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A

a - Variable in class loci.formats.in.VentanaReader.Overlap
 
About - Class in loci.plugins
Displays a small information dialog about the Bio-Formats Plugins package.
About() - Constructor for class loci.plugins.About
 
about() - Static method in class loci.plugins.About
 
abs() - Method in class loci.plugins.util.RecordedImageProcessor
 
absoluteTime - Variable in class loci.formats.in.OperettaReader.Plane
 
absoluteTime - Variable in class loci.formats.in.PrairieMetadata.Frame
absoluteTime attribute of this <Frame>.
AbstractOMEXMLMetadata - Class in loci.formats.ome
 
AbstractOMEXMLMetadata() - Constructor for class loci.formats.ome.AbstractOMEXMLMetadata
 
ac - Variable in class loci.formats.in.FakeReader
Channel of last opened image plane.
accept(File) - Method in class loci.formats.gui.ComboFileFilter
Accepts files with the proper filename prefix.
accept(File) - Method in class loci.formats.gui.ExtensionFileFilter
Accepts files with the proper extensions.
accept(File) - Method in class loci.formats.gui.FormatFileFilter
Accepts files in accordance with the file format reader.
accept(File) - Method in class loci.formats.gui.NoExtensionFileFilter
Accepts files with no extension.
accept(String) - Method in class loci.formats.NumberFilter
Tests if a specified file should be included in a file list.
accept(File) - Method in class loci.formats.NumberFilter
Tests if a specified file should be included in a file list.
accumulate - Variable in class loci.formats.in.SDTInfo
 
ACCUMULATION - Static variable in class loci.formats.in.CellSensReader
 
ACCUMULATION_MODE - Static variable in class loci.formats.in.CellSensReader
 
acqType - Variable in class loci.formats.in.OperettaReader.Plane
 
acquire - Variable in class loci.formats.in.ZeissLSMReader.SubBlock
 
acquiredDate - Variable in class loci.formats.in.LIFReader
 
acquiredDate - Variable in class loci.formats.in.ZeissCZIReader
 
acquiredDate - Variable in class loci.formats.in.ZeissLSMReader
 
ACQUISITION_CYCLE_TIME - Static variable in class loci.formats.in.FluoviewReader
 
ACQUISITION_FILE - Static variable in class loci.formats.in.ScanrReader
 
ACQUISITION_PROPERTIES - Static variable in class loci.formats.in.CellSensReader
 
ACQUISITION_TIME_TAG - Static variable in class loci.formats.in.FlowSightReader
 
acquisitionDate - Variable in class loci.formats.in.BaseZeissReader
 
acquisitionDate - Variable in class loci.formats.in.BioRadSCNReader
 
acquisitionDate - Variable in class loci.formats.in.ColumbusReader
 
acquisitionDate - Variable in class loci.formats.in.OIRReader
 
acquisitionDate - Variable in class loci.formats.in.SISReader
 
acquisitionDates - Variable in class loci.formats.in.FlexReader
 
acquisitionMode - Variable in class loci.formats.in.ZeissCZIReader.Channel
 
acquisitions - Variable in class loci.formats.in.ZeissCZIReader
 
acquisitionTime - Variable in class loci.formats.in.CellSensReader.Pyramid
 
act - Variable in class loci.formats.in.GIFReader
Active color table.
actionPerformed(ActionEvent) - Method in class loci.formats.gui.CacheComponent
Handles combo box changes.
actionPerformed(ActionEvent) - Method in class loci.formats.gui.DataConverter
 
actionPerformed(ActionEvent) - Method in class loci.formats.gui.ImageViewer
Handles menu commands.
actionPerformed(ActionEvent) - Method in class loci.formats.tools.EditTiffG
 
actionPerformed(ActionEvent) - Method in class loci.plugins.config.ConfigWindow
 
actionPerformed(ActionEvent) - Method in class loci.plugins.in.SeriesDialog
 
actionPerformed(ActionEvent) - Method in class loci.plugins.shortcut.ShortcutPanel
Handles button presses.
actionPerformed(ActionEvent) - Method in class loci.plugins.util.DataBrowser
 
actionPerformed(ActionEvent) - Method in class loci.plugins.util.SearchableWindow
 
actionPerformed(ActionEvent) - Method in class loci.plugins.util.SearchableWindow.SearchBox
 
active - Variable in class loci.formats.in.FV1000Reader.ChannelData
 
active - Variable in class loci.formats.in.LeicaHandler.Detector
 
active - Variable in class loci.formats.in.LeicaReader.Detector
 
ACTIVE_CHANNEL - Static variable in class loci.formats.in.CellSensReader
 
ACTIVE_LAYER_INDEX_VECTOR - Static variable in class loci.formats.in.CellSensReader
 
