in interface loci.formats.cache.ICacheStrategy
backwardsStageX - Variable in class loci.formats.in.DeltavisionReader
  Whether or not the stage moved backwards.
backwardsStageY - Variable in class loci.formats.in.DeltavisionReader
bandUsed - Variable in class loci.formats.in.NDPISReader
bankData - Variable in class loci.formats.gui.SignedByteBuffer
bankData - Variable in class loci.formats.gui.UnsignedIntBuffer
barcode - Variable in class loci.formats.in.LeicaSCNReader.ImageCollection
barrierFilter - Variable in class loci.formats.in.FV1000Reader.ChannelData
base - Variable in class loci.formats.ClassList
  Base class to which all classes are assignable.
Base64Codec - Class in loci.formats.codec
  Implements encoding (compress) and decoding (decompress) methods for Base64.
Base64Codec() - Constructor for class loci.formats.codec.Base64Codec
BASE_OFFSET - Static variable in class loci.formats.in.BioRadGelReader
BaseCodec - Class in loci.formats.codec
  BaseCodec contains default implementation and testing for classes implementing the Codec interface, and acts as a base class for any of the compression classes.
BaseCodec() - Constructor for class loci.formats.codec.BaseCodec
basedir - Variable in class loci.formats.in.ZeissTIFFReader.TIFFInfo
BASELINE_CLAMP - Static variable in class loci.formats.in.FluoviewReader
BASELINE_OFFSET - Static variable in class loci.formats.in.FluoviewReader
BASELINE_OFFSET_CLAMP - Static variable in class loci.formats.in.CellSensReader
BaseMetadata - Interface in loci.formats.meta
baseName - Variable in class loci.formats.in.OIRReader
basename - Variable in class loci.formats.in.ZeissTIFFHandler.Plane
baseReader - Variable in class loci.plugins.in.ImportProcess
baseTiff - Variable in class loci.formats.in.MicromanagerReader.Position
BaseTiffReader - Class in loci.formats.in
  BaseTiffReader is the superclass for file format readers compatible with or derived from the TIFF 6.0 file format.
BaseTiffReader(String, String) - Constructor for class loci.formats.in.BaseTiffReader
  Constructs a new BaseTiffReader.
BaseTiffReader(String, String[]) - Constructor for class loci.formats.in.BaseTiffReader
  Constructs a new BaseTiffReader.
baseTileHeight - Variable in class loci.formats.out.DicomWriter
baseTileWidth - Variable in class loci.formats.out.DicomWriter
baseX - Variable in class loci.formats.in.VentanaReader.TIFFTile
baseY - Variable in class loci.formats.in.VentanaReader.TIFFTile
BaseZeissReader - Class in loci.formats.in
  BaseZeissReader contains common functionality required by readers for Zeiss AxioVision formats.
BaseZeissReader(String, String) - Constructor for class loci.formats.in.BaseZeissReader
  Constructs a new ZeissZVI reader.
BaseZeissReader(String, String[]) - Constructor for class loci.formats.in.BaseZeissReader
  Constructs a new ZeissZVI reader.
BaseZeissReader.Charset - Enum in loci.formats.in
BaseZeissReader.Context - Enum in loci.formats.in
BaseZeissReader.DrawStyle - Enum in loci.formats.in
  Line drawing styles.
BaseZeissReader.FeatureType - Enum in loci.formats.in
  Feature types.
BaseZeissReader.FillStyle - Enum in loci.formats.in
  Fill styles.
BaseZeissReader.Layer - Class in loci.formats.in
  Layer class representing an AxioVision layer; used to contain a collection of shapes.
BaseZeissReader.LineEndPositions - Enum in loci.formats.in
BaseZeissReader.LineEndStyle - Enum in loci.formats.in
  Line ending styles.
BaseZeissReader.PointStyle - Enum in loci.formats.in
  Point styles.
BaseZeissReader.Shape - Class in loci.formats.in
  Shape class representing the metadata within an AxioVision Shape ROI
BaseZeissReader.Tag - Class in loci.formats.in
  Content of a single tag from a Tags block.
BaseZeissReader.TextAlignment - Enum in loci.formats.in
bayerPattern - Variable in class loci.formats.in.MRWReader
bbox - Variable in class loci.formats.in.BDVReader
BBOX - Static variable in class loci.formats.in.BDVReader.H5Constants
BBOX - Static variable in class loci.formats.in.CellH5Reader.CellH5Constants
BDReader - Class in loci.formats.in
  BDReader is the file format reader for BD Pathway datasets.
BDReader() - Constructor for class loci.formats.in.BDReader
  Constructs a new ScanR reader.
BDV_MAGIC_STRING - Static variable in class loci.formats.in.BDVReader
BDVReader - Class in loci.formats.in
  Reader for BDV files.
BDVReader() - Constructor for class loci.formats.in.BDVReader
  Constructs a new BDV reader.
BDVReader.BDVXMLHandler - Class in loci.formats.in
BDVReader.H5Constants - Class in loci.formats.in
BDVReader.H5Coordinate - Class in loci.formats.in
bdvxml - Variable in class loci.formats.in.BDVReader
BDVXMLHandler() - Constructor for class loci.formats.in.BDVReader.BDVXMLHandler
BEAM_SPLITTER_FILTER - Static variable in class loci.formats.in.ZeissLSMReader
BEAM_SPLITTER_FILTER_SET - Static variable in class loci.formats.in.ZeissLSMReader
BeamSplitter() - Constructor for class loci.formats.in.ZeissLSMReader.BeamSplitter
begin - Variable in class loci.formats.FilePatternBlock
BEZIER_WITH_ARROW - Static variable in class loci.formats.in.ZeissLSMReader
BF - Class in loci.plugins
  Miscellaneous plugins utility methods.
BF() - Constructor for class loci.plugins.BF
BFVirtualStack - Class in loci.plugins.util
  Subclass of VirtualStack that uses Bio-Formats to read planes on demand.
BFVirtualStack(String, IFormatReader, boolean, boolean, boolean) - Constructor for class loci.plugins.util.BFVirtualStack
BGR - Static variable in class loci.formats.in.CellSensReader
bgr - Variable in class loci.formats.in.CellSensReader
BGR_24 - Static variable in class loci.formats.in.ZeissCZIReader
BGR_24 - Static variable in class loci.formats.services.JPEGXRServiceImpl
BGR_32 - Static variable in class loci.formats.services.JPEGXRServiceImpl
BGR_48 - Static variable in class loci.formats.in.ZeissCZIReader
BGR_FLOAT - Static variable in class loci.formats.in.ZeissCZIReader
BGRA_32 - Static variable in class loci.formats.services.JPEGXRServiceImpl
BGRA_8 - Static variable in class loci.formats.in.ZeissCZIReader
bgrToRgb(byte[], boolean, int, int) - Static method in class loci.formats.ImageTools
BH_HEADER_CHKSUM - Static variable in class loci.formats.in.SDTInfo
BH_HEADER_NOT_VALID - Static variable in class loci.formats.in.SDTInfo
BH_HEADER_VALID - Static variable in class loci.formats.in.SDTInfo
BIFormatReader - Class in loci.formats.in
  BIFormatReader is the superclass for file format readers that use java.awt.image.BufferedImage as the native data type.
BIFormatReader(String, String) - Constructor for class loci.formats.in.BIFormatReader
  Constructs a new BIFormatReader.
BIFormatReader(String, String[]) - Constructor for class loci.formats.in.BIFormatReader
  Constructs a new BIFormatReader.
BIG - Static variable in class loci.formats.tiff.TiffConstants
BIG_TIFF - Static variable in class loci.formats.tiff.IFD
BIG_TIFF_BYTES_PER_ENTRY - Static variable in class loci.formats.tiff.TiffConstants
  The number of bytes in each IFD entry of a BigTIFF file.
BIG_TIFF_CUTOFF - Static variable in class loci.formats.tiff.TiffConstants
  Number of bytes at which to automatically switch to BigTIFF This is approximately 3.9 GB instead of 4 GB, to allow space for the IFDs.
BIG_TIFF_MAGIC_NUMBER - Static variable in class loci.formats.tiff.TiffConstants
BIG_TIFF_SUFFIXES - Static variable in class loci.formats.out.TiffWriter
bigEndianTransferSyntax - Variable in class loci.formats.dicom.DicomTag
bigTiff - Variable in class loci.formats.out.DicomWriter
bigTiff - Variable in class loci.formats.tiff.TiffParser
  Whether or not the TIFF file contains BigTIFF data.
bigTiff - Variable in class loci.formats.tiff.TiffSaver
  Whether or not to write BigTIFF data.
bin - Variable in class loci.formats.in.InCellReader
binary - Variable in class loci.formats.in.EPSReader
  Flag indicating binary data.
BINARY_SETUP - Static variable in class loci.formats.in.SDTInfo
binData - Variable in class loci.formats.in.OMEXMLReader
BinData(int, int) - Constructor for class loci.formats.in.OMEXMLReader.BinData
binDataOffsets - Variable in class loci.formats.in.OMEXMLReader
binning - Variable in class loci.formats.in.BDReader
binning - Variable in class loci.formats.in.BioRadSCNReader
binning - Variable in class loci.formats.in.CV7000Reader.Channel
binning - Variable in class loci.formats.in.MetamorphHandler
binning - Variable in class loci.formats.in.MetamorphReader
binning - Variable in class loci.formats.in.MicromanagerReader.Position
binning - Variable in class loci.formats.in.ND2Handler
binning - Variable in class loci.formats.in.PCIReader
binning - Variable in class loci.formats.in.SimplePCITiffReader
binning - Variable in class loci.formats.in.ZeissLSMReader
binning - Variable in class loci.formats.in.ZeissLSMReader.Recording
binnings - Variable in class loci.formats.in.FlexReader
binnings - Variable in class loci.formats.in.ZeissCZIReader
binningX - Variable in class loci.formats.in.CellSensReader.Pyramid
binningY - Variable in class loci.formats.in.CellSensReader.Pyramid
binSize - Variable in class loci.formats.in.SPCReader
binX - Variable in class loci.formats.in.FlexReader
  Camera binning values.
binX - Variable in class loci.formats.in.IvisionReader
binY - Variable in class loci.formats.in.FlexReader
  Camera binning values.
binY - Variable in class loci.formats.in.IvisionReader
BioFormatsExtensionPrinter - Class in loci.formats.tools
  This class is used to generate a text file containing all of the image file extensions supported by Bio-Formats.
BioFormatsExtensionPrinter() - Constructor for class loci.formats.tools.BioFormatsExtensionPrinter
BioRadGelReader - Class in loci.formats.in
  BioRadGelReader is the file format reader for Bio-Rad gel files.
BioRadGelReader() - Constructor for class loci.formats.in.BioRadGelReader
  Constructs a new Bio-Rad gel reader.
BioRadHandler() - Constructor for class loci.formats.in.BioRadReader.BioRadHandler
BioRadReader - Class in loci.formats.in
  BioRadReader is the file format reader for Bio-Rad PIC files.
BioRadReader() - Constructor for class loci.formats.in.BioRadReader
  Constructs a new BioRadReader.
BioRadReader.BioRadHandler - Class in loci.formats.in
  SAX handler for parsing XML.
BioRadReader.Note - Class in loci.formats.in
BioRadSCNReader - Class in loci.formats.in
  BioRadSCNReader is the reader for Bio-Rad .scn files
BioRadSCNReader() - Constructor for class loci.formats.in.BioRadSCNReader
  Constructs a new Bio-Rad .scn reader.
BioRadSCNReader.SCNHandler - Class in loci.formats.in
biReader - Variable in class loci.formats.gui.DataConverter
BIT - Static variable in class loci.formats.FormatTools
  Identifies the BIT data type used to store pixel values.
BIT_DEPTH - Static variable in class loci.formats.in.CellSensReader
BitBuffer - Class in loci.formats.codec
  Deprecated.
  Use loci.common.RandomAccessInputStream instead
BitBuffer(byte[]) - Constructor for class loci.formats.codec.BitBuffer
  Deprecated.
  Default constructor.
bitDepth - Variable in class loci.formats.in.CellSensReader.Pyramid
bitInc - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.Channel
BITMASK_COMPRESSION - Static variable in class loci.formats.in.FlowSightReader
bits - Variable in class loci.formats.in.BrukerReader
bits - Variable in class loci.formats.in.TargaReader
BITS_PER_SAMPLE - Static variable in class loci.formats.tiff.IFD
bitsPerPixel - Variable in class loci.formats.CoreMetadata
  Number of valid bits per pixel.
bitsPerPixel - Variable in class loci.formats.in.QTReader
  Pixel depth.
bitsPerSample - Variable in class loci.formats.codec.CodecOptions
  Number of bits per channel.
BitWriter - Class in loci.formats.codec
  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
blockSizeZPerResolution - Variable in class loci.formats.in.ImarisHDFReader
blocksPerPlane - Variable in class loci.formats.in.KLBReader
blocksPerPlane - Variable in class loci.formats.in.OIRReader
blockType - Variable in class loci.formats.in.APNGReader.PNGInputStream
blockType - Variable in class loci.formats.in.SDTInfo
  See blockType defines below.
BLUE_GAIN - Static variable in class loci.formats.in.CellSensReader
BLUE_MIN - Static variable in class loci.plugins.in.Colorizer
BLUE_MULTIPLIER - Static variable in class loci.formats.in.NDPIReader
BLUE_OFFSET - Static variable in class loci.formats.in.CellSensReader
BLUE_TO_GREEN_MIN - Static variable in class loci.plugins.in.Colorizer
blueGain - Variable in class loci.formats.in.CellSensReader.Pyramid
blueOffset - Variable in class loci.formats.in.CellSensReader.Pyramid
blueOffset - Static variable in class org.libjpegturbo.turbojpeg.TJ
blueShort - Variable in class loci.formats.gui.Index16ColorModel
  Lookup tables.
BMP - Static variable in class loci.formats.in.CellSensReader
BMP_MAGIC_STRING - Static variable in class loci.formats.in.BMPReader
bmpBitsPerPixel - Variable in class loci.formats.in.AVIReader
bmpColorsUsed - Variable in class loci.formats.in.AVIReader
bmpCompression - Variable in class loci.formats.in.AVIReader
BMPReader - Class in loci.formats.in
  BMPReader is the file format reader for Microsoft Bitmap (BMP) files.
BMPReader() - Constructor for class loci.formats.in.BMPReader
  Constructs a new BMP reader.
bmpScanLineSize - Variable in class loci.formats.in.AVIReader
bmpWidth - Variable in class loci.formats.in.AVIReader
bold - Variable in class loci.formats.in.BaseZeissReader.Shape
BOOLEAN - Static variable in class loci.formats.in.CellSensReader
BooleanIM3Record(String, int, long, int) - Constructor for class loci.formats.in.IM3Reader.BooleanIM3Record
BooleanOption - Class in loci.plugins.prefs
  A boolean option for one of the plugins.
BooleanOption(HashMap<String, String>) - Constructor for class loci.plugins.prefs.BooleanOption
  Constructs a boolean option with the parameters from the given map.
BooleanOption(String, boolean, String, String, boolean) - Constructor for class loci.plugins.prefs.BooleanOption
  Constructs a boolean option with the given parameters.
BORDER - Static variable in class loci.plugins.shortcut.ShortcutPanel
  Number of pixels for window border.
bordL - Variable in class loci.formats.in.SDTInfo
bordU - Variable in class loci.formats.in.SDTInfo
boundingBox - Variable in class loci.formats.in.VentanaReader.AreaOfInterest
boundValues - Variable in class loci.formats.services.MDBServiceImpl
BOX_SIZE - Static variable in class loci.formats.in.FakeReader
boxes - Variable in class loci.plugins.in.SeriesDialog
bpp - Variable in class loci.formats.in.BaseZeissReader
  Number of bytes per pixel.
bpp - Variable in class loci.formats.in.BMPReader
  Number of bits per pixel.
bpp - Variable in class loci.formats.in.MIASReader
bpp - Variable in class loci.formats.in.SPCReader
bpp - Variable in class loci.formats.out.CellH5Writer
BRIGHTNESS - Static variable in class loci.formats.in.CellSensReader
BRIGHTNESS_VALUE - Static variable in class loci.formats.tiff.IFD
brokenNotes - Variable in class loci.formats.in.BioRadReader
BrowserOptionsWindow - Class in loci.plugins.util
  Extension of JFrame that allows the user to adjust caching settings.
BrowserOptionsWindow(String, Cache, String[]) - Constructor for class loci.plugins.util.BrowserOptionsWindow
BrukerReader - Class in loci.formats.in
  BrukerReader is the file format reader for Bruker MRI files.
BrukerReader() - Constructor for class loci.formats.in.BrukerReader
  Constructs a new Bruker reader.
btsType - Variable in class loci.formats.in.CV7000Reader.MeasurementDataHandler
buffer - Variable in class loci.formats.codec.BitBuffer
  Deprecated.
buffer - Variable in class loci.formats.in.ImarisHDFReader
BUFFER_SIZE - Static variable in class loci.formats.in.ND2Reader
BUFFER_SIZE - Static variable in class loci.formats.in.OIRReader
BUFFER_SIZE - Static variable in class loci.formats.in.ZeissCZIReader
BufferedImageReader - Class in loci.formats.gui
  A reader wrapper for reading image planes as BufferedImage objects.
BufferedImageReader() - Constructor for class loci.formats.gui.BufferedImageReader
  Constructs a BufferedImageReader around a new image reader.
BufferedImageReader(IFormatReader) - Constructor for class loci.formats.gui.BufferedImageReader
  Constructs a BufferedImageReader with the given reader.
BufferedImageSource - Class in loci.formats.gui
  Retrieves BufferedImages from a data source using Bio-Formats.
BufferedImageSource(IFormatReader) - Constructor for class loci.formats.gui.BufferedImageSource
BufferedImageWriter - Class in loci.formats.gui
  A writer wrapper for writing image planes from BufferedImage objects.
BufferedImageWriter() - Constructor for class loci.formats.gui.BufferedImageWriter
  Constructs a BufferedImageWriter around a new image writer.
BufferedImageWriter(IFormatWriter) - Constructor for class loci.formats.gui.BufferedImageWriter
  Constructs a BufferedImageWriter with the given writer.
bufLength - Variable in class loci.formats.in.SPCReader
bufSize(int, int, int) - Static method in class org.libjpegturbo.turbojpeg.TJ
  Returns the maximum size of the buffer (in bytes) required to hold a JPEG image with the given width and height, and level of chrominance subsampling.
bufSizeYUV(int, int, int) - Static method in class org.libjpegturbo.turbojpeg.TJ
  Returns the size of the buffer (in bytes) required to hold a YUV planar image with the given width, height, and level of chrominance subsampling.
BUILDER - Static variable in class loci.formats.meta.OriginalMetadataAnnotation
buildExtensions() - Method in class loci.plugins.macro.MacroFunctions
  Builds the list of extensions, using reflection, from public methods of this class.
buildFileChooser(IFormatHandler) - Static method in class loci.formats.gui.GUITools
  Constructs a file chooser for the given file format handler.
buildFileChooser(IFormatHandler, boolean) - Static method in class loci.formats.gui.GUITools
  Constructs a file chooser for the given file format handler.
buildFileChooser(FileFilter[]) - Static method in class loci.formats.gui.GUITools
  Builds a file chooser with the given file filters, as well as an "All supported file types" combo filter.
buildFileChooser(FileFilter[], boolean) - Static method in class loci.formats.gui.GUITools
  Builds a file chooser with the given file filters, as well as an "All supported file types" combo filter, if one is not already specified.
buildFileFilters(IFormatHandler) - Static method in class loci.formats.gui.GUITools
  Constructs a list of file filters for the given file format handler.
buildFiles(String, int, List<String>) - Method in class loci.formats.FilePattern
buildTIFFList(int) - Method in class loci.formats.in.MicromanagerReader
buildTIFFList(int, String) - Method in class loci.formats.in.MicromanagerReader
  Populate the list of TIFF files using the given file name as a pattern.
BurleighReader - Class in loci.formats.in
  BurleighReader is the file format reader for Burleigh .img files.
BurleighReader() - Constructor for class loci.formats.in.BurleighReader
  Constructs a new Burleigh reader.
BYTE - Static variable in class loci.formats.in.GatanReader
BYTE_COUNT_HIGH_BYTES - Static variable in class loci.formats.in.NDPIReader
BYTE_COUNT_OFFSET - Static variable in class loci.formats.out.QTWriter
  Seek to this offset to update the total number of pixel bytes.
ByteArraySource - Class in loci.formats.cache
  Retrieves byte arrays from a data source (e.g., a file) using Bio-Formats.
ByteArraySource(IFormatReader) - Constructor for class loci.formats.cache.ByteArraySource
  Constructs a byte array source from the given Bio-Formats reader.
ByteArraySource(String) - Constructor for class loci.formats.cache.ByteArraySource
  Constructs a byte array source that draws from the given file.
ByteArrayToInt(byte[], int) - Method in class loci.formats.in.SlideBook7Reader.CNpyHeader
ByteArrayToShort(byte[], int) - Method in class loci.formats.in.SlideBook7Reader.CNpyHeader
ByteArrayToShort(byte[], int) - Method in class loci.formats.in.SlideBook7Reader.DataLoader
byteOrder - Variable in class org.libjpegturbo.turbojpeg.TJCompressor
byteOrder - Variable in class org.libjpegturbo.turbojpeg.TJDecompressor
bytes - Variable in class loci.formats.tiff.TiffSaver
  Output bytes.
BYTES_PER_ENTRY - Static variable in class loci.formats.tiff.TiffConstants
  The number of bytes in each IFD entry.
bytesFromReader(IFormatReader) - Method in class loci.formats.Memoizer.RandomAccessDeser
bytesInc - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.Channel
bytesInc - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.Dimension
bytesPerAxis - Variable in class loci.formats.in.LeicaHandler
bytesPerElement - Variable in enum loci.formats.tiff.IFDType
  Number of bytes per element of this type.
bytesPerImage - Variable in class loci.formats.in.DCIMGReader
bytesPerLine - Variable in class loci.formats.in.PCXReader
  Number of bytes per scan line - may be different than image width.
bytesPerPixel - Variable in class loci.formats.in.AmiraReader.ASCII
bytesPerPixel - Variable in class loci.formats.in.OpenlabRawReader
  Number of bytes per pixel.
bytesPerPixel - Variable in class loci.formats.out.AVIWriter
bytesPerPlane - Variable in class loci.formats.in.AVIReader
bytesPerRow - Variable in class loci.formats.in.DCIMGReader
bytesPerSample - Variable in class loci.formats.in.OBFReader.Stack
byteValue() - Method in class loci.formats.tiff.TiffRational
  Returns the value of the specified number as a byte.
ByteVector - Class in loci.formats.codec
  A growable array of bytes.
ByteVector() - Constructor for class loci.formats.codec.ByteVector
ByteVector(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.OIRReader.CZTKey
c - Variable in class loci.formats.in.OperettaReader.Plane
c - Variable in class loci.formats.tools.AmiraParameters
C01_MAGIC_BYTES - Static variable in class loci.formats.in.CellomicsReader
C_AXIS - Static variable in class loci.formats.AxisGuesser
  Axis type for channels.
C_KEY - Static variable in class loci.formats.in.LiFlimReader
C_PREFIXES - Static variable in class loci.formats.AxisGuesser
  Prefixes indicating channel dimension.
C_STRING - Static variable in class loci.formats.in.SDTInfo
Cache - Class in loci.formats.cache
  Cache provides a means of managing subsets of large collections of image planes in memory.
Cache(ICacheStrategy, ICacheSource, boolean) - Constructor for class loci.formats.cache.Cache
  Constructs an object cache with the given cache strategy and source.
cache - Variable in class loci.formats.cache.Cache
  Master array containing cached objects.
cache - Variable in class loci.formats.cache.CacheUpdater
cache - Variable in class loci.formats.gui.CacheComponent
  The cache that this component controls.
cache - Variable in class loci.formats.gui.CacheIndicator
cache - Variable in class loci.plugins.util.BFVirtualStack
CacheComponent - Class in loci.formats.gui
  GUI component for managing a cache.
CacheComponent(Cache, String[]) - Constructor for class loci.formats.gui.CacheComponent
  Creates a cache GUI component.
CacheComponent(Cache, String[], String) - Constructor for class loci.formats.gui.CacheComponent
  Creates a cache GUI component with the ability to change between the various source types (mainly for debugging purposes).
CacheConsole - Class in loci.formats.tools
  CacheConsole provides an interactive interpreter for testing the Bio-Formats caching implementation.
CacheConsole() - Constructor for class loci.formats.tools.CacheConsole
cachedTileBuffer - Variable in class loci.formats.in.MIASReader
  Cached tile buffer to avoid re-allocations when reading tiles.
cachedTileBuffer - Variable in class loci.formats.tiff.TiffParser
  Cached tile buffer to avoid re-allocations when reading tiles.
CacheEvent - Class in loci.formats.cache
  A event indicating a cache update.
CacheEvent(Object, int) - Constructor for class loci.formats.cache.CacheEvent
  Constructs a cache event.
CacheEvent(Object, int, int) - Constructor for class loci.formats.cache.CacheEvent
  Constructs a cache event.
CacheException - Exception in loci.formats.cache
  CacheException is the exception thrown when something goes wrong performing a cache operation.
CacheException() - Constructor for exception loci.formats.cache.CacheException
CacheException(String) - Constructor for exception loci.formats.cache.CacheException
CacheException(String, Throwable) - Constructor for exception loci.formats.cache.CacheException
CacheException(Throwable) - Constructor for exception loci.formats.cache.CacheException
CacheIndicator - Class in loci.formats.gui
  Indicator GUI component showing which planes are currently in the cache for a given dimensional axis at a particular dimensional position.
CacheIndicator(Cache, int) - Constructor for class loci.formats.gui.CacheIndicator
  Creates a new cache indicator for the given cache.
CacheIndicator(Cache, int, Component, int, int) - Constructor for class loci.formats.gui.CacheIndicator
  Creates a new cache indicator.
CacheListener - Interface in loci.formats.cache
  A listener for cache updates.
CacheReporter - Interface in loci.formats.cache
  Interface for components capable of reporting cache updates.
CacheSource - Class in loci.formats.cache
  Superclass of cache sources that retrieve image planes from a data source (e.g., a file) using Bio-Formats.
CacheSource(IFormatReader) - Constructor for class loci.formats.cache.CacheSource
  Constructs a cache source from the given Bio-Formats reader.
CacheSource(String) - Constructor for class loci.formats.cache.CacheSource
  Constructs a cache source that draws from the given file.
CacheStrategy - Class in loci.formats.cache
  Superclass of cache strategies.
CacheStrategy(int[]) - Constructor for class loci.formats.cache.CacheStrategy
  Constructs a cache strategy.
cacheUpdated(CacheEvent) - Method in interface loci.formats.cache.CacheListener
  Called when cache is updated.
cacheUpdated(CacheEvent) - Method in class loci.formats.gui.CacheComponent
  Updates GUI to match latest cache state.
cacheUpdated(CacheEvent) - Method in class loci.formats.gui.CacheIndicator
CacheUpdater - Class in loci.formats.cache
  Thread responsible for updating the cache (loading and dropping planes) in the background.
CacheUpdater(Cache) - Constructor for class loci.formats.cache.CacheUpdater
calcPhotons - Variable in class loci.formats.in.SDTInfo
  No of photons.
calculateDimensions() - Method in class loci.formats.in.ZeissCZIReader
calculateDimensions(int, boolean) - Method in class loci.formats.in.ZeissCZIReader
calculatePixelsOffsets(long) - Method in class loci.formats.in.DicomReader
  Calculate offsets to all pixel data (tiles or planes) in the file, starting from the given offset.
CALIBRATION - Static variable in class loci.formats.in.CellSensReader
CALIBRATION - Static variable in class loci.formats.in.OpenlabReader
calibrationTable - Variable in class loci.plugins.util.BFVirtualStack
calibrationUnit - Variable in class loci.formats.in.TiffReader
Calibrator - Class in loci.plugins.in
  Logic for calibrating images.
Calibrator(ImportProcess) - Constructor for class loci.plugins.in.Calibrator
CAlignManipRecord70() - Constructor for class loci.formats.in.SlideBook7Reader.CAlignManipRecord70
callDeferredSetters(ReaderWrapper) - Method in class loci.formats.WrappedReader
  A helper may not exist before initFile() is called.
callLegacyReader() - Method in class loci.formats.DelegateReader
CAMERA_GAIN - Static variable in class loci.formats.in.CellSensReader
CAMERA_GAMMA - Static variable in class loci.formats.in.CellSensReader
CAMERA_OFFSET - Static variable in class loci.formats.in.CellSensReader
CAMERA_SERIAL_SETTING - Static variable in class loci.formats.in.FluoviewReader
cameraIDs - Variable in class loci.formats.in.FlexReader
cameraMode - Variable in class loci.formats.in.MicromanagerReader.Position
cameraModel - Variable in class loci.formats.in.ND2Handler
cameraName - Variable in class loci.formats.in.SimplePCITiffReader
cameraName - Variable in class loci.formats.in.SISReader
cameraNumber - Variable in class loci.formats.in.CV7000Reader.Channel
cameraRef - Variable in class loci.formats.in.MicromanagerReader.Position
cameraRefs - Variable in class loci.formats.in.FlexReader
cameraType - Variable in class loci.formats.in.SimplePCITiffReader
CAN_GROUP - Static variable in class loci.formats.FormatTools
CAN_GROUP - Static variable in interface loci.formats.IFormatReader
canAdjustDimensions - Variable in class loci.formats.in.ND2Handler
cancel - Variable in class loci.plugins.in.ImportProcess
  Whether the process has been canceled.
cancel() - Method in class loci.plugins.in.ImportProcess
  Cancels the import process.
canceled - Variable in class loci.plugins.LociImporter
  Flag indicating whether last operation was canceled.
canceled - Variable in class loci.plugins.Slicer
  Flag indicating whether last operation was canceled.
canceled - Variable in class loci.plugins.Updater
  Flag indicating whether last operation was canceled.
canChangePattern() - Method in class loci.formats.FileStitcher
canClose - Variable in class loci.formats.tiff.TiffParser
canCloseReader - Variable in class loci.formats.gui.ImageViewer
canDetectBigTiff - Variable in class loci.formats.out.TiffWriter
  Whether or not BigTIFF can be used automatically.
canDoStacks() - Method in class loci.formats.FormatWriter
canDoStacks() - Method in interface loci.formats.IFormatWriter
  Reports whether the writer can save multiple images to a single file.
canDoStacks() - Method in class loci.formats.ImageWriter
canDoStacks() - Method in class loci.formats.out.APNGWriter
canDoStacks() - Method in class loci.formats.out.AVIWriter
canDoStacks() - Method in class loci.formats.out.CellH5Writer
canDoStacks() - Method in class loci.formats.out.DicomWriter
canDoStacks() - Method in class loci.formats.out.ICSWriter
canDoStacks() - Method in class loci.formats.out.JavaWriter
canDoStacks() - Method in class loci.formats.out.JPEG2000Writer
  Overridden to indicate that stacks are not supported.
canDoStacks() - Method in class loci.formats.out.OMEXMLWriter
canDoStacks() - Method in class loci.formats.out.QTWriter
canDoStacks() - Method in class loci.formats.out.TiffWriter
canDoStacks() - Method in class loci.formats.out.V3DrawWriter
canDoStacks() - Method in class loci.formats.WriterWrapper
canDoUpgradeCheck() - Method in class loci.formats.UpgradeChecker
  Return whether or not we are ever allowed to perform an upgrade check.
canImport(JComponent, DataFlavor[]) - Method in class loci.plugins.shortcut.ShortcutTransferHandler
canLookForND - Variable in class loci.formats.in.MetamorphReader
canMerge() - Method in class loci.formats.ChannelMerger
  Determines whether the channels in the file can be merged.
CANNOT_GROUP - Static variable in class loci.formats.FormatTools
CANNOT_GROUP - Static variable in interface loci.formats.IFormatReader
CAnnotation70() - Constructor for class loci.formats.in.SlideBook7Reader.CAnnotation70
CAnnotations() - Constructor for class loci.formats.in.SlideBook7Reader.CImageGroup.CAnnotations
CANON_TAG - Static variable in class loci.formats.in.DNGReader
CanonRawReader - Class in loci.formats.in
  CanonRawReader is the file format reader for Canon RAW files.
CanonRawReader() - Constructor for class loci.formats.in.CanonRawReader
  Constructs a new Canon RAW reader.
canParse - Variable in class loci.formats.in.LeicaHandler
canReadAttachments() - Method in class loci.formats.in.ZeissCZIReader
canSeparateSeries - Variable in class loci.formats.in.MinimalTiffReader
  Whether or not IFDs with different dimensions can be split into separate series.
canUseBankDataDirectly(WritableRaster, int, Class<? extends DataBuffer>) - Static method in class loci.formats.gui.AWTImageTools
  Whether we can return the data buffer's bank data without performing any copy or conversion operations.
canUsePrecompressedTiles(IFormatReader, IFormatWriter, int, int) - Static method in class loci.formats.FormatTools
  Compare the given reader and writer at the specified series and resolution to see if pre-compressed tiles can be transferred directly from the reader to the writer.
canUsePrevious - Variable in class loci.formats.in.QTReader
  Flag indicating whether we can safely use prevPixels.
CANVAS_COLOR_1 - Static variable in class loci.formats.in.CellSensReader
CANVAS_COLOR_2 - Static variable in class loci.formats.in.CellSensReader
CAPTURE_EDITOR_DATA - Static variable in class loci.formats.in.NikonReader
CAPTURE_MODE - Static variable in class loci.formats.in.NDPIReader
cast(Class<?>) - Method in class loci.formats.ClassList
  Cast the given class to something that extends the base class.
category - Variable in class loci.formats.in.BaseZeissReader.Tag
category - Variable in class loci.formats.in.ZeissTIFFHandler.Scaling
category - Variable in class loci.formats.in.ZeissTIFFHandler.Tag
CAuxDoubleData() - Constructor for class loci.formats.in.SlideBook7Reader.CImageGroup.CAuxDoubleData
CAuxFloatData() - Constructor for class loci.formats.in.SlideBook7Reader.CImageGroup.CAuxFloatData
CAuxSInt32Data() - Constructor for class loci.formats.in.SlideBook7Reader.CImageGroup.CAuxSInt32Data
CAuxSInt64Data() - Constructor for class loci.formats.in.SlideBook7Reader.CImageGroup.CAuxSInt64Data
CAuxXmlData() - Constructor for class loci.formats.in.SlideBook7Reader.CImageGroup.CAuxXmlData
cBegin - Variable in class loci.plugins.in.ImporterOptions
CCD_SENSITIVITY - Static variable in class loci.formats.in.CellSensReader
CChannelDef70() - Constructor for class loci.formats.in.SlideBook7Reader.CChannelDef70
CChannelRecord70() - Constructor for class loci.formats.in.SlideBook7Reader.CChannelRecord70
cChoice - Variable in class loci.formats.gui.DataConverter
cChoice - Variable in class loci.plugins.in.SwapDialog
CCompressionBase() - Constructor for class loci.formats.in.SlideBook7Reader.CCompressionBase
CCube() - Constructor for class loci.formats.in.SlideBook7Reader.CCube
CCubeAnnotation70() - Constructor for class loci.formats.in.SlideBook7Reader.CCubeAnnotation70
cdata - Variable in class loci.formats.in.LeicaSCNReader.LeicaSCNHandler
cdata - Variable in class loci.formats.in.ZeissTIFFHandler
CDataTableHeaderRecord70() - Constructor for class loci.formats.in.SlideBook7Reader.CDataTableHeaderRecord70
CELL_LENGTH - Static variable in class loci.formats.tiff.IFD
CELL_WIDTH - Static variable in class loci.formats.tiff.IFD
CellH5Constants() - Constructor for class loci.formats.in.CellH5Reader.CellH5Constants
CellH5Coordinate(String, String, String) - Constructor for class loci.formats.in.CellH5Reader.CellH5Coordinate
CellH5PathsToImageData - Variable in class loci.formats.in.CellH5Reader
CellH5PositionList - Variable in class loci.formats.in.CellH5Reader
CellH5Reader - Class in loci.formats.in
  Reader for CellH5 (HDF) files.
CellH5Reader() - Constructor for class loci.formats.in.CellH5Reader
  Constructs a new CellH5 HDF reader.
CellH5Reader.CellH5Constants - Class in loci.formats.in
CellH5Reader.CellH5Coordinate - Class in loci.formats.in
CellH5Writer - Class in loci.formats.out
  CellH5Writer is the file format writer for CellH5 format.
CellH5Writer() - Constructor for class loci.formats.out.CellH5Writer
CellH5Writer(String, String[]) - Constructor for class loci.formats.out.CellH5Writer
cellObjectNames - Variable in class loci.formats.in.BDVReader
cellObjectNames - Variable in class loci.formats.in.CellH5Reader
cellomicsPattern - Variable in class loci.formats.in.CellomicsReader
CellomicsReader - Class in loci.formats.in
  Reader for Cellomics C01 files.
CellomicsReader() - Constructor for class loci.formats.in.CellomicsReader
  Constructs a new Cellomics reader.
CellomicsReader.ChannelFile - Class in loci.formats.in
CellSensReader - Class in loci.formats.in
  CellSensReader is the file format reader for cellSens .vsi files.
CellSensReader() - Constructor for class loci.formats.in.CellSensReader
  Constructs a new cellSens reader.
CellSensReader.Pyramid - Class in loci.formats.in
CellSensReader.TileCoordinate - Class in loci.formats.in
CellSensWidgets - Class in loci.plugins.config
  Custom widgets for configuring Bio-Formats CellSens .vsi support.
CellSensWidgets() - Constructor for class loci.plugins.config.CellSensWidgets
CellVoyagerReader - Class in loci.formats.in
  A bioformat reader for the Yokagawa Cellvoyager CV1000 automated microscope ( http://www.yokogawa.com/scanner/products/cv1000e.htm).
CellVoyagerReader() - Constructor for class loci.formats.in.CellVoyagerReader
CellVoyagerReader.AreaInfo - Class in loci.formats.in
CellVoyagerReader.ChannelInfo - Class in loci.formats.in
CellVoyagerReader.FieldInfo - Class in loci.formats.in
CellVoyagerReader.WellInfo - Class in loci.formats.in
CellWorxReader - Class in loci.formats.in
  CellWorxReader is the file format reader for CellWorx .pnl files.
CellWorxReader() - Constructor for class loci.formats.in.CellWorxReader
  Constructs a new CellWorx reader.
CellWorxReader(String, String[]) - Constructor for class loci.formats.in.CellWorxReader
cEnd - Variable in class loci.plugins.in.ImporterOptions
CENTERED_ORDER - Static variable in interface loci.formats.cache.ICacheStrategy
centerPixelValue - Variable in class loci.formats.in.DicomReader
centerX - Variable in class loci.formats.in.CellVoyagerReader.WellInfo
centerY - Variable in class loci.formats.in.CellVoyagerReader.WellInfo
certain - Variable in class loci.formats.AxisGuesser
  Whether the guesser is confident that all axis types are correct.
certain - Variable in class loci.formats.in.OMETiffReader.OMETiffPlane
  Certainty flag, for dealing with unspecified NumPlanes.
CExposureRecord70() - Constructor for class loci.formats.in.SlideBook7Reader.CExposureRecord70
cf - Variable in class org.libjpegturbo.turbojpeg.TJTransform
  Custom filter instance
CFA_PATTERN - Static variable in class loci.formats.tiff.IFD
cfaPattern - Variable in class loci.formats.in.DNGReader
cfaPattern - Variable in class loci.formats.in.NikonReader
cfdHF - Variable in class loci.formats.in.SDTInfo
cfdLH - Variable in class loci.formats.in.SDTInfo
cfdLL - Variable in class loci.formats.in.SDTInfo
cfdZC - Variable in class loci.formats.in.SDTInfo
CFG_SUFFIX - Static variable in class loci.formats.in.PerkinElmerReader
CFG_SUFFIX - Static variable in class loci.formats.in.PrairieReader
cfgFile - Variable in class loci.formats.in.PrairieReader
  The associated XML files.
CFluorDef70() - Constructor for class loci.formats.in.SlideBook7Reader.CFluorDef70
CFRAPRegionAnnotation70() - Constructor for class loci.formats.in.SlideBook7Reader.CFRAPRegionAnnotation70
CFRETManipRecord70() - Constructor for class loci.formats.in.SlideBook7Reader.CFRETManipRecord70
CHAINED_LAYERS - Static variable in class loci.formats.in.CellSensReader
chan - Variable in class loci.formats.in.SDTInfo
  Routing channel number.
CHANDESC - Static variable in class loci.formats.in.LeicaReader
changeOutputFile(String) - Method in class loci.formats.FormatWriter
changeOutputFile(String) - Method in interface loci.formats.IFormatWriter
  Switch the output file for the current dataset.
changeOutputFile(String) - Method in class loci.formats.ImageWriter
changeOutputFile(String) - Method in class loci.formats.WriterWrapper
chanMax - Variable in class loci.formats.MinMaxCalculator
  Max values for each channel.
chanMin - Variable in class loci.formats.MinMaxCalculator
  Min values for each channel.
channel - Variable in class loci.formats.dicom.DicomTile
CHANNEL - Static variable in class loci.formats.FormatTools
  Identifies the Channel dimensional type, representing a generic channel dimension.
channel - Variable in class loci.formats.in.CellomicsReader.ChannelFile
channel - Variable in class loci.formats.in.ColumbusReader.Plane
Channel() - Constructor for class loci.formats.in.CV7000Reader.Channel
Channel(CV7000Reader.Channel) - Constructor for class loci.formats.in.CV7000Reader.Channel
channel - Variable in class loci.formats.in.CV7000Reader.Plane
Channel() - Constructor for class loci.formats.in.LeicaHandler.Channel
channel - Variable in class loci.formats.in.LeicaHandler.Detector
channel - Variable in class loci.formats.in.LeicaHandler.MultiBand
Channel - Class in loci.formats.in.LeicaMicrosystemsMetadata
  This class represents image channels extracted from LMS image xmls.
Channel(int, int, double, double, String, String, long) - Constructor for class loci.formats.in.LeicaMicrosystemsMetadata.Channel
Channel() - Constructor for class loci.formats.in.OIRReader.Channel
Channel(OIRReader.Channel) - Constructor for class loci.formats.in.OIRReader.Channel
Channel() - Constructor for class loci.formats.in.OperettaReader.Channel
channel - Variable in class loci.formats.in.PrairieMetadata.PFile
  `channel` of this `<File>`.
channel - Variable in class loci.formats.in.SPCReader
Channel(String) - Constructor for class loci.formats.in.TecanReader.Channel
Channel() - Constructor for class loci.formats.in.TissueFAXSReader.Channel
Channel() - Constructor for class loci.formats.in.ZeissCZIReader.Channel
Channel.ChannelType - Enum in loci.formats.in.LeicaMicrosystemsMetadata
CHANNEL_ACQUIRE - Static variable in class loci.formats.in.ZeissLSMReader
CHANNEL_AMPLIFIER_GAIN - Static variable in class loci.formats.in.ZeissLSMReader
CHANNEL_CONTRAST_BRIGHTNESS - Static variable in class loci.formats.in.CellSensReader
CHANNEL_COUNT_TAG - Static variable in class loci.formats.in.FlowSightReader
CHANNEL_DESCS_TAG - Static variable in class loci.formats.in.FlowSightReader
CHANNEL_DETECTOR_GAIN - Static variable in class loci.formats.in.ZeissLSMReader
CHANNEL_DIM - Static variable in class loci.formats.in.CellSensReader
CHANNEL_FILTER - Static variable in class loci.formats.in.ZeissLSMReader
CHANNEL_FILTER_SET - Static variable in class loci.formats.in.ZeissLSMReader
CHANNEL_GAMMA_CORRECTION - Static variable in class loci.formats.in.CellSensReader
CHANNEL_INFO_PROPERTIES - Static variable in class loci.formats.in.CellSensReader
CHANNEL_NAME - Static variable in class loci.formats.FormatTools
CHANNEL_NAME - Static variable in class loci.formats.in.CellSensReader
CHANNEL_NAME - Static variable in class loci.formats.in.ZeissLSMReader
CHANNEL_NAMES_TAG - Static variable in class loci.formats.in.FlowSightReader
CHANNEL_NUM - Static variable in class loci.formats.FormatTools
CHANNEL_OVERFLOW - Static variable in class loci.formats.in.CellSensReader
CHANNEL_PINHOLE_DIAMETER - Static variable in class loci.formats.in.ZeissLSMReader
CHANNEL_PREFIX - Static variable in class loci.formats.in.KLBReader
  Prefixes indicating dimensions and projections
CHANNEL_PRIORITIES - Static variable in class loci.formats.in.LIFReader
CHANNEL_PROPERTIES - Static variable in class loci.formats.in.CellSensReader
CHANNEL_TAG - Static variable in class loci.formats.in.SlidebookTiffReader
CHANNEL_TRANSPARENCY_VALUE - Static variable in class loci.formats.in.CellSensReader
CHANNEL_VISIBLE - Static variable in class loci.formats.in.CellSensReader
channelBytesIncs - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.LMSMetadataExtractor
channelColor - Variable in class loci.formats.in.ColumbusReader.Plane
channelColor - Variable in class loci.formats.in.LeicaReader
channelColor - Variable in class loci.formats.in.ZeissLSMReader
channelColors - Variable in class loci.formats.in.BaseZeissReader
channelColors - Variable in class loci.formats.in.ImprovisionTiffReader
channelColors - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataTempBuffer
channelColors - Variable in class loci.formats.in.MicromanagerReader.Position
channelColors - Variable in class loci.formats.in.ND2Reader
channelCount - Variable in class loci.formats.in.CellSensReader
ChannelData() - Constructor for class loci.formats.in.FV1000Reader.ChannelData
channelDescs - Variable in class loci.formats.in.FlowSightReader
ChannelFile(String, int, int, int, int) - Constructor for class loci.formats.in.CellomicsReader.ChannelFile
ChannelFiller - Class in loci.formats
  For indexed color data representing true color, factors out the indices, replacing them with the color table values directly.
ChannelFiller() - Constructor for class loci.formats.ChannelFiller
  Constructs a ChannelFiller around a new image reader.
ChannelFiller(IFormatReader) - Constructor for class loci.formats.ChannelFiller
  Constructs a ChannelFiller with a given reader.
channelFiller - Variable in class loci.plugins.in.ImportProcess
channelId - Variable in class loci.formats.in.OIRReader.Detector
channelID - Variable in class loci.formats.in.OperettaReader.Channel
channelIDs - Variable in class loci.formats.in.IonpathMIBITiffReader
channelIndex - Variable in class loci.formats.in.CV7000Reader.Plane
channelIndexes - Variable in class loci.formats.in.BDVReader
channelIndices - Variable in class loci.formats.in.BaseZeissReader
ChannelInfo() - Constructor for class loci.formats.in.CellVoyagerReader.ChannelInfo
channelInfos - Variable in class loci.formats.in.CellVoyagerReader
channelLengths - Variable in class loci.formats.in.ICSReader
  The length of each channel axis.
channelMax - Variable in class loci.formats.in.ImarisHDFReader
ChannelMerger - Class in loci.formats
  Logic to automatically merge channels in a file.
ChannelMerger() - Constructor for class loci.formats.ChannelMerger
  Constructs a ChannelMerger around a new image reader.
ChannelMerger(IFormatReader) - Constructor for class loci.formats.ChannelMerger
  Constructs a ChannelMerger with the given reader.
channelMin - Variable in class loci.formats.in.ImarisHDFReader
channelName - Variable in class loci.formats.in.BaseZeissReader
channelName - Variable in class loci.formats.in.ColumbusReader.Plane
channelName - Variable in class loci.formats.in.ImarisHDFReader
channelName - Variable in class loci.formats.in.MetamorphHandler
channelName - Variable in class loci.formats.in.OpenlabReader.PlaneInfo
channelName - Variable in class loci.formats.in.OperettaReader.Channel
channelName - Variable in class loci.formats.in.OperettaReader.Plane
channelName - Variable in class loci.formats.in.PrairieMetadata.PFile
  `channelName` attribute of this `<File>`.
channelName - Variable in class loci.formats.in.SISReader
channelName - Variable in class loci.formats.in.TecanReader.Image
channelName - Variable in class loci.formats.in.ZeissLSMReader.DetectionChannel
channelNames - Variable in class loci.formats.dicom.DicomFileInfo
channelNames - Variable in class loci.formats.in.BDReader
channelNames - Variable in class loci.formats.in.CellSensReader.Pyramid
channelNames - Variable in class loci.formats.in.DicomReader
channelNames - Variable in class loci.formats.in.FlexReader
channelNames - Variable in class loci.formats.in.FlowSightReader
channelNames - Variable in class loci.formats.in.FluoviewReader
channelNames - Variable in class loci.formats.in.InCellReader
channelNames - Variable in class loci.formats.in.IonpathMIBITiffReader
channelNames - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataTempBuffer
channelNames - Variable in class loci.formats.in.LeicaReader
channelNames - Variable in class loci.formats.in.LIFReader
channelNames - Variable in class loci.formats.in.MetamorphHandler
channelNames - Variable in class loci.formats.in.ND2Handler
channelNames - Variable in class loci.formats.in.ScanrReader
channelNames - Variable in class loci.formats.in.SlidebookTiffReader
channelNames - Variable in class loci.formats.in.VolocityReader.Stack
channelNames - Variable in class loci.formats.in.ZeissLSMReader
channelNumber - Variable in class loci.formats.in.CellVoyagerReader.ChannelInfo
channelNumber - Variable in class loci.plugins.util.RecordedImageProcessor
channelOrder - Variable in class loci.formats.in.PhotoshopTiffReader
channelPrios - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataTempBuffer
channels - Variable in class loci.formats.codec.CodecOptions
  Number of channels.
channels - Variable in class loci.formats.in.CV7000Reader
channels - Variable in class loci.formats.in.FV1000Reader
channels - Variable in class loci.formats.in.KLBReader
channels - Variable in class loci.formats.in.LeicaHandler
channels - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataTempBuffer
channels - Variable in class loci.formats.in.LiFlimReader
channels - Variable in class loci.formats.in.MicromanagerReader.Position
channels - Variable in class loci.formats.in.OIRReader
channels - Variable in class loci.formats.in.OperettaReader.OperettaHandler
channels - Variable in class loci.formats.in.PrairieReader
  List of active channels.
channels - Variable in class loci.formats.in.SDTInfo
channels - Variable in class loci.formats.in.SDTReader
  Number of spectral channels.
channels - Variable in class loci.formats.in.TecanReader
channels - Variable in class loci.formats.in.TextReader
  List of channel labels.
channels - Variable in class loci.formats.in.TissueFAXSReader.ScanRegion
channels - Variable in class loci.formats.in.ZeissCZIReader
ChannelSeparator - Class in loci.formats
  Logic to automatically separate the channels in a file.
ChannelSeparator() - Constructor for class loci.formats.ChannelSeparator
  Constructs a ChannelSeparator around a new image reader.
ChannelSeparator(IFormatReader) - Constructor for class loci.formats.ChannelSeparator
  Constructs a ChannelSeparator with the given reader.
channelSeparator - Variable in class loci.plugins.in.ImportProcess
channelsPerTimepoint - Variable in class loci.formats.in.InCellReader
channelTag - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.Channel
channelType - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.Channel
ChannelType() - Constructor for enum loci.formats.in.LeicaMicrosystemsMetadata.Channel.ChannelType
channelType - Variable in class loci.formats.in.OperettaReader.Channel
channelType - Variable in class loci.formats.in.OperettaReader.Plane
channelTypes - Variable in class loci.formats.in.ICSReader
  The type of each channel axis.
channelWavelengths - Variable in class loci.formats.in.CellSensReader.Pyramid
CHAR - Static variable in class loci.formats.in.CellSensReader
CHAR - Static variable in class loci.formats.in.GatanReader
characters(char[], int, int) - Method in class loci.formats.in.AFIReader.AFIHandler
characters(char[], int, int) - Method in class loci.formats.in.BDVReader.BDVXMLHandler
characters(char[], int, int) - Method in class loci.formats.in.BioRadSCNReader.SCNHandler
characters(char[], int, int) - Method in class loci.formats.in.ColumbusReader.MeasurementHandler
characters(char[], int, int) - Method in class loci.formats.in.CV7000Reader.MeasurementDataHandler
characters(char[], int, int) - Method in class loci.formats.in.CV7000Reader.MeasurementSettingsHandler
characters(char[], int, int) - Method in class loci.formats.in.FEITiffReader.FEIHandler
characters(char[], int, int) - Method in class loci.formats.in.FlexReader.FlexHandler
characters(char[], int, int) - Method in class loci.formats.in.ImaconReader.ImaconHandler
characters(char[], int, int) - Method in class loci.formats.in.InCellReader.InCellHandler
characters(char[], int, int) - Method in class loci.formats.in.IvisionReader.IvisionHandler
characters(char[], int, int) - Method in class loci.formats.in.LeicaSCNReader.LeicaSCNHandler
characters(char[], int, int) - Method in class loci.formats.in.OMEXMLReader.OMEXMLHandler
characters(char[], int, int) - Method in class loci.formats.in.OperettaReader.OperettaHandler
characters(char[], int, int) - Method in class loci.formats.in.ScanrReader.ScanrHandler
characters(char[], int, int) - Method in class loci.formats.in.ZeissTIFFHandler
characters(char[], int, int) - Method in class loci.formats.out.OMEXMLWriter.OMEHandler
charData - Variable in class loci.formats.in.FlexReader.FlexHandler
CHARS - Static variable in class loci.formats.tools.AsciiImage
Charset(int, String) - Constructor for enum loci.formats.in.BaseZeissReader.Charset
charset - Variable in class loci.formats.in.BaseZeissReader.Shape
CHECK - Static variable in class loci.formats.in.ZeissLMSReader
checkBufferSize(IFormatReader, int) - Static method in class loci.formats.FormatTools
checkBufferSize(IFormatReader, int, int, int) - Static method in class loci.formats.FormatTools
  Checks that the given buffer size is large enough to hold a w * h image as returned by the given reader.
checkClass(String) - Static method in class loci.plugins.util.LibraryChecker
  Checks whether the given class is available.
checkCommentImageJ(String) - Method in class loci.formats.in.TiffReader
checkCommentMetamorph(String) - Method in class loci.formats.in.TiffReader
checkElement(Element, String) - Method in class loci.formats.in.PrairieMetadata
  Checks that the given element has the specified name.
checkFlip(boolean, Length) - Method in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataStoreInitializer
checkFlip(boolean, Length) - Method in class loci.formats.in.LIFReader
checkForLofLayout(RandomAccessInputStream, String) - Method in class loci.formats.in.LOFReader
  Checks if file layout meets lof file specifications
checkHeader() - Method in class loci.formats.tiff.TiffParser
  Checks the TIFF header.
checkImageFormat() - Method in class loci.formats.in.LeicaMicrosystemsMetadata.XlifDocument
checkImageIndex(int) - Method in class loci.formats.ome.OMEPyramidStore
  Verify that the given index is non-negative and less than the Image count.
checkImageJ() - Static method in class loci.plugins.util.LibraryChecker
  Checks whether ImageJ is new enough for the Bio-Formats plugins.
checkImageJ(String, String) - Static method in class loci.plugins.util.LibraryChecker
  Returns true the current ImageJ version is greater than or equal to the specified version.
checkImageJ(String, String, String) - Static method in class loci.plugins.util.LibraryChecker
  Returns true the current ImageJ version is greater than or equal to the specified version.
checkJava() - Static method in class loci.plugins.util.LibraryChecker
  Checks for a new enough version of the Java Runtime Environment.
checkKey(String, String) - Method in class loci.formats.in.MetamorphHandler
  Check if the value needs to be saved.
checkKey(String, String) - Method in class loci.plugins.in.ImporterOptions
  Tests whether the given boolean key is set in the specified options.
checkLatest(String, String) - Static method in class loci.plugins.config.InstallWizard
checkLibrary(LibraryChecker.Library, HashSet<String>) - Static method in class loci.plugins.util.LibraryChecker
  Checks for a required library.
checkLibrary(String, String, HashSet<String>) - Static method in class loci.plugins.util.LibraryChecker
  Checks whether the given class is available; if not, adds the specified JAR file name to the hash set (presumably to report it missing to the user).
checkMissing(HashSet<String>) - Static method in class loci.plugins.util.LibraryChecker
  Reports missing libraries in the given hash set to the user.
checkObsoleteOptions() - Method in class loci.plugins.in.ImporterOptions
  Handles obsolete macro keys, for backward compatibility.
checkPALM(String) - Method in class loci.formats.in.ZeissCZIReader
checkParams(int, byte[], int, int, int, int) - Method in class loci.formats.FormatWriter
  Ensure that the arguments that are being passed to saveBytes(...) are valid.
checkParams - Variable in class loci.formats.out.TiffWriter
  Whether or not to check the parameters passed to saveBytes.
checkPerformed - Static variable in class loci.plugins.in.UpgradeDialog
  Whether an upgrade check has already been performed this session.
checkPixelCount(boolean) - Method in class loci.formats.out.DicomWriter
checkPlaneNumber(IFormatReader, int) - Static method in class loci.formats.FormatTools
  Checks that the given plane number is valid for the given reader.
checkPlaneParameters(IFormatReader, int, int, int, int, int, int) - Static method in class loci.formats.FormatTools
  Convenience method for checking that the plane number, tile size and buffer sizes are all valid for the given reader.
checkPoints(int) - Method in enum loci.formats.in.BaseZeissReader.FeatureType
checkPrecompressedSupport() - Method in class loci.formats.out.DicomWriter
  Check if pre-compressed tiles are supported with the current options.
checkResolutionIndex(int, int) - Method in class loci.formats.ome.OMEPyramidStore
  Verify that the given image and resolution indices are valid.
checkSuffix(String, String) - Static method in class loci.formats.FormatHandler
  Performs suffix matching for the given filename.
checkSuffix(String, String[]) - Static method in class loci.formats.FormatHandler
  Performs suffix matching for the given filename.
checkTileSize(IFormatReader, int, int, int, int) - Static method in class loci.formats.FormatTools
  Checks that the given tile size is valid for the given reader.
checkTime(long, int, long, long) - Method in class loci.formats.in.TextReader
checkUnit(String, String...) - Method in class loci.formats.in.ICSReader
  Verifies that a unit matches the expected value.
children - Variable in class loci.formats.dicom.DicomTag
children - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.LMSCollectionXmlDocument
CHIP_SIZE_X - Static variable in class loci.formats.in.FluoviewReader
CHIP_SIZE_Y - Static variable in class loci.formats.in.FluoviewReader
CHistogramRecord70() - Constructor for class loci.formats.in.SlideBook7Reader.CHistogramRecord70
chksum - Variable in class loci.formats.in.SDTInfo
CHUNK_SIZE - Static variable in class loci.formats.UpgradeChecker
  Number of bytes to read from the CI server at a time.
chunkFilePositions - Variable in class loci.formats.in.OBFReader.Stack
chunkFileStart - Variable in class loci.formats.in.OBFReader.State
chunkLogicalPositions - Variable in class loci.formats.in.OBFReader.Stack
chunkLogicalStart - Variable in class loci.formats.in.OBFReader.State
ChunkMapEntry() - Constructor for class loci.formats.in.ND2Reader.ChunkMapEntry
chunkSize - Variable in class loci.formats.in.OBFReader.State
chunkSizes - Variable in class loci.formats.in.QTReader
  Number of bytes in each plane.
CI_SERVER - Static variable in class loci.formats.UpgradeChecker
  Location of the OME continuous integration server.
CImageData() - Constructor for class loci.formats.in.SlideBook7Reader.CImageData
CImageGroup(SlideBook7Reader.CSBFile70, String) - Constructor for class loci.formats.in.SlideBook7Reader.CImageGroup
CImageRecord70() - Constructor for class loci.formats.in.SlideBook7Reader.CImageRecord70
cIndex - Variable in class loci.formats.in.BaseZeissReader
cIndex - Variable in class loci.plugins.util.DataBrowser
CIRCLE - Static variable in class loci.formats.in.FV1000Reader
CIRCLE - Static variable in class loci.formats.in.ZeissLSMReader
CIRCLE_3POINT - Static variable in class loci.formats.in.ZeissLSMReader
cLabel - Variable in class loci.formats.gui.DataConverter
CLASS_IMAGE_5D - Static variable in class loci.plugins.in.ImporterOptions
CLASS_LABELS - Static variable in class loci.formats.in.BDVReader.H5Constants
CLASS_LABELS - Static variable in class loci.formats.in.CellH5Reader.CellH5Constants
CLASS_VIEW_5D - Static variable in class loci.plugins.in.ImporterOptions
ClassDecoder() - Constructor for class loci.formats.in.SlideBook7Reader.ClassDecoder
classes - Variable in class loci.formats.ClassList
  List of classes.
classes - Variable in class loci.formats.in.BDVReader
classes - Variable in class loci.formats.in.CellH5Reader
ClassList<T> - Class in loci.formats
  ClassList is a list of classes for use with `ImageReader` or `ImageWriter`, parsed from a configuration file such as readers.txt or writers.txt.
ClassList(Class<T>) - Constructor for class loci.formats.ClassList
  Constructs a list of classes, initially empty.
ClassList(String, Class<T>) - Constructor for class loci.formats.ClassList
  Constructs a list of classes from the given configuration file.
ClassList(String, Class<T>, Class<?>) - Constructor for class loci.formats.ClassList
  Constructs a list of classes from the given configuration file.
classList - Variable in class loci.formats.FileStitcher
cleanup() - Method in class loci.formats.Memoizer
clear() - Method in class loci.formats.codec.ByteVector
clear() - Method in class loci.formats.MetadataList
  Clear the array.
clear(int) - Method in class loci.formats.MetadataList
  Clear the specified primary array element.
clearSeries() - Method in class loci.plugins.in.ImporterOptions
clearXML() - Method in class loci.formats.in.ZeissCZIReader.Metadata
cLengths - Variable in class loci.plugins.util.DataBrowser
CLensDef70() - Constructor for class loci.formats.in.SlideBook7Reader.CLensDef70
CLIPPING - Static variable in class loci.formats.in.CellSensReader
CLIPPING_MAGIC_STRING - Static variable in class loci.formats.in.VolocityClippingReader
CLIPPING_STATE - Static variable in class loci.formats.in.CellSensReader
clippingData - Variable in class loci.formats.in.VolocityReader.Stack
CLOCKWISE - Static variable in class loci.formats.in.FluoviewReader
clone() - Method in class loci.formats.CoreMetadata
clone(IFormatReader, int) - Method in class loci.formats.CoreMetadata
clone() - Method in class loci.formats.SwappableMetadata
clone(IFormatReader, int) - Method in class loci.formats.SwappableMetadata
close(boolean) - Method in class loci.formats.ChannelSeparator
close() - Method in class loci.formats.codec.JPEGTileDecoder
close(boolean) - Method in class loci.formats.DelegateReader
close() - Method in class loci.formats.FileStitcher
close(boolean) - Method in class loci.formats.FileStitcher
close() - Method in class loci.formats.FileStitcher.ExternalSeries
close(boolean) - Method in class loci.formats.FileStitcher.ExternalSeries
close(boolean) - Method in class loci.formats.FormatReader
close() - Method in class loci.formats.FormatReader
close() - Method in class loci.formats.FormatWriter
close() - Method in class loci.formats.gui.PreviewPane
  Closes the underlying image reader.
close(boolean) - Method in interface loci.formats.IFormatReader
  Closes the currently open file.
close(boolean) - Method in class loci.formats.ImageReader
close() - Method in class loci.formats.ImageReader
close() - Method in class loci.formats.ImageWriter
close(boolean) - Method in class loci.formats.in.AFIReader
close(boolean) - Method in class loci.formats.in.AIMReader
close(boolean) - Method in class loci.formats.in.AliconaReader
close(boolean) - Method in class loci.formats.in.AmiraReader
close(boolean) - Method in class loci.formats.in.AnalyzeReader
close(boolean) - Method in class loci.formats.in.APLReader
close(boolean) - Method in class loci.formats.in.APNGReader
close(boolean) - Method in class loci.formats.in.AVIReader
close(boolean) - Method in class loci.formats.in.BaseZeissReader
close(boolean) - Method in class loci.formats.in.BDReader
close(boolean) - Method in class loci.formats.in.BDVReader
close(boolean) - Method in class loci.formats.in.BioRadReader
close(boolean) - Method in class loci.formats.in.BioRadSCNReader
close(boolean) - Method in class loci.formats.in.BMPReader
close(boolean) - Method in class loci.formats.in.BrukerReader
close(boolean) - Method in class loci.formats.in.BurleighReader
close(boolean) - Method in class loci.formats.in.CanonRawReader
close(boolean) - Method in class loci.formats.in.CellH5Reader
close(boolean) - Method in class loci.formats.in.CellomicsReader
close(boolean) - Method in class loci.formats.in.CellSensReader
close(boolean) - Method in class loci.formats.in.CellWorxReader
close(boolean) - Method in class loci.formats.in.ColumbusReader
close(boolean) - Method in class loci.formats.in.CV7000Reader
close(boolean) - Method in class loci.formats.in.DCIMGReader
close(boolean) - Method in class loci.formats.in.DeltavisionReader
close(boolean) - Method in class loci.formats.in.DicomReader
close(boolean) - Method in class loci.formats.in.DNGReader
close(boolean) - Method in class loci.formats.in.EPSReader
close(boolean) - Method in class loci.formats.in.FakeReader
close(boolean) - Method in class loci.formats.in.FEIReader
close(boolean) - Method in class loci.formats.in.FEITiffReader
close(boolean) - Method in class loci.formats.in.FitsReader
close(boolean) - Method in class loci.formats.in.FlexReader
close(boolean) - Method in class loci.formats.in.FlowSightReader
close(boolean) - Method in class loci.formats.in.FluoviewReader
close(boolean) - Method in class loci.formats.in.FujiReader
close(boolean) - Method in class loci.formats.in.FV1000Reader
close(boolean) - Method in class loci.formats.in.GatanDM2Reader
close(boolean) - Method in class loci.formats.in.GatanReader
close(boolean) - Method in class loci.formats.in.GIFReader
close(boolean) - Method in class loci.formats.in.HamamatsuVMSReader
close(boolean) - Method in class loci.formats.in.HitachiReader
close(boolean) - Method in class loci.formats.in.HRDGDFReader
close(boolean) - Method in class loci.formats.in.ICSReader
close(boolean) - Method in class loci.formats.in.IM3Reader
close(boolean) - Method in class loci.formats.in.ImaconReader
close(boolean) - Method in class loci.formats.in.ImageIOReader
close(boolean) - Method in class loci.formats.in.ImagicReader
close(boolean) - Method in class loci.formats.in.ImarisHDFReader
close(boolean) - Method in class loci.formats.in.ImarisReader
close(boolean) - Method in class loci.formats.in.IMODReader
close(boolean) - Method in class loci.formats.in.ImprovisionTiffReader
close(boolean) - Method in class loci.formats.in.ImspectorReader
close(boolean) - Method in class loci.formats.in.InCell3000Reader
close(boolean) - Method in class loci.formats.in.InCellReader
close(boolean) - Method in class loci.formats.in.InveonReader
close(boolean) - Method in class loci.formats.in.IonpathMIBITiffReader
close(boolean) - Method in class loci.formats.in.IPLabReader
close(boolean) - Method in class loci.formats.in.IPWReader
close(boolean) - Method in class loci.formats.in.IvisionReader
close(boolean) - Method in class loci.formats.in.JDCEReader
close(boolean) - Method in class loci.formats.in.JEOLReader
close(boolean) - Method in class loci.formats.in.JPEG2000Reader
close(boolean) - Method in class loci.formats.in.JPEGReader
close(boolean) - Method in class loci.formats.in.JPXReader
close(boolean) - Method in class loci.formats.in.KhorosReader
close(boolean) - Method in class loci.formats.in.KLBReader
close(boolean) - Method in class loci.formats.in.KodakReader
close(boolean) - Method in class loci.formats.in.L2DReader
close(boolean) - Method in class loci.formats.in.LeicaMicrosystemsMetadata.LMSFileReader
close(boolean) - Method in class loci.formats.in.LeicaMicrosystemsMetadata.MultipleImagesReader
close(boolean) - Method in class loci.formats.in.LeicaReader
close(boolean) - Method in class loci.formats.in.LeicaSCNReader
close(boolean) - Method in class loci.formats.in.LiFlimReader
close(boolean) - Method in class loci.formats.in.LIFReader
close(boolean) - Method in class loci.formats.in.LIMReader
close(boolean) - Method in class loci.formats.in.LOFReader
close(boolean) - Method in class loci.formats.in.MetamorphReader
close(boolean) - Method in class loci.formats.in.MetamorphTiffReader
close(boolean) - Method in class loci.formats.in.MIASReader
close(boolean) - Method in class loci.formats.in.MicroCTReader
close(boolean) - Method in class loci.formats.in.MicromanagerReader
close(boolean) - Method in class loci.formats.in.MINCReader
close(boolean) - Method in class loci.formats.in.MinimalTiffReader
close(boolean) - Method in class loci.formats.in.MNGReader
close(boolean) - Method in class loci.formats.in.MolecularImagingReader
close(boolean) - Method in class loci.formats.in.MRCReader
close(boolean) - Method in class loci.formats.in.MRWReader
close(boolean) - Method in class loci.formats.in.NAFReader
close(boolean) - Method in class loci.formats.in.ND2Reader
close(boolean) - Method in class loci.formats.in.NDPIReader
close(boolean) - Method in class loci.formats.in.NDPISReader
close(boolean) - Method in class loci.formats.in.NiftiReader
close(boolean) - Method in class loci.formats.in.NikonElementsTiffReader
close(boolean) - Method in class loci.formats.in.NikonReader
close(boolean) - Method in class loci.formats.in.NikonTiffReader
close(boolean) - Method in class loci.formats.in.NRRDReader
close(boolean) - Method in class loci.formats.in.OBFReader
close(boolean) - Method in class loci.formats.in.OIRReader
close(boolean) - Method in class loci.formats.in.OlympusTileReader
close(boolean) - Method in class loci.formats.in.OMETiffReader
close(boolean) - Method in class loci.formats.in.OMEXMLReader
close(boolean) - Method in class loci.formats.in.OpenlabRawReader
close(boolean) - Method in class loci.formats.in.OpenlabReader
close(boolean) - Method in class loci.formats.in.OperettaReader
close(boolean) - Method in class loci.formats.in.PCIReader
close(boolean) - Method in class loci.formats.in.PCORAWReader
close(boolean) - Method in class loci.formats.in.PCXReader
close(boolean) - Method in class loci.formats.in.PDSReader
close(boolean) - Method in class loci.formats.in.PerkinElmerReader
close(boolean) - Method in class loci.formats.in.PGMReader
close(boolean) - Method in class loci.formats.in.PhotoshopTiffReader
close(boolean) - Method in class loci.formats.in.PictReader
close(boolean) - Method in class loci.formats.in.PQBinReader
close(boolean) - Method in class loci.formats.in.PrairieReader
close(boolean) - Method in class loci.formats.in.PSDReader
close(boolean) - Method in class loci.formats.in.QTReader
close(boolean) - Method in class loci.formats.in.QuesantReader
close(boolean) - Method in class loci.formats.in.RHKReader
close(boolean) - Method in class loci.formats.in.SBIGReader
close(boolean) - Method in class loci.formats.in.ScanrReader
close(boolean) - Method in class loci.formats.in.SDTReader
close(boolean) - Method in class loci.formats.in.SEQReader
close(boolean) - Method in class loci.formats.in.SIFReader
close(boolean) - Method in class loci.formats.in.SimplePCITiffReader
close(boolean) - Method in class loci.formats.in.SISReader
close(boolean) - Method in class loci.formats.in.SlideBook7Reader
close(boolean) - Method in class loci.formats.in.SlidebookReader
close(boolean) - Method in class loci.formats.in.SlidebookTiffReader
close(boolean) - Method in class loci.formats.in.SPCReader
close(boolean) - Method in class loci.formats.in.SPEReader
close(boolean) - Method in class loci.formats.in.SpiderReader
close(boolean) - Method in class loci.formats.in.SVSReader
close(boolean) - Method in class loci.formats.in.TargaReader
close(boolean) - Method in class loci.formats.in.TCSReader
close(boolean) - Method in class loci.formats.in.TecanReader
close(boolean) - Method in class loci.formats.in.TextReader
close(boolean) - Method in class loci.formats.in.TiffReader
close(boolean) - Method in class loci.formats.in.TileJPEGReader
close(boolean) - Method in class loci.formats.in.TillVisionReader
close(boolean) - Method in class loci.formats.in.TissueFAXSReader
close(boolean) - Method in class loci.formats.in.TopometrixReader
close(boolean) - Method in class loci.formats.in.TrestleReader
close(boolean) - Method in class loci.formats.in.UBMReader
close(boolean) - Method in class loci.formats.in.UnisokuReader
close(boolean) - Method in class loci.formats.in.VarianFDFReader
close(boolean) - Method in class loci.formats.in.VectraReader
close(boolean) - Method in class loci.formats.in.VeecoReader
close(boolean) - Method in class loci.formats.in.VentanaReader
close(boolean) - Method in class loci.formats.in.VisitechReader
close(boolean) - Method in class loci.formats.in.VolocityClippingReader
close(boolean) - Method in class loci.formats.in.VolocityReader
close(boolean) - Method in class loci.formats.in.XLEFReader
close(boolean) - Method in class loci.formats.in.ZeissCZIReader
close() - 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.ZeissXRMReader
close(boolean) - Method in class loci.formats.in.ZeissZVIReader
close(boolean) - Method in class loci.formats.in.ZipReader
close() - Method in class loci.formats.Memoizer
close(boolean) - Method in class loci.formats.Memoizer
close() - Method in interface loci.formats.Memoizer.Deser
close() - Method in class loci.formats.Memoizer.KryoDeser
close(boolean) - Method in class loci.formats.MinMaxCalculator
close() - Method in class loci.formats.out.APNGWriter
close() - Method in class loci.formats.out.AVIWriter
close() - Method in class loci.formats.out.CellH5Writer
close() - Method in class loci.formats.out.DicomWriter
close() - Method in class loci.formats.out.ICSWriter
close() - Method in class loci.formats.out.JavaWriter
close() - Method in class loci.formats.out.OMETiffWriter
close() - Method in class loci.formats.out.OMEXMLWriter
close() - Method in class loci.formats.out.PyramidOMETiffWriter
close() - Method in class loci.formats.out.QTWriter
close() - Method in class loci.formats.out.TiffWriter
close() - Method in class loci.formats.out.V3DrawWriter
close(boolean) - Method in class loci.formats.ReaderWrapper
close() - Method in class loci.formats.ReaderWrapper
close() - Method in interface loci.formats.services.EXIFService
close() - Method in class loci.formats.services.EXIFServiceImpl
close() - Method in interface loci.formats.services.JHDFService
  Closes and resets the service.
close() - Method in class loci.formats.services.JHDFServiceImpl
close() - Method in interface loci.formats.services.JPEGTurboService
  Free resources associated with the initialized stream.
close() - Method in class loci.formats.services.JPEGTurboServiceImpl
close() - Method in interface loci.formats.services.MDBService
  Close the currently initialized file.
close() - Method in class loci.formats.services.MDBServiceImpl
close() - Method in interface loci.formats.services.MetakitService
close() - Method in class loci.formats.services.MetakitServiceImpl
close() - Method in interface loci.formats.services.NetCDFService
  Closes and resets the service.
close() - Method in class loci.formats.services.NetCDFServiceImpl
close() - Method in interface loci.formats.services.POIService
  Close the current POI file system.
close() - Method in class loci.formats.services.POIServiceImpl
close(boolean) - Method in class loci.formats.SubResolutionFormatReader
close() - Method in class loci.formats.tiff.OnDemandLongArray
close() - Method in class loci.formats.tiff.TiffParser
  Close the underlying stream, if this TiffParser was constructed with a file path.
close() - Method in class loci.formats.tiff.TiffSaver
  Closes the output stream if not null.
close(boolean) - Method in class loci.formats.WrappedReader
close() - Method in class loci.formats.WrappedReader
close() - Method in class loci.formats.WriterWrapper
close() - Method in class loci.plugins.config.TextAreaWriter
  Closing a TextAreaWriter does nothing.
close() - Method in class loci.plugins.macro.LociFunctions
close() - Method in class loci.plugins.util.VirtualImagePlus
close() - Method in class loci.plugins.util.VirtualReader
close() - Method in class org.libjpegturbo.turbojpeg.TJCompressor
  Free the native structures associated with this compressor instance.
close() - Method in class org.libjpegturbo.turbojpeg.TJDecompressor
  Free the native structures associated with this decompressor instance.
CLOSED_ARROW - Static variable in class loci.formats.in.ZeissLSMReader
CLOSED_BEZIER - Static variable in class loci.formats.in.ZeissLSMReader
CLOSED_POLYLINE - Static variable in class loci.formats.in.ZeissLSMReader
CloseFile() - Method in class loci.formats.in.SlideBook7Reader.DataLoader
closeFileOnly() - Method in class loci.plugins.macro.LociFunctions
cm - Variable in class loci.formats.FormatWriter
  Default color model.
CMainViewRecord70() - Constructor for class loci.formats.in.SlideBook7Reader.CMainViewRecord70
CMaskPositions() - Constructor for class loci.formats.in.SlideBook7Reader.CImageGroup.CMaskPositions
CMaskRecord70() - Constructor for class loci.formats.in.SlideBook7Reader.CMaskRecord70
cNames - Variable in class loci.formats.in.ImprovisionTiffReader
CNpyHeader() - Constructor for class loci.formats.in.SlideBook7Reader.CNpyHeader
co2Percent - Variable in class loci.formats.in.ZeissCZIReader
COARSE_FRAME_IFD - Static variable in class loci.formats.in.CellSensReader
COARSE_PYRAMID_LEVEL - Static variable in class loci.formats.in.CellSensReader
code - Variable in enum loci.formats.codec.CompressionType
  Code for the compression.
code - Variable in enum loci.formats.codec.JPEG2000BoxType
  Code for the box type.
code - Variable in enum loci.formats.codec.JPEG2000SegmentMarker
  Code for the segment marker.
code - Variable in enum loci.formats.dicom.DicomVR
code - Variable in class loci.formats.in.FV1000Reader
code - Variable in enum loci.formats.tiff.IFDType
  Code for the IFD type in the actual TIFF file.
code - Variable in enum loci.formats.tiff.PhotoInterp
  Code for the IFD type in the actual TIFF file.
code - Variable in enum loci.formats.tiff.TiffCompression
  Code for the TIFF compression in the actual TIFF file.
codeBlockSize - Variable in class loci.formats.codec.JPEG2000CodecOptions
  The maximum code-block size to use per tile-component as it would be provided to: `J2KImageWriteParam.setCodeBlockSize(int[])` (WRITE).
Codec - Interface in loci.formats.codec
  This class is an interface for any kind of compression or decompression.
codec - Variable in class loci.formats.codec.WrappedCodec
codec - Variable in class loci.formats.gui.DataConverter
codec - Variable in class loci.formats.in.ND2Reader
  Codec to use when decompressing pixel data.
codec - Variable in class loci.formats.in.QTReader
  Video codec used by this movie.
codec - Variable in class loci.formats.out.QTWriter
  The codec to use.
codec - Variable in enum loci.formats.tiff.TiffCompression
  TIFF compression codec.
CODEC_ANIMATION - Static variable in class loci.formats.out.QTWriter
  Value indicating Animation codec.
CODEC_CINEPAK - Static variable in class loci.formats.out.QTWriter
  Value indicating Cinepak codec.
CODEC_H_263 - Static variable in class loci.formats.out.QTWriter
  Value indicating H.263 codec.
CODEC_MOTION_JPEG_B - Static variable in class loci.formats.out.QTWriter
  Value indicating Motion JPEG-B codec.
CODEC_MPEG_4 - Static variable in class loci.formats.out.QTWriter
  Value indicating MPEG-4 codec.
CODEC_RAW - Static variable in class loci.formats.out.QTWriter
  Value indicating Raw codec.
CODEC_SORENSON - Static variable in class loci.formats.out.QTWriter
  Value indicating Sorenson codec.
CODEC_SORENSON_3 - Static variable in class loci.formats.out.QTWriter
  Value indicating Sorenson 3 codec.
codecName - Variable in enum loci.formats.tiff.TiffCompression
  Name of the TIFF compression codec.
CodecOptions - Class in loci.formats.codec
  Options for compressing and decompressing data.
CodecOptions() - Constructor for class loci.formats.codec.CodecOptions
  Construct a new CodecOptions.
CodecOptions(CodecOptions) - Constructor for class loci.formats.codec.CodecOptions
  Construct a new CodecOptions using the given CodecOptions.
codecOptions - Variable in class loci.formats.tiff.TiffParser
  Codec options to be used when decoding compressed pixel data.
codestreamOffset - Variable in class loci.formats.in.JPEG2000MetadataParser
  Offset to first contiguous codestream.
codestreamPixelType - Variable in class loci.formats.in.JPEG2000MetadataParser
  Pixel type as specified in the JPEG 2000 codestream..
codestreamSizeC - Variable in class loci.formats.in.JPEG2000MetadataParser
  Number of channels the image as specified in the JPEG 2000 codestream.
codestreamSizeX - Variable in class loci.formats.in.JPEG2000MetadataParser
  Width of the image as specified in the JPEG 2000 codestream.
codestreamSizeY - Variable in class loci.formats.in.JPEG2000MetadataParser
  Height of the image as specified in the JPEG 2000 codestream.
cOffset - Variable in class loci.formats.out.DicomWriter.PlaneOffset
col - Variable in class loci.formats.in.CellomicsReader.ChannelFile
col - Variable in class loci.formats.in.CellVoyagerReader.WellInfo
col - Variable in class loci.formats.in.ColumbusReader.Plane
col - Variable in class loci.formats.in.OperettaReader.Plane
col - Variable in class loci.formats.in.ZeissCZIReader.SubBlock
colCount - Variable in class loci.formats.in.BaseZeissReader
collection - Variable in class loci.formats.in.LeicaHandler
collection - Variable in class loci.formats.in.LeicaSCNReader.LeicaSCNHandler
COLLECTION_VOLUME - Static variable in class loci.formats.in.CellSensReader
colName - Variable in class loci.formats.in.InCellReader
color - Variable in class loci.formats.in.CellVoyagerReader.ChannelInfo
color - Variable in class loci.formats.in.CV7000Reader.Channel
color - Variable in class loci.formats.in.LeicaHandler.ROI
color - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.ROI
color - Variable in class loci.formats.in.LIFReader.ROI
color - Variable in class loci.formats.in.OIRReader.Channel
color - Variable in class loci.formats.in.TissueFAXSReader.Channel
color - Variable in class loci.formats.in.ZeissCZIReader.Channel
color16 - Variable in class loci.formats.in.IvisionReader
COLOR_BAR - Static variable in class loci.formats.in.FV1000Reader
COLOR_MAP - Static variable in class loci.formats.in.CanonRawReader
COLOR_MAP - Static variable in class loci.formats.in.DNGReader
COLOR_MAP - Static variable in class loci.formats.in.NikonReader
COLOR_MAP - Static variable in class loci.formats.tiff.IFD
COLOR_MAP_1 - Static variable in class loci.formats.in.MRWReader
COLOR_MAP_2 - Static variable in class loci.formats.in.MRWReader
COLOR_MODE - Static variable in class loci.formats.in.NikonReader
COLOR_MODE_COLORIZED - Static variable in class loci.plugins.in.ImporterOptions
COLOR_MODE_COMPOSITE - Static variable in class loci.plugins.in.ImporterOptions
COLOR_MODE_CUSTOM - Static variable in class loci.plugins.in.ImporterOptions
COLOR_MODE_DEFAULT - Static variable in class loci.plugins.in.ImporterOptions
COLOR_MODE_GRAYSCALE - Static variable in class loci.plugins.in.ImporterOptions
COLOR_SPACE - Static variable in class loci.formats.in.CellSensReader
COLOR_SPACE - Static variable in class loci.formats.tiff.IFD
ColorDialog - Class in loci.plugins.in
  Bio-Formats Importer custom color chooser dialog box.
ColorDialog(ImportProcess) - Constructor for class loci.plugins.in.ColorDialog
colorize - Variable in class loci.plugins.util.BFVirtualStack
Colorizer - Class in loci.plugins.in
  Logic for colorizing images.
Colorizer(ImportProcess) - Constructor for class loci.plugins.in.Colorizer
colorMap - Variable in class loci.formats.in.TargaReader
colorModeChoice - Variable in class loci.plugins.in.MainDialog
colorModel - Variable in class loci.formats.codec.CodecOptions
  Color model to use when constructing an image (WRITE).
COLORS - Variable in class loci.formats.in.BDVReader
COLORS - Variable in class loci.formats.in.CellH5Reader
colors - Variable in class loci.formats.in.ImarisHDFReader
colors - Variable in class loci.formats.in.IMODReader
colors - Variable in class loci.formats.in.ND2Handler
colors - Variable in class loci.formats.in.ND2Reader
COLORSPACE - Static variable in class loci.formats.in.CellSensReader
colorTables - Variable in class loci.formats.in.GIFReader
cols - Variable in class loci.formats.in.CellSensReader
colT - Variable in class loci.formats.in.SDTInfo
ColumbusReader - Class in loci.formats.in
  ColumbusReader is the file format reader for screens exported from PerkinElmer Columbus.
ColumbusReader() - Constructor for class loci.formats.in.ColumbusReader
  Constructs a new Columbus reader.
ColumbusReader.MeasurementHandler - Class in loci.formats.in
ColumbusReader.Plane - Class in loci.formats.in
column - Variable in class loci.formats.in.CV7000Reader.Field
column - Variable in class loci.formats.in.FlexReader.FlexFile
column - Variable in class loci.formats.in.OMEXMLReader.BinData
column - Variable in class loci.formats.tools.AmiraParameters
columnIndex - Variable in class loci.formats.internal.WellContainer
COLUMNS - Static variable in class loci.formats.gui.DataConverter
ComboFileFilter - Class in loci.formats.gui
  A file filter that recognizes files from a union of other filters.
ComboFileFilter(FileFilter[], String) - Constructor for class loci.formats.gui.ComboFileFilter
  Constructs a new filter from a list of other filters.
comment - Variable in class loci.formats.in.FluoviewReader
comment - Variable in class loci.formats.in.MicromanagerReader.Position
comment - Variable in class loci.formats.in.QuesantReader
comment - Variable in class loci.formats.in.SVSCoreMetadata
COMMENT_STYLE_END - Static variable in class loci.formats.gui.XMLCellRenderer
COMMENT_STYLE_START - Static variable in class loci.formats.gui.XMLCellRenderer
comments - Variable in class loci.formats.in.JPEG2000MetadataParser
  List of comments stored in the file.
comments - Variable in class loci.formats.in.SVSReader
comp - Variable in class loci.formats.gui.CacheIndicator
COMPANION_KEY - Static variable in class loci.formats.out.OMETiffWriter
COMPANION_SUFFIXES - Static variable in class loci.formats.in.TiffReader
companionFile - Variable in class loci.formats.in.TiffReader
companionFiles - Variable in class loci.formats.in.DCIMGReader
companionFiles - Variable in class loci.formats.in.DicomReader
comparator - Static variable in class loci.formats.CoreMetadataList
compare(Object, Object) - Method in class loci.formats.cache.CacheStrategy
  Default comparator orders dimensional positions based on distance from the current position, taking into account axis priorities and planar ordering.
compare(String, String) - Method in class loci.formats.in.MetamorphTiffReader.NumericComparator
compare(File, File) - Method in class loci.formats.in.XLEFReader.PathComparator
compareTo(DicomFileInfo) - Method in class loci.formats.dicom.DicomFileInfo
compareTo(DicomTag) - Method in class loci.formats.dicom.DicomTag
compareTo(Object) - Method in class loci.formats.gui.ComboFileFilter
  Compares two FileFilter objects alphanumerically.
compareTo(Object) - Method in class loci.formats.gui.ExtensionFileFilter
  Compares two FileFilter objects alphanumerically.
compareTo(Object) - Method in class loci.formats.gui.FormatFileFilter
  Compares two FileFilter objects alphanumerically.
compareTo(Object) - Method in class loci.formats.gui.NoExtensionFileFilter
  Compares two FileFilter objects alphanumerically.
compareTo(OlympusTileReader.Tile) - Method in class loci.formats.in.OlympusTileReader.Tile
compareTo(VentanaReader.Overlap) - Method in class loci.formats.in.VentanaReader.Overlap
compareTo(WellContainer) - Method in class loci.formats.internal.WellContainer
compareTo(Object) - Method in class loci.formats.tiff.TiffIFDEntry
compareTo(TiffRational) - Method in class loci.formats.tiff.TiffRational
  Compares this object with the specified object for order.
compareTo(Object) - Method in class loci.plugins.config.FormatEntry
compareTo(Object) - Method in class loci.plugins.config.LibraryEntry
compareTo(ThumbLoader.SeriesInfo) - Method in class loci.plugins.in.ThumbLoader.SeriesInfo
compareTokens(String[], int, String[], int) - Method in class loci.formats.in.ICSReader
COMPLEX - Static variable in class loci.formats.in.CellSensReader
COMPLEX - Static variable in class loci.formats.in.ZeissCZIReader
COMPLEX_FLOAT - Static variable in class loci.formats.in.ZeissCZIReader
COMPONENT_HEIGHT - Static variable in class loci.formats.gui.CacheIndicator
COMPONENT_WIDTH - Static variable in class loci.formats.gui.CacheIndicator
COMPONENTS_CONFIGURATION - Static variable in class loci.formats.tiff.IFD
compress(byte[][], CodecOptions) - Method in class loci.formats.codec.BaseCodec
  2D data block encoding default implementation.
compress(byte[], CodecOptions) - Method in interface loci.formats.codec.Codec
  Compresses a block of data.
compress(byte[][], CodecOptions) - Method in interface loci.formats.codec.Codec
  Compresses a block of data.
compress(byte[], CodecOptions) - Method in class loci.formats.codec.JPEGXRCodec
compress(byte[], CodecOptions) - Method in class loci.formats.codec.NikonCodec
compress(byte[], CodecOptions) - Method in class loci.formats.codec.TargaRLECodec
compress(byte[], CodecOptions) - Method in class loci.formats.codec.WrappedCodec
compress(byte[][], CodecOptions) - Method in class loci.formats.codec.WrappedCodec
compress(byte[]) - Method in class loci.formats.out.OMEXMLWriter
  Compress the given byte array using the current codec.
compress(byte[], CodecOptions) - Method in enum loci.formats.tiff.TiffCompression
  Encodes a strip of data.
compress(byte[], int) - Method in class org.libjpegturbo.turbojpeg.TJCompressor
  Compress the uncompressed source image associated with this compressor instance and output a JPEG image to the given destination buffer.
compress(int) - Method in class org.libjpegturbo.turbojpeg.TJCompressor
  Compress the uncompressed source image associated with this compressor instance and return a buffer containing a JPEG image.
compress(BufferedImage, byte[], int) - Method in class org.libjpegturbo.turbojpeg.TJCompressor
  Compress the uncompressed source image stored in `srcImage` and output a JPEG image to the given destination buffer.
compress(BufferedImage, int) - Method in class org.libjpegturbo.turbojpeg.TJCompressor
  Compress the uncompressed source image stored in `srcImage` and return a buffer containing a JPEG image.
compress(byte[], int, int, int, int, byte[], int, int, int) - Method in class org.libjpegturbo.turbojpeg.TJCompressor
compress(int[], int, int, int, int, byte[], int, int, int) - Method in class org.libjpegturbo.turbojpeg.TJCompressor
compressBuffer(int, byte[], int, int, int, int) - Method in class loci.formats.out.JPEG2000Writer
  Compresses the buffer.
compressed - Variable in class loci.formats.in.NAFReader
compressed - Variable in class loci.formats.in.OpenlabReader.PlaneInfo
compressed - Variable in class loci.formats.in.PSDReader
compressed - Variable in class loci.formats.in.SBIGReader
compressed - Variable in class loci.formats.in.TargaReader
COMPRESSED_BITS_PER_PIXEL - Static variable in class loci.formats.tiff.IFD
compressedSize - Variable in class loci.formats.in.AmiraReader.HxRLE
compressedSize - Variable in class loci.formats.in.AmiraReader.HxZip
compressedSize - Variable in class org.libjpegturbo.turbojpeg.TJCompressor
compression - Variable in enum loci.formats.codec.CompressionType
  The compression used.
compression - Variable in class loci.formats.FormatWriter
  Current compression type.
compression - Variable in class loci.formats.in.AmiraReader
compression - Variable in class loci.formats.in.APNGReader
compression - Variable in class loci.formats.in.BMPReader
  Compression type
compression - Variable in class loci.formats.in.LiFlimReader
compression - Variable in class loci.formats.in.OBFReader.Stack
compression - Variable in class loci.formats.in.OMEXMLReader
compression - Variable in class loci.formats.in.PhotoshopTiffReader
compression - Variable in class loci.formats.in.ZeissCZIReader.DirectoryEntry
COMPRESSION - Static variable in class loci.formats.tiff.IFD
COMPRESSION_BZIP2 - Static variable in class loci.formats.in.KLBReader
COMPRESSION_GZIP - Static variable in class loci.formats.in.LiFlimReader
COMPRESSION_J2K - Static variable in class loci.formats.out.TiffWriter
COMPRESSION_J2K_LOSSY - Static variable in class loci.formats.out.TiffWriter
COMPRESSION_JPEG - Static variable in class loci.formats.out.TiffWriter
COMPRESSION_KEY - Static variable in class loci.formats.in.LiFlimReader
COMPRESSION_LZW - Static variable in class loci.formats.out.TiffWriter
COMPRESSION_NONE - Static variable in class loci.formats.in.KLBReader
COMPRESSION_NONE - Static variable in class loci.formats.in.LiFlimReader
COMPRESSION_SUFFIXES - Static variable in class loci.formats.FormatHandler
  Suffixes for supported compression types.
COMPRESSION_UNCOMPRESSED - Static variable in class loci.formats.out.TiffWriter
COMPRESSION_ZLIB - Static variable in class loci.formats.in.KLBReader
COMPRESSION_ZLIB - Static variable in class loci.formats.out.TiffWriter
compressionMethodPointer - Variable in class loci.formats.out.DicomWriter
CompressionType - Enum in loci.formats.codec
  An enumeration of compression types.
CompressionType(int, String) - Constructor for enum loci.formats.codec.CompressionType
  Default constructor.
compressionType - Variable in class loci.formats.in.CellSensReader
compressionType - Variable in class loci.formats.in.KLBReader
compressionTypes - Variable in class loci.formats.FormatWriter
  Available compression types.
computeAxisLengths() - Method in class loci.formats.FileStitcher
  Computes axis length arrays, and total axis lengths.
computeIndices(int) - Method in class loci.formats.FileStitcher
  Gets the file index, and image index into that file, corresponding to the given global image index.
computeNameAndLocation() - Method in class loci.plugins.in.ImportProcess
  Initializes the idName and idLoc derived values.
computePhysicalSize(int, String, String) - Method in class loci.formats.in.VarianFDFReader
  Return the physical size of a pixel, in microns, along an arbitrary axis based on the supplied physical and pixel lengths of the axis.
computeSeriesLabels(IFormatReader) - Method in class loci.plugins.in.ImportProcess
computeSizeT(int) - Method in class loci.formats.in.PrairieReader
  Scans the parsed metadata to determine the number of actual time points versus the number of actual stage positions.
computeVariableTimeInterval(IMetadata, int) - Method in class loci.plugins.in.Calibrator
concatenate(List<ImagePlus>) - Method in class loci.plugins.in.Concatenator
  Concatenates the list of images as appropriate.
concatenate(List<ImagePlus>) - Method in class loci.plugins.in.ImagePlusReader
concatenateBox - Variable in class loci.plugins.in.MainDialog
concatenateTokens(String[], int, int) - Method in class loci.formats.in.ICSReader
concatenationIndex - Variable in class loci.formats.dicom.DicomFileInfo
concatenationNumber - Variable in class loci.formats.in.DicomReader
Concatenator - Class in loci.plugins.in
  Logic for concatenating multiple images together.
Concatenator() - Constructor for class loci.plugins.in.Concatenator
confidence - Variable in class loci.formats.in.VentanaReader.Overlap
config - Variable in class loci.formats.in.PrairieMetadata
  Key/value pairs from CFG and/or ENV files.
ConfigWindow - Class in loci.plugins.config
  A window for managing configuration of the Bio-Formats plugins.
ConfigWindow() - Constructor for class loci.plugins.config.ConfigWindow
constructDialog() - Method in class loci.plugins.in.ColorDialog
constructDialog() - Method in class loci.plugins.in.CropDialog
constructDialog() - Method in class loci.plugins.in.FilePatternDialog
constructDialog() - Method in class loci.plugins.in.IdDialog
constructDialog() - Method in class loci.plugins.in.ImporterDialog
constructDialog() - Method in class loci.plugins.in.LocationDialog
constructDialog() - Method in class loci.plugins.in.MainDialog
constructDialog() - Method in class loci.plugins.in.MemoryDialog
constructDialog() - Method in class loci.plugins.in.RangeDialog
constructDialog() - Method in class loci.plugins.in.SeriesDialog
constructDialog() - Method in class loci.plugins.in.SwapDialog
constructDialog() - Method in class loci.plugins.in.UpgradeDialog
constructImage(int, int, int, int, boolean, boolean, DataBuffer) - Static method in class loci.formats.gui.AWTImageTools
  Creates an image with the given DataBuffer.
constructImage(int, int, int, int, boolean, boolean, DataBuffer, ColorModel) - Static method in class loci.formats.gui.AWTImageTools
  Creates an image with the given DataBuffer.
constructImageTitle(IFormatReader, String, String, boolean) - Method in class loci.plugins.in.ImagePlusReader
constructSliceLabel(int, IFormatReader, IMetadata, int, int, int, int) - Method in class loci.plugins.in.ImagePlusReader
CONTAINER_TYPES - Static variable in class loci.formats.in.QTReader
  List of identifiers for each container atom.
ContainerRecord(String, int, long, int) - Constructor for class loci.formats.in.IM3Reader.ContainerRecord
contentFileType - Variable in class loci.formats.in.ZeissCZIReader.AttachmentEntry
contentGUID - Variable in class loci.formats.in.ZeissCZIReader.AttachmentEntry
Context() - Constructor for enum loci.formats.in.BaseZeissReader.Context
context - Variable in class loci.formats.in.BaseZeissReader.Tag
CONTRAST - Static variable in class loci.formats.in.CellSensReader
CONTRAST - Static variable in class loci.formats.tiff.IFD
CONTRAST_BRIGHTNESS - Static variable in class loci.formats.in.CellSensReader
CONTRAST_TARGET - Static variable in class loci.formats.in.CellSensReader
convert(String, String) - Static method in class loci.formats.FormatTools
  Convenience method for converting the specified input file to the specified output file.
convert(IFormatReader, IFormatWriter, String) - Static method in class loci.formats.FormatTools
  Convenience method for writing all of the images and metadata obtained from the specified IFormatReader into the specified IFormatWriter.
convert - Variable in class loci.formats.gui.DataConverter
convert12to16LSB(byte[]) - Static method in class loci.formats.in.LiFlimReader
convert12to16MSB(byte[]) - Static method in class loci.formats.in.LiFlimReader
convertMetadata(MetadataRetrieve, MetadataStore) - Static method in class loci.formats.meta.MetadataConverter
  Deprecated.
  Copies information from a metadata retrieval object (source) into a metadata store (destination).
convertMetadata(String, MetadataStore) - Method in interface loci.formats.services.OMEXMLService
  Converts information from an OME-XML string (source) into a metadata store (destination).
convertMetadata(MetadataRetrieve, MetadataStore) - Method in interface loci.formats.services.OMEXMLService
  Copies information from a metadata retrieval object (source) into a metadata store (destination).
convertMetadata(String, MetadataStore) - Method in class loci.formats.services.OMEXMLServiceImpl
convertMetadata(MetadataRetrieve, MetadataStore) - Method in class loci.formats.services.OMEXMLServiceImpl
convertPixelType(int) - Method in class loci.formats.in.CellSensReader
convertPixelType(int) - Method in class loci.formats.in.JPEG2000MetadataParser
convertPixelType(CoreMetadata, int) - Method in class loci.formats.in.KLBReader
convertPixelType(int) - Method in class loci.formats.in.TillVisionReader
convertPixelType(int) - Method in class loci.formats.in.ZeissCZIReader
convertPixelType(CoreMetadata, int) - Method in class loci.formats.in.ZeissCZIReader
convertRenderedImage(RenderedImage) - Static method in class loci.formats.gui.AWTImageTools
  Converts a java.awt.image.RenderedImage into a java.awt.image.BufferedImage.
convertTo8Bit(short[][]) - Method in class loci.plugins.util.ImageProcessorReader
convertToByte(boolean) - Method in class loci.plugins.util.RecordedImageProcessor
convertToFloat() - Method in class loci.plugins.util.RecordedImageProcessor
convertToLong(byte[], int) - Method in class loci.formats.in.SlideBook7Reader.CCompressionBase
convertToRGB() - Method in class loci.plugins.util.RecordedImageProcessor
convertToShort(boolean) - Method in class loci.plugins.util.RecordedImageProcessor
convertUnits(String) - Method in class loci.formats.in.GatanReader
convertUnits(int) - Method in class loci.formats.in.IMODReader
convolve(float[], int, int) - Method in class loci.plugins.util.RecordedImageProcessor
convolve3x3(int[]) - Method in class loci.plugins.util.RecordedImageProcessor
COOKIE - Static variable in class loci.formats.in.IM3Reader
  First 4 bytes of file is "1985"
COOLING_ON - Static variable in class loci.formats.in.CellSensReader
coordinate - Variable in class loci.formats.in.CellSensReader.TileCoordinate
Coordinate(int, int, int) - Constructor for class loci.formats.in.ZeissCZIReader.Coordinate
coordinates - Variable in class loci.formats.in.BaseZeissReader
COptovarDef70() - Constructor for class loci.formats.in.SlideBook7Reader.COptovarDef70
copy(OperettaReader.Plane) - Method in class loci.formats.in.OperettaReader.Channel
  Copy data from this Channel to the given Plane.
copyBits(ImageProcessor, int, int, int) - Method in class loci.plugins.util.RecordedImageProcessor
copyCorrectionImageToBuffer(TissueFAXSReader.ScanRegion, Region, int[], byte[]) - Method in class loci.formats.in.TissueFAXSReader
copyOptions(CodecOptions, CodecOptions) - Static method in class loci.formats.codec.WrappedCodec
copyPixelBlock(OIRReader.PixelBlock, byte[], int, int, int, int, int) - Method in class loci.formats.in.OIRReader
copyPixels(int, int, int, int, int, int, byte[], byte[], boolean) - Method in class loci.formats.in.ND2Reader
copyRegion(Region, byte[], Region, byte[], int) - Method in class loci.formats.in.TissueFAXSReader
copyRegionToBuffer(TissueFAXSReader.ScanRegion, int, Region, int[], byte[]) - Method in class loci.formats.in.TissueFAXSReader
COPYRIGHT - Static variable in class loci.formats.tiff.IFD
copyScaled(BufferedImage, BufferedImage, Object) - Static method in class loci.formats.gui.AWTImageTools
  Copies the source image into the target, applying scaling.
copyTile(IFD, byte[], int, int) - Method in class loci.formats.in.MinimalTiffReader
core - Variable in class loci.formats.DimensionSwapper
  Core metadata associated with this dimension swapper.
core - Variable in class loci.formats.FileStitcher
  Core metadata.
core - Variable in class loci.formats.FormatReader
  Core metadata values.
core - Variable in class loci.formats.in.LeicaHandler
core - Variable in class loci.formats.in.ND2Handler
core - Variable in class loci.formats.in.VolocityReader.Stack
core - Variable in class loci.formats.SubResolutionFormatReader
  List of `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 - Variable in class loci.formats.dicom.DicomFileInfo
coreMetaData - Static variable in class loci.formats.in.SPEReader
CoreMetadataList - Class in loci.formats
CoreMetadataList() - Constructor for class loci.formats.CoreMetadataList
CoreMetadataList(CoreMetadataList) - Constructor for class loci.formats.CoreMetadataList
CoreMetadataList(int) - Constructor for class loci.formats.CoreMetadataList
  Construct a list containing a specified number of primary elements.
CoreMetadataList(int, int) - Constructor for class loci.formats.CoreMetadataList
  Construct a list containing a specified number of primary elements and a fixed number of secondary elements.
CoreMetadataList(int[]) - Constructor for class loci.formats.CoreMetadataList
  Construct a list containing a specified number of primary and secondary elements.
CoreMetadataList(List<CoreMetadata>) - Constructor for class loci.formats.CoreMetadataList
correction - Variable in class loci.formats.in.ND2Handler
correction - Variable in class loci.formats.in.NikonTiffReader
correction - Variable in class loci.formats.in.ZeissLSMReader.Recording
correctionCollar - Variable in class loci.formats.in.ZeissCZIReader
correctionFile - Variable in class loci.formats.in.CV7000Reader.Channel
correctionImageCoreIndex - Variable in class loci.formats.in.TissueFAXSReader.ScanRegion
correctionImageIDs - Variable in class loci.formats.in.TissueFAXSReader.ScanRegion
corrections - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataTempBuffer
corrections - Variable in class loci.formats.in.LIFReader
correctUnits(Double, String) - Method in class loci.formats.in.ColumbusReader
  Calculate value in micrometers based on input value and units.
cortime - Variable in class loci.formats.in.SDTInfo
  Correlation time [ms].
count - Variable in class loci.formats.in.LeicaHandler
count() - Method in class loci.formats.in.LeicaSCNReader.LeicaSCNHandler
count - Variable in class loci.formats.in.ZeissTIFFHandler.TagSet
COUNTER_CLOCKWISE - Static variable in class loci.formats.in.FluoviewReader
CountImageDataFiles() - Method in class loci.formats.in.SlideBook7Reader.CImageGroup
countImages() - Method in class loci.formats.in.BaseZeissReader
countImages() - Method in class loci.formats.in.ZeissTIFFReader
countImages() - Method in class loci.formats.in.ZeissZVIReader
CRatioManipRecord70() - Constructor for class loci.formats.in.SlideBook7Reader.CRatioManipRecord70
crc(byte[]) - Method in class loci.formats.out.APNGWriter
crc(byte[], int, int) - Method in class loci.formats.out.APNGWriter
create(Map<String, Object>) - Method in class loci.formats.filter.LZ4Filter.LZ4FilterProvider
createAngle(Double, Unit<Angle>) - Static method in class loci.formats.FormatTools
createAngle(Integer, Unit<Angle>) - Static method in class loci.formats.FormatTools
createAngle(T, Unit<Angle>) - Static method in class loci.formats.FormatTools
createBaseReader() - Method in class loci.plugins.in.ImportProcess
  Initializes an `IFormatReader` according to the current configuration.
createChannelDimension(int, long) - Static method in class loci.formats.in.LeicaMicrosystemsMetadata.Dimension
createChannelPriorities() - Static method in class loci.formats.in.LIFReader
createCodec(boolean) - Method in class loci.formats.in.ND2Reader
createColorModel() - Method in class loci.plugins.util.ImageProcessorReader
createCompatibleWritableRaster(int, int) - Method in class loci.formats.gui.Index16ColorModel
createCompatibleWritableRaster(int, int) - Method in class loci.formats.gui.SignedColorModel
createCompatibleWritableRaster(int, int) - Method in class loci.formats.gui.UnsignedIntColorModel
created - Variable in class loci.formats.out.QTWriter
  Time the file was created.
createElectricPotential(Double, Unit<ElectricPotential>) - Static method in class loci.formats.FormatTools
createElectricPotential(Integer, Unit<ElectricPotential>) - Static method in class loci.formats.FormatTools
createElectricPotential(T, Unit<ElectricPotential>) - Static method in class loci.formats.FormatTools
createFileInfo(String) - Method in class loci.formats.in.DicomReader
  Construct a DicomFileInfo for the given file.
createFileInfo() - Method in class loci.plugins.in.ImagePlusReader
createFrequency(Double, Unit<Frequency>) - Static method in class loci.formats.FormatTools
createFrequency(Integer, Unit<Frequency>) - Static method in class loci.formats.FormatTools
createFrequency(T, Unit<Frequency>) - Static method in class loci.formats.FormatTools
createGroup(String) - Method in interface loci.formats.services.JHDFService
  Writes an array as sub-slice into an existing HDF5 dataset
createGroup(String) - Method in class loci.formats.services.JHDFServiceImpl
createImage(String, List<ImageProcessor>) - Static method in class loci.plugins.in.ImagePlusReader
  Creates an `ImagePlus` from the given image processors.
createImage(String, ImageStack, List<LUT>) - Static method in class loci.plugins.in.ImagePlusReader
  Creates an `ImagePlus` from the given image stack.
createImage() - Method in class loci.plugins.util.RecordedImageProcessor
createIndexMap(int) - Method in class loci.formats.in.FakeReader
  Creates a mapping between indices and color values.
createInputStream() - Method in class loci.formats.out.TiffWriter
createKeys() - Static method in class loci.formats.in.ZeissLSMReader
createLength(Double, Unit<Length>) - Static method in class loci.formats.FormatTools
createLength(Integer, Unit<Length>) - Static method in class loci.formats.FormatTools
createLength(T, Unit<Length>) - Static method in class loci.formats.FormatTools
createLSID(String, int...) - Static method in class loci.formats.MetadataTools
  Constructs an LSID, given the object type and indices.
createMetadata(String, CoreMetadata) - Method in class loci.formats.tools.MakeTestOmeTiff
createModulo(OMEXMLMetadata, Modulo, StructuredAnnotations, Image, int, int, int) - Method in class loci.formats.services.OMEXMLServiceImpl
  Create a ModuloAlong* annotation corresponding to the given `Modulo`.
createOMEXMLMetadata() - Static method in class loci.formats.MetadataTools
  Creates an OME-XML metadata object using reflection, to avoid direct dependencies on the optional `loci.formats.ome` package.
createOMEXMLMetadata() - Method in interface loci.formats.services.OMEXMLService
  Creates an OME-XML metadata object using reflection, to avoid direct dependencies on the optional `loci.formats.ome` package.
createOMEXMLMetadata(String) - Method in interface loci.formats.services.OMEXMLService
  Creates an OME-XML metadata object using reflection, to avoid direct dependencies on the optional `loci.formats.ome` package, wrapping a DOM representation of the given OME-XML string.
createOMEXMLMetadata(String, String) - Method in interface loci.formats.services.OMEXMLService
  Creates an OME-XML metadata object using reflection, to avoid direct dependencies on the optional `loci.formats.ome` package, wrapping a DOM representation of the given OME-XML string.
createOMEXMLMetadata() - Method in class loci.formats.services.OMEXMLServiceImpl
createOMEXMLMetadata(String) - Method in class loci.formats.services.OMEXMLServiceImpl
createOMEXMLMetadata(String, String) - Method in class loci.formats.services.OMEXMLServiceImpl
createOMEXMLRoot(String) - Method in interface loci.formats.services.OMEXMLService
  Constructs an OME root node.
createOMEXMLRoot(String) - Method in class loci.formats.services.OMEXMLServiceImpl
createOutputStream() - Method in class loci.formats.FormatWriter
  Create an output stream for the current file path.
createPlane(String, CoreMetadata, int) - Method in class loci.formats.tools.MakeTestOmeTiff
createPower(Double, Unit<Power>) - Static method in class loci.formats.FormatTools
createPower(Integer, Unit<Power>) - Static method in class loci.formats.FormatTools
createPower(T, Unit<Power>) - Static method in class loci.formats.FormatTools
createPressure(Double, Unit<Pressure>) - Static method in class loci.formats.FormatTools
createPressure(Integer, Unit<Pressure>) - Static method in class loci.formats.FormatTools
createPressure(T, Unit<Pressure>) - Static method in class loci.formats.FormatTools
createProcessor(int, int) - Method in class loci.plugins.util.RecordedImageProcessor
createROI(MetadataStore, int) - Method in class loci.formats.in.GatanReader
  Create an empty ROI and link it to the Image.
createRoot(String) - Method in class loci.formats.services.OMEXMLServiceImpl
  Constructs an OME root node.
createStack(List<ImageProcessor>, List<String>, List<LUT>) - Static method in class loci.plugins.in.ImagePlusReader
  Creates an image stack from the given image processors.
createSwatch(Color) - Method in class loci.plugins.in.ColorDialog
createTemperature(Double, Unit<Temperature>) - Static method in class loci.formats.FormatTools
createTemperature(Integer, Unit<Temperature>) - Static method in class loci.formats.FormatTools
createTemperature(T, Unit<Temperature>) - Static method in class loci.formats.FormatTools
createTiffSaver() - Method in class loci.formats.out.TiffWriter
createTime(Double, Unit<Time>) - Static method in class loci.formats.FormatTools
createTime(Integer, Unit<Time>) - Static method in class loci.formats.FormatTools
createTime(T, Unit<Time>) - Static method in class loci.formats.FormatTools
createVirtualStack(ImportProcess, int, List<LUT>) - Method in class loci.plugins.in.ImagePlusReader
createWriter(String, CoreMetadata, String) - Method in class loci.formats.tools.MakeTestOmeTiff
CREATION_TIME - Static variable in class loci.formats.in.CellSensReader
creationDate - Variable in class loci.formats.in.FV1000Reader
creationDate - Variable in class loci.formats.in.ImaconReader
creationDate - Variable in class loci.formats.in.InCellReader
creationDate - Variable in class loci.formats.in.IvisionReader
creationDate - Variable in class loci.formats.in.LeicaSCNReader.Image
creationDate - Variable in class loci.formats.in.PCIReader
CREATOR - Static variable in class loci.formats.FormatTools
  Value to use when setting creator/software fields in exported files.
CREATOR_KEY - Static variable in class loci.formats.out.OMETiffWriter
CREATOR_KEY - Static variable in class loci.formats.out.OMEXMLWriter
CREATOR_TAG - Static variable in class loci.formats.in.ImaconReader
CRemapChannelLUT70() - Constructor for class loci.formats.in.SlideBook7Reader.CRemapChannelLUT70
CRemapManipRecord70() - Constructor for class loci.formats.in.SlideBook7Reader.CRemapManipRecord70
CRemapPoint() - Constructor for class loci.formats.in.SlideBook7Reader.CRemapPoint
crop() - Method in class loci.plugins.util.RecordedImageProcessor
cropBox - Variable in class loci.plugins.in.MainDialog
CropDialog - Class in loci.plugins.in
  Bio-Formats Importer crop options dialog box.
CropDialog(ImportProcess) - Constructor for class loci.plugins.in.CropDialog
  Creates a crop options dialog for the Bio-Formats Importer.
cropRegion - Variable in class loci.plugins.in.ImporterOptions
crossChan - Variable in class loci.formats.in.SDTInfo
  Cross FCS routing channel number when chan = crossChan and mod == crossMod - Auto FCS otherwise - Cross FCS.
CrosshairStrategy - Class in loci.formats.cache
  A crosshair strategy caches planes extending from the the current dimensional position along each individual axis, but not combinations of axes.
CrosshairStrategy(int[]) - Constructor for class loci.formats.cache.CrosshairStrategy
  Constructs a crosshair strategy.
crossMod - Variable in class loci.formats.in.SDTInfo
  Cross FCS module number.
crossMtResol - Variable in class loci.formats.in.SDTInfo
  Macro time clock of cross FCS module in 0.1 ns units.
CS_2C - Static variable in class loci.formats.gui.TwoChannelColorSpace
CSBFile70(String) - Constructor for class loci.formats.in.SlideBook7Reader.CSBFile70
CSBPoint() - Constructor for class loci.formats.in.SlideBook7Reader.CSBPoint
cScroll - Variable in class loci.plugins.util.DataBrowser
cSlider - Variable in class loci.formats.gui.ImageViewer
CSlideRecord70() - Constructor for class loci.formats.in.SlideBook7Reader.CSlideRecord70
cSliders - Variable in class loci.plugins.util.DataBrowser
cStep - Variable in class loci.plugins.in.ImporterOptions
CSV_SUFFIX - Static variable in class loci.formats.in.PerkinElmerReader
CUnknownAnnotation70() - Constructor for class loci.formats.in.SlideBook7Reader.CUnknownAnnotation70
curCycle - Variable in class loci.formats.in.SDTInfo
  Current cycle (accumulation cycle in FLOW mode) - (if multi-cycle measurement).
curPage - Variable in class loci.formats.in.SDTInfo
  Current measured page.
current - Variable in class loci.formats.ImageReader
  Current form index.
current - Variable in class loci.formats.ImageWriter
  Current form index.
current - Variable in class loci.formats.in.ZeissXRMReader
current_layer - Variable in class loci.formats.in.ZeissTIFFHandler
current_scaling - Variable in class loci.formats.in.ZeissTIFFHandler
current_shape - Variable in class loci.formats.in.ZeissTIFFHandler
current_tag - Variable in class loci.formats.in.ZeissTIFFHandler
current_tagset - Variable in class loci.formats.in.ZeissTIFFHandler
currentBlock - Variable in class loci.formats.in.APNGReader.PNGInputStream
currentBlock - Variable in class loci.formats.in.PQBinReader
  Block of time bins currently stored for faster loading.
currentBlock - Variable in class loci.formats.in.SDTReader
  Block of time bins currently stored for faster loading.
currentChannel - Variable in class loci.formats.in.CV7000Reader.MeasurementSettingsHandler
currentChunk - Variable in class loci.formats.in.OBFReader.State
currentCol - Variable in class loci.formats.in.InCellReader.InCellHandler
currentElement - Variable in class loci.formats.in.AFIReader.AFIHandler
currentElement - Variable in class loci.formats.in.IvisionReader.IvisionHandler
currentField - Variable in class loci.formats.in.CV7000Reader.MeasurementDataHandler
currentField - Variable in class loci.formats.in.InCellReader.InCellHandler
currentFile - Variable in class loci.formats.services.JHDFServiceImpl
currentFile - Variable in class loci.formats.services.NetCDFServiceImpl
currentFragment - Variable in class loci.formats.out.OMEXMLWriter
currentFrame - Variable in class loci.formats.in.SPCReader
currentIcsId - Variable in class loci.formats.in.ICSReader
  Current filename.
currentId - Variable in class loci.formats.FormatHandler
  Name of current file.
currentId - Variable in class loci.formats.ImageReader
  Name of current file.
currentId - Variable in class loci.formats.ImageWriter
  Name of current file.
currentIdsId - Variable in class loci.formats.in.ICSReader
currentImage - Variable in class loci.formats.in.InCellReader.InCellHandler
currentImage - Variable in class loci.formats.in.LeicaSCNReader.LeicaSCNHandler
currentImageFile - Variable in class loci.formats.in.InCellReader.MinimalInCellHandler
currentLine - Variable in class loci.formats.in.SPCReader
currentName - Variable in class loci.formats.in.ColumbusReader.MeasurementHandler
currentName - Variable in class loci.formats.in.OperettaReader.OperettaHandler
currentNo - Variable in class loci.formats.in.AmiraReader.HxRLE
currentNo - Variable in class loci.formats.in.AmiraReader.HxZip
currentPixel - Variable in class loci.formats.in.SPCReader
currentPlane - Variable in class loci.formats.in.InCellReader.InCellHandler
currentPlane - Variable in class loci.formats.in.ZeissZVIReader
currentPlane - Variable in class loci.formats.out.DicomWriter
currentPlaneIndex - Variable in class loci.formats.in.ZeissZVIReader
currentPos - Variable in class loci.formats.cache.Cache
  Current dimensional position.
currentProcessor - Variable in class loci.plugins.util.BFVirtualStack
currentQName - Variable in class loci.formats.in.BDVReader.BDVXMLHandler
currentQName - Variable in class loci.formats.in.InCellReader.InCellHandler
currentQName - Variable in class loci.formats.in.OMEXMLReader.OMEXMLHandler
currentRow - Variable in class loci.formats.in.InCellReader.InCellHandler
currentSetupIndex - Variable in class loci.formats.in.BDVReader.BDVXMLHandler
currentSlice - Variable in class loci.plugins.util.BFVirtualStack
currentStreamPosition - Variable in class loci.formats.in.DCIMGReader
currentThumbnail - Variable in class loci.formats.in.InCellReader.MinimalInCellHandler
currentTileFile - Variable in class loci.formats.in.DicomReader
currentTileStream - Variable in class loci.formats.in.DicomReader
currentValue - Variable in class loci.formats.in.ColumbusReader.MeasurementHandler
currentValue - Variable in class loci.formats.in.CV7000Reader.MeasurementDataHandler
currentValue - Variable in class loci.formats.in.CV7000Reader.MeasurementSettingsHandler
currentValue - Variable in class loci.formats.in.OperettaReader.OperettaHandler
currentValue - Variable in class loci.formats.in.ScanrReader.ScanrHandler
curStep - Variable in class loci.formats.in.SDTInfo
  Current step (if multi-step measurement).
curve - Variable in class loci.formats.codec.NikonCodecOptions
CURVE - Static variable in class loci.formats.in.NikonReader
curve - Variable in class loci.formats.in.NikonReader
CUSTOM_BITS - Static variable in class loci.formats.in.SimplePCITiffReader
CUSTOM_GRAYSCALE - Static variable in class loci.formats.in.CellSensReader
CUSTOM_RENDERED - Static variable in class loci.formats.tiff.IFD
customColors - Variable in class loci.plugins.in.ImporterOptions
customFilter(ShortBuffer, Rectangle, Rectangle, int, int, TJTransform) - Method in interface org.libjpegturbo.turbojpeg.TJCustomFilter
  A callback function that can be used to modify the DCT coefficients after they are losslessly transformed but before they are transcoded to a new JPEG file.
cutIn - Variable in class loci.formats.in.LeicaHandler.MultiBand
cutInPopulated - Variable in class loci.formats.in.LeicaReader
cutIns - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataTempBuffer
cutIns - Variable in class loci.formats.in.LIFReader
cutOut - Variable in class loci.formats.in.LeicaHandler.MultiBand
cutOutPopulated - Variable in class loci.formats.in.LeicaReader
cutOuts - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataTempBuffer
cutOuts - Variable in class loci.formats.in.LIFReader
CV7000Reader - Class in loci.formats.in
CV7000Reader() - Constructor for class loci.formats.in.CV7000Reader
  Constructs a new Yokogawa CV7000 reader.
CV7000Reader.Channel - Class in loci.formats.in
CV7000Reader.Field - Class in loci.formats.in
CV7000Reader.LightSource - Class in loci.formats.in
CV7000Reader.MeasurementDataHandler - Class in loci.formats.in
CV7000Reader.MeasurementDetailHandler - Class in loci.formats.in
CV7000Reader.MeasurementSettingsHandler - Class in loci.formats.in
CV7000Reader.MinMax - Class in loci.formats.in
CV7000Reader.Plane - Class in loci.formats.in
CV7000Reader.WPIHandler - Class in loci.formats.in
cycle - Variable in class loci.formats.in.PrairieMetadata.Sequence
  `cycle` of this `<Sequence>`.
cycle - Variable in class loci.formats.in.TecanReader.Image
cycleMax - Variable in class loci.formats.in.PrairieMetadata
  Maximum cycle value.
cycleMin - Variable in class loci.formats.in.PrairieMetadata
  Minimum cycle value.
cycles - Variable in class loci.formats.in.SDTInfo
  Cycles (accumulation cycles in FLOW mode).
CYTELL_MAGIC_STRING - Static variable in class loci.formats.in.InCellReader
CZI_MAGIC_STRING - Static variable in class loci.formats.in.ZeissCZIReader
CZTKey(int, int, int) - Constructor for class loci.formats.in.OIRReader.CZTKey
cztToPixelBlocks - Variable in class loci.formats.in.OIRReader

## D

d(String) - Method in class loci.formats.in.PrairieMetadata
  Converts the given string to a `Double`, or `null` if incompatible.
DAILY - Static variable in class loci.plugins.Updater
DAILY_BUILD - Static variable in class loci.formats.UpgradeChecker
  Location of the JAR artifacts for Bio-Formats' daily build.
DarkImage - Variable in class loci.formats.in.LiFlimReader
DarkImage_KEY - Static variable in class loci.formats.in.LiFlimReader
data - Variable in class loci.formats.in.ICSReader
  Image data.
data - Variable in class loci.formats.in.IM3Reader
data - Variable in class loci.formats.in.TextReader
  Because we have no way of indexing into the text file efficiently in general, we cheat and store the entire file's data in a giant array.
data - Variable in class loci.formats.MetadataList
DATA_CHANNEL_ACQUIRE - Static variable in class loci.formats.in.ZeissLSMReader
DATA_CHANNEL_NAME - Static variable in class loci.formats.in.ZeissLSMReader
DATA_DIR - Static variable in class loci.formats.in.VolocityReader
DATA_IDENTIFIER - Static variable in class loci.formats.in.SDTInfo
  For normal .sdt files (setup + data).
DATA_SIGNATURE - Static variable in class loci.formats.out.AVIWriter
dataBlockLength - Variable in class loci.formats.in.SDTInfo
dataBlockOffs - Variable in class loci.formats.in.SDTInfo
  Offset of the first data block.
DataBrowser - Class in loci.plugins.util
  Extension of StackWindow with additional UI trimmings for animation, virtual stack caching options, metadata, and general beautification.
DataBrowser(ImagePlus) - Constructor for class loci.plugins.util.DataBrowser
DataBrowser(ImagePlus, ImageCanvas, String[], int[]) - Constructor for class loci.plugins.util.DataBrowser
DataBrowser(ImagePlus, ImageCanvas, String[], int[], XMLWindow) - Constructor for class loci.plugins.util.DataBrowser
DataChannel() - Constructor for class loci.formats.in.ZeissLSMReader.DataChannel
DataConverter - Class in loci.formats.gui
  A utility for reorganizing and converting QuickTime movies, TIFF series and other 4D datasets.
DataConverter() - Constructor for class loci.formats.gui.DataConverter
DataConverter.RowPanel - Class in loci.formats.gui
dataFile - Variable in class loci.formats.in.NRRDReader
  Name of data file, if the current extension is 'nhdr'.
dataId - Variable in class loci.formats.in.OIRReader.Laser
DataLoader(String) - Constructor for class loci.formats.in.SlideBook7Reader.DataLoader
dataOffs - Variable in class loci.formats.in.SDTInfo
  Offset of the data block from the beginning of the file.
dataOffset - Variable in class loci.formats.in.DCIMGReader
dataOffset - Variable in class loci.formats.in.LiFlimReader
  Offset to start of pixel data.
dataOffset - Variable in class loci.formats.in.ZeissCZIReader.Attachment
dataOffset - Variable in class loci.formats.in.ZeissCZIReader.SubBlock
dataPointers - Variable in class loci.formats.in.InveonReader
DATASET - Static variable in class loci.formats.in.ZeissXRMReader
datasetDescription - Variable in class loci.formats.FormatReader
  Short description of the structure of the dataset.
dataSets - Variable in class loci.formats.in.IM3Reader
dataSize - Variable in class loci.formats.in.MRWReader
dataSize - Variable in class loci.formats.in.ZeissCZIReader.Attachment
dataSize - Variable in class loci.formats.in.ZeissCZIReader.SubBlock
dataStore - Variable in class loci.formats.in.PQBinReader
dataStore - Variable in class loci.formats.in.SDTReader
dataType - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.Channel
datatype - Variable in class loci.formats.in.LiFlimReader
DATATYPE_INT16 - Static variable in class loci.formats.in.LiFlimReader
DATATYPE_INT32 - Static variable in class loci.formats.in.LiFlimReader
DATATYPE_INT8 - Static variable in class loci.formats.in.LiFlimReader
DATATYPE_KEY - Static variable in class loci.formats.in.LiFlimReader
DATATYPE_REAL32 - Static variable in class loci.formats.in.LiFlimReader
DATATYPE_REAL64 - Static variable in class loci.formats.in.LiFlimReader
DATATYPE_UINT12 - Static variable in class loci.formats.in.LiFlimReader
DATATYPE_UINT16 - Static variable in class loci.formats.in.LiFlimReader
DATATYPE_UINT32 - Static variable in class loci.formats.in.LiFlimReader
DATATYPE_UINT8 - Static variable in class loci.formats.in.LiFlimReader
DATE - Static variable in class loci.formats.FormatTools
  Date on which this release was built.
DATE - Static variable in class loci.formats.in.CellSensReader
date - Variable in class loci.formats.in.DicomReader
date - Variable in class loci.formats.in.FEITiffReader
date - Variable in class loci.formats.in.FluoviewReader
date - Variable in class loci.formats.in.LEOReader
date - Variable in class loci.formats.in.MetamorphHandler
date - Variable in class loci.formats.in.MicroCTReader
date - Variable in class loci.formats.in.ND2Handler
date - Variable in class loci.formats.in.PrairieMetadata
  The date of the acquisition.
date - Variable in class loci.formats.in.QuesantReader
date - Variable in class loci.formats.in.SDTInfo
  Date of creation.
date - Variable in class loci.formats.in.SimplePCITiffReader
date - Variable in class loci.formats.in.SVSReader
DATE_FORMAT - Static variable in class loci.formats.in.BrukerReader
DATE_FORMAT - Static variable in class loci.formats.in.CellWorxReader
DATE_FORMAT - Static variable in class loci.formats.in.DeltavisionReader
  Deprecated.
  Use `DeltavisionReader.DATE_FORMATS` instead
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
DATESTAMP - Static variable in class loci.formats.in.ZeissXRMReader
datestamps - Variable in class loci.formats.in.ZeissXRMReader
datFile - Variable in class loci.formats.in.InveonReader
datFile - Variable in class loci.formats.in.UnisokuReader
dBlock - Variable in class loci.formats.in.GIFReader
  Current data block.
DCIMG_PIXELTYPE_MONO16 - Static variable in class loci.formats.in.DCIMGReader
DCIMG_PIXELTYPE_MONO8 - Static variable in class loci.formats.in.DCIMGReader
DCIMG_VERSION_0 - Static variable in class loci.formats.in.DCIMGReader
DCIMG_VERSION_1 - Static variable in class loci.formats.in.DCIMGReader
DCIMGReader - Class in loci.formats.in
  DCIMGReader reads Hamamatsu DCIMG files.
DCIMGReader() - Constructor for class loci.formats.in.DCIMGReader
deadTimeComp - Variable in class loci.formats.in.SDTInfo
debug(String) - Static method in class loci.plugins.BF
decode(byte[]) - Method in class loci.formats.filter.LZ4Filter
decode(APNGReader.PNGInputStream) - Method in class loci.formats.in.APNGReader
decode(APNGReader.PNGInputStream, int, int) - Method in class loci.formats.in.APNGReader
Decode(MappingNode, int) - Method in class loci.formats.in.SlideBook7Reader.CChannelDef70
Decode(MappingNode, int) - Method in class loci.formats.in.SlideBook7Reader.CChannelRecord70
Decode(MappingNode, int) - Method in class loci.formats.in.SlideBook7Reader.CCubeAnnotation70
Decode(MappingNode, int) - Method in class loci.formats.in.SlideBook7Reader.CFRAPRegionAnnotation70
Decode(MappingNode) - Method in class loci.formats.in.SlideBook7Reader.CImageRecord70
Decode(MappingNode) - Method in class loci.formats.in.SlideBook7Reader.ClassDecoder
Decode(MappingNode, int) - Method in class loci.formats.in.SlideBook7Reader.ClassDecoder
Decode(MappingNode, int) - Method in class loci.formats.in.SlideBook7Reader.CUnknownAnnotation70
decode12BitCamera(byte[], int) - Method in class loci.formats.in.ZeissCZIReader
decodeDate(int) - Static method in class loci.formats.in.MetamorphReader
  Converts a Julian date value into a human-readable string.
decodeImageData() - Method in class loci.formats.in.GIFReader
  Decodes LZW image data into a pixel array.
decoder - Variable in class loci.formats.codec.JPEGTileDecoder
decodeTile(int, int, int) - Method in class loci.formats.in.CellSensReader
decodeTime(int) - Static method in class loci.formats.in.MetamorphReader
  Converts a time value in milliseconds into a human-readable string.
DecodeUnknownString(String, Node) - Method in class loci.formats.in.SlideBook7Reader.CAnnotation70
DecodeUnknownString(String, Node) - Method in class loci.formats.in.SlideBook7Reader.ClassDecoder
decompress(byte[]) - Method in class loci.formats.codec.BaseCodec
decompress(byte[][]) - Method in class loci.formats.codec.BaseCodec
decompress(byte[], CodecOptions) - Method in class loci.formats.codec.BaseCodec
decompress(RandomAccessInputStream, CodecOptions) - Method in class loci.formats.codec.BaseCodec
decompress(byte[][], CodecOptions) - Method in class loci.formats.codec.BaseCodec
  2D data block decoding default implementation.
decompress(byte[], CodecOptions) - Method in interface loci.formats.codec.Codec
  Decompresses a block of data.
decompress(byte[][], CodecOptions) - Method in interface loci.formats.codec.Codec
  Decompresses a block of data.
decompress(byte[]) - Method in interface loci.formats.codec.Codec
  Decompresses a block of data.
decompress(byte[][]) - Method in interface loci.formats.codec.Codec
  Decompresses a block of data.
decompress(RandomAccessInputStream, CodecOptions) - Method in interface loci.formats.codec.Codec
  Decompresses data from the given RandomAccessInputStream.
decompress(RandomAccessInputStream, CodecOptions) - Method in class loci.formats.codec.JPEGXRCodec
decompress(byte[], CodecOptions) - Method in class loci.formats.codec.JPEGXRCodec
  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[], int, int) - Method in class loci.formats.codec.ZstdCodec
decompress(byte[]) - Method in interface loci.formats.services.JPEGXRService
  Decompress the given JPEG-XR compressed byte array and return as a byte array.
decompress(byte[]) - Method in class loci.formats.services.JPEGXRServiceImpl
decompress(byte[], CodecOptions) - Method in enum loci.formats.tiff.TiffCompression
  Decodes a strip of data.
decompress(byte[], int, int, int, int, int) - Method in class org.libjpegturbo.turbojpeg.TJDecompressor
  Decompress the JPEG source image associated with this decompressor instance and output a decompressed image to the given destination buffer.
decompress(int, int, int, int, int) - Method in class org.libjpegturbo.turbojpeg.TJDecompressor
  Decompress the JPEG source image associated with this decompressor instance and return a buffer containing the decompressed image.
decompress(BufferedImage, int) - Method in class org.libjpegturbo.turbojpeg.TJDecompressor
  Decompress the JPEG source image associated with this decompressor instance and output a decompressed image to the given `BufferedImage` instance.
decompress(int, int, int, int) - Method in class org.libjpegturbo.turbojpeg.TJDecompressor
  Decompress the JPEG source image associated with this decompressor instance and return a `BufferedImage` instance containing the decompressed image.
decompress(byte[], int, byte[], int, int, int, int, int) - Method in class org.libjpegturbo.turbojpeg.TJDecompressor
decompress(byte[], int, int[], int, int, int, int, int) - Method in class org.libjpegturbo.turbojpeg.TJDecompressor
DecompressBuffer(byte[]) - Method in class loci.formats.in.SlideBook7Reader.CCompressionBase
decompressHeader(byte[], int) - Method in class org.libjpegturbo.turbojpeg.TJDecompressor
decompressor - Variable in class loci.formats.filter.LZ4Filter
decompressor - Variable in class loci.formats.in.AmiraReader.HxZip
decompressToYUV(byte[], int) - Method in class org.libjpegturbo.turbojpeg.TJDecompressor
  Decompress the JPEG source image associated with this decompressor instance and output a YUV planar image to the given destination buffer.
decompressToYUV(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_RGB_DIMENSION_ORDER - Static variable in class loci.formats.in.FakeReader
DEFAULT_SAMPLE_IFD - Static variable in class loci.formats.in.CellSensReader
DEFAULT_SERIES - Static variable in class loci.formats.in.KLBReader
DEFAULT_SIZE_C - Static variable in class loci.formats.in.FakeReader
DEFAULT_SIZE_T - Static variable in class loci.formats.in.FakeReader
DEFAULT_SIZE_X - Static variable in class loci.formats.in.FakeReader
DEFAULT_SIZE_Y - Static variable in class loci.formats.in.FakeReader
DEFAULT_SIZE_Z - Static variable in class loci.formats.in.FakeReader
defaultClasses - Static variable in class loci.formats.ImageReader
  Default list of reader classes, for use with noargs constructor.
defaultClasses - Static variable in class loci.formats.ImageWriter
  Default list of writer classes, for use with noargs constructor.
defaultDateEnabled - Static variable in class loci.formats.MetadataTools
defaultExposureTime - Variable in class loci.formats.in.CellSensReader.Pyramid
DefaultJPEGReader() - Constructor for class loci.formats.in.JPEGReader.DefaultJPEGReader
DefaultMetadataOptions - Class in loci.formats.in
  Default implementation of `MetadataOptions`.
DefaultMetadataOptions() - Constructor for class loci.formats.in.DefaultMetadataOptions
  Construct a new `DefaultMetadataOptions`.
DefaultMetadataOptions(MetadataLevel) - Constructor for class loci.formats.in.DefaultMetadataOptions
  Construct a new `DefaultMetadataOptions`.
defaultMinMax(int) - Static method in class loci.formats.FormatTools
  Get the default range for the specified pixel type.
defaultValue - Variable in class loci.plugins.prefs.BooleanOption
  The option's default value.
defaultValue - Variable in class loci.plugins.prefs.DoubleOption
  The option's default value.
defaultValue - Variable in class loci.plugins.prefs.StringOption
  The option's default value.
defaultVR - Variable in enum loci.formats.dicom.DicomAttribute
defaultXMLSkip - Variable in class loci.formats.in.OIRReader
DEFINITION - Static variable in class loci.formats.in.BDVReader.H5Constants
DEFINITION - Static variable in class loci.formats.in.CellH5Reader.CellH5Constants
delegate - Variable in class loci.formats.in.SimplePCITiffReader
DelegateReader - Class in loci.formats
  DelegateReader is a file format reader that selects which reader to use for a format if there are two readers which handle the same format.
DelegateReader(String, String) - Constructor for class loci.formats.DelegateReader
  Constructs a new delegate reader.
DelegateReader(String, String[]) - Constructor for class loci.formats.DelegateReader
  Constructs a new delegate reader.
deleteMemo() - Method in class loci.formats.Memoizer
  Force the current memo file to be deleted, if it exists.
deleteQuietly(File) - Method in class loci.formats.Memoizer
  Attempts to delete an existing file, logging at warn if the deletion returns false or at error if an exception is thrown.
DELIMITERS - Static variable in class loci.formats.in.ImarisHDFReader
deltaT - Variable in class loci.formats.in.ColumbusReader.Plane
deltaT - Variable in class loci.formats.in.FV1000Reader.PlaneData
deltaT - Variable in class loci.formats.in.InCellReader.Image
deltaT - Variable in class loci.formats.in.IvisionReader
deltaT - Variable in class loci.formats.in.LeicaHandler
deltaT - Variable in class loci.formats.in.NiftiReader
deltaT - Variable in class loci.formats.in.OperettaReader.Plane
deltaT - Variable in class loci.formats.in.ScanrReader
DeltavisionReader - Class in loci.formats.in
  DeltavisionReader is the file format reader for Deltavision files.
DeltavisionReader() - Constructor for class loci.formats.in.DeltavisionReader
  Constructs a new Deltavision reader.
DeltavisionReader.DVExtHdrFields - Class in loci.formats.in
  This private class structure holds the details for the extended header.
denom - Variable in class loci.formats.tiff.TiffRational
  Components of the rational's fractional representation.
denom - Variable in class org.libjpegturbo.turbojpeg.TJScalingFactor
  Denominator
depth - Variable in class loci.formats.tools.AmiraParameters
desc - Variable in class loci.formats.gui.ComboFileFilter
  Description.
desc - Variable in class loci.formats.gui.ExtensionFileFilter
  Description.
desc - Variable in class loci.formats.gui.FormatFileFilter
  Description.
description - Variable in enum loci.formats.dicom.DicomAttribute
description - Variable in class loci.formats.in.CV7000Reader.WPIHandler
description - Variable in class loci.formats.in.NiftiReader
description() - Method in interface loci.formats.in.PrairieMetadata.Value
description - Variable in class loci.formats.in.PrairieMetadata.ValueItem
description() - Method in class loci.formats.in.PrairieMetadata.ValueItem
description() - Method in class loci.formats.in.PrairieMetadata.ValueTable
description - Variable in class loci.formats.in.TiffReader
description - Variable in class loci.formats.in.VolocityReader.Stack
description - Variable in class loci.formats.in.ZeissCZIReader
description - Variable in class loci.formats.in.ZeissLSMReader.Recording
DESCRIPTION_MARKER - Static variable in class loci.formats.in.TillVisionReader
descriptions - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataTempBuffer
descriptions - Variable in class loci.formats.in.LIFReader
destroy() - Method in class org.libjpegturbo.turbojpeg.TJCompressor
destroy() - Method in class org.libjpegturbo.turbojpeg.TJDecompressor
detailPath - Variable in class loci.formats.in.CV7000Reader
details - Variable in class loci.formats.in.PerkinElmerReader
DetectionChannel() - Constructor for class loci.formats.in.ZeissLSMReader.DetectionChannel
detector - Variable in class loci.formats.in.LeicaHandler.Channel
Detector() - Constructor for class loci.formats.in.LeicaHandler.Detector
Detector() - Constructor for class loci.formats.in.LeicaReader.Detector
Detector() - Constructor for class loci.formats.in.OIRReader.Detector
detector - Variable in class loci.formats.in.VolocityReader.Stack
detectorChannel - Variable in class loci.formats.in.LeicaHandler
detectorGain - Variable in class loci.formats.in.BaseZeissReader
detectorID - Variable in class loci.formats.in.MicromanagerReader.Position
detectorIDs - Variable in class loci.formats.in.ZeissCZIReader
detectorIndexes - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataTempBuffer
detectorIndexes - Variable in class loci.formats.in.LIFReader
detectorManufacturer - Variable in class loci.formats.in.FluoviewReader
detectorManufacturer - Variable in class loci.formats.in.MicromanagerReader.Position
detectorModel - Variable in class loci.formats.in.MicromanagerReader.Position
detectorModels - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataTempBuffer
detectorModels - Variable in class loci.formats.in.LIFReader
detectorOffset - Variable in class loci.formats.in.BaseZeissReader
detectorOffset - Variable in class loci.formats.in.OpenlabReader
detectorOffsets - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataTempBuffer
detectorOffsets - Variable in class loci.formats.in.LIFReader
detectorRefs - Variable in class loci.formats.in.ZeissCZIReader
detectors - Variable in class loci.formats.in.FEITiffReader
detectors - Variable in class loci.formats.in.LeicaHandler
detectors - Variable in class loci.formats.in.LeicaReader
detectors - Variable in class loci.formats.in.OIRReader
detType - Variable in class loci.formats.in.SDTInfo
  Detector type (SPC-930 in camera mode).
DEVICE_ID - Static variable in class loci.formats.in.CellSensReader
DEVICE_MANUFACTURER - Static variable in class loci.formats.in.CellSensReader
DEVICE_NAME - Static variable in class loci.formats.in.CellSensReader
DEVICE_SUBTYPE - Static variable in class loci.formats.in.CellSensReader
deviceIDs - Variable in class loci.formats.in.CellSensReader.Pyramid
deviceManufacturers - Variable in class loci.formats.in.CellSensReader.Pyramid
deviceNames - Variable in class loci.formats.in.CellSensReader.Pyramid
deviceTypes - Variable in class loci.formats.in.CellSensReader.Pyramid
devModel - Variable in class loci.formats.in.LeicaSCNReader.Image
devVersion - Variable in class loci.formats.in.LeicaSCNReader.Image
dialog - Variable in class loci.plugins.in.ThumbLoader
dichroic - Variable in class loci.formats.in.FlexReader.FilterGroup
dichroicMap - Variable in class loci.formats.in.FlexReader
dichroicModels - Variable in class loci.formats.in.NikonTiffReader
DICOM_MAGIC_STRING - Static variable in class loci.formats.in.DicomReader
DICOM_SUFFIXES - Static variable in class loci.formats.in.DicomReader
DicomAttribute - Enum in loci.formats.dicom
  Describes a DICOM attribute (integer tag, associated description, and expected VR).
DicomAttribute(int) - Constructor for enum loci.formats.dicom.DicomAttribute
DicomFileInfo - Class in loci.formats.dicom
  Structure containing metadata for one DICOM file (instance).
DicomFileInfo() - Constructor for class loci.formats.dicom.DicomFileInfo
  Construct an empty object to be populated later.
DicomFileInfo(String) - Constructor for class loci.formats.dicom.DicomFileInfo
  Construct an object from the given file.
DicomJSONProvider - Class in loci.formats.dicom
  Provide DICOM tags from a file containing JSON.
DicomJSONProvider() - Constructor for class loci.formats.dicom.DicomJSONProvider
DicomReader - Class in loci.formats.in
  DicomReader is the file format reader for DICOM files.
DicomReader() - Constructor for class loci.formats.in.DicomReader
  Constructs a new DICOM reader.
DicomTag - Class in loci.formats.dicom
  Represents a complete DICOM tag, including the dictionary attribute, actual VR, value, and any "child" tags (in the case of a sequence).
DicomTag(DicomAttribute) - Constructor for class loci.formats.dicom.DicomTag
DicomTag(DicomAttribute, DicomVR) - Constructor for class loci.formats.dicom.DicomTag
DicomTag(int, DicomVR) - Constructor for class loci.formats.dicom.DicomTag
DicomTag(RandomAccessInputStream, boolean, long, boolean) - Constructor for class loci.formats.dicom.DicomTag
  Read a complete tag and value from the given input stream.
DicomTag(RandomAccessInputStream, boolean, long, boolean, boolean) - Constructor for class loci.formats.dicom.DicomTag
  Read a complete tag and optionally a value from the given input stream.
DicomTile - Class in loci.formats.dicom
  Represents a tile stored in a DICOM file.
DicomTile() - Constructor for class loci.formats.dicom.DicomTile
DicomVR - Enum in loci.formats.dicom
  Enumeration of valid DICOM value representations (VRs).
DicomVR(int, int) - Constructor for enum loci.formats.dicom.DicomVR
DicomWriter - Class in loci.formats.out
  DicomWriter is the file format writer for DICOM files.
DicomWriter() - Constructor for class loci.formats.out.DicomWriter
DicomWriter.PlaneOffset - Class in loci.formats.out
DicomWriter.UIDCreator - Class in loci.formats.out
  Helper class for creating UIDs.
dict - Static variable in enum loci.formats.dicom.DicomAttribute
diff - Variable in class loci.formats.in.BioRadGelReader
difference(byte[], IFD) - Static method in enum loci.formats.tiff.TiffCompression
  Performs in-place differencing according to the given predictor value.
DIGITAL_ZOOM_RATIO - Static variable in class loci.formats.tiff.IFD
digits(int) - Static method in class loci.plugins.in.ImporterMetadata
  Computes the given value's number of digits.
dilate() - Method in class loci.plugins.util.RecordedImageProcessor
DIM_INDEX_1 - Static variable in class loci.formats.in.CellSensReader
DIM_INDEX_2 - Static variable in class loci.formats.in.CellSensReader
DIMDESCR - Static variable in class loci.formats.in.LeicaReader
Dimension - Class in loci.formats.in.LeicaMicrosystemsMetadata
  This class represents image dimensions extracted from LMS image xmls.
Dimension(Dimension.DimensionKey, int, long, String, Double, boolean) - Constructor for class loci.formats.in.LeicaMicrosystemsMetadata.Dimension
Dimension() - Constructor for class loci.formats.in.LeicaMicrosystemsMetadata.Dimension
Dimension(Attributes) - Constructor for class loci.formats.in.LeicaSCNReader.Dimension
dimension - Variable in class loci.formats.in.ZeissCZIReader.DimensionEntry
Dimension(Integer) - Constructor for class loci.formats.in.ZeissTIFFHandler.Scaling.Dimension
  Constructor.
dimension - Variable in class loci.formats.in.ZeissTIFFHandler.Scaling.Dimension
Dimension.DimensionKey - Enum in loci.formats.in.LeicaMicrosystemsMetadata
DIMENSION_DESCRIPTION_VOLUME - Static variable in class loci.formats.in.CellSensReader
DIMENSION_INCREMENT_ID - Static variable in class loci.formats.in.CellSensReader
DIMENSION_MEANING - Static variable in class loci.formats.in.CellSensReader
DIMENSION_NAME - Static variable in class loci.formats.in.CellSensReader
DIMENSION_NAMES - Static variable in class loci.formats.in.LeicaReader
DIMENSION_SIZE - Static variable in class loci.formats.in.CellSensReader
DIMENSION_START_ID - Static variable in class loci.formats.in.CellSensReader
DIMENSION_VALUE_ID - Static variable in class loci.formats.in.CellSensReader
dimensionCount - Variable in class loci.formats.in.ZeissCZIReader.DirectoryEntry
dimensionEntries - Variable in class loci.formats.in.ZeissCZIReader.DirectoryEntry
DimensionEntry(RandomAccessInputStream) - Constructor for class loci.formats.in.ZeissCZIReader.DimensionEntry
dimensionIndex - Variable in class loci.formats.out.DicomWriter.PlaneOffset
DimensionKey(int, char) - Constructor for enum loci.formats.in.LeicaMicrosystemsMetadata.Dimension.DimensionKey
dimensionLength - Variable in class loci.formats.out.ICSWriter
dimensionM - Variable in class loci.formats.in.ZeissLSMReader
dimensionOffset - Variable in class loci.formats.out.ICSWriter
dimensionOrder - Variable in class loci.formats.CoreMetadata
  Order in which dimensions are stored.
dimensionOrder - Variable in class loci.formats.in.FluoviewReader
dimensionOrdering - Variable in class loci.formats.in.CellSensReader.Pyramid
dimensionP - Variable in class loci.formats.in.ZeissLSMReader
dimensions - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataTempBuffer
DIMENSIONS_STRING - Static variable in class loci.formats.in.KodakReader
dimensionsSwapped - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.MultipleImagesReader
DimensionSwapper - Class in loci.formats
  Handles swapping the dimension order of an image series.
DimensionSwapper() - Constructor for class loci.formats.DimensionSwapper
  Constructs a DimensionSwapper around a new image reader.
DimensionSwapper(IFormatReader) - Constructor for class loci.formats.DimensionSwapper
  Constructs a DimensionSwapper with the given reader.
dimensionSwapper - Variable in class loci.plugins.in.ImportProcess
dimensionTag - Variable in class loci.formats.in.CellSensReader
dimOrder - Variable in class loci.formats.AxisGuesser
  Original ordering of internal dimensional axes.
dims - Variable in class loci.formats.in.LeicaSCNReader.Pixels
dims - Variable in class loci.formats.in.ZeissTIFFHandler.Scaling
dims_blockSize - Variable in class loci.formats.in.KLBReader
dims_xyzct - Variable in class loci.formats.in.KLBReader
dir - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.LMSXmlDocument
dir - Variable in class loci.formats.in.VolocityReader
direction - Variable in class loci.formats.in.VentanaReader.Overlap
Directory() - Constructor for class loci.formats.in.ZeissCZIReader.Directory
directory - Variable in class loci.formats.Memoizer
  Directory where all memo files should be created.
directory - Variable in class loci.formats.services.EXIFServiceImpl
directoryCache - Variable in class loci.formats.in.ZeissTIFFReader
DirectoryEntry(RandomAccessInputStream) - Constructor for class loci.formats.in.ZeissCZIReader.DirectoryEntry
directoryEntry - Variable in class loci.formats.in.ZeissCZIReader.SubBlock
directoryList - Variable in class loci.formats.in.CellWorxReader
directoryPosition - Variable in class loci.formats.in.ZeissCZIReader.FileHeader
directoryRoot - Variable in class loci.formats.tools.FakeImage
dirty - Variable in class loci.formats.cache.CacheStrategy
  Whether load order array needs to be recomputed before building the next load list.
disableChromaSubsampling - Variable in class loci.formats.codec.CodecOptions
  Whether or not to use chroma subsampling.
DISPLAY_COLOR - Static variable in class loci.formats.in.CellSensReader
DISPLAY_CONTRAST_BRIGHTNESS - Static variable in class loci.formats.in.CellSensReader
DISPLAY_GAMMA_CORRECTION - Static variable in class loci.formats.in.CellSensReader
DISPLAY_LIMITS - Static variable in class loci.formats.in.CellSensReader
DISPLAY_LUT - Static variable in class loci.formats.in.CellSensReader
DISPLAY_MAPPING_VOLUME - Static variable in class loci.formats.in.CellSensReader
DISPLAY_PROCESSOR_TYPE - Static variable in class loci.formats.in.CellSensReader
DISPLAY_STACK_ID - Static variable in class loci.formats.in.CellSensReader
DISPLAY_STACK_INDEX - Static variable in class loci.formats.in.CellSensReader
DISPLAY_VISIBLE - Static variable in class loci.formats.in.CellSensReader
displayColor - Variable in class loci.formats.in.SVSReader
displayDataBrowser(ImagePlus) - Method in class loci.plugins.in.DisplayHandler
displayDialog(GenericDialog) - Method in class loci.plugins.in.IdDialog
  Asks user whether Bio-Formats should automatically check for upgrades, and if so, checks for an upgrade and prompts user to install it.
displayDialog(GenericDialog) - Method in class loci.plugins.in.ImporterDialog
  Displays the dialog, or grabs values from macro options.
displayDialog(GenericDialog) - Method in class loci.plugins.in.SeriesDialog
displayDialog(GenericDialog) - Method in class loci.plugins.in.UpgradeDialog
  Asks user whether Bio-Formats should automatically check for upgrades, and if so, checks for an upgrade and prompts user to install it.
DISPLAYED_LUT_ID - Static variable in class loci.formats.in.CellSensReader
DisplayHandler - Class in loci.plugins.in
  Logic for displaying images and metadata onscreen using ImageJ.
DisplayHandler(ImportProcess) - Constructor for class loci.plugins.in.DisplayHandler
displayImage(ImagePlus) - Method in class loci.plugins.in.DisplayHandler
  Displays the given image according to the configured options.
displayImage5D(ImagePlus) - Method in class loci.plugins.in.DisplayHandler
displayImages(ImagePlus[]) - Method in class loci.plugins.in.DisplayHandler
  Displays the given images according to the configured options.
displayName - Variable in class loci.formats.in.OperettaReader.OperettaHandler
displayNormal(ImagePlus) - Method in class loci.plugins.in.DisplayHandler
  Displays in a normal ImageJ window.
displayOMEXML() - Method in class loci.plugins.in.DisplayHandler
  Displays OME-XML metadata in a tree in its own window.
displayOriginalMetadata() - Method in class loci.plugins.in.DisplayHandler
  Displays standard metadata in a table in its own window.
displayROIs(ImagePlus[]) - Method in class loci.plugins.in.DisplayHandler
displayTag - Variable in class loci.formats.in.BaseZeissReader.Shape
displayUsage() - Method in class loci.formats.tools.MakeTestOmeTiff
displayView5D(ImagePlus) - Method in class loci.plugins.in.DisplayHandler
dispose() - Method in class loci.formats.gui.CacheComponent
dispose - Variable in class loci.formats.in.GIFReader
distance(int, int) - Method in class loci.formats.cache.CacheStrategy
  Computes the distance from the given axis value to the axis center, taking into account the axis ordering scheme.
dither - Variable in class loci.formats.in.SDTInfo
DLL_DATA_IDENTIFIER - Static variable in class loci.formats.in.SDTInfo
  For .sdt files created using DLL function SPC_save_data_to_sdtfile (no setup, only data).
DM2_MAGIC_BYTES - Static variable in class loci.formats.in.GatanDM2Reader
DM3_MAGIC_BYTES - Static variable in class loci.formats.in.GatanReader
DM4_MAGIC_BYTES - Static variable in class loci.formats.in.GatanReader
DNGReader - Class in loci.formats.in
  DNGReader is the file format reader for Canon DNG (TIFF) files.
DNGReader() - Constructor for class loci.formats.in.DNGReader
  Constructs a new DNG reader.
doc - Variable in class loci.formats.gui.XMLWindow
doc - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.LMSXmlDocument
doCaching - Variable in class loci.formats.tiff.TiffParser
doChannels - Variable in class loci.formats.in.CellWorxReader
doCrop() - Method in class loci.plugins.in.ImporterOptions
DOCUMENT_AUTHOR - Static variable in class loci.formats.in.CellSensReader
DOCUMENT_COMPANY - Static variable in class loci.formats.in.CellSensReader
DOCUMENT_CREATOR_BUILD_NUMBER - Static variable in class loci.formats.in.CellSensReader
DOCUMENT_CREATOR_MAJOR_VERSION - Static variable in class loci.formats.in.CellSensReader
DOCUMENT_CREATOR_MINOR_VERSION - Static variable in class loci.formats.in.CellSensReader
DOCUMENT_CREATOR_NAME - Static variable in class loci.formats.in.CellSensReader
DOCUMENT_CREATOR_PACKAGE - Static variable in class loci.formats.in.CellSensReader
DOCUMENT_CREATOR_SUB_VERSION - Static variable in class loci.formats.in.CellSensReader
DOCUMENT_KEYS - Static variable in class loci.formats.in.ICSReader
DOCUMENT_NAME - Static variable in class loci.formats.in.CellSensReader
DOCUMENT_NAME - Static variable in class loci.formats.tiff.IFD
DOCUMENT_NOTE - Static variable in class loci.formats.in.CellSensReader
DOCUMENT_PRODUCT - Static variable in class loci.formats.in.CellSensReader
DOCUMENT_PRODUCT_NAME - Static variable in class loci.formats.in.CellSensReader
DOCUMENT_PRODUCT_VERSION - Static variable in class loci.formats.in.CellSensReader
DOCUMENT_PROPERTIES - Static variable in class loci.formats.in.CellSensReader
DOCUMENT_THUMB - Static variable in class loci.formats.in.CellSensReader
DOCUMENT_TIME - Static variable in class loci.formats.in.CellSensReader
DOCUMENT_TYPE_HINT - Static variable in class loci.formats.in.CellSensReader
doFormatLayout(FormatEntry) - Method in class loci.plugins.config.ConfigWindow
doInPlaceCaching - Variable in class loci.formats.Memoizer
  If `true`, then all memo files will be created in the same directory as the original file.
domains - Variable in class loci.formats.FormatReader
  List of domains in which this format is used.
doMustGroup() - Method in class loci.plugins.in.ImporterOptions
doNotChangePattern - Variable in class loci.formats.FileStitcher
doRecording - Variable in class loci.plugins.util.RecordedImageProcessor
doStitchTiles() - Method in class loci.plugins.in.ImporterOptions
doT - Variable in class loci.formats.in.InCellReader.MinimalInCellHandler
DOT - Static variable in class loci.formats.ResourceNamer
DOT_RANGE - Static variable in class loci.formats.tiff.IFD
DOUBLE - Static variable in class loci.formats.FormatTools
  Identifies the DOUBLE data type used to store pixel values.
DOUBLE - Static variable in class loci.formats.in.CellSensReader
DOUBLE - Static variable in class loci.formats.in.GatanReader
DOUBLE_2 - Static variable in class loci.formats.in.CellSensReader
DOUBLE_2_2 - Static variable in class loci.formats.in.CellSensReader
DOUBLE_3 - Static variable in class loci.formats.in.CellSensReader
DOUBLE_3_3 - Static variable in class loci.formats.in.CellSensReader
DOUBLE_4 - Static variable in class loci.formats.in.CellSensReader
DOUBLE_4_4 - Static variable in class loci.formats.in.CellSensReader
DOUBLE_ARRAY_2 - Static variable in class loci.formats.in.CellSensReader
DOUBLE_ARRAY_3 - Static variable in class loci.formats.in.CellSensReader
DOUBLE_INTERVAL - Static variable in class loci.formats.in.CellSensReader
DOUBLE_RECT - Static variable in class loci.formats.in.CellSensReader
doubleCapacity() - Method in class loci.formats.codec.ByteVector
DoubleOption - Class in loci.plugins.prefs
  A double option for one of the plugins.
DoubleOption(HashMap<String, String>) - Constructor for class loci.plugins.prefs.DoubleOption
  Constructs a double option with the parameters from the given map.
DoubleOption(String, boolean, String, String, double) - Constructor for class loci.plugins.prefs.DoubleOption
  Constructs a double option with the given parameters.
doubleValue() - Method in class loci.formats.tiff.TiffRational
  Returns the value of the specified number as a double.
doUpgradeCheck() - Method in class loci.plugins.in.ImporterOptions
download(URLConnection) - Static method in class loci.plugins.config.InstallWizard
download(URLConnection, File) - Static method in class loci.plugins.config.InstallWizard
doZ - Variable in class loci.formats.in.InCellReader.MinimalInCellHandler
DP80_FRAME_CENTERING - Static variable in class loci.formats.in.CellSensReader
drawColour - Variable in class loci.formats.in.BaseZeissReader.Shape
drawDot(int, int) - Method in class loci.plugins.util.RecordedImageProcessor
drawLine(int, int, int, int) - Method in class loci.plugins.util.RecordedImageProcessor
drawOval(int, int, int, int) - Method in class loci.plugins.util.RecordedImageProcessor
drawPixel(int, int) - Method in class loci.plugins.util.RecordedImageProcessor
drawPolygon(Polygon) - Method in class loci.plugins.util.RecordedImageProcessor
drawRect(int, int, int, int) - Method in class loci.plugins.util.RecordedImageProcessor
drawString(String) - Method in class loci.plugins.util.RecordedImageProcessor
drawString(String, int, int) - Method in class loci.plugins.util.RecordedImageProcessor
DrawStyle(int) - Constructor for enum loci.formats.in.BaseZeissReader.DrawStyle
drawStyle - Variable in class loci.formats.in.BaseZeissReader.Shape
DRI - Static variable in class loci.formats.services.JPEGTurboServiceImpl
drivePictDecoder(int) - Method in class loci.formats.in.PictReader
  Handles the opcodes in the PICT file.
dualCamera - Variable in class loci.formats.in.MetamorphHandler
dualCamera - Variable in class loci.formats.in.MetamorphTiffReader
DUMMY_PIXEL - Static variable in class loci.formats.out.EPSWriter
DummyMetadata - Class in loci.formats.meta
DummyMetadata() - Constructor for class loci.formats.meta.DummyMetadata
dumpXML() - Method in class loci.formats.ome.OMEPyramidStore
duplicate(Class<? extends IFormatReader>) - Method in class loci.formats.ReaderWrapper
  Performs a deep copy of the reader, including nested wrapped readers.
duplicate(Class<? extends IFormatWriter>) - Method in class loci.formats.WriterWrapper
  Performs a deep copy of the writer, including nested wrapped writers.
duplicate() - Method in class loci.plugins.util.RecordedImageProcessor
DUPLICATE_PLANES_DEFAULT - Static variable in class loci.formats.in.CV7000Reader
DUPLICATE_PLANES_DEFAULT - Static variable in class loci.formats.in.InCellReader
DUPLICATE_PLANES_KEY - Static variable in class loci.formats.in.CV7000Reader
DUPLICATE_PLANES_KEY - Static variable in class loci.formats.in.InCellReader
duplicatePlanes() - Method in class loci.formats.in.CV7000Reader
duplicatePlanes() - Method in class loci.formats.in.InCellReader
duplicateRecurse(Class<? extends IFormatReader>) - Method in class loci.formats.ReaderWrapper
duplicateRecurse(Class<? extends IFormatWriter>) - Method in class loci.formats.WriterWrapper
DV_MAGIC_BYTES_1 - Static variable in class loci.formats.in.DeltavisionReader
DV_MAGIC_BYTES_2 - Static variable in class loci.formats.in.DeltavisionReader
DVExtHdrFields(RandomAccessInputStream) - Constructor for class loci.formats.in.DeltavisionReader.DVExtHdrFields
DWORD - Static variable in class loci.formats.in.CellSensReader
dyeName - Variable in class loci.formats.in.FV1000Reader.ChannelData
dyeName - Variable in class loci.formats.in.LeicaHandler.MultiBand
dyeNames - Variable in class loci.formats.in.SVSReader
dyes - Variable in class loci.formats.in.ND2Handler
DYNAMIC_PROPERTIES - Static variable in class loci.formats.in.CellSensReader
DynamicMetadataOptions - Class in loci.formats.in
  Configuration object for readers and writers.
DynamicMetadataOptions() - Constructor for class loci.formats.in.DynamicMetadataOptions
  Creates an options object with metadata level set to `DynamicMetadataOptions.METADATA_LEVEL_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.
eCompressionJetRaw - Static variable in class loci.formats.in.SlideBook7Reader.CCompressionBase
eCompressionLz4 - Static variable in class loci.formats.in.SlideBook7Reader.CCompressionBase
eCompressionNone - Static variable in class loci.formats.in.SlideBook7Reader.CCompressionBase
eCompressionRLE - Static variable in class loci.formats.in.SlideBook7Reader.CCompressionBase
eCompressionZlib - Static variable in class loci.formats.in.SlideBook7Reader.CCompressionBase
eCompressionZstd - Static variable in class loci.formats.in.SlideBook7Reader.CCompressionBase
edf - Variable in class loci.formats.dicom.DicomFileInfo
edf - Variable in class loci.formats.in.DicomReader
EditTiffG - Class in loci.formats.tools
  Provides a GUI for editing TIFF file comments.
EditTiffG() - Constructor for class loci.formats.tools.EditTiffG
effectiveFieldCount - Variable in class loci.formats.in.FlexReader
EFI_HEIGHT_MAP - Static variable in class loci.formats.in.CellSensReader
EFI_SHARPNESS_MAP - Static variable in class loci.formats.in.CellSensReader
EFI_STACK - Static variable in class loci.formats.in.CellSensReader
EFI_TEXTURE_MAP - Static variable in class loci.formats.in.CellSensReader
EGraphicType() - Constructor for enum loci.formats.in.SlideBook7Reader.EGraphicType
el(NodeList, int) - Method in class loci.formats.in.PrairieMetadata
  Gets the `index`th element from the given list of nodes.
ELEMENT_STYLE_END - Static variable in class loci.formats.gui.XMLCellRenderer
ELEMENT_STYLE_START - Static variable in class loci.formats.gui.XMLCellRenderer
elementLength - Variable in class loci.formats.dicom.DicomTag
elementName - Variable in class loci.formats.in.LeicaHandler
elements - Variable in class loci.formats.FilePatternBlock
  Elements within this block, e.g.
ELLIPSE - Static variable in class loci.formats.in.FV1000Reader
ELLIPSE - Static variable in class loci.formats.in.GatanReader
ELLIPSE - Static variable in class loci.formats.in.ZeissLSMReader
ellipses - Variable in class loci.formats.in.FakeReader
EM_DAC - Static variable in class loci.formats.in.FluoviewReader
EM_DOMAIN - Static variable in class loci.formats.FormatTools
  Identifies the electron microscopy domain.
EM_GAIN - Static variable in class loci.formats.in.CellSensReader
EMBEDDED_STREAM - Static variable in class loci.formats.in.VolocityReader
embeddedImages - Variable in class loci.formats.in.TillVisionReader
embeddedOffset - Variable in class loci.formats.in.TillVisionReader
emFilters - Variable in class loci.formats.in.InCellReader
emission - Variable in class loci.formats.in.FlexReader.FilterGroup
emission - Variable in class loci.formats.in.OIRReader.Channel
emission - Variable in class loci.formats.in.ZeissCZIReader.Channel
emissionFilter - Variable in class loci.formats.in.FV1000Reader.ChannelData
emissionWavelength - Variable in class loci.formats.in.SVSReader
emissionWavelengths - Variable in class loci.formats.in.FakeReader
EMPTY_STRING - Static variable in class loci.formats.in.IM3Reader
emWave - Variable in class loci.formats.in.BDReader
emWave - Variable in class loci.formats.in.FV1000Reader.ChannelData
emWave - Variable in class loci.formats.in.ImarisHDFReader
emWave - Variable in class loci.formats.in.ND2Handler
emWave - Variable in class loci.formats.in.NikonTiffReader
emWave - Variable in class loci.formats.in.TissueFAXSReader.Channel
emWavelen - Variable in class loci.formats.in.DeltavisionReader.DVExtHdrFields
  Emission filter wavelength.
emWavelength - Variable in class loci.formats.in.BaseZeissReader
emWavelength - Variable in class loci.formats.in.ColumbusReader.Plane
emWavelength - Variable in class loci.formats.in.MetamorphReader
  The TIFF's emWavelength
emWavelength - Variable in class loci.formats.in.OperettaReader.Channel
emWavelength - Variable in class loci.formats.in.OperettaReader.Plane
emWaves - Variable in class loci.formats.in.InCellReader
emWaves - Variable in class loci.formats.in.LeicaReader
enabledBox - Variable in class loci.plugins.config.ConfigWindow
encloses(Region, Region) - Method in class loci.formats.in.DicomReader
encode(byte[]) - Method in class loci.formats.filter.LZ4Filter
encodeYUV(byte[], int) - Method in class org.libjpegturbo.turbojpeg.TJCompressor
  Encode the uncompressed source image associated with this compressor instance and output a YUV planar image to the given destination buffer.
encodeYUV(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 - Static variable in class loci.formats.in.LOFReader
  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
endOffset - Variable in class loci.formats.dicom.DicomTile
endPointer - Variable in class loci.formats.in.LIFReader
endPointer - Variable in class loci.formats.in.LOFReader
endPos - Variable in class loci.formats.out.AVIWriter
endTime - Variable in class loci.formats.in.CV7000Reader
endTime - Variable in class loci.formats.in.SDTInfo
  Macro time of the last photon.
endX - Variable in class loci.formats.in.SPEReader.SpeROI
endY - Variable in class loci.formats.in.SPEReader.SpeROI
energyConvFactor - Variable in class loci.formats.in.DeltavisionReader.DVExtHdrFields
  Energy conversion factor.
ENHANCED_DYNAMIC_RANGE - Static variable in class loci.formats.in.CellSensReader
ensureNonExisting(String) - Method in class loci.formats.tools.MakeTestOmeTiff
entries - Variable in class loci.formats.in.ZeissCZIReader.AttachmentDirectory
entries - Variable in class loci.formats.in.ZeissCZIReader.Directory
entryName - Variable in class loci.formats.in.ZipReader
entryToString(Object, String) - Static method in class loci.formats.tools.AmiraParameters
ENV_SUFFIX - Static variable in class loci.formats.in.PrairieReader
envFile - Variable in class loci.formats.in.PrairieReader
  The associated XML files.
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.CV7000Reader.Field
equals(Object) - Method in class loci.formats.in.MetamorphTiffReader.Well
equals(Object) - Method in class loci.formats.in.OIRReader.CZTKey
equals(Object) - Method in class loci.formats.in.ZeissCZIReader.Coordinate
equals(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
excitationWavelengths - Variable in class loci.formats.in.FakeReader
exclude - Variable in class loci.formats.in.InCellReader
execute() - Method in class loci.plugins.in.ImportProcess
  Performs the import preparation process, notifying status listeners at each step.
exFilters - Variable in class loci.formats.in.InCellReader
EXIF - Static variable in class loci.formats.tiff.IFD
EXIF_VERSION - Static variable in class loci.formats.tiff.IFD
EXIFService - Interface in loci.formats.services
EXIFServiceImpl - Class in loci.formats.services
EXIFServiceImpl() - Constructor for class loci.formats.services.EXIFServiceImpl
exists - Variable in class loci.formats.in.OMETiffReader.OMETiffPlane
  Whether or not the file meant to contain this plane exists.
exists(String) - Method in interface loci.formats.services.JHDFService
  Checks if path in HDF5 file exists.
exists(String) - Method in class loci.formats.services.JHDFServiceImpl
exit() - Method in class loci.formats.tools.EditTiffG
exp() - Method in class loci.plugins.util.RecordedImageProcessor
expandPixels(int, byte[], byte[], int) - Method in class loci.formats.in.PictReader
  Expand an array of bytes.
EXPANSION_TABLE - Static variable in class loci.formats.in.PictReader
  Table used in expanding pixels that use less than 8 bits.
expectETS - Variable in class loci.formats.in.CellSensReader
EXPERIMENT - Static variable in class loci.formats.in.LeicaReader
EXPERIMENT_FILE - Static variable in class loci.formats.in.BDReader
EXPERIMENT_FILE - Static variable in class loci.formats.in.ScanrReader
experimenterName - Variable in class loci.formats.in.ImaconReader
explode() - Method in class loci.formats.FilePatternBlock
exporter - Variable in class loci.plugins.LociExporter
Exporter - Class in loci.plugins.out
  Core logic for the Bio-Formats Exporter ImageJ plugin.
Exporter(LociExporter, ImagePlus) - Constructor for class loci.plugins.out.Exporter
exposure - Variable in class loci.formats.in.BDReader
exposure - Variable in class loci.formats.in.InCellReader.Image
exposure - Variable in class loci.formats.in.InCellReader.InCellHandler
exposure - Variable in class loci.formats.in.ZeissCZIReader.Channel
EXPOSURE_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.JDCEReader.PlaneMetadata
exposureTime - Variable in class loci.formats.in.LeicaReader
exposureTime - Variable in class loci.formats.in.LiFlimReader
exposureTime - Variable in class loci.formats.in.MetamorphReader
exposureTime - Variable in class loci.formats.in.MicroCTReader
exposureTime - Variable in class loci.formats.in.MicromanagerReader.Position
exposureTime - Variable in class loci.formats.in.ND2Handler
exposureTime - Variable in class loci.formats.in.ND2Reader
exposureTime - Variable in class loci.formats.in.OperettaReader.Channel
exposureTime - Variable in class loci.formats.in.OperettaReader.Plane
exposureTime - Variable in class loci.formats.in.SVSReader
exposureTime - Variable in class loci.formats.in.TecanReader.Channel
exposureTime - Variable in class loci.formats.in.TecanReader.Image
exposureTime - Variable in class loci.formats.in.ZeissCZIReader.SubBlock
exposureTimes - Variable in class loci.formats.in.CellSensReader.Pyramid
exposureTimes - Variable in class loci.formats.in.LeicaHandler
exposureTimes - Variable in class loci.formats.in.SimplePCITiffReader
exposureTimes - Variable in class loci.formats.in.TillVisionReader
exposureTimes - Variable in class loci.formats.in.ZeissXRMReader
exposureTimeUnit - Variable in class loci.formats.in.LiFlimReader
expTime - Variable in class loci.formats.in.DeltavisionReader.DVExtHdrFields
  Exposure time in seconds.
expTimes - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataTempBuffer
expTimes - Variable in class loci.formats.in.LIFReader
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.CellSensReader
extraFiles - Variable in class loci.formats.in.CV7000Reader
extraFiles - Variable in class loci.formats.in.OlympusTileReader
extraFiles - Variable in class loci.formats.in.TecanReader
extraFiles - Variable in class loci.formats.in.VolocityReader
extraImages - Variable in class loci.formats.in.SVSReader
extraImages - Variable in class loci.formats.in.ZeissCZIReader
extras - Variable in class loci.formats.in.LeicaHandler
extras - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.LMSMetadataExtractor
exts - Variable in class loci.formats.gui.ExtensionFileFilter
  List of valid extensions.
extSize - Variable in class loci.formats.in.DeltavisionReader
  Size of extended header.
exWave - Variable in class loci.formats.in.BDReader
exWave - Variable in class loci.formats.in.FV1000Reader.ChannelData
exWave - Variable in class loci.formats.in.ImarisHDFReader
exWave - Variable in class loci.formats.in.LeicaHandler.Channel
exWave - Variable in class loci.formats.in.ND2Handler
exWave - Variable in class loci.formats.in.NikonTiffReader
exWave - Variable in class loci.formats.in.TissueFAXSReader.Channel
exWavelen - Variable in class loci.formats.in.DeltavisionReader.DVExtHdrFields
  Excitation filter wavelength.
exWavelength - Variable in class loci.formats.in.BaseZeissReader
exWavelength - Variable in class loci.formats.in.ColumbusReader.Plane
exWavelength - Variable in class loci.formats.in.OperettaReader.Channel
exWavelength - Variable in class loci.formats.in.OperettaReader.Plane
exWaves - Variable in class loci.formats.in.InCellReader
exWaves - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataTempBuffer
exWaves - Variable in class loci.formats.in.LeicaReader
exWaves - Variable in class loci.formats.in.LIFReader