ACTIVE_LAYER_VECTOR - Static variable in class loci.formats.in.CellSensReader
 
ACTIVE_STACK_DIMENSION - Static variable in class loci.formats.in.CellSensReader
 
activeChannelIndices - Variable in class loci.formats.in.LeicaReader
 
activeChannels - Variable in class loci.formats.in.PrairieMetadata
Set of active channel indices.
activeDetector - Variable in class loci.formats.in.LIFReader
 
activePlane - Variable in class loci.formats.in.OperettaReader.OperettaHandler
 
ACTUAL_TEMPERATURE - Static variable in class loci.formats.in.FluoviewReader
 
adcDE - Variable in class loci.formats.in.SDTInfo
ADC sample delay (SPC-930).
adcRE - Variable in class loci.formats.in.SDTInfo
 
adcResShift - Variable in class loci.formats.in.SPCReader
 
adcZoom - Variable in class loci.formats.in.SDTInfo
 
add(byte) - Method in class loci.formats.codec.ByteVector
 
add(byte[]) - Method in class loci.formats.codec.ByteVector
 
add(byte[], int, int) - Method in class loci.formats.codec.ByteVector
 
add(int, CoreMetadata) - Method in class loci.formats.CoreMetadataList
Add a secondary array element to the specified primary array
add() - Method in class loci.formats.MetadataList
Add a empty primary array element.
add(int) - Method in class loci.formats.MetadataList
Add a empty primary array element.
add(int, T) - Method in class loci.formats.MetadataList
Add a secondary array element to the specified primary array
add(T) - Method in class loci.formats.MetadataList
Add a new primary element containing a single specified value.
add(List<T>) - Method in class loci.formats.MetadataList
Add a new primary element containing the specified values.
add(double) - Method in class loci.plugins.util.RecordedImageProcessor
 
add(int) - Method in class loci.plugins.util.RecordedImageProcessor
 
addCacheListener(CacheListener) - Method in class loci.formats.cache.Cache
 
addCacheListener(CacheListener) - Method in interface loci.formats.cache.CacheReporter
Adds a listener for status update events.
addCacheListener(CacheListener) - Method in class loci.formats.cache.CacheStrategy
 
addCheckbox(GenericDialog, String) - Method in class loci.plugins.prefs.OptionsDialog
Adds a checkbox to the given dialog object corresponding to the boolean option identified by the specified key.
addChoice(GenericDialog, String) - Method in class loci.plugins.prefs.OptionsDialog
Adds a choice to the given dialog object corresponding to the string option identified by the specified key.
addClass(int, Class<? extends T>) - Method in class loci.formats.ClassList
Adds the given class, which must be assignable to the base class, to the list.
addClass(Class<? extends T>) - Method in class loci.formats.ClassList
Adds the given class, which must be assignable to the base class, to the list.
addDirectory(String, int) - Method in class loci.formats.in.L2DReader
Recursively add all of the files in the given directory to the used file list.
addEntry(Comparable<Object>, DefaultListModel) - Static method in class loci.plugins.config.ConfigWindow
 