## F

F_KEY - Static variable in class loci.formats.in.LiFlimReader
F_NUMBER - Static variable in class loci.formats.tiff.IFD
factor - Variable in class loci.formats.in.ZeissTIFFHandler.Scaling.Dimension
factors - Variable in class loci.formats.in.FlexReader.FlexFile
factors - Variable in class loci.formats.in.FlexReader.FlexHandler
factory - Variable in class loci.formats.FormatReader
FAIL_ON_MISSING_DEFAULT - Static variable in class loci.formats.in.CellSensReader
FAIL_ON_MISSING_DEFAULT - Static variable in class loci.formats.in.OMETiffReader
FAIL_ON_MISSING_KEY - Static variable in class loci.formats.in.CellSensReader
FAIL_ON_MISSING_KEY - Static variable in class loci.formats.in.OMETiffReader
failOnMissingETS() - Method in class loci.formats.in.CellSensReader
failOnMissingTIFF() - Method in class loci.formats.in.OMETiffReader
FAKE_EXT - Static variable in class loci.formats.ResourceNamer
fakeBigTiff - Variable in class loci.formats.tiff.TiffParser
  Whether or not 64-bit offsets are used for non-BigTIFF files.
FakeImage - Class in loci.formats.tools
  Generates fake image structures.
FakeImage(Location) - Constructor for class loci.formats.tools.FakeImage
FakeReader - Class in loci.formats.in
  FakeReader is the file format reader for faking input data.
FakeReader() - Constructor for class loci.formats.in.FakeReader
  Constructs a new fake reader.
FakeReader.TextLine - Class in loci.formats.in
fakeSeries - Variable in class loci.formats.in.FakeReader
  List of used files if the fake is a SPW structure
falseColor - Variable in class loci.formats.CoreMetadata
  Indicates whether or not we can ignore the color map (if present).
FAN_SPEED - Static variable in class loci.formats.in.CellSensReader
fb - Variable in class loci.formats.in.BaseZeissReader.Shape
fcc - Variable in class loci.formats.in.AVIReader
FCS_DATA_IDENTIFIER - Static variable in class loci.formats.in.SDTInfo
  For .sdt files created in FIFO mode (setup, data blocks = Decay, FCS, FIDA, FILDA & MCS curves for each used routing channel).
fcsDecayCalc - Variable in class loci.formats.in.SDTInfo
  Bit 0 = 1 - decay curve calculated.
fcsPoints - Variable in class loci.formats.in.SDTInfo
  No of FCS values.
fcsType - Variable in class loci.formats.in.SDTInfo
  0 - linear FCS with log binning (100 bins/log) when bit 15 = 1 (0x8000) - Multi-Tau FCS where bits 14-0 = ktau parameter.
fctlCount - Variable in class loci.formats.in.APNGReader.PNGInputStream
fdatValid - Variable in class loci.formats.in.APNGReader.PNGInputStream
FEATURE - Static variable in class loci.formats.in.BDVReader.H5Constants
FEATURE - Static variable in class loci.formats.in.CellH5Reader.CellH5Constants
FeatureType(int, int) - Constructor for enum loci.formats.in.BaseZeissReader.FeatureType
FEI_MAGIC_STRING - Static variable in class loci.formats.in.FEIReader
FEIHandler() - Constructor for class loci.formats.in.FEITiffReader.FEIHandler
FEIReader - Class in loci.formats.in
  FEIReader is the file format reader for FEI and Philips .img files.
FEIReader() - Constructor for class loci.formats.in.FEIReader
  Constructs a new FEI reader.
FEITiffReader - Class in loci.formats.in
  FEITiffReader is the file format reader for TIFF files produced by various FEI software.
FEITiffReader() - Constructor for class loci.formats.in.FEITiffReader
FEITiffReader.FEIHandler - Class in loci.formats.in
fetchRow(MdbTableDef) - Method in class loci.formats.services.MDBServiceImpl
  Fetches the next row from the table, ignoring potential parsing exceptions.
fetchXMLId() - Method in class loci.formats.in.BDVReader
fidaPoints - Variable in class loci.formats.in.SDTInfo
  No of FIDA values.
fidaTime - Variable in class loci.formats.in.SDTInfo
  Interval time [ms] for FIDA histogram.
field - Variable in class loci.formats.in.CellomicsReader.ChannelFile
field - Variable in class loci.formats.in.ColumbusReader.Plane
Field() - Constructor for class loci.formats.in.CV7000Reader.Field
field - Variable in class loci.formats.in.CV7000Reader.Field
field - Variable in class loci.formats.in.CV7000Reader.Plane
field - Variable in class loci.formats.in.FlexReader.FlexFile
field - Variable in class loci.formats.in.OperettaReader.Plane
field - Variable in class loci.formats.in.TecanReader.Image
FIELD - Static variable in class loci.formats.ResourceNamer
FIELD_AUX_FLAGS - Static variable in class loci.formats.in.IM3Reader
FIELD_BAND_INDEX - Static variable in class loci.formats.in.IM3Reader
FIELD_BANDS - Static variable in class loci.formats.in.IM3Reader
FIELD_CLASS_ID - Static variable in class loci.formats.in.IM3Reader
FIELD_DATA - Static variable in class loci.formats.in.IM3Reader
FIELD_DATA_SET - Static variable in class loci.formats.in.IM3Reader
FIELD_EXPOSURE - Static variable in class loci.formats.in.IM3Reader
FIELD_FILE_VERSION - Static variable in class loci.formats.in.IM3Reader
FIELD_FILTER_PAIR - Static variable in class loci.formats.in.IM3Reader
FIELD_FIXED_FILTER - Static variable in class loci.formats.in.IM3Reader
FIELD_HOMOGENEOUS - Static variable in class loci.formats.in.IM3Reader
FIELD_INDEX - Static variable in class loci.formats.in.ND2Handler
FIELD_MAGNITUDES - Static variable in class loci.formats.in.IM3Reader
FIELD_MANUFACTURER - Static variable in class loci.formats.in.IM3Reader
FIELD_MILLIMETERS_PER_PIXEL - Static variable in class loci.formats.in.IM3Reader
FIELD_NAME - Static variable in class loci.formats.in.IM3Reader
FIELD_NUANCE_FLAGS - Static variable in class loci.formats.in.IM3Reader
FIELD_OBJECTIVE - Static variable in class loci.formats.in.IM3Reader
FIELD_PART_NUMBER - Static variable in class loci.formats.in.IM3Reader
FIELD_PROTOCOL - Static variable in class loci.formats.in.IM3Reader
FIELD_PROXY_PARENT_FILE_NAME - Static variable in class loci.formats.in.IM3Reader
FIELD_SAMPLE_ID - Static variable in class loci.formats.in.IM3Reader
FIELD_SHAPE - Static variable in class loci.formats.in.IM3Reader
FIELD_SOURCE_FILE_NAME - Static variable in class loci.formats.in.IM3Reader
FIELD_SPECTRA - Static variable in class loci.formats.in.IM3Reader
FIELD_SPECTRAL_BASIS_INFO - Static variable in class loci.formats.in.IM3Reader
FIELD_SPECTRAL_LIBRARY - Static variable in class loci.formats.in.IM3Reader
FIELD_SPECTRUM - Static variable in class loci.formats.in.IM3Reader
FIELD_THUMBNAIL - Static variable in class loci.formats.in.IM3Reader
FIELD_TIMESTAMP - Static variable in class loci.formats.in.IM3Reader
FIELD_TYPE - Static variable in class loci.formats.in.CellSensReader
FIELD_TYPE_ID - Static variable in class loci.formats.in.IM3Reader
FIELD_USER_COMMENTS - Static variable in class loci.formats.in.IM3Reader
FIELD_VALUES - Static variable in class loci.formats.in.IM3Reader
FIELD_WAVELENGTH - Static variable in class loci.formats.in.IM3Reader
FIELD_WAVELENGTHS - Static variable in class loci.formats.in.IM3Reader
fieldCol - Variable in class loci.formats.in.MetamorphTiffReader.Well
fieldCols - Variable in class loci.formats.in.BDReader
fieldColumnCount - Variable in class loci.formats.in.MetamorphTiffReader
fieldColumns - Variable in class loci.formats.in.ScanrReader
fieldCount - Variable in class loci.formats.in.CellWorxReader
fieldCount - Variable in class loci.formats.in.FlexReader
fieldCount - Variable in class loci.formats.in.InCellReader
fieldCount - Variable in class loci.formats.internal.WellContainer
fieldIndex - Variable in class loci.formats.in.FluoviewReader
fieldIndex - Variable in class loci.formats.in.ND2Reader
FieldInfo() - Constructor for class loci.formats.in.CellVoyagerReader.FieldInfo
fieldMap - Variable in class loci.formats.in.CellWorxReader
fieldNames - Variable in class loci.formats.in.ZeissCZIReader
fieldOffsets - Variable in class loci.formats.in.FluoviewReader
fieldPositionX - Variable in class loci.formats.in.ScanrReader
fieldPositionY - Variable in class loci.formats.in.ScanrReader
fieldPosX - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataTempBuffer
fieldPosX - Variable in class loci.formats.in.LIFReader
fieldPosY - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataTempBuffer
fieldPosY - Variable in class loci.formats.in.LIFReader
fieldRow - Variable in class loci.formats.in.MetamorphTiffReader.Well
fieldRowCount - Variable in class loci.formats.in.MetamorphTiffReader
fieldRows - Variable in class loci.formats.in.BDReader
fieldRows - Variable in class loci.formats.in.ScanrReader
fields - Variable in class loci.formats.in.CellVoyagerReader.AreaInfo
fields - Variable in class loci.formats.in.CV7000Reader
fields - Variable in class loci.formats.in.FakeReader
fifoTyp - Variable in class loci.formats.in.SDTInfo
fildaPoints - Variable in class loci.formats.in.SDTInfo
  No of FILDA values.
fildaTime - Variable in class loci.formats.in.SDTInfo
  Interval time [ms] for FILDA histogram.
file - Variable in class loci.formats.dicom.DicomFileInfo
file - Variable in class loci.formats.dicom.DicomTile
file - Variable in class loci.formats.in.ColumbusReader.Plane
file - Variable in class loci.formats.in.CV7000Reader.Plane
file - Variable in class loci.formats.in.FlexReader.FlexFile
file - Variable in class loci.formats.in.OIRReader.PixelBlock
file - Variable in class loci.formats.in.OlympusTileReader.Tile
file - Variable in class loci.formats.in.TecanReader.Image
file - Variable in class loci.formats.in.TissueFAXSReader.ScanRegion
file - Variable in class loci.formats.tools.EditTiffG
FILE_LENGTH - Static variable in class loci.formats.in.CanonRawReader
FILE_MAGIC_STRING - Static variable in class loci.formats.in.OBFReader
FILE_SOURCE - Static variable in class loci.formats.tiff.IFD
file_version - Variable in class loci.formats.in.OBFReader
fileBox - Variable in class loci.formats.tools.EditTiffG
fileExists(String) - Static method in class loci.formats.in.LeicaMicrosystemsMetadata.LMSFileReader
  Checks if file at path exists
fileExists(String) - Static method in class loci.formats.in.LeicaMicrosystemsMetadata.LMSXmlDocument
  Checks if file at path exists and corrects paths to be case sensitive
fileGroupOption(String) - Method in class loci.formats.FormatReader
fileGroupOption(String) - Method in interface loci.formats.IFormatReader
  Returns an indication of whether the files in a multi-file dataset can be handled individually.
fileGroupOption(String) - Method in class loci.formats.ImageReader
fileGroupOption(String) - Method in class loci.formats.in.AFIReader
fileGroupOption(String) - Method in class loci.formats.in.AnalyzeReader
fileGroupOption(String) - Method in class loci.formats.in.APLReader
fileGroupOption(String) - Method in class loci.formats.in.BDReader
fileGroupOption(String) - Method in class loci.formats.in.BioRadReader
fileGroupOption(String) - Method in class loci.formats.in.BrukerReader
fileGroupOption(String) - Method in class loci.formats.in.CellomicsReader
fileGroupOption(String) - Method in class loci.formats.in.CellSensReader
fileGroupOption(String) - Method in class loci.formats.in.CellVoyagerReader
fileGroupOption(String) - Method in class loci.formats.in.CellWorxReader
fileGroupOption(String) - Method in class loci.formats.in.ColumbusReader
fileGroupOption(String) - Method in class loci.formats.in.CV7000Reader
fileGroupOption(String) - Method in class loci.formats.in.DCIMGReader
fileGroupOption(String) - Method in class loci.formats.in.DicomReader
fileGroupOption(String) - Method in class loci.formats.in.FlexReader
fileGroupOption(String) - Method in class loci.formats.in.FujiReader
fileGroupOption(String) - Method in class loci.formats.in.FV1000Reader
fileGroupOption(String) - Method in class loci.formats.in.HitachiReader
fileGroupOption(String) - Method in class loci.formats.in.ICSReader
fileGroupOption(String) - Method in class loci.formats.in.ImagicReader
fileGroupOption(String) - Method in class loci.formats.in.InCellReader
fileGroupOption(String) - Method in class loci.formats.in.JDCEReader
fileGroupOption(String) - Method in class loci.formats.in.KLBReader
fileGroupOption(String) - Method in class loci.formats.in.L2DReader
fileGroupOption(String) - Method in class loci.formats.in.LeicaReader
fileGroupOption(String) - Method in class loci.formats.in.MetamorphReader
fileGroupOption(String) - Method in class loci.formats.in.MIASReader
fileGroupOption(String) - Method in class loci.formats.in.MicroCTReader
fileGroupOption(String) - Method in class loci.formats.in.MicromanagerReader
fileGroupOption(String) - Method in class loci.formats.in.NDPIReader
fileGroupOption(String) - Method in class loci.formats.in.NDPISReader
fileGroupOption(String) - Method in class loci.formats.in.NiftiReader
fileGroupOption(String) - Method in class loci.formats.in.NRRDReader
fileGroupOption(String) - Method in class loci.formats.in.OIRReader
fileGroupOption(String) - Method in class loci.formats.in.OlympusTileReader
fileGroupOption(String) - Method in class loci.formats.in.OMETiffReader
fileGroupOption(String) - Method in class loci.formats.in.OperettaReader
fileGroupOption(String) - Method in class loci.formats.in.PerkinElmerReader
fileGroupOption(String) - Method in class loci.formats.in.PrairieReader
fileGroupOption(String) - Method in class loci.formats.in.ScanrReader
fileGroupOption(String) - Method in class loci.formats.in.SPCReader
fileGroupOption(String) - Method in class loci.formats.in.SVSReader
fileGroupOption(String) - Method in class loci.formats.in.TCSReader
fileGroupOption(String) - Method in class loci.formats.in.TecanReader
fileGroupOption(String) - Method in class loci.formats.in.TillVisionReader
fileGroupOption(String) - Method in class loci.formats.in.TrestleReader
fileGroupOption(String) - Method in class loci.formats.in.VentanaReader
fileGroupOption(String) - Method in class loci.formats.in.VisitechReader
fileGroupOption(String) - Method in class loci.formats.in.XLEFReader
fileGroupOption(String) - Method in class loci.formats.in.ZeissLSMReader
fileGroupOption(String) - Method in class loci.formats.in.ZeissTIFFReader
fileGroupOption(String) - Method in class loci.formats.ReaderWrapper
fileGroupOption(String, String[]) - Method in class loci.plugins.macro.LociFunctions
fileGUID - Variable in class loci.formats.in.ZeissCZIReader.FileHeader
FileHeader() - Constructor for class loci.formats.in.ZeissCZIReader.FileHeader
fileIndex - Variable in class loci.formats.dicom.DicomTile
fileIndex - Variable in class loci.formats.in.ColumbusReader.Plane
FileInfo - Class in loci.formats
  Encompasses basic metadata about a file.
FileInfo() - Constructor for class loci.formats.FileInfo
FILEINFO_STRING - Static variable in class loci.formats.in.KodakReader
fileLength - Variable in class loci.formats.in.LeicaReader
  Length of each file name.
fileList - Variable in class loci.formats.in.DicomReader
filelist - Variable in class loci.formats.in.KLBReader
fileMap - Variable in class loci.formats.in.CellSensReader
fileMetaLengthPointer - Variable in class loci.formats.out.DicomWriter
filename - Variable in class loci.formats.FileInfo
  Absolute path to this file.
filename - Variable in class loci.formats.gui.ImageViewer
filename - Variable in class loci.formats.in.CellomicsReader.ChannelFile
filename - Variable in class loci.formats.in.InCellReader.Image
filename - Variable in class loci.formats.in.MIASReader.AnalysisFile
filename - Variable in class loci.formats.in.OperettaReader.Plane
filename - Variable in class loci.formats.in.PrairieMetadata.PFile
  `filename` attribute of this `<File>`.
filename - Variable in class loci.formats.in.ZeissCZIReader.Segment
filename - Variable in class loci.formats.in.ZeissTIFFReader.Plane
filename - Variable in class loci.formats.tiff.TiffSaver
  Output filename.
fileNameMap - Variable in class loci.formats.in.MicromanagerReader.Position
filenames - Variable in class loci.formats.in.FV1000Reader
fileOffset - Variable in class loci.formats.dicom.DicomTile
fileOffset - Variable in class loci.formats.in.LIFReader.MemoryBlock
filePart - Variable in class loci.formats.in.ZeissCZIReader.AttachmentEntry
filePart - Variable in class loci.formats.in.ZeissCZIReader.DirectoryEntry
filePart - Variable in class loci.formats.in.ZeissCZIReader.FileHeader
filepath - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.LMSXmlDocument
filePath - Variable in class loci.formats.services.POIServiceImpl
FilePattern - Class in loci.formats
  Represents a collection of files meant to be part of the same data series.
FilePattern(Location) - Constructor for class loci.formats.FilePattern
  Creates a pattern object using the given file as a template.
FilePattern(String, String) - Constructor for class loci.formats.FilePattern
  Creates a pattern object using the given filename and directory path as a template.
FilePattern(String) - Constructor for class loci.formats.FilePattern
  Creates a pattern object for files with the given pattern string.
FilePatternBlock - Class in loci.formats
  FilePatternBlock represents a single block in a `FilePattern`.
FilePatternBlock(String) - Constructor for class loci.formats.FilePatternBlock
  Builds a FilePatternBlock from a block string.
FilePatternDialog - Class in loci.plugins.in
  Bio-Formats Importer file pattern dialog box.
FilePatternDialog(ImportProcess) - Constructor for class loci.plugins.in.FilePatternDialog
  Creates a file pattern dialog for the Bio-Formats Importer.
FilePatternReader - Class in loci.formats.in
FilePatternReader() - Constructor for class loci.formats.in.FilePatternReader
  Constructs a new pattern reader.
filePosition - Variable in class loci.formats.in.ZeissCZIReader.AttachmentEntry
filePosition - Variable in class loci.formats.in.ZeissCZIReader.DirectoryEntry
fileReader - Variable in class loci.formats.gui.ImageViewer
  Reader for files on disk.
files - Variable in class loci.formats.FilePattern
  File listing for this file pattern.
files - Variable in class loci.formats.FileStitcher.ExternalSeries
files - Variable in class loci.formats.in.CellomicsReader
files - Variable in class loci.formats.in.HamamatsuVMSReader
files - Variable in class loci.formats.in.ImprovisionTiffReader
files - Variable in class loci.formats.in.LeicaReader
  Array of image file names.
files - Variable in class loci.formats.in.MetamorphTiffReader
files - Variable in class loci.formats.in.OlympusTileReader.Tile
files - Variable in class loci.formats.in.PerkinElmerReader
  List of files to open.
files - Variable in class loci.formats.in.PrairieMetadata.Frame
  `<File>` elements beneath this `<Frame>`, keyed on each file's `channel`.
files - Variable in class loci.formats.in.SEQReader
files - Variable in class loci.formats.in.SlidebookTiffReader
files - Variable in class loci.formats.in.TrestleReader
files - Variable in class loci.formats.in.VarianFDFReader
files - Variable in class loci.formats.in.VisitechReader
  Files in this dataset.
files - Variable in class loci.formats.in.ZeissZVIReader
files - Variable in class loci.formats.internal.WellContainer
files - Variable in class loci.formats.services.POIServiceImpl
fileSave - Variable in class loci.formats.gui.ImageViewer
fileSizes - Variable in class loci.formats.services.POIServiceImpl
FileStitcher - 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
fillChannelWavelengths(MetadataStore) - Method in class loci.formats.in.FakeReader
fillColor - Variable in class loci.formats.FormatReader
  Fill value for undefined pixels.
fillColour - Variable in class loci.formats.in.BaseZeissReader.Shape
filled - Variable in class loci.formats.ChannelFiller
  Whether to fill in the indices.
fillExposureTime(MetadataStore) - Method in class loci.formats.in.FakeReader
fillInData() - Method in class loci.formats.in.ZeissCZIReader.Attachment
fillInData() - Method in class loci.formats.in.ZeissCZIReader.AttachmentDirectory
fillInData() - Method in class loci.formats.in.ZeissCZIReader.Directory
fillInData() - Method in class loci.formats.in.ZeissCZIReader.FileHeader
fillInData() - Method in class loci.formats.in.ZeissCZIReader.Metadata
fillInData() - Method in class loci.formats.in.ZeissCZIReader.Segment
fillInData() - Method in class loci.formats.in.ZeissCZIReader.SubBlock
fillInIFD(IFD) - Method in class loci.formats.tiff.TiffParser
  Fill in IFD entries that are stored at an arbitrary offset.
fillInstrumentRefs(MetadataStore) - Method in class loci.formats.in.FakeReader
fillMetadataPass1(MetadataStore) - Method in class loci.formats.in.BaseZeissReader
  Read and store basic dimensions in model
fillMetadataPass1(MetadataStore) - Method in class loci.formats.in.ZeissTIFFReader
fillMetadataPass1(MetadataStore) - Method in class loci.formats.in.ZeissZVIReader
fillMetadataPass2(MetadataStore) - Method in class loci.formats.in.BaseZeissReader
  Read and store basic dimensions in model
fillMetadataPass2(MetadataStore) - Method in class loci.formats.in.ZeissTIFFReader
fillMetadataPass3(MetadataStore) - Method in class loci.formats.in.BaseZeissReader
  Read and store basic dimensions in model
fillMetadataPass3(MetadataStore) - Method in class loci.formats.in.ZeissZVIReader
fillMetadataPass4(MetadataStore) - Method in class loci.formats.in.BaseZeissReader
  Read and store basic dimensions in model
fillMetadataPass5(MetadataStore) - Method in class loci.formats.in.BaseZeissReader
  Read and store basic dimensions in model
fillMetadataPass5(MetadataStore) - Method in class loci.formats.in.ZeissTIFFReader
fillMetadataPass5(MetadataStore) - Method in class loci.formats.in.ZeissZVIReader
fillMetadataPass6(MetadataStore) - Method in class loci.formats.in.BaseZeissReader
  Read and store basic dimensions in model
fillMetadataPass7(MetadataStore) - Method in class loci.formats.in.BaseZeissReader
  Store basic dimensions in model
fillMetadataStore(MetadataStore, int, int, int, int) - Method in class loci.formats.internal.WellContainer
fillMetadataStore(MetadataStore, int, int, int, int, int) - Method in class loci.formats.internal.WellContainer
fillOval(int, int, int, int) - Method in class loci.plugins.util.RecordedImageProcessor
fillPhysicalSizes(MetadataStore) - Method in class loci.formats.in.FakeReader
fillPolygon(Polygon) - Method in class loci.plugins.util.RecordedImageProcessor
fillRegions(MetadataStore, int) - Method in class loci.formats.in.FakeReader
FillStyle(int) - Constructor for enum loci.formats.in.BaseZeissReader.FillStyle
fillStyle - Variable in class loci.formats.in.BaseZeissReader.Shape
filter - Variable in class loci.formats.in.ZeissLSMReader.BeamSplitter
filter - Variable in class loci.formats.in.ZeissLSMReader.DetectionChannel
filter(int) - Method in class loci.plugins.util.RecordedImageProcessor
FILTER_SET_NAME - Static variable in class loci.formats.in.NDPIReader
FilterGroup() - Constructor for class loci.formats.in.FlexReader.FilterGroup
filterMap - Variable in class loci.formats.in.FlexReader
filterMetadata - Variable in class loci.formats.FormatReader
  Whether or not to filter out invalid metadata.
FilterMetadata - Class in loci.formats.meta
FilterMetadata(MetadataStore, boolean) - Constructor for class loci.formats.meta.FilterMetadata
filterModels - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataTempBuffer
filterModels - Variable in class loci.formats.in.LIFReader
filterModels - Variable in class loci.formats.in.NikonTiffReader
filterRefPopulated - Variable in class loci.formats.in.LeicaReader
filterSet - Variable in class loci.formats.in.FlexReader.FlexHandler
FILTERSET - Static variable in class loci.formats.in.LeicaReader
filterSet - Variable in class loci.formats.in.ZeissLSMReader.BeamSplitter
filterSet - Variable in class loci.formats.in.ZeissLSMReader.DetectionChannel
filterSetMap - Variable in class loci.formats.in.FlexReader
filterSetRef - Variable in class loci.formats.in.ZeissCZIReader.Channel
filterSets - Variable in class loci.formats.in.FlexReader
filts - Variable in class loci.formats.gui.ComboFileFilter
  List of filters to be combined.
finalize() - Method in class org.libjpegturbo.turbojpeg.TJCompressor
finalize() - Method in class org.libjpegturbo.turbojpeg.TJDecompressor
find(String[]) - Method in class loci.formats.in.PrairieReader
  Finds the first file with one of the given suffixes.
find(String, String) - Static method in class loci.plugins.Updater
findAllFiles(Location, ArrayList<String>, boolean) - Method in class loci.formats.in.SlideBook7Reader
findAllFiles(Location, ArrayList<String>) - Method in class loci.formats.in.TecanReader
findChildWithID(Node, String, String) - Method in class loci.formats.services.OMEXMLServiceImpl
  Return the child node with specified value for the "ID" attribute.
findDBFiles() - Method in class loci.formats.in.TissueFAXSReader
  If a .tfcyto file was provided, then that is the only file that should be read.
findEdges() - Method in class loci.plugins.util.RecordedImageProcessor
findExtraMetadata() - Method in class loci.formats.in.TecanReader
findFiles(Location) - Method in class loci.formats.in.FlexReader
  Search for files that correspond to the given file.
findFiles(Location, String[]) - Method in class loci.formats.in.FlexReader
findImages(Connection, HashMap<Integer, String>) - Method in class loci.formats.in.TecanReader
findImages(RandomAccessInputStream) - Method in class loci.formats.in.TillVisionReader
findKeyValue(String[], String[][]) - Method in class loci.formats.in.ICSReader
findKeyValueForCategory(String[], String[][]) - Method in class loci.formats.in.ICSReader
findKeyValueOther(String[], String[][]) - Method in class loci.formats.in.ICSReader
findLEIFile(String) - Method in class loci.formats.in.LeicaReader
  Find the .lei file that belongs to the same dataset as the given file.
findLogFiles() - Method in class loci.formats.in.DeltavisionReader
  Find the log files.
findLogFiles() - Method in class loci.formats.in.FakeReader
findMetadataFiles() - Method in class loci.formats.in.PrairieReader
findNextBlock() - Method in class loci.formats.in.OpenlabReader
FindNextClass(MappingNode, int) - Method in class loci.formats.in.SlideBook7Reader.ClassDecoder
findNextOffset(RandomAccessInputStream) - Method in class loci.formats.in.TillVisionReader
findNextOffset(RandomAccessInputStream, byte[]) - Method in class loci.formats.in.TillVisionReader
findNextXMLBlock(RandomAccessInputStream) - Method in class loci.formats.in.OIRReader
findOffset() - Method in class loci.formats.in.ImspectorReader
  Find the offset to the next block of pixel data.
findOffset(boolean) - Method in class loci.formats.in.ImspectorReader
findOIFFile(String) - Method in class loci.formats.in.FV1000Reader
findPattern(String) - Static method in class loci.formats.FilePattern
  Identifies the group pattern from a given file within that group.
findPattern(Location) - Static method in class loci.formats.FilePattern
  Identifies the group pattern from a given file within that group.
findPattern(File) - Static method in class loci.formats.FilePattern
  Identifies the group pattern from a given file within that group.
findPattern(String, String) - Static method in class loci.formats.FilePattern
  Identifies the group pattern from a given filename and directory.
findPattern(String, String, String[]) - Static method in class loci.formats.FilePattern
  Identifies the group pattern from a given filename, directory and list of candidate filenames.
findPattern(String, String, String[], int[]) - Static method in class loci.formats.FilePattern
  Identifies the group pattern from a given filename, directory and list of candidate filenames.
findPattern(String[]) - Static method in class loci.formats.FilePattern
  Generate a pattern from a list of file names.
findPattern(String, String[], int, int, String) - Static method in class loci.formats.FilePattern
findPattern(String) - Method in class loci.formats.FileStitcher
findPatterns(String) - Method in class loci.formats.FileStitcher
  Finds the file pattern for the given ID, based on the state of the file stitcher.
findPixelOffsets() - Method in class loci.formats.in.JPXReader
findPixelsFiles() - Method in class loci.formats.in.CellWorxReader
findPixelsFiles() - Method in class loci.formats.in.MetaxpressTiffReader
findPixelsOffset(int) - Method in class loci.formats.in.VisitechReader
findPlateDimensions(Connection) - Method in class loci.formats.in.TecanReader
findRootNode(Node) - Method in class loci.formats.services.OMEXMLServiceImpl
  Return the absolute root node for the specified child node.
findSeriesPatterns(String) - Static method in class loci.formats.FilePattern
  Works like `FilePattern.findSeriesPatterns(String, String, String[])`, but dir and nameList are inferred from the given file's absolute path.
findSeriesPatterns(String, String, String[]) - Static method in class loci.formats.FilePattern
  Similar to `FilePattern.findPattern(String, String, String[])`, but this does not merge series indices into a pattern block.
findString(String) - Method in class loci.formats.in.KodakReader
findTIFFs() - Method in class loci.formats.in.MetamorphTiffReader
findXML(String) - Static method in class loci.formats.in.ColumbusReader
findZipEntries() - Method in class loci.formats.in.ZipReader
finish(ImportProcess) - Method in class loci.plugins.in.Importer
finishTime - Variable in class loci.formats.in.PerkinElmerReader
finishTiming() - Method in class loci.plugins.in.ImagePlusReader
FIRMWARE_VERSION - Static variable in class loci.formats.in.NDPIReader
FIRMWARE_VERSION - Static variable in class loci.formats.in.NikonReader
firstAvailable(int...) - Method in class loci.plugins.in.SwapDialog
firstDataStream - Variable in class loci.formats.tools.AmiraParameters
firstFile - Variable in class loci.formats.in.PrairieMetadata.Frame
  The first actual `<File>` element for this `<Frame>`.
firstFrame - Variable in class loci.formats.in.PrairieMetadata.Sequence
  The first actual `<Frame>` element for this `<Sequence>`.
firstIFD - Variable in class loci.formats.tiff.TiffParser
  Cached first IFD in the current file.
firstIndex - Variable in class loci.formats.in.PerkinElmerReader.PixelsFile
firstSequence - Variable in class loci.formats.in.PrairieMetadata
  The first actual `<Sequence>` element.
firstSeriesChannels - Variable in class loci.formats.in.MetamorphReader
firstStamp - Variable in class loci.formats.in.LeicaHandler
firstTimeLoop - Variable in class loci.formats.in.ND2Handler
firstTimepoint - Variable in class loci.formats.in.BDVReader
firstWellPlanes() - Method in class loci.formats.in.FlexReader
  Returns the number of planes in the first well that has data.
fis - Variable in class loci.formats.Memoizer.KryoDeser
FitsReader - Class in loci.formats.in
  FitsReader is the file format reader for Flexible Image Transport System (FITS) images.
FitsReader() - Constructor for class loci.formats.in.FitsReader
  Constructs a new FitsReader.
fixed - Variable in class loci.formats.FilePatternBlock
  Whether or not this is a fixed-width block.
fixUnits(Length) - Method in class loci.formats.out.DicomWriter
  Check if the unit for the given Length is "pixel" or "referenceframe".
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.
FLIM_DOMAIN - Static variable in class loci.formats.FormatTools
  Identifies the fluorescence-lifetime domain.
flip - Variable in class loci.formats.in.QTReader
flipHorizontal() - Method in class loci.plugins.util.RecordedImageProcessor
flipVertical() - Method in class loci.plugins.util.RecordedImageProcessor
flipX - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataTempBuffer
flipX - Variable in class loci.formats.in.LIFReader
flipY - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataTempBuffer
flipY - Variable in class loci.formats.in.LIFReader
FLOAT - Static variable in class loci.formats.FormatTools
  Identifies the FLOAT data type used to store pixel values.
FLOAT - Static variable in class loci.formats.in.CellSensReader
FLOAT - Static variable in class loci.formats.in.GatanReader
FLOAT - Static variable in class loci.formats.in.SPEReader
FLOAT32_TYPE - Static variable in class loci.formats.in.KLBReader
FLOAT64_TYPE - Static variable in class loci.formats.in.KLBReader
FloatIM3Record(String, int, long, int) - Constructor for class loci.formats.in.IM3Reader.FloatIM3Record
floatValue() - Method in class loci.formats.tiff.TiffRational
  Returns the value of the specified number as a float.
FLOW_DATA_IDENTIFIER - Static variable in class loci.formats.in.SDTInfo
  For .sdt files created automatically in Continuous Flow mode measurement (no setup, only data).
FlowSightReader - Class in loci.formats.in
FlowSightReader() - Constructor for class loci.formats.in.FlowSightReader
fluor - Variable in class loci.formats.in.CV7000Reader.Channel
fluor - Variable in class loci.formats.in.ZeissCZIReader.Channel
FLUOVIEW_MAGIC_STRING - Static variable in class loci.formats.in.FluoviewReader
  String identifying a Fluoview file.
FluoviewReader - Class in loci.formats.in
  FluoviewReader is the file format reader for Olympus Fluoview TIFF files AND Andor Bio-imaging Division (ABD) TIFF files.
FluoviewReader() - Constructor for class loci.formats.in.FluoviewReader
  Constructs a new Fluoview TIFF reader.
flush() - Method in class loci.plugins.config.TextAreaWriter
  Flushing a TextAreaWriter does nothing .
flushBlockSize - Variable in class loci.formats.in.OBFReader.Stack
flushPoints - Variable in class loci.formats.in.OBFReader.Stack
fmt - Variable in class loci.formats.in.GelReader
fmt - Variable in class loci.formats.in.OpenlabReader
FOCAL_LENGTH - Static variable in class loci.formats.tiff.IFD
FOCAL_LENGTH_35MM_FILM - Static variable in class loci.formats.tiff.IFD
FOCAL_PLANE_RESOLUTION_UNIT - Static variable in class loci.formats.tiff.IFD
FOCAL_PLANE_X_RESOLUTION - Static variable in class loci.formats.tiff.IFD
FOCAL_PLANE_Y_RESOLUTION - Static variable in class loci.formats.tiff.IFD
FOCUS_IMAGE - Static variable in class loci.formats.in.CellSensReader
FOCUS_MODE - Static variable in class loci.formats.in.NikonReader
FOCUS_OFFSET - Static variable in class loci.formats.in.NDPIReader
FOCUS_POINT_REGIONS - Static variable in class loci.formats.in.NDPIReader
FOCUS_TIME - Static variable in class loci.formats.in.NDPIReader
focusGained(FocusEvent) - Method in class loci.plugins.in.MainDialog
  Handles information pane updates when component focus changes.
focusLost(FocusEvent) - Method in class loci.plugins.in.MainDialog
focusOffset - Variable in class loci.formats.in.TecanReader.Channel
font - Variable in class loci.formats.in.FakeReader.TextLine
font - Variable in class loci.formats.tools.MakeTestOmeTiff.TextLine
fontName - Variable in class loci.formats.in.BaseZeissReader.Shape
fontName - Variable in class loci.formats.in.LeicaHandler.ROI
fontName - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.ROI
fontName - Variable in class loci.formats.in.LIFReader.ROI
fontSize - Variable in class loci.formats.in.BaseZeissReader.Shape
fontSize - Variable in class loci.formats.in.GatanReader.ROIShape
fontSize - Variable in class loci.formats.in.LeicaHandler.ROI
fontSize - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.ROI
fontSize - Variable in class loci.formats.in.LIFReader.ROI
fontWeight - Variable in class loci.formats.in.BaseZeissReader.Shape
FOOTER_SIZE - Static variable in class loci.formats.in.SIFReader
footerPointer - Variable in class loci.formats.out.APNGWriter
force - Variable in class loci.formats.gui.DataConverter
forceType - Variable in class loci.formats.gui.DataConverter
forkFile - Variable in class loci.formats.in.QTReader
format - Variable in class loci.formats.FormatHandler
  Name of this file format.
formatCompression(IFD) - Method in class loci.formats.out.TiffWriter
  Sets the compression code for the specified IFD.
formatDouble(double) - Method in class loci.formats.in.ZeissXRMReader
  Format double value to 2 decimal places, rounding to nearest.
FormatEntry - Class in loci.plugins.config
  A list entry for the configuration window's Formats tab.
FormatEntry(PrintWriter, Object) - Constructor for class loci.plugins.config.FormatEntry
FormatException - Exception 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.
formatFixedWidth(double, int) - Static method in class loci.formats.out.DicomWriter
  Format the given double as a string with no more than `width` characters.
FormatHandler - Class in loci.formats
  Abstract superclass of all biological file format readers and writers.
FormatHandler(String, String) - Constructor for class loci.formats.FormatHandler
  Constructs a format handler with the given name and default suffix.
FormatHandler(String, String[]) - Constructor for class loci.formats.FormatHandler
  Constructs a format handler with the given name and default suffixes.
formatHex(int) - Method in class loci.formats.in.BaseZeissReader.Shape
formatInfo - Variable in class loci.plugins.config.ConfigWindow
formatLabel - Variable in class loci.formats.gui.PreviewPane
  Labels containing thumbnail and dimensional information.
formatMetadata(String, String) - Static method in class loci.formats.in.IonpathMIBITiffReader
formatName - Variable in class loci.plugins.config.FormatEntry
FormatReader - Class in loci.formats
  Abstract superclass of all biological file format readers.
FormatReader(String, String) - Constructor for class loci.formats.FormatReader
  Constructs a format reader with the given name and default suffix.
FormatReader(String, String[]) - Constructor for class loci.formats.FormatReader
  Constructs a format reader with the given name and default suffixes.
FORMATS - Static variable in class loci.formats.in.GelReader
formatsList - Variable in class loci.plugins.config.ConfigWindow
formatsListModel - Variable in class loci.plugins.config.ConfigWindow
formatTag(int) - Static method in enum loci.formats.dicom.DicomAttribute
  Format the given tag as a pair of comma-separated hex strings.
formatText - Variable in class loci.formats.gui.PreviewPane
formatTip - Variable in class loci.formats.gui.PreviewPane
FormatTools - Class in loci.formats
  A utility class for format reader and writer implementations.
FormatTools() - Constructor for class loci.formats.FormatTools
FormatWriter - Class in loci.formats
  Abstract superclass of all biological file format writers.
FormatWriter(String, String) - Constructor for class loci.formats.FormatWriter
  Constructs a format writer with the given name and default suffix.
FormatWriter(String, String[]) - Constructor for class loci.formats.FormatWriter
  Constructs a format writer with the given name and default suffixes.
FORWARD_ORDER - Static variable in interface loci.formats.cache.ICacheStrategy
fos - Variable in class loci.formats.Memoizer.KryoDeser
found - Variable in class loci.formats.in.ZeissTIFFHandler.TagSet
foundChannelTag - Variable in class loci.formats.in.CellSensReader
foundHTDFile(String) - Method in class loci.formats.in.CellWorxReader
foundMontage - Variable in class loci.formats.in.GatanReader
foundPlateLayout - Variable in class loci.formats.in.ScanrReader.ScanrHandler
foundPositions - Variable in class loci.formats.in.ScanrReader
fourPixelCorrectionInFooter - Variable in class loci.formats.in.DCIMGReader
fourPixelCorrectionLine - Variable in class loci.formats.in.DCIMGReader
fourPixelCorrectionOffset - Variable in class loci.formats.in.DCIMGReader
fourPixelOffsetInFrame - Variable in class loci.formats.in.DCIMGReader
fovs - Variable in class loci.formats.in.TissueFAXSReader.ScanRegion
fp - Variable in class loci.formats.AxisGuesser
  File pattern identifying dimensional axis blocks.
fp - Variable in class loci.plugins.in.FilePatternDialog
fps - Variable in class loci.formats.FormatWriter
  Frame rate to use when writing in frames per second, if applicable.
fps - Variable in class loci.formats.gui.DataConverter
fps - Variable in class loci.formats.gui.ImageViewer
fpsSpin - Variable in class loci.plugins.util.DataBrowser
Frame(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
frameFooterSize - Variable in class loci.formats.in.DCIMGReader
frameIndex - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.Dimension
frameIndex(PrairieMetadata.Sequence, int, int, int) - Method in class loci.formats.in.PrairieReader
  Gets the frame index associated with the given (Z, T) position of the specified series.
frames - Variable in class loci.formats.in.PrairieMetadata.Sequence
  `<Frame>` elements beneath this `<Sequence>`, keyed on each frame's `index`.
framesAreTime - Variable in class loci.formats.in.PrairieReader
  Whether a series uses `Frame`s 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
fullResolutionCoreIndex - Variable in class loci.formats.in.TissueFAXSReader.ScanRegion
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.LeicaMicrosystemsMetadata.MetadataTempBuffer
gains - Variable in class loci.formats.in.LIFReader
gains - Variable in class loci.formats.in.ZeissCZIReader
gamma - Variable in class loci.formats.in.GatanReader
gamma(double) - Method in class loci.plugins.util.RecordedImageProcessor
GAMMA_CORRECTION - Static variable in class loci.formats.in.CellSensReader
GatanDM2Reader - Class in loci.formats.in
  GatanDM2Reader is the file format reader for Gatan .dm2 files.
GatanDM2Reader() - Constructor for class loci.formats.in.GatanDM2Reader
  Constructs a new Gatan .dm2 reader.
GatanReader - Class in loci.formats.in
  GatanReader is the file format reader for Gatan files.
GatanReader() - Constructor for class loci.formats.in.GatanReader
  Constructs a new Gatan reader.
GatanReader.ROIShape - Class in loci.formats.in
gct - Variable in class loci.formats.in.GIFReader
  Global color table.
GEL_DOMAIN - Static variable in class loci.formats.FormatTools
  Identifies the gel and blot imaging domain.
GelReader - Class in loci.formats.in
  GelReader is the file format reader for Molecular Dynamics GEL TIFF files.
GelReader() - Constructor for class loci.formats.in.GelReader
  Constructs a new GEL reader.
GENERAL_PARAMS - Static variable in class loci.formats.in.ZeissXRMReader
generateMemo(String) - Method in class loci.formats.Memoizer
  Convenience method to generate (or regenerate) the memo file for a given file.
generateScreen(int, int, int, int, int) - Method in class loci.formats.tools.FakeImage
  Creates a fake SPW file/directory structure.
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(Codec) - Static method in enum loci.formats.codec.CompressionType
  Look up the compression type by Codec instance.
get(int) - Static method in enum loci.formats.codec.JPEG2000BoxType
  Retrieves the box type by reverse lookup of its "code".
get(int) - Static method in enum loci.formats.codec.JPEG2000SegmentMarker
  Retrieves the segment marker by reverse lookup of its "code".
get(int) - Static method in enum loci.formats.dicom.DicomAttribute
  Lookup the attribute for the given tag.
get(int) - Static method in enum loci.formats.dicom.DicomVR
get(int) - Static method in enum loci.formats.in.BaseZeissReader.Charset
get(int) - Static method in enum loci.formats.in.BaseZeissReader.DrawStyle
get(int) - Static method in enum loci.formats.in.BaseZeissReader.FeatureType
get(int) - Static method in enum loci.formats.in.BaseZeissReader.FillStyle
get(int) - Static method in enum loci.formats.in.BaseZeissReader.LineEndPositions
get(int) - Static method in enum loci.formats.in.BaseZeissReader.LineEndStyle
get(int) - Static method in enum loci.formats.in.BaseZeissReader.PointStyle
get(int) - Static method in enum loci.formats.in.BaseZeissReader.TextAlignment
get(String) - Method in class loci.formats.in.DynamicMetadataOptions
  Get the value of property `name`.
get(String, String) - Method in class loci.formats.in.DynamicMetadataOptions
  Get the value of property `name`.
get(Object) - Method in interface loci.formats.in.PrairieMetadata.Value
get(int) - Method in interface loci.formats.in.PrairieMetadata.Value
get(Object) - Method in class loci.formats.in.PrairieMetadata.ValueItem
get(int) - Method in class loci.formats.in.PrairieMetadata.ValueItem
get(int) - Method in class loci.formats.in.PrairieMetadata.ValueTable
get(int, int) - Method in class loci.formats.MetadataList
  Get the array element for the specified indexes.
get(int) - Static method in enum loci.formats.tiff.IFDType
  Retrieves a IFD type by reverse lookup of its "code".
get(int) - Method in class loci.formats.tiff.OnDemandLongArray
get(int) - Static method in enum loci.formats.tiff.PhotoInterp
  Retrieves a photometric interpretation by reverse lookup of its "code".
get(int) - Static method in enum loci.formats.tiff.TiffCompression
  Retrieves a TIFF compression instance by code.
get(List<T>, int, T) - Method in class loci.plugins.in.ImporterOptions
get(int) - Method in class loci.plugins.util.RecordedImageProcessor
get(int, int) - Method in class loci.plugins.util.RecordedImageProcessor
get16BitLookupTable() - Method in class loci.formats.ChannelFiller
get16BitLookupTable() - Method in class loci.formats.DelegateReader
get16BitLookupTable() - Method in class loci.formats.FileStitcher
get16BitLookupTable() - Method in class loci.formats.FormatReader
get16BitLookupTable() - Method in interface loci.formats.IFormatReader
  Gets the 16-bit color lookup table associated with the most recently opened image.
get16BitLookupTable() - Method in class loci.formats.ImageReader
get16BitLookupTable() - Method in class loci.formats.in.BaseZeissReader
get16BitLookupTable() - Method in class loci.formats.in.DicomReader
get16BitLookupTable() - Method in class loci.formats.in.FakeReader
get16BitLookupTable() - Method in class loci.formats.in.FilePatternReader
get16BitLookupTable() - Method in class loci.formats.in.FV1000Reader
get16BitLookupTable() - Method in class loci.formats.in.ImarisHDFReader
get16BitLookupTable() - Method in class loci.formats.in.ImprovisionTiffReader
get16BitLookupTable() - Method in class loci.formats.in.InCellReader
get16BitLookupTable() - Method in class loci.formats.in.JPEG2000Reader
get16BitLookupTable() - Method in class loci.formats.in.JPXReader
get16BitLookupTable() - Method in class loci.formats.in.LeicaReader
get16BitLookupTable() - Method in class loci.formats.in.LIFReader
get16BitLookupTable() - Method in class loci.formats.in.LOFReader
get16BitLookupTable() - Method in class loci.formats.in.MIASReader
get16BitLookupTable() - Method in class loci.formats.in.MinimalTiffReader
get16BitLookupTable() - Method in class loci.formats.in.ND2Reader
get16BitLookupTable() - Method in class loci.formats.in.OIRReader
get16BitLookupTable() - Method in class loci.formats.in.OMETiffReader
get16BitLookupTable() - Method in class loci.formats.in.PDSReader
get16BitLookupTable() - Method in class loci.formats.in.PerkinElmerReader
get16BitLookupTable() - Method in class loci.formats.in.SlidebookTiffReader
get16BitLookupTable() - Method in class loci.formats.in.TCSReader
get16BitLookupTable() - Method in class loci.formats.in.VentanaReader
get16BitLookupTable() - Method in class loci.formats.in.ZeissCZIReader
get16BitLookupTable() - Method in class loci.formats.in.ZeissLSMReader
get16BitLookupTable() - Method in class loci.formats.in.ZipReader
get16BitLookupTable() - Method in class loci.formats.ReaderWrapper
get16BitLookupTable() - Method in class loci.formats.WrappedReader
get8BitLookupTable() - Method in class loci.formats.ChannelFiller
get8BitLookupTable() - Method in class loci.formats.DelegateReader
get8BitLookupTable() - Method in class loci.formats.FileStitcher
get8BitLookupTable() - Method in class loci.formats.FormatReader
get8BitLookupTable(ColorModel) - Static method in class loci.formats.gui.AWTImageTools
  Converts an IndexColorModel to a 2D byte array.
get8BitLookupTable() - Method in interface loci.formats.IFormatReader
  Gets the 8-bit color lookup table associated with the most recently opened image.
get8BitLookupTable() - Method in class loci.formats.ImageReader
get8BitLookupTable() - Method in class loci.formats.in.AmiraReader
get8BitLookupTable() - Method in class loci.formats.in.APNGReader
get8BitLookupTable() - Method in class loci.formats.in.AVIReader
get8BitLookupTable() - Method in class loci.formats.in.BaseZeissReader
get8BitLookupTable() - Method in class loci.formats.in.BDVReader
get8BitLookupTable() - Method in class loci.formats.in.BioRadReader
get8BitLookupTable() - Method in class loci.formats.in.BMPReader
get8BitLookupTable() - Method in class loci.formats.in.CellH5Reader
get8BitLookupTable() - Method in class loci.formats.in.DicomReader
get8BitLookupTable() - Method in class loci.formats.in.FakeReader
get8BitLookupTable() - Method in class loci.formats.in.FilePatternReader
get8BitLookupTable() - Method in class loci.formats.in.GIFReader
get8BitLookupTable() - Method in class loci.formats.in.ImarisHDFReader
get8BitLookupTable() - Method in class loci.formats.in.ImprovisionTiffReader
get8BitLookupTable() - Method in class loci.formats.in.InCellReader
get8BitLookupTable() - Method in class loci.formats.in.IPWReader
get8BitLookupTable() - Method in class loci.formats.in.JPEG2000Reader
get8BitLookupTable() - Method in class loci.formats.in.JPXReader
get8BitLookupTable() - Method in class loci.formats.in.KhorosReader
get8BitLookupTable() - Method in class loci.formats.in.LeicaReader
get8BitLookupTable() - Method in class loci.formats.in.LIFReader
get8BitLookupTable() - Method in class loci.formats.in.LOFReader
get8BitLookupTable() - Method in class loci.formats.in.MIASReader
get8BitLookupTable() - Method in class loci.formats.in.MinimalTiffReader
get8BitLookupTable() - Method in class loci.formats.in.ND2Reader
get8BitLookupTable() - Method in class loci.formats.in.OIRReader
get8BitLookupTable() - Method in class loci.formats.in.OMETiffReader
get8BitLookupTable() - Method in class loci.formats.in.OpenlabReader
get8BitLookupTable() - Method in class loci.formats.in.PCXReader
get8BitLookupTable() - Method in class loci.formats.in.PerkinElmerReader
get8BitLookupTable() - Method in class loci.formats.in.PictReader
get8BitLookupTable() - Method in class loci.formats.in.PSDReader
get8BitLookupTable() - Method in class loci.formats.in.SlidebookTiffReader
get8BitLookupTable() - Method in class loci.formats.in.TargaReader
get8BitLookupTable() - Method in class loci.formats.in.TCSReader
get8BitLookupTable() - Method in class loci.formats.in.VentanaReader
get8BitLookupTable() - Method in class loci.formats.in.ZeissCZIReader
get8BitLookupTable() - Method in class loci.formats.in.ZeissLMSReader
get8BitLookupTable() - Method in class loci.formats.in.ZeissLSMReader
get8BitLookupTable() - Method in class loci.formats.in.ZipReader
get8BitLookupTable() - Method in class loci.formats.ReaderWrapper
get8BitLookupTable() - Method in class loci.formats.WrappedReader
getAbsoluteTime() - Method in class loci.formats.in.PrairieMetadata.Frame
  Gets the `absoluteTime` associated with this `Frame`.
getAcquisitionMode(String) - Method in class loci.formats.FormatReader
  Deprecated.
  Use `MetadataTools.getAcquisitionMode(String)`.
getAcquisitionMode(String) - Method in class loci.formats.in.OperettaReader
  Deprecated.
getAcquisitionMode(String) - Static method in class loci.formats.MetadataTools
  Retrieves an `AcquisitionMode` enumeration value for the given String.
getActiveChannels() - Method in class loci.formats.in.PrairieMetadata
  Gets the list of active channel indices, in sorted order.
getAdjustedIndex(int) - Method in class loci.formats.FileStitcher
  Gets the local reader index for use with the given image plane.
getAdjustedOrder() - Method in class loci.formats.AxisGuesser
  Gets the adjusted dimension order.
getAdvancedSeriesUsedFiles(boolean) - Method in class loci.formats.FileStitcher
getAdvancedSeriesUsedFiles(boolean) - Method in class loci.formats.FormatReader
getAdvancedSeriesUsedFiles(boolean) - Method in interface loci.formats.IFormatReader
  Returns an array of FileInfo objects representing the files needed to open the current series.
getAdvancedSeriesUsedFiles(boolean) - Method in class loci.formats.ImageReader
getAdvancedSeriesUsedFiles(boolean) - Method in class loci.formats.ReaderWrapper
getAdvancedUsedFiles(boolean) - Method in class loci.formats.FileStitcher
getAdvancedUsedFiles(boolean) - Method in class loci.formats.FormatReader
getAdvancedUsedFiles(boolean) - Method in interface loci.formats.IFormatReader
  Returns an array of FileInfo objects representing the files needed to open this dataset.
getAdvancedUsedFiles(boolean) - Method in class loci.formats.ImageReader
getAdvancedUsedFiles(boolean) - Method in class loci.formats.ReaderWrapper
getAllChildren(Integer) - Method in class loci.formats.in.VolocityReader
getAllFiles(String) - Method in class loci.formats.FilePattern
getAllFiles() - Method in class loci.formats.internal.WellContainer
getAllRegions(int) - Method in class loci.formats.in.TissueFAXSReader
getAlpha(int) - Method in class loci.formats.gui.Index16ColorModel
getAlpha(int) - Method in class loci.formats.gui.SignedColorModel
getAlpha(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
  Deprecated.
  Use `MetadataTools.getArcType(String)`.
getArcType(String) - Static method in class loci.formats.MetadataTools
  Retrieves an `ArcType` enumeration value for the given String.
getArray(String, int[], int[]) - Method in interface loci.formats.services.NetCDFService
  Retrieves an HDF path's values.
getArray(String, int[], int[]) - Method in class loci.formats.services.NetCDFServiceImpl
getAttr(Node, String) - Method in class loci.formats.in.LeicaMicrosystemsMetadata.LMSXmlDocument
  Returns the value of an attribute of a node, if existing
getAttributeList() - Method in interface loci.formats.services.NetCDFService
  Retrieves an exhaustive list of the HDF paths for all attributes in the HDF document.
getAttributeList() - Method in class loci.formats.services.NetCDFServiceImpl
getAttributeValue(String) - Method in interface loci.formats.services.NetCDFService
  Retrieves an attribute's value.
getAttributeValue(String) - Method in class loci.formats.services.NetCDFServiceImpl
getAutoscaleInfo() - Method in class loci.plugins.in.ImporterOptions
getAutoThreshold() - Method in class loci.plugins.util.RecordedImageProcessor
getAutoThreshold(int[]) - Method in class loci.plugins.util.RecordedImageProcessor
getAvailableMemory() - Method in class loci.plugins.in.MemoryDialog
getAvailableOptions() - Method in class loci.formats.FormatReader
  Returns the list of available metadata options.
getAvailableOptions() - Method in class loci.formats.in.CellSensReader
getAvailableOptions() - Method in class loci.formats.in.CV7000Reader
getAvailableOptions() - Method in class loci.formats.in.GatanReader
getAvailableOptions() - Method in class loci.formats.in.InCellReader
getAvailableOptions() - Method in class loci.formats.in.LIFReader
getAvailableOptions() - Method in class loci.formats.in.ND2Reader
getAvailableOptions() - Method in class loci.formats.in.OMETiffReader
getAvailableOptions() - Method in class loci.formats.in.ScanrReader
getAvailableOptions() - Method in class loci.formats.in.SVSReader
getAvailableOptions() - Method in class loci.formats.in.VentanaReader
getAvailableOptions() - Method in class loci.formats.in.ZeissCZIReader
getAxisCount(int) - Method in class loci.formats.AxisGuesser
  Gets the number of axes in the pattern of the given type.
getAxisCountC() - Method in class loci.formats.AxisGuesser
  Gets the number of C axes in the pattern.
getAxisCountS() - Method in class loci.formats.AxisGuesser
  Gets the number of S axes in the pattern.
getAxisCountT() - Method in class loci.formats.AxisGuesser
  Gets the number of T axes in the pattern.
getAxisCountZ() - Method in class loci.formats.AxisGuesser
  Gets the number of Z axes in the pattern.
getAxisGuesser() - Method in class loci.formats.FileStitcher.ExternalSeries
getAxisGuesser() - Method in class loci.formats.FileStitcher
  Gets the axis guesser object used to guess which dimensional axes are which.
getAxisType(String) - Static method in class loci.formats.AxisGuesser
  Convert the given label to an axis type.
getAxisTypes() - Method in class loci.formats.AxisGuesser
  Gets the guessed axis type for each dimensional block.
getAxisTypes() - Method in class loci.formats.FileStitcher
  Gets the axis type for each dimensional block.
getBackgroundValue() - Method in class loci.plugins.util.RecordedImageProcessor
getBaseReader() - Method in class loci.plugins.in.ImportProcess
  Valid only after `ImportStep.READER`.
getBestIndex(Color) - Method in class loci.plugins.util.RecordedImageProcessor
getBGRComponents(short[]) - Method in class loci.formats.services.JPEGXRServiceImpl
getBinaryOnlyOMEXML(String, String, String) - Method in class loci.formats.out.OMETiffWriter
getBinning(String) - Method in class loci.formats.FormatReader
  Deprecated.
  Use `MetadataTools.getBinning(String)`.
getBinning() - Method in class loci.formats.in.MetamorphHandler
getBinning(String) - Static method in class loci.formats.MetadataTools
  Retrieves an `Binning` enumeration value for the given String.
getBinnings() - Method in class loci.formats.in.ND2Handler
getBitDepth() - Method in class loci.formats.in.PrairieMetadata
  Gets the `bitDepth` recorded in the configuration.
getBits(int) - Method in class loci.formats.codec.BitBuffer
  Deprecated.
  Returns an int value representing the value of the bits read from the byte array, from the current position.
getBitsPerPixel() - Method in class loci.formats.ChannelFiller
getBitsPerPixel() - Method in class loci.formats.FileStitcher
getBitsPerPixel() - Method in class loci.formats.FormatReader
getBitsPerPixel() - Method in interface loci.formats.IFormatReader
  Gets the number of valid bits per pixel.
getBitsPerPixel() - Method in class loci.formats.ImageReader
getBitsPerPixel() - Method in class loci.formats.in.LeicaMicrosystemsMetadata.MultipleImagesReader
getBitsPerPixel(int) - Method in class loci.formats.in.OBFReader
getBitsPerPixel() - Method in class loci.formats.ReaderWrapper
getBitsPerPixel() - Method in class loci.formats.WrappedReader
getBitsPerSample(int) - Method in class loci.formats.in.NDPIReader
  Get the number of bits per sample associated with the given capture mode.
getBitsPerSample() - Method in class loci.formats.tiff.IFD
  Retrieves the image's bits per sample (TIFF tag BitsPerSample) from a given TIFF IFD.
getBlankThumbBytes() - Method in class loci.formats.FileStitcher.ExternalSeries
getBlock(int) - Method in class loci.formats.FilePattern
  Gets the specified file pattern block (e.g., <0-9>).
getBlock() - Method in class loci.formats.FilePatternBlock
  Gets the block string.
getBlock(String) - Method in class loci.formats.in.OIRReader
getBlock(int, String) - Method in class loci.formats.in.ScanrReader
getBlocks() - Method in class loci.formats.FilePattern
  Gets all file pattern blocks.
getBlue(int) - Method in class loci.formats.gui.Index16ColorModel
getBlue(int) - Method in class loci.formats.gui.SignedColorModel
getBlue(Object) - Method in class loci.formats.gui.SignedColorModel
getBlue(int) - Method in class loci.formats.gui.UnsignedIntColorModel
getBlue(Object) - Method in class loci.formats.gui.UnsignedIntColorModel
getBlueOffset(int) - Static method in class org.libjpegturbo.turbojpeg.TJ
  For the given pixel format, returns the number of bytes that the blue component is offset from the start of the pixel.
getBlues() - Method in class loci.formats.gui.Index16ColorModel
  Return the array of blue color components.
getBoolean(String) - Method in class loci.formats.in.DynamicMetadataOptions
  Get the value of property `name` as a Boolean.
getBoolean(String, Boolean) - Method in class loci.formats.in.DynamicMetadataOptions
  Get the value of property `name` as a Boolean.
getBooleanOption(String) - Method in class loci.plugins.prefs.OptionsList
  Gets the boolean option with the given key.
getBooleanValue(String) - Method in class loci.plugins.Slicer
  Gets the value of the given macro key as a boolean.
getBounds(BigInteger[], boolean) - Static method in class loci.formats.FilePattern
  Gets a string containing start, end and step values for a sorted list of numbers.
getBufferedImage() - Method in class loci.plugins.util.RecordedImageProcessor
getBuildDate(String[]) - Method in class loci.plugins.macro.LociFunctions
getByte(SPEReader.SpeHeaderEntry) - Method in class loci.formats.in.SPEReader.SpeHeader
  Method used to retrieve data values for Byte entries into the SPE header table
getByte(int) - Method in class loci.formats.in.SPEReader.SpeHeader
  Private method used to retrieve a Byte value from the SPE header
getByteBuffer() - Method in class loci.formats.codec.BitBuffer
  Deprecated.
  Return the backing byte array.
getByteCount(boolean) - Method in class loci.formats.tiff.IFD
  Get the maximum number of bytes needed to represent this IFD.
getBytes(BufferedImage) - Static method in class loci.formats.gui.AWTImageTools
  Extracts pixel data as arrays of unsigned bytes, one per channel.
getBytes(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() - Method in class loci.formats.in.SlideBook7Reader.CImageGroup
getBytesPerSample() - Method in class loci.formats.tiff.IFD
  Retrieves the image's bytes per sample (derived from tag BitsPerSample) from this IFD.
getC() - Method in class loci.formats.gui.ImageViewer
  Gets the C value of the currently displayed image.
getC(String) - Method in class loci.formats.in.OIRReader
getCache() - Method in class loci.formats.gui.CacheComponent
getCache() - Method in class loci.plugins.util.BFVirtualStack
getCacheListeners() - Method in class loci.formats.cache.Cache
getCacheListeners() - Method in interface loci.formats.cache.CacheReporter
  Gets a list of all registered status update listeners.
getCacheListeners() - Method in class loci.formats.cache.CacheStrategy
getCalibrationTable() - Method in class loci.plugins.util.RecordedImageProcessor
getCameraModel() - Method in class loci.formats.in.ND2Handler
getCaptureMode(int) - Method in class loci.formats.in.NDPIReader
  Get the description of the given capture mode.
getCategory() - Method in class loci.formats.in.BaseZeissReader.Tag
getCBegin(int) - Method in class loci.plugins.in.ImporterOptions
getCBegin(int) - Method in class loci.plugins.in.ImportProcess
getCCount(int) - Method in class loci.plugins.in.ImportProcess
  Valid only after `ImportStep.SERIES`.
getCEnd(int) - Method in class loci.plugins.in.ImporterOptions
getCEnd(int) - Method in class loci.plugins.in.ImportProcess
  Valid only after `ImportStep.STACK`.
getChannel(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.LeicaMicrosystemsMetadata.LMSMetadataExtractor
getChannelDescriptionNodes(Element) - Method in class loci.formats.in.LIFReader
getChannelDimCount(Double[]) - Method in class loci.plugins.macro.LociFunctions
getChannelDimensionBytesInc(int) - Method in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataTempBuffer
getChannelDimLength(Double, Double[]) - Method in class loci.plugins.macro.LociFunctions
getChannelDimType(Double, String[]) - Method in class loci.plugins.macro.LociFunctions
getChannelFiller() - Method in class loci.plugins.in.ImportProcess
  Valid only after `ImportStep.STACK`.
getChannelGlobalMaximum(int) - Method in class loci.formats.MinMaxCalculator
  Retrieves a specified channel's global maximum.
getChannelGlobalMinimum(int) - Method in class loci.formats.MinMaxCalculator
  Retrieves a specified channel's global minimum.
getChannelIndex(CV7000Reader.Plane) - Method in class loci.formats.in.CV7000Reader
getChannelIndex(Element) - Static method in class loci.formats.in.LeicaMicrosystemsMetadata.LMSMetadataExtractor
getChannelIndex(Element) - Method in class loci.formats.in.LIFReader
getChannelIndexOfCellObjectName(String) - Method in class loci.formats.in.BDVReader
getChannelIndexOfCellObjectName(String) - Method in class loci.formats.in.CellH5Reader
GetChannelIndexOfPath(String) - Method in class loci.formats.in.SlideBook7Reader.CSBFile70
getChannelKnownMaximum(int) - Method in class loci.formats.MinMaxCalculator
  Retrieves the specified channel's maximum based on the images that have been read.
getChannelKnownMinimum(int) - Method in class loci.formats.MinMaxCalculator
  Retrieves the specified channel's minimum based on the images that have been read.
getChannelLabel(int) - Method in class loci.formats.in.TextReader
  Gets the label for the given channel.
getChannelName() - Method in class loci.formats.in.MetamorphHandler
getChannelName() - Method in class loci.formats.in.PrairieMetadata.PFile
  Gets the `channelName` associated with this `File`.
GetChannelName(int) - Method in class loci.formats.in.SlideBook7Reader.CImageGroup
getChannelNames() - Method in class loci.formats.in.DicomReader
getChannelNames() - Method in class loci.formats.in.MetamorphHandler
getChannelNames() - Method in class loci.formats.in.ND2Handler
getChannelPriority(String) - Method in class loci.formats.in.LeicaMicrosystemsMetadata.LMSMetadataExtractor
getChannelSeparator() - Method in class loci.plugins.in.ImportProcess
  Valid only after `ImportStep.STACK`.
getChar(int) - Method in class loci.formats.tools.AsciiImage
getCheckboxes(GenericDialog) - Static method in class loci.plugins.util.WindowTools
getChild(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
getChildNode(Element, String) - Method in class loci.formats.in.OlympusTileReader
getChildNodes(Element) - Method in class loci.formats.in.OBFReader
getChildren(Element, String) - Static method in class loci.formats.in.CellVoyagerReader
getChildrenFiles(boolean) - Method in class loci.formats.in.LeicaMicrosystemsMetadata.LMSCollectionXmlDocument
  Returns filepaths of all files which are referenced by this document.
getChildText(Element, String[]) - Static method in class loci.formats.in.CellVoyagerReader
getChildText(Element, String) - Static method in class loci.formats.in.CellVoyagerReader
getChildValue(Element, String) - Method in class loci.formats.in.OlympusTileReader
GetChildWithName(Node, String) - Method in class loci.formats.in.LeicaMicrosystemsMetadata.LMSXmlDocument
getChoices(GenericDialog) - Static method in class loci.plugins.util.WindowTools
getClass(String) - Method in class loci.formats.in.DynamicMetadataOptions
  Get the value of property `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.dicom.DicomVR
getCode() - Method in enum loci.formats.tiff.IFDType
getCode() - Method in enum loci.formats.tiff.PhotoInterp
getCode() - Method in enum loci.formats.tiff.TiffCompression
getCodec() - Method in interface loci.formats.ICompressedTileWriter
getCodec() - Method in class loci.formats.ImageWriter
getCodec(int) - Method in class loci.formats.in.TissueFAXSReader
getCodec() - Method in class loci.formats.out.DicomWriter
getCodec() - Method in class loci.formats.out.TiffWriter
getCodec() - Method in enum loci.formats.tiff.TiffCompression
getCodec() - Method in class loci.formats.WriterWrapper
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.FormatWriter
getCodecOptions() - Method in interface loci.formats.ICompressedTileWriter
getCodecOptions() - Method in class loci.formats.ImageWriter
getCodecOptions(TissueFAXSReader.ScanRegion) - Method in class loci.formats.in.TissueFAXSReader
getCodecOptions() - Method in class loci.formats.tiff.TiffParser
  Retrieves the current set of codec options being used to decompress pixel data.
getCodecOptions() - Method in class loci.formats.WriterWrapper
getCodestreamOffset() - Method in class loci.formats.in.JPEG2000MetadataParser
  Retrieves the offset to the first contiguous codestream.
getCodestreamPixelType() - Method in class loci.formats.in.JPEG2000MetadataParser
  Returns the pixel type as specified in the header.
getCodestreamSizeC() - Method in class loci.formats.in.JPEG2000MetadataParser
  Returns the number of channels the image has as specified in the header.
getCodestreamSizeX() - Method in class loci.formats.in.JPEG2000MetadataParser
  Returns the width of the image as specified in the header.
getCodestreamSizeY() - Method in class loci.formats.in.JPEG2000MetadataParser
  Returns the height of the image as specified in the header.
getColor(Double) - Method in class loci.formats.in.OperettaReader
  Translate emission wavelength to color, based upon: https://www.perkinelmer.com/CMSResources/Images/44-6551APP_PhotocellApplicationNotes.pdf
getColor() - Method in class loci.formats.in.TissueFAXSReader.Channel
  Color returned by DB is ARGB, OME model is RGBA.
getColorMap(IFD) - Method in class loci.formats.tiff.TiffParser
  Retrieve the color map associated with the given IFD.
getColorMode() - Method in class loci.plugins.in.ImporterOptions
getColorModeInfo() - Method in class loci.plugins.in.ImporterOptions
getColorModel() - Method in class loci.formats.FormatWriter
getColorModel() - Method in interface loci.formats.IFormatWriter
  Gets the color model.
getColorModel() - Method in class loci.formats.ImageWriter
getColorModel() - Method in class loci.formats.WriterWrapper
getColorModel() - Method in class loci.plugins.util.RecordedImageProcessor
getColorModes() - Method in class loci.plugins.in.ImporterOptions
getColorValue(TextField) - Method in class loci.plugins.in.ColorDialog
getColumn() - Method in class loci.formats.in.OMEXMLReader.BinData
getColumn(int, int, int[], int) - Method in class loci.plugins.util.RecordedImageProcessor
getColumNames(int) - Method in interface loci.formats.services.MetakitService
getColumNames(int) - Method in class loci.formats.services.MetakitServiceImpl
getColumnIndex() - Method in class loci.formats.internal.WellContainer
getColumnNames(String) - Method in interface loci.formats.services.MetakitService
getColumnNames(String) - Method in class loci.formats.services.MetakitServiceImpl
getColumnTypes(int) - Method in interface loci.formats.services.MetakitService
getColumnTypes(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
  Get the value of the `COMPANION_KEY` option.
getComponent(int, int) - Method in class loci.formats.gui.UnsignedIntColorModel
getCompressedByteCount(IFD, int, int) - Method in class loci.formats.in.MinimalTiffReader
getCompressedSize() - Method in class org.libjpegturbo.turbojpeg.TJCompressor
  Returns the size of the image (in bytes) generated by the most recent compress/encode operation.
getCompressedTile(int, int) - Method in interface loci.formats.services.JPEGTurboService
  Similar to getTile(int, int), but returns the JPEG-compressed bytes.
getCompressedTile(byte[], int, int) - Method in interface loci.formats.services.JPEGTurboService
  Similar to getTile(int, int), but returns the JPEG-compressed bytes.
getCompressedTile(int, int) - Method in class loci.formats.services.JPEGTurboServiceImpl
getCompressedTile(byte[], int, int) - Method in class loci.formats.services.JPEGTurboServiceImpl
getCompression() - Method in enum loci.formats.codec.CompressionType
  Returns the compression.
getCompression(String) - Method in class loci.formats.FormatReader
  Deprecated.
  Use `MetadataTools.getCompression(String)`.
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
getCompressionMethod() - Method in class loci.formats.out.DicomWriter
getCompressionTypes() - Method in class loci.formats.FormatWriter
getCompressionTypes() - Method in interface loci.formats.IFormatWriter
  Gets the available compression types.
getCompressionTypes() - Method in class loci.formats.ImageWriter
getCompressionTypes() - Method in class loci.formats.WriterWrapper
getConcatenateInfo() - Method in class loci.plugins.in.ImporterOptions
getConcatenationIndex() - Method in class loci.formats.in.DicomReader
getConfig(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
  Deprecated.
  Use `MetadataTools.getContrastMethod(String)`.
getContrastMethod(String) - Static method in class loci.formats.MetadataTools
  Retrieves an `ContrastMethod` enumeration value for the given String.
getCore() - Method in class loci.formats.in.LeicaMicrosystemsMetadata.LMSFileReader
getCoreIndex() - Method in class loci.formats.FileStitcher
getCoreIndex() - Method in class loci.formats.FormatReader
getCoreIndex() - Method in interface loci.formats.IFormatReader
  Deprecated.
  This method is no longer required for sub-resolution support.
getCoreIndex() - Method in class loci.formats.ImageReader
getCoreIndex() - Method in class loci.formats.ReaderWrapper
getCoreIndex() - Method in class loci.formats.SubResolutionFormatReader
getCoreIndex() - Method in class loci.formats.WrappedReader
getCoreMetadataList() - Method in class loci.formats.DimensionSwapper
getCoreMetadataList() - Method in class loci.formats.FileStitcher
getCoreMetadataList() - Method in class loci.formats.FormatReader
getCoreMetadataList() - Method in interface loci.formats.IFormatReader
  Deprecated.
  Reader internals should not be accessed by reader users
getCoreMetadataList() - Method in class loci.formats.ImageReader
getCoreMetadataList() - Method in class loci.formats.in.FilePatternReader
getCoreMetadataList() - Method in class loci.formats.in.LeicaHandler
getCoreMetadataList() - Method in class loci.formats.in.ND2Handler
getCoreMetadataList() - Method in class loci.formats.ReaderWrapper
getCoreMetadataList() - Method in class loci.formats.SubResolutionFormatReader
getCoreMetadataList() - Method in class loci.formats.WrappedReader
getCorrection(String) - Method in class loci.formats.FormatReader
  Deprecated.
  Use `MetadataTools.getCorrection(String)`.
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.
getCurrentPyramid() - Method in class loci.formats.in.CellSensReader
  Get an object representing the pyramid which contains the current series/resolution.
getCurrentPyramidIndex() - Method in class loci.formats.in.CellSensReader
  Get an index to the pyramid which contains the current series/resolution.
getCustomColor(int, int) - Method in class loci.plugins.in.ImporterOptions
getCustomColorKey(int, int) - Method in class loci.plugins.in.ImporterOptions
getCutIn(Double) - Static method in class loci.formats.FormatTools
getCutOut(Double) - Static method in class loci.formats.FormatTools
getCycle() - Method in class loci.formats.in.PrairieMetadata.Sequence
  Gets the `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
GetDataOffsetForBlock(int) - Method in class loci.formats.in.SlideBook7Reader.CCompressionBase
getDatasetStructureDescription() - Method in class loci.formats.FormatReader
getDatasetStructureDescription() - Method in interface loci.formats.IFormatReader
  Returns a short description of the dataset structure.
getDatasetStructureDescription() - Method in class loci.formats.ImageReader
getDatasetStructureDescription() - Method in class loci.formats.ReaderWrapper
getDatasetStructureDescription() - Method in class loci.formats.WrappedReader
GetDataSizeForBlock(int) - Method in class loci.formats.in.SlideBook7Reader.CCompressionBase
getDate() - Method in class loci.formats.in.MetamorphHandler
getDate() - Method in class loci.formats.in.ND2Handler
getDate() - Method in class loci.formats.in.PrairieMetadata
  Gets the date of the acquisition.
getDatestamp() - Method in class loci.formats.in.SVSReader
getDecompressedStream(String) - Method in class loci.formats.in.CellomicsReader
getDefault() - Method in class loci.plugins.prefs.BooleanOption
  Gets the default value of the option.
getDefault() - Method in class loci.plugins.prefs.DoubleOption
  Gets the default value of the option.
getDefault() - Method in class loci.plugins.prefs.StringOption
  Gets the default value of the option.
getDefaultColorModel() - Method in class loci.plugins.util.RecordedImageProcessor
getDefaultConfiguration() - Static method in class loci.formats.gui.AWTImageTools
  Gets the default graphics configuration for the environment.
getDefaultCustomColor(int) - Method in class loci.plugins.in.ImporterOptions
getDefaultOptions() - Static method in class loci.formats.codec.CodecOptions
  Return CodecOptions with reasonable default values.
getDefaultOptions() - Static method in class loci.formats.codec.JPEG2000CodecOptions
  Return JPEG2000CodecOptions with reasonable default values.
getDefaultOptions(CodecOptions) - Static method in class loci.formats.codec.JPEG2000CodecOptions
  Return JPEG2000CodecOptions using the given CodecOptions as the default.
getDefaultReaderClasses() - Static method in class loci.formats.ImageReader
getDefaultValue(String) - Method in class loci.plugins.prefs.OptionsList
  Gets the default value of the string option with the given key.
getDefaultVR() - Method in enum loci.formats.dicom.DicomAttribute
  Get the known default VR for this attribute, or IMPLICIT if our dictionary does not include a default VR.
getDefaultVR(int) - Static method in enum loci.formats.dicom.DicomAttribute
getDefaultWriterClasses() - Static method in class loci.formats.ImageWriter
getDeltaT() - Method in class loci.formats.in.LeicaHandler
getDenom() - Method in class org.libjpegturbo.turbojpeg.TJScalingFactor
  Returns denominator
getDenominator() - Method in class loci.formats.tiff.TiffRational
  Gets this number's denominator.
getDescription() - Method in enum loci.formats.dicom.DicomAttribute
  Get the human-readable description associated with this attribute.
getDescription(int) - Static method in enum loci.formats.dicom.DicomAttribute
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
  Deprecated.
  Use `MetadataTools.getDetectorType(String)`.
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(int, Dimension.DimensionKey) - Method in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataTempBuffer
getDimension(String) - Method in class loci.formats.in.ZeissTIFFHandler.Scaling
  Get a dimension by its index.
getDimension(String) - Method in interface loci.formats.services.NetCDFService
  Retrieves the length of a dimension.
getDimension(String) - Method in class loci.formats.services.NetCDFServiceImpl
getDimensionDescriptionNodes(Element) - Method in class loci.formats.in.LeicaMicrosystemsMetadata.LMSMetadataExtractor
getDimensionDescriptionNodes(Element) - Method in class loci.formats.in.LIFReader
getDimensionEntry(String) - Method in class loci.formats.in.ZeissCZIReader.DirectoryEntry
getDimensionOrder() - Method in class loci.formats.ChannelMerger
getDimensionOrder() - Method in class loci.formats.ChannelSeparator
getDimensionOrder() - Method in class loci.formats.DimensionSwapper
getDimensionOrder() - Method in class loci.formats.FileStitcher
getDimensionOrder() - Method in class loci.formats.FormatReader
getDimensionOrder(String) - Method in class loci.formats.FormatReader
  Deprecated.
  Use `MetadataTools.getDimensionOrder(String)`.
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(int) - Method in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataTempBuffer
  Returns the dimension order as a string
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
getDimensions(int) - Method in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataTempBuffer
getDimensionSwapper() - Method in class loci.plugins.in.ImportProcess
  Valid only after `ImportStep.STACK`.
getDirectory(String) - Method in class loci.formats.services.NetCDFServiceImpl
getDisplayColor() - Method in class loci.formats.in.SVSReader
getDoc() - Method in class loci.formats.in.LeicaMicrosystemsMetadata.LMSXmlDocument
getDocument() - Method in class loci.formats.gui.XMLWindow
  Gets the XML document currently being displayed within the window.
getDocumentBytes(String) - Method in interface loci.formats.services.POIService
  Retrieve all of the raw bytes that correspond to the given file name.
getDocumentBytes(String, 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.
GetDoubleArray(Node, String, Boolean) - Method in class loci.formats.in.SlideBook7Reader.ClassDecoder
getDoubles(BufferedImage) - Static method in class loci.formats.gui.AWTImageTools
  Extracts pixel data as arrays of doubles, one per channel.
getDoubles(WritableRaster) - Static method in class loci.formats.gui.AWTImageTools
  Extracts pixel data as arrays of doubles, one per channel.
getDoubles(WritableRaster, int, int, int, int) - Static method in class loci.formats.gui.AWTImageTools
  Extracts pixel data as arrays of doubles, one per channel.
getDoubleValue(int) - Method in class loci.formats.in.ZeissLSMReader.SubBlock
getDyeNames() - Method in class loci.formats.in.SVSReader
getEffectiveSeries(int) - Method in class loci.formats.in.ZeissLSMReader
getEffectiveSizeC() - Method in class loci.formats.FormatReader
getEffectiveSizeC() - Method in interface loci.formats.IFormatReader
  Gets the effective size of the C dimension, guaranteeing that getEffectiveSizeC() * getSizeZ() * getSizeT() == getImageCount() regardless of the result of isRGB().
getEffectiveSizeC() - Method in class loci.formats.ImageReader
getEffectiveSizeC() - Method in class loci.formats.ReaderWrapper
getEffectiveSizeC() - Method in class loci.formats.WrappedReader
getEffectiveSizeC(Double[]) - Method in class loci.plugins.macro.LociFunctions
GetElapsedTime(int) - Method in class loci.formats.in.SlideBook7Reader.CImageGroup
getElem(int) - Method in class loci.formats.gui.SignedByteBuffer
getElem(int, 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
getElementNode() - Method in class loci.formats.in.LeicaMicrosystemsMetadata.XlifDocument
getElements() - Method in class loci.formats.FilePattern
  Gets individual elements for each pattern block.
getElements() - Method in class loci.formats.FilePatternBlock
  Gets all block elements.
getElementSize(String) - Method in interface loci.formats.services.JHDFService
  Retrieves the Element Size of a dataset in Byte.
getElementSize(String) - Method in class loci.formats.services.JHDFServiceImpl
getElemFloat(int) - Method in class loci.formats.gui.UnsignedIntBuffer
getElemFloat(int, int) - Method in class loci.formats.gui.UnsignedIntBuffer
getEmission() - Method in class loci.formats.in.SVSReader
getEmissionWavelength(Double) - Static method in class loci.formats.FormatTools
getEmissionWavelengths() - Method in class loci.formats.in.ND2Handler
getEndPointer() - Method in class loci.formats.dicom.DicomTag
  Get the file pointer at which the value ends (useful for sequences and byte streams).
getEndX() - Method in class loci.formats.in.SPEReader.SpeROI
getEndY() - Method in class loci.formats.in.SPEReader.SpeROI
getEntries(IRandomAccess) - Method in class loci.formats.in.IM3Reader.FloatIM3Record
  Return all entries as an array
getEntry(IRandomAccess, int) - Method in class loci.formats.in.IM3Reader.BooleanIM3Record
  Get the boolean value at the given index
getEntry(IRandomAccess, int) - Method in class loci.formats.in.IM3Reader.FloatIM3Record
  Get the floating-point value at the given index
getEntry(IRandomAccess, int) - Method in class loci.formats.in.IM3Reader.IntIM3Record
  Get the integer value at the given index
getEnum(String, T) - Method in class loci.formats.in.DynamicMetadataOptions
  Get the value of property `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
  Deprecated.
  Use `MetadataTools.getExperimentType(String)`.
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(int) - Method in class loci.formats.in.SlideBook7Reader.CImageGroup
getExposureTime() - Method in class loci.formats.in.SVSReader
getExposureTimes() - Method in class loci.formats.in.LeicaHandler
getExposureTimes() - Method in class loci.formats.in.ND2Handler
getExtension() - Method in class loci.formats.gui.ExtensionFileFilter
  Gets the filter's first valid extension.
getExtensionFunctions() - Method in class loci.plugins.macro.MacroFunctions
getExtensions() - Method in class loci.formats.gui.ExtensionFileFilter
  Gets the filter's valid extensions.
getExternalSeries() - Method in class loci.formats.FileStitcher
getExternalSeries(int) - Method in class loci.formats.FileStitcher
getExtraSeries(String) - Method in class loci.formats.in.ZeissLSMReader
getf(int) - Method in class loci.plugins.util.RecordedImageProcessor
getf(int, int) - Method in class loci.plugins.util.RecordedImageProcessor
getField(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
getFieldCount() - Method in class loci.formats.internal.WellContainer
getFieldFromSeries(int) - Method in class loci.formats.in.InCellReader
getFieldIndex() - Method in class loci.formats.in.ND2Handler
getFieldName(int) - Static method in class loci.formats.tiff.IFD
  This method uses reflection to scan the values of this class's static fields, returning the first matching field's name.
getFilamentType(String) - Method in class loci.formats.FormatReader
  Deprecated.
  Use `MetadataTools.getFilamentType(String)`.
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.JDCEReader
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, String) - Method in class loci.formats.in.VolocityReader
getFile(int, int) - Method in class loci.formats.internal.WellContainer
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`.
getFilename(int, int) - Method in class loci.formats.out.DicomWriter
getFilenames(String, IFormatReader) - Static method in class loci.formats.FormatTools
getFilepath() - Method in class loci.formats.in.LeicaMicrosystemsMetadata.LMSXmlDocument
getFilePattern() - Method in class loci.formats.AxisGuesser
  Gets the file pattern.
getFilePattern() - Method in class loci.formats.FileStitcher.ExternalSeries
getFilePattern() - Method in class loci.formats.FileStitcher
  Gets the file pattern object used to build the list of files.
getFiles() - Method in class loci.formats.FilePattern
  Gets a listing of all files matching this file pattern.
getFiles() - Method in class loci.formats.FileStitcher.ExternalSeries
getFiles(int) - Method in class loci.formats.in.JDCEReader.JDCEWell
getFiles(int) - Method in class loci.formats.internal.WellContainer
getFileSize(String) - Method in interface loci.formats.services.POIService
  Retrieve the total number of bytes in the given file.
getFileSize(String) - Method in class loci.formats.services.POIServiceImpl
getFileStitcher() - Method in class loci.plugins.in.ImportProcess
  Valid only after `ImportStep.STACK`.
getFileVersion(RandomAccessInputStream) - Method in class loci.formats.in.OBFReader
getFillColor() - Method in class loci.formats.FormatReader
getFillColor() - Method in interface loci.formats.IFormatReader
  Return the fill value for undefined pixels.
getFillColor() - Method in class loci.formats.ImageReader
getFillColor() - Method in class loci.formats.in.ZeissCZIReader
getFillColor() - Method in class loci.formats.ReaderWrapper
getFillRule(String) - Method in class loci.formats.FormatReader
  Deprecated.
  Use `MetadataTools.getFillRule(String)`.
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
  Deprecated.
  Use `MetadataTools.getFilterType(String)`.
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(Node, String, Boolean) - Method in class loci.formats.in.SlideBook7Reader.ClassDecoder
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
  Deprecated.
  Use `MetadataTools.getFontFamily(String)`.
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
  Deprecated.
  Use `MetadataTools.getFontStyle(String)`.
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
getForegroundValue() - Method in class loci.plugins.util.RecordedImageProcessor
getFormat() - Method in class loci.formats.FormatHandler
getFormat() - Method in interface loci.formats.IFormatHandler
  Gets the name of this file format.
getFormat(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
getFourPixelCorrectionLine() - Method in class loci.formats.in.DCIMGReader
getFourPixelCorrectionOffset() - Method in class loci.formats.in.DCIMGReader
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 `c`th 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
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(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
GetHistogramDataFile(String, Integer, Integer) - Method in class loci.formats.in.SlideBook7Reader.CSBFile70
getHistogramMax() - Method in class loci.plugins.util.RecordedImageProcessor
getHistogramMin() - Method in class loci.plugins.util.RecordedImageProcessor
getHistogramSize() - Method in class loci.plugins.util.RecordedImageProcessor
getId() - Method in class loci.formats.filter.LZ4Filter
getId() - Method in class loci.formats.filter.LZ4Filter.LZ4FilterProvider
getId(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(int) - Method in class loci.formats.in.SVSReader
  Get the IFD corresponding to the given plane in the current series.
getIFD(long) - Method in class loci.formats.tiff.TiffParser
  Gets the IFD stored at the given offset.
getIFDComment(int) - Method in class loci.formats.in.VectraReader
getIFDIndex() - Method in class loci.formats.in.CellSensReader
getIFDIndex(int, 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) - Method in class loci.formats.in.VentanaReader
  Note that all planes for a particular resolution or extra image are packed into a single IFD, so the IFD index does not depend upon the plane (e.g.
getIFDIntArray(int) - Method in class loci.formats.tiff.IFD
  Gets the given directory entry values in int format from this IFD, performing some error checking.
getIFDIntValue(int) - Method in class loci.formats.tiff.IFD
  Gets the given directory entry value in int format from this IFD, or -1 if the given directory does not exist.
getIFDIntValue(int, int) - Method in class loci.formats.tiff.IFD
  Gets the given directory entry value in int format from this IFD, performing some error checking.
getIFDLongArray(int) - Method in class loci.formats.tiff.IFD
  Gets the given directory entry values in long format from this IFD, performing some error checking.
getIFDLongValue(int, long) - Method in class loci.formats.tiff.IFD
  Gets the given directory entry value in long format from this IFD, performing some error checking.
getIFDOffsets() - Method in class loci.formats.tiff.TiffParser
  Gets the offsets to every IFD in the file.
getIFDRationalValue(int) - Method in class loci.formats.tiff.IFD
  Gets the given directory entry value in rational format from this IFD, performing some error checking.
getIFDs() - Method in class loci.formats.in.MinimalTiffReader
  Gets the list of IFDs associated with the current TIFF's image planes.
getIFDs() - Method in class loci.formats.tiff.TiffParser
  Deprecated.
  Use `TiffParser.getMainIFDs()` and `TiffParser.getSubIFDs(IFD)` instead.
getIFDShortArray(int) - Method in class loci.formats.tiff.IFD
  Gets the given directory entry values in short format from this IFD, performing some error checking.
getIFDStringValue(int) - Method in class loci.formats.tiff.IFD
  Gets the given directory entry value as a string from this IFD, performing some error checking.
getIFDTagName(int) - Static method in class loci.formats.tiff.IFD
  Gets the name of the IFD tag encoded by the given number.
getIFDTextValue(int) - Method in class loci.formats.tiff.IFD
  Gets the given directory entry value as a string (regardless of type).
getIFDValue(int) - Method in class loci.formats.tiff.IFD
  Gets the given directory entry value from this IFD.
getIFDValue(int, Class) - Method in class loci.formats.tiff.IFD
  Gets the given directory entry value from this IFD, performing some error checking.
getIFDValue(TiffIFDEntry) - Method in class loci.formats.tiff.TiffParser
  Retrieve the value corresponding to the given TiffIFDEntry.
getIlluminationType(String) - Method in class loci.formats.FormatReader
  Deprecated.
  Use `MetadataTools.getIlluminationType(String)`.
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.
getImageCount() - Method in class loci.formats.ChannelMerger
getImageCount() - Method in class loci.formats.ChannelSeparator
getImageCount() - Method in class loci.formats.FileStitcher
getImageCount() - Method in class loci.formats.FormatReader
getImageCount() - Method in interface loci.formats.IFormatReader
  Determines the number of image planes in the current file.
getImageCount() - Method in class loci.formats.ImageReader
getImageCount() - Method in class loci.formats.in.LeicaMicrosystemsMetadata.XlefDocument
  Returns number of images which are referenced by xlifs
getImageCount() - Method in class loci.formats.ReaderWrapper
getImageCount() - Method in class loci.formats.WrappedReader
getImageCount(Double[]) - Method in class loci.plugins.macro.LociFunctions
getImageCreationDate() - Method in class loci.formats.in.BaseTiffReader
  Retrieves the image creation date.
getImageCreationDate(String[]) - Method in class loci.plugins.macro.LociFunctions
getImageData(int, int, int, 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.
GetImageDataFile(String, Integer, Integer) - Method in class loci.formats.in.SlideBook7Reader.CSBFile70
getImageDescription(Element) - Method in class loci.formats.in.LeicaMicrosystemsMetadata.LMSMetadataExtractor
getImageDescription(Element) - Method in class loci.formats.in.LIFReader
getImageFile(String) - Method in class loci.formats.in.TecanReader
  Turn a relative image file path into an absolute path.
getImageFormat() - Method in class loci.formats.in.LeicaMicrosystemsMetadata.LMSFileReader
  Returns the file format in which actual image bytes are stored
getImageFormat() - Method in class loci.formats.in.LeicaMicrosystemsMetadata.MultipleImagesReader
getImageFormat() - Method in class loci.formats.in.LeicaMicrosystemsMetadata.XlifDocument
getImageFormat() - Method in class loci.formats.in.LOFReader
getImageFormat() - Method in class loci.formats.in.XLEFReader
GetImageGroup(int) - Method in class loci.formats.in.SlideBook7Reader.DataLoader
GetImageGroupDirectory(String) - Method in class loci.formats.in.SlideBook7Reader.CSBFile70
getImageIndex() - Method in class loci.formats.gui.ImageViewer
  Gets the index of the currently displayed image.
getImageIndex(int) - Method in class loci.formats.in.FluoviewReader
getImageIndex(String) - Method in class loci.formats.in.PCIReader
  Get the image index from the image file name.
getImageLength() - Method in class loci.formats.tiff.IFD
  Retrieves the image's length (TIFF tag ImageLength) from a given TIFF IFD.
getImageName() - Method in class loci.formats.in.LeicaMicrosystemsMetadata.LMSImageXmlDocument
  Returns the name of the image (it might be contained in the XML or otherwise e.g.
getImageName() - Method in class loci.formats.in.LeicaMicrosystemsMetadata.LofXmlDocument
getImageName() - Method in class loci.formats.in.LeicaMicrosystemsMetadata.XlifDocument
getImageName() - Method in class loci.formats.in.MetamorphHandler
getImageName(int) - Method in class loci.formats.in.VectraReader
getImageNode() - Method in class loci.formats.in.LeicaMicrosystemsMetadata.LMSImageXmlDocument
  Returns the image node of the xml document which contains image metadata
getImageNode() - Method in class loci.formats.in.LeicaMicrosystemsMetadata.LofXmlDocument
getImageNode() - Method in class loci.formats.in.LeicaMicrosystemsMetadata.XlifDocument
getImageNumber(String, int) - Method in class loci.formats.in.ZeissZVIReader
getImagePaths() - Method in class loci.formats.in.LeicaMicrosystemsMetadata.XlifDocument
getImageReader() - Method in class loci.plugins.in.ImportProcess
  Valid only after `ImportStep.READER`.
getImageSequence(int) - Method in class loci.formats.in.DeltavisionReader
  Get the image sequence string.
getImagesPerFile() - Method in class loci.formats.FileStitcher.ExternalSeries
getImagesPerFile(String, IFormatReader) - Static method in class loci.formats.FormatTools
getImageType() - Method in class loci.formats.in.DicomReader
getImageType(int) - Method in class loci.formats.in.VectraReader
getImageType(String, int, boolean, int) - Method in class loci.formats.out.DicomWriter
getImageWidth() - Method in class loci.formats.tiff.IFD
  Retrieves the image's width (TIFF tag ImageWidth) from a given TIFF IFD.
getImagingDevice() - Method in class loci.formats.in.PrairieMetadata.Frame
  Gets the imaging device associated with this `Frame`.
getImmersion(String) - Method in class loci.formats.FormatReader
  Deprecated.
  Use `MetadataTools.getImmersion(String)`.
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(String) - Method in class loci.formats.in.JDCEReader.JDCEWell
getIndex() - Method in class loci.formats.in.PrairieMetadata.Frame
  Gets the `index` associated with this `Frame`.
getIndex(int, int) - Method in class loci.formats.out.DicomWriter
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.formats.in.SlideBook7Reader.CImageGroup
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
getInstrumentType() - Method in class loci.formats.in.OperettaReader.OperettaHandler
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.
GetIntegerArray(Node, String, Boolean) - Method in class loci.formats.in.SlideBook7Reader.ClassDecoder
GetIntegerValue(MappingNode, int, String) - Method in class loci.formats.in.SlideBook7Reader.ClassDecoder
GetInterplaneSpacing() - Method in class loci.formats.in.SlideBook7Reader.CImageGroup
getInterpolate() - Method in class loci.plugins.util.RecordedImageProcessor
getInterpolatedPixel(double, double) - Method in class loci.plugins.util.RecordedImageProcessor
getInts(BufferedImage) - Static method in class loci.formats.gui.AWTImageTools
  Extracts pixel data as arrays of signed integers, one per channel.
getInts(WritableRaster) - Static method in class loci.formats.gui.AWTImageTools
  Extracts pixel data as arrays of signed integers, one per channel.
getInts(WritableRaster, int, int, int, int) - Static method in class loci.formats.gui.AWTImageTools
  Extracts pixel data as arrays of signed integers, one per channel.
getIntValue(int) - Method in class loci.formats.in.ZeissLSMReader.SubBlock
getJPEGBuf() - Method in class org.libjpegturbo.turbojpeg.TJDecompressor
  Returns the JPEG image buffer associated with this decompressor instance.
getJPEGSize() - Method in class org.libjpegturbo.turbojpeg.TJDecompressor
  Returns the size of the JPEG image (in bytes) associated with this decompressor instance.
getKey() - Method in class loci.formats.in.BaseZeissReader.Tag
getKey(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
getL(String) - Method in class loci.formats.in.OIRReader
getLabel() - Method in class loci.plugins.prefs.Option
  Gets label describing the option.
getLabel(String) - Method in class loci.plugins.prefs.OptionsList
  Gets the label for the option with the given key.
getLabels() - Method in class loci.plugins.config.CellSensWidgets
getLabels() - Method in interface loci.plugins.config.IFormatWidgets
getLabels() - Method in class loci.plugins.config.LIFWidgets
getLabels() - Method in class loci.plugins.config.ND2Widgets
getLabels() - Method in class loci.plugins.config.SDTWidgets
getLabels() - Method in class loci.plugins.config.TiffDelegateWidgets
getLabels() - Method in class loci.plugins.config.ZeissCZIWidgets
getLaserMedium(String) - Method in class loci.formats.FormatReader
  Deprecated.
  Use `MetadataTools.getLaserMedium(String)`.
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
  Deprecated.
  Use `MetadataTools.getLaserType(String)`.
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) - Method in class loci.formats.dicom.DicomTag
  Get the length of the next value in the given input stream.
getLength() - Method in class loci.formats.in.LeicaMicrosystemsMetadata.Dimension
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
GetLensName() - Method in class loci.formats.in.SlideBook7Reader.CImageGroup
getLensRI() - Method in class loci.formats.in.MetamorphHandler
getLetter() - Method in class loci.formats.ResourceNamer
  Returns a `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).
getLevel() - Method in class loci.formats.in.TissueFAXSReader
getLine(double, double, double, double) - Method in class loci.plugins.util.RecordedImageProcessor
getLinesPerFrame() - Method in class loci.formats.in.PrairieMetadata.Frame
  Gets the lines per frame for this `Frame`.
GetListOfHistogramDataFiles(String) - Method in class loci.formats.in.SlideBook7Reader.CSBFile70
GetListOfHistogramSummaryFiles(String) - Method in class loci.formats.in.SlideBook7Reader.CSBFile70
GetListOfImageDataFiles(String) - Method in class loci.formats.in.SlideBook7Reader.CSBFile70
GetListOfImageGroupTitles() - Method in class loci.formats.in.SlideBook7Reader.CSBFile70
GetListOfMaskDataFiles(String) - Method in class loci.formats.in.SlideBook7Reader.CSBFile70
getListOfNpyDataFiles(String, String) - Method in class loci.formats.in.SlideBook7Reader.CSBFile70
getLoadList(int[]) - Method in class loci.formats.cache.CacheStrategy
getLoadList(int[]) - Method in interface loci.formats.cache.ICacheStrategy
  Gets the indices of the objects to cache, surrounding the object at the given position.
getLocation() - Method in class loci.plugins.in.ImporterOptions
getLocationFromResourceName(Location, String, int, String) - Method in class loci.formats.ResourceNamer
  Creates a new `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(Node, String, Boolean) - Method in class loci.formats.in.SlideBook7Reader.ClassDecoder
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() - 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.SlideBook7Reader.CImageGroup
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
  Deprecated.
  Use `MetadataTools.getMarker(String)`.
getMarker(String) - Static method in class loci.formats.MetadataTools
  Retrieves an `Marker` enumeration value for the given String.
getMarkers(IFD) - Method in class loci.formats.in.NDPIReader
  Get the array of restart markers (offsets) for the given IFD.
getMask() - Method in class loci.plugins.util.RecordedImageProcessor
getMaskArray() - Method in class loci.plugins.util.RecordedImageProcessor
GetMaskDataFile(String, Integer) - Method in class loci.formats.in.SlideBook7Reader.CSBFile70
getMax() - Method in class loci.plugins.util.RecordedImageProcessor
getMaxFieldCount(Integer) - Static method in class loci.formats.FormatTools
getMaximumSize() - Method in class loci.formats.gui.CacheIndicator
getMaximumSize() - Method in class loci.formats.gui.DataConverter.RowPanel
getMaxThreshold() - Method in class loci.plugins.util.RecordedImageProcessor
getMCUHeight(int) - Static method in class org.libjpegturbo.turbojpeg.TJ
  Returns the MCU block height for the given level of chrominance subsampling.
getMCUWidth(int) - Static method in class org.libjpegturbo.turbojpeg.TJ
  Returns the MCU block width for the given level of chrominance subsampling.
getMDBFile(String) - Method in class loci.formats.in.ZeissLSMReader
getMeasurementID() - Method in class loci.formats.in.ColumbusReader.MeasurementHandler
getMeasurementID() - Method in class loci.formats.in.OperettaReader.OperettaHandler
getMeasurementName() - Method in class loci.formats.in.ColumbusReader.MeasurementHandler
getMeasurementTime() - Method in class loci.formats.in.OperettaReader.OperettaHandler
getMedium(String) - Method in class loci.formats.FormatReader
  Deprecated.
  Use `MetadataTools.getMedium(String)`.
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.
getMemoFile() - Method in class loci.formats.Memoizer
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
getMetadataOptionsFile(String) - Static method in class loci.formats.in.DynamicMetadataOptions
getMetadataPixelType(int) - Method in class loci.formats.in.ZeissXRMReader
getMetadataRetrieve() - Method in class loci.formats.FormatWriter
getMetadataRetrieve() - Method in interface loci.formats.IFormatWriter
  Retrieves the current metadata retrieval object for this writer.
getMetadataRetrieve() - Method in class loci.formats.ImageWriter
getMetadataRetrieve() - Method in class loci.formats.WriterWrapper
getMetadataRoot(String) - Method in class loci.formats.in.LIFReader
getMetadataRoot(String) - Method in class loci.formats.in.OlympusTileReader
getMetadataStore() - Method in class loci.formats.FileStitcher
getMetadataStore() - Method in class loci.formats.FormatReader
getMetadataStore() - Method in interface loci.formats.IFormatReader
  Retrieves the current metadata store for this reader.
getMetadataStore() - Method in class loci.formats.ImageReader
getMetadataStore() - Method in class loci.formats.in.FilePatternReader
getMetadataStore() - Method in class loci.formats.Memoizer
getMetadataStore() - Method in class loci.formats.ReaderWrapper
getMetadataStoreForConversion() - Method in class loci.formats.in.OMETiffReader
  Deprecated.
  Use the general `FormatReader.getMetadataStore()` method.
getMetadataStoreForDisplay() - Method in class loci.formats.in.OMETiffReader
  Deprecated.
  Use the general `FormatReader.getMetadataStore()` method.
getMetadataStoreRoot() - Method in class loci.formats.FileStitcher
getMetadataStoreRoot() - Method in class loci.formats.FormatReader
getMetadataStoreRoot() - Method in interface loci.formats.IFormatReader
  Retrieves the current metadata store's root object.
getMetadataStoreRoot() - Method in class loci.formats.ImageReader
getMetadataStoreRoot() - Method in class loci.formats.ReaderWrapper
getMetadataStoreRoot() - Method in class loci.formats.WrappedReader
getMetadataString(String) - Method in class loci.plugins.in.ImporterMetadata
  Returns a string with each key/value pair on its own line.
getMetadataType() - Method in enum loci.formats.tiff.PhotoInterp
  Retrieves the metadata type of the photometric interpretation.
getMetadataValue(String) - Method in class loci.formats.FormatReader
getMetadataValue(String) - Method in interface loci.formats.IFormatReader
  Obtains the specified metadata field's value for the current file.
getMetadataValue(String) - Method in class loci.formats.ImageReader
getMetadataValue(String) - Method in class loci.formats.ReaderWrapper
getMetadataValue(String) - Method in class loci.formats.WrappedReader
getMetadataValue(String, String[]) - Method in class loci.plugins.macro.LociFunctions
getMethodStack() - Method in class loci.plugins.util.BFVirtualStack
getMethodStack() - Method in class loci.plugins.util.RecordedImageProcessor
getMicrobeamManipulationType(String) - Method in class loci.formats.FormatReader
  Deprecated.
  Use `MetadataTools.getMicrobeamManipulationType(String)`.
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
  Deprecated.
  Use `MetadataTools.getMicroscopeType(String)`.
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
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
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() - Method in class loci.formats.filter.LZ4Filter
getName() - Method in class loci.formats.filter.LZ4Filter.LZ4FilterProvider
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() - Method in class loci.formats.in.LeicaMicrosystemsMetadata.XlifDocument
getName(Node) - Method in class loci.formats.in.OlympusTileReader
GetName() - Method in class loci.formats.in.SlideBook7Reader.CImageGroup
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
  Deprecated.
  Use `MetadataTools.getNamingConvention(String)`.
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.ReaderWrapper
getNativeDataType() - Method in class loci.formats.TileStitcher
getNativeDataType() - Method in class loci.formats.WrappedReader
getNativeDataType() - Method in class loci.formats.WriterWrapper
getNativeDataType() - Method in class loci.plugins.util.ImageProcessorReader
getNChannels() - Method in class loci.plugins.util.RecordedImageProcessor
getNDVersionSuffix(Location) - Method in class loci.formats.in.MetamorphReader
  Parses the given ND file to determined the version and return the expected file suffix
getNextLine(byte[]) - Method in class loci.formats.in.MicromanagerReader
getNextLine(List<String>) - Method in class loci.formats.in.TextReader
getNextOffset(long) - Method in class loci.formats.tiff.TiffParser
  Read a file offset.
getNextTag(RandomAccessInputStream) - Method in class loci.formats.dicom.DicomTag
  Get the next 4 byte DICOM tag from the given input stream.
getNextTag(RandomAccessInputStream) - Method in class loci.formats.in.ZeissZVIReader
getNodes(Element, String) - Method in class loci.formats.in.LeicaMicrosystemsMetadata.LMSMetadataExtractor
  Returns all (grand*n)children nodes with given node name
getNodes(Element, String) - Method in class loci.formats.in.LIFReader
getNonThumbnailIFDs() - Method in class loci.formats.tiff.TiffParser
  Returns non-thumbnail IFDs.
getNormalizedName() - Method in class loci.formats.in.ZeissCZIReader.AttachmentEntry
getNum() - Method in class org.libjpegturbo.turbojpeg.TJScalingFactor
  Returns numerator
getNumber(String) - Method in class loci.formats.NumberFilter
  Gets numbers filling the asterisk positions.
getNumberValue() - Method in class loci.formats.dicom.DicomTag
  Get a number representation of the current value, or null if not a number.
getNumBytes(int) - Method in class loci.formats.in.GatanReader
GetNumCaptures() - Method in class loci.formats.in.SlideBook7Reader.DataLoader
GetNumChannels() - Method in class loci.formats.in.SlideBook7Reader.CImageGroup
GetNumColumns() - Method in class loci.formats.in.SlideBook7Reader.CImageGroup
getNumComponents() - Method in class loci.formats.gui.TwoChannelColorSpace
getNumEntries(IRandomAccess) - Method in class loci.formats.in.IM3Reader.BooleanIM3Record
  Get the # of boolean values in this record
getNumEntries(IRandomAccess) - Method in class loci.formats.in.IM3Reader.FloatIM3Record
  Get the # of floating-point values in this record
getNumEntries(IRandomAccess) - Method in class loci.formats.in.IM3Reader.IntIM3Record
  Get the # of integer values in this record
getNumerator() - Method in class loci.formats.tiff.TiffRational
  Gets this number's numerator.
getNumericalAperture() - Method in class loci.formats.in.ND2Handler
getNumericFields(GenericDialog) - Method in class loci.plugins.in.ColorDialog
getNumericFields(GenericDialog) - Static method in class loci.plugins.util.WindowTools
GetNumPlanes() - Method in class loci.formats.in.SlideBook7Reader.CImageGroup
GetNumPositions() - Method in class loci.formats.in.SlideBook7Reader.CImageGroup
GetNumRows() - Method in class loci.formats.in.SlideBook7Reader.CImageGroup
GetNumTimepoints() - Method in class loci.formats.in.SlideBook7Reader.CImageGroup
getObject(int) - Method in class loci.formats.cache.ByteArraySource
getObject(int[]) - Method in class loci.formats.cache.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
getOffset(int) - Method in class loci.formats.in.PrairieMetadata.Frame
  Gets the `c`th offset for this `Frame`.
getOffsets() - Method in class loci.formats.in.ND2Reader
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.DicomReader
getOptimalTileHeight() - Method in class loci.formats.in.EPSReader
getOptimalTileHeight() - Method in class loci.formats.in.FlexReader
getOptimalTileHeight() - Method in class loci.formats.in.FV1000Reader
getOptimalTileHeight() - Method in class loci.formats.in.HamamatsuVMSReader
getOptimalTileHeight() - Method in class loci.formats.in.ImageIOReader
getOptimalTileHeight() - Method in class loci.formats.in.ImarisHDFReader
getOptimalTileHeight() - Method in class loci.formats.in.InCellReader
getOptimalTileHeight() - Method in class loci.formats.in.IPWReader
getOptimalTileHeight() - Method in class loci.formats.in.JDCEReader
getOptimalTileHeight() - Method in class loci.formats.in.L2DReader
getOptimalTileHeight() - Method in class loci.formats.in.LeicaReader
getOptimalTileHeight() - Method in class loci.formats.in.LeicaSCNReader
getOptimalTileHeight() - Method in class loci.formats.in.LIFReader
getOptimalTileHeight() - Method in class loci.formats.in.LOFReader
getOptimalTileHeight() - Method in class loci.formats.in.MIASReader
getOptimalTileHeight() - Method in class loci.formats.in.MicromanagerReader
getOptimalTileHeight() - Method in class loci.formats.in.MinimalTiffReader
getOptimalTileHeight() - Method in class loci.formats.in.NDPIReader
getOptimalTileHeight() - Method in class loci.formats.in.NDPISReader
getOptimalTileHeight() - Method in class loci.formats.in.NRRDReader
getOptimalTileHeight() - Method in class loci.formats.in.OIRReader
getOptimalTileHeight() - Method in class loci.formats.in.OlympusTileReader
getOptimalTileHeight() - Method in class loci.formats.in.OMETiffReader
getOptimalTileHeight() - Method in class loci.formats.in.OpenlabReader
getOptimalTileHeight() - Method in class loci.formats.in.PCIReader
getOptimalTileHeight() - Method in class loci.formats.in.PerkinElmerReader
getOptimalTileHeight() - Method in class loci.formats.in.PrairieReader
getOptimalTileHeight() - Method in class loci.formats.in.PyramidTiffReader
getOptimalTileHeight() - Method in class loci.formats.in.ScanrReader
getOptimalTileHeight() - Method in class loci.formats.in.SVSReader
getOptimalTileHeight() - Method in class loci.formats.in.TissueFAXSReader
getOptimalTileHeight() - Method in class loci.formats.in.TrestleReader
getOptimalTileHeight() - Method in class loci.formats.in.VectraReader
getOptimalTileHeight() - Method in class loci.formats.in.VentanaReader
getOptimalTileHeight() - Method in class loci.formats.in.VisitechReader
getOptimalTileHeight() - Method in class loci.formats.in.ZeissCZIReader
getOptimalTileHeight() - Method in class loci.formats.in.ZeissLSMReader
getOptimalTileHeight() - Method in class loci.formats.ReaderWrapper
getOptimalTileHeight() - Method in class loci.formats.WrappedReader
getOptimalTileWidth() - Method in class loci.formats.DelegateReader
getOptimalTileWidth() - Method in class loci.formats.FormatReader
getOptimalTileWidth() - Method in interface loci.formats.IFormatReader
  Returns the optimal sub-image width for use with openBytes.
getOptimalTileWidth() - Method in class loci.formats.ImageReader
getOptimalTileWidth() - Method in class loci.formats.in.AFIReader
getOptimalTileWidth() - Method in class loci.formats.in.APLReader
getOptimalTileWidth() - Method in class loci.formats.in.BDReader
getOptimalTileWidth() - Method in class loci.formats.in.CellSensReader
getOptimalTileWidth() - Method in class loci.formats.in.DicomReader
getOptimalTileWidth() - Method in class loci.formats.in.EPSReader
getOptimalTileWidth() - Method in class loci.formats.in.FlexReader
getOptimalTileWidth() - Method in class loci.formats.in.FV1000Reader
getOptimalTileWidth() - Method in class loci.formats.in.HamamatsuVMSReader
getOptimalTileWidth() - Method in class loci.formats.in.ImarisHDFReader
getOptimalTileWidth() - Method in class loci.formats.in.InCellReader
getOptimalTileWidth() - Method in class loci.formats.in.IPWReader
getOptimalTileWidth() - Method in class loci.formats.in.JDCEReader
getOptimalTileWidth() - Method in class loci.formats.in.L2DReader
getOptimalTileWidth() - Method in class loci.formats.in.LeicaReader