addFileToList(String, boolean) - Method in class loci.formats.in.DicomReader
Determine if the given file belongs in the same dataset as this file.
addGlobalMeta(String, Object) - Method in class loci.formats.FormatReader
Adds an entry to the global metadata table.
addGlobalMeta(String, boolean) - Method in class loci.formats.FormatReader
Adds an entry to the global metadata table.
addGlobalMeta(String, byte) - Method in class loci.formats.FormatReader
Adds an entry to the global metadata table.
addGlobalMeta(String, short) - Method in class loci.formats.FormatReader
Adds an entry to the global metadata table.
addGlobalMeta(String, int) - Method in class loci.formats.FormatReader
Adds an entry to the global metadata table.
addGlobalMeta(String, long) - Method in class loci.formats.FormatReader
Adds an entry to the global metadata table.
addGlobalMeta(String, float) - Method in class loci.formats.FormatReader
Adds an entry to the global metadata table.
addGlobalMeta(String, double) - Method in class loci.formats.FormatReader
Adds an entry to the global metadata table.
addGlobalMeta(String, char) - Method in class loci.formats.FormatReader
Adds an entry to the global metadata table.
addGlobalMetaList(String, Object) - Method in class loci.formats.FormatReader
Add the given key/value pair to the global metadata hashtable.
addInfo(int, String) - Method in class loci.formats.in.DicomReader
 
addInfo(int, int) - Method in class loci.formats.in.DicomReader
 
addMeta(String, Object, Hashtable<String, Object>) - Method in class loci.formats.FormatReader
Adds an entry to the specified Hashtable.
addMetadataOnly(OMEXMLMetadata, int) - Method in interface loci.formats.services.OMEXMLService
Insert a MetadataOnly element under the Image specified by 'index' in the given OME-XML metadata object.
addMetadataOnly(OMEXMLMetadata, int, boolean) - Method in interface loci.formats.services.OMEXMLService
Insert a MetadataOnly element under the Image specified by 'index' in the given OME-XML metadata object.
addMetadataOnly(OMEXMLMetadata, int) - Method in class loci.formats.services.OMEXMLServiceImpl
 
addMetadataOnly(OMEXMLMetadata, int, boolean) - Method in class loci.formats.services.OMEXMLServiceImpl
 
addMetaList(String, Object, Hashtable<String, Object>) - Method in class loci.formats.FormatReader
Add the given key/value pair to the given hashtable.
addModuloAlong(OMEXMLMetadata, CoreMetadata, int) - Method in interface loci.formats.services.OMEXMLService
Adds ModuloAlong* annotations to the given OME-XML metadata object, using the given CoreMetadata object to determine modulo dimensions.
addModuloAlong(OMEXMLMetadata, CoreMetadata, int) - Method in class loci.formats.services.OMEXMLServiceImpl
 
addOption(String, String) - Method in class loci.formats.ClassList
Add a key/value pair to the list of options.
addPossible(String) - Method in class loci.plugins.prefs.StringOption
Adds a possible value to the list.
addProp(HashMap<String, String>, String, String, HashMap<String, String>) - Method in class loci.plugins.config.ConfigWindow
 
addPtyFiles() - Method in class loci.formats.in.FV1000Reader
 
addScrollBars(Container) - Static method in class loci.plugins.util.WindowTools
Adds AWT scroll bars to the given container.
addSeriesMeta(String, Object) - Method in class loci.formats.FormatReader
Adds an entry to the metadata table for the current series.
addSeriesMeta(String, boolean) - Method in class loci.formats.FormatReader
Adds an entry to the metadata table for the current series.
addSeriesMeta(String, byte) - Method in class loci.formats.FormatReader
Adds an entry to the metadata table for the current series.
addSeriesMeta(String, short) - Method in class loci.formats.FormatReader
Adds an entry to the metadata table for the current series.
addSeriesMeta(String, int) - Method in class loci.formats.FormatReader
Adds an entry to the metadata table for the current series.
addSeriesMeta(String, long) - Method in class loci.formats.FormatReader
Adds an entry to the metadata table for the current series.
addSeriesMeta(String, float) - Method in class loci.formats.FormatReader
Adds an entry to the metadata table for the current series.
addSeriesMeta(String, double) - Method in class loci.formats.FormatReader
Adds an entry to the metadata table for the current series.
addSeriesMeta(String, char) - Method in class loci.formats.FormatReader
Adds an entry to the metadata table for the current series.
addSeriesMetaList(String, Object) - Method in class loci.formats.FormatReader
Add the given key/value pair to the current series metadata hashtable.
addStatusListener(StatusListener) - Method in class loci.plugins.in.ImagePlusReader
 
addStatusListener(StatusListener) - Method in class loci.plugins.in.ImportProcess
 