getOptimalTileWidth() - Method in class loci.formats.in.LeicaSCNReader
getOptimalTileWidth() - Method in class loci.formats.in.MIASReader
getOptimalTileWidth() - Method in class loci.formats.in.MicromanagerReader
getOptimalTileWidth() - Method in class loci.formats.in.MinimalTiffReader
getOptimalTileWidth() - Method in class loci.formats.in.NDPIReader
getOptimalTileWidth() - Method in class loci.formats.in.NDPISReader
getOptimalTileWidth() - Method in class loci.formats.in.OIRReader
getOptimalTileWidth() - Method in class loci.formats.in.OlympusTileReader
getOptimalTileWidth() - Method in class loci.formats.in.OMETiffReader
getOptimalTileWidth() - Method in class loci.formats.in.PCIReader
getOptimalTileWidth() - Method in class loci.formats.in.PerkinElmerReader
getOptimalTileWidth() - Method in class loci.formats.in.PrairieReader
getOptimalTileWidth() - Method in class loci.formats.in.PyramidTiffReader
getOptimalTileWidth() - Method in class loci.formats.in.ScanrReader
getOptimalTileWidth() - Method in class loci.formats.in.SVSReader
getOptimalTileWidth() - Method in class loci.formats.in.TissueFAXSReader
getOptimalTileWidth() - Method in class loci.formats.in.TrestleReader
getOptimalTileWidth() - Method in class loci.formats.in.VectraReader
getOptimalTileWidth() - Method in class loci.formats.in.VentanaReader
getOptimalTileWidth() - Method in class loci.formats.in.ZeissCZIReader
getOptimalTileWidth() - Method in class loci.formats.ReaderWrapper
getOptimalTileWidth() - Method in class loci.formats.WrappedReader
getOptimalWidth() - Method in class loci.formats.in.ZeissLSMReader
getOption(String) - Method in class loci.plugins.prefs.OptionsList
  Gets the option with the given key.
getOptions() - Method in class loci.formats.ClassList
  Gets the list of options as a map.
getOptions(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.
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
getPacking(String) - Static method in class loci.formats.in.LIPixelFormat
getPage() - Method in class loci.formats.in.PrairieMetadata.PFile
  Gets the `page` associated with this `File`.
getParent(int) - Method in class loci.formats.in.LeicaSCNReader
getParentFiles() - Method in class loci.formats.in.LeicaMicrosystemsMetadata.LMSXmlDocument
  Returns all files which directly or indirectly reference this LMS xml file.
getParentName(Integer) - Method in class loci.formats.in.VolocityReader
getPath(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
getPathToImageData() - Method in class loci.formats.in.CellH5Reader.CellH5Coordinate
getPathToSegmentationData() - Method in class loci.formats.in.CellH5Reader.CellH5Coordinate
getPattern() - Method in class loci.formats.FilePattern
  Gets the file pattern string.
getPhotometricInterpretation() - Method in class loci.formats.tiff.IFD
  Retrieves the image's photometric interpretation (TIFF tag PhotometricInterpretation) from this IFD.
getPhysicalHeight() - Method in class loci.formats.in.ZeissCZIReader.SubBlock
getPhysicalSize(Double, String) - Static method in class loci.formats.FormatTools
getPhysicalSize(Length) - Method in class loci.formats.out.DicomWriter
getPhysicalSizes() - Method in class loci.formats.in.SVSReader
getPhysicalSizeX(Double) - Static method in class loci.formats.FormatTools
  Formats the input value for the physical size in X into a length in microns
getPhysicalSizeX(Double, String) - Static method in class loci.formats.FormatTools
  Formats the input value for the physical size in X into a length of the given unit.
getPhysicalSizeX(Double, Unit<Length>) - Static method in class loci.formats.FormatTools
  Formats the input value for the physical size in X into a length of the given unit.
getPhysicalSizeY(Double) - Static method in class loci.formats.FormatTools
  Formats the input value for the physical size in Y into a length in microns
getPhysicalSizeY(Double, String) - Static method in class loci.formats.FormatTools
  Formats the input value for the physical size in Y into a length of the given unit.
getPhysicalSizeY(Double, Unit<Length>) - Static method in class loci.formats.FormatTools
  Formats the input value for the physical size in Y into a length of the given unit.
getPhysicalSizeZ(Double) - Static method in class loci.formats.FormatTools
  Formats the input value for the physical size in Z into a length in microns.
getPhysicalSizeZ(Double, String) - Static method in class loci.formats.FormatTools
  Formats the input value for the physical size in Z into a length of the given unit.
getPhysicalSizeZ(Double, Unit<Length>) - Static method in class loci.formats.FormatTools
  Formats the input value for the physical size in Z into a length of the given unit.
getPhysicalWidth() - Method in class loci.formats.in.ZeissCZIReader.SubBlock
getPinholeSize() - Method in class loci.formats.in.ND2Handler
getPixel(int, int) - Method in class loci.plugins.util.RecordedImageProcessor
getPixel(int, int, int[]) - Method in class loci.plugins.util.RecordedImageProcessor
getPixelBytes(BufferedImage, boolean) - Static method in class loci.formats.gui.AWTImageTools
  Return a 2D array of bytes representing the image.
getPixelBytes(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.DicomReader
getPixelSizeX() - Method in class loci.formats.in.MetamorphHandler
getPixelSizeX() - Method in class loci.formats.in.ND2Handler
getPixelSizeY() - Method in class loci.formats.in.DicomReader
getPixelSizeY() - Method in class loci.formats.in.MetamorphHandler
getPixelSizeY() - Method in class loci.formats.in.ND2Handler
getPixelSizeZ() - Method in class loci.formats.in.DicomReader
getPixelSizeZ() - Method in class loci.formats.in.ND2Handler
getPixelsPerLine() - Method in class loci.formats.in.PrairieMetadata.Frame
  Gets the pixels per line for this `Frame`.
getPixelsPhysicalSizeX(Double[]) - Method in class loci.plugins.macro.LociFunctions
getPixelsPhysicalSizeY(Double[]) - Method in class loci.plugins.macro.LociFunctions
getPixelsPhysicalSizeZ(Double[]) - Method in class loci.plugins.macro.LociFunctions
getPixelsTimeIncrement(Double[]) - Method in class loci.plugins.macro.LociFunctions
getPixelString(int) - Method in class loci.formats.in.DeltavisionReader
  Get a descriptive string representing the pixel type.
getPixelType() - Method in class loci.formats.FileStitcher
getPixelType() - Method in class loci.formats.FormatReader
getPixelType(String) - Method in class loci.formats.FormatReader
  Deprecated.
  Use `MetadataTools.getPixelType(String)`.
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() - Method in class loci.formats.in.LeicaMicrosystemsMetadata.MultipleImagesReader
getPixelType(int) - Method in class loci.formats.in.OBFReader
getPixelType(int) - Method in class loci.formats.in.ZeissXRMReader
  Convert an XRM data type to a Bio-Formats pixel type.
getPixelType(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 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.DicomWriter
getPixelTypes(String) - Method in class loci.formats.out.EPSWriter
getPixelTypes(String) - Method in class loci.formats.out.ICSWriter
getPixelTypes(String) - Method in class loci.formats.out.ImageIOWriter
getPixelTypes(String) - Method in class loci.formats.out.JavaWriter
getPixelTypes(String) - Method in class loci.formats.out.JPEG2000Writer
  Overridden to return the formats supported by the writer.
getPixelTypes(String) - Method in class loci.formats.out.JPEGWriter
getPixelTypes(String) - Method in class loci.formats.out.OMEXMLWriter
getPixelTypes(String) - Method in class loci.formats.out.QTWriter
getPixelTypes(String) - Method in class loci.formats.out.TiffWriter
getPixelTypes(String) - Method in class loci.formats.out.V3DrawWriter
getPixelTypes() - 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.
getPlaneMetadata(int, int[]) - Method in class loci.formats.in.JDCEReader.JDCEWell
getPlaneMinimum(int) - Method in class loci.formats.MinMaxCalculator
  Retrieves the minimum pixel value for the specified plane.
getPlanePositionX(Double[], Double) - Method in class loci.plugins.macro.LociFunctions
getPlanePositionY(Double[], Double) - Method in class loci.plugins.macro.LociFunctions
getPlanePositionZ(Double[], Double) - Method in class loci.plugins.macro.LociFunctions
getPlanes() - Method in class loci.formats.in.CV7000Reader.MeasurementDataHandler
getPlanes() - Method in class loci.formats.in.OperettaReader.OperettaHandler
getPlaneSize(IFormatReader) - Static method in class loci.formats.FormatTools
  Returns the size in bytes of a single plane.
getPlaneSize(IFormatReader, int, int) - Static method in class loci.formats.FormatTools
  Returns the size in bytes of a w * h tile.
getPlanesToLoad(int) - Method in class loci.plugins.in.ImagePlusReader
getPlaneTimingDeltaT(Double[], Double) - Method in class loci.plugins.macro.LociFunctions
getPlaneTimingExposureTime(Double[], Double) - Method in class loci.plugins.macro.LociFunctions
getPlateAcquisition() - Method in class loci.formats.internal.WellContainer
getPlateColumns() - Method in class loci.formats.in.ColumbusReader.MeasurementHandler
getPlateColumns() - Method in class loci.formats.in.CV7000Reader.WPIHandler
getPlateColumns() - Method in class loci.formats.in.OperettaReader.OperettaHandler
getPlateDescription() - Method in class loci.formats.in.CV7000Reader.WPIHandler
getPlateDescription() - Method in class loci.formats.in.OperettaReader.OperettaHandler
getPlateID() - Method in class loci.formats.in.CV7000Reader.WPIHandler
getPlateIdentifier() - Method in class loci.formats.in.OperettaReader.OperettaHandler
getPlateName(String) - Method in class loci.formats.in.CellomicsReader
getPlateName(String) - Method in class loci.formats.in.CellWorxReader
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.DicomReader
getPositionX() - Method in class loci.formats.in.PrairieMetadata.Frame
  Gets the X stage position associated with this `Frame`.
getPositionY() - Method in class loci.formats.in.DicomReader
getPositionY() - Method in class loci.formats.in.PrairieMetadata.Frame
  Gets the Y stage position associated with this `Frame`.
getPositionZ() - Method in class loci.formats.in.DicomReader
getPositionZ() - Method in class loci.formats.in.PrairieMetadata.Frame
  Gets the Z stage position associated with this `Frame`.
getPossible(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
  Deprecated.
  Use `MetadataTools.getPulse(String)`.
getPulse(String) - Static method in class loci.formats.MetadataTools
  Retrieves an `Pulse` enumeration value for the given String.
getPyramidHeight() - Method in class loci.formats.in.NDPIReader
getQuietInfo() - Method in class loci.plugins.in.ImporterOptions
getRange() - Method in class loci.formats.cache.CacheStrategy
getRange() - Method in interface loci.formats.cache.ICacheStrategy
  Retrieves the number of objects to cache along each axis.
getRasterLength(int[]) - Static method in class loci.formats.FormatTools
  Computes the number of raster values for a positional array with the given lengths.
getReader(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(String, boolean) - Method in class loci.formats.in.MetaxpressTiffReader
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
getReaderIndex(int) - Method in class loci.formats.in.XLEFReader
  Returns the index of the correct reader for the series index.
getReaders() - Method in class loci.formats.FileStitcher.ExternalSeries
getReaders() - Method in class loci.formats.ImageReader
  Gets all constituent file format readers.
getReadOutRate() - Method in class loci.formats.in.MetamorphHandler
getRealSTKFile(Location) - Method in class loci.formats.in.MetamorphReader
  Check that the given STK file exists.
getRecordedProcessor() - Method in class loci.plugins.util.BFVirtualStack
getRed(int) - Method in class loci.formats.gui.Index16ColorModel
getRed(int) - Method in class loci.formats.gui.SignedColorModel
getRed(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
getRegion() - Method in class loci.formats.in.TissueFAXSReader
getRegion(int) - Method in class loci.formats.in.TissueFAXSReader
getRelativeTime() - Method in class loci.formats.in.PrairieMetadata.Frame
  Gets the `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.in.TecanReader
getRequiredDirectories(String[]) - Method in class loci.formats.ReaderWrapper
getResolution() - Method in class loci.formats.FileStitcher
getResolution() - Method in class loci.formats.FormatReader
getResolution() - Method in class loci.formats.FormatWriter
getResolution() - Method in class loci.formats.ImageReader
getResolution() - Method in class loci.formats.ImageWriter
getResolution() - Method in interface loci.formats.IPyramidHandler
  Get the current resolution level.
getResolution() - Method in class loci.formats.ReaderWrapper
getResolution() - Method in class loci.formats.SubResolutionFormatReader
getResolution() - Method in class loci.formats.WrappedReader
getResolution() - Method in class loci.formats.WriterWrapper
getResolutionCount() - Method in class loci.formats.FormatReader
getResolutionCount() - Method in class loci.formats.FormatWriter
getResolutionCount() - Method in class loci.formats.ImageReader
getResolutionCount() - Method in class loci.formats.ImageWriter
getResolutionCount() - Method in interface loci.formats.IPyramidHandler
  Return the number of resolutions for the current series.
getResolutionCount(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
getResolutionIndex() - Method in class loci.formats.in.CellSensReader
  Get the current pyramid resolution, accounting for flattened resolutions as needed.
getResolutionLevels() - Method in class loci.formats.in.JPEG2000MetadataParser
  Returns the number of resolution levels the file JPEG 2000 data has.
getResolutionMultiplier() - Method in class loci.formats.tiff.IFD
  Retrieve the value by which to multiply the X and Y resolution so that the resolutions are in microns per pixel.
getResolutions() - Method in class loci.formats.FormatWriter
getResolutions() - Method in interface loci.formats.IFormatWriter
  Get a list of resolution objects for the current series.
getResolutions() - Method in class loci.formats.ImageWriter
getResolutions() - Method in class loci.formats.WriterWrapper
getResolutionSizeX(int, int) - Method in interface loci.formats.meta.IPyramidStore
  Retrieve the image width in pixels of the given pyramid resolution.
getResolutionSizeX(int, int) - Method in class loci.formats.ome.OMEPyramidStore
getResolutionSizeY(int, int) - Method in interface loci.formats.meta.IPyramidStore
  Retrieve the image height in pixels of the given pyramid resolution.
getResolutionSizeY(int, int) - Method in class loci.formats.ome.OMEPyramidStore
getResolutionUnitFromComment(IFD) - Method in class loci.formats.in.BaseTiffReader
  Extracts the resolution unit symbol from the comment field
getRestartMarkers() - Method in interface loci.formats.services.JPEGTurboService
getRestartMarkers() - Method in class loci.formats.services.JPEGTurboServiceImpl
getRevision(String[]) - Method in class loci.plugins.macro.LociFunctions
getRgbChannel(int, byte[]) - Method in class loci.formats.in.XLEFReader
  Returns single channel data for an rgb plane
getRGBChannelCount() - Method in class loci.formats.FormatReader
getRGBChannelCount() - Method in interface loci.formats.IFormatReader
  Gets the number of channels returned with each call to openBytes.
getRGBChannelCount() - Method in class loci.formats.ImageReader
getRGBChannelCount() - Method in class loci.formats.in.LeicaMicrosystemsMetadata.MultipleImagesReader
getRGBChannelCount() - Method in class loci.formats.ReaderWrapper
getRGBChannelCount() - Method in class loci.formats.WrappedReader
getRGBChannelCount(Double[]) - Method in class loci.plugins.macro.LociFunctions
getRoi() - Method in class loci.plugins.util.RecordedImageProcessor
getROIs() - Method in class loci.formats.in.ND2Handler
getROIs() - Method in class loci.formats.in.SPEReader.SpeHeader
  Method used to read and return meta data for upto 10 rectangular ROI's stored in the SPE header table
getROIsMode() - Method in class loci.plugins.in.ImporterOptions
getROIsModeInfo() - Method in class loci.plugins.in.ImporterOptions
getROIsModes() - Method in class loci.plugins.in.ImporterOptions
GetRootDirectory() - Method in class loci.formats.in.SlideBook7Reader.DataLoader
getRotationTransform(double) - Method in class loci.formats.FormatReader
  Construct an `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
getRowIndex() - Method in class loci.formats.internal.WellContainer
getRowsPerStrip() - Method in class loci.formats.tiff.IFD
  Retrieves the number of rows per strip for image (TIFF tag RowsPerStrip) from this IFD.
getSample(BitBuffer, CodecOptions) - Method in class loci.formats.codec.HuffmanCodec
  Deprecated.
getSample(RandomAccessInputStream, CodecOptions) - Method in class loci.formats.codec.HuffmanCodec
getSampleData() - Method in class loci.formats.in.ImarisHDFReader
getSamples(IFD, byte[]) - Method in class loci.formats.tiff.TiffParser
getSamples(IFD, byte[], int, int, long, long) - Method in class loci.formats.tiff.TiffParser
getSamples(IFD, byte[], int, int, long, long, int, int) - Method in class loci.formats.tiff.TiffParser
getSamplesPerPixel() - Method in class loci.formats.FormatWriter
  Retrieve the number of samples per pixel for the current series.
getSamplesPerPixel(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.
GetSBClassName() - Method in class loci.formats.in.SlideBook7Reader.ClassDecoder
getScale(int) - Method in class loci.formats.in.VentanaReader
getScaled(int) - Method in class org.libjpegturbo.turbojpeg.TJScalingFactor
  Returns the scaled value of `dimension`.
getScaledHeight(int, int) - Method in class org.libjpegturbo.turbojpeg.TJDecompressor
  Returns the height of the largest scaled down image that the TurboJPEG decompressor can generate without exceeding the desired image width and height.
getScaledWidth(int, int) - Method in class org.libjpegturbo.turbojpeg.TJDecompressor
  Returns the width of the largest scaled down image that the TurboJPEG decompressor can generate without exceeding the desired image width and height.
getScalingFactors() - Static method in class org.libjpegturbo.turbojpeg.TJ
  Returns a list of fractional scaling factors that the JPEG decompressor in this implementation of TurboJPEG supports.
getScanline(int) - Method in class loci.formats.codec.JPEGTileDecoder
getScanlinePad() - Method in class loci.formats.in.ND2Reader
getScanNames() - Method in class loci.formats.in.L2DReader
  Return a list of scan names.
getScanProfileXML() - Method in class loci.formats.in.VectraReader
  Returns an XML string corresponding to the ScanProfile node.
getScientificNotationPattern(int, int, int) - Static method in class loci.formats.out.DicomWriter
getScreenName() - Method in class loci.formats.in.ColumbusReader.MeasurementHandler
getSequence() - Method in class loci.formats.in.PrairieMetadata.Frame
  Gets the `<Sequence>` containing this `<Frame>`.
getSequence(int) - Method in class loci.formats.in.PrairieMetadata
  Gets the `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
getSeriesPerReaderIndex(int) - Method in class loci.formats.in.XLEFReader
  Returns the index of the series (tile) in the corresponding reader
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.DCIMGReader
getSeriesUsedFiles(boolean) - Method in class loci.formats.in.DeltavisionReader
getSeriesUsedFiles(boolean) - Method in class loci.formats.in.DicomReader
getSeriesUsedFiles(boolean) - Method in class loci.formats.in.FakeReader
getSeriesUsedFiles(boolean) - Method in class loci.formats.in.FilePatternReader
getSeriesUsedFiles(boolean) - Method in class loci.formats.in.FlexReader
getSeriesUsedFiles(boolean) - Method in class loci.formats.in.FujiReader
getSeriesUsedFiles(boolean) - Method in class loci.formats.in.FV1000Reader
getSeriesUsedFiles(boolean) - Method in class loci.formats.in.HamamatsuVMSReader
getSeriesUsedFiles(boolean) - Method in class loci.formats.in.HitachiReader
getSeriesUsedFiles(boolean) - Method in class loci.formats.in.ICSReader
getSeriesUsedFiles(boolean) - Method in class loci.formats.in.ImagicReader
getSeriesUsedFiles(boolean) - Method in class loci.formats.in.ImprovisionTiffReader
getSeriesUsedFiles(boolean) - Method in class loci.formats.in.InCellReader
getSeriesUsedFiles(boolean) - Method in class loci.formats.in.JDCEReader
getSeriesUsedFiles(boolean) - Method in class loci.formats.in.JEOLReader
getSeriesUsedFiles(boolean) - Method in class loci.formats.in.JPEGReader
getSeriesUsedFiles(boolean) - Method in class loci.formats.in.L2DReader
getSeriesUsedFiles(boolean) - Method in class loci.formats.in.LeicaReader
getSeriesUsedFiles(boolean) - Method in class loci.formats.in.LIFReader
getSeriesUsedFiles(boolean) - Method in class loci.formats.in.LOFReader
getSeriesUsedFiles(boolean) - Method in class loci.formats.in.MetamorphReader
getSeriesUsedFiles(boolean) - Method in class loci.formats.in.MetaxpressTiffReader
getSeriesUsedFiles(boolean) - Method in class loci.formats.in.MIASReader
getSeriesUsedFiles(boolean) - Method in class loci.formats.in.MicroCTReader
getSeriesUsedFiles(boolean) - Method in class loci.formats.in.MicromanagerReader
getSeriesUsedFiles(boolean) - Method in class loci.formats.in.NDPISReader
getSeriesUsedFiles(boolean) - Method in class loci.formats.in.NiftiReader
getSeriesUsedFiles(boolean) - Method in class loci.formats.in.NRRDReader
getSeriesUsedFiles(boolean) - Method in class loci.formats.in.OIRReader
getSeriesUsedFiles(boolean) - Method in class loci.formats.in.OlympusTileReader
getSeriesUsedFiles(boolean) - Method in class loci.formats.in.OMETiffReader
getSeriesUsedFiles(boolean) - Method in class loci.formats.in.OperettaReader
getSeriesUsedFiles(boolean) - Method in class loci.formats.in.PCORAWReader
getSeriesUsedFiles(boolean) - Method in class loci.formats.in.PDSReader
getSeriesUsedFiles(boolean) - Method in class loci.formats.in.PerkinElmerReader
getSeriesUsedFiles(boolean) - Method in class loci.formats.in.PrairieReader
getSeriesUsedFiles(boolean) - Method in class loci.formats.in.QTReader
getSeriesUsedFiles(boolean) - Method in class loci.formats.in.ScanrReader
getSeriesUsedFiles(boolean) - Method in class loci.formats.in.SEQReader
getSeriesUsedFiles(boolean) - Method in class loci.formats.in.SlidebookTiffReader
getSeriesUsedFiles(boolean) - Method in class loci.formats.in.SPCReader
getSeriesUsedFiles(boolean) - Method in class loci.formats.in.TCSReader
getSeriesUsedFiles(boolean) - Method in class loci.formats.in.TecanReader
getSeriesUsedFiles(boolean) - Method in class loci.formats.in.TiffReader
getSeriesUsedFiles(boolean) - Method in class loci.formats.in.TillVisionReader
getSeriesUsedFiles(boolean) - Method in class loci.formats.in.TissueFAXSReader
getSeriesUsedFiles(boolean) - Method in class loci.formats.in.TrestleReader
getSeriesUsedFiles(boolean) - Method in class loci.formats.in.VarianFDFReader
getSeriesUsedFiles(boolean) - Method in class loci.formats.in.VectraReader
getSeriesUsedFiles(boolean) - Method in class loci.formats.in.VisitechReader
getSeriesUsedFiles(boolean) - Method in class loci.formats.in.VolocityReader
getSeriesUsedFiles(boolean) - Method in class loci.formats.in.XLEFReader
getSeriesUsedFiles(boolean) - Method in class loci.formats.in.ZeissCZIReader
getSeriesUsedFiles(boolean) - Method in class loci.formats.in.ZeissLSMReader
getSeriesUsedFiles(boolean) - Method in class loci.formats.in.ZeissTIFFReader
getSeriesUsedFiles() - 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
GetSingleTimepointFile() - Method in class loci.formats.in.SlideBook7Reader.CImageGroup
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.in.LeicaMicrosystemsMetadata.MultipleImagesReader
getSizeC() - Method in class loci.formats.ReaderWrapper
getSizeC() - Method in class loci.formats.WrappedReader
getSizeC(Double[]) - Method in class loci.plugins.macro.LociFunctions
getSizeT() - Method in class loci.formats.DimensionSwapper
getSizeT() - Method in class loci.formats.FileStitcher
getSizeT() - Method in class loci.formats.FormatReader
getSizeT() - Method in interface loci.formats.IFormatReader
  Gets the size of the T dimension.
getSizeT() - Method in class loci.formats.ImageReader
getSizeT() - Method in class loci.formats.ReaderWrapper
getSizeT() - Method in class loci.formats.WrappedReader
getSizeT(Double[]) - Method in class loci.plugins.macro.LociFunctions
getSizeX() - Method in class loci.formats.DimensionSwapper
getSizeX() - Method in class loci.formats.FileStitcher
getSizeX() - Method in class loci.formats.FormatReader
getSizeX() - Method in class loci.formats.FormatWriter
getSizeX() - Method in interface loci.formats.IFormatReader
  Gets the size of the X dimension.
getSizeX() - Method in class loci.formats.ImageReader
getSizeX() - Method in class loci.formats.ReaderWrapper
getSizeX() - Method in class loci.formats.TileStitcher
getSizeX() - Method in class loci.formats.WrappedReader
getSizeX(Double[]) - Method in class loci.plugins.macro.LociFunctions
getSizeY() - Method in class loci.formats.DimensionSwapper
getSizeY() - Method in class loci.formats.FileStitcher
getSizeY() - Method in class loci.formats.FormatReader
getSizeY() - Method in class loci.formats.FormatWriter
getSizeY() - Method in interface loci.formats.IFormatReader
  Gets the size of the Y dimension.
getSizeY() - Method in class loci.formats.ImageReader
getSizeY() - Method in class loci.formats.ReaderWrapper
getSizeY() - Method in class loci.formats.TileStitcher
getSizeY() - Method in class loci.formats.WrappedReader
getSizeY(Double[]) - Method in class loci.plugins.macro.LociFunctions
getSizeZ() - Method in class loci.formats.DimensionSwapper
getSizeZ() - Method in class loci.formats.FileStitcher
getSizeZ() - Method in class loci.formats.FormatReader
getSizeZ() - Method in interface loci.formats.IFormatReader
  Gets the size of the Z dimension.
getSizeZ() - Method in class loci.formats.ImageReader
getSizeZ() - Method in class loci.formats.ReaderWrapper
getSizeZ() - Method in class loci.formats.WrappedReader
getSizeZ(Double[]) - Method in class loci.plugins.macro.LociFunctions
getSliceLabelBaseIndex() - Static method in class loci.plugins.util.LociPrefs
getSliceLabelPattern() - Static method in class loci.plugins.util.LociPrefs
GetSlideRootDirectory() - Method in class loci.formats.in.SlideBook7Reader.CSBFile70
getSnapshotPixels() - Method in class loci.plugins.util.RecordedImageProcessor
getSource() - Method in class loci.formats.cache.Cache
  Gets the cache's caching source.
getSource() - Method in class loci.formats.cache.CacheEvent
  Gets the source of the cache update.
getSpecifyRangesInfo() - Method in class loci.plugins.in.ImporterOptions
getSpectra() - Method in class loci.formats.in.IM3Reader
  If a Nuance file is a spectral library set (.csl) file, there is a spectral library inside that contains a profile of spectral bin magnitudes for each of several measured fluorophores (or auto fluorescence).
getSpeeds() - Method in class loci.formats.in.ND2Handler
getSplitChannelsInfo() - Method in class loci.plugins.in.ImporterOptions
getSplitFocalPlanesInfo() - Method in class loci.plugins.in.ImporterOptions
getSplitTimepointsInfo() - Method in class loci.plugins.in.ImporterOptions
getStackFormat() - Method in class loci.plugins.in.ImporterOptions
getStackFormatInfo() - Method in class loci.plugins.in.ImporterOptions
getStackFormats() - Method in class loci.plugins.in.ImporterOptions
getStackOrder() - Method in class loci.plugins.in.ImporterOptions
getStackOrder() - Method in class loci.plugins.in.ImportProcess
  Valid only after `ImportStep.STACK`.
getStackOrderInfo() - Method in class loci.plugins.in.ImporterOptions
getStackOrders() - Method in class loci.plugins.in.ImporterOptions
getStackSize() - Method in class loci.formats.in.SPEReader.SpeHeader
  Method used to determined the stack size of the SPE file.
getStackType(String) - Method in class loci.formats.in.CellSensReader
getStageLabel() - Method in class loci.formats.in.MetamorphHandler
getStagePosition(Double, 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
getStageX() - Method in class loci.formats.in.MetamorphReader
getStageY() - Method in class loci.formats.in.MetamorphReader
getStart(Hashtable<String, Object>) - Method in class loci.formats.in.MINCReader
getStartX() - Method in class loci.formats.in.SPEReader.SpeROI
getStartY() - Method in class loci.formats.in.SPEReader.SpeROI
getStatistics(int, int, double, double) - Method in class loci.plugins.util.VirtualImagePlus
getStep() - Method in class loci.formats.FilePattern
  Gets the STEP element for all blocks.
getStep() - Method in class loci.formats.FilePatternBlock
  Gets the difference between consecutive elements in a range block.
getStep(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
getStoredLength(DicomTag) - Method in class loci.formats.out.DicomWriter
getStrategy() - Method in class loci.formats.cache.Cache
  Gets the cache's caching strategy.
getStream(String) - Method in class loci.formats.in.DicomReader
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
GetStringArray(Node, String, Boolean, Boolean) - Method in class loci.formats.in.SlideBook7Reader.ClassDecoder
getStringOption(String) - Method in class loci.plugins.prefs.OptionsList
  Gets the string option with the given key.
getStringValue() - Method in class loci.formats.dicom.DicomTag
  Get a string representation of the current value.
GetStringValue(MappingNode, int, String, Boolean) - Method in class loci.formats.in.SlideBook7Reader.ClassDecoder
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.
getSubC(Modulo, int) - Static method in class loci.plugins.in.ImagePlusReader
getSubCTypes(Modulo) - Static method in class loci.plugins.in.ImagePlusReader
getSubIFDs(IFD) - Method in class loci.formats.tiff.TiffParser
  Returns the SUBIFDS belonging to a given IFD.
getSubimage(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
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 enum loci.formats.dicom.DicomAttribute
  Get the 4 byte integer tag.
getTag(String) - Static method in enum loci.formats.dicom.DicomAttribute
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 class loci.formats.dicom.DicomJSONProvider
getTags() - Method in interface loci.formats.dicom.ITagProvider
  Retrieve the tags defined by this provider.
getTags() - Method in class loci.formats.in.DicomReader
  Provide the complete hierarchy of DICOM tags.
getTags() - Method in interface loci.formats.services.EXIFService
getTags() - Method in class loci.formats.services.EXIFServiceImpl
getTBegin(int) - Method in class loci.plugins.in.ImporterOptions
getTBegin(int) - Method in class loci.plugins.in.ImportProcess
getTCount(int) - Method in class loci.plugins.in.ImportProcess
  Valid only after `ImportStep.SERIES`.
getTemperature() - Method in class loci.formats.in.MetamorphHandler
getTemperatures() - Method in class loci.formats.in.ND2Handler
getTEnd(int) - Method in class loci.plugins.in.ImporterOptions
getTEnd(int) - Method in class loci.plugins.in.ImportProcess
  Valid only after `ImportStep.STACK`.
getThumbnailIFDs() - Method in class loci.formats.in.MinimalTiffReader
  Gets the list of IFDs associated with the current TIFF's thumbnails.
getThumbnailIFDs() - Method in class loci.formats.tiff.TiffParser
  Returns thumbnail IFDs.
getThumbSizeX() - Method in class loci.formats.FileStitcher
getThumbSizeX() - Method in class loci.formats.FormatReader
getThumbSizeX() - Method in interface loci.formats.IFormatReader
  Get the size of the X dimension for the thumbnail.
getThumbSizeX() - Method in class loci.formats.ImageReader
getThumbSizeX() - Method in class loci.formats.in.LeicaSCNReader
getThumbSizeX() - Method in class loci.formats.in.MinimalTiffReader
getThumbSizeX() - Method in class loci.formats.in.VentanaReader
getThumbSizeX() - Method in class loci.formats.ReaderWrapper
getThumbSizeX() - Method in class loci.formats.WrappedReader
getThumbSizeY() - Method in class loci.formats.FileStitcher
getThumbSizeY() - Method in class loci.formats.FormatReader
getThumbSizeY() - Method in interface loci.formats.IFormatReader
  Get the size of the Y dimension for the thumbnail.
getThumbSizeY() - Method in class loci.formats.ImageReader
getThumbSizeY() - Method in class loci.formats.in.LeicaSCNReader
getThumbSizeY() - Method in class loci.formats.in.MinimalTiffReader
getThumbSizeY() - Method in class loci.formats.in.VentanaReader
getThumbSizeY() - Method in class loci.formats.ReaderWrapper
getThumbSizeY() - Method in class loci.formats.WrappedReader
getTIFFCompression() - Method in class loci.formats.out.DicomWriter
getTIFFCompression() - Method in class loci.formats.out.TiffWriter
  Get the TIFF compression enum value that corresponds to the current compression type.
getTiffFiles(String, char, int, int, int, int) - Method in class loci.formats.in.MetaxpressTiffReader
getTIFFList() - Method in class loci.formats.in.LeicaReader
getTiffs() - Method in class loci.formats.in.BDReader
getTile(DicomTile, byte[], int, int, int, int) - Method in class loci.formats.in.DicomReader
  Decompress pixel data associated with the given DicomTile.
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
  Get the uncompressed bytes representing the given bounding box.
getTile(int, int) - Method in interface loci.formats.services.JPEGTurboService
  Get the uncompressed bytes representing the given tile index.
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
getTileCodec(int) - Method in class loci.formats.ChannelFiller
getTileCodec(int) - Method in class loci.formats.ChannelMerger
getTileCodec(int) - Method in class loci.formats.ChannelSeparator
getTileCodec(int) - Method in class loci.formats.DimensionSwapper
getTileCodec(int) - Method in class loci.formats.FileStitcher
getTileCodec(int) - Method in interface loci.formats.ICompressedTileReader
  Retrieve a codec that can be used to decompress compressed tiles.
getTileCodec(int) - Method in class loci.formats.ImageReader
getTileCodec(int) - Method in class loci.formats.in.DicomReader
getTileCodec(DicomTile) - Method in class loci.formats.in.DicomReader
  Get a Codec that can be used to decompress the given tile.
getTileCodec(int) - Method in class loci.formats.in.NDPIReader
getTileCodec(int) - Method in class loci.formats.in.SVSReader
getTileCodec(int) - Method in class loci.formats.ReaderWrapper
getTileCodec(int) - Method in class loci.formats.TileStitcher
getTileCodecOptions(int, int, int) - Method in class loci.formats.ChannelFiller
getTileCodecOptions(int, int, int) - Method in class loci.formats.ChannelMerger
getTileCodecOptions(int, int, int) - Method in class loci.formats.ChannelSeparator
getTileCodecOptions(int, int, int) - Method in class loci.formats.DimensionSwapper
getTileCodecOptions(int, int, int) - Method in class loci.formats.FileStitcher
getTileCodecOptions(int, int, int) - Method in interface loci.formats.ICompressedTileReader
  Retrieve codec options that can be used to decompressed the specified tile.
getTileCodecOptions(int, int, int) - Method in class loci.formats.ImageReader
getTileCodecOptions(int, int, int) - Method in class loci.formats.in.DicomReader
getTileCodecOptions(DicomTile) - Method in class loci.formats.in.DicomReader
  Get a CodecOptions that can be used to decompress the given tile.
getTileCodecOptions(int, int, int) - Method in class loci.formats.in.NDPIReader
getTileCodecOptions(int, int, int) - Method in class loci.formats.in.SVSReader
getTileCodecOptions(int, int, int) - Method in class loci.formats.ReaderWrapper
getTileCodecOptions(int, int, int) - Method in class loci.formats.TileStitcher
getTileColumn(int, int, int) - Method in class loci.formats.in.VentanaReader
getTileColumns(int) - Method in class loci.formats.FormatReader
getTileColumns(int) - Method in interface loci.formats.ICompressedTileReader
  Get the number of columns of tiles in the specified plane in the current series.
getTileColumns(int) - Method in class loci.formats.ImageReader
getTileColumns(int) - Method in class loci.formats.in.DicomReader
getTileColumns(int) - Method in class loci.formats.in.NDPIReader
getTileColumns(int) - Method in class loci.formats.in.SVSReader
getTileColumns(int) - Method in class loci.formats.ReaderWrapper
getTileColumns() - Method in interface loci.formats.services.JPEGTurboService
getTileColumns() - Method in class loci.formats.services.JPEGTurboServiceImpl
getTileColumns(int) - Method in class loci.formats.TileStitcher
getTileCount() - Method in class loci.formats.in.LeicaMicrosystemsMetadata.XlifDocument
  Returns the number of tiles referenced by this xlif
getTileFilename(int, int, int, String) - Static method in class loci.formats.FormatTools
getTileHeight() - Method in interface loci.formats.services.JPEGTurboService
getTileHeight() - Method in class loci.formats.services.JPEGTurboServiceImpl
getTileIndex(int) - Method in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataStoreInitializer
getTileIndex(int) - Method in class loci.formats.in.LIFReader
getTileIndex(int) - Method in class loci.formats.in.LOFReader
getTileIndex(IFD, int, int) - Method in class loci.formats.in.MinimalTiffReader
  Get the index of the tile corresponding to given IFD (plane) and tile XY indexes.
getTileLength() - Method in class loci.formats.tiff.IFD
  Returns the length of an image tile.
getTileList(int, Region, boolean) - Method in class loci.formats.in.DicomReader
  Get a list of tiles corresponding to the given plane.
getTileRows(int) - Method in class loci.formats.FormatReader
getTileRows(int) - Method in interface loci.formats.ICompressedTileReader
  Get the number of rows of tiles in the specified plane in the current series.
getTileRows(int) - Method in class loci.formats.ImageReader
getTileRows(int) - Method in class loci.formats.in.DicomReader
getTileRows(int) - Method in class loci.formats.in.NDPIReader
getTileRows(int) - Method in class loci.formats.in.SVSReader
getTileRows(int) - Method in class loci.formats.ReaderWrapper
getTileRows() - Method in interface loci.formats.services.JPEGTurboService
getTileRows() - Method in class loci.formats.services.JPEGTurboServiceImpl
getTileRows(int) - Method in class loci.formats.TileStitcher
getTiles() - Method in class loci.formats.in.DicomReader
getTileSize() - Method in class loci.formats.in.CellSensReader
  Get the expected decompressed size of a single tile, in bytes.
getTileSizeX() - Method in class loci.formats.FormatWriter
getTileSizeX() - Method in interface loci.formats.IFormatWriter
  Retrieves the current tile width Defaults to 0 if not supported
getTileSizeX() - Method in class loci.formats.ImageWriter
getTileSizeX() - Method in class loci.formats.out.DicomWriter
getTileSizeX() - Method in class loci.formats.out.TiffWriter
getTileSizeX() - Method in class loci.formats.WriterWrapper
getTileSizeY() - Method in class loci.formats.FormatWriter
getTileSizeY() - Method in interface loci.formats.IFormatWriter
  Retrieves the current tile height Defaults to 0 if not supported
getTileSizeY() - Method in class loci.formats.ImageWriter
getTileSizeY() - Method in class loci.formats.out.DicomWriter
getTileSizeY() - Method in class loci.formats.out.TiffWriter
getTileSizeY() - Method in class loci.formats.WriterWrapper
getTilesPerColumn() - Method in class loci.formats.tiff.IFD
  Returns the number of image tiles per column.
getTilesPerRow() - Method in class loci.formats.tiff.IFD
  Returns the number of image tiles per row.
getTileWidth() - Method in interface loci.formats.services.JPEGTurboService
getTileWidth() - Method in class loci.formats.services.JPEGTurboServiceImpl
getTileWidth() - Method in class loci.formats.tiff.IFD
  Returns the width of an image tile.
getTime(Double, String) - Static method in class loci.formats.FormatTools
  Formats the input value for the time into a length of the given unit.
getTimeBinCount() - Method in class loci.formats.in.SDTReader
  Gets the number of bins in the lifetime histogram.
GetTimepointOfPath(String) - Method in class loci.formats.in.SlideBook7Reader.CSBFile70
getTimepoints() - Method in class loci.formats.in.ND2Handler
getTimestamp(String) - Method in class loci.formats.in.BDReader
getTimestamp() - Method in class loci.formats.in.DicomReader
getTimestamp(String) - Method in class loci.formats.in.SlidebookTiffReader
getTimestampIndex(String) - Method in class loci.formats.in.PCIReader
getTimestampMicroseconds(String) - Method in class loci.formats.in.DicomReader
  Convert the timestamp from a TM value to microseconds.
getTimestamps() - Method in class loci.formats.in.MetamorphHandler
getTotalPlaneHeaderSize() - Method in class loci.formats.in.DeltavisionReader
getTransferSyntax() - Method in class loci.formats.out.DicomWriter
getTransformedSizes() - Method in class org.libjpegturbo.turbojpeg.TJTransformer
  Returns an array containing the sizes of the transformed JPEG images from the most recent call to `transform()`.
getTreeCellRendererComponent(JTree, Object, boolean, boolean, boolean, int, boolean) - Method in class loci.formats.gui.XMLCellRenderer
getTStep(int) - Method in class loci.plugins.in.ImporterOptions
getTStep(int) - Method in class loci.plugins.in.ImportProcess
getType() - Method in class loci.formats.cache.CacheEvent
  Gets the type of cache update.
getType() - Method in class loci.formats.gui.TwoChannelColorSpace
getType() - Method in class loci.formats.in.PrairieMetadata.Sequence
  Gets the `type` associated with this `Sequence`.
getType(Object, boolean) - Static method in enum loci.formats.tiff.IFDType
  Get the type corresponding to the given value.
getType() - Method in class loci.formats.tiff.TiffIFDEntry
  Retrieves the entry's Type value.
getUID() - Method in class loci.formats.out.DicomWriter.UIDCreator
getUIDRoot() - Method in class loci.formats.out.DicomWriter
getUnderlyingReaders() - Method in class loci.formats.FileStitcher
getUnderlyingReaders() - Method in class loci.formats.FormatReader
getUnderlyingReaders() - Method in interface loci.formats.IFormatReader
  Retrieves all underlying readers.
getUnderlyingReaders() - Method in class loci.formats.ImageReader
getUnderlyingReaders() - Method in class loci.formats.ReaderWrapper
getUnderlyingReaders() - Method in class loci.formats.WrappedReader
getUngroupFilesInfo() - Method in class loci.plugins.in.ImporterOptions
getUpgradeCheckInfo() - Method in class loci.plugins.in.ImporterOptions
getUsedFile(Double, String[]) - Method in class loci.plugins.macro.LociFunctions
getUsedFileCount(Double[]) - Method in class loci.plugins.macro.LociFunctions
getUsedFiles() - Method in class loci.formats.FileStitcher
getUsedFiles(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.CV7000Reader
getUsedFiles(boolean) - Method in class loci.formats.in.FilePatternReader
getUsedFiles(boolean) - Method in class loci.formats.in.InveonReader
getUsedFiles(boolean) - Method in class loci.formats.in.KLBReader
getUsedFiles(boolean) - Method in class loci.formats.in.MetamorphTiffReader
getUsedFiles(boolean) - Method in class loci.formats.in.MetaxpressTiffReader
getUsedFiles(boolean) - Method in class loci.formats.in.OperettaReader
getUsedFiles(boolean) - Method in class loci.formats.in.SlideBook7Reader
getUsedFiles(boolean) - Method in class loci.formats.in.TecanReader
getUsedFiles(boolean) - Method in class loci.formats.in.UnisokuReader
getUsedFiles(boolean) - Method in class loci.formats.in.XLEFReader
getUsedFiles() - 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.
getValueStartPointer() - Method in class loci.formats.dicom.DicomTag
  Get the file pointer at which the value starts (useful for sequences and byte streams).
getVariableAttributes(String) - Method in interface loci.formats.services.NetCDFService
  Retrieves all of a variable's attributes.
getVariableAttributes(String) - Method in class loci.formats.services.NetCDFServiceImpl
getVariableList() - Method in interface loci.formats.services.NetCDFService
  Retrieves an exhaustive list of the HDF paths for all variables in the HDF document.
getVariableList() - Method in class loci.formats.services.NetCDFServiceImpl
getVariableValue(String) - Method in interface loci.formats.services.NetCDFService
  Retrieves a variable's value.
getVariableValue(String) - Method in class loci.formats.services.NetCDFServiceImpl
getVersion() - Method in class loci.formats.in.LiFlimReader
getVersionNumber(String[]) - Method in class loci.plugins.macro.LociFunctions
getVirtualInfo() - Method in class loci.plugins.in.ImporterOptions
getVirtualReader() - Method in class loci.plugins.in.ImportProcess
  Valid only after `ImportStep.STACK`.
getVoltage() - Method in class loci.formats.in.ND2Handler
getVolumeName(int) - Method in class loci.formats.in.CellSensReader
GetVoxelSize() - Method in class loci.formats.in.SlideBook7Reader.CImageGroup
getWaitTime() - Method in class loci.formats.in.PrairieMetadata
  Gets the `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
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
getWellIndex() - Method in class loci.formats.internal.WellContainer
getWellLabels(Connection) - Method in class loci.formats.in.TecanReader
getWellLink(PreparedStatement, String) - Method in class loci.formats.in.TecanReader
  Get the well identifier and field indexfor the given Id in the ImagingResult table.
getWellName(int, int) - Static method in class loci.formats.FormatTools
  Create a simple name for the well at the given row and column.
getWellName(String) - Method in class loci.formats.in.CellomicsReader
getWellRow(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
getWellRowName(int) - Static method in class loci.formats.FormatTools
  Create a simple name for the given row of wells.
getWidgets() - Method in class loci.plugins.config.CellSensWidgets
getWidgets() - Method in interface loci.plugins.config.IFormatWidgets
getWidgets() - Method in class loci.plugins.config.LIFWidgets
getWidgets() - Method in class loci.plugins.config.ND2Widgets
getWidgets() - Method in class loci.plugins.config.SDTWidgets
getWidgets() - Method in class loci.plugins.config.TiffDelegateWidgets
getWidgets() - Method in class loci.plugins.config.ZeissCZIWidgets
getWidth() - Method in class loci.formats.codec.JPEGTileDecoder
getWidth() - Method in enum loci.formats.dicom.DicomVR
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
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
getXlifs() - Method in class loci.formats.in.LeicaMicrosystemsMetadata.LMSCollectionXmlDocument
  Returns all XlifDocuments referenced by this and by all referenced XlcfDocuments
getXML() - Method in class loci.formats.tools.EditTiffG
GetXPosition(int) - Method in class loci.formats.in.SlideBook7Reader.CImageGroup
getXPositions() - Method in class loci.formats.in.ND2Handler
getXResolution() - Method in class loci.formats.tiff.IFD
  Retrieve the X resolution (TIFF tag XResolution) from this IFD.
getY(int) - Method in class loci.formats.in.FakeReader
getY(double[]) - Method in class loci.formats.in.TextReader
getYesNo(RandomAccessInputStream) - Method in class loci.formats.in.ZeissXRMReader
GetYPosition(int) - Method in class loci.formats.in.SlideBook7Reader.CImageGroup
getYPositions() - Method in class loci.formats.in.ND2Handler
getYResolution() - Method in class loci.formats.tiff.IFD
  Retrieve the Y resolution (TIFF tag YResolution) from this IFD.
getZ() - Method in class loci.formats.gui.ImageViewer
  Gets the Z value of the currently displayed image.
getZ(String) - Method in class loci.formats.in.OIRReader
getZBegin(int) - Method in class loci.plugins.in.ImporterOptions
getZBegin(int) - Method in class loci.plugins.in.ImportProcess
getZCount(int) - Method in class loci.plugins.in.ImportProcess
  Valid only after `ImportStep.SERIES`.
getZCTCoords(int) - Method in class loci.formats.ChannelMerger
getZCTCoords(int) - Method in class loci.formats.ChannelSeparator
getZCTCoords(int) - Method in class loci.formats.DimensionSwapper
getZCTCoords(int) - Method in class loci.formats.FileStitcher
getZCTCoords(int) - Method in class loci.formats.FormatReader
getZCTCoords(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.out.DicomWriter
getZCTCoords(int) - Method in class loci.formats.ReaderWrapper
getZCTCoords(int) - Method in class loci.formats.WrappedReader
getZCTCoords(Double, Double[], Double[], Double[]) - Method in class loci.plugins.macro.LociFunctions
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
getZOffsets() - Method in class loci.formats.in.DicomReader
getZoom() - Method in class loci.formats.in.MetamorphHandler
GetZPosition(int, int) - Method in class loci.formats.in.SlideBook7Reader.CImageGroup
getZPositions() - Method in class loci.formats.in.MetamorphHandler
getZPositions() - Method in class loci.formats.in.ND2Handler
getZSections() - Method in class loci.formats.in.ND2Handler
getZStep(int) - Method in class loci.plugins.in.ImporterOptions
getZStep(int) - Method in class loci.plugins.in.ImportProcess
GIF_MAGIC_STRING - Static variable in class loci.formats.in.GIFReader
GIFReader - Class in loci.formats.in
  GIFReader is the file format reader for Graphics Interchange Format (GIF) files.
GIFReader() - Constructor for class loci.formats.in.GIFReader
  Constructs a new GIF reader.
global - Variable in class loci.formats.in.BMPReader
  Offset to image data.
globalMetadata - Variable in class loci.formats.in.LeicaHandler
gradient(int, int, int) - Method in class loci.formats.tools.MakeTestOmeTiff
GRADIENT_LUT - Static variable in class loci.formats.in.CellSensReader
GRAPHICS - Static variable in class loci.formats.in.GIFReader
GRAPHICS_DOMAIN - Static variable in class loci.formats.FormatTools
  Identifies the graphics domain.
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
handleFilter(Element, int) - Method in class loci.formats.in.VectraReader
handleKeyValue(String, String) - Method in class loci.formats.in.MicromanagerReader
  Process a piece of metadata represented by a key/value pair.
handleMetadataStore(IFormatReader) - Method in class loci.formats.Memoizer
  Return the `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
handleReferencedFile(DicomTag, String) - Method in class loci.formats.in.DicomReader
handleSize - Variable in class loci.formats.in.BaseZeissReader.Shape
handleTXMMetadata(String, RandomAccessInputStream) - Method in class loci.formats.in.ZeissXRMReader
  Parse metadata fields specific to .txm files.
handleTXRMMetadata(String, RandomAccessInputStream) - Method in class loci.formats.in.ZeissXRMReader
  Parse metadata fields specific to .txrm files.
HARMONY_MAGIC - Static variable in class loci.formats.in.OperettaReader
harvestResults(GenericDialog) - Method in class loci.plugins.in.ColorDialog
harvestResults(GenericDialog) - Method in class loci.plugins.in.CropDialog
harvestResults(GenericDialog) - Method in class loci.plugins.in.FilePatternDialog
harvestResults(GenericDialog) - Method in class loci.plugins.in.IdDialog
harvestResults(GenericDialog) - Method in class loci.plugins.in.ImporterDialog
harvestResults(GenericDialog) - Method in class loci.plugins.in.LocationDialog
harvestResults(GenericDialog) - Method in class loci.plugins.in.MainDialog
harvestResults(GenericDialog) - Method in class loci.plugins.in.MemoryDialog
harvestResults(GenericDialog) - Method in class loci.plugins.in.RangeDialog
harvestResults(GenericDialog) - Method in class loci.plugins.in.SeriesDialog
harvestResults(GenericDialog) - Method in class loci.plugins.in.SwapDialog
harvestResults(GenericDialog) - Method in class loci.plugins.in.UpgradeDialog
HAS_EXTERNAL_FILE - Static variable in class loci.formats.in.CellSensReader
hasAbsoluteZ - Variable in class loci.formats.in.MetamorphReader
hasAbsoluteZValid - Variable in class loci.formats.in.MetamorphReader
HasAssociatedEtsFile - Variable in class loci.formats.in.CellSensReader.Pyramid
hasChipOffsets - Variable in class loci.formats.in.MetamorphReader
hasCompanionFiles - Variable in class loci.formats.FormatReader
  Whether this format supports multi-file datasets.
hasCompanionFiles() - Method in class loci.formats.FormatReader
hasCompanionFiles() - Method in interface loci.formats.IFormatReader
  Returns true if this format supports multi-file datasets.
hasCompanionFiles() - Method in class loci.formats.ImageReader
hasCompanionFiles() - Method in class loci.formats.in.FilePatternReader
hasCompanionFiles() - Method in class loci.formats.ReaderWrapper
hasCompanionFiles() - Method in class loci.formats.WrappedReader
hasDetectorSettings - Variable in class loci.formats.in.ZeissCZIReader
hasDualCamera() - Method in class loci.formats.in.MetamorphHandler
hasExtendedMeasureInfo - Variable in class loci.formats.in.SDTInfo
hasFlattenedResolutions() - Method in class loci.formats.FormatReader
hasFlattenedResolutions() - Method in interface loci.formats.IFormatReader
  Return whether or not resolution flattening is enabled.
hasFlattenedResolutions() - Method in class loci.formats.ImageReader
hasFlattenedResolutions() - Method in class loci.formats.in.FilePatternReader
hasFlattenedResolutions() - Method in class loci.formats.ReaderWrapper
hashCode() - Method in class loci.formats.in.CV7000Reader.Field
hashCode() - Method in class loci.formats.in.MetamorphTiffReader.Well
hashCode - Variable in class loci.formats.in.OIRReader.CZTKey
hashCode() - Method in class loci.formats.in.OIRReader.CZTKey
hashCode() - Method in class loci.formats.in.ZeissCZIReader.Coordinate
hashCode() - Method in class loci.formats.tiff.TiffRational
  Reasonable hash value for use with hashtables.
hashCode() - Method in class loci.plugins.config.FormatEntry
hashCode() - Method in class loci.plugins.prefs.OptionsList
hasInstrumentData - Variable in class loci.formats.in.ICSReader
hasMeasFCSInfo - Variable in class loci.formats.in.SDTInfo
hasMeasHISTInfo - Variable in class loci.formats.in.SDTInfo
hasMeasStopInfo - Variable in class loci.formats.in.SDTInfo
hasMeasureInfo - Variable in class loci.formats.in.SDTInfo
hasPaddingByte - Variable in class loci.formats.in.IvisionReader
hasPlaneReader - Variable in class loci.formats.in.AmiraReader
hasResolutions() - Method in class loci.formats.FormatWriter
hasSPW - Variable in class loci.formats.in.OMETiffReader
hasSPW - Variable in class loci.formats.in.OMEXMLReader
hasStagePositions - Variable in class loci.formats.in.MetamorphReader
HCS_DOMAIN - Static variable in class loci.formats.FormatTools
  Identifies the high content screening domain.
HDF_MAGIC_STRING - Static variable in class loci.formats.in.BDVReader
HDF_MAGIC_STRING - Static variable in class loci.formats.in.CellH5Reader
HDF_MAGIC_STRING - Static variable in class loci.formats.in.ImarisHDFReader
hdfReader - Variable in class loci.formats.services.JHDFServiceImpl
  Root of the HDF5 file.
hdfWriter - Variable in class loci.formats.services.JHDFServiceImpl
  Root of the HDF5 file.
HDRI_EXPOSURE_RANGE - Static variable in class loci.formats.in.CellSensReader
HDRI_FRAMES - Static variable in class loci.formats.in.CellSensReader
HDRI_MAP_MODE - Static variable in class loci.formats.in.CellSensReader
HDRI_ON - Static variable in class loci.formats.in.CellSensReader
HEADER - 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_LENGTH - Static variable in class loci.formats.in.DicomReader
HEADER_MARKER - Static variable in class loci.formats.in.VisitechReader
HEADER_SIZE - Static variable in class loci.formats.in.Ecat7Reader
HEADER_SIZE - Static variable in class loci.formats.in.GatanDM2Reader
HEADER_SIZE - Static variable in class loci.formats.in.I2IReader
HEADER_SIZE - Static variable in class loci.formats.in.INRReader
HEADER_SIZE - Static variable in class loci.formats.in.MRCReader
HEADER_SIZE - Static variable in class loci.formats.in.OpenlabRawReader
HEADER_SIZE - Static variable in class loci.formats.in.PovrayReader
HEADER_SIZE - Static variable in class loci.formats.in.PQBinReader
HEADER_SIZE - Static variable in class loci.formats.in.RHKReader
HEADER_SIZE - Static variable in class loci.formats.in.SBIGReader
HEADER_SIZE - Static variable in class loci.formats.in.SeikoReader
HEADER_SIZE - Static variable in class loci.formats.in.SMCameraReader
HEADER_SIZE - Static variable in class loci.formats.in.UBMReader
HEADER_SIZE - Static variable in class loci.formats.in.WATOPReader
HEADER_SIZE - Static variable in class loci.formats.in.ZeissCZIReader
headerIFDs - Variable in class loci.formats.in.LeicaReader
  Array of IFD-like structures containing metadata.
headerPixelType - Variable in class loci.formats.in.JPEG2000MetadataParser
  Pixel type as specified in the header.
headerSize - Variable in class loci.formats.in.DCIMGReader
headerSize - Variable in class loci.formats.in.FEIReader
headerSize - Variable in class loci.formats.in.KLBReader
headerSize - Variable in class loci.formats.in.MicroCTReader
headerSize - Variable in class loci.formats.in.OxfordInstrumentsReader
headerSize - Static variable in class loci.formats.in.SPEReader.SpeHeader
headerSize - Variable in class loci.formats.in.SpiderReader
headerSizeC - Variable in class loci.formats.in.JPEG2000MetadataParser
  Number of channels the image has as specified in the header.
headerSizeX - Variable in class loci.formats.in.JPEG2000MetadataParser
  Width of the image as specified in the header.
headerSizeY - Variable in class loci.formats.in.JPEG2000MetadataParser
  Height of the image as specified in the header.
headerValid - Variable in class loci.formats.in.SDTInfo
headerVersion - Variable in class loci.formats.in.KLBReader
height - Variable in class loci.formats.codec.CodecOptions
  Height, in pixels, of the image.
height - Variable in class loci.formats.in.BaseZeissReader.Shape
height - Variable in class loci.formats.in.CellSensReader.Pyramid
height - Variable in class loci.formats.in.CellVoyagerReader.AreaInfo
height - Variable in class loci.formats.in.CellVoyagerReader.ChannelInfo
height - Variable in class loci.formats.in.OpenlabReader.PlaneInfo
height - Variable in class loci.formats.in.SDTInfo
height - Variable in class loci.formats.tools.AmiraParameters
HELIOS_TAG - Static variable in class loci.formats.in.FEITiffReader
HELP_MENU - Static variable in class loci.plugins.shortcut.ShortcutPanel
  Name of the 'About Plugins' submenu.
helper - Variable in class loci.formats.gui.SignedColorModel
helper - Variable in class loci.formats.gui.SignedShortBuffer
helper - Variable in class loci.formats.gui.UnsignedIntColorModel
helper - Variable in class loci.formats.in.FilePatternReader
helper - Variable in class loci.formats.in.JDCEReader
helper - Variable in class loci.formats.in.NRRDReader
  Helper reader.
helperReader - Variable in class loci.formats.in.HitachiReader
helperReader - Variable in class loci.formats.in.OlympusTileReader
helperReader - Variable in class loci.formats.in.TecanReader
hex2Rgb(String) - Static method in class loci.formats.in.BDVReader
hex2Rgb(String) - Static method in class loci.formats.in.CellH5Reader
HIDDEN_LAYER - Static variable in class loci.formats.in.CellSensReader
HIGH_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
ICompressedTileReader - Interface in loci.formats
  Interface for reading pre-compressed image tiles.
ICompressedTileWriter - Interface in loci.formats
  Interface for writing pre-compressed image tiles.
icon - Variable in class loci.formats.gui.ImageViewer
icon - Variable in class loci.formats.gui.PreviewPane
iconLabel - Variable in class loci.formats.gui.ImageViewer
iconLabel - Variable in class loci.formats.gui.PreviewPane
  Labels containing thumbnail and dimensional information.
iconText - Variable in class loci.formats.gui.PreviewPane
iconTip - Variable in class loci.formats.gui.PreviewPane
ICSReader - Class in loci.formats.in
  ICSReader is the file format reader for ICS (Image Cytometry Standard) files.
ICSReader() - Constructor for class loci.formats.in.ICSReader
  Constructs a new ICSReader.
ICSWriter - Class in loci.formats.out
  ICSWriter is the file format writer for ICS files.
ICSWriter() - Constructor for class loci.formats.out.ICSWriter
id - Static variable in class loci.formats.filter.LZ4Filter
id - Variable in class loci.formats.gui.CacheComponent
  File name that the cache is working with (debugging only).
id - Variable in class loci.formats.in.BaseZeissReader.Shape
id - Variable in class loci.formats.in.FlexReader.FilterGroup
id - Variable in class loci.formats.in.LeicaHandler.Laser
id - Variable in enum loci.formats.in.LeicaMicrosystemsMetadata.Dimension.DimensionKey
id - Variable in class loci.formats.in.LeicaReader.Detector
id - Variable in class loci.formats.in.LIFReader.MemoryBlock
id - Variable in class loci.formats.in.OIRReader.Channel
id - Variable in class loci.formats.in.OIRReader.Detector
id - Variable in class loci.formats.in.OIRReader.Laser
id - Variable in class loci.formats.in.OMETiffReader.OMETiffPlane
  File containing this plane.
id - Variable in class loci.formats.in.TissueFAXSReader.Channel
id - Variable in class loci.formats.in.TissueFAXSReader.ScanRegion
id - Variable in class loci.formats.in.ZeissCZIReader.Segment
id - Variable in class loci.plugins.util.BFVirtualStack
idatCount - Variable in class loci.formats.in.APNGReader
IdDialog - Class in loci.plugins.in
  Bio-Formats Importer id chooser dialog box.
IdDialog(ImportProcess) - Constructor for class loci.plugins.in.IdDialog
  Creates an id chooser dialog for the Bio-Formats Importer.
IDENTIFIER - Static variable in class loci.formats.in.OIRReader
idLoc - Variable in class loci.plugins.in.ImportProcess
idName - Variable in class loci.plugins.in.ImportProcess
idx1Pos - Variable in class loci.formats.out.AVIWriter
IExtraMetadataWriter - Interface in loci.formats.out
ifd - Variable in class loci.formats.in.LeicaSCNReader.Dimension
ifd - Variable in class loci.formats.in.OMETiffReader.OMETiffPlane
  IFD number of this plane.
ifd - Variable in class loci.formats.in.VentanaReader.TIFFTile
IFD - Class in loci.formats.tiff
  Data structure for working with TIFF Image File Directories (IFDs).
IFD() - Constructor for class loci.formats.tiff.IFD
IFD(IFD) - Constructor for class loci.formats.tiff.IFD
ifdBuffer - Variable in class loci.formats.tiff.TiffSaver
ifdCounts - Variable in class loci.formats.out.OMETiffWriter
ifdIndex - Variable in class loci.formats.in.SVSCoreMetadata
IFDList - Class in loci.formats.tiff
  Data structure for working with a list of TIFF `IFD`s.
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.
ifds - Variable in class loci.formats.out.DicomWriter
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(Attributes) - Constructor for class loci.formats.in.LeicaSCNReader.Image
Image() - Constructor for class loci.formats.in.TecanReader.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_DETAILS - Static variable in class loci.formats.in.ZeissXRMReader
IMAGE_FRAME_VOLUME - Static variable in class loci.formats.in.CellSensReader
IMAGE_INFO_PATH - Static variable in class loci.formats.in.ZeissXRMReader
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
imageDirectory - Variable in class loci.formats.in.TecanReader
imageFile - Variable in class loci.formats.in.PCORAWReader
imageFileCSV - Variable in class loci.formats.in.JDCEReader
imageFiles - Variable in class loci.formats.in.BaseZeissReader
imageFiles - Variable in class loci.formats.in.InCellReader
imageFiles - Variable in class loci.formats.in.IPWReader
  List of embedded image file names (one per image plane).
imageFiles - Variable in class loci.formats.in.PCIReader
imageFolder - Variable in class loci.formats.in.CellVoyagerReader
ImageFormat() - Constructor for enum loci.formats.in.LeicaMicrosystemsMetadata.LMSFileReader.ImageFormat
imageFormat - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.MultipleImagesReader
imageFormat - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.XlifDocument
imageHeight - Variable in class loci.formats.in.InCellReader
imageHeight - Variable in class loci.formats.services.JPEGTurboServiceImpl
imageIFD(int) - Method in class loci.formats.in.LeicaSCNReader
imageIndex - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.MultipleImagesReader
ImageIOReader - Class in loci.formats.in
  ImageIOReader is the superclass for file format readers that use the javax.imageio package.
ImageIOReader(String, String) - Constructor for class loci.formats.in.ImageIOReader
  Constructs a new ImageIOReader.
ImageIOReader(String, String[]) - Constructor for class loci.formats.in.ImageIOReader
  Constructs a new ImageIOReader.
ImageIOWriter - Class in loci.formats.out
  ImageIOWriter is the superclass for file format writers that use the javax.imageio library.
ImageIOWriter(String, String, String) - Constructor for class loci.formats.out.ImageIOWriter
  Constructs an ImageIO-based writer with the given name, default 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
imageMetadataLVExists - Variable in class loci.formats.in.ND2Handler
imageMetadataLVOrder - Variable in class loci.formats.in.ND2Reader
imageMetadataLVProcessed - Variable in class loci.formats.in.ND2Reader
imageName - Variable in class loci.formats.in.BioRadSCNReader
imageName - Variable in class loci.formats.in.FEITiffReader
imageName - Variable in class loci.formats.in.ImaconReader
imageName - Variable in class loci.formats.in.MetamorphHandler
imageName - Variable in class loci.formats.in.MetamorphReader
  The TIFF's name
imageName - Variable in class loci.formats.in.SISReader
imageName - Variable in class loci.formats.in.ZeissCZIReader
imageNames - Variable in class loci.formats.in.BrukerReader
imageNames - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataTempBuffer
imageNames - Variable in class loci.formats.in.LIFReader
imageNames - Variable in class loci.formats.in.TillVisionReader
imageNames - Variable in class loci.formats.in.ZeissCZIReader
imageNames - Variable in class loci.formats.in.ZeissLSMReader
imageNumber - Variable in class loci.formats.in.APNGReader.PNGInputStream
imageNumEnd - Variable in class loci.formats.in.LeicaSCNReader.Image
imageNumStart - Variable in class loci.formats.in.LeicaSCNReader.Image
imageOffset - Variable in class loci.formats.in.IvisionReader
imagePaths - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.XlifDocument
imagePaths - Variable in class loci.formats.in.ZeissXRMReader
ImagePlusReader - Class in loci.plugins.in
  A high-level reader for `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.LeicaMicrosystemsMetadata.MetadataTempBuffer
imageROIs - Variable in class loci.formats.in.LIFReader
imageRX - Variable in class loci.formats.in.SDTInfo
imageRY - Variable in class loci.formats.in.SDTInfo
images - Variable in class loci.formats.gui.ImageViewer
images - Variable in class loci.formats.in.GIFReader
IMAGES - Static variable in class loci.formats.in.LeicaReader
images - Variable in class loci.formats.in.LeicaSCNReader.ImageCollection
images - Variable in class loci.formats.in.TecanReader
imagesDir - Variable in class loci.formats.in.OperettaReader
imageSequence - Variable in class loci.formats.in.DeltavisionReader
imagesNumber - Variable in class loci.formats.in.InCellReader
imagesPerFile - Variable in class loci.formats.FileStitcher.ExternalSeries
imagesPerFile - Variable in class loci.formats.in.DicomReader
imageThumbnail - Variable in class loci.formats.in.LeicaSCNReader.Image
ImageTools - Class in loci.formats
  A utility class with convenience methods for manipulating images in primitive array form.
ImageTools() - Constructor for class loci.formats.ImageTools
imageType - Variable in class loci.formats.dicom.DicomFileInfo
imageType - Variable in class loci.formats.in.DicomReader
ImageViewer - Class in loci.formats.gui
  ImageViewer is a simple viewer/converter for the Bio-Formats image formats.
ImageViewer() - Constructor for class loci.formats.gui.ImageViewer
  Constructs an image viewer.
ImageViewer(boolean) - Constructor for class loci.formats.gui.ImageViewer
  Constructs an image viewer.
imageWidth - Variable in class loci.formats.in.InCellReader
imageWidth - Variable in class loci.formats.services.JPEGTurboServiceImpl
ImageWriter - Class in loci.formats
  ImageWriter is the master file format writer for all supported formats.
ImageWriter() - Constructor for class loci.formats.ImageWriter
  Constructs a new ImageWriter with the default list of writer classes from writers.txt.
ImageWriter(ClassList<IFormatWriter>) - Constructor for class loci.formats.ImageWriter
  Constructs a new ImageWriter from the given list of writer classes.
imageX - Variable in class loci.formats.in.SDTInfo
  4 subsequent fields valid only for Camera mode or FIFO_IMAGE mode.
imageY - Variable in class loci.formats.in.SDTInfo
ImagicReader - Class in loci.formats.in
  ImagicReader is the file format reader for IMAGIC files.
ImagicReader() - Constructor for class loci.formats.in.ImagicReader
  Constructs a new IMAGIC reader.
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.LeicaMicrosystemsMetadata.MetadataTempBuffer
immersions - Variable in class loci.formats.in.LIFReader
IMODReader - Class in loci.formats.in
  Reader for IMOD binary files.
IMODReader() - Constructor for class loci.formats.in.IMODReader
  Constructs a new IMOD reader.
IMODSTAMP_OFFSET - Static variable in class loci.formats.in.MRCReader
imp - Variable in class loci.plugins.out.Exporter
  Current stack.
imp - Variable in class loci.plugins.Slicer
  Current image stack.
implementationUID - Variable in class loci.formats.out.DicomWriter
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.TecanReader.Channel
index - Variable in class loci.formats.in.VentanaReader.AreaOfInterest
index - Variable in class loci.formats.in.ZeissTIFFHandler.Tag
index - Variable in class loci.formats.Resolution
index - Variable in class loci.plugins.in.ThumbLoader.SeriesInfo
index - Variable in class loci.plugins.util.SearchableWindow
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
initChildren() - Method in class loci.formats.in.LeicaMicrosystemsMetadata.LMSCollectionXmlDocument
  Adds all referenced xlcfs and valid xlifs as children
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
initDetectorModels(int) - Method in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataStoreInitializer
  Adds detector and channel color details from the reader's `MetadataTempBuffer` to its `MetadataStore`
initExtraMetadata() - Method in class loci.formats.in.DeltavisionReader
initFile(String) - Method in class loci.formats.FileStitcher
  Initializes the given file or file pattern.
initFile(String) - Method in class loci.formats.FormatReader
  Initializes the given file (parsing header information, etc.).
initFile(String) - Method in class loci.formats.in.AFIReader
initFile(String) - Method in class loci.formats.in.AIMReader
initFile(String) - Method in class loci.formats.in.AliconaReader
initFile(String) - Method in class loci.formats.in.AmiraReader
initFile(String) - Method in class loci.formats.in.AnalyzeReader
initFile(String) - Method in class loci.formats.in.APLReader
initFile(String) - Method in class loci.formats.in.APNGReader
initFile(String) - Method in class loci.formats.in.ARFReader
initFile(String) - Method in class loci.formats.in.AVIReader
initFile(String) - Method in class loci.formats.in.BaseTiffReader
initFile(String) - Method in class loci.formats.in.BDReader
initFile(String) - Method in class loci.formats.in.BDVReader
initFile(String) - Method in class loci.formats.in.BioRadGelReader
initFile(String) - Method in class loci.formats.in.BioRadReader
initFile(String) - Method in class loci.formats.in.BioRadSCNReader
initFile(String) - Method in class loci.formats.in.BMPReader
initFile(String) - Method in class loci.formats.in.BrukerReader
initFile(String) - Method in class loci.formats.in.BurleighReader
initFile(String) - Method in class loci.formats.in.CanonRawReader
initFile(String) - Method in class loci.formats.in.CellH5Reader
initFile(String) - Method in class loci.formats.in.CellomicsReader
initFile(String) - Method in class loci.formats.in.CellSensReader
initFile(String) - Method in class loci.formats.in.CellVoyagerReader
initFile(String) - Method in class loci.formats.in.CellWorxReader
initFile(String) - Method in class loci.formats.in.ColumbusReader
initFile(String) - Method in class loci.formats.in.CV7000Reader
initFile(String) - Method in class loci.formats.in.DCIMGReader
initFile(String) - Method in class loci.formats.in.DeltavisionReader
initFile(String) - Method in class loci.formats.in.DicomReader
initFile(String) - Method in class loci.formats.in.DNGReader
initFile(String) - Method in class loci.formats.in.Ecat7Reader
initFile(String) - Method in class loci.formats.in.EPSReader
initFile(String) - Method in class loci.formats.in.FakeReader
initFile(String) - Method in class loci.formats.in.FEIReader
initFile(String) - Method in class loci.formats.in.FilePatternReader
initFile(String) - Method in class loci.formats.in.FitsReader
initFile(String) - Method in class loci.formats.in.FlexReader
initFile(String) - Method in class loci.formats.in.FlowSightReader
initFile(String) - Method in class loci.formats.in.FujiReader
initFile(String) - Method in class loci.formats.in.FV1000Reader
initFile(String) - Method in class loci.formats.in.GatanDM2Reader
initFile(String) - Method in class loci.formats.in.GatanReader
initFile(String) - Method in class loci.formats.in.GIFReader
initFile(String) - Method in class loci.formats.in.HamamatsuVMSReader
initFile(String) - Method in class loci.formats.in.HISReader
initFile(String) - Method in class loci.formats.in.HitachiReader
initFile(String) - Method in class loci.formats.in.HRDGDFReader
initFile(String) - Method in class loci.formats.in.I2IReader
initFile(String) - Method in class loci.formats.in.ICSReader
initFile(String) - Method in class loci.formats.in.IM3Reader
initFile(String) - Method in class loci.formats.in.ImageIOReader
initFile(String) - Method in class loci.formats.in.ImagicReader
initFile(String) - Method in class loci.formats.in.ImarisHDFReader
initFile(String) - Method in class loci.formats.in.ImarisReader
initFile(String) - Method in class loci.formats.in.ImarisTiffReader
initFile(String) - Method in class loci.formats.in.IMODReader
initFile(String) - Method in class loci.formats.in.ImspectorReader
initFile(String) - Method in class loci.formats.in.InCell3000Reader
initFile(String) - Method in class loci.formats.in.InCellReader
initFile(String) - Method in class loci.formats.in.INRReader
initFile(String) - Method in class loci.formats.in.InveonReader
initFile(String) - Method in class loci.formats.in.IPLabReader
initFile(String) - Method in class loci.formats.in.IPWReader
initFile(String) - Method in class loci.formats.in.IvisionReader
initFile(String) - Method in class loci.formats.in.JDCEReader
initFile(String) - Method in class loci.formats.in.JEOLReader
initFile(String) - Method in class loci.formats.in.JPEG2000Reader
initFile(String) - Method in class loci.formats.in.JPEGReader.DefaultJPEGReader
initFile(String) - Method in class loci.formats.in.JPXReader
initFile(String) - Method in class loci.formats.in.KhorosReader
initFile(String) - Method in class loci.formats.in.KLBReader
initFile(String) - Method in class loci.formats.in.KodakReader
initFile(String) - Method in class loci.formats.in.L2DReader
initFile(String) - Method in class loci.formats.in.LeicaReader
initFile(String) - Method in class loci.formats.in.LiFlimReader
initFile(String) - Method in class loci.formats.in.LIFReader
initFile(String) - Method in class loci.formats.in.LIMReader
initFile(String) - Method in class loci.formats.in.LOFReader
initFile(String) - Method in class loci.formats.in.MetamorphReader
initFile(String) - Method in class loci.formats.in.MetamorphTiffReader
initFile(String) - Method in class loci.formats.in.MIASReader
initFile(String) - Method in class loci.formats.in.MicroCTReader
initFile(String) - Method in class loci.formats.in.MicromanagerReader
initFile(String) - Method in class loci.formats.in.MINCReader
initFile(String) - Method in class loci.formats.in.MinimalTiffReader
initFile(String) - Method in class loci.formats.in.MNGReader
initFile(String) - Method in class loci.formats.in.MolecularImagingReader
initFile(String) - Method in class loci.formats.in.MRCReader
initFile(String) - Method in class loci.formats.in.MRWReader
initFile(String) - Method in class loci.formats.in.NAFReader
initFile(String) - Method in class loci.formats.in.ND2Reader
initFile(String) - Method in class loci.formats.in.NDPIReader
initFile(String) - Method in class loci.formats.in.NDPISReader
initFile(String) - Method in class loci.formats.in.NiftiReader
initFile(String) - Method in class loci.formats.in.NikonReader
initFile(String) - Method in class loci.formats.in.NRRDReader
initFile(String) - Method in class loci.formats.in.OBFReader
initFile(String) - Method in class loci.formats.in.OIRReader
initFile(String) - Method in class loci.formats.in.OlympusTileReader
initFile(String) - Method in class loci.formats.in.OMETiffReader
initFile(String) - Method in class loci.formats.in.OMEXMLReader
initFile(String) - Method in class loci.formats.in.OpenlabRawReader
initFile(String) - Method in class loci.formats.in.OpenlabReader
initFile(String) - Method in class loci.formats.in.OperettaReader
initFile(String) - Method in class loci.formats.in.OxfordInstrumentsReader
initFile(String) - Method in class loci.formats.in.PCIReader
initFile(String) - Method in class loci.formats.in.PCORAWReader
initFile(String) - Method in class loci.formats.in.PCXReader
initFile(String) - Method in class loci.formats.in.PDSReader
initFile(String) - Method in class loci.formats.in.PerkinElmerReader
initFile(String) - Method in class loci.formats.in.PGMReader
initFile(String) - Method in class loci.formats.in.PhotoshopTiffReader
initFile(String) - Method in class loci.formats.in.PictReader
initFile(String) - Method in class loci.formats.in.PovrayReader
initFile(String) - Method in class loci.formats.in.PQBinReader
initFile(String) - Method in class loci.formats.in.PrairieReader
initFile(String) - Method in class loci.formats.in.PSDReader
initFile(String) - Method in class loci.formats.in.QTReader
initFile(String) - Method in class loci.formats.in.QuesantReader
initFile(String) - Method in class loci.formats.in.RHKReader
initFile(String) - Method in class loci.formats.in.SBIGReader
initFile(String) - Method in class loci.formats.in.ScanrReader
initFile(String) - Method in class loci.formats.in.SDTReader
initFile(String) - Method in class loci.formats.in.SeikoReader
initFile(String) - Method in class loci.formats.in.SEQReader
initFile(String) - Method in class loci.formats.in.SIFReader
initFile(String) - Method in class loci.formats.in.SlideBook7Reader
initFile(String) - Method in class loci.formats.in.SlidebookReader
initFile(String) - Method in class loci.formats.in.SMCameraReader
initFile(String) - Method in class loci.formats.in.SPCReader
initFile(String) - Method in class loci.formats.in.SPEReader
initFile(String) - Method in class loci.formats.in.SpiderReader
initFile(String) - Method in class loci.formats.in.TargaReader
initFile(String) - Method in class loci.formats.in.TCSReader
initFile(String) - Method in class loci.formats.in.TecanReader
initFile(String) - Method in class loci.formats.in.TextReader
initFile(String) - Method in class loci.formats.in.TiffJAIReader
initFile(String) - Method in class loci.formats.in.TileJPEGReader
initFile(String) - Method in class loci.formats.in.TillVisionReader
initFile(String) - Method in class loci.formats.in.TissueFAXSReader
initFile(String) - Method in class loci.formats.in.TopometrixReader
initFile(String) - Method in class loci.formats.in.TrestleReader
initFile(String) - Method in class loci.formats.in.UBMReader
initFile(String) - Method in class loci.formats.in.UnisokuReader
initFile(String) - Method in class loci.formats.in.VarianFDFReader
initFile(String) - Method in class loci.formats.in.VeecoReader
initFile(String) - Method in class loci.formats.in.VGSAMReader
initFile(String) - Method in class loci.formats.in.VisitechReader
initFile(String) - Method in class loci.formats.in.VolocityClippingReader
initFile(String) - Method in class loci.formats.in.VolocityReader
initFile(String) - Method in class loci.formats.in.WATOPReader
initFile(String) - Method in class loci.formats.in.XLEFReader
initFile(String) - Method in class loci.formats.in.ZeissCZIReader
initFile(String) - Method in class loci.formats.in.ZeissLMSReader
initFile(String) - Method in class loci.formats.in.ZeissLSMReader
initFile(String) - Method in class loci.formats.in.ZeissTIFFReader
initFile(String) - Method in class loci.formats.in.ZeissXRMReader
initFile(String) - Method in class loci.formats.in.ZeissZVIReader
initFile(String) - Method in class loci.formats.in.ZipReader
initFile(String) - Method in class loci.formats.SubResolutionFormatReader
  Initializes the given file (parsing header information, etc.).
initFileMain(String) - Method in class loci.formats.in.BaseZeissReader
initFilterModels(int) - Method in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataStoreInitializer
  Adds filter details from the reader's `MetadataTempBuffer` to its `MetadataStore`
initFlexFile(String) - Method in class loci.formats.in.FlexReader
InitFrom() - Constructor for enum loci.formats.in.LeicaMicrosystemsMetadata.LMSXmlDocument.InitFrom
initFromFilepath(String) - Method in class loci.formats.in.LeicaMicrosystemsMetadata.LMSXmlDocument
initFromXmlString(String) - Method in class loci.formats.in.LeicaMicrosystemsMetadata.LMSXmlDocument
initialize(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(long, int, int, int, int, int) - Method in class loci.formats.in.SlideBook7Reader.CCompressionBase
Initialize(long, int, int, int, int, int, int) - Method in class loci.formats.in.SlideBook7Reader.CCompressionBase
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 the given stream, which represents an image of the given width and height.
initialize(RandomAccessInputStream, int, int) - Method in class loci.formats.services.JPEGTurboServiceImpl
initialize(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.
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.
initialUseLegacy - Variable in class loci.formats.in.JPEGReader
  setId may alter the "useLegacy" variable depending upon the type of JPEG encountered.
initImage() - Method in class loci.formats.in.ImageIOReader
initImageDetails(int) - Method in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataStoreInitializer
  Adds image and ROI details from the reader's `MetadataTempBuffer` to its `MetadataStore`
initImagePaths() - Method in class loci.formats.in.LeicaMicrosystemsMetadata.XlifDocument
  Searches the xml for referenced images and adds image paths
initIntArray(String, long[], long) - Method in interface loci.formats.services.JHDFService
  Creates an HDF5 dataset in path consisting of integers specified by bytes per pixel bpp.
initIntArray(String, long[], long) - Method in class loci.formats.services.JHDFServiceImpl
initLasers(int) - Method in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataStoreInitializer
  Adds laser and light source details from the reader's `MetadataTempBuffer` to its `MetadataStore`
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.LeicaMicrosystemsMetadata.MetadataStoreInitializer
  Translates metadata information from the reader's `MetadataTempBuffer` and adds it to its `MetadataStore`
initMetadataStore() - Method in class loci.formats.in.LeicaSCNReader
initMetadataStore() - Method in class loci.formats.in.LEOReader
initMetadataStore() - Method in class loci.formats.in.NDPIReader
initMetadataStore() - Method in class loci.formats.in.NikonElementsTiffReader
initMetadataStore() - Method in class loci.formats.in.NikonTiffReader
initMetadataStore() - Method in class loci.formats.in.PyramidTiffReader
initMetadataStore() - Method in class loci.formats.in.SimplePCITiffReader
initMetadataStore() - Method in class loci.formats.in.SISReader
initMetadataStore() - Method in class loci.formats.in.SlidebookTiffReader
initMetadataStore() - Method in class loci.formats.in.SVSReader
initMetadataStore() - Method in class loci.formats.in.TiffReader
initMetadataStore() - Method in class loci.formats.in.TrestleReader
initMetadataStore() - Method in class loci.formats.in.VectraReader
initMetadataStore() - Method in class loci.formats.in.VentanaReader
initMinMax() - Method in class loci.formats.MinMaxCalculator
  Ensures internal min/max variables are initialized properly.
initOMEMetadata() - Method in class loci.formats.in.LiFlimReader
initOriginalMetadata() - Method in class loci.formats.in.LiFlimReader
initPixels() - Method in class loci.formats.in.DeltavisionReader
initPlaneReader() - Method in class loci.formats.in.AmiraReader
initPOIService() - Method in class loci.formats.in.FV1000Reader
initPOIService() - Method in class loci.formats.in.IPWReader
initPOIService() - Method in class loci.formats.in.PCIReader
initPOIService() - Method in class loci.formats.in.ZeissXRMReader
initPOIService() - Method in class loci.formats.in.ZeissZVIReader
initReader(int, int) - Method in class loci.formats.FileStitcher
initReader(IFormatReader, String, boolean) - Method in class loci.formats.in.CellWorxReader
initReaders(List<String>) - Method in class loci.formats.in.LeicaMicrosystemsMetadata.MultipleImagesReader
  Creates an internal reader for each image file
initResFile(String) - Method in class loci.formats.in.FlexReader
  Initialize the dataset from a .res file.
initStack(long) - Method in class loci.formats.in.OBFReader
initStandardMetadata() - Method in class loci.formats.in.BaseTiffReader
  Parses standard metadata.
initStandardMetadata() - Method in class loci.formats.in.DNGReader
initStandardMetadata() - Method in class loci.formats.in.FEITiffReader
initStandardMetadata() - Method in class loci.formats.in.FluoviewReader
initStandardMetadata() - Method in class loci.formats.in.ImaconReader
initStandardMetadata() - Method in class loci.formats.in.ImprovisionTiffReader
initStandardMetadata() - Method in class loci.formats.in.IonpathMIBITiffReader
initStandardMetadata() - Method in class loci.formats.in.JPKReader
initStandardMetadata() - Method in class loci.formats.in.LeicaSCNReader
initStandardMetadata() - Method in class loci.formats.in.LEOReader
initStandardMetadata() - Method in class loci.formats.in.MetamorphReader
initStandardMetadata() - Method in class loci.formats.in.NDPIReader
initStandardMetadata() - Method in class loci.formats.in.NikonElementsTiffReader
initStandardMetadata() - Method in class loci.formats.in.NikonReader
initStandardMetadata() - Method in class loci.formats.in.NikonTiffReader
initStandardMetadata() - Method in class loci.formats.in.PyramidTiffReader
initStandardMetadata() - Method in class loci.formats.in.SEQReader
initStandardMetadata() - Method in class loci.formats.in.SimplePCITiffReader
initStandardMetadata() - Method in class loci.formats.in.SISReader
initStandardMetadata() - Method in class loci.formats.in.SlidebookTiffReader
initStandardMetadata() - Method in class loci.formats.in.SVSReader
initStandardMetadata() - Method in class loci.formats.in.TiffReader
initStandardMetadata() - Method in class loci.formats.in.TrestleReader
initStandardMetadata() - Method in class loci.formats.in.VectraReader
initStandardMetadata() - Method in class loci.formats.in.VentanaReader
initStandDetails(int) - Method in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataStoreInitializer
  Adds microscope and objective details from the reader's `MetadataTempBuffer` to its `MetadataStore`
initTiffParser() - Method in class loci.formats.in.LeicaSCNReader
initTiffParser() - Method in class loci.formats.in.LEOReader
initTiffParser() - Method in class loci.formats.in.MinimalTiffReader
  Reinitialize the underlying TiffParser.
initVars(String) - Method in class loci.formats.in.BaseZeissReader
initVars(String) - Method in class loci.formats.in.ZeissTIFFReader
initVars(String) - Method in class loci.formats.in.ZeissZVIReader
INK_NAMES - Static variable in class loci.formats.tiff.IFD
INK_SET - Static variable in class loci.formats.tiff.IFD
inPixels - Variable in class loci.formats.in.BDVReader.BDVXMLHandler
inPixels - Variable in class loci.formats.in.OMEXMLReader.OMEXMLHandler
input - Variable in class loci.formats.gui.DataConverter
input - Variable in class loci.formats.Memoizer.KryoDeser
inputOrder - Variable in class loci.formats.SwappableMetadata
  Order in which dimensions are stored.
inputOrder - Variable in class loci.plugins.in.ImporterOptions
INR_MAGIC - Static variable in class loci.formats.in.INRReader
INRReader - Class in loci.formats.in
  INRReader is the file format reader for INR files.
INRReader() - Constructor for class loci.formats.in.INRReader
  Constructs a new INR reader.
insert(ImageProcessor, int, int) - Method in class loci.plugins.util.RecordedImageProcessor
insertChannel(int, OIRReader.Channel) - Method in class loci.formats.in.OIRReader
  Insert the given Channel into the list of channels, at the given index.
insertResolution(OMEPyramidStore.Resolution, int, int) - Method in class loci.formats.ome.OMEPyramidStore
  Store the given Resolution object at the given indices.
insertWarningComment(String) - Method in class loci.formats.out.OMETiffWriter
install(String, 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
instanceUID - Variable in class loci.formats.in.DicomReader
instanceUIDValue - Variable in class loci.formats.out.DicomWriter
institutions - Variable in class loci.formats.in.BrukerReader
instrumentModel - Variable in class loci.formats.in.NDPIReader
instrumentType - Variable in class loci.formats.in.OperettaReader.OperettaHandler
INT - 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.
intensity - Variable in class loci.formats.in.TecanReader.Channel
intensity - Variable in class loci.formats.in.ZeissCZIReader.Channel
interlace - Variable in class loci.formats.in.APNGReader
interlace - Variable in class loci.formats.in.GIFReader
  Interlace flag.
interlaced - Variable in class loci.formats.codec.MJPBCodecOptions
  Indicates whether or not channels are interlaced.
interlaced - Variable in class loci.formats.in.QTReader
  Set to true if the scanlines in a plane are interlaced (mjpb only).
interleaved - Variable in class loci.formats.codec.CodecOptions
  Indicates whether or not channels are interleaved.
interleaved - Variable in class loci.formats.CoreMetadata
  True if channels are stored RGBRGBRGB...; false if channels are stored RRR...GGG...BBB...
interleaved - Variable in class loci.formats.FormatWriter
  Whether the channels in an RGB image are interleaved.
internalOffsets - Variable in class loci.formats.in.AmiraReader.HxRLE
internalStamps - Variable in class loci.formats.in.MetamorphReader
interpolate(short[], byte[], int[], int, int, boolean) - Static method in class loci.formats.ImageTools
intFormat(int, int) - Static method in class loci.formats.in.MetamorphReader
  Formats an integer value with leading 0s if needed.
intFormatMax(int, int) - Static method in class loci.formats.in.MetamorphReader
  Formats an integer with leading 0 using maximum sequence number.
IntIM3Record(String, int, long, int) - Constructor for class loci.formats.in.IM3Reader.IntIM3Record
IntIntPair(Integer, Integer) - Constructor for class loci.formats.in.SlideBook7Reader.IntIntPair
intValue() - Method in class loci.formats.tiff.TiffRational
  Returns the value of the specified number as an int.
INVALID_PIXELS - Static variable in class loci.formats.in.FEIReader
invalidAndMark(int) - Method in class loci.formats.in.SPCReader
invalidAndMarkInit(int) - Method in class loci.formats.in.SPCReader
InveonReader - Class in loci.formats.in
  InveonReader is the file format reader for Inveon files.
InveonReader() - Constructor for class loci.formats.in.InveonReader
  Constructs a new Inveon reader.
inverseRgb - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataTempBuffer
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_GLITCHED - Static variable in class loci.plugins.prefs.OptionsDialog
  Flag indicating whether to invoke workaround for AWT refresh bug.
IS_LITTLE - Static variable in class loci.formats.in.DCIMGReader
IS_LITTLE - Static variable in class loci.formats.in.ImarisReader
  Specifies endianness.
IS_TRANSMISSION - Static variable in class loci.formats.in.CellSensReader
isAllowedKey(String) - Method in class loci.formats.ClassList
  Returns whether a given key is an allowed option.
isAutoscale() - Method in class loci.plugins.in.ImporterOptions
isBGR(short[]) - Method in class loci.formats.services.JPEGXRServiceImpl
isBigTiff - Variable in class loci.formats.out.TiffWriter
  Whether or not the output file is a BigTIFF file.
isBigTiff() - Method in class loci.formats.tiff.IFD
  Gets whether this is a BigTIFF IFD.
isBigTiff() - Method in class loci.formats.tiff.TiffParser
  Returns whether or not the current TIFF file contains BigTIFF data.
isBigTiff() - Method in class loci.formats.tiff.TiffSaver
  Returns whether or not we are writing BigTIFF data.
isBitOnByteBoundary() - Method in class loci.formats.codec.BitBuffer
  Deprecated.
  Checks if the current position is on a byte boundary, that is the next bit in the byte array is the first bit in a byte.
isCellsensFailOnMissing() - Static method in class loci.plugins.util.LociPrefs
isCertain() - Method in class loci.formats.AxisGuesser
  Gets whether the guesser is confident that all axes are correct.
isColorLut() - Method in class loci.plugins.util.RecordedImageProcessor
isColorModeColorized() - Method in class loci.plugins.in.ImporterOptions
isColorModeComposite() - Method in class loci.plugins.in.ImporterOptions
isColorModeCustom() - Method in class loci.plugins.in.ImporterOptions
isColorModeDefault() - Method in class loci.plugins.in.ImporterOptions
isColorModeGrayscale() - Method in class loci.plugins.in.ImporterOptions
isCompatibleRaster(Raster) - Method in class loci.formats.gui.Index16ColorModel
isCompatibleRaster(Raster) - Method in class loci.formats.gui.SignedColorModel
isCompatibleRaster(Raster) - Method in class loci.formats.gui.UnsignedIntColorModel
isCompressed - Variable in class loci.formats.in.LIMReader
isConcatenate() - Method in class loci.plugins.in.ImporterOptions
isContainer(String) - Method in class loci.formats.in.QTReader
  Checks if the given String is a container atom type.
isCorrectionImage(TissueFAXSReader.ScanRegion) - Method in class loci.formats.in.TissueFAXSReader
isCS_sRGB() - Method in class loci.formats.gui.TwoChannelColorSpace
isCurrentFile(String) - Method in class loci.formats.in.OIRReader
isDeflate - Variable in class loci.formats.dicom.DicomTile
isDeflate - Variable in class loci.formats.in.DicomReader
isDimensions(String) - Method in class loci.formats.in.ND2Handler
  Returns whether or not the specified key is denotes dimensions.
isEnabled - Variable in class loci.formats.in.CellVoyagerReader.ChannelInfo
isEqual(OMEXMLMetadata, OMEXMLMetadata) - Method in interface loci.formats.services.OMEXMLService
  Determine whether or not two OMEXMLMetadata objects are equal.
isEqual(OMEXMLMetadata, OMEXMLMetadata) - Method in class loci.formats.services.OMEXMLServiceImpl
isExtendedDepthOfField() - Method in class loci.formats.in.DicomReader
isFalseColor() - Method in class loci.formats.FileStitcher
isFalseColor() - Method in class loci.formats.FormatReader
isFalseColor() - Method in interface loci.formats.IFormatReader
  Returns false if `IFormatReader.isIndexed()` is false, or 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.dicom.DicomTile
isJP2K - Variable in class loci.formats.in.DicomReader
isJPEG - Variable in class loci.formats.dicom.DicomTile
isJPEG - Variable in class loci.formats.in.BaseZeissReader
isJPEG - Variable in class loci.formats.in.DicomReader
isJPEG - Variable in class loci.formats.in.ND2Reader
  Whether or not the pixel data is compressed using JPEG 2000.
isLegacy() - Method in class loci.formats.DelegateReader
  Gets whether to use the legacy reader by default.
isLeicaLIFPhysicalSizeBackwardsCompatible() - Static method in class loci.plugins.util.LociPrefs
isLibraryLoaded() - Method in interface loci.formats.services.JPEGTurboService
isLibraryLoaded() - Method in class loci.formats.services.JPEGTurboServiceImpl
isLittleEndian() - Method in class loci.formats.FileStitcher
isLittleEndian() - Method in class loci.formats.FormatReader
isLittleEndian() - Method in interface loci.formats.IFormatReader
  Gets whether the data is in little-endian format.
isLittleEndian() - Method in class loci.formats.ImageReader
isLittleEndian() - Method in class loci.formats.ReaderWrapper
isLittleEndian() - Method in class loci.formats.tiff.IFD
  Gets whether the TIFF information in this IFD is little-endian.
isLittleEndian() - Method in class loci.formats.tiff.TiffSaver
  Returns whether or not we are writing little-endian data.
isLittleEndian() - Method in class loci.formats.WrappedReader
isLittleEndian(String[]) - Method in class loci.plugins.macro.LociFunctions
isLoadedFromMemo() - Method in class loci.formats.Memoizer
  Returns whether the `ReaderWrapper.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.ND2Handler
isLossless() - Method in class loci.formats.in.ND2Handler
isLossless - Variable in class loci.formats.in.ND2Reader
  Whether or not the pixel data is losslessly compressed.
isLutInverted - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.Channel
isMetadataComplete() - Method in class loci.formats.FormatReader
isMetadataComplete() - Method in interface loci.formats.IFormatReader
  Returns true if this format's metadata is completely parsed.
isMetadataComplete() - Method in class loci.formats.ImageReader
isMetadataComplete() - Method in class loci.formats.ReaderWrapper
isMetadataComplete() - Method in class loci.formats.WrappedReader
isMetadataComplete(String[]) - Method in class loci.plugins.macro.LociFunctions
isMetadataFiltered() - Method in class loci.formats.FormatReader
isMetadataFiltered() - Method in interface loci.formats.IFormatReader
  Returns true if ugly metadata (entries with unprintable characters, and extremely large entries) are discarded from the metadata table.
isMetadataFiltered() - Method in class loci.formats.ImageReader
isMetadataFiltered() - Method in class loci.formats.in.FilePatternReader
isMetadataFiltered() - Method in class loci.formats.ReaderWrapper
isMetadataFiltered(String[]) - Method in class loci.plugins.macro.LociFunctions
isMINC2 - Variable in class loci.formats.in.MINCReader
isMinimumMetadata() - Method in class loci.formats.in.PrairieReader
  Gets whether to populate only the minimum required metadata.
isMinMaxPopulated() - Method in class loci.formats.MinMaxCalculator
  Returns true if the values returned by getChannelGlobalMinimum/Maximum can be trusted.
isModulo - Variable in class loci.formats.tools.MakeTestOmeTiff
isNormalized() - Method in class loci.formats.FormatReader
isNormalized() - Method in interface loci.formats.IFormatReader
  Returns true if we should normalize float data.
isNormalized() - Method in class loci.formats.ImageReader
isNormalized() - Method in class loci.formats.in.FilePatternReader
isNormalized() - Method in class loci.formats.ReaderWrapper
isNormalized(Boolean[]) - Method in class loci.plugins.macro.LociFunctions
isNumeric() - Method in class loci.formats.FilePatternBlock
  Whether or not this is a numeric block.
ISO - Static variable in class loci.formats.in.NikonReader
ISO_SENSITIVITY - Static variable in class loci.formats.in.CellSensReader
ISO_SPEED_RATINGS - Static variable in class loci.formats.tiff.IFD
isOIB - Variable in class loci.formats.in.FV1000Reader
  Flag indicating this is an OIB dataset.
isOmero(String) - Method in class loci.formats.FormatReader
isOmero(String) - Method in class loci.formats.ImageReader
isOMERO() - Method in class loci.plugins.in.ImporterOptions
isOMEXMLMetadata(Object) - Method in interface loci.formats.services.OMEXMLService
  Checks whether the given object is an OME-XML metadata object.
isOMEXMLMetadata(Object) - Method in class loci.formats.services.OMEXMLServiceImpl
isOMEXMLRoot(Object) - Method in interface loci.formats.services.OMEXMLService
  Checks whether the given object is an OME-XML root object.
isOMEXMLRoot(Object) - Method in class loci.formats.services.OMEXMLServiceImpl
isOne() - Method in class org.libjpegturbo.turbojpeg.TJScalingFactor
  Returns true or false, depending on whether this instance is equal to 1/1.
isOrderCertain() - Method in class loci.formats.FileStitcher
isOrderCertain() - Method in class loci.formats.FormatReader
isOrderCertain() - Method in interface loci.formats.IFormatReader
  Gets whether the dimension order and sizes are known, or merely guesses.
isOrderCertain() - Method in class loci.formats.ImageReader
isOrderCertain() - Method in class loci.formats.ReaderWrapper
isOrderCertain() - Method in class loci.formats.WrappedReader
isOrderCertain(String[]) - Method in class loci.plugins.macro.LociFunctions
isOriginalMetadataPopulated() - Method in class loci.formats.FormatReader
isOriginalMetadataPopulated() - Method in interface loci.formats.IFormatReader
  Returns true if we should save proprietary metadata in the MetadataStore.
isOriginalMetadataPopulated() - Method in class loci.formats.ImageReader
isOriginalMetadataPopulated() - Method in class loci.formats.in.FilePatternReader
isOriginalMetadataPopulated() - Method in class loci.formats.ReaderWrapper
isOriginalMetadataPopulated(Boolean[]) - Method in class loci.plugins.macro.LociFunctions
isPositiveValue(Double) - Static method in class loci.formats.FormatTools
isPossible(String, String) - Method in class loci.plugins.prefs.OptionsList
  Gets whether the specified value is a possible one for the string option with the given key.
isPreviewName(String) - Method in class loci.formats.in.FV1000Reader
isPrivateContentCreator() - Method in class loci.formats.dicom.DicomTag
  See https://dicom.nema.org/dicom/2013/output/chtml/part05/sect_7.8.html
isPseudoColorLut() - Method in class loci.plugins.util.RecordedImageProcessor
isPyramidResolution(int, int) - Method in class loci.formats.in.NDPISReader
isQuiet() - Method in class loci.plugins.in.ImporterOptions
isRawCodestream - Variable in class loci.formats.in.JPEG2000MetadataParser
  Whether or not the codestream is raw and not JP2 boxed.
isRawCodestream() - Method in class loci.formats.in.JPEG2000MetadataParser
  Whether or not the codestream is raw and not JP2 boxed.
isReaderEnabled(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
isReallySequential() - Method in class loci.formats.out.DicomWriter
isRegex - Variable in class loci.formats.FilePattern
  Whether or not this FilePattern represents a regular expression.
isRegex() - Method in class loci.formats.FilePattern
  Returns whether or not this pattern is a regular expression.
isRGB() - Method in class loci.formats.ChannelFiller
isRGB() - Method in class loci.formats.ChannelMerger
isRGB() - Method in class loci.formats.ChannelSeparator
isRGB() - Method in class loci.formats.FileStitcher
isRGB() - Method in class loci.formats.FormatReader
isRGB() - Method in interface loci.formats.IFormatReader
  Checks if the image planes in the file have more than one channel per `IFormatReader.openBytes(int)` call.
isRGB() - Method in class loci.formats.ImageReader
isRGB() - Method in class loci.formats.in.LeicaMicrosystemsMetadata.MultipleImagesReader
isRGB() - Method in class loci.formats.ReaderWrapper
isRGB() - Method in class loci.formats.WrappedReader
isRLE - Variable in class loci.formats.dicom.DicomTile
isRLE - Variable in class loci.formats.in.DicomReader
isSaved() - Method in class loci.plugins.prefs.Option
  Gets whether option should be saved to ImageJ preferences file.
isSaved(String) - Method in class loci.plugins.prefs.OptionsList
  Gets whether the option with the given key is saved to the ImageJ preferences file.
isSavedToMemo() - Method in class loci.formats.Memoizer
  Returns whether the `ReaderWrapper.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.
IsSFMT(String) - Method in class loci.formats.in.SlideBook7Reader.CImageGroup
isShowMetadata() - Method in class loci.plugins.in.ImporterOptions
isShowOMEXML() - Method in class loci.plugins.in.ImporterOptions
isSigned(int) - Static method in class loci.formats.FormatTools
  Determines whether the given pixel type is signed or unsigned.
isSIM - Variable in class loci.formats.in.ZeissLSMReader
isSingleFile(String) - Method in class loci.formats.FormatReader
isSingleFile(String) - Method in interface loci.formats.IFormatReader
  Returns true if the named file is expected to be the only file in the dataset.
isSingleFile(String) - Method in class loci.formats.ImageReader
isSingleFile(String) - Method in class loci.formats.in.AFIReader
isSingleFile(String) - Method in class loci.formats.in.AnalyzeReader
isSingleFile(String) - Method in class loci.formats.in.APLReader
isSingleFile(String) - Method in class loci.formats.in.BDReader
isSingleFile(String) - Method in class loci.formats.in.BioRadReader
isSingleFile(String) - Method in class loci.formats.in.BrukerReader
isSingleFile(String) - Method in class loci.formats.in.CellSensReader
isSingleFile(String) - Method in class loci.formats.in.CellVoyagerReader
isSingleFile(String) - Method in class loci.formats.in.ColumbusReader
isSingleFile(String) - Method in class loci.formats.in.CV7000Reader
isSingleFile(String) - Method in class loci.formats.in.DCIMGReader
isSingleFile(String) - Method in class loci.formats.in.DeltavisionReader
isSingleFile(String) - Method in class loci.formats.in.FakeReader
isSingleFile(String) - Method in class loci.formats.in.FilePatternReader
isSingleFile(String) - Method in class loci.formats.in.FlexReader
isSingleFile(String) - Method in class loci.formats.in.FujiReader
isSingleFile(String) - Method in class loci.formats.in.FV1000Reader
isSingleFile(String) - Method in class loci.formats.in.HitachiReader
isSingleFile(String) - Method in class loci.formats.in.ICSReader
isSingleFile(String) - Method in class loci.formats.in.ImagicReader
isSingleFile(String) - Method in class loci.formats.in.InCellReader
isSingleFile(String) - Method in class loci.formats.in.JDCEReader
isSingleFile(String) - Method in class loci.formats.in.L2DReader
isSingleFile(String) - Method in class loci.formats.in.LeicaReader
isSingleFile(String) - Method in class loci.formats.in.MetamorphReader
isSingleFile(String) - Method in class loci.formats.in.MIASReader
isSingleFile(String) - Method in class loci.formats.in.MicroCTReader
isSingleFile(String) - Method in class loci.formats.in.MicromanagerReader
isSingleFile(String) - Method in class loci.formats.in.NDPISReader
isSingleFile(String) - Method in class loci.formats.in.NiftiReader
isSingleFile(String) - Method in class loci.formats.in.NRRDReader
isSingleFile(String) - Method in class loci.formats.in.OIRReader
isSingleFile(String) - Method in class loci.formats.in.OlympusTileReader
isSingleFile(String) - Method in class loci.formats.in.OMETiffReader
isSingleFile(String) - Method in class loci.formats.in.OperettaReader
isSingleFile(String) - Method in class loci.formats.in.PerkinElmerReader
isSingleFile(String) - Method in class loci.formats.in.PrairieReader
isSingleFile(String) - Method in class loci.formats.in.ScanrReader
isSingleFile(String) - Method in class loci.formats.in.SlideBook7Reader
isSingleFile(String) - Method in class loci.formats.in.SPCReader
isSingleFile(String) - Method in class loci.formats.in.TCSReader
isSingleFile(String) - Method in class loci.formats.in.TecanReader
isSingleFile(String) - Method in class loci.formats.in.TillVisionReader
isSingleFile(String) - Method in class loci.formats.in.VisitechReader
isSingleFile(String) - Method in class loci.formats.in.XLEFReader
isSingleFile(String) - Method in class loci.formats.in.ZeissLSMReader
isSingleFile(String) - Method in class loci.formats.in.ZeissTIFFReader
isSingleFile(String) - Method in class loci.formats.ReaderWrapper
isSingleFile(String) - Method in class loci.formats.WrappedReader
isSpecifyRanges() - Method in class loci.plugins.in.ImporterOptions
isSpectralMode() - Method in class loci.formats.in.PrairieMetadata.Sequence
isSplitChannels() - Method in class loci.plugins.in.ImporterOptions
isSplitFocalPlanes() - Method in class loci.plugins.in.ImporterOptions
isSplitTimepoints() - Method in class loci.plugins.in.ImporterOptions
isSpool - Variable in class loci.formats.in.SlidebookReader
isSPWStructure(String) - Method in class loci.formats.in.FakeReader
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(RandomAccessInputStream) - Method in class loci.formats.in.DCIMGReader
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.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(RandomAccessInputStream) - Method in class loci.formats.in.LOFReader
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.MetaxpressTiffReader
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.ND2Reader
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(RandomAccessInputStream) - Method in class loci.formats.in.QTReader
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.SlideBook7Reader
isThisType(String, boolean) - Method in class loci.formats.in.SlideBook7Reader
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.SlidebookReader
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.SlidebookTiffReader
isThisType(RandomAccessInputStream) - Method in class loci.formats.in.SMCameraReader
isThisType(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(String, boolean) - Method in class loci.formats.in.TecanReader
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(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.ZeissXRMReader
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.
isValid() - Method in class loci.formats.in.LeicaMicrosystemsMetadata.XlifDocument
isValidate() - Method in class loci.formats.in.DefaultMetadataOptions
isValidate() - Method in class loci.formats.in.DynamicMetadataOptions
isValidate() - Method in interface loci.formats.in.MetadataOptions
  Checks whether file validation has been set.
isValidHeader() - Method in class loci.formats.tiff.TiffParser
  Tests this stream to see if it represents a TIFF file.
isValidRange(int, int, int) - Static method in class loci.formats.tools.FakeImage
isVersionChecking() - Method in class loci.formats.Memoizer
  Returns whether or not version checking is done based upon major/minor version numbers.
isViewBrowser() - Method in class loci.plugins.in.ImporterOptions
isViewHyperstack() - Method in class loci.plugins.in.ImporterOptions
isViewImage5D() - Method in class loci.plugins.in.ImporterOptions
isViewNone() - Method in class loci.plugins.in.ImporterOptions
isViewStandard() - Method in class loci.plugins.in.ImporterOptions
isViewView5D() - Method in class loci.plugins.in.ImporterOptions
isVirtual() - Method in class loci.plugins.in.ImporterOptions
isWellAcquired(int, int) - Method in class loci.formats.in.CV7000Reader
isWhitelistedKey(String) - Method in class loci.formats.ClassList
  Deprecated.
  Use `ClassList.isAllowedKey(String)` instead.
isWindowless() - Method in class loci.plugins.in.ImporterOptions
isWindowless() - Method in class loci.plugins.in.ImportProcess
isWindowless(IFormatReader) - Static method in class loci.plugins.util.LociPrefs
  Gets whether windowless mode should be used when opening this reader's currently initialized dataset.
isWritableDirectory(File) - Method in class loci.formats.Memoizer
  Test if the given `File` instance is a writable directory.
isZlib - Variable in class loci.formats.in.BaseZeissReader
ITagProvider - Interface in loci.formats.dicom
  Interface used to provide DICOM tags.
italic - Variable in class loci.formats.in.BaseZeissReader.Shape
itemStateChanged(ItemEvent) - Method in class loci.plugins.config.CellSensWidgets
itemStateChanged(ItemEvent) - Method in class loci.plugins.config.ConfigWindow
itemStateChanged(ItemEvent) - Method in class loci.plugins.config.LIFWidgets
itemStateChanged(ItemEvent) - Method in class loci.plugins.config.ND2Widgets
itemStateChanged(ItemEvent) - Method in class loci.plugins.config.SDTWidgets
itemStateChanged(ItemEvent) - Method in class loci.plugins.config.TiffDelegateWidgets
itemStateChanged(ItemEvent) - Method in class loci.plugins.config.ZeissCZIWidgets
itemStateChanged(ItemEvent) - Method in class loci.plugins.in.MainDialog
  Handles toggling of mutually exclusive options.
itemStateChanged(ItemEvent) - Method in class loci.plugins.in.SwapDialog
iterateIn(RandomAccessInputStream, Long) - Method in class loci.formats.in.ND2Reader
  Function for iterating through ND2 metaAttributes
iterateIn(RandomAccessInputStream, Long, boolean) - Method in class loci.formats.in.ND2Reader
  Function for iterating through ND2 metaAttributes
IvisionHandler() - Constructor for class loci.formats.in.IvisionReader.IvisionHandler
IvisionReader - Class in loci.formats.in
  IvisionReader is the file format reader for IVision (.IPM) files.
IvisionReader() - Constructor for class loci.formats.in.IvisionReader
  Constructs a new Ivision reader.
IvisionReader.IvisionHandler - Class in loci.formats.in
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
JDCEReader - Class in loci.formats.in
  JDCEReader is the file format reader for Molecular Devices JDCE plates.
JDCEReader() - Constructor for class loci.formats.in.JDCEReader
  Constructs a new JDCE reader.
JDCEReader.JDCEWell - Class in loci.formats.in
JDCEReader.PlaneMetadata - Class in loci.formats.in
JDCEWell(int, int, int) - Constructor for class loci.formats.in.JDCEReader.JDCEWell
JEOLReader - Class in loci.formats.in
  JEOLReader is the file format reader for JEOL files.
JEOLReader() - Constructor for class loci.formats.in.JEOLReader
  Constructs a new JEOL reader.
jhdf - Variable in class loci.formats.in.BDVReader
jhdf - Variable in class loci.formats.in.CellH5Reader
jhdf - Variable in class loci.formats.out.CellH5Writer
JHDFService - Interface in loci.formats.services
  Utility class for working with NetCDF/HDF files.
JHDFServiceImpl - Class in loci.formats.services
  Utility class for working with HDF files.
JHDFServiceImpl() - Constructor for class loci.formats.services.JHDFServiceImpl
  Default constructor.
JPEG - 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

## K

kAnnotationRecordFilename - Static variable in class loci.formats.in.SlideBook7Reader.CSBFile70
kAuxDataFilename - Static variable in class loci.formats.in.SlideBook7Reader.CSBFile70
kBinaryFileSuffix - Static variable in class loci.formats.in.SlideBook7Reader.CSBFile70
kChannelRecordFilename - Static variable in class loci.formats.in.SlideBook7Reader.CSBFile70
kElapsedTimesFilename - Static variable in class loci.formats.in.SlideBook7Reader.CSBFile70
key - Variable in class loci.formats.dicom.DicomTag
key - Variable in class loci.formats.in.BaseZeissReader.Layer
key - Variable in class loci.formats.in.BioRadSCNReader.SCNHandler
key - Variable in class loci.formats.in.FEITiffReader.FEIHandler
key - Variable in class loci.formats.in.ImaconReader.ImaconHandler
key - Variable in class loci.formats.in.IvisionReader.IvisionHandler
key - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.Dimension
key - Variable in class loci.formats.in.ScanrReader.ScanrHandler
key - Variable in class loci.formats.in.ZeissTIFFHandler.Scaling
key - Variable in class loci.formats.in.ZeissTIFFHandler.Tag
key - Variable in class loci.formats.meta.OriginalMetadataAnnotation
key - Variable in class loci.plugins.prefs.Option
  Key name for ImageJ preferences file.
KEY_AUTOSCALE - Static variable in class loci.plugins.in.ImporterOptions
KEY_COLOR_MODE - Static variable in class loci.plugins.in.ImporterOptions
KEY_CONCATENATE - Static variable in class loci.plugins.in.ImporterOptions
KEY_CROP - Static variable in class loci.plugins.in.ImporterOptions
KEY_FIRST - Static variable in class loci.plugins.in.ImporterOptions
KEY_FORCE_THUMBS - Static variable in class loci.plugins.in.ImporterOptions
KEY_GROUP_FILES - Static variable in class loci.plugins.in.ImporterOptions
KEY_ID - Static variable in class loci.plugins.in.ImporterOptions
KEY_LOCATION - Static variable in class loci.plugins.in.ImporterOptions
KEY_MUST_GROUP - Static variable in class loci.plugins.in.ImporterOptions
KEY_OPEN_ALL_SERIES - Static variable in class loci.plugins.in.ImporterOptions
KEY_PREFIX - Static variable in class loci.plugins.prefs.Option
  Prefix to use for all plugins preferences.
KEY_QUIET - Static variable in class loci.plugins.in.ImporterOptions
KEY_ROIS_MODE - Static variable in class loci.plugins.in.ImporterOptions
KEY_SHOW_METADATA - Static variable in class loci.plugins.in.ImporterOptions
KEY_SHOW_OME_XML - Static variable in class loci.plugins.in.ImporterOptions
KEY_SHOW_ROIS - Static variable in class loci.plugins.in.ImporterOptions
KEY_SPECIFY_RANGES - Static variable in class loci.plugins.in.ImporterOptions
KEY_SPLIT_C - Static variable in class loci.plugins.in.ImporterOptions
KEY_SPLIT_T - Static variable in class loci.plugins.in.ImporterOptions
KEY_SPLIT_Z - Static variable in class loci.plugins.in.ImporterOptions
KEY_STACK_FORMAT - Static variable in class loci.plugins.in.ImporterOptions
KEY_STACK_ORDER - Static variable in class loci.plugins.in.ImporterOptions
KEY_STITCH_TILES - Static variable in class loci.plugins.in.ImporterOptions
KEY_SWAP_DIMS - Static variable in class loci.plugins.in.ImporterOptions
KEY_UNGROUP_FILES - Static variable in class loci.plugins.in.ImporterOptions
KEY_UPGRADE_CHECK - Static variable in class loci.plugins.in.ImporterOptions
KEY_VIRTUAL - Static variable in class loci.plugins.in.ImporterOptions
KEY_WINDOWLESS - Static variable in class loci.plugins.in.ImporterOptions
keyid - Variable in class loci.formats.in.BaseZeissReader.Tag
keyPressed(KeyEvent) - Method in class loci.formats.gui.ImageViewer
  Handles key presses.
keyReleased(KeyEvent) - Method in class loci.formats.gui.ImageViewer
KEYS - 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.
kImageDirSuffix - Static variable in class loci.formats.in.SlideBook7Reader.CSBFile70
kImageRecordFilename - Static variable in class loci.formats.in.SlideBook7Reader.CSBFile70
kind - Variable in class loci.formats.out.ImageIOWriter
KINETIC_CYCLE_TIME - Static variable in class loci.formats.in.FluoviewReader
KLB_DATA_DIMS - Static variable in class loci.formats.in.KLBReader
KLB_DEFAULT_HEADER_VERSION - Static variable in class loci.formats.in.KLBReader
KLB_METADATA_SIZE - Static variable in class loci.formats.in.KLBReader
KLBReader - Class in loci.formats.in
  Reader for Keller Lab Block (KLB) files.
KLBReader() - Constructor for class loci.formats.in.KLBReader
  Constructs a new BDV reader.
kMaskRecordFilename - Static variable in class loci.formats.in.SlideBook7Reader.CSBFile70
kMaxNumberOpenFiles - Static variable in class loci.formats.in.SlideBook7Reader.DataLoader
KNOWN_VERSIONS - Static variable in class loci.formats.in.LiFlimReader
kNumDigitsInTimepoint - Static variable in class loci.formats.in.SlideBook7Reader.CSBFile70
KodakReader - Class in loci.formats.in
  KodakReader is the file format reader for Kodak Molecular Imaging .bip files.
KodakReader() - Constructor for class loci.formats.in.KodakReader
  Constructs a new Kodak reader.
kRootDirSuffix - Static variable in class loci.formats.in.SlideBook7Reader.CSBFile70
kryo - Variable in class loci.formats.Memoizer.KryoDeser
KryoDeser() - Constructor for class loci.formats.Memoizer.KryoDeser
kSAPositionDataFilename - Static variable in class loci.formats.in.SlideBook7Reader.CSBFile70
kSlideSuffix - Static variable in class loci.formats.in.SlideBook7Reader.CSBFile70
kStagePositionDataFilename - Static variable in class loci.formats.in.SlideBook7Reader.CSBFile70
kZBinaryFileSuffix - Static variable in class loci.formats.in.SlideBook7Reader.CSBFile70
kZSlideSuffix - Static variable in class loci.formats.in.SlideBook7Reader.CSBFile70

## L

L2DReader - Class in loci.formats.in
  L2DReader is the file format reader for Li-Cor L2D datasets.
L2DReader() - Constructor for class loci.formats.in.L2DReader
  Construct a new L2D reader.
label - Variable in class loci.plugins.prefs.Option
  Label describing the option, for use with ImageJ dialogs.
LABEL_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
labelIndex - Variable in class loci.formats.in.SVSReader
labelPlanes - Variable in class loci.formats.in.FakeReader
labels - Variable in class loci.formats.in.FakeReader
labels - Variable in class loci.formats.in.ICSReader
  Dimensional reordering for lifetime data
labels - Variable in class loci.formats.Modulo
labels - Variable in class loci.plugins.config.CellSensWidgets
labels - Variable in class loci.plugins.config.FormatEntry
labels - Variable in class loci.plugins.config.LIFWidgets
labels - Variable in class loci.plugins.config.ND2Widgets
labels - Variable in class loci.plugins.config.SDTWidgets
labels - Variable in class loci.plugins.config.TiffDelegateWidgets
labels - Variable in class loci.plugins.config.ZeissCZIWidgets
LAMBDA - Static variable in class loci.formats.in.CellSensReader
LAMBDA_INCREMENT - Static variable in class loci.formats.in.CellSensReader
LAMBDA_START - Static variable in class loci.formats.in.CellSensReader
LAMBDA_VALUE - Static variable in class loci.formats.in.CellSensReader
LAMP_AGE - Static variable in class loci.formats.in.NDPIReader
Laser() - Constructor for class loci.formats.in.LeicaHandler.Laser
Laser() - Constructor for class loci.formats.in.OIRReader.Laser
Laser() - Constructor for class loci.formats.in.ZeissLSMReader.Laser
LASER_ACQUIRE - Static variable in class loci.formats.in.ZeissLSMReader
LASER_NAME - Static variable in class loci.formats.in.ZeissLSMReader
LASER_POWER - Static variable in class loci.formats.in.ZeissLSMReader
laserActive - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataTempBuffer
laserActive - Variable in class loci.formats.in.LIFReader
laserCount - Variable in class loci.formats.in.LeicaHandler
laserFrap - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataTempBuffer
laserFrap - Variable in class loci.formats.in.LIFReader
laserIDs - Variable in class loci.formats.in.NikonTiffReader
laserIndex - Variable in class loci.formats.in.OIRReader.Channel
laserIntensity - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataTempBuffer
laserIntensity - Variable in class loci.formats.in.LIFReader
lasers - Variable in class loci.formats.in.LeicaHandler
lasers - Variable in class loci.formats.in.OIRReader
laserWavelength - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataTempBuffer
laserWavelength - Variable in class loci.formats.in.LIFReader
last - Variable in class loci.formats.dicom.DicomTile
lastChannel - Variable in class loci.formats.in.BDVReader
lastChannel - Variable in class loci.formats.in.BioRadReader
lastChannel - Variable in class loci.formats.in.CellH5Reader
lastChannel - Variable in class loci.formats.in.FV1000Reader
lastChannel - Variable in class loci.formats.in.ImarisHDFReader
lastChannel - Variable in class loci.formats.in.LIFReader
lastChannel - Variable in class loci.formats.in.LOFReader
lastChannel - Variable in class loci.formats.in.ND2Reader
lastChannel - Variable in class loci.formats.in.OIRReader
lastCodeOffset - Variable in class loci.formats.in.AmiraReader.HxRLE
lastDispose - Variable in class loci.formats.in.GIFReader
lastFile - Variable in class loci.formats.in.CellWorxReader
lastFile - Variable in class loci.formats.in.ImprovisionTiffReader
lastFile - Variable in class loci.formats.in.SlidebookTiffReader
lastId - Variable in class loci.formats.gui.PreviewPane
  Last ID loaded.
lastIFD - Variable in class loci.formats.in.LeicaSCNReader.Pixels
lastImage - Variable in class loci.formats.ChannelSeparator
  Last image opened.
lastImage - Variable in class loci.formats.in.APNGReader
lastImage - Variable in class loci.formats.in.AVIReader
lastImage - Variable in class loci.formats.in.InCellReader.MinimalInCellHandler
lastImageHeight - Variable in class loci.formats.ChannelSeparator
  Height of last image opened.
lastImageIndex - Variable in class loci.formats.ChannelSeparator
  Index of last image opened.
lastImageIndex - Variable in class loci.formats.in.APNGReader
lastImageNo - Variable in class loci.formats.in.AVIReader
lastImageRow - Variable in class loci.formats.in.APNGReader
lastImageSeries - Variable in class loci.formats.ChannelSeparator
  Series of last image opened.
lastImageWidth - Variable in class loci.formats.ChannelSeparator
  Width of last image opened.
lastImageX - Variable in class loci.formats.ChannelSeparator
  X index of last image opened.
lastImageY - Variable in class loci.formats.ChannelSeparator
  Y index of last image opened.
lastIndex - Variable in class loci.formats.in.DNGReader
lastIndex - Variable in class loci.formats.in.NikonReader
lastMaxZ - Variable in class loci.formats.in.ImarisHDFReader
lastMinZ - Variable in class loci.formats.in.ImarisHDFReader
lastPlane - Variable in class loci.formats.in.BaseZeissReader
lastPlane - Variable in class loci.formats.in.DNGReader
lastPlane - Variable in class loci.formats.in.JPXReader
lastPlane - Variable in class loci.formats.in.LeicaReader
lastPlane - Variable in class loci.formats.in.MinimalTiffReader
lastPlane - Variable in class loci.formats.in.NikonReader
lastPlane - Variable in class loci.formats.in.NRRDReader
lastPlane - Variable in class loci.formats.in.OMETiffReader
lastPlane - Variable in class loci.formats.in.OpenlabReader
lastPlane - Variable in class loci.formats.in.TCSReader
lastPlane - Variable in class loci.formats.out.ICSWriter
lastPlane - Variable in class loci.formats.out.V3DrawWriter
lastReader - Variable in class loci.formats.in.CellWorxReader
lastRes - Variable in class loci.formats.in.ImarisHDFReader
lastSeries - Variable in class loci.formats.in.BrukerReader
lastSeries - Variable in class loci.formats.in.JPEG2000Reader
lastSeries - Variable in class loci.formats.in.JPXReader
lastSeriesPlane - Variable in class loci.formats.in.JPEG2000Reader
lastSeriesPlane - Variable in class loci.formats.in.JPXReader
lastT - Variable in class loci.formats.in.ImarisHDFReader
lastTimepoint - Variable in class loci.formats.in.BDVReader
LATEST_VERSION - Static variable in class loci.formats.services.OMEXMLServiceImpl
  Latest OME-XML version namespace.
Layer() - Constructor for class loci.formats.in.BaseZeissReader.Layer
layer_count - Variable in class loci.formats.in.ZeissTIFFHandler
LAYER_INFO_PROPERTIES - Static variable in class loci.formats.in.CellSensReader
LAYER_SELECTION - Static variable in class loci.formats.in.CellSensReader
LAYER_SELECTION_INDEX - Static variable in class loci.formats.in.CellSensReader
LAYER_XY_FIXED - Static variable in class loci.formats.in.CellSensReader
layerNames - Variable in class loci.formats.in.PhotoshopTiffReader
layerOffset - Variable in class loci.formats.in.PhotoshopTiffReader
layers - Variable in class loci.formats.in.BaseZeissReader
layers - Variable in class loci.formats.in.ZeissTIFFHandler
LAYOUT_KEYS - Static variable in class loci.formats.in.ICSReader
LAYOUT_TABLE - Static variable in class loci.formats.in.LiFlimReader
lblockNo - Variable in class loci.formats.in.SDTInfo
  Long blockNo - see remarks below.
legacyReader - Variable in class loci.formats.DelegateReader
  Legacy reader.
legacyReaderInitialized - Variable in class loci.formats.DelegateReader
  Flag indicating that the legacy reader was successfully initialized.
LEI_SUFFIX - Static variable in class loci.formats.in.LeicaReader
LEICA_MAGIC_TAG - Static variable in class loci.formats.in.LeicaReader
  All Leica TIFFs have this tag.
LeicaHandler - Class in loci.formats.in
  SAX handler for parsing XML in Leica LIF and Leica TCS files.
LeicaHandler(MetadataStore, MetadataLevel) - Constructor for class loci.formats.in.LeicaHandler
LeicaHandler(MetadataStore, MetadataLevel, boolean) - Constructor for class loci.formats.in.LeicaHandler
LeicaHandler.Channel - Class in loci.formats.in
LeicaHandler.Detector - Class in loci.formats.in
LeicaHandler.Laser - Class in loci.formats.in
LeicaHandler.MultiBand - Class in loci.formats.in
LeicaHandler.ROI - Class in loci.formats.in
LeicaReader - Class in loci.formats.in
  LeicaReader is the file format reader for Leica files.
LeicaReader() - Constructor for class loci.formats.in.LeicaReader
  Constructs a new Leica reader.
LeicaReader.Detector - Class in loci.formats.in
LeicaSCNHandler() - Constructor for class loci.formats.in.LeicaSCNReader.LeicaSCNHandler
LeicaSCNReader - Class in loci.formats.in
  LeicaSCNReader is the file format reader for Leica SCN TIFF files.
LeicaSCNReader() - Constructor for class loci.formats.in.LeicaSCNReader
  Constructs a new LeicaSCN reader.
LeicaSCNReader.Dimension - Class in loci.formats.in
LeicaSCNReader.Image - Class in loci.formats.in
LeicaSCNReader.ImageCollection - Class in loci.formats.in
LeicaSCNReader.LeicaSCNHandler - Class in loci.formats.in
  SAX handler for parsing XML in Leica SCN files.
LeicaSCNReader.Pixels - Class in loci.formats.in
leiFilename - Variable in class loci.formats.in.LeicaReader
  Name of current LEI file
len - Variable in class loci.plugins.util.BFVirtualStack
lenC - Variable in class loci.formats.FileStitcher
  Component lengths for each axis type.
length() - 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.LeicaMicrosystemsMetadata.Dimension
length - Variable in class loci.formats.in.ND2Reader.ChunkMapEntry
length - Variable in class loci.formats.in.OBFReader.Stack
length - Variable in class loci.formats.in.OIRReader.PixelBlock
length() - Method in class loci.formats.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.LeicaMicrosystemsMetadata.MetadataTempBuffer
lensNA - Variable in class loci.formats.in.LIFReader
lensNA - Variable in class loci.formats.in.MetamorphHandler
lensNA - Variable in class loci.formats.in.ND2Reader
lensNA - Variable in class loci.formats.in.NikonTiffReader
lensNA - Variable in class loci.formats.in.OperettaReader.Channel
lensNA - Variable in class loci.formats.in.OperettaReader.Plane
lensNA - Variable in class loci.formats.in.ZeissLSMReader.Recording
lensRI - Variable in class loci.formats.in.MetamorphHandler
lenT - Variable in class loci.formats.FileStitcher
  Component lengths for each axis type.
lenZ - Variable in class loci.formats.FileStitcher
  Component lengths for each axis type.
LEO_TAG - Static variable in class loci.formats.in.LEOReader
LEOReader - Class in loci.formats.in
  LEOReader is the file format reader for LEO EM files.
LEOReader() - Constructor for class loci.formats.in.LEOReader
  Constructs a new LEO reader.
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
libraryLoaded - Static variable in class loci.formats.services.JPEGTurboServiceImpl
libsList - Variable in class loci.plugins.config.ConfigWindow
libsListModel - Variable in class loci.plugins.config.ConfigWindow
license - Variable in class loci.plugins.config.ConfigWindow
license - Variable in class loci.plugins.config.LibraryEntry
LICOR_MAGIC_STRING - Static variable in class loci.formats.in.L2DReader
LIF_MAGIC_BYTE - Static variable in class loci.formats.in.LIFReader
LIF_MEMORY_BYTE - Static variable in class loci.formats.in.LIFReader
LIFETIME - 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.MemoryBlock - Class in loci.formats.in
LIFReader.ROI - Class in loci.formats.in
LIFWidgets - Class in loci.plugins.config
  Custom widgets for configuring Bio-Formats Leica LIF support.
LIFWidgets() - Constructor for class loci.plugins.config.LIFWidgets
LIGHT_SOURCE - Static variable in class loci.formats.tiff.IFD
LIGHT_TYPE - Static variable in class loci.formats.in.NikonReader
LightSource() - Constructor for class loci.formats.in.CV7000Reader.LightSource
lightSourceCombinationIDs - Variable in class loci.formats.in.FlexReader
lightSourceCombinationRefs - Variable in class loci.formats.in.FlexReader
lightSourceID - Variable in class loci.formats.in.FlexReader.FlexHandler
lightSourceIDs - Variable in class loci.formats.in.FlexReader
lightSourceIDs - Variable in class loci.formats.in.ZeissCZIReader
lightSourceRef - Variable in class loci.formats.in.ZeissCZIReader.Channel
lightSourceRefs - Variable in class loci.formats.in.CV7000Reader.Channel
lightSources - Variable in class loci.formats.in.CV7000Reader
limitHeight(JComponent) - Method in class loci.formats.gui.DataConverter
LIMReader - Class in loci.formats.in
  LIMReader is the file format reader for Laboratory Imaging/Nikon LIM files.
LIMReader() - Constructor for class loci.formats.in.LIMReader
  Constructs a new LIM reader.
line - Variable in class loci.formats.in.FakeReader.TextLine
LINE - 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.LeicaMicrosystemsMetadata.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.LeicaMicrosystemsMetadata.ROI
linewidth - Variable in class loci.formats.in.LIFReader.ROI
linkedInstruments - Variable in class loci.formats.in.LeicaHandler
LIPixelFormat - Class in loci.formats.in
LIPixelFormat() - Constructor for class loci.formats.in.LIPixelFormat
listeners - Variable in class loci.formats.cache.Cache
  List of cache event listeners.
listeners - Variable in class loci.formats.cache.CacheStrategy
  List of cache event listeners.
listeners - Variable in class loci.plugins.in.ImagePlusReader
listeners - Variable in class loci.plugins.in.ImportProcess
listFakeSeries(String) - Method in class loci.formats.in.FakeReader
  Traverses a fake file folder structure indicated by traversedDirectory
listString - Variable in class loci.formats.in.AVIReader
LITTLE - Static variable in class loci.formats.tiff.TiffConstants
LITTLE_ENDIAN - Static variable in class loci.formats.in.BioRadReader
  Always little endian.
LITTLE_ENDIAN - Static variable in class loci.formats.in.DeltavisionReader
LITTLE_ENDIAN - Static variable in class loci.formats.in.OBFReader
LITTLE_ENDIAN - Static variable in class loci.formats.in.TextReader
LITTLE_ENDIAN - Static variable in class loci.formats.tiff.IFD
littleEndian - Variable in class loci.formats.codec.CodecOptions
  Indicates endianness of pixel data.
littleEndian - Variable in class loci.formats.CoreMetadata
  Indicates whether or not each pixel's bytes are in little endian order.
littleEndian - Variable in class loci.formats.out.APNGWriter
littleEndian - Variable in class loci.formats.tools.AmiraParameters
LIVE_OVERFLOW - Static variable in class loci.formats.in.CellSensReader
LM_DOMAIN - Static variable in class loci.formats.FormatTools
  Identifies the light microscopy domain.
LMSCollectionXmlDocument - Class in loci.formats.in.LeicaMicrosystemsMetadata
  This class represents an LMS xml file that references other LMS xml files such as xlcfs and xlifs.
LMSCollectionXmlDocument(String, LMSCollectionXmlDocument) - Constructor for class loci.formats.in.LeicaMicrosystemsMetadata.LMSCollectionXmlDocument
LMSFileReader - Class in loci.formats.in.LeicaMicrosystemsMetadata
  This class can be extended by readers of Leica Microsystems file formats that include LASX generated XML (e.g.
LMSFileReader(String, String) - Constructor for class loci.formats.in.LeicaMicrosystemsMetadata.LMSFileReader
LMSFileReader.ImageFormat - Enum in loci.formats.in.LeicaMicrosystemsMetadata
  file format in which actual image bytes are stored
LMSImageXmlDocument - Class in loci.formats.in.LeicaMicrosystemsMetadata
  This class loads and represents a Leica Microsystems image XML document that contains image metadata
LMSImageXmlDocument(String) - Constructor for class loci.formats.in.LeicaMicrosystemsMetadata.LMSImageXmlDocument
LMSImageXmlDocument(String, LMSCollectionXmlDocument) - Constructor for class loci.formats.in.LeicaMicrosystemsMetadata.LMSImageXmlDocument
LMSMetadataExtractor - Class in loci.formats.in.LeicaMicrosystemsMetadata
  This class extracts metadata information from Leica Microsystems image XML and stores it in the reader's CoreMetadata and MetadataTempBuffer
LMSMetadataExtractor(LMSFileReader) - Constructor for class loci.formats.in.LeicaMicrosystemsMetadata.LMSMetadataExtractor
LMSXmlDocument - Class in loci.formats.in.LeicaMicrosystemsMetadata
  This class loads and represents a Leica Microsystems XML document (from file or xml string)
LMSXmlDocument(String) - Constructor for class loci.formats.in.LeicaMicrosystemsMetadata.LMSXmlDocument
LMSXmlDocument(String, LMSCollectionXmlDocument) - Constructor for class loci.formats.in.LeicaMicrosystemsMetadata.LMSXmlDocument
LMSXmlDocument.InitFrom - Enum in loci.formats.in.LeicaMicrosystemsMetadata
Load() - Method in class loci.formats.in.SlideBook7Reader.CImageGroup
load(String, File, boolean) - Static method in class loci.formats.Memoizer
load() - Static method in class org.libjpegturbo.turbojpeg.TJLoader
LoadAnnotations() - Method in class loci.formats.in.SlideBook7Reader.CImageGroup
LoadAuxData() - Method in class loci.formats.in.SlideBook7Reader.CImageGroup
LoadChannelRecord() - Method in class loci.formats.in.SlideBook7Reader.CImageGroup
loadedFromMemo - Variable in class loci.formats.Memoizer
  Whether the `ReaderWrapper.reader` instance currently active was loaded from the memo file during `Memoizer.setId(String)`.
LoadElapsedTimes() - Method in class loci.formats.in.SlideBook7Reader.CImageGroup
loader - Variable in class loci.formats.gui.PreviewPane
  Thumbnail loading thread.
loader - Variable in class loci.plugins.in.ThumbLoader
loaderAlive - Variable in class loci.formats.gui.PreviewPane
  Flag indicating whether loader thread should keep running.
loadId - Variable in class loci.formats.gui.PreviewPane
  Current ID to load.
loadImage(Image) - Static method in class loci.formats.gui.AWTImageTools
  Ensures the given AWT image is fully loaded.
LoadImageRecord() - Method in class loci.formats.in.SlideBook7Reader.CImageGroup
LoadMaks() - Method in class loci.formats.in.SlideBook7Reader.CImageGroup
loadManifest() - Static method in class loci.formats.FormatTools
loadMemo() - Method in class loci.formats.Memoizer
  Load a memo file if possible, returning a null if not.
LoadMetadata() - Method in class loci.formats.in.SlideBook7Reader.DataLoader
loadOption() - Method in class loci.plugins.prefs.BooleanOption
loadOption() - Method in class loci.plugins.prefs.DoubleOption
loadOption() - Method in class loci.plugins.prefs.Option
  Loads the option's value from the ImageJ preferences file.
loadOption() - Method in class loci.plugins.prefs.StringOption
loadOptions(String, ArrayList<String>) - Method in class loci.formats.in.DynamicMetadataOptions
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
LoadSAPositions() - Method in class loci.formats.in.SlideBook7Reader.CImageGroup
LoadStagePosition() - Method in class loci.formats.in.SlideBook7Reader.CImageGroup
loadStart(File) - Method in interface loci.formats.Memoizer.Deser
loadStart(File) - Method in class loci.formats.Memoizer.KryoDeser
loadStart(File) - Method in class loci.formats.Memoizer.RandomAccessDeser
loadStop() - Method in interface loci.formats.Memoizer.Deser
loadStop() - Method in class loci.formats.Memoizer.KryoDeser
loadStop() - Method in class loci.formats.Memoizer.RandomAccessDeser
loadStream - Variable in class loci.formats.Memoizer.RandomAccessDeser
loadThumb(BufferedImageReader, int, Panel, boolean) - Static method in class loci.plugins.in.ThumbLoader
loadVersion() - Method in interface loci.formats.Memoizer.Deser
loadVersion() - Method in class loci.formats.Memoizer.KryoDeser
loadVersion() - Method in class loci.formats.Memoizer.RandomAccessDeser
locateExperimentFile(String) - Method in class loci.formats.in.BDReader
locateFirstValidFile() - Method in class loci.formats.in.MetamorphReader
  Locates the first valid file in the STK arrays.
LOCATION_HTTP - Static variable in class loci.plugins.in.ImporterOptions
LOCATION_LOCAL - Static variable in class loci.plugins.in.ImporterOptions
LOCATION_OMERO - Static variable in class loci.plugins.in.ImporterOptions
LocationDialog - Class in loci.plugins.in
  Bio-Formats Importer location chooser dialog box.
LocationDialog(ImportProcess) - Constructor for class loci.plugins.in.LocationDialog
  Creates a location chooser dialog for the Bio-Formats Importer.
locator - Variable in class loci.formats.in.OMEXMLReader.OMEXMLHandler
loci.formats - package loci.formats
  Bio-Formats: a library for reading and writing popular microscopy file formats.
loci.formats.cache - package loci.formats.cache
  Package containing Bio-Formats caching logic, for managing subsets of large collections of image planes in memory.
loci.formats.codec - package loci.formats.codec
loci.formats.dicom - package loci.formats.dicom
loci.formats.filter - package loci.formats.filter
loci.formats.gui - package loci.formats.gui
  Package containing Bio-Formats graphical user interface code.
loci.formats.in - package loci.formats.in
  Package containing Bio-Formats file format readers.
loci.formats.in.LeicaMicrosystemsMetadata - package loci.formats.in.LeicaMicrosystemsMetadata
loci.formats.internal - package loci.formats.internal
  Package containing common classes for internal use by Bio-Formats readers/writers.
loci.formats.meta - package loci.formats.meta
  Package containing core Bio-Formats metadata interfaces for the OME data model.
loci.formats.ome - package loci.formats.ome
  Package containing Bio-Formats OME-related logic for OME-XML metadata, and database import, upload and download.
loci.formats.out - package loci.formats.out
  Package containing Bio-Formats file format writers.
loci.formats.services - package loci.formats.services
loci.formats.tiff - package loci.formats.tiff
  Package containing Bio-Formats TIFF code of general utility.
loci.formats.tools - package loci.formats.tools
  Package containing utility methods corresponding to the Bio-Formats command line tools.
loci.plugins - package loci.plugins
  Bio-Formats Plugins: a collection of plugins for ImageJ, including the Bio-Formats Importer, Bio-Formats Exporter, Bio-Formats Macro Extensions, Data Browser and Stack Slicer.
loci.plugins.config - package loci.plugins.config
  Bio-Formats Plugins Configuration plugin for ImageJ.
loci.plugins.in - package loci.plugins.in
  Bio-Formats Importer plugin for ImageJ.
loci.plugins.macro - package loci.plugins.macro
  Bio-Formats Macro Extensions plugin for ImageJ.
loci.plugins.out - package loci.plugins.out
  Bio-Formats Exporter plugin for ImageJ.
loci.plugins.prefs - package loci.plugins.prefs
  Classes for managing Bio-Formats plugins preferences.
loci.plugins.shortcut - package loci.plugins.shortcut
  Bio-Formats Plugins Shortcut Window plugin for ImageJ.
loci.plugins.util - package loci.plugins.util
  Utility classes and methods for the Bio-Formats plugins for ImageJ.
LociConfig - Class in loci.plugins.config
  An ImageJ plugin for displaying the Bio-Formats plugins configuration dialog.
LociConfig() - Constructor for class loci.plugins.config.LociConfig
LociExporter - Class in loci.plugins
  ImageJ plugin for writing files using the OME Bio-Formats package.
LociExporter() - Constructor for class loci.plugins.LociExporter
LociFunctions - Class in loci.plugins.macro
  This class provides macro extensions in ImageJ for Bio-Formats.
LociFunctions() - Constructor for class loci.plugins.macro.LociFunctions
LociImporter - Class in loci.plugins
  ImageJ plugin for reading files using the OME Bio-Formats package.
LociImporter() - Constructor for class loci.plugins.LociImporter
LociInstaller - Class in loci.plugins.config
  An ImageJ plugin for installing and upgrading libraries related to the Bio-Formats plugins.
LociInstaller() - Constructor for class loci.plugins.config.LociInstaller
LociPrefs - Class in loci.plugins.util
  Utility methods for ImageJ preferences for Bio-Formats plugins.
LociPrefs() - Constructor for class loci.plugins.util.LociPrefs
LOF_MAGIC_BYTE - Static variable in class loci.formats.in.LOFReader
LOF_MEMORY_BYTE - Static variable in class loci.formats.in.LOFReader
LOFReader - Class in loci.formats.in
  LOFReader is the file format reader for Leica Microsystems' LOF files.
LOFReader() - Constructor for class loci.formats.in.LOFReader
  Constructs a new Leica LOF reader.
LOFReader(XlifDocument) - Constructor for class loci.formats.in.LOFReader
LOFReader.MetadataSource - Enum in loci.formats.in
LofXmlDocument - Class in loci.formats.in.LeicaMicrosystemsMetadata
  This class loads and represents a Leica Microsystems XML document that has been extracted from a LOF file
LofXmlDocument(String, String) - Constructor for class loci.formats.in.LeicaMicrosystemsMetadata.LofXmlDocument
log - Static variable in class loci.formats.in.LeicaMicrosystemsMetadata.LMSFileReader
log - Variable in class loci.plugins.config.ConfigWindow
log() - Method in class loci.plugins.util.RecordedImageProcessor
logFile - Variable in class loci.formats.in.DeltavisionReader
logFiles - Variable in class loci.formats.in.CellWorxReader
LOGGER - Static variable in class loci.formats.cache.CacheUpdater
LOGGER - Static variable in class loci.formats.ChannelMerger
LOGGER - Static variable in class loci.formats.ClassList
LOGGER - Static variable in class loci.formats.codec.BaseCodec
LOGGER - Static variable in class loci.formats.dicom.DicomJSONProvider
LOGGER - Static variable in class loci.formats.FileStitcher
LOGGER - Static variable in class loci.formats.FormatHandler
LOGGER - Static variable in class loci.formats.FormatTools
LOGGER - Static variable in class loci.formats.gui.AWTImageTools
LOGGER - Static variable in class loci.formats.gui.CacheComponent
LOGGER - Static variable in class loci.formats.gui.DataConverter
LOGGER - Static variable in class loci.formats.gui.ImageViewer
LOGGER - Static variable in class loci.formats.gui.PreviewPane
LOGGER - Static variable in class loci.formats.ImageReader
LOGGER - Static variable in class loci.formats.ImageWriter
LOGGER - Static variable in class loci.formats.in.BaseTiffReader
  Logger for this class.
LOGGER - Static variable in class loci.formats.in.CV7000Reader
LOGGER - Static variable in class loci.formats.in.DNGReader
  Logger for this class.
LOGGER - Static variable in class loci.formats.in.DynamicMetadataOptions
LOGGER - Static variable in class loci.formats.in.IM3Reader
  Logger for outputting summary diagnostics.
LOGGER - Static variable in class loci.formats.in.ImarisTiffReader
  Logger for this class.
LOGGER - Static variable in class loci.formats.in.JPEG2000MetadataParser
  Logger for this class.
LOGGER - Static variable in class loci.formats.in.JPEG2000Reader
  Logger for this class.
LOGGER - Static variable in class loci.formats.in.JPXReader
  Logger for this class.
LOGGER - Static variable in class loci.formats.in.LeicaHandler
  Logger for this class.
LOGGER - Static variable in class loci.formats.in.LeicaMicrosystemsMetadata.LMSXmlDocument
LOGGER - Static variable in class loci.formats.in.LeicaReader
LOGGER - Static variable in class loci.formats.in.LeicaSCNReader
  Logger for this class.
LOGGER - Static variable in class loci.formats.in.MetamorphHandler
LOGGER - Static variable in class loci.formats.in.MetamorphReader
  Logger for this class.
LOGGER - Static variable in class loci.formats.in.MikroscanTiffReader
  Logger for this class.
LOGGER - Static variable in class loci.formats.in.MinimalTiffReader
  Logger for this class.
LOGGER - Static variable in class loci.formats.in.ND2Handler
LOGGER - Static variable in class loci.formats.in.NikonReader
  Logger for this class.
LOGGER - Static variable in class loci.formats.in.PyramidTiffReader
  Logger for this class.
LOGGER - Static variable in class loci.formats.in.SlideBook7Reader
LOGGER - Static variable in class loci.formats.in.SVSReader
  Logger for this class.
LOGGER - Static variable in class loci.formats.in.TecanReader
LOGGER - Static variable in class loci.formats.in.TiffReader
  Logger for this class.
LOGGER - Static variable in class loci.formats.in.TissueFAXSReader
LOGGER - Static variable in class loci.formats.in.TrestleReader
  Logger for this class.
LOGGER - Static variable in class loci.formats.in.VectraReader
  Logger for this class.
LOGGER - Static variable in class loci.formats.in.VentanaReader
  Logger for this class.
LOGGER - Static variable in class loci.formats.in.ZeissTIFFHandler
LOGGER - Static variable in class loci.formats.Memoizer
  Default `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.AmiraParameters
LOGGER - Static variable in class loci.formats.tools.EditTiffG
LOGGER - Static variable in class loci.formats.tools.FakeImage
LOGGER - Static variable in class loci.formats.UpgradeChecker
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.dicom.DicomAttribute
lookup - Static variable in enum loci.formats.dicom.DicomVR
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.
lookupChannel(CV7000Reader.Plane) - Method in class loci.formats.in.CV7000Reader
lookupChannelIndex(String) - Method in class loci.formats.in.TecanReader
lookupChild(DicomAttribute) - Method in class loci.formats.dicom.DicomTag
  Find the first child tag with the given attribute, or null if one does not exist.
lookupDimension(int, int, int) - Method in class loci.formats.in.LeicaSCNReader.Pixels
lookupFile(int, 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
lookupImage(int, int, boolean, boolean) - Method in class loci.formats.in.TecanReader
lookupPlane(int, 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.
lookupTag(String, JSONObject) - Method in class loci.formats.dicom.DicomJSONProvider
  Get the tag code corresponding to the given JSON object.
lookupTag(List<DicomTag>, DicomTag) - Method in class loci.formats.out.DicomWriter
lookupVR(Integer, JSONObject) - Method in class loci.formats.dicom.DicomJSONProvider
  Get the VR associated with the given tag code and JSON object.
lookupWell(int, int, int) - Method in class loci.formats.in.JDCEReader
lossless - Variable in class loci.formats.codec.CodecOptions
  Used with codecs allowing lossy and lossless compression.
LOSSLESS_DECODER_CONFIGURATION_12 - Static variable in class loci.formats.codec.NikonCodec
LOSSLESS_DECODER_CONFIGURATION_14 - Static variable in class loci.formats.codec.NikonCodec
LosslessJPEGCodec - Class in loci.formats.codec
  Decompresses lossless JPEG images.
LosslessJPEGCodec() - Constructor for class loci.formats.codec.LosslessJPEGCodec
LOSSY_DECODER_CONFIGURATION_12 - Static variable in class loci.formats.codec.NikonCodec
LOSSY_DECODER_CONFIGURATION_14 - Static variable in class loci.formats.codec.NikonCodec
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
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.
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.
lutName - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.Channel
lutNames - Variable in class loci.formats.in.FV1000Reader
lutNames - Variable in class loci.formats.in.LeicaHandler
lutNames - Variable in class loci.formats.in.LIFReader
luts - Variable in class loci.formats.in.OpenlabReader
luts - Variable in class loci.plugins.util.VirtualImagePlus
LZ4Filter - Class in loci.formats.filter
LZ4Filter(Map<String, Object>) - Constructor for class loci.formats.filter.LZ4Filter
LZ4Filter.LZ4FilterProvider - Class in loci.formats.filter
LZ4FilterProvider() - Constructor for class loci.formats.filter.LZ4Filter.LZ4FilterProvider
LZOCodec - Class in loci.formats.codec
  This class implements LZO decompression.
LZOCodec() - Constructor for class loci.formats.codec.LZOCodec
LZW - 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
MACRO_IMAGE - Static variable in class loci.formats.in.CellSensReader
macroFile - Variable in class loci.formats.in.HamamatsuVMSReader
MacroFunctions - Class in loci.plugins.macro
  Convenience class that simplifies implemention of ImageJ macro extensions.
MacroFunctions() - Constructor for class loci.plugins.macro.MacroFunctions
macroIndex - Variable in class loci.formats.in.SVSReader
mActualMagnification - Variable in class loci.formats.in.SlideBook7Reader.CLensDef70
mag - Variable in class loci.formats.in.FluoviewReader
mag - Variable in class loci.formats.in.GatanReader
mag - Variable in class loci.formats.in.ND2Handler
MAG_MULTIPLIER - Static variable in class loci.formats.in.FEITiffReader
MAGIC - Static variable in class loci.formats.in.AnalyzeReader
MAGIC - Static variable in class loci.formats.in.BioRadSCNReader
MAGIC - Static variable in class loci.formats.in.ColumbusReader
MAGIC - Static variable in class loci.formats.in.HitachiReader
MAGIC_BYTES - Static variable in class loci.formats.in.BioRadGelReader
MAGIC_NUMBER - Static variable in class loci.formats.in.OBFReader
MAGIC_NUMBER - Static variable in class loci.formats.tiff.TiffConstants
MAGIC_STRING - Static variable in class loci.formats.in.HRDGDFReader
MAGIC_STRING - Static variable in class loci.formats.in.IMODReader
MAGIC_STRING - Static variable in class loci.formats.in.ImspectorReader
  The header for each file contains this string.
MAGIC_STRING - Static variable in class loci.formats.in.KodakReader
MAGIC_STRING - Static variable in class loci.formats.in.MolecularImagingReader
MAGIC_STRING - Static variable in class loci.formats.in.SIFReader
MAGIC_STRING - Static variable in class loci.formats.in.SimplePCITiffReader
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.LeicaMicrosystemsMetadata.MetadataTempBuffer
magnification - Variable in class loci.formats.in.LIFReader
magnification - Variable in class loci.formats.in.NDPIReader
magnification - Variable in class loci.formats.in.NikonTiffReader
magnification - Variable in class loci.formats.in.OIRReader.Objective
magnification - Variable in class loci.formats.in.OperettaReader.Channel
magnification - Variable in class loci.formats.in.OperettaReader.Plane
magnification - Variable in class loci.formats.in.SimplePCITiffReader
magnification - Variable in class loci.formats.in.SISReader
magnification - Variable in class loci.formats.in.SVSReader
magnification - Variable in class loci.formats.in.VentanaReader
magnification - Variable in class loci.formats.in.VolocityReader.Stack
magnification - Variable in class loci.formats.in.ZeissLSMReader.Recording
MAGNIFICATION_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
  Build a list of files that belong with the current file.
makeFilterMetadata() - Method in class loci.formats.FormatReader
  Return a properly configured loci.formats.meta.FilterMetadata.
makeFilterMetadata() - Method in class loci.formats.in.LeicaMicrosystemsMetadata.LMSFileReader
makeGrid(Container, int, int, int, int, int, int) - Static method in class loci.plugins.config.SpringUtilities
  Aligns the first `rows` * `cols` components of `parent` in a grid.
makeHeavyPanel(Component) - Static method in class loci.plugins.util.DataBrowser
  Makes AWT play nicely with Swing components.
makeIFD() - Method in class loci.formats.out.PyramidOMETiffWriter
makeIFD() - Method in class loci.formats.out.TiffWriter
makeImage(byte[], int, int, boolean) - Static method in class loci.formats.gui.AWTImageTools
  Creates an image from the given 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.
makeItem() - Method in class loci.formats.out.DicomWriter
makeItemDelimitation() - Method in class loci.formats.out.DicomWriter
makeJTree(Document) - Static method in class loci.formats.gui.XMLCellRenderer
  Constructs a Swing JTree that displays the given XML DOM document.
makeLabel(String, boolean) - Method in class loci.plugins.config.ConfigWindow
makeLabel(String, int, int) - Method in class loci.plugins.in.ColorDialog
makeList(DefaultListModel) - Method in class loci.plugins.config.ConfigWindow
makeLUT(int, int) - Method in class loci.plugins.in.Colorizer
makeLUT(Color) - Method in class loci.plugins.in.Colorizer
makeLUTs(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'.
makeShortArray(int) - Method in class loci.formats.out.DicomWriter
makeSplitPane(JList, JPanel) - Method in class loci.plugins.config.ConfigWindow
makeStack(ImageStack) - Method in class loci.plugins.Slicer
  Returns a new ImageStack using the given ImageStack as a template.
MakeTestOmeTiff - Class in loci.formats.tools
  Creates sample OME-TIFF datasets according to the given parameters.
MakeTestOmeTiff() - Constructor for class loci.formats.tools.MakeTestOmeTiff
MakeTestOmeTiff.TextLine - Class in loci.formats.tools
makeTextField() - Static method in class loci.plugins.config.ConfigWindow
makeTileStitcher(IFormatReader) - Static method in class loci.formats.TileStitcher
  Converts the given reader into a TileStitcher, wrapping if needed.
makeTreeNode(Node) - Static method in class loci.formats.gui.XMLCellRenderer
  Recursively builds JTree node structure from DOM node structure.
makeUnsigned(BufferedImage) - Static method in class loci.formats.gui.AWTImageTools
  Converts the given BufferedImage into an image with unsigned pixel data.
makeValidIFD(IFD, int, int) - Method in class loci.formats.tiff.TiffSaver
  Makes a valid IFD.
makeWellLabel(int, int) - Method in class loci.formats.in.TecanReader
mAlgorythm - Variable in class loci.formats.in.SlideBook7Reader.CCompressionBase
mAlignManipRecordList - Variable in class loci.formats.in.SlideBook7Reader.CImageGroup
mAltSourcePosition - Variable in class loci.formats.in.SlideBook7Reader.CFluorDef70
mAnn - Variable in class loci.formats.in.SlideBook7Reader.CCubeAnnotation70
mAnn - Variable in class loci.formats.in.SlideBook7Reader.CFRAPRegionAnnotation70
mAnn - Variable in class loci.formats.in.SlideBook7Reader.CUnknownAnnotation70
mAnnotationList - Variable in class loci.formats.in.SlideBook7Reader.CImageGroup
mAnnotationTablePtr - Variable in class loci.formats.in.SlideBook7Reader.CImageRecord70
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
MARKER_TAG_HIGH_BYTES - 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
mAuxCaptureFlags - Variable in class loci.formats.in.SlideBook7Reader.CExposureRecord70
mAuxDataTablePtr - Variable in class loci.formats.in.SlideBook7Reader.CImageRecord70
mAuxDoubleDataList - Variable in class loci.formats.in.SlideBook7Reader.CImageGroup
mAuxFilterWheel2Pos - Variable in class loci.formats.in.SlideBook7Reader.CFluorDef70
mAuxFilterWheel3Pos - Variable in class loci.formats.in.SlideBook7Reader.CFluorDef70
mAuxFilterWheel4Pos - Variable in class loci.formats.in.SlideBook7Reader.CFluorDef70
mAuxFilterWheel5Pos - Variable in class loci.formats.in.SlideBook7Reader.CFluorDef70
mAuxFilterWheel6Pos - Variable in class loci.formats.in.SlideBook7Reader.CFluorDef70
mAuxFilterWheel7Pos - Variable in class loci.formats.in.SlideBook7Reader.CFluorDef70
mAuxFilterWheelPos - Variable in class loci.formats.in.SlideBook7Reader.CFluorDef70
mAuxFloatDataList - Variable in class loci.formats.in.SlideBook7Reader.CImageGroup
mAuxNDPos - Variable in class loci.formats.in.SlideBook7Reader.CFluorDef70
mAuxSInt32DataList - Variable in class loci.formats.in.SlideBook7Reader.CImageGroup
mAuxSInt64DataList - Variable in class loci.formats.in.SlideBook7Reader.CImageGroup
mAuxXmlDataList - Variable in class loci.formats.in.SlideBook7Reader.CImageGroup
mAuxZStageIncreaseTowardsSample - Variable in class loci.formats.in.SlideBook7Reader.CAnnotation70
mAuxZStageMicrons - Variable in class loci.formats.in.SlideBook7Reader.CAnnotation70
mAuxZStageMicronsSet - Variable in class loci.formats.in.SlideBook7Reader.CAnnotation70
mAuxZStartPosition - Variable in class loci.formats.in.SlideBook7Reader.CExposureRecord70
max - Variable in class loci.formats.gui.SignedColorModel
max - Variable in class loci.formats.in.InCellReader.Image
max - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.Channel
max(double) - Method in class loci.plugins.util.RecordedImageProcessor
MAX_APERTURE_VALUE - Static variable in class loci.formats.tiff.IFD
MAX_BLOCK_SIZE - Static variable in class loci.formats.services.POIServiceImpl
MAX_CHANNELS - Static variable in class loci.formats.in.DeltavisionReader
MAX_COMPONENTS - Static variable in class loci.plugins.in.SeriesDialog
MAX_HEADER_SIZE - Static variable in class loci.formats.in.QuesantReader
MAX_JPEG_SIZE - Static variable in class loci.formats.in.HamamatsuVMSReader
MAX_LEN - Static variable in class loci.formats.out.DicomWriter.UIDCreator
MAX_MAJOR_VERSION - Static variable in class loci.formats.in.MicromanagerReader
  Defines maximum Micro-Manager version supported.
MAX_PRIORITY - Static variable in interface loci.formats.cache.ICacheStrategy
MAX_READERS - Static variable in class loci.formats.FileStitcher
MAX_SAMPLE_VALUE - Static variable in class loci.formats.tiff.IFD
MAX_SERIES_THUMBS - Static variable in class loci.plugins.in.SeriesDialog
MAX_SERIES_TOGGLES - Static variable in class loci.plugins.in.SeriesDialog
MAX_SIZE - Static variable in class loci.formats.in.HamamatsuVMSReader
MAX_SIZE - Static variable in class loci.formats.in.JPEGReader
MAX_SIZE - Static variable in class loci.formats.in.NDPIReader
MAX_STACK_SIZE - Static variable in class loci.formats.in.GIFReader
  Maximum buffer size.
MAX_VERSION - Static variable in class loci.formats.in.MicromanagerReader
maxAdcRate - Variable in class loci.formats.in.SDTInfo
maxBufferSize - Variable in class loci.formats.in.ImarisHDFReader
maxBytes - Variable in class loci.formats.codec.CodecOptions
  If compressing, this is the maximum number of raw bytes to compress.
maxC - Variable in class loci.formats.in.CV7000Reader.MinMax
maxCfdRate - Variable in class loci.formats.in.SDTInfo
  (-1.0 - not set).
maxCycle - Variable in class loci.formats.in.TecanReader
maxField - Variable in class loci.formats.in.TecanReader
MAXIMAL_NUMBER_OF_DIMENSIONS - Static variable in class loci.formats.in.OBFReader
maximumReadOffset - Variable in class loci.formats.in.JPEG2000MetadataParser
  Maximum read offset within in the stream.
maxInten - Variable in class loci.formats.in.DeltavisionReader.DVExtHdrFields
  Maxiumum intensity.
maxOffsetIndex - Variable in class loci.formats.in.AmiraReader.HxRLE
maxPixelRange - Variable in class loci.formats.in.DicomReader
maxResolution - Variable in class loci.formats.in.ZeissCZIReader
maxSyncRate - Variable in class loci.formats.in.SDTInfo
  Maximum rates during the measurement.
maxT - Variable in class loci.formats.in.CV7000Reader.MinMax
maxTacRate - Variable in class loci.formats.in.SDTInfo
maxValue() - Method in class loci.plugins.util.RecordedImageProcessor
maxX - Variable in class loci.formats.in.ImarisHDFReader
maxY - Variable in class loci.formats.in.ImarisHDFReader
maxZ - Variable in class loci.formats.in.CV7000Reader.MinMax
maxZ - Variable in class loci.formats.in.ImarisHDFReader
mBackX1 - Variable in class loci.formats.in.SlideBook7Reader.CRatioManipRecord70
mBackX2 - Variable in class loci.formats.in.SlideBook7Reader.CRatioManipRecord70
mBackY1 - Variable in class loci.formats.in.SlideBook7Reader.CRatioManipRecord70
mBackY2 - Variable in class loci.formats.in.SlideBook7Reader.CRatioManipRecord70
mBaseAnnotationList - Variable in class loci.formats.in.SlideBook7Reader.CImageGroup.CAnnotations
mBeta - Variable in class loci.formats.in.SlideBook7Reader.CRatioManipRecord70
mBinning - Variable in class loci.formats.in.SlideBook7Reader.CExposureRecord70
mBitDepth - Variable in class loci.formats.in.SlideBook7Reader.CMainViewRecord70
mBkgndChannel - Variable in class loci.formats.in.SlideBook7Reader.CMainViewRecord70
mBlendFraction - Variable in class loci.formats.in.SlideBook7Reader.CMainViewRecord70
mBlockDictionary - Variable in class loci.formats.in.SlideBook7Reader.CCompressionBase
mBlockDictionarySize - Variable in class loci.formats.in.SlideBook7Reader.CCompressionBase
mBlueChannel - Variable in class loci.formats.in.SlideBook7Reader.CMainViewRecord70
mBorderFillPixels - Variable in class loci.formats.in.SlideBook7Reader.CAnnotation70
mBottomX - Variable in class loci.formats.in.SlideBook7Reader.CCube
mBottomY - Variable in class loci.formats.in.SlideBook7Reader.CCube
mBottomZ - Variable in class loci.formats.in.SlideBook7Reader.CCube
mBrightfieldPos - Variable in class loci.formats.in.SlideBook7Reader.CLensDef70
mBufLenBY - Variable in class loci.formats.in.SlideBook7Reader.CCompressionBase
mBuiltTable - Variable in class loci.formats.in.SlideBook7Reader.CRemapChannelLUT70
mByteOrdering - Variable in class loci.formats.in.SlideBook7Reader.CAlignManipRecord70
mByteOrdering - Variable in class loci.formats.in.SlideBook7Reader.CAnnotation70
mByteOrdering - Variable in class loci.formats.in.SlideBook7Reader.CChannelDef70
mByteOrdering - Variable in class loci.formats.in.SlideBook7Reader.CChannelRecord70
mByteOrdering - Variable in class loci.formats.in.SlideBook7Reader.CDataTableHeaderRecord70
mByteOrdering - Variable in class loci.formats.in.SlideBook7Reader.CExposureRecord70
mByteOrdering - Variable in class loci.formats.in.SlideBook7Reader.CFluorDef70
mByteOrdering - Variable in class loci.formats.in.SlideBook7Reader.CFRETManipRecord70
mByteOrdering - Variable in class loci.formats.in.SlideBook7Reader.CHistogramRecord70
mByteOrdering - Variable in class loci.formats.in.SlideBook7Reader.CImageRecord70
mByteOrdering - Variable in class loci.formats.in.SlideBook7Reader.CLensDef70
mByteOrdering - Variable in class loci.formats.in.SlideBook7Reader.CMainViewRecord70
mByteOrdering - Variable in class loci.formats.in.SlideBook7Reader.CMaskRecord70
mByteOrdering - Variable in class loci.formats.in.SlideBook7Reader.COptovarDef70
mByteOrdering - Variable in class loci.formats.in.SlideBook7Reader.CRatioManipRecord70
mByteOrdering - Variable in class loci.formats.in.SlideBook7Reader.CRemapManipRecord70
mByteOrdering - Variable in class loci.formats.in.SlideBook7Reader.CSlideRecord70
mBytesPerPixel - Variable in class loci.formats.in.SlideBook7Reader.CNpyHeader
mCalibDataPtrHigh - Variable in class loci.formats.in.SlideBook7Reader.CRemapManipRecord70
mCalibDataPtrLow - Variable in class loci.formats.in.SlideBook7Reader.CRemapManipRecord70
mCamera - Variable in class loci.formats.in.SlideBook7Reader.CFluorDef70
mCameraBitDepth - Variable in class loci.formats.in.SlideBook7Reader.CFluorDef70
mCameraGain - Variable in class loci.formats.in.SlideBook7Reader.CFluorDef70
mCameraIntensification - Variable in class loci.formats.in.SlideBook7Reader.CFluorDef70
mCameraMagnificationChange - Variable in class loci.formats.in.SlideBook7Reader.CLensDef70
mCameraName - Variable in class loci.formats.in.SlideBook7Reader.CChannelDef70
mCameraName - Variable in class loci.formats.in.SlideBook7Reader.CLensDef70
mCameraParameter1 - Variable in class loci.formats.in.SlideBook7Reader.CFluorDef70
mCameraPixelSize - Variable in class loci.formats.in.SlideBook7Reader.CLensDef70
mCameraPort - Variable in class loci.formats.in.SlideBook7Reader.CFluorDef70
mCameraSpeed - Variable in class loci.formats.in.SlideBook7Reader.CFluorDef70
mCameraVideoTurretPos - Variable in class loci.formats.in.SlideBook7Reader.CFluorDef70
mCaptureFlags - Variable in class loci.formats.in.SlideBook7Reader.CExposureRecord70
mCaptureSetId - Variable in class loci.formats.in.SlideBook7Reader.CExposureRecord70
mCaptureStatus - Variable in class loci.formats.in.SlideBook7Reader.CSlideRecord70
mCaptureType - Variable in class loci.formats.in.SlideBook7Reader.CExposureRecord70
mCentroidChannel - Variable in class loci.formats.in.SlideBook7Reader.CMaskRecord70
mCentroidFeature - Variable in class loci.formats.in.SlideBook7Reader.CMaskRecord70
mChannelDef - Variable in class loci.formats.in.SlideBook7Reader.CChannelRecord70
mChannelEnabled - Variable in class loci.formats.in.SlideBook7Reader.CMainViewRecord70
mChannelIndex - Variable in class loci.formats.in.SlideBook7Reader.CDataTableHeaderRecord70
mChannelIndex - Variable in class loci.formats.in.SlideBook7Reader.CHistogramRecord70
mChannelMask - Variable in class loci.formats.in.SlideBook7Reader.CAnnotation70
mChannelPtr - Variable in class loci.formats.in.SlideBook7Reader.CImageRecord70
mChannelRecordList - Variable in class loci.formats.in.SlideBook7Reader.CImageGroup
mChannelType - Variable in class loci.formats.in.SlideBook7Reader.CFluorDef70
mCheckpointImagePtr - Variable in class loci.formats.in.SlideBook7Reader.CSlideRecord70
mCheckpointMaxImages - Variable in class loci.formats.in.SlideBook7Reader.CSlideRecord70
mCheckpointNumImages - Variable in class loci.formats.in.SlideBook7Reader.CSlideRecord70
mCImageGroupList - Variable in class loci.formats.in.SlideBook7Reader.DataLoader
mCoefficients - Variable in class loci.formats.in.SlideBook7Reader.CRemapChannelLUT70
mColorDisplay - Variable in class loci.formats.in.SlideBook7Reader.CMainViewRecord70
mColumns - Variable in class loci.formats.in.SlideBook7Reader.CDataTableHeaderRecord70
mCompressedSizes - Variable in class loci.formats.in.SlideBook7Reader.CImageGroup.CMaskPositions
mCompressionFlag - Variable in class loci.formats.in.SlideBook7Reader.CImageGroup
mCompressionFlag - Variable in class loci.formats.in.SlideBook7Reader.CNpyHeader
mCompressor - Variable in class loci.formats.in.SlideBook7Reader.CImageGroup
mCounterToPathMap - Variable in class loci.formats.in.SlideBook7Reader.DataLoader
mcsPoints - Variable in class loci.formats.in.SDTInfo
  No of MCS values.
mcstaPoints - Variable in class loci.formats.in.SDTInfo
  Number of MCS_TA points.
mcsTime - Variable in class loci.formats.in.SDTInfo
  Interval time [ms] for MCS histogram.
mCube - Variable in class loci.formats.in.SlideBook7Reader.CRemapPoint
mCubeAnnotationList - Variable in class loci.formats.in.SlideBook7Reader.CImageGroup.CAnnotations
mcuHeight - Variable in class loci.formats.services.JPEGTurboServiceImpl
mcuHeight - Static variable in class org.libjpegturbo.turbojpeg.TJ
mCurrentFileCounter - Variable in class loci.formats.in.SlideBook7Reader.DataLoader
mcuWidth - Variable in class loci.formats.services.JPEGTurboServiceImpl
mcuWidth - Static variable in class org.libjpegturbo.turbojpeg.TJ
MD_FILE_UNITS - Static variable in class loci.formats.in.GelReader
MD_FILETAG - Static variable in class loci.formats.in.GelReader
MD_LAB_NAME - Static variable in class loci.formats.in.GelReader
MD_PREP_DATE - Static variable in class loci.formats.in.GelReader
MD_PREP_TIME - Static variable in class loci.formats.in.GelReader
MD_SAMPLE_INFO - Static variable in class loci.formats.in.GelReader
MD_SCALE_PIXEL - Static variable in class loci.formats.in.GelReader
mDarkfieldPos - Variable in class loci.formats.in.SlideBook7Reader.CLensDef70
mDarkValue - Variable in class loci.formats.in.SlideBook7Reader.CFRETManipRecord70
mDataBlockSize - Variable in class loci.formats.in.SlideBook7Reader.CHistogramRecord70
mDataLenBY - Variable in class loci.formats.in.SlideBook7Reader.CCompressionBase
mDataLoader - Variable in class loci.formats.in.SlideBook7Reader
mDataPosition - Variable in class loci.formats.in.SlideBook7Reader.CCompressionBase
mDataTablePtr - Variable in class loci.formats.in.SlideBook7Reader.CChannelRecord70
mDataType - Variable in class loci.formats.in.SlideBook7Reader.CChannelRecord70
mDataType - Variable in class loci.formats.in.SlideBook7Reader.CNpyHeader
mDay - Variable in class loci.formats.in.SlideBook7Reader.CImageRecord70
mdb - Variable in class loci.formats.services.MDBServiceImpl
MDB_SUFFIX - Static variable in class loci.formats.in.ZeissLSMReader
MDBService - Interface in loci.formats.services
  Interface defining methods for parsing MDB database files.
MDBServiceImpl - Class in loci.formats.services
  Implementation of `MDBService` for parsing MDB database files.
MDBServiceImpl() - Constructor for class loci.formats.services.MDBServiceImpl
  Default constructor.
mDefault - Variable in class loci.formats.in.SlideBook7Reader.CLensDef70
mDefault - Variable in class loci.formats.in.SlideBook7Reader.COptovarDef70
mDefaultColor - Variable in class loci.formats.in.SlideBook7Reader.CFluorDef70
mDefaultColorDisplay - Variable in class loci.formats.in.SlideBook7Reader.CFluorDef70
mDemoFlag - Variable in class loci.formats.in.SlideBook7Reader.CSlideRecord70
mDenBackground - Variable in class loci.formats.in.SlideBook7Reader.CRatioManipRecord70
mDenMax - Variable in class loci.formats.in.SlideBook7Reader.CRatioManipRecord70
mDenMin - Variable in class loci.formats.in.SlideBook7Reader.CRatioManipRecord70
mDependencyRef - Variable in class loci.formats.in.SlideBook7Reader.CAnnotation70
mDependencyType70 - Variable in class loci.formats.in.SlideBook7Reader.CAnnotation70
mDeprecatedMagnification - Variable in class loci.formats.in.SlideBook7Reader.CLensDef70
mDescriptorFileOffset - Variable in class loci.formats.in.SlideBook7Reader.CDataTableHeaderRecord70
mDescriptorSize - Variable in class loci.formats.in.SlideBook7Reader.CDataTableHeaderRecord70
mDescriptorVersion - Variable in class loci.formats.in.SlideBook7Reader.CDataTableHeaderRecord70
mDesiredValue - Variable in class loci.formats.in.SlideBook7Reader.CRemapPoint
mdf - Variable in class loci.formats.in.SlideBook7Reader.CLensDef70
mDICPos - Variable in class loci.formats.in.SlideBook7Reader.CLensDef70
mDICPrismPos - Variable in class loci.formats.in.SlideBook7Reader.CLensDef70
mDictionaryPosition - Variable in class loci.formats.in.SlideBook7Reader.CCompressionBase
mDictionaryRead - Variable in class loci.formats.in.SlideBook7Reader.CCompressionBase
mDisplayHigh - Variable in class loci.formats.in.SlideBook7Reader.CFRETManipRecord70
mDisplayLow - Variable in class loci.formats.in.SlideBook7Reader.CFRETManipRecord70
mDisplayNormalization - Variable in class loci.formats.in.SlideBook7Reader.CFRETManipRecord70
mDonor1Lifetime - Variable in class loci.formats.in.SlideBook7Reader.CFRETManipRecord70
mDonor1X - Variable in class loci.formats.in.SlideBook7Reader.CFRETManipRecord70
mDonor1Y - Variable in class loci.formats.in.SlideBook7Reader.CFRETManipRecord70
mDonor2Lifetime - Variable in class loci.formats.in.SlideBook7Reader.CFRETManipRecord70
mDoubleData - Variable in class loci.formats.in.SlideBook7Reader.CImageGroup.CAuxDoubleData
MEA_SUFFIX - Static variable in class loci.formats.in.FlexReader
MeaHandler() - Constructor for class loci.formats.in.FlexReader.MeaHandler
measDescBlockLength - Variable in class loci.formats.in.SDTInfo
measDescBlockNo - Variable in class loci.formats.in.SDTInfo
  Number of the measurement description block corresponding to this data block.
measDescBlockOffs - Variable in class loci.formats.in.SDTInfo
measMode - Variable in class loci.formats.in.SDTInfo
MEASUREMENT_DETAIL - Static variable in class loci.formats.in.CV7000Reader
MEASUREMENT_FILE - Static variable in class loci.formats.in.CV7000Reader
MEASUREMENT_SUFFIXES - Static variable in class loci.formats.in.FlexReader
MeasurementDataHandler(String) - Constructor for class loci.formats.in.CV7000Reader.MeasurementDataHandler
MeasurementDetailHandler() - Constructor for class loci.formats.in.CV7000Reader.MeasurementDetailHandler
measurementFiles - Variable in class loci.formats.in.FlexReader
MeasurementHandler() - Constructor for class loci.formats.in.ColumbusReader.MeasurementHandler
measurementID - Variable in class loci.formats.in.ColumbusReader.MeasurementHandler
measurementID - Variable in class loci.formats.in.OperettaReader.OperettaHandler
measurementName - Variable in class loci.formats.in.ColumbusReader.MeasurementHandler
measurementPath - Variable in class loci.formats.in.CV7000Reader
measurementResultFile - Variable in class loci.formats.in.CellVoyagerReader
MeasurementSettingsHandler() - Constructor for class loci.formats.in.CV7000Reader.MeasurementSettingsHandler
measurementTime - Variable in class loci.formats.in.OperettaReader.OperettaHandler
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
mElapsedTimeOffset - Variable in class loci.formats.in.SlideBook7Reader.CImageRecord70
mElapsedTimes - Variable in class loci.formats.in.SlideBook7Reader.CImageGroup
mElapsedTimeTablePtr - Variable in class loci.formats.in.SlideBook7Reader.CImageRecord70
MEM_MODEL - Static variable in class loci.formats.in.CellSensReader
memBank - Variable in class loci.formats.in.SDTInfo
mEmissionWheelPos - Variable in class loci.formats.in.SlideBook7Reader.CFluorDef70
memoFile - Variable in class loci.formats.Memoizer
Memoizer - Class in loci.formats
  `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 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, File) - Constructor for class loci.formats.Memoizer
  Constructs a memoizer around the given `IFormatReader` creating memo file 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 100L 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.
MemoryBlock(long, String) - Constructor for class loci.formats.in.LIFReader.MemoryBlock
memoryBlocks - Variable in class loci.formats.in.LIFReader
  Memory blocks including offsets and ID
MemoryDialog - Class in loci.plugins.in
  Bio-Formats Importer memory usage confirmation dialog box.
MemoryDialog(ImportProcess) - Constructor for class loci.plugins.in.MemoryDialog
  Creates a memory confirmation dialog for the Bio-Formats Importer.
mEquationString - Variable in class loci.formats.in.SlideBook7Reader.CRemapChannelLUT70
merge(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.
mErrorMessage - Variable in class loci.formats.in.SlideBook7Reader.CCompressionBase
mErrorMessage - Variable in class loci.formats.in.SlideBook7Reader.DataLoader
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_TAG - Static variable in class loci.formats.in.NDPISReader
METADATA_XML_TAG - Static variable in class loci.formats.in.FlowSightReader
metadataComplete - Variable in class loci.formats.CoreMetadata
  Indicates whether or not we are confident that all of the metadata stored within the file has been parsed.
MetadataConverter - Class in loci.formats.meta
  Deprecated.
  Use ome.xml.meta.MetadataConverter.
MetadataConverter() - Constructor for class loci.formats.meta.MetadataConverter
  Deprecated.
  Private constructor; all methods in MetadataConverter are static, so this should not be called.
metadataFile - Variable in class loci.formats.in.MicromanagerReader.Position
metadataFile - Variable in class loci.formats.in.OMETiffReader
metadataFiles - Variable in class loci.formats.in.BDReader
metadataFiles - Variable in class loci.formats.in.CellomicsReader
metadataFiles - Variable in class loci.formats.in.ColumbusReader
metadataFiles - Variable in class loci.formats.in.InCellReader
metadataFiles - Variable in class loci.formats.in.L2DReader
  List of all metadata files in the dataset.
metadataFiles - Variable in class loci.formats.in.MicroCTReader
metadataFiles - Variable in class loci.formats.in.OperettaReader
metadataFiles - Variable in class loci.formats.in.ScanrReader
metadataIndex - Variable in class loci.formats.in.CellSensReader
metadataInPlanes - Variable in class loci.formats.in.SlidebookReader
metadataLevel - Variable in class loci.formats.in.DefaultMetadataOptions
MetadataLevel - Enum 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.
metadataMap - Variable in class loci.formats.in.JDCEReader.JDCEWell
metadataOffsets - Variable in class loci.formats.in.SlidebookReader
metadataOptions - Variable in class loci.formats.FormatHandler
  Metadata parsing options.
MetadataOptions - Interface in loci.formats.in
  Holds metadata-related options.
metadataPosition - Variable in class loci.formats.in.ZeissCZIReader.FileHeader
metadataRetrieve - Variable in class loci.formats.FormatWriter
  Current metadata retrieval object.
MetadataRetrieve - Interface in loci.formats.meta
metadataSize - Variable in class loci.formats.in.ZeissCZIReader.SubBlock
metadataSource - Variable in class loci.formats.in.LOFReader
MetadataSource() - Constructor for enum loci.formats.in.LOFReader.MetadataSource
metadataStore - Variable in class loci.formats.FormatReader
  Current metadata store.
MetadataStore - Interface in loci.formats.meta
MetadataStoreInitializer - Class in loci.formats.in.LeicaMicrosystemsMetadata
  This class initializes the `MetadataStore` of a given `LMSFileReader`, using its `MetadataTempBuffer`
MetadataStoreInitializer(LMSFileReader) - Constructor for class loci.formats.in.LeicaMicrosystemsMetadata.MetadataStoreInitializer
MetadataTempBuffer - Class in loci.formats.in.LeicaMicrosystemsMetadata
  This class is used to temporarily store metadata information extracted from Leica XML before it is written to the reader's MetadataStore
MetadataTempBuffer(int) - Constructor for class loci.formats.in.LeicaMicrosystemsMetadata.MetadataTempBuffer
  Constructs a MetadataTempBuffer for a given number of images.
MetadataTools - Class in loci.formats
  A utility class for working with metadata objects, including `MetadataStore`, `MetadataRetrieve`, and OME-XML strings.
MetadataTools() - Constructor for class loci.formats.MetadataTools
metadataType - Variable in enum loci.formats.tiff.PhotoInterp
  Metadata type of the photometric interpretation.
metaFile - Variable in class loci.formats.in.OMETiffReader
MetakitService - Interface in loci.formats.services
  Interface defining methods for interacting with the OME Metakit library.
MetakitServiceImpl - Class in loci.formats.services
  Implementation of MetakitService for interacting with the OME Metakit library.
MetakitServiceImpl() - Constructor for class loci.formats.services.MetakitServiceImpl
METAMORPH_ID - Static variable in class loci.formats.in.MetamorphReader
MetamorphHandler - Class in loci.formats.in
  MetamorphTiffReader is the file format reader for TIFF files produced by Metamorph software version 7.5 and above.
MetamorphHandler() - Constructor for class loci.formats.in.MetamorphHandler
MetamorphHandler(Hashtable) - Constructor for class loci.formats.in.MetamorphHandler
MetamorphReader - Class in loci.formats.in
  Reader is the file format reader for Metamorph STK files.
MetamorphReader() - Constructor for class loci.formats.in.MetamorphReader
  Constructs a new Metamorph reader.
MetamorphTiffReader - Class in loci.formats.in
  MetamorphTiffReader is the file format reader for TIFF files produced by Metamorph software version 7.5 and above.
MetamorphTiffReader() - Constructor for class loci.formats.in.MetamorphTiffReader
  Constructs a new Metamorph TIFF reader.
MetamorphTiffReader.NumericComparator - Class in loci.formats.in
MetamorphTiffReader.Well - Class in loci.formats.in
metaTemp - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.LMSFileReader
metaWindow - Variable in class loci.plugins.util.DataBrowser
MetaxpressTiffReader - Class in loci.formats.in
  MetaxpressTiffReader is the file format reader for MetaXpress .htd + TIFF files.
MetaxpressTiffReader() - Constructor for class loci.formats.in.MetaxpressTiffReader
  Constructs a new MetaXpress TIFF reader.
METER_MULTIPLY - Static variable in class loci.formats.in.LeicaMicrosystemsMetadata.Dimension
METER_MULTIPLY - Static variable in class loci.formats.in.LeicaMicrosystemsMetadata.LMSMetadataExtractor
METER_MULTIPLY - Static variable in class loci.formats.in.LeicaMicrosystemsMetadata.ROI
METER_MULTIPLY - Static variable in class loci.formats.in.LIFReader
METERING_MODE - Static variable in class loci.formats.tiff.IFD
method - Variable in class loci.plugins.util.RecordedImageProcessor.MethodEntry
MethodEntry() - Constructor for class loci.plugins.util.RecordedImageProcessor.MethodEntry
methodStack - Variable in class loci.plugins.util.RecordedImageProcessor
methodStacks - Variable in class loci.plugins.util.BFVirtualStack
mExcitationLambda - Variable in class loci.formats.in.SlideBook7Reader.CFluorDef70
mExcitationWheelPos - Variable in class loci.formats.in.SlideBook7Reader.CFluorDef70
mExposureFactor - Variable in class loci.formats.in.SlideBook7Reader.CRatioManipRecord70
mExposureRecord - Variable in class loci.formats.in.SlideBook7Reader.CChannelRecord70
mExposureTime - Variable in class loci.formats.in.SlideBook7Reader.CExposureRecord70
mFaAa - Variable in class loci.formats.in.SlideBook7Reader.CFRETManipRecord70
mFdDd - Variable in class loci.formats.in.SlideBook7Reader.CFRETManipRecord70
mFieldMicronsPerPixel - Variable in class loci.formats.in.SlideBook7Reader.CAnnotation70
mFieldOffsetMicrons - Variable in class loci.formats.in.SlideBook7Reader.CAnnotation70
mFieldOffsetSet - Variable in class loci.formats.in.SlideBook7Reader.CAnnotation70
mFile - Variable in class loci.formats.in.SlideBook7Reader.CImageGroup
mFile - Variable in class loci.formats.in.SlideBook7Reader.DataLoader
mFileOffsets - Variable in class loci.formats.in.SlideBook7Reader.CImageGroup.CMaskPositions
mFileVersion - Variable in class loci.formats.in.SlideBook7Reader.CSlideRecord70
mFilterSet - Variable in class loci.formats.in.SlideBook7Reader.CFluorDef70
mFloatData - Variable in class loci.formats.in.SlideBook7Reader.CCubeAnnotation70
mFloatData - Variable in class loci.formats.in.SlideBook7Reader.CImageGroup.CAuxFloatData
mFluorDef - Variable in class loci.formats.in.SlideBook7Reader.CChannelDef70
mFortranOrder - Variable in class loci.formats.in.SlideBook7Reader.CNpyHeader
mFRAPDevice - Variable in class loci.formats.in.SlideBook7Reader.CCubeAnnotation70
mFRAPRegionAnnotationList - Variable in class loci.formats.in.SlideBook7Reader.CImageGroup.CAnnotations
mFRETAddParameter - Variable in class loci.formats.in.SlideBook7Reader.CFRETManipRecord70
mFRETManipRecList - Variable in class loci.formats.in.SlideBook7Reader.CImageGroup
mFRETMethod - Variable in class loci.formats.in.SlideBook7Reader.CFRETManipRecord70
mFRETParadigm - Variable in class loci.formats.in.SlideBook7Reader.CFRETManipRecord70
mGamma - Variable in class loci.formats.in.SlideBook7Reader.CMainViewRecord70
mGivenValue - Variable in class loci.formats.in.SlideBook7Reader.CRemapPoint
mGraphicType70 - Variable in class loci.formats.in.SlideBook7Reader.CAnnotation70
mGreenChannel - Variable in class loci.formats.in.SlideBook7Reader.CMainViewRecord70
mGroupId - Variable in class loci.formats.in.SlideBook7Reader.CAnnotation70
mHardwareFileLen - Variable in class loci.formats.in.SlideBook7Reader.CSlideRecord70
mHardwareFileOffset - Variable in class loci.formats.in.SlideBook7Reader.CSlideRecord70
mHeaderSize - Variable in class loci.formats.in.SlideBook7Reader.CNpyHeader
mHeight - Variable in class loci.formats.in.SlideBook7Reader.CImageRecord70
mHigh - Variable in class loci.formats.in.SlideBook7Reader.CMainViewRecord70
mHighDesired - Variable in class loci.formats.in.SlideBook7Reader.CRemapChannelLUT70
mHighestCount - Variable in class loci.formats.in.SlideBook7Reader.CSlideRecord70
mHighGiven - Variable in class loci.formats.in.SlideBook7Reader.CRemapChannelLUT70
mHistogramRecordList - Variable in class loci.formats.in.SlideBook7Reader.CImageGroup
mHistogramSummaryPtr - Variable in class loci.formats.in.SlideBook7Reader.CChannelRecord70
mHistogramTablePtr - Variable in class loci.formats.in.SlideBook7Reader.CChannelRecord70
mHistogramType - Variable in class loci.formats.in.SlideBook7Reader.CHistogramRecord70
mHour - Variable in class loci.formats.in.SlideBook7Reader.CImageRecord70
mHue - Variable in class loci.formats.in.SlideBook7Reader.CFluorDef70
mHue - Variable in class loci.formats.in.SlideBook7Reader.CMainViewRecord70
MIASReader - Class in loci.formats.in
  MIASReader is the file format reader for Maia Scientific MIAS-2 datasets.
MIASReader() - Constructor for class loci.formats.in.MIASReader
  Constructs a new MIAS reader.
MIASReader.AnalysisFile - Class in loci.formats.in
MicroCTReader - Class in loci.formats.in
  MicroCTReader is the file format reader for VFF files from a GE MicroCT scanner.
MicroCTReader() - Constructor for class loci.formats.in.MicroCTReader
  Constructs a new MicroCT reader.
MicromanagerHandler() - Constructor for class loci.formats.in.MicromanagerReader.MicromanagerHandler
MicromanagerReader - Class in loci.formats.in
  MicromanagerReader is the file format reader for Micro-Manager files.
MicromanagerReader() - Constructor for class loci.formats.in.MicromanagerReader
  Constructs a new Micromanager reader.
MicromanagerReader.Index - Class in loci.formats.in
MicromanagerReader.MicromanagerHandler - Class in loci.formats.in
  SAX handler for parsing Acqusition.xml.
MicromanagerReader.Position - Class in loci.formats.in
microscopeModel - Variable in class loci.formats.in.FEITiffReader
microscopeModels - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataTempBuffer
microscopeModels - Variable in class loci.formats.in.LIFReader
microscopyMode - Variable in class loci.formats.in.ImarisHDFReader
microSecPerFrame - Variable in class loci.formats.out.AVIWriter
MIKROSCAN_IMAGE_DESCRIPTION_PREFIX - Static variable in class loci.formats.in.MikroscanTiffReader
  TIFF image description prefix for Mikroscan TIF files.
MikroscanTiffReader - Class in loci.formats.in
  MikroscanTiffReader is the file format reader for Mikroscan TIFF files.
MikroscanTiffReader() - Constructor for class loci.formats.in.MikroscanTiffReader
  Constructs a new Mikroscan TIF reader.
mIlluminationMode - Variable in class loci.formats.in.SlideBook7Reader.CFluorDef70
mImageDataList - Variable in class loci.formats.in.SlideBook7Reader.CImageGroup
mImageGroupIndex - Variable in class loci.formats.in.SlideBook7Reader.CImageRecord70
mImageIndex - Variable in class loci.formats.in.SlideBook7Reader.CHistogramRecord70
mImagePtr - Variable in class loci.formats.in.SlideBook7Reader.CSlideRecord70
mImageRecord - Variable in class loci.formats.in.SlideBook7Reader.CImageGroup
mImageTitle - Variable in class loci.formats.in.SlideBook7Reader.CImageGroup
mImagingMode - Variable in class loci.formats.in.SlideBook7Reader.CFluorDef70
mImported - Variable in class loci.formats.in.SlideBook7Reader.CImageRecord70
min - Variable in class loci.formats.in.InCellReader.Image
min - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.Channel
min(double) - Method in class loci.plugins.util.RecordedImageProcessor
MIN_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.
mInfo - Variable in class loci.formats.in.SlideBook7Reader.CImageRecord70
MINIMAL_TAGS - Static variable in class loci.formats.in.FlowSightReader
  The tags that must be present for this reader to function properly
MinimalInCellHandler() - Constructor for class loci.formats.in.InCellReader.MinimalInCellHandler
MinimalTiffReader - Class in loci.formats.in
  MinimalTiffReader is the superclass for file format readers compatible with or derived from the TIFF 6.0 file format.
MinimalTiffReader() - Constructor for class loci.formats.in.MinimalTiffReader
  Constructs a new MinimalTiffReader.
MinimalTiffReader(String, String) - Constructor for class loci.formats.in.MinimalTiffReader
  Constructs a new MinimalTiffReader.
MinimalTiffReader(String, String[]) - Constructor for class loci.formats.in.MinimalTiffReader
  Constructs a new MinimalTiffReader.
MINIMUM_MEMORY_PADDING - Static variable in class loci.plugins.in.MemoryDialog
  Minimum amount of wiggle room for available memory, in bytes.
minimumElapsed - Variable in class loci.formats.Memoizer
  Minimum number of milliseconds which must elapse during the call to `Memoizer.setId(java.lang.String)` before a memo file will be created.
minInten - Variable in class loci.formats.in.DeltavisionReader.DVExtHdrFields
  Minimum intensity
mInitialOffset - Variable in class loci.formats.in.SlideBook7Reader.CExposureRecord70
MinMax() - Constructor for class loci.formats.in.CV7000Reader.MinMax
MinMaxCalculator - 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
mInsideRange - Variable in class loci.formats.in.SlideBook7Reader.CRemapChannelLUT70
minSyncRate - Variable in class loci.formats.in.SDTInfo
  Minimum rates during the measurement.
minT - Variable in class loci.formats.in.CV7000Reader.MinMax
minT - Variable in class loci.formats.in.OIRReader
mInt - Variable in class loci.formats.in.SlideBook7Reader.StrIntPair
mInt1 - Variable in class loci.formats.in.SlideBook7Reader.IntIntPair
mInt2 - Variable in class loci.formats.in.SlideBook7Reader.IntIntPair
minTacRate - Variable in class loci.formats.in.SDTInfo
mIntData - Variable in class loci.formats.in.SlideBook7Reader.CCubeAnnotation70
mIntegerData - Variable in class loci.formats.in.SlideBook7Reader.CImageGroup.CAuxSInt32Data
mInterplaneSpacing - Variable in class loci.formats.in.SlideBook7Reader.CExposureRecord70
minValue() - Method in class loci.plugins.util.RecordedImageProcessor
minX - Variable in class loci.formats.in.ImarisHDFReader
minY - Variable in class loci.formats.in.ImarisHDFReader
minZ - Variable in class loci.formats.in.CV7000Reader.MinMax
minZ - Variable in class loci.formats.in.ImarisHDFReader
minZ - Variable in class loci.formats.in.OIRReader
mipmapLevel - Variable in class loci.formats.in.BDVReader.H5Coordinate
MIRROR_H - Static variable in class loci.formats.in.CellSensReader
MIRROR_V - Static variable in class loci.formats.in.CellSensReader
mIsBackground - Variable in class loci.formats.in.SlideBook7Reader.CCubeAnnotation70
mIsCompressed - Variable in class loci.formats.in.SlideBook7Reader.CSBFile70
mIsFloatSet - Variable in class loci.formats.in.SlideBook7Reader.CCubeAnnotation70
mIsFRAP - Variable in class loci.formats.in.SlideBook7Reader.CCubeAnnotation70
mIsIntSet - Variable in class loci.formats.in.SlideBook7Reader.CCubeAnnotation70
mIsLLS - Variable in class loci.formats.in.SlideBook7Reader.CCubeAnnotation70
mIsNoLabel - Variable in class loci.formats.in.SlideBook7Reader.CCubeAnnotation70
MISSING - Static variable in class loci.plugins.config.LibraryEntry
  HTML markup for missing library.
MISSING_VERSION_CODE - Static variable in class loci.plugins.config.LibraryEntry
  Version code to indicate a missing library.
MissingLibraryException - Exception 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
mIsStimulation - Variable in class loci.formats.in.SlideBook7Reader.CCubeAnnotation70
MJPBCodec - Class in loci.formats.codec
  Methods for compressing and decompressing QuickTime Motion JPEG-B data.
MJPBCodec() - Constructor for class loci.formats.codec.MJPBCodec
MJPBCodecOptions - Class in loci.formats.codec
  Options for compressing and decompressing MJPB data.
MJPBCodecOptions() - Constructor for class loci.formats.codec.MJPBCodecOptions
MJPEG_HUFFMAN_TABLE - Static variable in class loci.formats.in.AVIReader
  Huffman table for MJPEG data.
mKd - Variable in class loci.formats.in.SlideBook7Reader.CRatioManipRecord70
mLambda - Variable in class loci.formats.in.SlideBook7Reader.CFluorDef70
mLambdaOptions - Variable in class loci.formats.in.SlideBook7Reader.CFluorDef70
mLaserPowerPos - Variable in class loci.formats.in.SlideBook7Reader.CFluorDef70
mLastChannel - Variable in class loci.formats.in.SlideBook7Reader.CImageGroup
mLastTimepoint - Variable in class loci.formats.in.SlideBook7Reader.CImageGroup
mLCDPos - Variable in class loci.formats.in.SlideBook7Reader.CFluorDef70
mLensDef - Variable in class loci.formats.in.SlideBook7Reader.CImageRecord70
mLightSource - Variable in class loci.formats.in.SlideBook7Reader.CFluorDef70
mLittleEndian - Variable in class loci.formats.in.SlideBook7Reader.CNpyHeader
mLongData - Variable in class loci.formats.in.SlideBook7Reader.CImageGroup.CAuxSInt64Data
mLow - Variable in class loci.formats.in.SlideBook7Reader.CMainViewRecord70
mLowDesired - Variable in class loci.formats.in.SlideBook7Reader.CRemapChannelLUT70
mLowGiven - Variable in class loci.formats.in.SlideBook7Reader.CRemapChannelLUT70
MM_JSON_TAG - Static variable in class loci.formats.in.MicromanagerReader
mMagnification - Variable in class loci.formats.in.SlideBook7Reader.COptovarDef70
mMainFrequency - Variable in class loci.formats.in.SlideBook7Reader.CFRETManipRecord70
mMainViewRecord - Variable in class loci.formats.in.SlideBook7Reader.CImageRecord70
mMajorVersion - Variable in class loci.formats.in.SlideBook7Reader.CNpyHeader
mManipID - Variable in class loci.formats.in.SlideBook7Reader.CAlignManipRecord70
mManipID - Variable in class loci.formats.in.SlideBook7Reader.CFRETManipRecord70
mManipID - Variable in class loci.formats.in.SlideBook7Reader.CRatioManipRecord70
mManipID - Variable in class loci.formats.in.SlideBook7Reader.CRemapManipRecord70
mManipPtr - Variable in class loci.formats.in.SlideBook7Reader.CChannelRecord70
mManipPtr - Variable in class loci.formats.in.SlideBook7Reader.CMaskRecord70
mMaskDataTablePtr - Variable in class loci.formats.in.SlideBook7Reader.CMaskRecord70
mMaskPosList - Variable in class loci.formats.in.SlideBook7Reader.CImageGroup
mMaskPtr - Variable in class loci.formats.in.SlideBook7Reader.CImageRecord70
mMaskRecordList - Variable in class loci.formats.in.SlideBook7Reader.CImageGroup
mMax - Variable in class loci.formats.in.SlideBook7Reader.CHistogramRecord70
mMean - Variable in class loci.formats.in.SlideBook7Reader.CHistogramRecord70
mMedium - Variable in class loci.formats.in.SlideBook7Reader.CLensDef70
MMHEADER - Static variable in class loci.formats.in.FluoviewReader
  Private TIFF tags
mMicronPerPixel - Variable in class loci.formats.in.SlideBook7Reader.CLensDef70
mMin - Variable in class loci.formats.in.SlideBook7Reader.CHistogramRecord70
mMinorVersion - Variable in class loci.formats.in.SlideBook7Reader.CNpyHeader
mMinute - Variable in class loci.formats.in.SlideBook7Reader.CImageRecord70
mModulationFlatFieldCorrected - Variable in class loci.formats.in.SlideBook7Reader.CFRETManipRecord70
mModZero - Variable in class loci.formats.in.SlideBook7Reader.CFRETManipRecord70
mMonth - Variable in class loci.formats.in.SlideBook7Reader.CImageRecord70
mMoveFieldDownSign - Variable in class loci.formats.in.SlideBook7Reader.CExposureRecord70
mMoveFieldRightSign - Variable in class loci.formats.in.SlideBook7Reader.CExposureRecord70
mmPlanes - Variable in class loci.formats.in.MetamorphReader
MMSTAMP - Static variable in class loci.formats.in.FluoviewReader
mNA - Variable in class loci.formats.in.SlideBook7Reader.CLensDef70
mName - Variable in class loci.formats.in.SlideBook7Reader.CChannelDef70
mName - Variable in class loci.formats.in.SlideBook7Reader.CFluorDef70
mName - Variable in class loci.formats.in.SlideBook7Reader.CImageRecord70
mName - Variable in class loci.formats.in.SlideBook7Reader.CLensDef70
mName - Variable in class loci.formats.in.SlideBook7Reader.CMaskRecord70
mName - Variable in class loci.formats.in.SlideBook7Reader.COptovarDef70
mName - Variable in class loci.formats.in.SlideBook7Reader.CSlideRecord70
mNDPos - Variable in class loci.formats.in.SlideBook7Reader.CFluorDef70
mNextTableFileOffset - Variable in class loci.formats.in.SlideBook7Reader.CDataTableHeaderRecord70
MNG_MAGIC_BYTES - Static variable in class loci.formats.in.MNGReader
MNGReader - Class in loci.formats.in
  MNGReader is the file format reader for Multiple-image Network Graphics (MNG) files.
MNGReader() - Constructor for class loci.formats.in.MNGReader
  Constructs a new MNG reader.
MNGReader.SeriesInfo - Class in loci.formats.in
mNotesLen - Variable in class loci.formats.in.SlideBook7Reader.CImageRecord70
mNotesLen - Variable in class loci.formats.in.SlideBook7Reader.CSlideRecord70
mNotesPtr - Variable in class loci.formats.in.SlideBook7Reader.CImageRecord70
mNotesPtr - Variable in class loci.formats.in.SlideBook7Reader.CSlideRecord70
mNpyHeader - Variable in class loci.formats.in.SlideBook7Reader.CImageGroup
mNumAuxDataTables - Variable in class loci.formats.in.SlideBook7Reader.CImageRecord70
mNumBackground - Variable in class loci.formats.in.SlideBook7Reader.CRatioManipRecord70
mNumberOfThreads - Variable in class loci.formats.in.SlideBook7Reader.CCompressionBase
mNumBins - Variable in class loci.formats.in.SlideBook7Reader.CHistogramRecord70
mNumBlocks - Variable in class loci.formats.in.SlideBook7Reader.CCompressionBase
mNumCalibPoints - Variable in class loci.formats.in.SlideBook7Reader.CRemapManipRecord70
mNumChannels - Variable in class loci.formats.in.SlideBook7Reader.CImageRecord70
mNumExposuresAverage - Variable in class loci.formats.in.SlideBook7Reader.CFluorDef70
mNumImages - Variable in class loci.formats.in.SlideBook7Reader.CSlideRecord70
mNumManip - Variable in class loci.formats.in.SlideBook7Reader.CChannelRecord70
mNumManip - Variable in class loci.formats.in.SlideBook7Reader.CMaskRecord70
mNumMasks - Variable in class loci.formats.in.SlideBook7Reader.CImageRecord70
mNumMax - Variable in class loci.formats.in.SlideBook7Reader.CRatioManipRecord70
mNumMin - Variable in class loci.formats.in.SlideBook7Reader.CRatioManipRecord70
mNumPhases - Variable in class loci.formats.in.SlideBook7Reader.CFRETManipRecord70
mNumPlanes - Variable in class loci.formats.in.SlideBook7Reader.CChannelRecord70
mNumPlanes - Variable in class loci.formats.in.SlideBook7Reader.CExposureRecord70
mNumPlanes - Variable in class loci.formats.in.SlideBook7Reader.CImageRecord70
mNumTimepoints - Variable in class loci.formats.in.SlideBook7Reader.CImageRecord70
mNumViews - Variable in class loci.formats.in.SlideBook7Reader.CImageRecord70
mNumX - Variable in class loci.formats.in.SlideBook7Reader.CCompressionBase
mNumY - Variable in class loci.formats.in.SlideBook7Reader.CCompressionBase
mNumZ - Variable in class loci.formats.in.SlideBook7Reader.CCompressionBase
mNuTSACSampleSize - Variable in class loci.formats.in.SlideBook7Reader.CExposureRecord70
mObjectId - Variable in class loci.formats.in.SlideBook7Reader.CAnnotation70
mOcularPhotoTurretPos - Variable in class loci.formats.in.SlideBook7Reader.CFluorDef70
mod - Variable in class loci.formats.in.SDTInfo
  Module number.
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
MODELS_WITHOUT_CORRECTION - Static variable in class loci.formats.in.LeicaSCNReader
modFpgaVer - Variable in class loci.formats.in.SDTInfo
  New in v.8.4.
modSerNo - Variable in class loci.formats.in.SDTInfo
  Serial number of the module.
modType - Variable in class loci.formats.in.SDTInfo
  Module type.
modTypeCode - Variable in class loci.formats.in.SDTInfo
modulo - Variable in class loci.formats.meta.ModuloAnnotation
Modulo - Class in loci.formats
  Represents a subdimension of Z, C, or T as needed for supporting Modulo annotations.
Modulo(String) - Constructor for class loci.formats.Modulo
Modulo(Modulo) - Constructor for class loci.formats.Modulo
MODULO_NS - Static variable in class loci.formats.meta.ModuloAnnotation
ModuloAnnotation - Class in loci.formats.meta
ModuloAnnotation() - Constructor for class loci.formats.meta.ModuloAnnotation
moduloC - Variable in class loci.formats.CoreMetadata
moduloT - Variable in class loci.formats.CoreMetadata
moduloZ - Variable in class loci.formats.CoreMetadata
MolecularImagingReader - Class in loci.formats.in
  MolecularImagingReader is the file format reader for Molecular Imaging files.
MolecularImagingReader() - Constructor for class loci.formats.in.MolecularImagingReader
  Constructs a new Molecular Imaging reader.
montageIndex - Variable in class loci.formats.in.FluoviewReader
montageOffsets - Variable in class loci.formats.in.FluoviewReader
mOptovarDef - Variable in class loci.formats.in.SlideBook7Reader.CImageRecord70
mosaics - Variable in class loci.formats.in.ZeissCZIReader
mouseClicked(MouseEvent) - Method in class loci.plugins.in.MainDialog
mouseDragged(MouseEvent) - Method in class loci.formats.gui.ImageViewer
  Handles cursor probes.
mouseEntered(MouseEvent) - Method in class loci.plugins.in.MainDialog
  Focuses the component upon mouseover.
mouseExited(MouseEvent) - Method in class loci.plugins.in.MainDialog
mouseMoved(MouseEvent) - Method in class loci.formats.gui.ImageViewer
  Handles cursor probes.
mousePressed(MouseEvent) - Method in class loci.plugins.in.MainDialog
mouseReleased(MouseEvent) - Method in class loci.plugins.in.MainDialog
mouseWheelMoved(MouseWheelEvent) - Method in class loci.plugins.util.DataBrowser
mOutputBuffer - Variable in class loci.formats.in.SlideBook7Reader.CCompressionBase
moveTo(int, int) - Method in class loci.plugins.util.RecordedImageProcessor
mParcentricOffsetX - Variable in class loci.formats.in.SlideBook7Reader.CLensDef70
mParcentricOffsetY - Variable in class loci.formats.in.SlideBook7Reader.CLensDef70
mParentRecordPtr - Variable in class loci.formats.in.SlideBook7Reader.CDataTableHeaderRecord70
mParfocalOffset - Variable in class loci.formats.in.SlideBook7Reader.CLensDef70
mParfocalOffset2 - Variable in class loci.formats.in.SlideBook7Reader.CLensDef70
mPathToStreamMap - Variable in class loci.formats.in.SlideBook7Reader.DataLoader
mPersistentSubmasks - Variable in class loci.formats.in.SlideBook7Reader.CMaskRecord70
mPhaseFlatFieldCorrected - Variable in class loci.formats.in.SlideBook7Reader.CFRETManipRecord70
mPhasePos - Variable in class loci.formats.in.SlideBook7Reader.CLensDef70
mPhaseZero - Variable in class loci.formats.in.SlideBook7Reader.CFRETManipRecord70
mPlaneId - Variable in class loci.formats.in.SlideBook7Reader.CAnnotation70
mPlanes - Variable in class loci.formats.in.SlideBook7Reader.CDataTableHeaderRecord70
mPoints - Variable in class loci.formats.in.SlideBook7Reader.CRemapChannelLUT70
mPolarizerPos - Variable in class loci.formats.in.SlideBook7Reader.CLensDef70
mPrefsFileLen - Variable in class loci.formats.in.SlideBook7Reader.CSlideRecord70
mPrefsOffset - Variable in class loci.formats.in.SlideBook7Reader.CSlideRecord70
mProjectFolder - Variable in class loci.formats.in.SlideBook7Reader.CSlideRecord70
mPseudoFrom - Variable in class loci.formats.in.SlideBook7Reader.CMainViewRecord70
mPseudoTo - Variable in class loci.formats.in.SlideBook7Reader.CMainViewRecord70
mRatioManipRecordList - Variable in class loci.formats.in.SlideBook7Reader.CImageGroup
MRC_SUFFIXES - Static variable in class loci.formats.in.MRCReader
MRCReader - Class in loci.formats.in
  MRCReader is the file format reader for MRC files.
MRCReader() - Constructor for class loci.formats.in.MRCReader
  Constructs a new MRC reader.
mRedChannel - Variable in class loci.formats.in.SlideBook7Reader.CMainViewRecord70
mRegionIndex - Variable in class loci.formats.in.SlideBook7Reader.CCubeAnnotation70
mRegions - Variable in class loci.formats.in.SlideBook7Reader.CFRAPRegionAnnotation70
mRelativePower - Variable in class loci.formats.in.SlideBook7Reader.CAnnotation70
mRemapChannelLUTList - Variable in class loci.formats.in.SlideBook7Reader.CImageGroup
mRemapManipRecList - Variable in class loci.formats.in.SlideBook7Reader.CImageGroup
mRemapType - Variable in class loci.formats.in.SlideBook7Reader.CRemapChannelLUT70
mRemapType - Variable in class loci.formats.in.SlideBook7Reader.CRemapManipRecord70
mReserved1 - Variable in class loci.formats.in.SDTInfo
mReserved2 - Variable in class loci.formats.in.SDTInfo
mReserved2 - Variable in class loci.formats.in.SlideBook7Reader.CRemapManipRecord70
mReservedBuf - Variable in class loci.formats.in.SlideBook7Reader.CCubeAnnotation70
mRGBFactor - Variable in class loci.formats.in.SlideBook7Reader.CFluorDef70
mRhigh - Variable in class loci.formats.in.SlideBook7Reader.CRatioManipRecord70
mRlow - Variable in class loci.formats.in.SlideBook7Reader.CRatioManipRecord70
mRmax - Variable in class loci.formats.in.SlideBook7Reader.CRatioManipRecord70
mRmin - Variable in class loci.formats.in.SlideBook7Reader.CRatioManipRecord70
mRows - Variable in class loci.formats.in.SlideBook7Reader.CDataTableHeaderRecord70
MRW_MAGIC_STRING - Static variable in class loci.formats.in.MRWReader
MRWReader - Class in loci.formats.in
  MRWReader is the file format reader for Minolta MRW files.
MRWReader() - Constructor for class loci.formats.in.MRWReader
  Constructs a new MRW reader.
MS_VIDEO - Static variable in class loci.formats.in.AVIReader
mSamplingStdDev - Variable in class loci.formats.in.SlideBook7Reader.CRemapPoint
mSAPositionList - Variable in class loci.formats.in.SlideBook7Reader.CImageGroup
mSAPositionTablePtr - Variable in class loci.formats.in.SlideBook7Reader.CImageRecord70
mSaturation - Variable in class loci.formats.in.SlideBook7Reader.CFluorDef70
mSaturation - Variable in class loci.formats.in.SlideBook7Reader.CMainViewRecord70
mScanning - Variable in class loci.formats.in.SlideBook7Reader.CExposureRecord70
mSecond - Variable in class loci.formats.in.SlideBook7Reader.CImageRecord70
mSequenceId - Variable in class loci.formats.in.SlideBook7Reader.CAnnotation70
msg - Variable in class loci.formats.FilePattern
  Error message generated during file pattern construction.
msg(String) - Method in class loci.formats.gui.DataConverter
mShape - Variable in class loci.formats.in.SlideBook7Reader.CNpyHeader
mSignalThreshold - Variable in class loci.formats.in.SlideBook7Reader.CFRETManipRecord70
mSingleTimepointFile - Variable in class loci.formats.in.SlideBook7Reader.CImageGroup
mSlidePath - Variable in class loci.formats.in.SlideBook7Reader.CSBFile70
mSlidePath - Variable in class loci.formats.in.SlideBook7Reader.DataLoader
mSlideRecord - Variable in class loci.formats.in.SlideBook7Reader.DataLoader
mSpecialBuildStr - Variable in class loci.formats.in.SlideBook7Reader.CSlideRecord70
MSRLE - Static variable in class loci.formats.in.AVIReader
  Supported compression types.
MSRLECodec - Class in loci.formats.codec
  Methods for compressing and decompressing data using Microsoft RLE.
MSRLECodec() - Constructor for class loci.formats.codec.MSRLECodec
mStageOffsetMicrons - Variable in class loci.formats.in.SlideBook7Reader.CAnnotation70
mStageOffsetSet - Variable in class loci.formats.in.SlideBook7Reader.CAnnotation70
mStagePositions - Variable in class loci.formats.in.SlideBook7Reader.CImageGroup
mStagePositionTablePtr - Variable in class loci.formats.in.SlideBook7Reader.CImageRecord70
mStartTime - Variable in class loci.formats.in.SlideBook7Reader.CDataTableHeaderRecord70
mStoreMicronPositions - Variable in class loci.formats.in.SlideBook7Reader.CAnnotation70
mStr - Variable in class loci.formats.in.SlideBook7Reader.StrIntPair
mStructID - Variable in class loci.formats.in.SlideBook7Reader.CAlignManipRecord70
mStructID - Variable in class loci.formats.in.SlideBook7Reader.CChannelDef70
mStructID - Variable in class loci.formats.in.SlideBook7Reader.CChannelRecord70
mStructID - Variable in class loci.formats.in.SlideBook7Reader.CDataTableHeaderRecord70
mStructID - Variable in class loci.formats.in.SlideBook7Reader.CExposureRecord70
mStructID - Variable in class loci.formats.in.SlideBook7Reader.CFluorDef70
mStructID - Variable in class loci.formats.in.SlideBook7Reader.CFRETManipRecord70
mStructID - Variable in class loci.formats.in.SlideBook7Reader.CHistogramRecord70
mStructID - Variable in class loci.formats.in.SlideBook7Reader.CImageRecord70
mStructID - Variable in class loci.formats.in.SlideBook7Reader.CLensDef70
mStructID - Variable in class loci.formats.in.SlideBook7Reader.CMainViewRecord70
mStructID - Variable in class loci.formats.in.SlideBook7Reader.CMaskRecord70
mStructID - Variable in class loci.formats.in.SlideBook7Reader.COptovarDef70
mStructID - Variable in class loci.formats.in.SlideBook7Reader.CRatioManipRecord70
mStructID - Variable in class loci.formats.in.SlideBook7Reader.CRemapManipRecord70
mStructLen - Variable in class loci.formats.in.SlideBook7Reader.CAlignManipRecord70
mStructLen - Variable in class loci.formats.in.SlideBook7Reader.CChannelDef70
mStructLen - Variable in class loci.formats.in.SlideBook7Reader.CChannelRecord70
mStructLen - Variable in class loci.formats.in.SlideBook7Reader.CDataTableHeaderRecord70
mStructLen - Variable in class loci.formats.in.SlideBook7Reader.CExposureRecord70
mStructLen - Variable in class loci.formats.in.SlideBook7Reader.CFluorDef70
mStructLen - Variable in class loci.formats.in.SlideBook7Reader.CFRETManipRecord70
mStructLen - Variable in class loci.formats.in.SlideBook7Reader.CHistogramRecord70
mStructLen - Variable in class loci.formats.in.SlideBook7Reader.CImageRecord70
mStructLen - Variable in class loci.formats.in.SlideBook7Reader.CLensDef70
mStructLen - Variable in class loci.formats.in.SlideBook7Reader.CMainViewRecord70
mStructLen - Variable in class loci.formats.in.SlideBook7Reader.CMaskRecord70
mStructLen - Variable in class loci.formats.in.SlideBook7Reader.COptovarDef70
mStructLen - Variable in class loci.formats.in.SlideBook7Reader.CRatioManipRecord70
mStructLen - Variable in class loci.formats.in.SlideBook7Reader.CRemapManipRecord70
mStructLen - Variable in class loci.formats.in.SlideBook7Reader.CSlideRecord70
mStructVersion - Variable in class loci.formats.in.SlideBook7Reader.CAlignManipRecord70
mStructVersion - Variable in class loci.formats.in.SlideBook7Reader.CChannelDef70
mStructVersion - Variable in class loci.formats.in.SlideBook7Reader.CChannelRecord70
mStructVersion - Variable in class loci.formats.in.SlideBook7Reader.CDataTableHeaderRecord70
mStructVersion - Variable in class loci.formats.in.SlideBook7Reader.CExposureRecord70
mStructVersion - Variable in class loci.formats.in.SlideBook7Reader.CFluorDef70
mStructVersion - Variable in class loci.formats.in.SlideBook7Reader.CFRETManipRecord70
mStructVersion - Variable in class loci.formats.in.SlideBook7Reader.CHistogramRecord70
mStructVersion - Variable in class loci.formats.in.SlideBook7Reader.CImageRecord70
mStructVersion - Variable in class loci.formats.in.SlideBook7Reader.CLensDef70
mStructVersion - Variable in class loci.formats.in.SlideBook7Reader.CMainViewRecord70
mStructVersion - Variable in class loci.formats.in.SlideBook7Reader.CMaskRecord70
mStructVersion - Variable in class loci.formats.in.SlideBook7Reader.COptovarDef70
mStructVersion - Variable in class loci.formats.in.SlideBook7Reader.CRatioManipRecord70
mStructVersion - Variable in class loci.formats.in.SlideBook7Reader.CRemapManipRecord70
mStructVersion - Variable in class loci.formats.in.SlideBook7Reader.CSlideRecord70
MSVideoCodec - Class in loci.formats.codec
  Methods for compressing and decompressing data using Microsoft Video 1.
MSVideoCodec() - Constructor for class loci.formats.codec.MSVideoCodec
mTableType - Variable in class loci.formats.in.SlideBook7Reader.CDataTableHeaderRecord70
mText - Variable in class loci.formats.in.SlideBook7Reader.CAnnotation70
mThumbNail - Variable in class loci.formats.in.SlideBook7Reader.CImageRecord70
mThumbPlane - Variable in class loci.formats.in.SlideBook7Reader.CMainViewRecord70
mThumbTimePoint - Variable in class loci.formats.in.SlideBook7Reader.CMainViewRecord70
mTimeBasis - Variable in class loci.formats.in.SlideBook7Reader.CDataTableHeaderRecord70
mTimeInterval - Variable in class loci.formats.in.SlideBook7Reader.CDataTableHeaderRecord70
mTimeLapse - Variable in class loci.formats.in.SlideBook7Reader.CExposureRecord70
mTimeLapseInterval - Variable in class loci.formats.in.SlideBook7Reader.CExposureRecord70
mTimePointsTableSize - Variable in class loci.formats.in.SlideBook7Reader.CDataTableHeaderRecord70
mTimePointsWritten - Variable in class loci.formats.in.SlideBook7Reader.CDataTableHeaderRecord70
mTIRFPos - Variable in class loci.formats.in.SlideBook7Reader.CFluorDef70
mTLApertureDiaphramPos - Variable in class loci.formats.in.SlideBook7Reader.CLensDef70
mTLFieldDiaphramPos - Variable in class loci.formats.in.SlideBook7Reader.CLensDef70
mTopLensPos - Variable in class loci.formats.in.SlideBook7Reader.CLensDef70
mTopX - Variable in class loci.formats.in.SlideBook7Reader.CCube
mTopY - Variable in class loci.formats.in.SlideBook7Reader.CCube
mTopZ - Variable in class loci.formats.in.SlideBook7Reader.CCube
mTransmittedModePrompt - Variable in class loci.formats.in.SlideBook7Reader.CFluorDef70
mtResol - Variable in class loci.formats.in.SDTInfo
  Macro time clock in 0.1 ns units.
mTurretPosition - Variable in class loci.formats.in.SlideBook7Reader.CFluorDef70
mTurretPosition - Variable in class loci.formats.in.SlideBook7Reader.CLensDef70
mTurretPosition - Variable in class loci.formats.in.SlideBook7Reader.COptovarDef70
mTwoLifetimeRatio - Variable in class loci.formats.in.SlideBook7Reader.CFRETManipRecord70
mUint16Size - Variable in class loci.formats.in.SlideBook7Reader.CCompressionBase
MultiBand() - Constructor for class loci.formats.in.LeicaHandler.MultiBand
multiBands - Variable in class loci.formats.in.LeicaHandler
MULTIDIM_IMAGE_VOLUME - Static variable in class loci.formats.in.CellSensReader
MULTIDIM_STACK_PROPERTIES - Static variable in class loci.formats.in.CellSensReader
multifile - Variable in class loci.formats.in.ZeissTIFFReader.TIFFInfo
MultipleImagesReader - Class in loci.formats.in.LeicaMicrosystemsMetadata
  MultipleImagesReader presents a number of image files as one image reference
MultipleImagesReader(XlifDocument, int) - Constructor for class loci.formats.in.LeicaMicrosystemsMetadata.MultipleImagesReader
multiply(double) - Method in class loci.plugins.util.RecordedImageProcessor
mUncompactedSpace - Variable in class loci.formats.in.SlideBook7Reader.CSlideRecord70
mUniqueId - Variable in class loci.formats.in.SlideBook7Reader.CImageRecord70
mUnknownAnnotationList - Variable in class loci.formats.in.SlideBook7Reader.CImageGroup.CAnnotations
MUST_GROUP - Static variable in class loci.formats.FormatTools
  File grouping options.
MUST_GROUP - Static variable in interface loci.formats.IFormatReader
  File grouping options.
mUV - Variable in class loci.formats.in.SlideBook7Reader.CFluorDef70
mUV - Variable in class loci.formats.in.SlideBook7Reader.CLensDef70
mValue - Variable in class loci.formats.in.SlideBook7Reader.CFluorDef70
mValue - Variable in class loci.formats.in.SlideBook7Reader.CMainViewRecord70
mValues - Variable in class loci.formats.in.SlideBook7Reader.CRemapChannelLUT70
mValueType - Variable in class loci.formats.in.SlideBook7Reader.CDataTableHeaderRecord70
mVersion - Variable in class loci.formats.in.SlideBook7Reader.CAnnotation70
mVertexes - Variable in class loci.formats.in.SlideBook7Reader.CAnnotation70
mViewID - Variable in class loci.formats.in.SlideBook7Reader.CMainViewRecord70
mViewOptions - Variable in class loci.formats.in.SlideBook7Reader.CMainViewRecord70
mViewPtr - Variable in class loci.formats.in.SlideBook7Reader.CImageRecord70
mWidth - Variable in class loci.formats.in.SlideBook7Reader.CImageRecord70
mX - Variable in class loci.formats.in.SlideBook7Reader.CSBPoint
mXExtent - Variable in class loci.formats.in.SlideBook7Reader.CExposureRecord70
mXFactor - Variable in class loci.formats.in.SlideBook7Reader.CExposureRecord70
mXML - Variable in class loci.formats.in.SlideBook7Reader.CFRAPRegionAnnotation70
mXmlData - Variable in class loci.formats.in.SlideBook7Reader.CImageGroup.CAuxXmlData
mXmlDescriptor - Variable in class loci.formats.in.SlideBook7Reader.CImageGroup.CAuxDoubleData
mXmlDescriptor - Variable in class loci.formats.in.SlideBook7Reader.CImageGroup.CAuxFloatData
mXmlDescriptor - Variable in class loci.formats.in.SlideBook7Reader.CImageGroup.CAuxSInt32Data
mXmlDescriptor - Variable in class loci.formats.in.SlideBook7Reader.CImageGroup.CAuxSInt64Data
mXOffset - Variable in class loci.formats.in.SlideBook7Reader.CAlignManipRecord70
mXOffset - Variable in class loci.formats.in.SlideBook7Reader.CExposureRecord70
mXStartPosition - Variable in class loci.formats.in.SlideBook7Reader.CExposureRecord70
mXYInterpolationFactor - Variable in class loci.formats.in.SlideBook7Reader.CImageRecord70
mY - Variable in class loci.formats.in.SlideBook7Reader.CSBPoint
mYear - Variable in class loci.formats.in.SlideBook7Reader.CImageRecord70
mYExtent - Variable in class loci.formats.in.SlideBook7Reader.CExposureRecord70
mYFactor - Variable in class loci.formats.in.SlideBook7Reader.CExposureRecord70
mYOffset - Variable in class loci.formats.in.SlideBook7Reader.CAlignManipRecord70
mYOffset - Variable in class loci.formats.in.SlideBook7Reader.CExposureRecord70
myReader - Variable in class loci.formats.gui.ImageViewer
  Current format reader.
mYStartPosition - Variable in class loci.formats.in.SlideBook7Reader.CExposureRecord70
myWriter - Variable in class loci.formats.gui.ImageViewer
  Current format writer.
mZ - Variable in class loci.formats.in.SlideBook7Reader.CSBPoint
mZInterpolationFactor - Variable in class loci.formats.in.SlideBook7Reader.CImageRecord70
mZOffset - Variable in class loci.formats.in.SlideBook7Reader.CAlignManipRecord70
mZStageDirectionsValid - Variable in class loci.formats.in.SlideBook7Reader.CAnnotation70
mZStageIncreaseTowardsSample - Variable in class loci.formats.in.SlideBook7Reader.CAnnotation70
mZStartPosition - Variable in class loci.formats.in.SlideBook7Reader.CExposureRecord70

## N

N_ACCUMULATIONS - Static variable in class loci.formats.in.FluoviewReader
N_FRAMES - Static variable in class loci.formats.in.FluoviewReader
na - Variable in class loci.formats.in.ND2Handler
na - Variable in class loci.formats.in.OIRReader.Objective
NAFReader - Class in loci.formats.in
  NAFReader is the file format reader for Hamamatsu Aquacosmos NAF files.
NAFReader() - Constructor for class loci.formats.in.NAFReader
  Constructs a new NAF reader.
name - Variable in enum 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 - Static variable in class loci.formats.filter.LZ4Filter
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.LeicaMicrosystemsMetadata.LofXmlDocument
name - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.ROI
name - Variable in class loci.formats.in.LeicaReader.Detector
name - Variable in class loci.formats.in.LeicaSCNReader.Image
name - Variable in class loci.formats.in.LeicaSCNReader.ImageCollection
name - Variable in class loci.formats.in.LiFlimReader.ROI
name - Variable in class loci.formats.in.LIFReader.ROI
name - Variable in class loci.formats.in.MicromanagerReader.Position
name - Variable in class loci.formats.in.ND2Reader.ChunkMapEntry
name - Variable in class loci.formats.in.OIRReader.Channel
name - Variable in class loci.formats.in.OIRReader.Laser
name - Variable in class loci.formats.in.OIRReader.Objective
name - Variable in class loci.formats.in.TecanReader.Channel
name - Variable in class loci.formats.in.TissueFAXSReader.Channel
name - Variable in class loci.formats.in.ZeissCZIReader.AttachmentEntry
name - Variable in class loci.formats.in.ZeissCZIReader.Channel
name - Variable in class loci.formats.in.ZeissLSMReader.DataChannel
name - Variable in class loci.formats.in.ZeissLSMReader.IlluminationChannel
name - Variable in class loci.formats.in.ZeissLSMReader.Recording
name - Variable in enum loci.formats.tiff.PhotoInterp
  Given name of the photometric interpretation.
name - Variable in class loci.plugins.config.LibraryEntry
name - Variable in class loci.plugins.in.IdDialog
name - Variable in class loci.plugins.util.RecordedImageProcessor.MethodEntry
nameLength - Variable in class loci.formats.in.LeicaReader
nameLookup - Static variable in enum loci.formats.dicom.DicomAttribute
nameOfMeasuredQuantity - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.Channel
names - Variable in class loci.formats.in.FlexReader.FlexHandler
names - Static variable in class loci.plugins.shortcut.ShortcutPanel
  Details for installed plugins.
NAMESPACE - Static variable in class loci.formats.ome.OMEPyramidStore
nameStack - Variable in class loci.formats.in.LeicaHandler
nameStack - Variable in class loci.formats.in.LeicaSCNReader.LeicaSCNHandler
nameStack - Variable in class loci.formats.in.ZeissTIFFHandler
NATIVE_LIB_CLASS - Static variable in class loci.formats.services.JPEGTurboServiceImpl
nativeReader - Variable in class loci.formats.DelegateReader
  Native reader.
nativeReaderInitialized - Variable in class loci.formats.DelegateReader
  Flag indicating that the native reader was successfully initialized.
nBuffers - Variable in class loci.formats.in.SPCReader
nChannels - Variable in class loci.formats.gui.SignedColorModel
nChannels - Variable in class loci.formats.gui.UnsignedIntColorModel
nChannels - Variable in class loci.formats.in.InCellReader.MinimalInCellHandler
nChannels - Variable in class loci.formats.in.SPCReader
  Number of spectral nChannels.
nColorPlanes - Variable in class loci.formats.in.PCXReader
nCols - Variable in class loci.formats.in.FlexReader
nCols - Variable in class loci.formats.in.HamamatsuVMSReader
ncx - Variable in class loci.formats.in.SDTInfo
ncy - Variable in class loci.formats.in.SDTInfo
ND2_MAGIC_BYTES_1 - Static variable in class loci.formats.in.ND2Reader
ND2_MAGIC_BYTES_2 - Static variable in class loci.formats.in.ND2Reader
ND2Handler - Class in loci.formats.in
  DefaultHandler implementation for handling XML produced by Nikon Elements.
ND2Handler(CoreMetadataList, 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.
ND2Reader.ChunkMapEntry - Class in loci.formats.in
ND2Widgets - Class in loci.plugins.config
  Custom widgets for configuring Bio-Formats ND2 support.
ND2Widgets() - Constructor for class loci.plugins.config.ND2Widgets
ND_ENCODING - Static variable in class loci.formats.in.MetamorphReader
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
NDINFOFILE_VER1 - Static variable in class loci.formats.in.MetamorphReader
NDINFOFILE_VER2 - Static variable in class loci.formats.in.MetamorphReader
ndpiFiles - Variable in class loci.formats.in.NDPISReader
NDPIReader - Class in loci.formats.in
  NDPIReader is the file format reader for Hamamatsu .ndpi files.
NDPIReader() - Constructor for class loci.formats.in.NDPIReader
  Constructs a new NDPI reader.
NDPISReader - Class in loci.formats.in
  NDPISReader is the file format reader for Hamamatsu .ndpis files.
NDPISReader() - Constructor for class loci.formats.in.NDPISReader
  Constructs a new NDPIS reader.
needMem - Variable in class loci.plugins.in.MemoryDialog
  Required memory for the dataset, in bytes.
needPrompt() - Method in class loci.plugins.in.ColorDialog
needPrompt() - Method in class loci.plugins.in.CropDialog
needPrompt() - Method in class loci.plugins.in.FilePatternDialog
needPrompt() - Method in class loci.plugins.in.IdDialog
needPrompt() - Method in class loci.plugins.in.ImporterDialog
needPrompt() - Method in class loci.plugins.in.LocationDialog
needPrompt() - Method in class loci.plugins.in.MainDialog
needPrompt() - Method in class loci.plugins.in.MemoryDialog
needPrompt() - Method in class loci.plugins.in.RangeDialog
needPrompt() - Method in class loci.plugins.in.SeriesDialog
needPrompt() - Method in class loci.plugins.in.SwapDialog
needPrompt() - Method in class loci.plugins.in.UpgradeDialog
NEF_SUFFIX - Static variable in class loci.formats.in.NikonReader
netcdf - Variable in class loci.formats.in.ImarisHDFReader
netcdf - Variable in class loci.formats.in.MINCReader
netcdf - Variable in class loci.formats.in.VeecoReader
netCDFFile - Variable in class loci.formats.services.NetCDFServiceImpl
  NetCDF file instance.
NetCDFService - Interface in loci.formats.services
  Utility class for working with NetCDF/HDF files.
NetCDFServiceImpl - Class in loci.formats.services
  Utility class for working with NetCDF/HDF files.
NetCDFServiceImpl() - Constructor for class loci.formats.services.NetCDFServiceImpl
  Default constructor.
NEW_MDIM_VOLUME_HEADER - Static variable in class loci.formats.in.CellSensReader
NEW_SUBFILE_TYPE - Static variable in class loci.formats.tiff.IFD
NEW_TYPE - Static variable in class loci.formats.in.DeltavisionReader
NEW_VOLUME_HEADER - Static variable in class loci.formats.in.CellSensReader
newFileType - Variable in class loci.formats.in.DeltavisionReader
newOrder - Variable in class loci.formats.AxisGuesser
  Adjusted ordering of internal dimensional axes.
newVersionAvailable(String) - Method in class loci.formats.UpgradeChecker
  Contact the OME registry and return true if a new version is available.
newVersionAvailable(String, String) - Method in class loci.formats.UpgradeChecker
  Contact the OME registry and return true if a new version is available.
nextBlockOffs - Variable in class loci.formats.in.SDTInfo
  Offset to the data block header of the next data block.
nextCamera - Variable in class loci.formats.in.FlexReader.FlexHandler
nextChannel - Variable in class loci.formats.in.LeicaHandler
nextChannel - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataStoreInitializer
nextChannel - Variable in class loci.formats.in.LeicaReader
nextChName - Variable in class loci.formats.in.BaseZeissReader
nextDetectChannel - Variable in class loci.formats.in.ZeissLSMReader
nextDetector - Variable in class loci.formats.in.LeicaReader
nextDetector - Variable in class loci.formats.in.ZeissLSMReader
nextDichroic - Variable in class loci.formats.in.FlexReader.FlexHandler
nextDichroic - Variable in class loci.formats.in.ZeissLSMReader
nextDichroicChannel - Variable in class loci.formats.in.ZeissLSMReader
nextEmWave - Variable in class loci.formats.in.BaseZeissReader
nextExWave - Variable in class loci.formats.in.BaseZeissReader
nextFilter - Variable in class loci.formats.in.FlexReader.FlexHandler
nextFilter - Variable in class loci.formats.in.LeicaHandler
nextFilter - Variable in class loci.formats.in.ZeissLSMReader
nextFilterSet - Variable in class loci.formats.in.FlexReader.FlexHandler
nextIFDPointer - Variable in class loci.formats.out.DicomWriter
nextIllumChannel - Variable in class loci.formats.in.ZeissLSMReader
nextImage - Variable in class loci.formats.in.FlexReader.FlexHandler
nextLaser - Variable in class loci.formats.in.FlexReader.FlexHandler
nextLaser - Variable in class loci.formats.in.ZeissLSMReader
nextLetter() - Method in class loci.formats.ResourceNamer
  Increments the internal alphabet pointer to the next element of the alphabet.
nextObjective - Variable in class loci.formats.in.FlexReader.FlexHandler
nextPlate - Variable in class loci.formats.in.FlexReader.FlexHandler
nextPlate - Variable in class loci.formats.in.InCellReader.InCellHandler
nextReadPosition - Variable in class loci.formats.in.OBFReader.State
nextROI - Variable in class loci.formats.in.LeicaHandler
nextSequenceNumber - Variable in class loci.formats.out.APNGWriter
nextSliderRef - Variable in class loci.formats.in.FlexReader.FlexHandler
nextTag - Variable in class loci.formats.in.OpenlabReader
nextXPos - Variable in class loci.formats.in.ScanrReader.ScanrHandler
nextYPos - Variable in class loci.formats.in.ScanrReader.ScanrHandler
nFields - Variable in class loci.formats.in.ColumbusReader
nFiles - Variable in class loci.formats.in.FlexReader
nFrames - Variable in class loci.formats.in.SPCReader
ni - Variable in class loci.formats.in.BrukerReader
NiftiReader - Class in loci.formats.in
  NiftiReader is the file format reader for NIfTI files.
NiftiReader() - Constructor for class loci.formats.in.NiftiReader
  Constructs a new NIfTI reader.
NIKON_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_NETCDF_MSG - Static variable in class loci.formats.services.NetCDFServiceImpl
NO_OME_XML_MSG - Static variable in class loci.formats.services.OMEXMLServiceImpl
node - Variable in class loci.formats.gui.XMLCellRenderer.XMLItem
nodeToString(Node) - Method in class loci.formats.in.LeicaMicrosystemsMetadata.LMSXmlDocument
NoExtensionFileFilter - Class in loci.formats.gui
  A file filter that selects files with no extension, for use with a JFileChooser.
NoExtensionFileFilter() - Constructor for class loci.formats.gui.NoExtensionFileFilter
noise(double) - Method in class loci.plugins.util.RecordedImageProcessor
NOISE_REDUCTION - Static variable in class loci.formats.in.CellSensReader
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
NORMAL_MENU - Static variable in class loci.plugins.shortcut.ShortcutPanel
  Name of the 'Bio-Formats' submenu.
NORMAL_PRIORITY - Static variable in interface loci.formats.cache.ICacheStrategy
normalize() - Method in class loci.formats.in.LeicaHandler.ROI
  Vertices and transformation values are not stored in pixel coordinates.
normalize() - Method in class loci.formats.in.LeicaMicrosystemsMetadata.ROI
  Vertices and transformation values are not stored in pixel coordinates.
normalize() - Method in class loci.formats.in.LIFReader.ROI
  Vertices and transformation values are not stored in pixel coordinates.
normalizeColor(String) - Method in class loci.formats.in.ZeissCZIReader
normalized - Variable in class loci.formats.in.LeicaHandler.ROI
normalized - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.ROI
normalized - Variable in class loci.formats.in.LIFReader.ROI
normalizeData - Variable in class loci.formats.FormatReader
  Whether or not to normalize float data.
normalizeFilename(String, String) - Method in class loci.formats.in.OMETiffReader
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.
nTimepoints - Variable in class loci.formats.in.CellWorxReader
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_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.
NUMBEROFDARKIMAGES_KEY - Static variable in class loci.formats.in.LiFlimReader
NUMBEROFFRAMES_KEY - Static variable in class loci.formats.in.LiFlimReader
numBlocks - Variable in class loci.formats.in.KLBReader
numBytes - Variable in class loci.formats.in.AliconaReader
  Number of bytes per pixel (either 1 or 2).
numBytes - Variable in class loci.formats.out.QTWriter
  Total number of pixel bytes.
numChannels - Variable in class loci.formats.in.LeicaHandler
numDatasets - Variable in class loci.formats.in.LeicaHandler
numDecompositionLevels - Variable in class loci.formats.codec.JPEG2000CodecOptions
  The number of decomposition levels as would be provided to: `J2KImageWriteParam.setNumDecompositionLevels(int)` (WRITE).
numer - Variable in class loci.formats.tiff.TiffRational
  Components of the rational's fractional representation.
numeric - Variable in class loci.formats.FilePatternBlock
  Whether or not this is a numeric block.
NUMERICAL_APERTURE - Static variable in class loci.formats.in.CellSensReader
numericalAperture - Variable in class loci.formats.in.CellSensReader.Pyramid
NumericComparator() - Constructor for class loci.formats.in.MetamorphTiffReader.NumericComparator
numFloatsPerSection - Variable in class loci.formats.in.DeltavisionReader
numFrames - Variable in class loci.formats.out.APNGWriter
numFramesPointer - Variable in class loci.formats.out.APNGWriter
numIntsPerSection - Variable in class loci.formats.in.DeltavisionReader
  The number of ints in each extended header section.
NUMOP - Static variable in class org.libjpegturbo.turbojpeg.TJTransform
  The number of lossless transform operations
NUMPF - Static variable in class org.libjpegturbo.turbojpeg.TJ
  The number of pixel formats
numPixelBytes - Variable in class loci.formats.in.GatanReader
numRegions - Variable in class loci.formats.in.LiFlimReader
NUMSAMP - Static variable in class org.libjpegturbo.turbojpeg.TJ
  The number of chrominance subsampling options
numSeries - Variable in class loci.formats.in.LeicaReader
  Number of series in the file.
numSeries - Variable in class loci.formats.in.ND2Handler
numWritten - Variable in class loci.formats.out.QTWriter
nXFields - Variable in class loci.formats.in.ND2Handler
nXFields - Variable in class loci.formats.in.ND2Reader
nYFields - Variable in class loci.formats.in.ND2Handler

## O

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
objectiveMag - Variable in class loci.formats.in.ND2Reader
objectiveManufacturer - Variable in class loci.formats.in.FluoviewReader
objectiveModel - Variable in class loci.formats.in.ND2Handler
objectiveModel - Variable in class loci.formats.in.ND2Reader
objectiveModels - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataTempBuffer
objectiveModels - Variable in class loci.formats.in.LIFReader
objectiveName - Variable in class loci.formats.in.CellSensReader.Pyramid
objectiveName - Variable in class loci.formats.in.FV1000Reader
objectiveNames - Variable in class loci.formats.in.CellSensReader.Pyramid
objectiveRefs - Variable in class loci.formats.in.FlexReader
objectives - Variable in class loci.formats.in.OIRReader
objectiveSettingsID - Variable in class loci.formats.in.ZeissCZIReader
objectiveTypes - Variable in class loci.formats.in.CellSensReader.Pyramid
objMag - Variable in class loci.formats.in.LeicaSCNReader.Image
OBS - Static variable in class loci.formats.gui.AWTImageTools
  ImageObserver for working with AWT images.
ocr - Variable in class loci.formats.in.LeicaSCNReader.ImageCollection
od - Variable in class loci.plugins.in.IdDialog
oddLocations - Variable in class loci.formats.dicom.DicomTag
OECF - Static variable in class loci.formats.tiff.IFD
offByOneLength - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.Dimension
offset - Variable in class loci.formats.in.APNGReader.PNGBlock
offset - Variable in class loci.formats.in.BDReader
offset - Variable in class loci.formats.in.BioRadGelReader
offset - Variable in class loci.formats.in.BioRadReader
offset - Variable in class loci.formats.in.CellSensReader.Pyramid
offset - Variable in class loci.formats.in.ICSReader
  Offset to pixel data.
offset - Variable in class loci.formats.in.IM3Reader.IM3Record
offset - Variable in class loci.formats.in.IvisionReader
offset - Variable in class loci.formats.in.KhorosReader
  Image offset.
offset - Variable in class loci.formats.in.LeicaHandler.Detector
offset - Variable in class loci.formats.in.LeicaReader.Detector
offset - Variable in class loci.formats.in.MRWReader
  Offset to image data.
offset - Variable in class loci.formats.in.NRRDReader
  Offset to pixel data.
offset - Variable in class loci.formats.in.OIRReader.Detector
offset - Variable in class loci.formats.in.OIRReader.PixelBlock
offset - Variable in class loci.formats.in.PCXReader
  Offset to pixel data.
offset - Variable in class loci.formats.in.PGMReader
  Offset to pixel data.
offset - Variable in class loci.formats.in.PSDReader
  Offset to pixel data.
offset - Variable in class loci.formats.in.SDTInfo
offset - Variable in enum 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.FlexReader.FlexFile
offsets - Variable in class loci.formats.in.FluoviewReader
offsets - Variable in class loci.formats.in.ImarisReader
  Offsets to each image.
offsets - Variable in class loci.formats.in.LOFReader
  Offsets to memory blocks, paired with their corresponding description.
offsets - Variable in class loci.formats.in.MNGReader.SeriesInfo
offsets - Variable in class loci.formats.in.NAFReader
offsets - Variable in class loci.formats.in.ND2Reader
  Array of image offsets.
offsets - Variable in class loci.formats.in.OpenlabRawReader
  Offset to each image's pixel data.
offsets - Variable in class loci.formats.in.QTReader
  Offsets to each plane's pixel data.
offsets - Variable in class loci.formats.in.ZeissLMSReader
offsets - Variable in class loci.formats.out.QTWriter
  Vector of plane offsets.
offsetToFooter - Variable in class loci.formats.in.DCIMGReader
offsetToFourPixels - Variable in class loci.formats.in.DCIMGReader
OIB_SUFFIX - Static variable in class loci.formats.in.FV1000Reader
oibMapping - Variable in class loci.formats.in.FV1000Reader
  File mappings for OIB file.
OIF_SUFFIX - Static variable in class loci.formats.in.FV1000Reader
OIRReader - Class in loci.formats.in
  OIRReader is the file format reader for Olympus .oir files.
OIRReader() - Constructor for class loci.formats.in.OIRReader
  Constructs a new OIR reader.
OIRReader.Channel - Class in loci.formats.in
OIRReader.CZTKey - Class in loci.formats.in
  This is a class that wraps three numbers c,z,t and an object can be used as a key in a hashmap.
OIRReader.Detector - Class in loci.formats.in
OIRReader.Laser - Class in loci.formats.in
OIRReader.Objective - Class in loci.formats.in
OIRReader.PixelBlock - Class in loci.formats.in
OLD_PHYSICAL_SIZE_DEFAULT - Static variable in class loci.formats.in.LeicaMicrosystemsMetadata.LMSFileReader
OLD_PHYSICAL_SIZE_DEFAULT - Static variable in class loci.formats.in.LIFReader
OLD_PHYSICAL_SIZE_KEY - Static variable in class loci.formats.in.LeicaMicrosystemsMetadata.LMSFileReader
OLD_PHYSICAL_SIZE_KEY - Static variable in class loci.formats.in.LIFReader
OLD_TOOLS - Static variable in class loci.formats.UpgradeChecker
  Deprecated.
  Removed in Bio-Formats 6.9.0
oldPhysicalSize - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.Dimension
OlympusTileReader - Class in loci.formats.in
  OlympusTileReader is the file format reader for Olympus .omp2info files.
OlympusTileReader() - Constructor for class loci.formats.in.OlympusTileReader
  Constructs a new Olympus .omp2info reader.
OlympusTileReader.Tile - Class in loci.formats.in
ome_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() - 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.DCIMGReader
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.DeltavisionReader
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.DicomReader
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.DNGReader
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.Ecat7Reader
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.EPSReader
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.FakeReader
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.FEIReader
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.FitsReader
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.FlexReader
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.FlowSightReader
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.FluoviewReader
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.FujiReader
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.FV1000Reader
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.GatanDM2Reader
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.GatanReader
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.GelReader
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.GIFReader
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.HamamatsuVMSReader
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.HISReader
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.HitachiReader
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.HRDGDFReader
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.I2IReader
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.ICSReader
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.IM3Reader
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.ImaconReader
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.ImagicReader
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.ImarisHDFReader
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.ImarisReader
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.IMODReader
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.ImprovisionTiffReader
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.ImspectorReader
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.InCell3000Reader
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.InCellReader
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.INRReader
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.InveonReader
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.IonpathMIBITiffReader
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.IPLabReader
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.IPWReader
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.IvisionReader
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.JDCEReader
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.JEOLReader
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.JPEG2000Reader
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.JPKReader
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.JPXReader
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.KhorosReader
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.KLBReader
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.KodakReader
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.L2DReader
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.LeicaMicrosystemsMetadata.MultipleImagesReader
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.LeicaReader
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.LeicaSCNReader
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.LiFlimReader
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.LIFReader
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.LIMReader
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.LOFReader
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.MetamorphReader
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.MetamorphTiffReader
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.MIASReader
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.MicroCTReader
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.MicromanagerReader
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.MINCReader
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.MinimalTiffReader
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.MolecularImagingReader
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.MRCReader
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.MRWReader
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.NAFReader
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.ND2Reader
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.NDPIReader
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.NDPISReader
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.NiftiReader
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.NikonReader
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.NRRDReader
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.OBFReader
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.OIRReader
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.OlympusTileReader
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.OMETiffReader
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.OMEXMLReader
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.OpenlabRawReader
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.OpenlabReader
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.OperettaReader
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.OxfordInstrumentsReader
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.PCIReader
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.PCORAWReader
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.PCXReader
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.PDSReader
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.PerkinElmerReader
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.PGMReader
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.PhotoshopTiffReader
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.PictReader
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.PovrayReader
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.PQBinReader
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.PrairieReader
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.PSDReader
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.PyramidTiffReader
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.QTReader
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.QuesantReader
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.RHKReader
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.SBIGReader
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.ScanrReader
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.SDTReader
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.SeikoReader
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.SEQReader
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.SIFReader
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.SimplePCITiffReader
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.SlideBook7Reader
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.SlidebookReader
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.SlidebookTiffReader
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.SMCameraReader
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.SPCReader
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.SPEReader
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.SpiderReader
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.SVSReader
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.TargaReader
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.TCSReader
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.TecanReader
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.TextReader
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.TiffDelegateReader
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.TileJPEGReader
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.TillVisionReader
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.TissueFAXSReader
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.TopometrixReader
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.TrestleReader
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.UBMReader
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.UnisokuReader
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.VarianFDFReader
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.VectraReader
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.VeecoReader
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.VentanaReader
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.VGSAMReader
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.VisitechReader
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.VolocityClippingReader
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.VolocityReader
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.WATOPReader
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.XLEFReader
openBytes(int, int, int, int, int) - Method in class loci.formats.in.XLEFReader
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.ZeissCZIReader
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.ZeissLMSReader
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.ZeissLSMReader
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.ZeissTIFFReader
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.ZeissXRMReader
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.ZeissZVIReader
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.ZipReader
openBytes(int) - 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
openBytesJpeg(int, byte[], int, int, int, int) - Method in class loci.formats.in.XLEFReader
  Gets bytes of jpeg images.
openCompressedBytes(int, int, int) - Method in class loci.formats.ChannelFiller
openCompressedBytes(int, byte[], int, int) - Method in class loci.formats.ChannelFiller
openCompressedBytes(int, int, int) - Method in class loci.formats.ChannelMerger
openCompressedBytes(int, byte[], int, int) - Method in class loci.formats.ChannelMerger
openCompressedBytes(int, int, int) - Method in class loci.formats.ChannelSeparator
openCompressedBytes(int, byte[], int, int) - Method in class loci.formats.ChannelSeparator
openCompressedBytes(int, int, int) - Method in class loci.formats.DimensionSwapper
openCompressedBytes(int, byte[], int, int) - Method in class loci.formats.DimensionSwapper
openCompressedBytes(int, int, int) - Method in class loci.formats.FileStitcher
openCompressedBytes(int, byte[], int, int) - Method in class loci.formats.FileStitcher
openCompressedBytes(int, int, int) - Method in interface loci.formats.ICompressedTileReader
  Retrieve the specified tile without performing any decompression.
openCompressedBytes(int, byte[], int, int) - Method in interface loci.formats.ICompressedTileReader
  Retrieve the specified tile without performing any decompression.
openCompressedBytes(int, int, int) - Method in class loci.formats.ImageReader
openCompressedBytes(int, byte[], int, int) - Method in class loci.formats.ImageReader
openCompressedBytes(int, int, int) - Method in class loci.formats.in.DicomReader
openCompressedBytes(int, byte[], int, int) - Method in class loci.formats.in.DicomReader
openCompressedBytes(int, int, int) - Method in class loci.formats.in.NDPIReader
openCompressedBytes(int, byte[], int, int) - Method in class loci.formats.in.NDPIReader
openCompressedBytes(int, int, int) - Method in class loci.formats.in.SVSReader
openCompressedBytes(int, byte[], int, int) - Method in class loci.formats.in.SVSReader
openCompressedBytes(int, int, int) - Method in class loci.formats.ReaderWrapper
openCompressedBytes(int, byte[], int, int) - Method in class loci.formats.ReaderWrapper
openCompressedBytes(int, int, int) - Method in class loci.formats.TileStitcher
openCompressedBytes(int, byte[], int, int) - Method in class loci.formats.TileStitcher
openConnection() - Method in class loci.formats.in.TecanReader
openConnection(String) - Method in class loci.formats.in.TecanReader
openConnection(String) - Method in class loci.formats.in.TissueFAXSReader
OPENER_PLUGIN - Static variable in class loci.plugins.shortcut.ShortcutPanel
  Name of plugin to use for opening dropped files.
openerIndex - Static variable in class loci.plugins.shortcut.ShortcutPanel
  Index of plugin to use to open dropped files.
openFile(int, int) - Method in class loci.formats.out.DicomWriter
openFile(File) - Method in class loci.formats.tools.EditTiffG
openFile(File, RandomAccessInputStream) - Method in class loci.formats.tools.EditTiffG
openFile(String) - Static method in class loci.formats.tools.EditTiffG
  Deprecated.
openFiles - Variable in class loci.formats.in.MetamorphReader
openGreyscaleBytes(IFD, int, int) - Method in class loci.formats.in.FlowSightReader
  Decode the whole IFD plane using greyscale compression
openImage(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.
openPixelTag() - Method in class loci.formats.in.PhotoshopTiffReader
openPlane(int, int, int, int, int) - Method in class loci.formats.FileStitcher
openPlane(int, int, int, int, int) - Method in class loci.formats.FormatReader
openPlane(int, int, int, int, int) - Method in interface loci.formats.IFormatReader
  Obtains the specified image plane (or sub-image thereof) in the reader's native data structure.
openPlane(int, int, int, int, int) - Method in class loci.formats.ImageReader
openPlane(int, int, int, int, int) - Method in class loci.formats.in.ImageIOReader
openPlane(int, int, int, int, int) - Method in class loci.formats.in.MNGReader
openPlane(int, int, int, int, int) - Method in class loci.formats.in.TextReader
openPlane(int, int, int, int, int) - Method in class loci.formats.in.TiffJAIReader
openPlane(int, int, int, int, int) - Method in class loci.formats.ReaderWrapper
openPlane(int, int, int, int, int) - Method in class loci.formats.WrappedReader
openPlane(int, int, int, int, int) - Method in class loci.plugins.util.ImageProcessorReader
openProcessors(int) - Method in class loci.plugins.util.ImageProcessorReader
  Creates an ImageJ image processor object for the image plane at the given position.
openProcessors(int, int, int, int, int) - Method in class loci.plugins.util.ImageProcessorReader
  Returns an array of ImageProcessors that represent the given slice.
openRaw() - Method in class loci.formats.in.IM3Reader
  Open the current series in raw-mode, returning the interleaved image bytes.
openROIs(IMetadata, ImagePlus[]) - Static method in class loci.plugins.util.ROIHandler
  Look for ROIs in the given OMEXMLMetadata; if any are present, apply them to the given images and display them in the ROI manager.
openROIs(IMetadata, ImagePlus[], boolean) - Static method in class loci.plugins.util.ROIHandler
  Opens the rois and converts them into ImageJ Rois.
openROIs(IMetadata, ImagePlus[], boolean, String) - Static method in class loci.plugins.util.ROIHandler
  Opens the rois and converts them into ImageJ Rois.
openSubImage(String, Double, Double, Double, Double, Double) - Method in class loci.plugins.macro.LociFunctions
openThumbBytes(int) - Method in class loci.formats.ChannelSeparator
openThumbBytes(int) - Method in class loci.formats.DimensionSwapper
openThumbBytes(int) - Method in class loci.formats.FileStitcher
openThumbBytes(int) - Method in class loci.formats.FormatReader
openThumbBytes(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
OPERETTA_MAGIC - Static variable in class loci.formats.in.OperettaReader
OperettaHandler() - Constructor for class loci.formats.in.OperettaReader.OperettaHandler
OperettaReader - Class in loci.formats.in
  OperettaReader is the file format reader for PerkinElmer Operetta data.
OperettaReader() - Constructor for class loci.formats.in.OperettaReader
  Constructs a new Operetta reader.
OperettaReader.Channel - Class in loci.formats.in
OperettaReader.OperettaHandler - Class in loci.formats.in
OperettaReader.Plane - Class in loci.formats.in
OPT_CROP - Static variable in class org.libjpegturbo.turbojpeg.TJTransform
  This option will enable lossless cropping.
OPT_GRAY - Static variable in class org.libjpegturbo.turbojpeg.TJTransform
  This option will discard the color data in the input image and produce a grayscale output image.
OPT_NOOUTPUT - Static variable in class org.libjpegturbo.turbojpeg.TJTransform
  This option will prevent `TJTransformer.transform()` from outputting a JPEG image for this particular transform.
OPT_PERFECT - Static variable in class org.libjpegturbo.turbojpeg.TJTransform
  This option will cause `TJTransformer.transform()` to throw an exception if the transform is not perfect.
OPT_TRIM - Static variable in class org.libjpegturbo.turbojpeg.TJTransform
  This option will discard any partial MCU blocks that cannot be transformed.
OPTICAL_PATH - Static variable in class loci.formats.in.CellSensReader
optimalTileHeight - Variable in class loci.formats.in.OIRReader
Option - Class in loci.plugins.prefs
  Base class for an option for one of the plugins.
Option(String, boolean, String, String) - Constructor for class loci.plugins.prefs.Option
  Constructs an option with the given parameters.
options - Variable in class loci.formats.ClassList
  List of options.
options - Variable in class loci.formats.FormatWriter
  The options if required.
options - Variable in class loci.formats.tiff.TiffSaver
  The codec options if set.
options - Variable in class loci.plugins.in.DisplayHandler
options - Variable in class loci.plugins.in.ImporterDialog
options - Variable in class loci.plugins.in.ImportProcess
  Associated importer options.
options - Variable in class loci.plugins.prefs.OptionsList
  Table of options defining this set of preferences.
options - Variable in class loci.plugins.util.DataBrowser
options - Variable in class org.libjpegturbo.turbojpeg.TJTransform
  Transform options (bitwise OR of one or more of `OPT_*`)
OptionsDialog - Class in loci.plugins.prefs
  Base class for options dialogs.
OptionsDialog(OptionsList) - Constructor for class loci.plugins.prefs.OptionsDialog
  Creates a new options dialog with the given associated options.
optionsList - Variable in class loci.plugins.prefs.OptionsDialog
  Options list associated with the dialog.
OptionsList - Class in loci.plugins.prefs
  Base class for ImageJ preferences for plugins.
OptionsList(String, Class<?>) - Constructor for class loci.plugins.prefs.OptionsList
OptionsList(IniList) - Constructor for class loci.plugins.prefs.OptionsList
optionsWindow - Variable in class loci.plugins.util.DataBrowser
or(int) - Method in class loci.plugins.util.RecordedImageProcessor
order - Variable in class loci.formats.cache.CacheStrategy
  The order in which planes should be loaded along each axis.
order - Variable in class loci.formats.gui.CacheComponent
  Combo boxes for choosing planar ordering.
ORDER - Static variable in class loci.plugins.out.Exporter
ORDER_CHANGED - Static variable in class loci.formats.cache.CacheEvent
  Event type indicating new planar ordering.
ORDER_DEFAULT - Static variable in class loci.plugins.in.ImporterOptions
ORDER_VALUES - Static variable in class loci.formats.gui.CacheComponent
ORDER_XYCTZ - Static variable in class loci.plugins.in.ImporterOptions
ORDER_XYCZT - Static variable in class loci.plugins.in.ImporterOptions
ORDER_XYTCZ - Static variable in class loci.plugins.in.ImporterOptions
ORDER_XYTZC - Static variable in class loci.plugins.in.ImporterOptions
ORDER_XYZCT - Static variable in class loci.plugins.in.ImporterOptions
ORDER_XYZTC - Static variable in class loci.plugins.in.ImporterOptions
orderCertain - Variable in class loci.formats.CoreMetadata
  Indicates whether or not we are confident that the dimension order is correct.
orderIndex(int) - Method in class loci.formats.gui.CacheComponent
  Converts enumerated order value to order chooser index.
ordering - Variable in class loci.formats.in.BrukerReader
ORDERS - Static variable in class loci.formats.gui.CacheComponent
orderValue(int) - Method in class loci.formats.gui.CacheComponent
  Converts order chooser index to enumerated order value.
org.libjpegturbo.turbojpeg - package org.libjpegturbo.turbojpeg
orientation - Variable in class loci.formats.in.TargaReader
ORIENTATION - Static variable in class loci.formats.tiff.IFD
orientationMatrix - Variable in class loci.formats.in.OperettaReader.Channel
orientationMatrix - Variable in class loci.formats.in.OperettaReader.Plane
origin - Variable in class loci.formats.in.ZeissTIFFHandler.Scaling.Dimension
original - Variable in class loci.formats.in.DNGReader
  The original IFD.
original - Variable in class loci.formats.in.NikonReader
  The original IFD.
ORIGINAL_FRAME_RATE - Static variable in class loci.formats.in.CellSensReader
ORIGINAL_METADATA_NS - Static variable in class loci.formats.meta.OriginalMetadataAnnotation
originalDate - Variable in class loci.formats.in.DicomReader
originalID - Variable in class loci.plugins.in.FilePatternDialog
originalInstance - Variable in class loci.formats.in.DicomReader
originalMetadata - Variable in class loci.formats.in.CellSensReader.Pyramid
OriginalMetadataAnnotation - Class in loci.formats.meta
OriginalMetadataAnnotation() - Constructor for class loci.formats.meta.OriginalMetadataAnnotation
originalName - Variable in class loci.formats.in.TecanReader.Channel
originalOrder - Variable in class loci.formats.FileStitcher.ExternalSeries
originalSeries - Variable in class loci.formats.in.DicomReader
originalSpecimen - Variable in class loci.formats.in.DicomReader
originalStudyTime - Variable in class loci.formats.in.DicomReader
originalTime - Variable in class loci.formats.in.DicomReader
originalX - Variable in class loci.formats.in.DicomReader
originalY - Variable in class loci.formats.in.DicomReader
originX - Variable in class loci.formats.in.CellSensReader.Pyramid
originX - Variable in class loci.formats.in.PerkinElmerReader
originX - Variable in class loci.formats.in.VarianFDFReader
originX - Variable in class loci.formats.in.ZeissLSMReader
originY - Variable in class loci.formats.in.CellSensReader.Pyramid
originY - Variable in class loci.formats.in.PerkinElmerReader
originY - Variable in class loci.formats.in.VarianFDFReader
originY - Variable in class loci.formats.in.ZeissLSMReader
originZ - Variable in class loci.formats.in.PerkinElmerReader
originZ - Variable in class loci.formats.in.VarianFDFReader
originZ - Variable in class loci.formats.in.ZeissLSMReader
origname - Variable in class loci.formats.in.ZeissTIFFReader.TIFFInfo
OTHER_KEYS - Static variable in class loci.formats.in.ICSReader
otherChannels - Variable in class loci.plugins.util.RecordedImageProcessor
otherExposureTimes - Variable in class loci.formats.in.CellSensReader.Pyramid
out - Variable in class loci.formats.FormatWriter
  Current file.
out - Variable in class loci.formats.tiff.TiffSaver
  Output stream to use when saving TIFF data.
output - Variable in class loci.formats.gui.DataConverter
output - Variable in class loci.formats.Memoizer.KryoDeser
outputOrder - Variable in class loci.formats.out.ICSWriter
outputOrder - Variable in class loci.formats.out.V3DrawWriter
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
overlapX - Variable in class loci.formats.in.TissueFAXSReader.ScanRegion
overlapY - Variable in class loci.formats.in.TissueFAXSReader.ScanRegion
overlay - Variable in class loci.formats.in.TecanReader.Image
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
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
packing - Variable in class loci.formats.in.LiFlimReader
PACKING_KEY - Static variable in class loci.formats.in.LiFlimReader
pad - Variable in class loci.formats.out.QTWriter
  Number of padding bytes in each row.
PAD - Static variable in class loci.plugins.config.ConfigWindow
padding - Variable in class loci.formats.in.UBMReader
PADDING_BYTES - Static variable in class loci.formats.out.AVIWriter
paddingZeros - Variable in class loci.plugins.in.FilePatternDialog
padImage(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.
padString(String) - Method in class loci.formats.out.DicomWriter
  Pad the given string so that the length is a multiple of 2.
padString(String, String) - Method in class loci.formats.out.DicomWriter
padString(String, String, int) - Method in class loci.formats.out.DicomWriter
padTagValues(DicomTag) - Method in class loci.formats.out.DicomWriter
padUID(String) - Method in class loci.formats.out.DicomWriter
  Pad the given string so that the length is a multiple of 2.
PAETH - Static variable in class loci.formats.in.APNGReader
page - Variable in class loci.formats.in.PrairieMetadata.PFile
  `page` attribute of this `<File>`.
page - Variable in class loci.formats.in.SDTInfo
PAGE_NAME - Static variable in class loci.formats.tiff.IFD
PAGE_NUMBER - Static variable in class loci.formats.tiff.IFD
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.dicom.DicomTag
parent - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.LMSXmlDocument
parentDimension - Variable in class loci.formats.Modulo
parentDir - Variable in class loci.formats.in.CV7000Reader.MeasurementDataHandler
parentNames - Variable in class loci.formats.in.FEITiffReader.FEIHandler
parentQName - Variable in class loci.formats.in.FlexReader.FlexHandler
parentType - Variable in class loci.formats.Modulo
parse(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.
parse(int, long, long) - Method in class loci.formats.in.QTReader
  Parse all of the atoms in the file.
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
parseDCAMVersion0Footer(RandomAccessInputStream) - Method in class loci.formats.in.DCIMGReader
parseDCAMVersion0Header(RandomAccessInputStream) - Method in class loci.formats.in.DCIMGReader
parseDCAMVersion1Header(RandomAccessInputStream) - Method in class loci.formats.in.DCIMGReader
parseDeconvolutionLog(RandomAccessInputStream, MetadataStore) - Method in class loci.formats.in.DeltavisionReader
  Parse deconvolution output, if it exists.
parseDimension(String) - Method in class loci.formats.in.APLReader
  Parse an integer from the given dimension String.
parseDimensionSizes(String[], String[]) - Method in class loci.formats.in.NikonTiffReader
parseDimensionTag(int) - Method in class loci.formats.in.LeicaReader
parseDOM(Location) - Method in class loci.formats.in.PrairieReader
  Parses a `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.LeicaMicrosystemsMetadata.LMSMetadataExtractor
parseDouble(String) - Method in class loci.formats.in.MetamorphHandler
  Remove '+' before parsing doubles.
parseDouble(String) - Method in class loci.formats.in.TiffReader
parseDouble(String) - Static method in class loci.formats.in.ZeissTIFFHandler
  Parse a Double from a String.
parseENV(Document) - Method in class loci.formats.in.PrairieMetadata
  Parses metadata from Prairie ENV file.
parseETSFile(RandomAccessInputStream, String, int, boolean) - Method in class loci.formats.in.CellSensReader
parseExperimentTag() - Method in class loci.formats.in.LeicaReader
parseExtraTags() - Method in class loci.formats.in.GatanDM2Reader
parseFDF(String) - Method in class loci.formats.in.VarianFDFReader
parseFile(String, Class<?>) - Method in class loci.formats.ClassList
  Parses a list of classes from a configuration file.
parseFile(String, MetamorphHandler) - Method in class loci.formats.in.MetamorphTiffReader
parseFile(DirectoryEntry) - Method in class loci.formats.services.POIServiceImpl
parseFileHeader(List<String>) - Method in class loci.formats.in.TextReader
  Parses the file looking for the file header.
parseFilename(String[], int, int) - Method in class loci.formats.in.APLReader
parseFilenames(int) - Method in class loci.formats.in.LeicaReader
parseFilePath(String) - Method in class loci.formats.in.LeicaMicrosystemsMetadata.LMSXmlDocument
  Translates Leica XML file paths to absolute url decoded paths
parseFlexFile(int, int, int, int, boolean, MetadataStore) - Method in class loci.formats.in.FlexReader
  Parses XML metadata from the Flex file corresponding to the given well.
parseFrameProperties(Element) - Method in class loci.formats.in.OIRReader
parseHeader() - Method in class loci.formats.in.LiFlimReader
parseHeaderRow(String[]) - Method in class loci.formats.in.TextReader
  Populates rowLength, xIndex, yIndex, and channels.
parseHTD() - Method in class loci.formats.in.CellWorxReader
parseImageNames(int) - Method in class loci.formats.in.OpenlabReader
parseImageProperties(Element) - Method in class loci.formats.in.OIRReader
parseImageTag(int) - Method in class loci.formats.in.LeicaReader
parseImageXML(String, int) - Method in class loci.formats.in.ColumbusReader
parseInstrumentData(MetadataStore, int) - Method in class loci.formats.in.LeicaReader
parseInt(String) - Static method in class loci.formats.in.BaseZeissReader
  Parse an Integer from a String.
parseInt(String, int) - Static method in class loci.formats.in.BaseZeissReader
  Parse an Integer from a String.
parseInt(String) - Method in class loci.formats.in.LeicaMicrosystemsMetadata.LMSMetadataExtractor
parseInt(String) - Method in class loci.formats.in.TiffReader
parseIntegerString(String) - Method in class loci.formats.in.BDVReader.BDVXMLHandler
parseIntValue(Number, int) - Method in class loci.formats.in.DicomReader
parseJSON() - Method in class loci.formats.in.TissueFAXSReader.ScanRegion
parseKeyAndValue(String, String, int, int, int) - Method in class loci.formats.in.MicromanagerReader
parseKeyAndValue(String, String, String) - Method in class loci.formats.in.ND2Handler
parseKeys(Element, PrairieMetadata.ValueTable) - Method in class loci.formats.in.PrairieMetadata
  Parses `<Key>` elements beneath the given element, into the specified table.
parseKeyValue(String, String) - Method in class loci.formats.in.LEOReader
parseKeyValue(String, String) - Method in class loci.formats.in.PerkinElmerReader
parseLength(String) - Static method in class loci.formats.FormatTools
  Parse a length composed of a value and an optional unit
parseLength(String, String) - Static method in class loci.formats.FormatTools
  Parse a length composed of a value and an optional unit
parseLine(String) - Method in class loci.formats.ClassList
  Parses a class from a string including options and comments.
parseLines(String[]) - Method in class loci.formats.in.BrukerReader
parseList(String) - Static method in class loci.plugins.prefs.StringOption
  Parses a string of comma-separated values into a list of tokens.
parseLogFile(MetadataStore) - Method in class loci.formats.in.DeltavisionReader
  Extract metadata from associated log file, if it exists.
parseLong(String) - Method in class loci.formats.in.LeicaMicrosystemsMetadata.LMSMetadataExtractor
parseLUT(int) - Method in class loci.formats.in.LeicaReader
parseLUT(Element, String) - Method in class loci.formats.in.OIRReader
parseMainTags(int, MetadataStore, ArrayList<BaseZeissReader.Tag>) - Method in class loci.formats.in.BaseZeissReader
parseMasks - Variable in class loci.formats.in.MIASReader
  Whether or not mask pixel data should be parsed in setId.
parseMasks(MetadataStore) - Method in class loci.formats.in.MIASReader
  Parse masks into a separate overlay-specific MetadataStore.
parseMasks(MetadataStore, int, int, String) - Method in class loci.formats.in.MIASReader
  Parse Mask ROIs from the given TIFF and place them in the given MetadataStore.
parseMDB(String) - Method in class loci.formats.in.ZeissLSMReader
  Parse a .mdb file and return a list of referenced .lsm files.
parseMetadata() - Method in class loci.formats.in.ZeissCZIReader.SubBlock
parseNotes(MetadataStore) - Method in class loci.formats.in.BioRadReader
ParseNpyHeader(RandomAccessInputStream) - Method in class loci.formats.in.SlideBook7Reader.CNpyHeader
parseObjectives(NodeList) - Method in class loci.formats.in.ZeissCZIReader
parseOption(String) - Method in class loci.plugins.prefs.BooleanOption
parseOption(String) - Method in class loci.plugins.prefs.DoubleOption
parseOption(String) - Method in class loci.plugins.prefs.Option
  Parses the option's value from the given argument string.
parseOption(String) - Method in class loci.plugins.prefs.StringOption
parseOptions(String) - Method in class loci.formats.ClassList
  Parses one or more options from a string.
parseOptions(String) - Method in class loci.plugins.in.Importer
  Parses core options.
parseOptions(String) - Method in class loci.plugins.prefs.OptionsList
  Parses option values from the given argument string.
parseOriginalMetadata(Node) - Method in class loci.formats.in.OIRReader
parseOriginalMetadata(Node) - Method in class loci.formats.in.OlympusTileReader
parseOverlays(int, long, String, MetadataStore) - Method in class loci.formats.in.ZeissLSMReader
  Parses overlay-related fields.
parsePageName() - Method in class loci.formats.in.FluoviewReader
parsePhysicalSize(String, String) - Method in class loci.formats.in.FakeReader
parsePixelSize(int) - Method in class loci.formats.in.NRRDReader
parsePixelSpacing(String) - Method in class loci.formats.in.DicomReader
parsePixelsSizeZFromKey(String) - Method in class loci.formats.in.ND2Handler
  Parses the physical size from a key.
parsePoints(String) - Static method in class loci.plugins.util.ROIHandler
  Parse (x, y) coordinates from a String returned by MetadataRetrieve.getPolygonpoints(...) or MetadataRetrieve.getPolylinepoints(...)
parsePosition(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
parseSOF() - Method in class loci.formats.services.JPEGTurboServiceImpl
parseSpectrumRecord(IRandomAccess, IM3Reader.ContainerRecord) - Method in class loci.formats.in.IM3Reader.Spectrum
  Parse the spectrum record
parseSpreadsheet() - Method in class loci.formats.in.TecanReader
parseString(IRandomAccess) - Static method in class loci.formats.in.IM3Reader
  Parse a string from the IM3 file at the current file pointer loc
parseStructure() - Method in class loci.formats.in.BDVReader
parseStructure() - Method in class loci.formats.in.CellH5Reader
parseTable(String) - Method in interface loci.formats.services.MDBService
  Read named table from a pre-initialized .mdb files.
parseTable(String) - Method in class loci.formats.services.MDBServiceImpl
parseTableData(List<String>, int) - Method in class loci.formats.in.TextReader
  Reads the tabular data into the data array.
parseTags(int, String, String) - Method in class loci.formats.in.GatanReader
  Parses Gatan DM3 tags.
parseTags(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.ND2Reader
parseTimestamp(String) - Method in class loci.formats.in.BaseZeissReader
  Parse timestamp from string.
parseTimeTag(int) - Method in class loci.formats.in.LeicaReader
parseTimFile(String) - Method in class loci.formats.in.PerkinElmerReader
parseUIC1Tags(long, int) - Method in class loci.formats.in.MetamorphReader
  UIC1 entry parser
parseUIC2Tags(long) - Method in class loci.formats.in.MetamorphReader
  Populates metadata fields with some contained in MetaMorph UIC2 Tag.
parseUIC4Tags(long) - Method in class loci.formats.in.MetamorphReader
  UIC4 metadata parser UIC4 Table contains per-plane blocks of metadata stage X/Y positions, camera chip offsets, stage labels...
parseWavelength(String, String) - Method in class loci.formats.in.FakeReader
parseWellLogFile(int, MetadataStore) - Method in class loci.formats.in.CellWorxReader
  Parse metadata from a well log file.
parseWellLogFile(int, MetadataStore) - Method in class loci.formats.in.MetaxpressTiffReader
parseXML(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
PathComparator() - Constructor for class loci.formats.in.XLEFReader.PathComparator
pathToImageData - Variable in class loci.formats.in.BDVReader.H5Coordinate
pathToPosition - Variable in class loci.formats.in.BDVReader.H5Coordinate
pathToPosition - Variable in class loci.formats.in.CellH5Reader.CellH5Coordinate
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.ND2Reader
pfsStateOffset - Variable in class loci.formats.in.ND2Reader
PGM_MAGIC_CHAR - Static variable in class loci.formats.in.PGMReader
PGMReader - Class in loci.formats.in
  PGMReader is the file format reader for Portable Gray Map (PGM) images.
PGMReader() - Constructor for class loci.formats.in.PGMReader
  Constructs a new PGMReader.
PHASE - Static variable in class loci.formats.FormatTools
  Identifies the Phase dimensional type, representing a dimension consisting of phases.
PHASE - Static variable in class loci.formats.in.CellSensReader
phaseLabels - Variable in class loci.formats.in.ZeissCZIReader
phases - Variable in class loci.formats.in.LiFlimReader
phases - Variable in class loci.formats.in.ZeissCZIReader
phases - Variable in class loci.formats.in.ZeissLSMReader
PHENIX_MAGIC - Static variable in class loci.formats.in.OperettaReader
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.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
physicalDistanceFromLeftEdge - Variable in class loci.formats.in.SVSReader
physicalDistanceFromTopEdge - Variable in class loci.formats.in.SVSReader
physicalPixelSize - Variable in class loci.formats.in.VentanaReader
physicalSizes - Variable in class loci.formats.in.LeicaReader
physicalSizeX - Variable in class loci.formats.in.BaseZeissReader
physicalSizeX - Variable in class loci.formats.in.BioRadSCNReader
physicalSizeX - Variable in class loci.formats.in.CellSensReader.Pyramid
physicalSizeX - Variable in class loci.formats.in.FakeReader
physicalSizeX - Variable in class loci.formats.in.LeicaHandler
physicalSizeX - Variable in class loci.formats.in.NikonTiffReader
physicalSizeX - Variable in class loci.formats.in.OIRReader
physicalSizeX - Variable in class loci.formats.in.SISReader
physicalSizeXs - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataTempBuffer
physicalSizeXs - Variable in class loci.formats.in.LIFReader
physicalSizeY - Variable in class loci.formats.in.BaseZeissReader
physicalSizeY - Variable in class loci.formats.in.BioRadSCNReader
physicalSizeY - Variable in class loci.formats.in.CellSensReader.Pyramid
physicalSizeY - Variable in class loci.formats.in.FakeReader
physicalSizeY - Variable in class loci.formats.in.LeicaHandler
physicalSizeY - Variable in class loci.formats.in.NikonTiffReader
physicalSizeY - Variable in class loci.formats.in.OIRReader
physicalSizeY - Variable in class loci.formats.in.SISReader
physicalSizeYs - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataTempBuffer
physicalSizeYs - Variable in class loci.formats.in.LIFReader
physicalSizeZ - Variable in class loci.formats.in.BaseZeissReader
physicalSizeZ - Variable in class loci.formats.in.FakeReader
physicalSizeZ - Variable in class loci.formats.in.NikonTiffReader
physicalSizeZ - Variable in class loci.formats.in.OIRReader
physicalSizeZ - Variable in class loci.formats.in.TiffReader
physicalX - Variable in class loci.formats.in.VolocityReader.Stack
physicalY - Variable in class loci.formats.in.VolocityReader.Stack
physicalZ - Variable in class loci.formats.in.VolocityReader.Stack
PIC_FILE_ID - Static variable in class loci.formats.in.BioRadReader
  Numerical ID of a valid Bio-Rad PIC file.
PIC_SUFFIX - Static variable in class loci.formats.in.BioRadReader
picFiles - Variable in class loci.formats.in.BioRadReader
pict - Variable in class loci.formats.in.OpenlabReader
  Helper reader to read PICT data.
pict - Variable in class loci.formats.in.OpenlabReader.PlaneInfo
PICT_9A - Static variable in class loci.formats.in.PictReader
PICT_BITSRECT - Static variable in class loci.formats.in.PictReader
PICT_BITSRGN - Static variable in class loci.formats.in.PictReader
PICT_CLIP_RGN - Static variable in class loci.formats.in.PictReader
PICT_END - Static variable in class loci.formats.in.PictReader
PICT_JPEG - Static variable in class loci.formats.in.PictReader
PICT_LONGCOMMENT - Static variable in class loci.formats.in.PictReader
PICT_PACKBITSRECT - Static variable in class loci.formats.in.PictReader
PICT_PACKBITSRGN - Static variable in class loci.formats.in.PictReader
PICT_TYPE_1 - Static variable in class loci.formats.in.PictReader
PICT_TYPE_2 - Static variable in class loci.formats.in.PictReader
PictReader - Class in loci.formats.in
  PictReader is the file format reader for Apple PICT files.
PictReader() - Constructor for class loci.formats.in.PictReader
  Constructs a new PICT reader.
pinhole - Variable in class loci.formats.in.ImarisHDFReader
pinhole - Variable in class loci.formats.in.LeicaHandler
pinhole - Variable in class loci.formats.in.LeicaReader
pinhole - Variable in class loci.formats.in.OIRReader.Channel
pinhole - Variable in class loci.formats.in.ZeissCZIReader.Channel
pinhole - Variable in class loci.formats.in.ZeissLSMReader.DetectionChannel
pinholes - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataTempBuffer
pinholes - Variable in class loci.formats.in.LIFReader
pinholeSize - Variable in class loci.formats.in.FV1000Reader
pinholeSize - Variable in class loci.formats.in.ND2Handler
pinholeSize - Variable in class loci.formats.in.NikonTiffReader
pix - Variable in class loci.formats.in.CanonRawReader
pixClk - Variable in class loci.formats.in.SDTInfo
PIXEL_CLOCK - Static variable in class loci.formats.in.CellSensReader
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_X_DIMENSION - Static variable in class loci.formats.tiff.IFD
PIXEL_Y_DIMENSION - Static variable in class loci.formats.tiff.IFD
pixelBits - Variable in class loci.formats.gui.SignedColorModel
PixelBlock() - Constructor for class loci.formats.in.OIRReader.PixelBlock
pixelBlocks - Variable in class loci.formats.in.OIRReader
pixelBytes - Variable in class loci.formats.in.QTReader
  Total number of bytes of pixel data.
pixelData - Variable in class loci.formats.in.MINCReader
pixelDataLengthPointer - Variable in class loci.formats.out.DicomWriter
pixelDataSize - Variable in class loci.formats.out.DicomWriter
pixelFile - Variable in class loci.formats.in.AnalyzeReader
  File containing the pixel data.
pixelFile - Variable in class loci.formats.in.NiftiReader
  File containing the pixel data.
PIXELFORMAT_BAYERBG12 - Static variable in class loci.formats.in.LIPixelFormat
PIXELFORMAT_BAYERBG12P - Static variable in class loci.formats.in.LIPixelFormat
PIXELFORMAT_BAYERBG12PMSB - Static variable in class loci.formats.in.LIPixelFormat
PIXELFORMAT_BAYERBG16 - Static variable in class loci.formats.in.LIPixelFormat
PIXELFORMAT_BAYERBG8 - Static variable in class loci.formats.in.LIPixelFormat
PIXELFORMAT_BAYERGB12 - Static variable in class loci.formats.in.LIPixelFormat
PIXELFORMAT_BAYERGB12P - Static variable in class loci.formats.in.LIPixelFormat
PIXELFORMAT_BAYERGB12PMSB - Static variable in class loci.formats.in.LIPixelFormat
PIXELFORMAT_BAYERGB16 - Static variable in class loci.formats.in.LIPixelFormat
PIXELFORMAT_BAYERGB8 - Static variable in class loci.formats.in.LIPixelFormat
PIXELFORMAT_BAYERGR10 - Static variable in class loci.formats.in.LIPixelFormat
PIXELFORMAT_BAYERGR12 - Static variable in class loci.formats.in.LIPixelFormat
PIXELFORMAT_BAYERGR12P - Static variable in class loci.formats.in.LIPixelFormat
PIXELFORMAT_BAYERGR12PMSB - Static variable in class loci.formats.in.LIPixelFormat
PIXELFORMAT_BAYERGR16 - Static variable in class loci.formats.in.LIPixelFormat
PIXELFORMAT_BAYERGR8 - Static variable in class loci.formats.in.LIPixelFormat
PIXELFORMAT_BAYERRG10 - Static variable in class loci.formats.in.LIPixelFormat
PIXELFORMAT_BAYERRG12 - Static variable in class loci.formats.in.LIPixelFormat
PIXELFORMAT_BAYERRG12P - Static variable in class loci.formats.in.LIPixelFormat
PIXELFORMAT_BAYERRG12PACKED - Static variable in class loci.formats.in.LIPixelFormat
PIXELFORMAT_BAYERRG12PMSB - Static variable in class loci.formats.in.LIPixelFormat
PIXELFORMAT_BAYERRG16 - Static variable in class loci.formats.in.LIPixelFormat
PIXELFORMAT_BAYERRG8 - Static variable in class loci.formats.in.LIPixelFormat
PIXELFORMAT_BGR8 - Static variable in class loci.formats.in.LIPixelFormat
PIXELFORMAT_BGR8PACKED - Static variable in class loci.formats.in.LIPixelFormat
PIXELFORMAT_KEY - Static variable in class loci.formats.in.LiFlimReader
PIXELFORMAT_MONO10 - Static variable in class loci.formats.in.LIPixelFormat
PIXELFORMAT_MONO10P - Static variable in class loci.formats.in.LIPixelFormat
PIXELFORMAT_MONO10PMSB - Static variable in class loci.formats.in.LIPixelFormat
PIXELFORMAT_MONO12 - Static variable in class loci.formats.in.LIPixelFormat
PIXELFORMAT_MONO12P - Static variable in class loci.formats.in.LIPixelFormat
PIXELFORMAT_MONO12PACKED - Static variable in class loci.formats.in.LIPixelFormat
PIXELFORMAT_MONO12PMSB - Static variable in class loci.formats.in.LIPixelFormat
PIXELFORMAT_MONO14 - Static variable in class loci.formats.in.LIPixelFormat
PIXELFORMAT_MONO14P - Static variable in class loci.formats.in.LIPixelFormat
PIXELFORMAT_MONO16 - Static variable in class loci.formats.in.LIPixelFormat
PIXELFORMAT_MONO8 - Static variable in class loci.formats.in.LIPixelFormat
PIXELFORMAT_RGB8 - Static variable in class loci.formats.in.LIPixelFormat
PIXELFORMAT_RGB8PACKED - Static variable in class loci.formats.in.LIPixelFormat
pixelFormatEqualsBitSize(Integer, String) - Static method in class loci.formats.in.LIPixelFormat
pixelLengths - Variable in class loci.formats.in.SlidebookReader
pixelOffset - Variable in class loci.formats.in.AIMReader
pixelOffset - Variable in class loci.formats.in.AnalyzeReader
  Offset to the pixel data in the .img file.
pixelOffset - Variable in class loci.formats.in.FitsReader
pixelOffset - Variable in class loci.formats.in.GatanReader
  Offset to pixel data.
pixelOffset - Variable in class loci.formats.in.HISReader
  Offsets to pixel data for each series.
pixelOffset - Variable in class loci.formats.in.JEOLReader
pixelOffset - Variable in class loci.formats.in.KodakReader
pixelOffset - Variable in class loci.formats.in.MolecularImagingReader
pixelOffset - Variable in class loci.formats.in.NiftiReader
  Offset to the pixel data in the .img file.
pixelOffset - Variable in class loci.formats.in.QTReader
  Offset to start of pixel data.
pixelOffset - Variable in class loci.formats.in.RHKReader
pixelOffset - Variable in class loci.formats.in.SIFReader
pixelOffset - Variable in class loci.formats.in.TopometrixReader
pixelOffset - Variable in class loci.formats.in.VolocityClippingReader
pixelOffset - Variable in class loci.formats.out.ICSWriter
pixelOffset - Variable in class loci.formats.out.V3DrawWriter
pixelOffsets - Variable in class loci.formats.in.JPXReader
pixelOffsets - Variable in class loci.formats.in.SlidebookReader
pixelOffsets - Variable in class loci.formats.in.VarianFDFReader
pixelOffsets - Variable in class loci.formats.in.VisitechReader
pixels - Variable in class loci.formats.in.AFIReader
pixels - Variable in class loci.formats.in.GIFReader
pixels - Variable in class loci.formats.in.ImagicReader
pixels - Variable in class loci.formats.in.LeicaSCNReader.Image
Pixels(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
PIXELS_MARKER - Static variable in class loci.formats.in.VisitechReader
PIXELS_OFFSET - Static variable in class loci.formats.in.ARFReader
PIXELS_OFFSET - Static variable in class loci.formats.in.LIMReader
PIXELS_STRING - Static variable in class loci.formats.in.KodakReader
PIXELS_SUFFIXES - Static variable in class loci.formats.in.InCellReader
PIXELS_TAG - Static variable in class loci.formats.in.ImaconReader
pixelsFile - Variable in class loci.formats.in.FujiReader
pixelsFile - Variable in class loci.formats.in.ImagicReader
pixelsFile - Variable in class loci.formats.in.PDSReader
PixelsFile() - Constructor for class loci.formats.in.PerkinElmerReader.PixelsFile
pixelsFilename - Variable in class loci.formats.in.AnalyzeReader
pixelsFilename - Variable in class loci.formats.in.NiftiReader
pixelsFiles - Variable in class loci.formats.in.BrukerReader
pixelsFiles - Variable in class loci.formats.in.TillVisionReader
pixelsFiles - Variable in class loci.formats.in.TissueFAXSReader
pixelsFiles - Variable in class loci.formats.in.VolocityReader.Stack
pixelSize - Variable in class loci.formats.in.FV1000Reader
pixelSize - Variable in class loci.formats.in.IPLabReader
pixelSize - Variable in class loci.formats.in.MicromanagerReader.Position
pixelSize - Variable in class loci.formats.in.ScanrReader
pixelSize - Variable in class loci.formats.in.SVSCoreMetadata
pixelSize - Variable in class loci.formats.in.TecanReader.Image
pixelSize - Variable in class loci.formats.in.ZeissXRMReader
pixelSize - Static variable in class org.libjpegturbo.turbojpeg.TJ
pixelSizes - Variable in class loci.formats.in.GatanReader
  List of pixel sizes.
pixelSizes - Variable in class loci.formats.in.NRRDReader
pixelSizeT - Variable in class loci.formats.in.FV1000Reader
pixelSizeT - Variable in class loci.formats.in.ImprovisionTiffReader
pixelSizeUnits - Variable in class loci.formats.in.GatanDM2Reader
pixelSizeX - Variable in class loci.formats.dicom.DicomFileInfo
pixelSizeX - Variable in class loci.formats.in.DicomReader
pixelSizeX - Variable in class loci.formats.in.FV1000Reader
pixelSizeX - Variable in class loci.formats.in.GatanDM2Reader
pixelSizeX - Variable in class loci.formats.in.ImarisHDFReader
pixelSizeX - Variable in class loci.formats.in.ImprovisionTiffReader
pixelSizeX - Variable in class loci.formats.in.MetamorphHandler
pixelSizeX - Variable in class loci.formats.in.ND2Handler
pixelSizeX - Variable in class loci.formats.in.PerkinElmerReader
pixelSizeX - Variable in class loci.formats.in.VarianFDFReader
pixelSizeX - Variable in class loci.formats.in.ZeissLSMReader
pixelSizeY - Variable in class loci.formats.dicom.DicomFileInfo
pixelSizeY - Variable in class loci.formats.in.DicomReader
pixelSizeY - Variable in class loci.formats.in.FV1000Reader
pixelSizeY - Variable in class loci.formats.in.GatanDM2Reader
pixelSizeY - Variable in class loci.formats.in.ImarisHDFReader
pixelSizeY - Variable in class loci.formats.in.ImprovisionTiffReader
pixelSizeY - Variable in class loci.formats.in.MetamorphHandler
pixelSizeY - Variable in class loci.formats.in.ND2Handler
pixelSizeY - Variable in class loci.formats.in.PerkinElmerReader
pixelSizeY - Variable in class loci.formats.in.VarianFDFReader
pixelSizeY - Variable in class loci.formats.in.ZeissLSMReader
pixelSizeZ - Variable in class loci.formats.dicom.DicomFileInfo
pixelSizeZ - Variable in class loci.formats.in.DicomReader
pixelSizeZ - Variable in class loci.formats.in.FV1000Reader
pixelSizeZ - Variable in class loci.formats.in.ImarisHDFReader
pixelSizeZ - Variable in class loci.formats.in.ImprovisionTiffReader
pixelSizeZ - Variable in class loci.formats.in.ND2Handler
pixelSizeZ - Variable in class loci.formats.in.VarianFDFReader
pixelSizeZ - Variable in class loci.formats.in.ZeissLSMReader
pixelsOffset - Variable in class loci.formats.in.BioRadSCNReader
pixelsOffset - Variable in class loci.formats.in.BurleighReader
pixelsOffset - Variable in class loci.formats.in.InCell3000Reader
pixelsOffset - Variable in class loci.formats.in.JPEG2000Reader
pixelsOffset - Variable in class loci.formats.in.QuesantReader
pixelsOffsets - Variable in class loci.formats.in.ImspectorReader
  List of offsets to each block of pixel data.
pixelsPerPlane - Variable in class loci.formats.in.AmiraReader.ASCII
pixelsStream - Variable in class loci.formats.in.TillVisionReader
pixelStack - Variable in class loci.formats.in.GIFReader
pixelType - Variable in class loci.formats.CoreMetadata
  Describes the number of bytes per pixel.
pixelType - Variable in class loci.formats.in.AmiraReader.ASCII
pixelType - Variable in class loci.formats.in.DCIMGReader
pixelType - Variable in class loci.formats.in.ZeissCZIReader.DirectoryEntry
pixelTypeFromBytes(int, boolean, boolean) - Static method in class loci.formats.FormatTools
  Returns an appropriate pixel type given the number of bytes per pixel.
pixelTypeFromString(String) - Static method in class loci.formats.FormatTools
  Takes a string value and maps it to one of the pixel type enumerations.
pixelTypeIndex - Variable in class loci.formats.in.ZeissCZIReader.SubBlock
pixelTypes - Static variable in class loci.formats.FormatTools
  Human readable pixel type.
pixTime - Variable in class loci.formats.in.SDTInfo
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.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.TecanReader.Image
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 - Variable in class loci.formats.in.JDCEReader.JDCEWell
planeCount() - Method in class loci.formats.out.OMETiffWriter
planeData - Variable in class loci.formats.in.CV7000Reader
PlaneData() - Constructor for class loci.formats.in.FV1000Reader.PlaneData
planeDeltaT - Variable in class loci.formats.in.FlexReader
planeExposureTime - Variable in class loci.formats.in.FlexReader
planeIndex - Variable in class loci.formats.in.ZeissCZIReader.SubBlock
planeIndexes - Variable in class loci.plugins.util.BFVirtualStack
PlaneInfo() - Constructor for class loci.formats.in.OpenlabReader.PlaneInfo
planeMax - Variable in class loci.formats.MinMaxCalculator
  Max values for each plane.
PlaneMetadata() - Constructor for class loci.formats.in.JDCEReader.PlaneMetadata
planeMin - Variable in class loci.formats.MinMaxCalculator
  Min values for each plane.
planeName - Variable in class loci.formats.in.OpenlabReader.PlaneInfo
planeNames - Variable in class loci.formats.in.ZeissTIFFHandler
planeOffset - Variable in class loci.formats.in.OpenlabReader.PlaneInfo
planeOffset - Variable in class loci.formats.in.SlidebookReader
PlaneOffset() - Constructor for class loci.formats.out.DicomWriter.PlaneOffset
planeOffset - Variable in class loci.formats.out.EPSWriter
planeOffsets - Variable in class loci.formats.in.OpenlabReader
planeOffsets - Variable in class loci.formats.out.DicomWriter
planePadding - Variable in class loci.formats.in.VolocityReader.Stack
planePositionX - Variable in class loci.formats.in.FlexReader
planePositionY - Variable in class loci.formats.in.FlexReader
planePositionZ - Variable in class loci.formats.in.FlexReader
planeReader - Variable in class loci.formats.in.AmiraReader
planes - Variable in class loci.formats.in.ColumbusReader
planes - Variable in class loci.formats.in.CV7000Reader.MeasurementDataHandler
planes - Variable in class loci.formats.in.FV1000Reader
planes - Variable in class loci.formats.in.OpenlabReader
planes - Variable in class loci.formats.in.OperettaReader.OperettaHandler
planes - Variable in class loci.formats.in.OperettaReader
planes - Variable in class loci.formats.in.ZeissCZIReader
planes - Variable in class loci.formats.in.ZeissTIFFHandler
planes - Variable in class loci.formats.in.ZeissTIFFReader
  Image planes
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
plateAcquisitionIndex - Variable in class loci.formats.internal.WellContainer
plateBarcode - Variable in class loci.formats.in.FlexReader
plateCols - Variable in class loci.formats.in.FakeReader
plateCols - Variable in class loci.formats.in.OperettaReader.OperettaHandler
plateColumns - Variable in class loci.formats.in.ColumbusReader.MeasurementHandler
plateColumns - Variable in class loci.formats.in.CV7000Reader.WPIHandler
plateColumns - Variable in class loci.formats.in.TecanReader
plateColumns - Variable in class loci.formats.in.ZeissCZIReader
plateCount - Variable in class loci.formats.in.FlexReader
plateDescription - Variable in class loci.formats.in.BDReader
plateDescription - Variable in class loci.formats.in.OperettaReader.OperettaHandler
plateID - Variable in class loci.formats.in.CV7000Reader.WPIHandler
plateID - Variable in class loci.formats.in.OperettaReader.OperettaHandler
plateLogFile - Variable in class loci.formats.in.CellWorxReader
plateMap - Variable in class loci.formats.in.InCellReader
plateName - Variable in class loci.formats.in.BDReader
plateName - Variable in class loci.formats.in.ColumbusReader.MeasurementHandler
plateName - Variable in class loci.formats.in.FlexReader
plateName - Variable in class loci.formats.in.OperettaReader.OperettaHandler
plateName - Variable in class loci.formats.in.ScanrReader
plateName - Variable in class loci.formats.in.TecanReader
platePositions - Variable in class loci.formats.in.ZeissCZIReader
plateRows - Variable in class loci.formats.in.ColumbusReader.MeasurementHandler
plateRows - Variable in class loci.formats.in.CV7000Reader.WPIHandler
plateRows - Variable in class loci.formats.in.FakeReader
plateRows - Variable in class loci.formats.in.OperettaReader.OperettaHandler
plateRows - Variable in class loci.formats.in.TecanReader
plateRows - Variable in class loci.formats.in.ZeissCZIReader
plates - Variable in class loci.formats.in.FakeReader
plateType - Variable in class loci.formats.in.ColumbusReader.MeasurementHandler
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.
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.ZeissXRMReader
poi - Variable in class loci.formats.in.ZeissZVIReader
POI_MAGIC_BYTES - Static variable in class loci.formats.services.POIServiceImpl
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.LeicaMicrosystemsMetadata.ROI
POLYGON - Static variable in class loci.formats.in.LIFReader.ROI
polygons - Variable in class loci.formats.in.FakeReader
POLYLINE - Static variable in class loci.formats.in.FV1000Reader
POLYLINE_ARROW - Static variable in class loci.formats.in.ZeissLSMReader
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
populateInstrument(MetadataStore) - Method in class loci.formats.in.FakeReader
populateLines(NodeList, int, int) - Method in class loci.formats.in.ZeissCZIReader
populateMaskPixels(int, int, int, MetadataStore) - Method in class loci.formats.in.MIASReader
  Populate the MaskPixels.BinData attribute for the Mask identified by the given Image index, ROI index, and Shape index.
populateMetadata() - Method in class loci.formats.in.CellWorxReader
populateMetadata() - Method in class loci.formats.in.MicromanagerReader
populateMetadata(MetadataStore, int, String, 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.ND2Reader
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.LeicaMicrosystemsMetadata.LMSMetadataExtractor
  Creates key value pairs from attributes of the root's child nodes (tag | attribute name : attribute value) and adds them to reader's `CoreMetadata`
populateOriginalMetadata(Element, Deque<String>, int[], int) - 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.ND2Reader.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.ND2Reader
positionInT - Variable in class loci.formats.in.DeltavisionReader
positions - Variable in class loci.formats.cache.CacheStrategy
  The list of dimensional positions to consider caching, in order of preference based on strategy, axis priority and planar ordering.
positions - Variable in class loci.formats.in.MicromanagerReader.Position
positions - Variable in class loci.formats.in.MicromanagerReader
positions - Variable in class loci.formats.in.ZeissCZIReader
POSITIONS - Static variable in class loci.formats.in.ZeissXRMReader
positionsMatch(int, int) - Method in class loci.formats.in.PrairieReader
  Verifies that stage coordinates match for all (P, Z) across time.
positionsX - Variable in class loci.formats.in.ZeissCZIReader
positionsY - Variable in class loci.formats.in.ZeissCZIReader
positionsZ - Variable in class loci.formats.in.ZeissCZIReader
positionToRaster(int[], int[]) - Static method in class loci.formats.FormatTools
  Computes a unique 1-D index corresponding to the given multidimensional position.
positionX - Variable in class loci.formats.dicom.DicomFileInfo
positionX - Variable in class loci.formats.in.ColumbusReader.Plane
positionX - Variable in class loci.formats.in.DicomReader
positionX - Variable in class loci.formats.in.FV1000Reader.PlaneData
positionX - Variable in class loci.formats.in.JDCEReader.PlaneMetadata
positionX - Variable in class loci.formats.in.MetamorphHandler
positionX - Variable in class loci.formats.in.OperettaReader.Plane
positionY - Variable in class loci.formats.dicom.DicomFileInfo
positionY - Variable in class loci.formats.in.ColumbusReader.Plane
positionY - Variable in class loci.formats.in.DicomReader
positionY - Variable in class loci.formats.in.FV1000Reader.PlaneData
positionY - Variable in class loci.formats.in.JDCEReader.PlaneMetadata
positionY - Variable in class loci.formats.in.MetamorphHandler
positionY - Variable in class loci.formats.in.OperettaReader.Plane
positionZ - Variable in class loci.formats.dicom.DicomFileInfo
positionZ - Variable in class loci.formats.in.ColumbusReader.Plane
positionZ - Variable in class loci.formats.in.DicomReader
positionZ - Variable in class loci.formats.in.FV1000Reader.PlaneData
positionZ - Variable in class loci.formats.in.JDCEReader.PlaneMetadata
positionZ - Variable in class loci.formats.in.OperettaReader.Plane
posMap - Variable in class loci.formats.in.JDCEReader.JDCEWell
posNames - Variable in class loci.formats.in.ND2Handler
possibleValues - Variable in class loci.plugins.prefs.StringOption
  List of possible values.
post - Variable in class loci.formats.NumberFilter
  String appearing after the numerical block.
POST_PROCESS - Static variable in class loci.formats.in.CV7000Reader
posX - Variable in class loci.formats.in.GatanReader
posX - Variable in class loci.formats.in.InCellReader
posX - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataTempBuffer
posX - Variable in class loci.formats.in.LIFReader
posX - Variable in class loci.formats.in.ND2Handler
posX - Variable in class loci.formats.in.ND2Reader
posY - Variable in class loci.formats.in.GatanReader
posY - Variable in class loci.formats.in.InCellReader
posY - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataTempBuffer
posY - Variable in class loci.formats.in.LIFReader
posY - Variable in class loci.formats.in.ND2Handler
posY - Variable in class loci.formats.in.ND2Reader
posZ - Variable in class loci.formats.in.GatanReader
posZ - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataTempBuffer
posZ - Variable in class loci.formats.in.LIFReader
posZ - Variable in class loci.formats.in.ND2Handler
posZ - Variable in class loci.formats.in.ND2Reader
PovrayReader - Class in loci.formats.in
  PovrayReader is the file format reader for POV-Ray .df3 files.
PovrayReader() - Constructor for class loci.formats.in.PovrayReader
  Constructs a new POV-Ray reader.
power - Variable in class loci.formats.in.CV7000Reader.LightSource
power - Variable in class loci.formats.in.ND2Handler
power - Variable in class loci.formats.in.OIRReader.Laser
power - Variable in class loci.formats.in.ZeissLSMReader.Laser
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_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.
preserveCreator() - Method in class loci.formats.out.OMETiffWriter
  Get the value of the `CREATOR_KEY` option.
preserveCreator() - Method in class loci.formats.out.OMEXMLWriter
  Get the value of the `CREATOR_KEY` option.
prestitched - Variable in class loci.formats.in.ZeissCZIReader
prevBuf - Variable in class loci.formats.in.ZeissLSMReader
prevChannel - Variable in class loci.formats.in.ZeissLSMReader
prevElement - Variable in class loci.formats.in.ND2Handler
PREVIEWNAME_PREFIXES - Static variable in class loci.formats.in.FV1000Reader
previewNames - Variable in class loci.formats.in.FV1000Reader
PreviewPane - Class in loci.formats.gui
  PreviewPane is a panel for use as a JFileChooser accessory, displaying a thumbnail for the selected image, loaded in a separate thread.
PreviewPane(JFileChooser) - Constructor for class loci.formats.gui.PreviewPane
  Constructs a preview pane for the given file chooser.
prevImage - Variable in class loci.formats.in.ICSReader
previousChannel - Variable in class loci.formats.in.ZeissCZIReader
previousImage - Variable in class loci.formats.codec.CodecOptions
  Pixels for preceding image (READ/WRITE).
previousTag - Variable in class loci.formats.in.CellSensReader
prevPixels - Variable in class loci.formats.in.QTReader
  Pixel data for the previous image plane.
prevPlane - Variable in class loci.formats.in.QTReader
  Previous plane number.
prevPlane - Variable in class loci.formats.in.ZeissLSMReader
prevRegion - Variable in class loci.formats.in.ZeissLSMReader
prevRuntype - Variable in class loci.formats.in.ND2Handler
PRIMARY_CHROMATICITIES - Static variable in class loci.formats.tiff.IFD
primaryFileGUID - Variable in class loci.formats.in.ZeissCZIReader.FileHeader
print(int, long, String) - Method in class loci.formats.in.QTReader
  Debugging method; prints information on an atom.
printArray(String, int[]) - Static method in class loci.formats.tools.CacheConsole
  Helper utility for outputing contents of an int array, used by main.
printIFD() - Method in class loci.formats.tiff.IFD
  Prints the contents of this IFD.
printOrder(String, Cache) - Static method in class loci.formats.tools.CacheConsole
  Helper utility for outputing cache strategy's order, used by main.
printReferences() - Method in class loci.formats.in.LeicaMicrosystemsMetadata.XlefDocument
printSizes(Component) - Static method in class loci.plugins.config.SpringUtilities
  A debugging utility that prints to stdout the component's minimum, preferred, and maximum sizes.
printSource(String, Cache) - Static method in class loci.formats.tools.CacheConsole
  Helper utility for outputing cache's associated source, used by main.
printStrategy(String, Cache) - Static method in class loci.formats.tools.CacheConsole
  Helper utility for outputing cache's associated strategy, used by main.
printXlifInfo() - Method in class loci.formats.in.LeicaMicrosystemsMetadata.XlifDocument
priorities - Variable in class loci.formats.cache.CacheStrategy
  Priority for caching each axis.
PRIORITIES - Static variable in class loci.formats.gui.CacheComponent
PRIORITIES_CHANGED - Static variable in class loci.formats.cache.CacheEvent
  Event type indicating new axis priorities.
priority - Variable in class loci.formats.gui.CacheComponent
  Combo boxes for choosing axis priority.
PRIORITY_VALUES - Static variable in class loci.formats.gui.CacheComponent
priorityIndex(int) - Method in class loci.formats.gui.CacheComponent
  Converts enumerated priority value to priority chooser index.
priorityValue(int) - Method in class loci.formats.gui.CacheComponent
  Converts priority chooser index to enumerated priority value.
privateContentHighWords - Variable in class loci.formats.in.DicomReader
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.
processParentNode(Node, String) - Method in class loci.formats.in.VectraReader
profileXML - Variable in class loci.formats.in.VectraReader
progress - Variable in class loci.formats.gui.DataConverter
progress(boolean, int, int) - Static method in class loci.plugins.BF
PROJECTION - Static variable in class loci.formats.in.ZeissXRMReader
PROJECTION_PREFIX - Static variable in class loci.formats.in.KLBReader
PROJECTION_SUFFIX - Static variable in class loci.formats.in.KLBReader
promptColors() - Method in class loci.plugins.in.ImporterPrompter
  Prompts for color details, if necessary.
promptCrop() - Method in class loci.plugins.in.ImporterPrompter
  Prompts for cropping details, if necessary.
promptFilePattern() - Method in class loci.plugins.in.ImporterPrompter
  Prompts for the file pattern, if necessary.
promptId() - Method in class loci.plugins.in.ImporterPrompter
promptLocation() - Method in class loci.plugins.in.ImporterPrompter
promptMain() - Method in class loci.plugins.in.ImporterPrompter
promptMemory() - Method in class loci.plugins.in.ImporterPrompter
  Prompts for confirmation of memory usage, if necessary.
promptRange() - Method in class loci.plugins.in.ImporterPrompter
  Prompts for the range of planes to import, if necessary.
promptSeries() - Method in class loci.plugins.in.ImporterPrompter
  Prompts for which series to import, if necessary.
promptSwap() - Method in class loci.plugins.in.ImporterPrompter
  Prompts for dimension swapping parameters, if necessary.
promptUpgrade() - Method in class loci.plugins.in.ImporterPrompter
PROP_LUT - Static variable in class loci.plugins.in.ImagePlusReader
  Special property prefix for storing planar LUTs.
PROP_SERIES - Static variable in class loci.plugins.in.ImagePlusReader
  Special property for storing series number associated with the image.
PROPERTY_FILE - Static variable in class loci.formats.FormatTools
  Deprecated.
  The property file is no longer used.
PROPERTY_SET_VOLUME - Static variable in class loci.formats.in.CellSensReader
propertyChange(PropertyChangeEvent) - Method in class loci.formats.gui.PreviewPane
  Property change event, to listen for when a new file is selected, or the file chooser closes.
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
QTReader - Class in loci.formats.in
  QTReader is the file format reader for QuickTime movie files.
QTReader() - Constructor for class loci.formats.in.QTReader
  Constructs a new QuickTime reader.
QTRLECodec - Class in loci.formats.codec
  Methods for compressing and decompressing data using QuickTime RLE.
QTRLECodec() - Constructor for class loci.formats.codec.QTRLECodec
QTWriter - Class in loci.formats.out
  QTWriter is the file format writer for uncompressed QuickTime movie files.
QTWriter() - Constructor for class loci.formats.out.QTWriter
quality - Variable in class loci.formats.codec.CodecOptions
  Compression quality level as it would be provided to: `ImageWriteParam.compressionQuality` (WRITE).
QUALITY - Static variable in class loci.formats.in.NikonReader
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.in.LeicaMicrosystemsMetadata.LMSMetadataExtractor
r - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataStoreInitializer
r - Variable in class loci.formats.in.LeicaSCNReader.Dimension
r - Variable in class loci.formats.in.TiffJAIReader
  Reflection tool for JAI calls.
r - Variable in class loci.plugins.macro.LociFunctions
r - Variable in class loci.plugins.util.VirtualImagePlus
raf - Variable in class loci.formats.services.NetCDFServiceImpl
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.QTReader
  Raw plane size, in bytes.
rc - Variable in class loci.formats.gui.DataConverter
RCPNLReader - Class in loci.formats.in
RCPNLReader() - Constructor for class loci.formats.in.RCPNLReader
read(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
readAsDoubles(RandomAccessInputStream) - Method in class loci.formats.in.ZeissXRMReader
readAsString(RandomAccessInputStream) - Method in class loci.formats.in.ZeissXRMReader
readAttachments() - Method in class loci.formats.in.ZeissCZIReader
readBlock() - Method in class loci.formats.in.GIFReader
  Reads the next variable length block.
readByte() - Method in class loci.formats.in.APNGReader.PNGInputStream
readByte() - Method in class loci.formats.tools.AmiraParameters
readByteArray(String) - Method in interface loci.formats.services.JHDFService
  Reads a multi-dimensional byte array from path.
readByteArray(String) - Method in class loci.formats.services.JHDFServiceImpl
readByteBlockArray(String, int[], int[]) - Method in interface loci.formats.services.JHDFService
  Reads a multi-dimensional sub-block byte array from path.
readByteBlockArray(String, int[], int[]) - Method in class loci.formats.services.JHDFServiceImpl
readChannel(Element) - Method in class loci.formats.in.CellVoyagerReader
readChunk() - Method in class loci.formats.in.AVIReader
readChunkHeader() - Method in class loci.formats.in.AVIReader
readCompoundArrayDataMap(String) - Method in interface loci.formats.services.JHDFService
  Reads Compound array of any type
readCompoundArrayDataMap(String) - Method in class loci.formats.services.JHDFServiceImpl
readCString(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
ReadData(RandomAccessInputStream, int) - Method in class loci.formats.in.SlideBook7Reader.CCompressionBase
readDate() - Method in class loci.formats.in.OxfordInstrumentsReader
ReadDictionary(RandomAccessInputStream) - Method in class loci.formats.in.SlideBook7Reader.CCompressionBase
readDoubleArray(int) - Method in class loci.formats.tools.AmiraParameters
readEntry() - Method in class loci.formats.in.ZeissLSMReader
reader - Variable in class loci.formats.cache.CacheSource
  Reader from which to draw image planes.
reader - Variable in class loci.formats.FileInfo
  IFormatReader implementation that would be used to read this file.
reader - Variable in class loci.formats.gui.BufferedImageSource
  Image reader from which to draw BufferedImages.
reader - Variable in class loci.formats.gui.DataConverter
reader - Variable in class loci.formats.gui.FormatFileFilter
  Associated file format reader.
reader - Variable in class loci.formats.gui.PreviewPane
  Reader for use when loading thumbnails.
reader - Variable in class loci.formats.in.AFIReader
reader - Variable in class loci.formats.in.BDReader
reader - Variable in class loci.formats.in.ColumbusReader
reader - Variable in class loci.formats.in.CV7000Reader
reader - Variable in class loci.formats.in.L2DReader
reader - Variable in class loci.formats.in.OMETiffReader.OMETiffPlane
  Reader to use for accessing this plane.
reader - Variable in class loci.formats.in.OperettaReader
reader - Variable in class loci.formats.in.PCORAWReader
reader - Variable in class loci.formats.in.ScanrReader
reader - Variable in class loci.formats.in.ZeissTIFFHandler
reader - Variable in class loci.formats.in.ZipReader
reader - Variable in class loci.formats.ReaderWrapper
  FormatReader used to read the file.
reader - Variable in class loci.formats.services.MetakitServiceImpl
reader - Variable in class loci.plugins.config.FormatEntry
reader - Variable in class loci.plugins.in.ImportProcess
reader - Variable in class loci.plugins.util.BFVirtualStack
reader - Variable in class loci.plugins.util.ImageProcessorSource
  Image reader from which to draw ImageProcessors.
READER_VALIDATE_DEFAULT - Static variable in class loci.formats.in.DynamicMetadataOptions
READER_VALIDATE_KEY - Static variable in class loci.formats.in.DynamicMetadataOptions
readerFromBytes(Class<IFormatReader>, byte[]) - Method in class loci.formats.Memoizer.RandomAccessDeser
readerName - Variable in class loci.plugins.config.FormatEntry
readers - Variable in class loci.formats.FileStitcher.ExternalSeries
readers - Variable in class loci.formats.ImageReader
  List of supported file format readers.
readers - Variable in class loci.formats.in.ImprovisionTiffReader
readers - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.MultipleImagesReader
readers - Variable in class loci.formats.in.MIASReader
  Delegate readers.
readers - Variable in class loci.formats.in.NDPISReader
readers - Variable in class loci.formats.in.SlidebookTiffReader
readers - Variable in class loci.formats.in.XLEFReader
ReaderWrapper - Class in loci.formats
  Abstract superclass of reader logic that wraps other readers.
ReaderWrapper() - Constructor for class loci.formats.ReaderWrapper
  Constructs a reader wrapper around a new image reader.
ReaderWrapper(IFormatReader) - Constructor for class loci.formats.ReaderWrapper
  Constructs a reader wrapper around the given reader.
readExtraMetadata(MetadataStore) - Method in class loci.formats.in.KodakReader
readField(Element) - Method in class loci.formats.in.CellVoyagerReader
readFile(String) - Method in class loci.formats.in.TextReader
readFile(String) - Method in class loci.formats.tools.AmiraParameters
readFile(RandomAccessInputStream) - Method in class loci.formats.tools.AmiraParameters
readFileInfoMetadata(MetadataStore) - Method in class loci.formats.in.KodakReader
readFlimFrame(OBFReader.Stack, int, byte[], int, int, int, int) - Method in class loci.formats.in.OBFReader
readFloat32() - Method in class loci.formats.in.KLBReader
readFrameInterval(Document) - Method in class loci.formats.in.CellVoyagerReader
readFromOverlays() - Static method in class loci.plugins.util.ROIHandler
  Returns rois if any from the overlay.
readFromRoiManager() - Static method in class loci.plugins.util.ROIHandler
  Returns the rois if any stored in the ROI manager.
readFromStack(OBFReader.Stack, byte[], int, int) - Method in class loci.formats.in.OBFReader
readFromStackRaw(OBFReader.Stack, byte[], int, int) - Method in class loci.formats.in.OBFReader
readGZIPPlane(String, int, byte[], int, int, int, int) - Method in class loci.formats.in.NRRDReader
  Read a tile in the specified plane from a GZIP-compressed file.
readHeader(CoreMetadata) - Method in class loci.formats.in.KLBReader
readImage(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
readMetadata(String) - Method in class loci.formats.in.OlympusTileReader
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
readPixelData() - Method in class loci.formats.in.ZeissCZIReader.SubBlock
readPixelData(RandomAccessInputStream) - Method in class loci.formats.in.ZeissCZIReader.SubBlock
readPixelData(RandomAccessInputStream, Region, byte[]) - Method in class loci.formats.in.ZeissCZIReader.SubBlock
readPixels(byte[], RandomAccessInputStream, ZipInputStream, long) - Method in class loci.formats.in.SDTReader
readPixels(ImagePlusReader, ImporterOptions, DisplayHandler) - Method in class loci.plugins.in.Importer
readPixelsFile(String, RandomAccessInputStream) - Method in class loci.formats.in.OIRReader
readPlane(RandomAccessInputStream, int, int, int, int, byte[]) - Method in class loci.formats.FormatReader
  Reads a raw plane from disk.
readPlane(RandomAccessInputStream, int, int, int, int, int, byte[]) - Method in class loci.formats.FormatReader
  Reads a raw plane from disk.
readPlane(RandomAccessInputStream, int, int, int, int, int, int, int, byte[]) - Method in class loci.formats.FormatReader
ReadPlane(int, byte[], int, int, int, int) - Method in class loci.formats.in.SlideBook7Reader.DataLoader
readPlaneData() - Method in class loci.formats.in.MetamorphReader
readPlanes(ImportProcess, int, List<LUT>, boolean) - Method in class loci.plugins.in.ImagePlusReader
readQuotedString() - Method in class loci.formats.tools.AmiraParameters
readRaster(InputStream, 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
readSequence(JSONObject, DicomTag) - Method in class loci.formats.dicom.DicomJSONProvider
readShortBlockArray(String, int[], int[]) - Method in interface loci.formats.services.JHDFService
  Reads a multi-dimensional sub-block short array from path.
readShortBlockArray(String, int[], int[]) - Method in class loci.formats.services.JHDFServiceImpl
ReadSld() - Method in class loci.formats.in.SlideBook7Reader.DataLoader
ReadSld(InputStream) - Method in class loci.formats.in.SlideBook7Reader.DataLoader
readSpecialPixels(byte[]) - Static method in class loci.formats.in.FakeReader
  Read byte-encoded metadata from the given plane.
readSpecialPixels(byte[], int, boolean) - Static method in class loci.formats.in.FakeReader
  Read byte-encoded metadata from the given plane.
readSpecialPixels(byte[], int, boolean, int, boolean) - Static method in class loci.formats.in.FakeReader
  Read byte-encoded metadata from the given plane.
readStackFrame(OBFReader.Stack, long, byte[], int, int, int) - Method in class loci.formats.in.OBFReader
readStackHeader() - Method in class loci.formats.in.ImspectorReader
  Read the header for an image stack.
readStageLabels() - Method in class loci.formats.in.MetamorphReader
readStagePositions() - Method in class loci.formats.in.MetamorphReader
readStamps() - Method in class loci.formats.in.FluoviewReader
readString() - Method in class loci.formats.in.OBFReader
readStringArray(String) - Method in interface loci.formats.services.JHDFService
  Reads String array array from path.
readStringArray(String) - Method in class loci.formats.services.JHDFServiceImpl
readTagHeader() - Method in class loci.formats.in.OpenlabReader
  Read the next tag.
readTags(RandomAccessInputStream, boolean, String) - Method in class loci.formats.in.CellSensReader
readTagSource(String) - Method in class loci.formats.dicom.DicomJSONProvider
readTagSource(String) - Method in interface loci.formats.dicom.ITagProvider
  Read tags from the given location.
readThumbImages() - Method in class loci.plugins.in.ImagePlusReader
readTiffIFDEntry() - Method in class loci.formats.tiff.TiffParser
readTimePoints(Document) - Method in class loci.formats.in.CellVoyagerReader
readTopLevel() - Method in class loci.formats.tools.AmiraParameters
readTypeAndSize() - Method in class loci.formats.in.AVIReader
readUInt32() - Method in class loci.formats.in.KLBReader
readUInt64() - Method in class loci.formats.in.KLBReader
readUnsignedLong(RandomAccessInputStream) - Method in class loci.formats.in.SDTInfo
readValue(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
readVarint(RandomAccessInputStream) - Method in class loci.formats.in.ZeissCZIReader
readWavelength(int, MetadataStore) - Method in class loci.formats.in.DeltavisionReader
readWellInfo(Element, double, double, int, int) - Method in class loci.formats.in.CellVoyagerReader
readXMLBlock(String, RandomAccessInputStream) - Method in class loci.formats.in.OIRReader
realChannel - Variable in class loci.formats.in.LIFReader
realColors - Variable in class loci.formats.in.ND2Handler
realFile - Variable in class loci.formats.Memoizer
realHeight - Variable in class loci.formats.in.BaseZeissReader
realWidth - Variable in class loci.formats.in.BaseZeissReader
realX - Variable in class loci.formats.in.VentanaReader.TIFFTile
realY - Variable in class loci.formats.in.VentanaReader.TIFFTile
rebuild(GenericDialog) - Method in class loci.plugins.in.FilePatternDialog
rebuildDialog(GenericDialog) - Method in class loci.plugins.in.MainDialog
  Fancies up the importer dialog to look much nicer.
rebuildDialog(GenericDialog, int) - Method in class loci.plugins.in.SeriesDialog
REC_BOOLEAN - Static variable in class loci.formats.in.IM3Reader
REC_CONTAINER - Static variable in class loci.formats.in.IM3Reader
  A record that is a container of other records.
REC_FLOAT - Static variable in class loci.formats.in.IM3Reader
REC_IMAGE - Static variable in class loci.formats.in.IM3Reader
  Image format int: pixel type? 3 = RGBA int: width int: height int: depth data bytes follow
REC_INT - Static variable in class loci.formats.in.IM3Reader
  32-bit integer values
REC_NESTED - Static variable in class loci.formats.in.IM3Reader
  A nested record of records
REC_STRING - Static variable in class loci.formats.in.IM3Reader
  A string int: ? int: length 8-byte characters follow
REC_SUFFIX - Static variable in class loci.formats.in.PerkinElmerReader
recache(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
RECON_SETTINGS - Static variable in class loci.formats.in.ZeissXRMReader
RECON_SETTINGS_PATH - Static variable in class loci.formats.in.ZeissXRMReader
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.LeicaMicrosystemsMetadata.ROI
RECTANGLE - Static variable in class loci.formats.in.LIFReader.ROI
RECTANGLE - Static variable in class loci.formats.in.ZeissLSMReader
rectangles - Variable in class loci.formats.in.FakeReader
RectangleStrategy - Class in loci.formats.cache
  A rectangle strategy caches planes extending from the the current dimensional position along each axis and combination of axes.
RectangleStrategy(int[]) - Constructor for class loci.formats.cache.RectangleStrategy
  Constructs a rectangle strategy.
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
REFERENCE_PATH - Static variable in class loci.formats.in.ZeissXRMReader
REFOCUS_INTERVAL - Static variable in class loci.formats.in.NDPIReader
refractive - Variable in class loci.formats.in.InCellReader
REFRACTIVE_INDEX - Static variable in class loci.formats.in.CellSensReader
refractiveIndex - Variable in class loci.formats.in.CellSensReader.Pyramid
refractiveIndex - Variable in class loci.formats.in.IvisionReader
refractiveIndex - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataTempBuffer
refractiveIndex - Variable in class loci.formats.in.LIFReader
refractiveIndex - Variable in class loci.formats.in.ND2Handler
refractiveIndex - Variable in class loci.formats.in.ND2Reader
refractiveIndex - Variable in class loci.formats.in.ZeissCZIReader
refresher - Variable in class loci.formats.gui.PreviewPane
  Method for syncing the view to the model.
region - Variable in class loci.formats.dicom.DicomTile
region - Variable in class loci.formats.in.OlympusTileReader.Tile
regionMetadata - Variable in class loci.formats.in.TissueFAXSReader.ScanRegion
regions - Variable in class loci.formats.in.TissueFAXSReader
registerServiceProviders() - Static method in class loci.formats.services.JAIIIOServiceImpl
  Register the JPEG-2000 readers with the reader service.
REGISTRY - Static variable in class loci.formats.UpgradeChecker
  Location of the OME registry.
REGISTRY_IMAGEJ - Static variable in class loci.formats.UpgradeChecker
  Registry ID identifying usage of Bio-Formats in ImageJ.
REGISTRY_LIBRARY - Static variable in class loci.formats.UpgradeChecker
  Registry ID identifying usage of Bio-Formats as a library in general.
REGISTRY_PROPERTIES - Static variable in class loci.formats.UpgradeChecker
  Properties that are sent to the OME registry.
RELATED_SOUND_FILE - Static variable in class loci.formats.tiff.IFD
RELATIVE_POSITIONS_DEFAULT - Static variable in class loci.formats.in.ZeissCZIReader
RELATIVE_POSITIONS_KEY - Static variable in class loci.formats.in.ZeissCZIReader
relativeTime - Variable in class loci.formats.in.PrairieMetadata.Frame
  `relativeTime` attribute of this `<Frame>`.
remainingBytesInChunk(OBFReader.Stack) - Method in class loci.formats.in.OBFReader
remove(int, int) - Method in class loci.formats.MetadataList
  Remove the array element at the specified indexes.
remove(int) - Method in class loci.formats.MetadataList
  Remove the entire primary array element at the specified index.
REMOVE_THUMBNAIL_DEFAULT - Static variable in class loci.formats.in.SVSReader
REMOVE_THUMBNAIL_KEY - Static variable in class loci.formats.in.SVSReader
removeBinData(OMEXMLMetadata) - Method in interface loci.formats.services.OMEXMLService
  Remove all of the BinData elements from the given OME-XML metadata object.
removeBinData(OMEXMLMetadata) - Method in class loci.formats.services.OMEXMLServiceImpl
removeCacheListener(CacheListener) - Method in class loci.formats.cache.Cache
removeCacheListener(CacheListener) - Method in interface loci.formats.cache.CacheReporter
  Removes a listener for status update events.
removeCacheListener(CacheListener) - Method in class loci.formats.cache.CacheStrategy
removeChannels(OMEXMLMetadata, int, int) - Method in interface loci.formats.services.OMEXMLService
  Remove all but the first sizeC valid Channel elements from the given OME-XML metadata object.
removeChannels(OMEXMLMetadata, int, int) - Method in class loci.formats.services.OMEXMLServiceImpl
removeClass(Class<? extends T>) - Method in class loci.formats.ClassList
  Removes the given class from the list.
removeExtension(String) - Method in class loci.plugins.out.Exporter
  Removes the extension of the specified name.
removeGST(String) - Method in class loci.formats.in.FV1000Reader
removeIFDComments(IFormatReader) - Method in class loci.formats.in.OMETiffReader
removePossible(String) - Method in class loci.plugins.prefs.StringOption
  Removes a possible value from the list.
removeStatusListener(StatusListener) - Method in class loci.plugins.in.ImagePlusReader
removeStatusListener(StatusListener) - Method in class loci.plugins.in.ImportProcess
removeThumbnail() - Method in class loci.formats.in.SVSReader
removeTiffData(OMEXMLMetadata) - Method in interface loci.formats.services.OMEXMLService
  Remove all of the TiffData elements from the given OME-XML metadata object.
removeTiffData(OMEXMLMetadata) - Method in class loci.formats.services.OMEXMLServiceImpl
RenamePathToTimepoint0(String) - Method in class loci.formats.in.SlideBook7Reader.CSBFile70
RENDER_OPERATION_ID - Static variable in class loci.formats.in.CellSensReader
reopenFile() - Method in class loci.formats.DelegateReader
reopenFile() - Method in class loci.formats.FileStitcher
reopenFile() - Method in class loci.formats.FormatReader
reopenFile() - Method in interface loci.formats.IFormatReader
  Reopen any files that were closed, and which are expected to be open while the reader is open.
reopenFile() - Method in class loci.formats.ImageReader
reopenFile() - Method in class loci.formats.in.AnalyzeReader
reopenFile() - Method in class loci.formats.in.BDVReader
reopenFile() - Method in class loci.formats.in.CellH5Reader
reopenFile() - Method in class loci.formats.in.CellSensReader
reopenFile() - Method in class loci.formats.in.FakeReader
reopenFile() - Method in class loci.formats.in.FlowSightReader
reopenFile() - Method in class loci.formats.in.HitachiReader
reopenFile() - Method in class loci.formats.in.ICSReader
reopenFile() - Method in class loci.formats.in.ImagicReader
reopenFile() - Method in class loci.formats.in.LeicaMicrosystemsMetadata.MultipleImagesReader
reopenFile() - Method in class loci.formats.in.MinimalTiffReader
reopenFile() - Method in class loci.formats.in.NiftiReader
reopenFile() - Method in class loci.formats.in.OMETiffReader
reopenFile() - Method in class loci.formats.in.SPCReader
reopenFile() - Method in class loci.formats.in.TileJPEGReader
reopenFile() - Method in class loci.formats.in.XLEFReader
reopenFile() - Method in class loci.formats.in.ZipReader
reopenFile() - Method in class loci.formats.ReaderWrapper
reopenFile() - Method in class loci.formats.WrappedReader
reorder() - Method in class loci.formats.CoreMetadataList
reorder(int) - Method in class loci.formats.DimensionSwapper
reorder(ImagePlus, String, String) - Static method in class loci.plugins.Slicer
  Reorder the given ImagePlus's stack.
reorderXSLT - Static variable in class loci.formats.services.OMEXMLServiceImpl
  Reordering stylesheet.
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
reserved1 - Variable in class loci.formats.in.SDTInfo
reserved2 - Variable in class loci.formats.in.SDTInfo
reset() - Method in class loci.formats.cache.Cache
  Reallocates the cache.
reset() - Method in class loci.plugins.util.RecordedImageProcessor
reset(ImageProcessor) - Method in class loci.plugins.util.RecordedImageProcessor
resetBinaryThreshold() - Method in class loci.plugins.util.RecordedImageProcessor
resetMinAndMax() - Method in class loci.plugins.util.RecordedImageProcessor
resetRoi() - Method in class loci.plugins.util.RecordedImageProcessor
resetSliceLabelButton - Variable in class loci.plugins.config.ConfigWindow
resetStream(IFD) - Method in class loci.formats.in.NDPIReader
resetThreshold() - Method in class loci.plugins.util.RecordedImageProcessor
ResHandler() - Constructor for class loci.formats.in.FlexReader.ResHandler
resize(int) - Method in class loci.plugins.util.RecordedImageProcessor
resize(int, int) - Method in class loci.plugins.util.RecordedImageProcessor
resLabel - Variable in class loci.formats.gui.PreviewPane
  Labels containing thumbnail and dimensional information.
reslice(ImagePlus, boolean, boolean, boolean, String) - Method in class loci.plugins.Slicer
resolution - Variable in class loci.formats.codec.JPEG2000CodecOptions
  The resolution level as would be provided to: `J2KImageReadParam.setResolution(int)` (READ).
resolution - Variable in class loci.formats.FormatReader
  The number of the current resolution.
resolution - Variable in class loci.formats.FormatWriter
  Current pyramid resolution.
resolution - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.Channel
Resolution() - 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.TissueFAXSReader.ScanRegion
resolutions - Variable in class loci.formats.in.VentanaReader
resolutions - Variable in class loci.formats.ome.OMEPyramidStore
ResolutionStrategy - Enum in loci.formats.dicom
ResolutionStrategy() - Constructor for enum loci.formats.dicom.ResolutionStrategy
resolutionX - Variable in class loci.formats.in.OperettaReader.Channel
resolutionX - Variable in class loci.formats.in.OperettaReader.Plane
resolutionY - Variable in class loci.formats.in.OperettaReader.Channel
resolutionY - Variable in class loci.formats.in.OperettaReader.Plane
resourceCount - Variable in class loci.formats.ResourceNamer
ResourceNamer - 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
RestoreSpecialCharacters(String) - Method in class loci.formats.in.SlideBook7Reader.ClassDecoder
result - Variable in class loci.formats.in.TecanReader.Image
resultFile - Variable in class loci.formats.in.MIASReader
  Path to file containing analysis results for all plates.
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 - Class in loci.formats.in.LeicaMicrosystemsMetadata
  This class helps saving ROI information to a reader's MetadataStore
ROI() - Constructor for class loci.formats.in.LeicaMicrosystemsMetadata.ROI
ROI() - Constructor for class loci.formats.in.LiFlimReader.ROI
ROI() - Constructor for class loci.formats.in.LIFReader.ROI
ROI_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.LeicaMicrosystemsMetadata.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.Field
row - Variable in class loci.formats.in.FlexReader.FlexFile
row - Variable in class loci.formats.in.OMEXMLReader.BinData
row - Variable in class loci.formats.in.OperettaReader.Plane
row - Variable in class loci.formats.in.TextReader
  Current row number.
row - Variable in class loci.formats.in.ZeissCZIReader.SubBlock
row - Variable in class loci.formats.tools.AmiraParameters
rowBytes - Variable in class loci.formats.in.PictReader
  Number of bytes in a row of pixel data (variable).
rowCount - Variable in class loci.formats.in.BaseZeissReader
rowIndex - Variable in class loci.formats.internal.WellContainer
rowLength - Variable in class loci.formats.in.TextReader
  Number of tokens per row.
rowName - Variable in class loci.formats.in.InCellReader
RowPanel() - Constructor for class loci.formats.gui.DataConverter.RowPanel
rows - Variable in class loci.formats.in.CellSensReader
ROWS_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.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.ND2Reader
  Remove control and invalid characters from the given string.
sanitizeFile(String, String) - Method in class loci.formats.in.FV1000Reader
sanitizeValue(String) - Method in class loci.formats.in.FV1000Reader
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.DicomWriter
saveBytes(int, byte[], int, int, int, int) - Method in class loci.formats.out.EPSWriter
saveBytes(int, byte[], int, int, int, int) - Method in class loci.formats.out.ICSWriter
saveBytes(int, byte[], int, int, int, int) - Method in class loci.formats.out.ImageIOWriter
saveBytes(int, byte[], int, int, int, int) - Method in class loci.formats.out.JavaWriter
saveBytes(int, byte[], int, int, int, int) - Method in class loci.formats.out.JPEG2000Writer
saveBytes(int, byte[], int, int, int, int) - Method in class loci.formats.out.OMETiffWriter
saveBytes(int, byte[], 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[]) - 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
saveCompressedBytes(int, byte[], int, int, int, int) - Method in interface loci.formats.ICompressedTileWriter
  Save a compressed tile to the current output file.
saveCompressedBytes(int, byte[], int, int, int, int) - Method in class loci.formats.ImageWriter
saveCompressedBytes(int, byte[], int, int, int, int) - Method in class loci.formats.out.DicomWriter
saveCompressedBytes(int, byte[], int, int, int, int) - Method in class loci.formats.out.OMETiffWriter
saveCompressedBytes(int, byte[], int, int, int, int) - Method in class loci.formats.out.TiffWriter
saveCompressedBytes(int, byte[], int, int, int, int) - Method in class loci.formats.WriterWrapper
savedbLength - Variable in class loci.formats.out.AVIWriter
saveDefaults() - Method in class loci.plugins.in.ImportProcess
  Performed following ImportStep.FILE notification.
savedToMemo - Variable in class loci.formats.Memoizer
  Whether the `ReaderWrapper.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) - 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.QTReader
  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.LeicaMicrosystemsMetadata.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.TissueFAXSReader.ScanRegion
scaleFactor - Variable in class loci.formats.in.ZeissCZIReader
scaleX - Variable in class loci.formats.in.LeicaHandler.ROI
scaleX - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.ROI
scaleX - Variable in class loci.formats.in.LIFReader.ROI
scaleY - Variable in class loci.formats.in.LeicaHandler.ROI
scaleY - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.ROI
scaleY - Variable in class loci.formats.in.LIFReader.ROI
scaling - Variable in class loci.formats.in.SimplePCITiffReader
Scaling() - Constructor for class loci.formats.in.ZeissTIFFHandler.Scaling
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) - Method in class loci.formats.in.DCIMGReader
scanDirectory(Location, boolean) - Method in class loci.formats.in.DicomReader
  Scan the given directory for files that belong to this dataset.
scanFormat(String, String) - Static method in class loci.formats.in.FV1000Reader
SCANNERSET - Static variable in class loci.formats.in.LeicaReader
ScanRegion() - Constructor for class loci.formats.in.TissueFAXSReader.ScanRegion
ScanrHandler() - Constructor for class loci.formats.in.ScanrReader.ScanrHandler
ScanrReader - Class in loci.formats.in
  ScanrReader is the file format reader for Olympus ScanR datasets.
ScanrReader() - Constructor for class loci.formats.in.ScanrReader
  Constructs a new ScanR reader.
ScanrReader.ScanrHandler - Class in loci.formats.in
scanRX - Variable in class loci.formats.in.SDTInfo
scanRY - Variable in class loci.formats.in.SDTInfo
scanValues - Variable in class loci.formats.in.PrairieMetadata
  Table of key/value pairs at the top level.
scanX - Variable in class loci.formats.in.SDTInfo
scanY - Variable in class loci.formats.in.SDTInfo
SCENE_CAPTURE_TYPE - Static variable in class loci.formats.tiff.IFD
SCENE_TYPE - Static variable in class loci.formats.tiff.IFD
SCHEMA_2010_03 - Static variable in class loci.formats.in.LeicaSCNReader
SCHEMA_2010_10 - Static variable in class loci.formats.in.LeicaSCNReader
SCHEMA_CLASSPATH_READER - Static variable in class loci.formats.services.OMEXMLServiceImpl
  Finds OME-XML schema definitions in specifications.jar.
SCHEMA_PATH - Static variable in class loci.formats.services.OMEXMLServiceImpl
SCHEMA_URL_PATTERN - Static variable in class loci.formats.services.OMEXMLServiceImpl
  The pattern of system ID URLs for OME-XML schema definitions.
schemaType - Variable in class loci.formats.in.ZeissCZIReader.AttachmentEntry
schemaType - Variable in class loci.formats.in.ZeissCZIReader.DirectoryEntry
SCNHandler() - Constructor for class loci.formats.in.BioRadSCNReader.SCNHandler
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
seekStartOfPlane(int, long, long) - Method in class loci.formats.in.LOFReader
seekToFrameStart(OBFReader.Stack, long) - Method in class loci.formats.in.OBFReader
seekToNextMarker() - Method in class loci.formats.in.ZeissLMSReader
seekToPlaneOffset(long, int, int) - Method in class loci.formats.FormatWriter
  Seek to the given (x, y) coordinate of the image that starts at the given offset.
Segment() - Constructor for class loci.formats.in.ZeissCZIReader.Segment
Segment(String) - Constructor for class loci.formats.in.ZeissCZIReader.Segment
Segment(ZeissCZIReader.Segment) - Constructor for class loci.formats.in.ZeissCZIReader.Segment
SEGMENTATION_PATH - Static variable in class loci.formats.in.BDVReader.H5Constants
SEGMENTATION_PATH - Static variable in class loci.formats.in.CellH5Reader.CellH5Constants
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.QTReader
  Flag indicating whether the resource and data fork are separated.
SEQ_FILTERSET - Static variable in class loci.formats.in.LeicaReader
SEQ_FILTERSET_END - Static variable in class loci.formats.in.LeicaReader
SEQ_SCANNERSET - Static variable in class loci.formats.in.LeicaReader
SEQ_SCANNERSET_END - Static variable in class loci.formats.in.LeicaReader
SEQReader - Class in loci.formats.in
  SEQReader is the file format reader for Image-Pro Sequence files.
SEQReader() - Constructor for class loci.formats.in.SEQReader
  Constructs a new Image-Pro SEQ reader.
sequence - Variable in class loci.formats.in.PrairieMetadata.Frame
  The `<Sequence>` containing this `<Frame>`.
Sequence(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.
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 `Sequence`s, ordered by cycle.
sequenceValues - Variable in class loci.formats.in.PrairieMetadata.Sequence
  Table of key/value pairs for this `<Sequence>`.
sequential - Variable in class loci.formats.FormatWriter
  Whether or not we are writing planes sequentially.
sequential - Variable in class loci.formats.in.LeicaReader
SEQUENTIALSET - Static variable in class loci.formats.in.LeicaReader
sequentialTileByteCounts - Variable in class loci.formats.tiff.TiffSaver
sequentialTileFilePointer - Variable in class loci.formats.tiff.TiffSaver
sequentialTileOffsets - Variable in class loci.formats.tiff.TiffSaver
  Store tile offsets and original file pointer when writing sequentially.
sequentialWrite - Variable in class loci.formats.tiff.TiffSaver
ser - Variable in class loci.formats.Memoizer
SERIAL_NUMBER - Static variable in class loci.formats.in.NDPIReader
SERIALIZED_MASK - Static variable in class loci.formats.in.CellSensReader
serialNumber - Variable in class loci.formats.in.BioRadSCNReader
serialNumber - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataTempBuffer
serialNumber - Variable in class loci.formats.in.LIFReader
serialNumber - Variable in class loci.formats.in.NDPIReader
serialVersionUID - Static variable in class org.libjpegturbo.turbojpeg.TJTransform
series - Variable in class loci.formats.FileStitcher
  The number of the current series (non flat).
series - Variable in class loci.formats.FormatReader
  The number of the current series (non flat).
series - Variable in class loci.formats.FormatWriter
  Current series.
series - Variable in class loci.formats.gui.DataConverter
series - Variable in class loci.formats.in.CellomicsReader.ChannelFile
series - Variable in class loci.formats.in.ColumbusReader.Plane
series - Variable in class loci.formats.in.CV7000Reader.Plane
series - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.MultipleImagesReader
SERIES - 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.TecanReader.Image
series - Variable in class loci.formats.in.ZeissCZIReader.Coordinate
series - Variable in class loci.plugins.macro.LociFunctions
series - Variable in class loci.plugins.util.BFVirtualStack
SERIES_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.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.DicomWriter
  Sets whether or not BigTIFF files should be written.
setBigTiff(boolean) - Method in class loci.formats.out.TiffWriter
  Sets whether or not BigTIFF files should be written.
setBigTiff(boolean) - Method in class loci.formats.tiff.TiffSaver
  Sets whether or not BigTIFF data should be written.
setBoolean(String, Boolean) - Method in class loci.formats.in.DynamicMetadataOptions
  Set property `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.
setChannelType() - Method in class loci.formats.in.LeicaMicrosystemsMetadata.Channel
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.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
setColumnIndex(int) - Method in class loci.formats.internal.WellContainer
setCompression(String) - Method in class loci.formats.FormatWriter
setCompression(String) - Method in interface loci.formats.IFormatWriter
  Sets the current compression type.
setCompression(String) - Method in class loci.formats.ImageWriter
setCompression(String) - Method in class loci.formats.WriterWrapper
setConcatenate(boolean) - Method in class loci.plugins.in.ImporterOptions
setCore(ArrayList<CoreMetadata>) - Method in class loci.formats.in.LeicaMicrosystemsMetadata.LMSFileReader
setCoreDimensionSizes(int) - Method in class loci.formats.in.LeicaMicrosystemsMetadata.LMSMetadataExtractor
  Writes extracted dimension sizes to CoreMetadata
setCoreIndex(int) - Method in class loci.formats.DelegateReader
setCoreIndex(int) - Method in class loci.formats.FileStitcher
setCoreIndex(int) - Method in class loci.formats.FormatReader
setCoreIndex(int) - Method in interface loci.formats.IFormatReader
  Deprecated.
  This method is no longer required for sub-resolution support.
setCoreIndex(int) - Method in class loci.formats.ImageReader
setCoreIndex(int) - Method in class loci.formats.in.ZeissLSMReader
setCoreIndex(int) - Method in class loci.formats.ReaderWrapper
setCoreIndex(int) - Method in class loci.formats.SubResolutionFormatReader
setCoreIndex(int) - Method in class loci.formats.WrappedReader
setCoreMetadata(CoreMetadata) - Method in class loci.formats.in.LeicaMicrosystemsMetadata.MultipleImagesReader
setCreator(OMEXMLMetadataRoot) - Method in class loci.formats.out.OMETiffWriter
  Set the Creator attribute on the given OME-XML root object.
setCrop(boolean) - Method in class loci.plugins.in.ImporterOptions
setCropRegion(int, Region) - Method in class loci.plugins.in.ImporterOptions
setCStep(int, int) - Method in class loci.plugins.in.ImporterOptions
setCurrentPos(int[]) - Method in class loci.formats.cache.Cache
  Sets the current dimensional position.
setCustomColor(int, int, Color) - Method in class loci.plugins.in.ImporterOptions
setDataType(String) - Method in class loci.formats.in.InveonReader
setDefaultCreationDate(MetadataStore, String, int) - Static method in class loci.formats.MetadataTools
  Sets a default creation date.
setDefaultDateEnabled(boolean) - Static method in class loci.formats.MetadataTools
  Disables the setting of a default creation date.
setDimensions(int, int, int) - Method in class loci.formats.in.ND2Reader
setDoCaching(boolean) - Method in class loci.formats.tiff.TiffParser
  Sets whether or not IFD entries should be cached.
setDocument(Document) - Method in class loci.formats.gui.XMLWindow
  Displays XML from the given document.
setDocumentLocator(Locator) - Method in class loci.formats.in.OMEXMLReader.OMEXMLHandler
setDoRecording(boolean) - Method in class loci.plugins.util.RecordedImageProcessor
setDouble(String, Double) - Method in class loci.formats.in.DynamicMetadataOptions
  Set property `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
setEncoding(String) - Method in class loci.formats.tiff.TiffParser
  Sets the encoding to use for tags with ASCII values.
setEnum(String, T) - Method in class loci.formats.in.DynamicMetadataOptions
  Set property `name` to enumerated type `value`.
setExtraMetadata(String) - Method in class loci.formats.out.DicomWriter
setExtraMetadata(String) - Method in interface loci.formats.out.IExtraMetadataWriter
  Provide additional metadata that should be written as part of this dataset.
setf(int, float) - Method in class loci.plugins.util.RecordedImageProcessor
setf(int, int, float) - Method in class loci.plugins.util.RecordedImageProcessor
setFieldCount(int) - Method in class loci.formats.internal.WellContainer
setFile(String, 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
setFillColor(Byte) - Method in class loci.formats.FormatReader
setFillColor(Byte) - Method in interface loci.formats.IFormatReader
  Set the fill value for undefined pixels.
setFillColor(Byte) - Method in class loci.formats.ImageReader
setFillColor(Byte) - Method in class loci.formats.ReaderWrapper
setFilled(boolean) - Method in class loci.formats.ChannelFiller
  Toggles whether the indices should be factored out.
setFirstTime(boolean) - Method in class loci.plugins.in.ImporterOptions
setFixed() - Method in class loci.formats.FilePatternBlock
setFlattenedList(List<CoreMetadata>) - Method in class loci.formats.CoreMetadataList
setFlattenedResolutions(boolean) - Method in class loci.formats.DelegateReader
setFlattenedResolutions(boolean) - Method in class loci.formats.FileStitcher
setFlattenedResolutions(boolean) - Method in class loci.formats.FormatReader
setFlattenedResolutions(boolean) - Method in interface loci.formats.IFormatReader
  Set whether or not to flatten resolutions into individual series.
setFlattenedResolutions(boolean) - Method in class loci.formats.ImageReader
setFlattenedResolutions(boolean) - Method in class loci.formats.in.FilePatternReader
setFlattenedResolutions(boolean) - Method in class loci.formats.ReaderWrapper
setFloat(String, Float) - Method in class loci.formats.in.DynamicMetadataOptions
  Set property `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.ChannelMerger
setId(String) - Method in class loci.formats.ChannelSeparator
setId(String) - Method in class loci.formats.DelegateReader
setId(String) - Method in class loci.formats.DimensionSwapper
setId(String) - Method in class loci.formats.FileStitcher
setId(String) - Method in class loci.formats.FormatReader
  Initialize a reader from the input file name.
setId(String) - Method in class loci.formats.FormatWriter
  Initializes a writer from the input file name.
setId(String) - Method in interface loci.formats.IFormatHandler
  Sets the current file name.
setId(String) - Method in class loci.formats.ImageReader
setId(String) - Method in class loci.formats.ImageWriter
setId(String) - Method in class loci.formats.in.JPEGReader
setId(String) - Method in class loci.formats.in.TiffDelegateReader
setId(String) - Method in class loci.formats.Memoizer
setId(String) - Method in class loci.formats.out.APNGWriter
setId(String) - Method in class loci.formats.out.AVIWriter
setId(String) - Method in class loci.formats.out.CellH5Writer
setId(String) - Method in class loci.formats.out.DicomWriter
setId(String) - Method in class loci.formats.out.ICSWriter
setId(String) - Method in class loci.formats.out.JavaWriter
setId(String) - Method in class loci.formats.out.OMETiffWriter
setId(String) - Method in class loci.formats.out.OMEXMLWriter
setId(String) - Method in class loci.formats.out.QTWriter
setId(String) - Method in class loci.formats.out.TiffWriter
setId(String) - Method in class loci.formats.out.V3DrawWriter
setId(String) - Method in class loci.formats.ReaderWrapper
setId(String) - Method in class loci.formats.TileStitcher
setId(String) - Method in class loci.formats.WriterWrapper
setId(String) - Method in class loci.plugins.in.ImporterOptions
setId(String) - Method in class loci.plugins.macro.LociFunctions
setIdWithMetadata(String, XlifDocument) - Method in class loci.formats.in.LOFReader
  Inits the LOFReader using passed xml (from XLIF) for metadata initiation, instead of reading the LOF's included xml
setImages(BufferedImage[]) - Method in class loci.formats.gui.ImageViewer
  Sets the viewer to display the given images.
setImages(IFormatReader, BufferedImage[]) - Method in class loci.formats.gui.ImageViewer
  Sets the viewer to display the given images, obtaining corresponding core metadata from the specified format reader.
setIndex(int) - Method in class loci.formats.in.BaseZeissReader.Tag
setInputOrder(int, String) - Method in class loci.plugins.in.ImporterOptions
setInt(int, int) - Method in class loci.formats.in.SPEReader.SpeHeader
  Private method used to set an Integer value in the SPE header
setIntArray(int[][]) - Method in class loci.plugins.util.RecordedImageProcessor
setInteger(String, Integer) - Method in class loci.formats.in.DynamicMetadataOptions
  Set property `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.
setLength(Double) - Method in class loci.formats.in.LeicaMicrosystemsMetadata.Dimension
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.
setMetadataOfMultipleImagesReaders() - Method in class loci.formats.in.XLEFReader
setMetadataOptions(MetadataOptions) - Method in class loci.formats.DelegateReader
setMetadataOptions(MetadataOptions) - Method in class loci.formats.FileStitcher
setMetadataOptions(MetadataOptions) - Method in class loci.formats.FormatHandler
setMetadataOptions(MetadataOptions) - Method in class loci.formats.ImageReader
setMetadataOptions(MetadataOptions) - Method in class loci.formats.ImageWriter
setMetadataOptions(MetadataOptions) - Method in interface loci.formats.IMetadataConfigurable
setMetadataOptions(MetadataOptions) - Method in class loci.formats.ReaderWrapper
setMetadataOptions(MetadataOptions) - Method in class loci.formats.WriterWrapper
setMetadataRetrieve(MetadataRetrieve) - Method in class loci.formats.FormatWriter
setMetadataRetrieve(MetadataRetrieve) - Method in interface loci.formats.IFormatWriter
  Sets the metadata retrieval object from which to retrieve standardized metadata.
setMetadataRetrieve(MetadataRetrieve) - Method in class loci.formats.ImageWriter
setMetadataRetrieve(MetadataRetrieve) - Method in class loci.formats.WriterWrapper
setMetadataStore(MetadataStore) - Method in class loci.formats.DelegateReader
setMetadataStore(MetadataStore) - Method in class loci.formats.FileStitcher
setMetadataStore(MetadataStore) - Method in class loci.formats.FormatReader
setMetadataStore(MetadataStore) - Method in interface loci.formats.IFormatReader
  Sets the default metadata store for this reader.
setMetadataStore(MetadataStore) - Method in class loci.formats.ImageReader
setMetadataStore(MetadataStore) - Method in class loci.formats.in.FilePatternReader
setMetadataStore(MetadataStore) - Method in class loci.formats.Memoizer
setMetadataStore(MetadataStore) - Method in class loci.formats.ReaderWrapper
setMetadataTempBuffer(MetadataTempBuffer) - Method in class loci.formats.in.LeicaMicrosystemsMetadata.MultipleImagesReader
setMinAndMax(double, double) - Method in class loci.plugins.util.RecordedImageProcessor
setMinMaxStore(IMinMaxStore) - Method in class loci.formats.MinMaxCalculator
  Sets the active min-max store for the calculator.
setModulo(OMEXMLMetadata, Modulo) - Method in class loci.formats.meta.ModuloAnnotation
  Set the value of this annotation using the given Modulo object
setMustGroup(boolean) - Method in class loci.plugins.in.ImporterOptions
setNormalized(boolean) - Method in class loci.formats.DelegateReader
setNormalized(boolean) - Method in class loci.formats.FileStitcher
setNormalized(boolean) - Method in class loci.formats.FormatReader
setNormalized(boolean) - Method in interface loci.formats.IFormatReader
  Specifies whether or not to normalize float data.
setNormalized(boolean) - Method in class loci.formats.ImageReader
setNormalized(boolean) - Method in class loci.formats.in.FilePatternReader
setNormalized(boolean) - Method in class loci.formats.ReaderWrapper
setNormalized(Boolean) - Method in class loci.plugins.macro.LociFunctions
setNumeric() - Method in class loci.formats.FilePatternBlock
setOffsetInfo(int, int, int, int) - Method in class loci.formats.in.DeltavisionReader
  This method calculates the size of a w, t, z section depending on which sequence is being used
setOffsets(String, long[][]) - Method in class loci.formats.in.ND2Reader
  Change the underlying file path and pixel data offsets, keeping all other metadata the same.
setOpenAllSeries(boolean) - Method in class loci.plugins.in.ImporterOptions
setOrder(int, int) - Method in class loci.formats.cache.CacheStrategy
setOrder(int, int) - Method in interface loci.formats.cache.ICacheStrategy
  Sets the order in which objects should be loaded along each axis.
setOriginalMetadataPopulated(boolean) - Method in class loci.formats.DelegateReader
setOriginalMetadataPopulated(boolean) - Method in class loci.formats.FileStitcher
setOriginalMetadataPopulated(boolean) - Method in class loci.formats.FormatReader
setOriginalMetadataPopulated(boolean) - Method in interface loci.formats.IFormatReader
  Specifies whether or not to save proprietary metadata in the MetadataStore.
setOriginalMetadataPopulated(boolean) - Method in class loci.formats.ImageReader
setOriginalMetadataPopulated(boolean) - Method in class loci.formats.in.FilePatternReader
setOriginalMetadataPopulated(boolean) - Method in class loci.formats.ReaderWrapper
setOriginalMetadataPopulated(Boolean) - Method in class loci.plugins.macro.LociFunctions
setOutputOrder(String) - Method in class loci.formats.DimensionSwapper
  Sets the output dimension order according to the given string (e.g., "XYZCT").
setOutputOrder(String) - Method in class loci.formats.out.ICSWriter
  Set the order in which dimensions should be written to the file.
setOutputOrder(String) - Method in class loci.formats.out.V3DrawWriter
  Set the order in which dimensions should be written to the file.
setPixels() - Method in class loci.formats.in.GIFReader
setPixels(int, FloatProcessor) - Method in class loci.plugins.util.RecordedImageProcessor
setPixels(Object) - Method in class loci.plugins.util.RecordedImageProcessor
setPixelType(int) - Method in class loci.formats.in.LeicaMicrosystemsMetadata.LMSMetadataExtractor
  Sets CoreMetadata.pixelType depending on extracted x bytesInc
setPlaneIndexes(int[]) - Method in class loci.plugins.util.BFVirtualStack
setPlaneMetadataInStore - Variable in class loci.formats.in.LeicaHandler
setPlateAcquisition(int) - Method in class loci.formats.internal.WellContainer
setPreLoad(boolean) - Method in class loci.formats.in.SDTReader
  Toggles whether the reader should pre-load data for increased performance.
setPriority(int, int) - Method in class loci.formats.cache.CacheStrategy
setPriority(int, int) - Method in interface loci.formats.cache.ICacheStrategy
  Sets the priority for caching the given axis.
setProgressBar(ProgressBar) - Method in class loci.plugins.util.RecordedImageProcessor
setQuality(int) - Method in class loci.formats.out.QTWriter
  Sets the quality of the encoded movie.
setQuiet(boolean) - Method in class loci.plugins.in.ImporterOptions
setRange(int, int) - Method in class loci.formats.cache.CacheStrategy
setRange(int, int) - Method in interface loci.formats.cache.ICacheStrategy
  Sets the number of objects to cache along the given axis.
setReader(IFormatReader) - Method in class loci.plugins.util.VirtualImagePlus
setReaderClassList(ClassList<IFormatReader>) - Method in class loci.formats.FileStitcher
  Set the ClassList object to use when constructing any helper readers.
setReaderEnabled(FormatEntry, boolean) - Method in class loci.plugins.config.ConfigWindow
setReaderPref(String, FormatEntry, boolean) - Method in class loci.plugins.config.ConfigWindow
setReaderWindowless(FormatEntry, boolean) - Method in class loci.plugins.config.ConfigWindow
setRefCount(int) - Method in class loci.plugins.util.VirtualReader
setResolution(int) - Method in class loci.formats.DelegateReader
setResolution(int) - Method in class loci.formats.FileStitcher
setResolution(int) - Method in class loci.formats.FormatReader
setResolution(int) - Method in class loci.formats.FormatWriter
setResolution(int) - Method in class loci.formats.ImageReader
setResolution(int) - Method in class loci.formats.ImageWriter
setResolution(int) - Method in interface loci.formats.IPyramidHandler
  Set the resolution level.
setResolution(int) - Method in class loci.formats.out.DicomWriter
setResolution(int) - Method in class loci.formats.ReaderWrapper
setResolution(int) - Method in class loci.formats.SubResolutionFormatReader
setResolution(int) - Method in class loci.formats.WrappedReader
setResolution(int) - Method in class loci.formats.WriterWrapper
setResolutionLevel(IFD) - Method in class loci.formats.in.MinimalTiffReader
  Sets the resolution level when we have JPEG 2000 compressed data.
setResolutions(List<Resolution>) - Method in class loci.formats.FormatWriter
setResolutions(List<Resolution>) - Method in interface loci.formats.IFormatWriter
  Specify a list of resolution objects for the current series.
setResolutions(List<Resolution>) - Method in class loci.formats.ImageWriter
setResolutions(List<Resolution>) - Method in class loci.formats.WriterWrapper
setResolutionSizeX(PositiveInteger, int, int) - Method in interface loci.formats.meta.IPyramidStore
  Define the image width in pixels of the given pyramid resolution.
setResolutionSizeX(PositiveInteger, int, int) - Method in class loci.formats.ome.OMEPyramidStore
setResolutionSizeY(PositiveInteger, int, int) - Method in interface loci.formats.meta.IPyramidStore
  Define the image height in pixels of the given pyramid resolution.
setResolutionSizeY(PositiveInteger, int, int) - Method in class loci.formats.ome.OMEPyramidStore
setRestartMarkers(long[]) - Method in interface loci.formats.services.JPEGTurboService
setRestartMarkers(long[]) - Method in class loci.formats.services.JPEGTurboServiceImpl
setRoi(int, int, int, int) - Method in class loci.plugins.util.RecordedImageProcessor
setRoi(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
setRowIndex(int) - Method in class loci.formats.internal.WellContainer
setSeries(int) - Method in class loci.formats.DelegateReader
setSeries(int) - Method in class loci.formats.FileStitcher
setSeries(int) - Method in class loci.formats.FormatReader
setSeries(int) - Method in class loci.formats.FormatWriter
setSeries(int) - Method in interface loci.formats.IFormatReader
  Activates the specified series.
setSeries(int) - Method in interface loci.formats.IFormatWriter
  Sets the current series.
setSeries(int) - Method in class loci.formats.ImageReader
setSeries(int) - Method in class loci.formats.ImageWriter
setSeries(int) - Method in class loci.formats.in.IM3Reader
setSeries(int) - Method in class loci.formats.in.LeicaMicrosystemsMetadata.MultipleImagesReader
  Sets the field MultipleImagesReader.series.
setSeries(int) - Method in class loci.formats.in.OMETiffReader
setSeries(int) - Method in class loci.formats.in.ZeissLSMReader
setSeries(int) - Method in class loci.formats.out.DicomWriter
setSeries(int) - Method in class loci.formats.ReaderWrapper
setSeries(int) - Method in class loci.formats.SubResolutionFormatReader
setSeries(int) - Method in class loci.formats.WrappedReader
setSeries(int) - Method in class loci.formats.WriterWrapper
setSeries(Double) - Method in class loci.plugins.macro.LociFunctions
setSeriesList(String) - Method in class loci.plugins.in.ImportProcess
setSeriesOn(int, boolean) - Method in class loci.plugins.in.ImporterOptions
setShort(int, int) - Method in class loci.formats.in.SPEReader.SpeHeader
  Private method used to set a Short value in the SPE header
setShowMetadata(boolean) - Method in class loci.plugins.in.ImporterOptions
setShowOMEXML(boolean) - Method in class loci.plugins.in.ImporterOptions
setShowROIs(boolean) - Method in class loci.plugins.in.ImporterOptions
setSize(int) - Method in class loci.formats.tiff.OnDemandLongArray
setSlice(int) - Method in class loci.plugins.util.VirtualImagePlus
setSliceLabelButton - Variable in class loci.plugins.config.ConfigWindow
setSnapshotCopyMode(boolean) - Method in class loci.plugins.util.RecordedImageProcessor
setSnapshotPixels(Object) - Method in class loci.plugins.util.RecordedImageProcessor
setSource(ICacheSource) - Method in class loci.formats.cache.Cache
  Sets the cache's caching source.
setSourceImage(byte[], int, int, int, int) - Method in class org.libjpegturbo.turbojpeg.TJCompressor
  Associate an uncompressed source image with this compressor instance.
setSpecifyRanges(boolean) - Method in class loci.plugins.in.ImporterOptions
setSplitChannels(boolean) - Method in class loci.plugins.in.ImporterOptions
setSplitFocalPlanes(boolean) - Method in class loci.plugins.in.ImporterOptions
setSplitTimepoints(boolean) - Method in class loci.plugins.in.ImporterOptions
setStackFormat(String) - Method in class loci.plugins.in.ImporterOptions
setStackOrder(String) - Method in class loci.plugins.in.ImporterOptions
setStitchTiles(boolean) - Method in class loci.plugins.in.ImporterOptions
setStrategy(ICacheStrategy) - Method in class loci.formats.cache.Cache
  Sets the cache's caching strategy.
setStream(RandomAccessInputStream) - Method in class loci.formats.tiff.OnDemandLongArray
setString(int, String) - Method in class loci.formats.in.SPEReader.SpeHeader
  Private method used to set a String value in the SPE header
setSubsamp(int) - Method in class org.libjpegturbo.turbojpeg.TJCompressor
  Set the level of chrominance subsampling for subsequent compress/encode operations.
setSwapDimensions(boolean) - Method in class loci.plugins.in.ImporterOptions
setTBegin(int, int) - Method in class loci.plugins.in.ImporterOptions
setTEnd(int, int) - Method in class loci.plugins.in.ImporterOptions
setThreshold(double, double, int) - Method in class loci.plugins.util.RecordedImageProcessor
setTileSizeX(int) - Method in class loci.formats.FormatWriter
setTileSizeX(int) - Method in interface loci.formats.IFormatWriter
  Will attempt to set the tile width to the desired value and return the actual value which will be used
setTileSizeX(int) - Method in class loci.formats.ImageWriter
setTileSizeX(int) - Method in class loci.formats.out.DicomWriter
setTileSizeX(int) - Method in class loci.formats.out.TiffWriter
setTileSizeX(int) - Method in class loci.formats.WriterWrapper
setTileSizeY(int) - Method in class loci.formats.FormatWriter
setTileSizeY(int) - Method in interface loci.formats.IFormatWriter
  Will attempt to set the tile height to the desired value and return the actual value which will be used
setTileSizeY(int) - Method in class loci.formats.ImageWriter
setTileSizeY(int) - Method in class loci.formats.out.DicomWriter
setTileSizeY(int) - Method in class loci.formats.out.TiffWriter
setTileSizeY(int) - Method in class loci.formats.WriterWrapper
settingsPath - Variable in class loci.formats.in.CV7000Reader
setTruncatedFileFlag(boolean) - Method in class loci.formats.in.DeltavisionReader
  This flag indicates if the file is known to be truncated.
setTStep(int, int) - Method in class loci.plugins.in.ImporterOptions
setUngroupFiles(boolean) - Method in class loci.plugins.in.ImporterOptions
setup - Variable in class loci.formats.in.BDVReader.H5Coordinate
setup - Variable in class loci.formats.in.SDTInfo
setup(String, ImagePlus) - Method in class loci.plugins.LociExporter
  Sets up the writer.
setup(String, ImagePlus) - Method in class loci.plugins.Slicer
SETUP_IDENTIFIER - Static variable in class loci.formats.in.SDTInfo
  For .set files (setup only).
setupAttributeList - Variable in class loci.formats.in.BDVReader
setUpgradeCheck(boolean) - Method in class loci.plugins.in.ImporterOptions
setupLength - Variable in class loci.formats.in.SDTInfo
  Length of the setup data.
setupOffs - Variable in class loci.formats.in.SDTInfo
  Offset of the setup text data (system parameters, display parameters, trace parameters etc.).
setupReader() - Method in class loci.formats.in.MicromanagerReader
  Initialize the TIFF reader with the first non-null file in the current series.
setupResolutionCounts - Variable in class loci.formats.in.BDVReader
setupService() - Method in class loci.formats.FormatReader
  Initialize the OMEXMLService needed by `FormatReader.setId(String)`
setupService() - Method in class loci.formats.in.OMETiffReader
setupServiceAndMetadata() - Method in class loci.formats.out.OMETiffWriter
setupTiffSaver() - Method in class loci.formats.out.TiffWriter
setupVoxelSizes - Variable in class loci.formats.in.BDVReader
setUse64BitOffsets(boolean) - Method in class loci.formats.tiff.TiffParser
  Sets whether or not 64-bit offsets are used for non-BigTIFF files.
setUsingPatternIds(boolean) - Method in class loci.formats.FileStitcher
  Sets whether the reader is using file patterns for IDs.
setUsingPatternIds(boolean) - Method in class loci.plugins.in.ImporterOptions
setValidate(boolean) - Method in class loci.formats.in.DefaultMetadataOptions
setValidate(boolean) - Method in class loci.formats.in.DynamicMetadataOptions
setValidate(boolean) - Method in interface loci.formats.in.MetadataOptions
  Specifies whether or not to validate files when reading.
setValidBitsPerPixel(int) - Method in class loci.formats.FormatWriter
setValidBitsPerPixel(int) - Method in interface loci.formats.IFormatWriter
  Sets the number of valid bits per pixel.
setValidBitsPerPixel(int) - Method in class loci.formats.ImageWriter
setValidBitsPerPixel(int) - Method in class loci.formats.WriterWrapper
setValue(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.
setWellIndex(int) - Method in class loci.formats.internal.WellContainer
setWindowless(boolean) - Method in class loci.plugins.in.ImporterOptions
setWriteSequentially(boolean) - Method in class loci.formats.FormatWriter
setWriteSequentially(boolean) - Method in interface loci.formats.IFormatWriter
  Sets whether or not we know that planes will be written sequentially.
setWriteSequentially(boolean) - Method in class loci.formats.ImageWriter
setWriteSequentially(boolean) - Method in class loci.formats.WriterWrapper
setWritingSequentially(boolean) - Method in class loci.formats.tiff.TiffSaver
  Sets whether or not we know that the planes will be written sequentially.
setXML(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
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.LeicaMicrosystemsMetadata.Dimension
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.JDCEReader.PlaneMetadata
sizeX - Variable in class loci.formats.in.LeicaSCNReader.Dimension
sizeX - Variable in class loci.formats.in.LeicaSCNReader.ImageCollection
sizeX - Variable in class loci.formats.in.LeicaSCNReader.Pixels
sizeX - Variable in class loci.formats.in.MetamorphReader
sizeX - Variable in class loci.formats.in.TextReader
  Image width.
sizeX - Variable in class loci.formats.Resolution
sizeY - Variable in class loci.formats.CoreMetadata
  Height (in pixels) of images in this series.
sizeY - Variable in class loci.formats.in.ColumbusReader.Plane
sizeY - Variable in class loci.formats.in.FakeReader
sizeY - Variable in class loci.formats.in.FEITiffReader
sizeY - Variable in class loci.formats.in.JDCEReader.PlaneMetadata
sizeY - Variable in class loci.formats.in.LeicaSCNReader.Dimension
sizeY - Variable in class loci.formats.in.LeicaSCNReader.ImageCollection
sizeY - Variable in class loci.formats.in.LeicaSCNReader.Pixels
sizeY - Variable in class loci.formats.in.MetamorphReader
sizeY - Variable in class loci.formats.in.TextReader
  Image height.
sizeY - Variable in class loci.formats.Resolution
sizeZ - Variable in class loci.formats.CoreMetadata
  Number of Z sections.
sizeZ - Variable in class loci.formats.FileStitcher
  Dimensional axis lengths per file.
sizeZ - Variable in class loci.formats.gui.ImageViewer
sizeZ - Variable in class loci.formats.in.FakeReader
sizeZ - Variable in class loci.formats.in.LeicaSCNReader.Pixels
sizeZ - Variable in class loci.formats.in.NDPIReader
sizeZsub - Variable in class loci.formats.tools.MakeTestOmeTiff
skip(InputStream, long) - Method in class loci.formats.in.LiFlimReader
SKIP_MISSING_WELLS - Static variable in class loci.formats.in.ScanrReader
SKIP_MISSING_WELLS_DEFAULT - Static variable in class loci.formats.in.ScanrReader
skipBits(long) - Method in class loci.formats.codec.BitBuffer
  Deprecated.
  Skips a number of bits in the BitBuffer.
skipBlocks() - Method in class loci.formats.in.GIFReader
skipBuffer - Variable in class loci.formats.in.OBFReader
skipBytes(OBFReader.Stack, long) - Method in class loci.formats.in.OBFReader
skipComment() - Method in class loci.formats.tools.AmiraParameters
skipData() - Method in class loci.formats.in.ZeissCZIReader.Metadata
skipHeader(RandomAccessInputStream) - Method in class loci.formats.in.MicroCTReader
  Skip the VFF header, which consists of a variable number of LF-terminated lines.
skipLoad - Variable in class loci.formats.Memoizer
skipMissingWells() - Method in class loci.formats.in.ScanrReader
skipPadding() - Method in class loci.formats.in.GatanReader
skipPixelBlock(String, RandomAccessInputStream, boolean) - Method in class loci.formats.in.OIRReader
skipSave - Variable in class loci.formats.Memoizer
skipSave(boolean) - Method in class loci.formats.Memoizer
  Set whether a memo file should be saved if a valid file is not present.
skipTagBlock() - Method in class loci.formats.in.ImspectorReader
  Skip an unknown tag.
skipTags(int) - Method in class loci.formats.in.ImspectorReader
  Skip a block of unknown string values.
skipWhiteSpace() - Method in class loci.formats.in.AmiraReader.ASCII
skipWhiteSpace() - Method in class loci.formats.tools.AmiraParameters
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
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
SlideBook7Reader - Class in loci.formats.in
SlideBook7Reader() - Constructor for class loci.formats.in.SlideBook7Reader
SlideBook7Reader.CAlignManipRecord70 - Class in loci.formats.in
SlideBook7Reader.CAnnotation70 - Class in loci.formats.in
SlideBook7Reader.CChannelDef70 - Class in loci.formats.in
SlideBook7Reader.CChannelRecord70 - Class in loci.formats.in
SlideBook7Reader.CCompressionBase - Class in loci.formats.in
SlideBook7Reader.CCube - Class in loci.formats.in
SlideBook7Reader.CCubeAnnotation70 - Class in loci.formats.in
SlideBook7Reader.CDataTableHeaderRecord70 - Class in loci.formats.in
SlideBook7Reader.CExposureRecord70 - Class in loci.formats.in
SlideBook7Reader.CFluorDef70 - Class in loci.formats.in
SlideBook7Reader.CFRAPRegionAnnotation70 - Class in loci.formats.in
SlideBook7Reader.CFRETManipRecord70 - Class in loci.formats.in
SlideBook7Reader.CHistogramRecord70 - Class in loci.formats.in
SlideBook7Reader.CImageData - Class in loci.formats.in
SlideBook7Reader.CImageGroup - Class in loci.formats.in
SlideBook7Reader.CImageGroup.CAnnotations - Class in loci.formats.in
SlideBook7Reader.CImageGroup.CAuxDoubleData - Class in loci.formats.in
SlideBook7Reader.CImageGroup.CAuxFloatData - Class in loci.formats.in
SlideBook7Reader.CImageGroup.CAuxSInt32Data - Class in loci.formats.in
SlideBook7Reader.CImageGroup.CAuxSInt64Data - Class in loci.formats.in
SlideBook7Reader.CImageGroup.CAuxXmlData - Class in loci.formats.in
SlideBook7Reader.CImageGroup.CMaskPositions - Class in loci.formats.in
SlideBook7Reader.CImageRecord70 - Class in loci.formats.in
SlideBook7Reader.ClassDecoder - Class in loci.formats.in
SlideBook7Reader.CLensDef70 - Class in loci.formats.in
SlideBook7Reader.CMainViewRecord70 - Class in loci.formats.in
SlideBook7Reader.CMaskRecord70 - Class in loci.formats.in
SlideBook7Reader.CNpyHeader - Class in loci.formats.in
SlideBook7Reader.COptovarDef70 - Class in loci.formats.in
SlideBook7Reader.CRatioManipRecord70 - Class in loci.formats.in
SlideBook7Reader.CRemapChannelLUT70 - Class in loci.formats.in
SlideBook7Reader.CRemapManipRecord70 - Class in loci.formats.in
SlideBook7Reader.CRemapPoint - Class in loci.formats.in
SlideBook7Reader.CSBFile70 - Class in loci.formats.in
SlideBook7Reader.CSBPoint<T> - Class in loci.formats.in
SlideBook7Reader.CSlideRecord70 - Class in loci.formats.in
SlideBook7Reader.CUnknownAnnotation70 - Class in loci.formats.in
SlideBook7Reader.DataLoader - Class in loci.formats.in
SlideBook7Reader.EGraphicType - Enum in loci.formats.in
SlideBook7Reader.IntIntPair - Class in loci.formats.in
SlideBook7Reader.StrIntPair - Class in loci.formats.in
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.
SOP_CLASS_UID_VALUE - Static variable in class loci.formats.out.DicomWriter
sortDimensions(int) - Method in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataTempBuffer
  Sorts list of existing dimensions by increasing bytesInc, beginning with X and Y, ending with stage position
sortFilters(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.
sortMultipleImagesReaders() - Method in class loci.formats.in.XLEFReader
  Sorts frames of all MultipleImagesReaders as per core dimension sizes and order
sortPaths(List<String>) - Method in class loci.formats.in.XLEFReader
  Sorts file paths by name and depth and moves current file path to the beginning
SOS - 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_ASSEMBLY - Static variable in class loci.formats.in.ZeissXRMReader
SOURCE_CHANGED - Static variable in class loci.formats.cache.CacheEvent
  Event type indicating a new cache source.
SOURCE_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
split - Variable in class loci.formats.codec.NikonCodecOptions
split - Variable in class loci.formats.in.ND2Reader
split - Variable in class loci.formats.in.NikonReader
SPLIT_LOSSY_DECODER_CONFIGURATION_12 - Static variable in class loci.formats.codec.NikonCodec
SPLIT_LOSSY_DECODER_CONFIGURATION_14 - Static variable in class loci.formats.codec.NikonCodec
SPLIT_MONTAGE - Static variable in class loci.formats.in.GatanReader
SPLIT_MONTAGE_DEFAULT - Static variable in class loci.formats.in.GatanReader
SPLIT_TILES_DEFAULT - Static variable in class loci.formats.in.VentanaReader
  Default value of `VentanaReader.SPLIT_TILES_KEY`
SPLIT_TILES_KEY - Static variable in class loci.formats.in.VentanaReader
  MetadataOptions key for determining whether to report each tile as a separate series.
splitCBox - Variable in class loci.plugins.in.MainDialog
splitChannels(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 `Double`s.
splitFOVs(TissueFAXSReader.ScanRegion, byte[], int) - Method in class loci.formats.in.TissueFAXSReader
  The largest resolution stores one field of view (FOV) per tile.
splitIFD(IFD, int) - Method in class loci.formats.in.VentanaReader
  Take the real IFD on disk and reshape it into something that represents only the given plane.
splitMontage() - Method in class loci.formats.in.GatanReader
splitPlanes - Variable in class loci.formats.in.ZeissLSMReader
splitTBox - Variable in class loci.plugins.in.MainDialog
splitTiles() - Method in class loci.formats.in.VentanaReader
splitZBox - Variable in class loci.plugins.in.MainDialog
SPM_DOMAIN - Static variable in class loci.formats.FormatTools
  Identifies the scanning probe microscopy domain.
SPREADSHEET_KEYS - Static variable in class loci.formats.in.TecanReader
SpringUtilities - Class in loci.plugins.config
  A 1.4 file that provides utility methods for creating form- or grid-style layouts with SpringLayout.
SpringUtilities() - Constructor for class loci.plugins.config.SpringUtilities
SPURIOUS_NOISE_REMOVAL - Static variable in class loci.formats.in.CellSensReader
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
STABLE - Static variable in class loci.plugins.Updater
STABLE_BUILD - Static variable in class loci.formats.UpgradeChecker
  Location of the JAR artifacts for the stable releases.
STABLE_VERSION - Static variable in class loci.formats.UpgradeChecker
  Deprecated.
  As of release 6.6.0
Stack() - Constructor for class loci.formats.in.OBFReader.Stack
Stack() - Constructor for class loci.formats.in.VolocityReader.Stack
STACK_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.dicom.DicomTag
start - Variable in class loci.formats.in.EPSReader
  Starting line of pixel data.
start - Variable in class loci.formats.in.MicromanagerReader
start - Variable in class loci.formats.in.ZeissCZIReader.DimensionEntry
start - Variable in class loci.formats.Modulo
start - Variable in class loci.formats.tiff.OnDemandLongArray
START_OFFSET - Static variable in class loci.formats.in.BioRadGelReader
START_TIME - Static variable in class loci.formats.in.ZeissLSMReader
startCoordinate - Variable in class loci.formats.in.ZeissCZIReader.DimensionEntry
startElement(String, String, String, Attributes) - Method in class loci.formats.in.AFIReader.AFIHandler
startElement(String, String, String, Attributes) - Method in class loci.formats.in.BDVReader.BDVXMLHandler
startElement(String, String, String, Attributes) - Method in class loci.formats.in.BioRadReader.BioRadHandler
startElement(String, String, String, Attributes) - Method in class loci.formats.in.BioRadSCNReader.SCNHandler
startElement(String, String, String, Attributes) - Method in class loci.formats.in.ColumbusReader.MeasurementHandler
startElement(String, String, String, Attributes) - Method in class loci.formats.in.CV7000Reader.MeasurementDataHandler
startElement(String, String, String, Attributes) - Method in class loci.formats.in.CV7000Reader.MeasurementDetailHandler
startElement(String, String, String, Attributes) - Method in class loci.formats.in.CV7000Reader.MeasurementSettingsHandler
startElement(String, String, String, Attributes) - Method in class loci.formats.in.CV7000Reader.WPIHandler
startElement(String, String, String, Attributes) - Method in class loci.formats.in.FEITiffReader.FEIHandler
startElement(String, String, String, Attributes) - Method in class loci.formats.in.FlexReader.FlexHandler
startElement(String, String, String, Attributes) - Method in class loci.formats.in.FlexReader.MeaHandler
startElement(String, String, String, Attributes) - Method in class loci.formats.in.FlexReader.ResHandler
startElement(String, String, String, Attributes) - Method in class loci.formats.in.ImaconReader.ImaconHandler
startElement(String, String, String, Attributes) - Method in class loci.formats.in.InCellReader.InCellHandler
startElement(String, String, String, Attributes) - Method in class loci.formats.in.InCellReader.MinimalInCellHandler
startElement(String, String, String, Attributes) - Method in class loci.formats.in.IvisionReader.IvisionHandler
startElement(String, String, String, Attributes) - Method in class loci.formats.in.LeicaHandler
startElement(String, String, String, Attributes) - Method in class loci.formats.in.LeicaSCNReader.LeicaSCNHandler
startElement(String, String, String, Attributes) - Method in class loci.formats.in.MetamorphHandler
startElement(String, String, String, Attributes) - Method in class loci.formats.in.MicromanagerReader.MicromanagerHandler
startElement(String, String, String, Attributes) - Method in class loci.formats.in.ND2Handler
startElement(String, String, String, Attributes) - Method in class loci.formats.in.OMEXMLReader.OMEXMLHandler
startElement(String, String, String, Attributes) - Method in class loci.formats.in.OperettaReader.OperettaHandler
startElement(String, String, String, Attributes) - Method in class loci.formats.in.ScanrReader.ScanrHandler
startElement(String, String, String, Attributes) - Method in class loci.formats.in.ZeissTIFFHandler
startElement(String, String, String, Attributes) - Method in class loci.formats.out.OMEXMLWriter.OMEHandler
startIndex - Variable in class loci.formats.FilePattern
  Indices into the pattern indicating the start of a numerical block.
startingPosition - Variable in class loci.formats.in.ZeissCZIReader.Segment
startTime - Variable in class loci.formats.in.CV7000Reader
startTime - Variable in class loci.formats.in.PerkinElmerReader
startTime - Variable in class loci.formats.in.ZeissLSMReader.Recording
startTime - Variable in class loci.plugins.in.ImagePlusReader
startTiming() - Method in class loci.plugins.in.ImagePlusReader
startX - Variable in class loci.formats.in.SPEReader.SpeROI
startY - Variable in class loci.formats.in.SPEReader.SpeROI
state - Variable in class loci.formats.in.OBFReader
State(int) - Constructor for class loci.formats.in.OBFReader.State
stateChanged(ChangeEvent) - Method in class loci.formats.gui.CacheComponent
  Handles range spinner changes.
stateChanged(ChangeEvent) - Method in class loci.formats.gui.DataConverter
stateChanged(ChangeEvent) - Method in class loci.formats.gui.ImageViewer
  Handles slider events.
stateChanged(ChangeEvent) - Method in class loci.plugins.util.SearchableWindow.SearchBox
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.in.DicomReader
stopWatch() - Method in class loci.formats.Memoizer
stopWatch() - Method in class loci.formats.out.DicomWriter
storageMethod - Variable in class loci.formats.in.MRWReader
store - Variable in class loci.formats.FileStitcher
store - Variable in class loci.formats.in.BDVReader
store - Variable in class loci.formats.in.CellH5Reader
store - Variable in class loci.formats.in.FlexReader.FlexHandler
store - Variable in class loci.formats.in.InCellReader.InCellHandler
store - Variable in class loci.formats.in.KLBReader
store - Variable in class loci.formats.in.LeicaHandler
store - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataStoreInitializer
store - Variable in class loci.formats.in.ZeissCZIReader
storedChannel - Variable in class loci.formats.in.SDTReader
storedChannel - Variable in class loci.formats.in.SPCReader
storedRGB - Variable in class loci.formats.in.ICSReader
storedSeries - Variable in class loci.formats.in.SDTReader
storedSize - Variable in class loci.formats.in.ZeissCZIReader.DimensionEntry
storedT - Variable in class loci.formats.in.SPCReader
storeKeyValue(Hashtable, String, String) - Method in class loci.formats.in.LeicaHandler
storeLine(Line, MetadataStore, int, int, int, int, int) - Static method in class loci.plugins.util.ROIHandler
  Stores the Line ROI into the specified metadata store.
storeOval(OvalRoi, MetadataStore, int, int, int, int, int) - Static method in class loci.plugins.util.ROIHandler
  Stores the Oval ROI into the specified metadata store.
storePoint(PointRoi, MetadataStore, int, int, int, int, int) - Static method in class loci.plugins.util.ROIHandler
  Stores the Point ROI into the specified metadata store.
storePolygon(PolygonRoi, MetadataStore, int, int, int, int, int) - Static method in class loci.plugins.util.ROIHandler
  Stores the Polygon ROI into the specified metadata store.
storeRectangle(Roi, MetadataStore, int, int, int, int, int) - Static method in class loci.plugins.util.ROIHandler
  Stores the Rectangle ROI into the specified metadata store.
storeRelativePositions() - Method in class loci.formats.in.ZeissCZIReader
storeROI(MetadataStore, int, int) - Method in class loci.formats.in.LeicaHandler.ROI
storeROI(MetadataStore, int, int, int, int, int, boolean, MetadataLevel) - Method in class loci.formats.in.LeicaMicrosystemsMetadata.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 - Variable in class loci.formats.dicom.DicomTag
STRATEGY_CHANGED - Static variable in class loci.formats.cache.CacheEvent
  Event type indicating a new cache strategy.
STRATEGY_PARAMS - Static variable in class loci.formats.gui.CacheComponent
STRATEGY_VALUES - Static variable in class loci.formats.gui.CacheComponent
strategyChooser - Variable in class loci.formats.gui.CacheComponent
  Combo box for choosing cache strategy.
strategyIndex(ICacheStrategy) - Method in class loci.formats.gui.CacheComponent
  Converts cache strategy to strategy chooser index.
strategyValue(int) - Method in class loci.formats.gui.CacheComponent
  Generates a new cache strategy matching the strategy chooser index.
stream - Variable in class loci.formats.in.ZeissCZIReader.Segment
stream - Variable in class loci.formats.services.POIServiceImpl
stream - Variable in class loci.formats.tiff.OnDemandLongArray
streamNames - Variable in class loci.formats.tools.AmiraParameters
streams - Variable in class loci.formats.tools.AmiraParameters
streamTypes - Variable in class loci.formats.tools.AmiraParameters
strikeout - Variable in class loci.formats.in.BaseZeissReader.Shape
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
StrIntPair(String, Integer) - Constructor for class loci.formats.in.SlideBook7Reader.StrIntPair
STRIP_BYTE_COUNTS - Static variable in class loci.formats.tiff.IFD
STRIP_OFFSETS - Static variable in class loci.formats.tiff.IFD
stripHeader() - Method in class loci.formats.in.QTReader
  Cut off header bytes from a resource fork file.
strips - Variable in class loci.formats.in.PictReader
  Vector of byte arrays representing individual rows.
strokeColor - Variable in class loci.formats.in.GatanReader.ROIShape
STRUCTURE_LABELS_1 - Static variable in class loci.formats.in.BioRadReader
  Structure labels.
STRUCTURE_LABELS_2 - Static variable in class loci.formats.in.BioRadReader
STRUCTURE_LABELS_3 - Static variable in class loci.formats.in.BioRadReader
STRUCTURE_LABELS_4 - Static variable in class loci.formats.in.BioRadReader
STRUCTURE_LABELS_5 - Static variable in class loci.formats.in.BioRadReader
STRUCTURE_LABELS_6 - Static variable in class loci.formats.in.BioRadReader
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 - 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.
sum(int[], int, int) - Method in class loci.formats.in.XLEFReader
  Sums up all values of an array, from start index to (including) end index
surfaceWind - Variable in class loci.formats.in.HRDGDFReader
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").
swapDimensions() - Method in class loci.formats.in.LeicaMicrosystemsMetadata.MultipleImagesReader
  Rearranges frame order from ZSTC order (used in XLIFs) to desired CoreMetadata.dimensionOrder
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.LeicaMicrosystemsMetadata.MetadataTempBuffer
swapXY - Variable in class loci.formats.in.LIFReader
SWATCH_SIZE - Static variable in class loci.plugins.in.ColorDialog
switchChunk(OBFReader.Stack, int) - Method in class loci.formats.in.OBFReader
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.OIRReader.CZTKey
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 - Variable in enum loci.formats.dicom.DicomAttribute
tag - Variable in class loci.formats.dicom.DicomTag
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
TAG_ENCODING - Static variable in class loci.formats.in.LEOReader
tagEncoding - Variable in class loci.formats.tiff.TiffParser
tagID - Variable in class loci.formats.in.BaseZeissReader.Shape
taglist - Variable in class loci.formats.in.ZeissTIFFReader.Plane
tagProviders - Variable in class loci.formats.out.DicomWriter
tags - Variable in class loci.formats.dicom.DicomJSONProvider
tags - Variable in class loci.formats.in.DicomReader
tags - Variable in class loci.formats.in.ZeissTIFFHandler.TagSet
tags - Variable in class loci.formats.in.ZeissTIFFReader.Plane
tagset - Variable in class loci.formats.in.ZeissTIFFHandler.Plane
tagset - Variable in class loci.formats.in.ZeissTIFFHandler.Scaling
TagSet() - Constructor for class loci.formats.in.ZeissTIFFHandler.TagSet
tagsToParse - Variable in class loci.formats.in.BaseZeissReader
TargaReader - Class in loci.formats.in
  File format reader for Truevision Targa files.
TargaReader() - Constructor for class loci.formats.in.TargaReader
  Constructs a new Targa reader.
TargaRLECodec - Class in loci.formats.codec
  This class implements Targa RLE decompression.
TargaRLECodec() - Constructor for class loci.formats.codec.TargaRLECodec
TARGET_PRINTER - Static variable in class loci.formats.tiff.IFD
tBegin - Variable in class loci.plugins.in.ImporterOptions
TCHAR - Static variable in class loci.formats.in.CellSensReader
tChoice - Variable in class loci.formats.gui.DataConverter
tChoice - Variable in class loci.plugins.in.SwapDialog
TCSReader - Class in loci.formats.in
  TCSReader is the file format reader for Leica TCS TIFF files and their companion XML file.
TCSReader() - Constructor for class loci.formats.in.TCSReader
tDim - Variable in class loci.formats.out.AVIWriter
TecanReader - Class in loci.formats.in
TecanReader() - Constructor for class loci.formats.in.TecanReader
  Constructs a new Tecan Spark Cyto reader.
TecanReader.Channel - Class in loci.formats.in
TecanReader.Image - Class in loci.formats.in
TEMPERATURE - 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.LeicaMicrosystemsMetadata.ROI
text - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.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.ND2Reader
textColour - Variable in class loci.formats.in.BaseZeissReader.Shape
textData - Variable in class loci.formats.in.ND2Reader
textEmissionWavelengths - Variable in class loci.formats.in.ND2Reader
TextLine(String, Font, int, int) - Constructor for class loci.formats.in.FakeReader.TextLine
TextLine(String, Font, int, int) - Constructor for class loci.formats.tools.MakeTestOmeTiff.TextLine
TextReader - Class in loci.formats.in
  Reader for text files containing tables of data.
TextReader() - Constructor for class loci.formats.in.TextReader
  Constructs a new text reader.
textureOffset - Variable in class loci.formats.in.AliconaReader
  Image offset.
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_KEY - Static variable in class loci.formats.out.DicomWriter
  Option for turning off TIFF metadata.
TIFF_SUFFIXES - Static variable in class loci.formats.in.TiffReader
TIFF_SUFFIXES - Static variable in class loci.formats.in.ZeissTIFFReader
TiffCompression - Enum 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.DicomWriter
tiffSaver - Variable in class loci.formats.out.TiffWriter
  The TiffSaver that will do most of the writing.
TiffSaver - Class in loci.formats.tiff
  Parses TIFF data from an input source.
TiffSaver(String) - Constructor for class loci.formats.tiff.TiffSaver
  Constructs a new TIFF saver from the given filename.
TiffSaver(RandomAccessOutputStream, String) - Constructor for class loci.formats.tiff.TiffSaver
  Constructs a new TIFF saver from the given output source.
TiffSaver(RandomAccessOutputStream, ByteArrayHandle) - Constructor for class loci.formats.tiff.TiffSaver
  Constructs a new TIFF saver from the given output source.
TIFFTile() - Constructor for class loci.formats.in.VentanaReader.TIFFTile
TiffWriter - Class in loci.formats.out
  TiffWriter is the file format writer for TIFF files.
TiffWriter() - Constructor for class loci.formats.out.TiffWriter
TiffWriter(String, String[]) - Constructor for class loci.formats.out.TiffWriter
Tile() - Constructor for class loci.formats.in.OlympusTileReader.Tile
TILE_BYTE_COUNTS - Static variable in class loci.formats.tiff.IFD
TILE_GRANULARITY - Static variable in class loci.formats.out.TiffWriter
  TIFF tiles must be of a height and width divisible by 16.
TILE_LENGTH - Static variable in class loci.formats.tiff.IFD
TILE_NUM - Static variable in class loci.formats.FormatTools
TILE_OFFSETS - Static variable in class loci.formats.tiff.IFD
TILE_ORIGIN - Static variable in class loci.formats.in.CellSensReader
TILE_SYSTEM - Static variable in class loci.formats.in.CellSensReader
TILE_WIDTH - Static variable in class loci.formats.tiff.IFD
TILE_X - Static variable in class loci.formats.FormatTools
TILE_Y - Static variable in class loci.formats.FormatTools
tileBytesInc - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataTempBuffer
tileBytesInc - Variable in class loci.formats.in.LIFReader
tileCols - Variable in class loci.formats.in.MIASReader
tileColumns - Variable in class loci.formats.in.VentanaReader.AreaOfInterest
TileCoordinate(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.LeicaMicrosystemsMetadata.MetadataTempBuffer
tileCount - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.MultipleImagesReader
tileCount - Variable in class loci.formats.in.LIFReader
tileCountPointer - Variable in class loci.formats.out.DicomWriter
tileFiles - Variable in class loci.formats.in.HamamatsuVMSReader
tileGridXOffset - Variable in class loci.formats.codec.CodecOptions
  Horizontal offset of the tile grid as it would be provided to: `ImageWriteParam.setTiling(int, int, int, int)` (WRITE).
tileGridYOffset - Variable in class loci.formats.codec.CodecOptions
  Vertical offset of the tile grid as it would be provided to: `ImageWriteParam.setTiling(int, int, int, int)` (WRITE).
tileHeight - Variable in class loci.formats.codec.CodecOptions
  Tile height as it would be provided to: `ImageWriteParam.setTiling(int, int, int, int)` (WRITE).
tileHeight - Variable in class loci.formats.in.CellVoyagerReader.ChannelInfo
tileHeight - Variable in class loci.formats.in.L2DReader
tileHeight - Variable in class loci.formats.in.LeicaReader
tileHeight - Variable in class loci.formats.in.MIASReader
tileHeight - Variable in class loci.formats.in.OMETiffReader.OMETiffCoreMetadata
  Tile size Y.
tileHeight - Variable in class loci.formats.in.ScanrReader
tileHeight - Variable in class loci.formats.in.VentanaReader
tileHeight - Variable in class loci.formats.in.ZeissCZIReader
tileHeight - Variable in class loci.formats.out.DicomWriter
tileHeight - Variable in class loci.formats.services.JPEGTurboServiceImpl
tileHeightPointer - Variable in class loci.formats.out.DicomWriter
tileIndices - Variable in class loci.formats.in.BaseZeissReader
TileJPEGReader - Class in loci.formats.in
  Reader for decoding JPEG images using java.awt.Toolkit and TurboJPEG.
TileJPEGReader() - Constructor for class loci.formats.in.TileJPEGReader
tileMap - Variable in class loci.formats.in.CellSensReader
tileMap - Variable in class loci.formats.TileStitcher
tileOffsets - Variable in class loci.formats.in.CellSensReader
tileOriginX - Variable in class loci.formats.in.CellSensReader.Pyramid
tileOriginY - Variable in class loci.formats.in.CellSensReader.Pyramid
tilePositions - Variable in class loci.formats.in.DicomReader
tileRangeX - Variable in class loci.formats.in.TissueFAXSReader.ScanRegion
tileRangeY - Variable in class loci.formats.in.TissueFAXSReader.ScanRegion
tileRows - Variable in class loci.formats.in.MIASReader
tileRows - Variable in class loci.formats.in.VentanaReader.AreaOfInterest
tiles - Variable in class loci.formats.dicom.DicomFileInfo
tiles - Variable in class loci.formats.in.BaseZeissReader
tiles - Variable in class loci.formats.in.OlympusTileReader
tiles - Variable in class loci.formats.in.VentanaReader
tileSizeX - Variable in class loci.formats.in.TissueFAXSReader.ScanRegion
tileSizeX - Variable in class loci.formats.out.TiffWriter
  The tile width which will be used for writing.
tileSizeY - Variable in class loci.formats.in.TissueFAXSReader.ScanRegion
tileSizeY - Variable in class loci.formats.out.TiffWriter
  The tile height which will be used for writing.
TileStitcher - 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
tileWidth - Variable in class loci.formats.out.DicomWriter
tileWidth - Variable in class loci.formats.services.JPEGTurboServiceImpl
tileWidthPointer - Variable in class loci.formats.out.DicomWriter
tileX - Variable in class loci.formats.in.CellSensReader
tileX - Variable in class loci.formats.TileStitcher
tileY - Variable in class loci.formats.in.CellSensReader
tileY - Variable in class loci.formats.TileStitcher
TillVisionReader - Class in loci.formats.in
  TillVisionReader is the file format reader for TillVision files.
TillVisionReader() - Constructor for class loci.formats.in.TillVisionReader
  Constructs a new TillVision reader.
TIM_SUFFIX - Static variable in class loci.formats.in.PerkinElmerReader
time - Variable in class loci.formats.in.DicomReader
time - Variable in class loci.formats.in.LEOReader
time - Variable in class loci.formats.in.MicroCTReader
time - Variable in class loci.formats.in.MicromanagerReader.Position
time - Variable in class loci.formats.in.SDTInfo
  Time of creation.
time - Variable in class loci.formats.in.SVSReader
time - Variable in class loci.plugins.in.ImagePlusReader
TIME_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_START - Static variable in class loci.formats.in.CellSensReader
TIME_SUFFIX - Static variable in class loci.formats.in.KLBReader
TIME_VALUE - Static variable in class loci.formats.in.CellSensReader
timeBins - Variable in class loci.formats.in.PQBinReader
timeBins - Variable in class loci.formats.in.SDTInfo
timeBins - Variable in class loci.formats.in.SDTReader
  Number of time bins in lifetime histogram.
timeIncrement - Variable in class loci.formats.in.FEITiffReader
timeIncrement - Variable in class loci.formats.in.IPLabReader
timeIncrement - Variable in class loci.formats.in.TiffReader
timeIncrement - Variable in class loci.formats.in.ZeissCZIReader
timeIncrement - Variable in class loci.formats.in.ZeissLSMReader.Track
timeIndex - Variable in class loci.formats.in.FluoviewReader
TIMEINFO - Static variable in class loci.formats.in.LeicaReader
timelineIndex - Variable in class loci.formats.in.CV7000Reader.Channel
timelineIndex - Variable in class loci.formats.in.CV7000Reader.MeasurementSettingsHandler
timelineIndex - Variable in class loci.formats.in.CV7000Reader.Plane
timepoint - Variable in class loci.formats.in.BaseZeissReader
timepoint - Variable in class loci.formats.in.BDVReader.H5Coordinate
timepoint - Variable in class loci.formats.in.ColumbusReader.Plane
timepoint - Variable in class loci.formats.in.CV7000Reader.Plane
timepoint - Variable in class loci.formats.in.OpenlabReader.PlaneInfo
timepoint - Variable in class loci.formats.in.TissueFAXSReader.ScanRegion
timepointIncrement - Variable in class loci.formats.in.BDVReader
timepointIndices - Variable in class loci.formats.in.BaseZeissReader
timePoints - Variable in class loci.formats.in.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
timestamp - Variable in class loci.formats.dicom.DicomFileInfo
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.JDCEReader.PlaneMetadata
timestamp - Variable in class loci.formats.in.OpenlabReader.PlaneInfo
timestamp - Variable in class loci.formats.in.TecanReader.Image
timestamp - Variable in class loci.formats.in.ZeissCZIReader.SubBlock
TIMESTAMP_KEY - Static variable in class loci.formats.in.LiFlimReader
timestampAdjustments - Variable in class loci.formats.in.OIRReader
timestampFile - Variable in class loci.formats.in.VolocityReader.Stack
timestamps - Variable in class loci.formats.in.BaseZeissReader
timestamps - Variable in class loci.formats.in.BrukerReader
timestamps - Variable in class loci.formats.in.CellWorxReader
timestamps - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataTempBuffer
timestamps - Variable in class loci.formats.in.LeicaReader
timestamps - Variable in class loci.formats.in.LiFlimReader
timestamps - Variable in class loci.formats.in.LIFReader
timestamps - Variable in class loci.formats.in.MetamorphHandler
timestamps - Variable in class loci.formats.in.MicromanagerReader.Position
timestamps - Variable in class loci.formats.in.PCIReader
timestamps - Variable in class loci.formats.in.VolocityReader
timestamps - Variable in class loci.formats.in.ZeissCZIReader
timestamps - Variable in class loci.formats.in.ZeissLSMReader
timeStampSeconds - Variable in class loci.formats.in.DeltavisionReader.DVExtHdrFields
  Time stamp in seconds since the experiment began.
timeUnit - Variable in class loci.formats.in.NiftiReader
TISSUE_INDEX - Static variable in class loci.formats.in.NDPIReader
TissueFAXSReader - Class in loci.formats.in
  Reader for TissueFAXS format from TissueGnostics.
TissueFAXSReader() - Constructor for class loci.formats.in.TissueFAXSReader
  Constructs a new TissueGnostics TissueFAXS reader.
TissueFAXSReader.Channel - Class in loci.formats.in
TissueFAXSReader.ScanRegion - Class in loci.formats.in
TITAN_TAG - Static variable in class loci.formats.in.FEITiffReader
TITLE - Static variable in class loci.formats.gui.DataConverter
TITLE - Static variable in class loci.formats.gui.ImageViewer
TITLE - Static variable in class loci.formats.tools.EditTiffG
TJ - Class in org.libjpegturbo.turbojpeg
  TurboJPEG utility class (cannot be instantiated)
TJ() - Constructor for class org.libjpegturbo.turbojpeg.TJ
TJCompressor - Class in org.libjpegturbo.turbojpeg
  TurboJPEG compressor
TJCompressor() - Constructor for class org.libjpegturbo.turbojpeg.TJCompressor
  Create a TurboJPEG compressor instance.
TJCompressor(byte[], int, int, int, int) - Constructor for class org.libjpegturbo.turbojpeg.TJCompressor
  Create a TurboJPEG compressor instance and associate the uncompressed source image stored in `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
tmaX - Variable in class loci.formats.in.TissueFAXSReader.ScanRegion
tmaY - Variable in class loci.formats.in.TissueFAXSReader.ScanRegion
tmpLetter - Variable in class loci.formats.ResourceNamer
toArray() - Method in class loci.formats.tiff.OnDemandLongArray
toByteArray() - Method in class loci.formats.codec.BitWriter
  Deprecated.
  Gets an array containing all bits written thus far.
toByteArray() - Method in class loci.formats.codec.ByteVector
toBytes(BufferedImage, IFormatWriter) - Static method in class loci.formats.gui.BufferedImageWriter
toCIEXYZ(float[]) - Method in class loci.formats.gui.TwoChannelColorSpace
toFloat(int, FloatProcessor) - Method in class loci.plugins.util.RecordedImageProcessor
toggleAnimation() - Method in class loci.plugins.util.DataBrowser
  Toggles whether the data browser is animating.
token - Variable in enum loci.formats.in.LeicaMicrosystemsMetadata.Dimension.DimensionKey
token(String, String, int) - Method in class loci.formats.in.PrairieMetadata
  Gets the `i`th 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
TOOLS - Static variable in class loci.formats.UpgradeChecker
  Name of the ueber tools JAR.
toOMExmlColor(Color) - Static method in class loci.plugins.util.ROIHandler
  Converts the Java Color into an OME-XML Color.
TOP_LEVEL_KEYS - Static variable in class loci.formats.in.NikonTiffReader
TopometrixReader - Class in loci.formats.in
  TopometrixReader is the file format reader for TopoMetrix .tfr, .ffr, .zfr, .zfp, and .2fl files.
TopometrixReader() - Constructor for class loci.formats.in.TopometrixReader
  Constructs a new TopoMetrix reader.
toRGB(float[]) - Method in class loci.formats.gui.TwoChannelColorSpace
toSPWCoordinates(int) - Method in class loci.formats.in.FakeReader
  Convert the given series (Image) index to a WellSample, Well, and Plate index.
toString() - Method in class loci.formats.cache.CacheEvent
toString() - Method in class loci.formats.CoreMetadata
toString() - Method in class loci.formats.dicom.DicomTag
toString() - Method in class loci.formats.FileInfo
toString() - Method in class loci.formats.gui.ComboFileFilter
  Gets a string representation of this file filter.
toString() - Method in class loci.formats.gui.ExtensionFileFilter
  Gets a string representation of this file filter.
toString() - Method in class loci.formats.gui.FormatFileFilter
  Gets a string representation of this file filter.
toString() - Method in class loci.formats.gui.NoExtensionFileFilter
  Gets a string representation of this file filter.
toString(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.CV7000Reader.Channel
toString() - Method in class loci.formats.in.DeltavisionReader.DVExtHdrFields
  Helper function which overrides toString, printing out the values in the header section.
toString() - Method in class loci.formats.in.IM3Reader.IM3Record
toString() - Method in class loci.formats.in.LeicaMicrosystemsMetadata.LMSXmlDocument
toString() - Method in class loci.formats.in.LIFReader.MemoryBlock
toString() - Method in class loci.formats.in.MicromanagerReader.Index
toString() - Method in class loci.formats.in.ND2Reader.ChunkMapEntry
toString() - Method in class loci.formats.in.OIRReader.CZTKey
toString() - Method in class loci.formats.in.OlympusTileReader.Tile
toString() - Method in class loci.formats.in.PrairieMetadata.ValueItem
toString() - Method in class loci.formats.in.VentanaReader.AreaOfInterest
toString() - Method in class loci.formats.in.VentanaReader.Overlap
toString() - Method in class loci.formats.in.ZeissCZIReader.AttachmentEntry
toString() - Method in class loci.formats.in.ZeissCZIReader.Coordinate
toString() - Method in class loci.formats.in.ZeissCZIReader.DimensionEntry
toString() - Method in class loci.formats.in.ZeissCZIReader.DirectoryEntry
toString() - Method in class loci.formats.in.ZeissCZIReader.SubBlock
toString() - Method in class loci.formats.in.ZeissTIFFHandler.Plane
toString() - Method in class loci.formats.in.ZeissTIFFHandler.Scaling
toString() - Method in class loci.formats.in.ZeissTIFFHandler.Tag
toString() - Method in class loci.formats.in.ZeissTIFFHandler.TagSet
toString() - Method in class loci.formats.in.ZeissTIFFHandler
toString() - Method in class loci.formats.in.ZeissTIFFReader.Plane
toString() - Method in class loci.formats.ome.OMEPyramidStore.Resolution
toString() - Method in class loci.formats.tiff.TiffIFDEntry
toString() - Method in class loci.formats.tiff.TiffRational
  Returns a string representation of the object.
toString() - Method in class loci.formats.tools.AmiraParameters
toString(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
transferSyntaxPointer - Variable in class loci.formats.out.DicomWriter
transform(byte[][], TJTransform[], int) - Method in class org.libjpegturbo.turbojpeg.TJTransformer
  Losslessly transform the JPEG image associated with this transformer instance into one or more JPEG images stored in the given destination buffers.
transform(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
transformBytes8To16(byte[], byte[], int) - Method in class loci.formats.in.XLEFReader
  Transforms an 8bit byte array to a 16bit byte array, optionally with bit upscaling (8-16bit)
transformCTProjectionInterpolation(String) - Method in class loci.formats.in.InveonReader
transformCTWarping(String) - Method in class loci.formats.in.InveonReader
transformedSizes - Variable in class org.libjpegturbo.turbojpeg.TJTransformer
transformEventType(String) - Method in class loci.formats.in.InveonReader
transformFileType(String) - Method in class loci.formats.in.InveonReader
transformFilter(String) - Method in class loci.formats.in.InveonReader
transformGantryRotation(String) - Method in class loci.formats.in.InveonReader
transformModality(String) - Method in class loci.formats.in.InveonReader
transformModalityConfiguration(String) - Method in class loci.formats.in.InveonReader
transformModel(String) - Method in class loci.formats.in.InveonReader
transformNormalizationApplied(String) - Method in class loci.formats.in.InveonReader
transformReconAlgorithm(String) - Method in class loci.formats.in.InveonReader
transformRegistrationAvailable(String) - Method in class loci.formats.in.InveonReader
transformRotationDirection(String) - Method in class loci.formats.in.InveonReader
transformSubjectLengthUnits(String) - Method in class loci.formats.in.InveonReader
transformSubjectOrientation(String) - Method in class loci.formats.in.InveonReader
transformSubjectWeightUnits(String) - Method in class loci.formats.in.InveonReader
transformToLatestVersion(String) - Method in interface loci.formats.services.OMEXMLService
  Transforms the given OME-XML string to the latest supported version of of the OME-XML schema.
transformToLatestVersion(String) - Method in class loci.formats.services.OMEXMLServiceImpl
transIndex - Variable in class loci.formats.in.GIFReader
  Transparent color index.
translate(int, int) - Method in class loci.plugins.util.RecordedImageProcessor
translateAttachmentNodes(Element, int) - Method in class loci.formats.in.LeicaMicrosystemsMetadata.LMSMetadataExtractor
  Extracts information from dimension descriptions and writes it to reader's `MetadataTempBuffer`
translateAttachmentNodes(Element, int) - Method in class loci.formats.in.LIFReader
translateChannelDescriptions(Element, int) - Method in class loci.formats.in.LeicaMicrosystemsMetadata.LMSMetadataExtractor
  Extracts i.a.
translateDetectors(Element, int) - Method in class loci.formats.in.LeicaMicrosystemsMetadata.LMSMetadataExtractor
  Extracts detector information and writes it to reader's `MetadataTempBuffer`
translateDetectors(Element, int) - Method in class loci.formats.in.LIFReader
translateDimensionDescriptions(Element, int) - Method in class loci.formats.in.LeicaMicrosystemsMetadata.LMSMetadataExtractor
  Extracts information from dimension descriptions and writes it to reader's `CoreMetadata` and `MetadataTempBuffer`
translateDisplaySettings(Element) - Method in class loci.formats.in.ZeissCZIReader
translateExperiment(Element) - Method in class loci.formats.in.ZeissCZIReader
translateFilterSettings(Element, int) - Method in class loci.formats.in.LeicaMicrosystemsMetadata.LMSMetadataExtractor
  Extracts filter information and writes it to reader's `MetadataTempBuffer`
translateFilterSettings(Element, int) - Method in class loci.formats.in.LIFReader
translateHardwareSettings(Element) - Method in class loci.formats.in.ZeissCZIReader
translateImage(Element, int) - Method in class loci.formats.in.LeicaMicrosystemsMetadata.LMSMetadataExtractor
  Extracts information from element node and writes it to reader's `CoreMetadata` and `MetadataTempBuffer`
translateImageNames(Element, int) - Method in class loci.formats.in.LIFReader
translateImageNodes(Element, int) - Method in class loci.formats.in.LIFReader
translateInformation(Element) - Method in class loci.formats.in.ZeissCZIReader
translateLaserLines(Element, int) - Method in class loci.formats.in.LeicaMicrosystemsMetadata.LMSMetadataExtractor
  Extracts laser information and writes it to reader's `MetadataTempBuffer`
translateLaserLines(Element, int) - Method in class loci.formats.in.LIFReader
translateLayers(Element) - Method in class loci.formats.in.ZeissCZIReader
translateLut(String) - Method in class loci.formats.in.LeicaMicrosystemsMetadata.LMSMetadataExtractor
  Translates Leica XML lut name / value to Color
translateLuts(List<String>, int) - Method in class loci.formats.in.LeicaMicrosystemsMetadata.LMSMetadataExtractor
  Translates raw channel luts of an image to Colors and writes it to reader's `MetadataTempBuffer`
translateMetadata(List<LMSImageXmlDocument>) - Method in class loci.formats.in.LeicaMicrosystemsMetadata.LMSFileReader
  Extracts metadata from a list of Leica image XML Documents and writes them to the reader's CoreMetadata, `MetadataTempBuffer` and MetadataStore
translateMetadata(LMSImageXmlDocument) - Method in class loci.formats.in.LeicaMicrosystemsMetadata.LMSFileReader
translateMetadata(List<LMSImageXmlDocument>) - Method in class loci.formats.in.LeicaMicrosystemsMetadata.LMSMetadataExtractor
  Extracts all information from Leica image xml Documents and writes it to reader's `CoreMetadata` and `MetadataTempBuffer`
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.LeicaMicrosystemsMetadata.LMSMetadataExtractor
  Extracts ROIs and writes them to reader's `MetadataTempBuffer`
translateROIs(Element, int) - Method in class loci.formats.in.LIFReader
translateScaling(Element) - Method in class loci.formats.in.ZeissCZIReader
translateScannerSettings(Element, int) - Method in class loci.formats.in.LeicaMicrosystemsMetadata.LMSMetadataExtractor
  Extracts scanner information and writes it to reader's `CoreMetadata` and `MetadataTempBuffer`
translateScannerSettings(Element, int) - Method in class loci.formats.in.LIFReader
translateSingleROIs(Element, int) - Method in class loci.formats.in.LeicaMicrosystemsMetadata.LMSMetadataExtractor
  Extracts single ROIs and writes them to reader's `MetadataTempBuffer`
translateSingleROIs(Element, int) - Method in class loci.formats.in.LIFReader
translateSingleTimestamp(String) - Method in class loci.formats.in.LeicaMicrosystemsMetadata.LMSMetadataExtractor
  Translates hex timestamp string to double value
translateSingleTimestamp(Element) - Method in class loci.formats.in.LeicaMicrosystemsMetadata.LMSMetadataExtractor
  Translates the content of a timestamp node to double value
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.LeicaMicrosystemsMetadata.LMSMetadataExtractor
  Extracts timestamps and writes them to reader's `MetadataTempBuffer`
translateTimestamps(Element, int) - Method in class loci.formats.in.LIFReader
transmissivity - Variable in class loci.formats.in.OIRReader.Laser
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.LeicaMicrosystemsMetadata.ROI
transX - Variable in class loci.formats.in.LIFReader.ROI
transY - Variable in class loci.formats.in.LeicaHandler.ROI
transY - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.ROI
transY - Variable in class loci.formats.in.LIFReader.ROI
TrestleReader - Class in loci.formats.in
  TrestleReader is the file format reader for Trestle slide datasets.
TrestleReader() - Constructor for class loci.formats.in.TrestleReader
  Constructs a new Trestle reader.
trigger - Variable in class loci.formats.in.SDTInfo
TRIM_DIMENSIONS_DEFAULT - Static variable in class loci.formats.in.ZeissCZIReader
TRIM_DIMENSIONS_KEY - Static variable in class loci.formats.in.ZeissCZIReader
trimDimensions() - Method in class loci.formats.in.ZeissCZIReader
TRUE_ALPHA - Static variable in class loci.formats.in.APNGReader
TRUE_COLOR - Static variable in class loci.formats.in.APNGReader
trueSizeX - Variable in class loci.formats.in.ND2Reader
trueSizeY - Variable in class loci.formats.in.ND2Reader
trueSizeZ - Variable in class loci.formats.in.ND2Reader
truncatedFileFlag - Variable in class loci.formats.in.DeltavisionReader
TRUNK - Static variable in class loci.plugins.Updater
TRUNK_BUILD - Static variable in class loci.formats.UpgradeChecker
  Location of the JAR artifacts for Bio-Formats' trunk build.
ts - Variable in class loci.formats.in.ND2Handler
tScroll - Variable in class loci.plugins.util.DataBrowser
tSize - Variable in class loci.formats.in.DeltavisionReader
  Size of one time element in the extended header.
tSlider - Variable in class loci.formats.gui.ImageViewer
tsT - Variable in class loci.formats.in.ND2Reader
tStart - Variable in class loci.formats.in.OIRReader
tStep - Variable in class loci.formats.in.OIRReader
tStep - Variable in class loci.plugins.in.ImporterOptions
tSteps - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataTempBuffer
tSteps - Variable in class loci.formats.in.LIFReader
Tstore - Variable in class loci.formats.in.SPCReader
tstoreb - Variable in class loci.formats.in.SPCReader
tValues - Variable in class loci.formats.in.CellSensReader.Pyramid
TWO - Static variable in class loci.formats.AxisGuesser
TwoChannelColorSpace - Class in loci.formats.gui
  ColorSpace for 2-channel images.
TwoChannelColorSpace(int, int) - Constructor for class loci.formats.gui.TwoChannelColorSpace
type - Variable in class loci.formats.cache.CacheEvent
  Type of cache event.
type - Variable in class loci.formats.in.APNGReader.PNGBlock
type - Variable in class loci.formats.in.AVIReader
type - Variable in class loci.formats.in.BaseZeissReader.Shape
type - Variable in class loci.formats.in.BioRadReader.Note
type - Variable in class loci.formats.in.CV7000Reader.LightSource
type - Variable in class loci.formats.in.GatanReader.ROIShape
type - Variable in class loci.formats.in.IM3Reader.IM3Record
type - Variable in class loci.formats.in.LeicaHandler.Detector
type - Variable in class loci.formats.in.LeicaHandler.ROI
type - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.ROI
type - Variable in class loci.formats.in.LIFReader.ROI
type - Variable in class loci.formats.in.PrairieMetadata.Sequence
  `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.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
UIC1TAG - Static variable in class loci.formats.in.MetamorphReader
UIC2TAG - Static variable in class loci.formats.in.MetamorphReader
UIC3TAG - Static variable in class loci.formats.in.MetamorphReader
UIC4TAG - Static variable in class loci.formats.in.MetamorphReader
UID - Variable in class loci.formats.in.CellVoyagerReader.AreaInfo
UID - Variable in class loci.formats.in.CellVoyagerReader.WellInfo
UID_DEFAULT_ROOT - Static variable in class loci.formats.out.DicomWriter
UID_ROOT_KEY - Static variable in class loci.formats.out.DicomWriter
  Option for setting the organization root for UIDs.
UIDCreator() - Constructor for class loci.formats.out.DicomWriter.UIDCreator
uids - Variable in class loci.formats.out.DicomWriter
UINT - Static variable in class loci.formats.in.CellSensReader
UINT - Static variable in class loci.formats.in.GatanReader
UINT12stream - Variable in class loci.formats.in.LiFlimReader
UINT12streamPos - Variable in class loci.formats.in.LiFlimReader
UINT12streamSeries - Variable in class loci.formats.in.LiFlimReader
UINT16 - Static variable in class loci.formats.FormatTools
  Identifies the UINT16 data type used to store pixel values.
UINT16_TYPE - Static variable in class loci.formats.in.KLBReader
UINT32 - Static variable in class loci.formats.FormatTools
  Identifies the UINT32 data type used to store pixel values.
UINT32_TYPE - Static variable in class loci.formats.in.KLBReader
UINT64_TYPE - Static variable in class loci.formats.in.KLBReader
UINT8 - Static variable in class loci.formats.FormatTools
  Identifies the UINT8 data type used to store pixel values.
UINT8_TYPE - Static variable in class loci.formats.in.KLBReader
ULONG - Static variable in class loci.formats.in.CellSensReader
uncompress(int, byte[]) - Method in class loci.formats.in.AVIReader
uncompress(byte[], String) - Method in class loci.formats.in.QTReader
  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.in.DCIMGReader
uniqueFiles - Variable in class loci.formats.out.ICSWriter
uniquePMTs - Variable in class loci.formats.in.ImspectorReader
  List of PMTs active during acquisition.
uniqueZ - Variable in class loci.formats.in.PCIReader
UNISOKU_MAGIC_STRING - Static variable in class loci.formats.in.UnisokuReader
UnisokuReader - Class in loci.formats.in
  UnisokuReader is the file format reader for Unisoku STM files.
UnisokuReader() - Constructor for class loci.formats.in.UnisokuReader
  Constructs a new Unisoku reader.
unit - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.Channel
unit - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.Dimension
unit - Variable in class loci.formats.in.ZeissTIFFHandler.Scaling.Dimension
unit - Variable in class loci.formats.Modulo
units - Variable in class loci.formats.in.GatanReader
units - Variable in class loci.formats.in.VarianFDFReader
UNITS_METER - Static variable in class loci.formats.in.NiftiReader
  Code for meters.
UNITS_MM - Static variable in class loci.formats.in.NiftiReader
  Code for millimeters.
UNITS_MSEC - Static variable in class loci.formats.in.NiftiReader
  Code for milliseconds.
UNITS_USEC - Static variable in class loci.formats.in.NiftiReader
  Code for microseconds.
UNKNOWN - 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
update() - Method in enum loci.formats.dicom.DicomAttribute
update2003FC - Static variable in class loci.formats.services.OMEXMLServiceImpl
  Stylesheets for updating from previous schema releases.
update200706 - Static variable in class loci.formats.services.OMEXMLServiceImpl
update200802 - Static variable in class loci.formats.services.OMEXMLServiceImpl
update200809 - Static variable in class loci.formats.services.OMEXMLServiceImpl
update200909 - Static variable in class loci.formats.services.OMEXMLServiceImpl
update201004 - Static variable in class loci.formats.services.OMEXMLServiceImpl
update201006 - Static variable in class loci.formats.services.OMEXMLServiceImpl
update201106 - Static variable in class loci.formats.services.OMEXMLServiceImpl
update201206 - Static variable in class loci.formats.services.OMEXMLServiceImpl
update201306 - Static variable in class loci.formats.services.OMEXMLServiceImpl
update201501 - Static variable in class loci.formats.services.OMEXMLServiceImpl
updateComposite(int[], int) - Method in class loci.plugins.util.RecordedImageProcessor
updateCoreMetadata(CoreMetadata) - Method in class loci.formats.in.DicomReader
updateIfGlitched() - Method in class loci.plugins.in.SeriesDialog
updateLabel(int, int) - Method in class loci.formats.gui.ImageViewer
  Updates cursor probe label.
updateLabels(String) - Method in class loci.formats.gui.DataConverter
updateMetadataLists(Hashtable<String, Object>) - Method in class loci.formats.FormatReader
  For the given metadata hashtable, replace any value that is a list with one key/value pair per list entry.
updateMinMax(int, byte[], int) - Method in class loci.formats.MinMaxCalculator
  Updates min/max values based on the given byte array.
updateOrder(int) - Method in class loci.formats.gui.CacheComponent
  Updates cache order to match the state of the GUI.
updatePending - Variable in class loci.formats.in.ZeissCZIReader.FileHeader
updatePriority(int) - Method in class loci.formats.gui.CacheComponent
  Updates cache priority to match the state of the GUI.
Updater - Class in loci.plugins
  A plugin for updating the Bio-Formats plugins.
Updater() - Constructor for class loci.plugins.Updater
updateRange(int) - Method in class loci.formats.gui.CacheComponent
  Updates cache range to match the state of the GUI.
updateSource() - Method in class loci.formats.gui.CacheComponent
  Updates cache source to match the state of the GUI.
updateStrategy() - Method in class loci.formats.gui.CacheComponent
  Updates cache strategy to match the state of the GUI.
updateTiming(int, int, int, int) - Method in class loci.plugins.in.ImagePlusReader
UPGRADE_CHECK_ALLOWED_PROPERTY - Static variable in class loci.formats.UpgradeChecker
  System property indicating whether the upgrade check is ever allowed.
UPGRADE_CHECK_KEY - Static variable in class loci.plugins.config.ConfigWindow
UPGRADE_CHECK_PROPERTY - Static variable in class loci.formats.UpgradeChecker
  System property to set once the upgrade check is performed.
upgradeBox - Variable in class loci.plugins.config.ConfigWindow
UpgradeCheck - Class in loci.formats.tools
  Utility that checks for a new stable version, and optionally installs a new version of Bio-Formats ueber tools.
UpgradeCheck() - Constructor for class loci.formats.tools.UpgradeCheck
UpgradeChecker - Class in loci.formats
  Class that allows checking for new versions of Bio-Formats, as well as updating to the latest stable, daily, or trunk version.
UpgradeChecker() - Constructor for class loci.formats.UpgradeChecker
UpgradeDialog - Class in loci.plugins.in
  Bio-Formats Importer upgrade checker dialog box.
UpgradeDialog(ImportProcess) - Constructor for class loci.plugins.in.UpgradeDialog
  Creates an upgrade checker dialog for the Bio-Formats Importer.
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_OME_TIFF - Static variable in class loci.formats.FormatTools
  URL of OME-TIFF web page.
URL_SOFTWARE - Static variable in class loci.plugins.About
  URL of the Bio-Formats web page.
urlPath - Variable in class loci.plugins.Updater
  Path to bioformats_package.jar uber-jar.
use64Bit - Variable in class loci.formats.in.MinimalTiffReader
USE_CHUNKMAP_DEFAULT - Static variable in class loci.formats.in.ND2Reader
USE_CHUNKMAP_KEY - Static variable in class loci.formats.in.ND2Reader
USE_CHUNKMAP_LEGACY_KEY - Static variable in class loci.formats.in.ND2Reader
  Deprecated.
USE_ORIGINAL_FRAME_RATE - Static variable in class loci.formats.in.CellSensReader
useChunkMap() - Method in class loci.formats.in.ND2Reader
used - Variable in class loci.formats.in.APLReader
used - Variable in class loci.formats.in.BioRadReader
used - Variable in class loci.formats.in.OMETiffReader
  List of used files.
usedFile(String) - Method in class loci.formats.in.LeicaReader
usedFiles - Variable in class loci.formats.in.CellSensReader
usedFiles - Variable in class loci.formats.in.FV1000Reader
  Used file list.
usedSize - Variable in class loci.formats.in.ZeissCZIReader.Segment
usedToInitialize - Variable in class loci.formats.FileInfo
  Whether or not this file can be passed to the appropriate reader's setId(String) method.
useLegacy - Variable in class loci.formats.DelegateReader
  Flag indicating whether to use legacy reader by default.
useMotor - Variable in class loci.formats.in.SDTInfo
useND2Chunkmap() - Static method in class loci.plugins.util.LociPrefs
useOldPhysicalSizeCalculation() - Method in class loci.formats.in.LeicaMicrosystemsMetadata.LMSFileReader
useOldPhysicalSizeCalculation() - Method in class loci.formats.in.LIFReader
usePatternIds - Variable in class loci.plugins.in.ImporterOptions
USER - Static variable in class loci.formats.in.OpenlabReader
USER_COMMENT - Static variable in class loci.formats.tiff.IFD
userDisplayName - Variable in class loci.formats.in.ZeissCZIReader
userEmail - Variable in class loci.formats.in.ZeissCZIReader
userFirstName - Variable in class loci.formats.in.ZeissCZIReader
userInstitution - Variable in class loci.formats.in.ZeissCZIReader
userLastName - Variable in class loci.formats.in.ZeissCZIReader
userMetadataStore - Variable in class loci.formats.Memoizer
  `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.ND2Reader
USHORT - Static variable in class loci.formats.in.CellSensReader
USHORT - Static variable in class loci.formats.in.GatanReader
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(List<DicomTag>) - Method in class loci.formats.dicom.DicomTag
  Check this tag against a list of existing tags.
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
validateValue() - Method in class loci.formats.dicom.DicomTag
  Compare the value type to the VR.
validBits - Variable in class loci.formats.FormatWriter
  The number of valid bits per pixel.
validBits - Variable in class loci.formats.in.FV1000Reader
validChannel - Variable in class loci.formats.in.ScanrReader.ScanrHandler
validLoopState - Variable in class loci.formats.in.ND2Handler
validPixelCount - Variable in class loci.formats.out.DicomWriter
validStream(RandomAccessInputStream, int, boolean) - Static method in class loci.formats.FormatTools
  Returns true if the given RandomAccessInputStream conatins at least 'len' bytes.
validZ - Variable in class loci.formats.in.MetamorphReader
value - Variable in class loci.formats.dicom.DicomTag
value - Variable in enum 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.dicom.DicomAttribute
  Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum loci.formats.dicom.DicomVR
  Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum loci.formats.dicom.ResolutionStrategy
  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.LeicaMicrosystemsMetadata.Channel.ChannelType
  Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum loci.formats.in.LeicaMicrosystemsMetadata.Dimension.DimensionKey
  Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum loci.formats.in.LeicaMicrosystemsMetadata.LMSFileReader.ImageFormat
  Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum loci.formats.in.LeicaMicrosystemsMetadata.LMSXmlDocument.InitFrom
  Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum loci.formats.in.LOFReader.MetadataSource
  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.SlideBook7Reader.EGraphicType
  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.dicom.DicomAttribute
  Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum loci.formats.dicom.DicomVR
  Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum loci.formats.dicom.ResolutionStrategy
  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.LeicaMicrosystemsMetadata.Channel.ChannelType
  Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum loci.formats.in.LeicaMicrosystemsMetadata.Dimension.DimensionKey
  Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum loci.formats.in.LeicaMicrosystemsMetadata.LMSFileReader.ImageFormat
  Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum loci.formats.in.LeicaMicrosystemsMetadata.LMSXmlDocument.InitFrom
  Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum loci.formats.in.LOFReader.MetadataSource
  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.SlideBook7Reader.EGraphicType
  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
variableZ - Variable in class loci.formats.in.InCellReader
VarianFDFReader - Class in loci.formats.in
  VarianFDFReader is the file format reader for Varian FDF files.
VarianFDFReader() - Constructor for class loci.formats.in.VarianFDFReader
  Constructs a new Varian FDF reader.
VCLOCK_AMPLITUDE - Static variable in class loci.formats.in.CellSensReader
VCS_REVISION - Static variable in class loci.formats.FormatTools
  Current VCS revision.
VCS_SHORT_REVISION - Static variable in class loci.formats.FormatTools
  Deprecated.
  Use the general `FormatTools.VCS_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.DCIMGReader
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
vmid - Variable in class loci.formats.out.DicomWriter.UIDCreator
vOffsetX - Variable in class loci.formats.in.LeicaSCNReader.Image
vOffsetY - Variable in class loci.formats.in.LeicaSCNReader.Image
VolocityClippingReader - Class in loci.formats.in
  VolocityClippingReader is the file format reader for Volocity library clipping files.
VolocityClippingReader() - Constructor for class loci.formats.in.VolocityClippingReader
  Constructs a new Volocity clipping reader.
VolocityReader - Class in loci.formats.in
  VolocityReader is the file format reader for Volocity library files.
VolocityReader() - Constructor for class loci.formats.in.VolocityReader
  Constructs a new Volocity reader.
VolocityReader.Stack - Class in loci.formats.in
voltage - Variable in class loci.formats.in.FV1000Reader.ChannelData
voltage - Variable in class loci.formats.in.GatanReader
voltage - Variable in class loci.formats.in.LeicaHandler.Detector
voltage - Variable in class loci.formats.in.LeicaReader.Detector
voltage - Variable in class loci.formats.in.MicromanagerReader.Position
voltage - Variable in class loci.formats.in.ND2Handler
voltage - Variable in class loci.formats.in.OIRReader.Detector
voltage - Variable in class loci.formats.in.ZeissXRMReader
voltages - Variable in class loci.formats.in.FluoviewReader
VOLUME_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
vPredictor - Variable in class loci.formats.codec.NikonCodecOptions
vPredictor - Variable in class loci.formats.in.NikonReader
vr - Variable in class loci.formats.dicom.DicomTag
vSizeX - Variable in class loci.formats.in.LeicaSCNReader.Image
vSizeY - Variable in class loci.formats.in.LeicaSCNReader.Image
vSpacingZ - Variable in class loci.formats.in.LeicaSCNReader.Image

## W

wait(boolean) - Method in class loci.formats.gui.ImageViewer
  Toggles wait cursor.
waitTime - Variable in class loci.formats.in.PrairieMetadata
  The wait time of the acquisition.
warn(boolean, String) - Static method in class loci.plugins.BF
warnFile(PrairieMetadata.Sequence, int, int) - Method in class loci.formats.in.PrairieReader
  Emits a warning about a missing `<File>`.
warnFilename(PrairieMetadata.Sequence, int, int) - Method in class loci.formats.in.PrairieReader
  Emits a warning about a `<File>`'s 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
WAVE_MAX - Static variable in class loci.formats.in.TissueFAXSReader
WAVE_MIN - Static variable in class loci.formats.in.TissueFAXSReader
wavelength - Variable in class loci.formats.in.CV7000Reader.LightSource
wavelength - Variable in class loci.formats.in.IvisionReader
wavelength - Variable in class loci.formats.in.LeicaHandler.Laser
WAVELENGTH - 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.CellWorxReader
wavelengths - Variable in class loci.formats.in.FV1000Reader
wavelengths - Variable in class loci.formats.in.IM3Reader.Spectrum
wavelengths - Variable in class loci.formats.in.MetamorphHandler
waveMax - Variable in class loci.formats.in.PrairieMetadata.PFile
  `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
wellColumn - Variable in class loci.formats.in.TecanReader.Image
wellColumns - Variable in class loci.formats.in.FlexReader
wellColumns - Variable in class loci.formats.in.MIASReader
wellColumns - Variable in class loci.formats.in.ScanrReader
WellContainer - Class in loci.formats.internal
  Represents a well in a plate.
WellContainer() - Constructor for class loci.formats.internal.WellContainer
WellContainer(int, int, int, int) - Constructor for class loci.formats.internal.WellContainer
wellCoordinates - Variable in class loci.formats.in.InCellReader
wellCount - Variable in class loci.formats.in.CellWorxReader
wellCount - Variable in class loci.formats.in.FlexReader
wellCount - Variable in class loci.formats.in.MetamorphTiffReader
wellCount - Variable in class loci.formats.in.ScanrReader
wellFiles - Variable in class loci.formats.in.CellWorxReader
wellIndex - Variable in class loci.formats.in.ScanrReader.ScanrHandler
wellIndex - Variable in class loci.formats.internal.WellContainer
WellInfo() - Constructor for class loci.formats.in.CellVoyagerReader.WellInfo
wellLabels - Variable in class loci.formats.in.BDReader
wellLabels - Variable in class loci.formats.in.ScanrReader
wellList - Variable in class loci.formats.in.BDReader
wellNumber - Variable in class loci.formats.in.FlexReader
  Specifies the row and column index into 'flexFiles' for a given well.
wellNumber - Variable in class loci.formats.in.MIASReader
wellNumbers - Variable in class loci.formats.in.ScanrReader
wellRow - Variable in class loci.formats.in.InCellReader.MinimalInCellHandler
wellRow - Variable in class loci.formats.in.TecanReader.Image
wellRows - Variable in class loci.formats.in.BDReader
wellRows - Variable in class loci.formats.in.FlexReader
wellRows - Variable in class loci.formats.in.InCellReader
wellRows - Variable in class loci.formats.in.ScanrReader
wells - Variable in class loci.formats.in.CellVoyagerReader
wells - Variable in class loci.formats.in.JDCEReader
WHITE_BALANCE - Static variable in class loci.formats.tiff.IFD
WHITE_BALANCE_FINE - Static variable in class loci.formats.in.NikonReader
WHITE_BALANCE_RGB_COEFFS - Static variable in class loci.formats.in.DNGReader
WHITE_BALANCE_RGB_COEFFS - Static variable in class loci.formats.in.NikonReader
WHITE_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
WIDER - Static variable in class loci.formats.in.CellSensReader
WIDER_ENABLED - Static variable in class loci.formats.in.CellSensReader
widgets - Variable in class loci.plugins.config.CellSensWidgets
widgets - Variable in class loci.plugins.config.FormatEntry
widgets - Variable in class loci.plugins.config.LIFWidgets
widgets - Variable in class loci.plugins.config.ND2Widgets
widgets - Variable in class loci.plugins.config.SDTWidgets
widgets - Variable in class loci.plugins.config.TiffDelegateWidgets
widgets - Variable in class loci.plugins.config.ZeissCZIWidgets
width - Variable in class loci.formats.codec.CodecOptions
  Width, in pixels, of the image.
width - Variable in enum loci.formats.dicom.DicomVR
width - Variable in class loci.formats.in.BaseZeissReader.Shape
width - Variable in class loci.formats.in.CellSensReader.Pyramid
width - Variable in class loci.formats.in.CellVoyagerReader.AreaInfo
width - Variable in class loci.formats.in.CellVoyagerReader.ChannelInfo
width - Variable in class loci.formats.in.OpenlabReader.PlaneInfo
width - Variable in class loci.formats.in.SDTInfo
width - Variable in class loci.formats.tools.AmiraParameters
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
with(int) - Static method in enum loci.formats.in.LeicaMicrosystemsMetadata.Dimension.DimensionKey
withinPixels(long) - Method in class loci.formats.in.SlidebookReader
WORKING_DISTANCE - Static variable in class loci.formats.in.CellSensReader
workingDistance - Variable in class loci.formats.in.CellSensReader.Pyramid
workingDistance - Variable in class loci.formats.in.FV1000Reader
workingDistance - Variable in class loci.formats.in.LEOReader
workingDistance - Variable in class loci.formats.in.NikonTiffReader
WPIHandler() - Constructor for class loci.formats.in.CV7000Reader.WPIHandler
wppPath - Variable in class loci.formats.in.CV7000Reader
WrappedCodec - Class in loci.formats.codec
  Generic wrapper for codecs from ome-codecs.
WrappedCodec(Codec) - Constructor for class loci.formats.codec.WrappedCodec
  Construct with a codec implementation to wrap.
WrappedReader - Class in loci.formats
  Helper class for readers which wrap other readers.
WrappedReader(String, String[]) - Constructor for class loci.formats.WrappedReader
  Constructs a new wrapped reader with the given name and suffixes.
write(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
writeDualPersonality() - Method in class loci.formats.out.DicomWriter
  Checks the writer's associated MetadataOptions to see if dual personality writing has been explicitly enabled or disabled.
writeFCTL(int, int) - Method in class loci.formats.out.APNGWriter
writeFooter() - Method in class loci.formats.out.APNGWriter
writeFooter() - Method in class loci.formats.out.JavaWriter
writeFooter() - Method in class loci.formats.out.QTWriter
writeHeader() - Method in class loci.formats.out.DicomWriter
  Write the preamble, prefix, and file meta elements.
writeHeader() - Method in class loci.formats.out.EPSWriter
writeHeader() - Method in class loci.formats.out.JavaWriter
writeHeader() - Method in class loci.formats.tiff.TiffSaver
  Writes the TIFF file header.
writeIFD(IFD, long) - Method in class loci.formats.tiff.TiffSaver
  Write the given IFD to the open stream.
writeIFD(IFD, long, boolean) - Method in class loci.formats.tiff.TiffSaver
  Write the given IFD to the open stream.
writeIFDs(int) - Method in class loci.formats.out.DicomWriter
writeIFDStrips(IFD, int, byte[][], int, boolean, int, int, long) - Method in class loci.formats.tiff.TiffSaver
writeIFDValue(RandomAccessOutputStream, long, int, Object) - Method in class loci.formats.tiff.TiffSaver
  Writes the given IFD value to the given output object.
writeImage(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
writeTag(DicomTag) - Method in class loci.formats.out.DicomWriter
writeTag(DicomTag, RandomAccessOutputStream) - Method in class loci.formats.out.DicomWriter
written - Variable in class loci.formats.ome.OMEPyramidStore
written - Variable in class loci.formats.out.DicomWriter.PlaneOffset
wsi - Variable in class loci.formats.in.DicomReader
wSize - Variable in class loci.formats.in.DeltavisionReader
  Size of one wave in the extended header.

## X

x - Variable in class loci.formats.in.BioRadReader.Note
x - Variable in class loci.formats.in.CellVoyagerReader.FieldInfo
x - Variable in class loci.formats.in.InCellReader
x - Variable in class loci.formats.in.LeicaHandler.ROI
x - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.ROI
x - Variable in class loci.formats.in.LIFReader.ROI
x - Variable in class loci.formats.in.OperettaReader.Channel
x - Variable in class loci.formats.in.OperettaReader.Plane
x - Variable in class loci.formats.in.VentanaReader.Overlap
x - Variable in class loci.formats.in.ZeissCZIReader.SubBlock
x - Variable in class loci.formats.ome.OMEPyramidStore.Resolution
x - Variable in class loci.formats.TileStitcher.TileCoordinate
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.
XlcfDocument - Class in loci.formats.in.LeicaMicrosystemsMetadata
  This class loads and represents a Leica Microsystems XLCF xml document
XlcfDocument(String, LMSCollectionXmlDocument) - Constructor for class loci.formats.in.LeicaMicrosystemsMetadata.XlcfDocument
XlefDocument - Class in loci.formats.in.LeicaMicrosystemsMetadata
  This class represents a Leica Microsystems XLEF xml document, a project file which references xlifs and optionally xlcfs
XlefDocument(String) - Constructor for class loci.formats.in.LeicaMicrosystemsMetadata.XlefDocument
XLEFReader - Class in loci.formats.in
  XLEFReader is the file format reader for Leica Microsystems' XLEF files.
XLEFReader() - Constructor for class loci.formats.in.XLEFReader
  Constructs a new Leica XLEF reader.
XLEFReader.PathComparator - Class in loci.formats.in
  Helper class to sort file paths by name and depth
xLen - Variable in class loci.formats.in.LiFlimReader
XlifDocument - Class in loci.formats.in.LeicaMicrosystemsMetadata
  This class loads and represents a Leica Microsystems XLIF xml document
XlifDocument(String, LMSCollectionXmlDocument) - Constructor for class loci.formats.in.LeicaMicrosystemsMetadata.XlifDocument
xLocation - Variable in class loci.formats.in.VolocityReader.Stack
XML - 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.in.FakeReader.TextLine
xoff - Variable in class loci.formats.tools.MakeTestOmeTiff.TextLine
xOffset - Variable in class loci.formats.in.ND2Reader
xOffset - Variable in class loci.formats.out.DicomWriter.PlaneOffset
xOffsetReal - Variable in class loci.formats.out.DicomWriter.PlaneOffset
xOffsetSize - Variable in class loci.formats.out.DicomWriter.PlaneOffset
xor(int) - Method in class loci.plugins.util.RecordedImageProcessor
xOrigin - Variable in class loci.formats.in.TiffReader
xOrigin - Variable in class loci.formats.in.VentanaReader.AreaOfInterest
xPad - Variable in class loci.formats.out.AVIWriter
xPath - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.LMSXmlDocument
xPath(String) - Method in class loci.formats.in.LeicaMicrosystemsMetadata.LMSXmlDocument
  Searches the XML document for expressions using xPath.
xPath(Node, String) - Method in class loci.formats.in.LeicaMicrosystemsMetadata.LMSXmlDocument
  Searches a node for expressions using xPath.
xpixels - Variable in class loci.formats.in.CellVoyagerReader.FieldInfo
xpos - Variable in class loci.formats.in.CV7000Reader.Plane
xPos - Variable in class loci.formats.in.LeicaHandler
xPos - Variable in class loci.formats.in.OpenlabReader
xPos - Variable in class loci.formats.in.ZeissXRMReader
xPositions - Variable in class loci.formats.in.FlexReader
xSize - Variable in class loci.formats.in.CV7000Reader.Channel
xSize - Variable in class loci.formats.in.LEOReader
xSize - Variable in class loci.formats.in.QuesantReader
xSizes - Variable in class loci.formats.in.FlexReader
XSLT_2003FC - Static variable in class loci.formats.services.OMEXMLServiceImpl
XSLT_200706 - Static variable in class loci.formats.services.OMEXMLServiceImpl
XSLT_200802 - Static variable in class loci.formats.services.OMEXMLServiceImpl
XSLT_200809 - Static variable in class loci.formats.services.OMEXMLServiceImpl
XSLT_200909 - Static variable in class loci.formats.services.OMEXMLServiceImpl
XSLT_201004 - Static variable in class loci.formats.services.OMEXMLServiceImpl
XSLT_201006 - Static variable in class loci.formats.services.OMEXMLServiceImpl
XSLT_201106 - Static variable in class loci.formats.services.OMEXMLServiceImpl
XSLT_201206 - Static variable in class loci.formats.services.OMEXMLServiceImpl
XSLT_201306 - Static variable in class loci.formats.services.OMEXMLServiceImpl
XSLT_201501 - Static variable in class loci.formats.services.OMEXMLServiceImpl
XSLT_PATH - Static variable in class loci.formats.services.OMEXMLServiceImpl
xTiles - Variable in class loci.formats.in.DeltavisionReader
  Number of tiles in X direction.
xTiles - Variable in class loci.formats.services.JPEGTurboServiceImpl
xyGain - Variable in class loci.formats.in.SDTInfo
  Gain for XY ADCs (SPC930).
xyw(CellConstraints, int, int, int) - Method in class loci.plugins.in.MainDialog
  Convenience method for creating a left-aligned, vertically centered cell constraints object.

## Y

y - Variable in class loci.formats.in.BioRadReader.Note
y - Variable in class loci.formats.in.CellVoyagerReader.FieldInfo
y - Variable in class loci.formats.in.InCellReader
y - Variable in class loci.formats.in.LeicaHandler.ROI
y - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.ROI
y - Variable in class loci.formats.in.LIFReader.ROI
y - Variable in class loci.formats.in.OperettaReader.Channel
y - Variable in class loci.formats.in.OperettaReader.Plane
y - Variable in class loci.formats.in.VentanaReader.Overlap
y - Variable in class loci.formats.in.ZeissCZIReader.SubBlock
y - Variable in class loci.formats.ome.OMEPyramidStore.Resolution
y - Variable in class loci.formats.TileStitcher.TileCoordinate
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.
yEnd - Variable in class loci.formats.in.OIRReader.PixelBlock
yIndex - Variable in class loci.formats.in.TextReader
  Column index for Y coordinate.
yLen - Variable in class loci.formats.in.LiFlimReader
yLocation - Variable in class loci.formats.in.VolocityReader.Stack
yOffset - Variable in class loci.formats.in.ND2Reader
yOffset - Variable in class loci.formats.out.DicomWriter.PlaneOffset
yOffsetReal - Variable in class loci.formats.out.DicomWriter.PlaneOffset
yOffsetSize - Variable in class loci.formats.out.DicomWriter.PlaneOffset
yOrigin - Variable in class loci.formats.in.TiffReader
yOrigin - Variable in class loci.formats.in.VentanaReader.AreaOfInterest
ypad - Variable in class loci.formats.in.FakeReader.TextLine
ypad - Variable in class loci.formats.tools.MakeTestOmeTiff.TextLine
ypixels - Variable in class loci.formats.in.CellVoyagerReader.FieldInfo
ypos - Variable in class loci.formats.in.CV7000Reader.Plane
yPos - Variable in class loci.formats.in.LeicaHandler
yPos - Variable in class loci.formats.in.OpenlabReader
yPos - Variable in class loci.formats.in.ZeissXRMReader
yPositions - Variable in class loci.formats.in.FlexReader
ySize - Variable in class loci.formats.in.CV7000Reader.Channel
ySizes - Variable in class loci.formats.in.FlexReader
yStart - Variable in class loci.formats.in.OIRReader.PixelBlock
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.ColumbusReader.Plane
z - Variable in class loci.formats.in.CV7000Reader.Plane
z - Variable in class loci.formats.in.LeicaSCNReader.Dimension
z - Variable in class loci.formats.in.MicromanagerReader.Index
z - Variable in class loci.formats.in.OIRReader.CZTKey
z - Variable in class loci.formats.in.OperettaReader.Plane
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_TAG - Static variable in class loci.formats.in.VentanaReader
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
ZeissXRMReader - Class in loci.formats.in
  ZeissXRMReader is the file format reader for Zeiss X-Ray Microscopy .txm and .txrm files.
ZeissXRMReader() - Constructor for class loci.formats.in.ZeissXRMReader
  Constructs a new Zeiss XRM reader.
ZeissZVIReader - Class in loci.formats.in
  ZeissZVIReader is the file format reader for Zeiss ZVI files.
ZeissZVIReader() - Constructor for class loci.formats.in.ZeissZVIReader
  Constructs a new ZeissZVI reader.
zEnd - Variable in class loci.plugins.in.ImporterOptions
zeroes - Variable in class loci.formats.FilePatternBlock
  The number of leading zeroes.
zIncrement - Variable in class loci.formats.in.CellSensReader.Pyramid
zIndices - Variable in class loci.formats.in.BaseZeissReader
ZIP - Static variable in class loci.formats.in.PhotoshopTiffReader
ZipReader - Class in loci.formats.in
  Reader for Zip files.
ZipReader() - Constructor for class loci.formats.in.ZipReader
zLabel - Variable in class loci.formats.gui.DataConverter
zLen - Variable in class loci.formats.in.LiFlimReader
ZlibCodec - Class in loci.formats.codec
  This class implements ZLIB decompression.
ZlibCodec() - Constructor for class loci.formats.codec.ZlibCodec
zLocation - Variable in class loci.formats.in.VolocityReader.Stack
zMapFile - Variable in class loci.formats.in.CellWorxReader
zOffset - Variable in class loci.formats.dicom.DicomTile
zOffset - Variable in class loci.formats.in.ND2Reader
zOffset - Variable in class loci.formats.out.DicomWriter.PlaneOffset
zOffsets - Variable in class loci.formats.dicom.DicomFileInfo
zOffsets - Variable in class loci.formats.in.DicomReader
zOffsetSize - Variable in class loci.formats.out.DicomWriter.PlaneOffset
zoom - Variable in class loci.formats.in.LeicaHandler.Detector
zoom - Variable in class loci.formats.in.LeicaHandler
zoom - Variable in class loci.formats.in.MetamorphHandler
zoom - Variable in class loci.formats.in.MetamorphReader
zoom - Variable in class loci.formats.in.ZeissCZIReader
zoom - Variable in class loci.formats.in.ZeissLSMReader
zooms - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataTempBuffer
zooms - Variable in class loci.formats.in.LIFReader
ZPO_SUFFIX - Static variable in class loci.formats.in.PerkinElmerReader
zpos - Variable in class loci.formats.in.CV7000Reader.Plane
zPos - Variable in class loci.formats.in.LeicaHandler
zPos - Variable in class loci.formats.in.OpenlabReader
zPos - Variable in class loci.formats.in.ZeissXRMReader
zPosition - Variable in class loci.formats.in.InCellReader.Image
zPosition - Variable in class loci.formats.in.InCellReader.InCellHandler
zPosition - Variable in class loci.formats.in.OpenlabReader.PlaneInfo
zPosition - Variable in class loci.formats.in.SVSReader
zPositions - Variable in class loci.formats.in.FluoviewReader
zPositions - Variable in class loci.formats.in.MetamorphHandler
zs - Variable in class loci.formats.in.ND2Handler
zScroll - Variable in class loci.plugins.util.DataBrowser
zSize - Variable in class loci.formats.in.DeltavisionReader
  Size of one z section in the extended header.
zSlider - Variable in class loci.formats.gui.ImageViewer
zStart - Variable in class loci.formats.in.CellSensReader.Pyramid
zStart - Variable in class loci.formats.in.MetamorphReader
zStart - Variable in class loci.formats.in.OIRReader
ZSTD_0 - Static variable in class loci.formats.in.ZeissCZIReader
ZSTD_1 - Static variable in class loci.formats.in.ZeissCZIReader
ZstdCodec - Class in loci.formats.codec
ZstdCodec() - Constructor for class loci.formats.codec.ZstdCodec
zStep - Variable in class loci.formats.in.OIRReader
zStep - Variable in class loci.formats.in.ZeissCZIReader
zStep - Variable in class loci.plugins.in.ImporterOptions
zSteps - Variable in class loci.formats.in.CellWorxReader
zSteps - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataTempBuffer
zSteps - Variable in class loci.formats.in.LIFReader
zSteps - Variable in class loci.formats.in.TissueFAXSReader.ScanRegion
zValues - Variable in class loci.formats.in.CellSensReader.Pyramid
ZVI_MAGIC_BYTES - Static variable in class loci.formats.in.ZeissZVIReader

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