addSubResolutions() - Method in class loci.formats.in.OMETiffReader
 
addToHashtable() - Method in class loci.formats.in.ZeissLSMReader.SubBlock
 
addUsedFile(String, String) - Method in class loci.formats.in.PerkinElmerReader
Add the given file to the used files list.
addUserCommentMeta(Element, int) - Method in class loci.formats.in.LIFReader
 
adjust - Variable in class loci.formats.in.SlidebookReader
 
adjustEndianness - Variable in class loci.formats.in.GatanReader
 
adjustForWhiteBalance(short, int) - Method in class loci.formats.in.DNGReader
 
adjustForWhiteBalance(short, int) - Method in class loci.formats.in.NikonReader
 
adjustmentValueChanged(AdjustmentEvent) - Method in class loci.plugins.util.DataBrowser
 
adjustWellDimensions() - Method in class loci.formats.in.ScanrReader
 
advanceBlock() - Method in class loci.formats.in.APNGReader.PNGInputStream
 
AE - Static variable in class loci.formats.in.DicomReader
 
AFIHandler() - Constructor for class loci.formats.in.AFIReader.AFIHandler
 
AFIReader - Class in loci.formats.in
AFIReader is the file format reader for Aperio AFI files.
AFIReader() - Constructor for class loci.formats.in.AFIReader
Constructs a new AFI reader.
AFIReader.AFIHandler - Class in loci.formats.in
 
ag - Variable in class loci.formats.FileStitcher.ExternalSeries
 
AIMReader - Class in loci.formats.in
AIMReader is the file format reader for .aim files.
AIMReader() - Constructor for class loci.formats.in.AIMReader
Constructs a new AIM reader.
airPressure - Variable in class loci.formats.in.ZeissCZIReader
 
AISF - Static variable in class loci.formats.in.VolocityClippingReader
 
AL3D_MAGIC_STRING - Static variable in class loci.formats.in.AliconaReader
 
AliconaReader - Class in loci.formats.in
AliconaReader is the file format reader for Alicona AL3D files.
AliconaReader() - Constructor for class loci.formats.in.AliconaReader
Constructs a new Alicona reader.
ALIGNMENT - Static variable in class loci.formats.in.ZeissCZIReader
 
ALL_DOMAINS - Static variable in class loci.formats.FormatTools
List of all supported domains.
ALL_TYPES - Static variable in class loci.formats.gui.GUITools
String to use for "all types" combination filter.
allBlockLengths - Variable in class loci.formats.in.SDTInfo
 
allBlockOffsets - Variable in class loci.formats.in.SDTInfo
 
allFiles - Variable in class loci.formats.in.BrukerReader
 
allFiles - Variable in class loci.formats.in.CV7000Reader
 
allFiles - Variable in class loci.formats.in.PerkinElmerReader
List of all files to open
allFiles - Variable in class loci.formats.in.SPCReader
List of all files to open
allFiles - Variable in class loci.formats.in.VectraReader
 
allocatedSize - Variable in class loci.formats.in.ZeissCZIReader.Segment
 
ALLOW_AUTOSTITCHING_DEFAULT - Static variable in class loci.formats.in.ZeissCZIReader
 
ALLOW_AUTOSTITCHING_KEY - Static variable in class loci.formats.in.ZeissCZIReader
 
allowAutostitching() - Method in class loci.formats.in.ZeissCZIReader
 
allowCZIAutostitch() - Static method in class loci.plugins.util.LociPrefs
 
allowOpen - Variable in class loci.formats.gui.FormatFileFilter
Whether it is ok to open a file to determine its type.
allowOpen - Variable in class loci.formats.ImageReader
 
allowShow - Variable in class loci.plugins.util.DataBrowser
 
ALPHABET_LENGTH - Static variable in class loci.formats.ResourceNamer
 
alphabeticIndexCount(String) - Static method in class loci.formats.ResourceNamer
 
alphaShort - Variable in class loci.formats.gui.Index16ColorModel
Lookup tables.
alreadyChecked() - Method in class loci.formats.UpgradeChecker
Return true if an upgrade check has already been performed in this JVM session.
altCodec - Variable in class loci.formats.in.NativeQTReader
Some movies use two video codecs -- this is the second codec.
alternateCenter - Variable in class loci.formats.in.LeicaHandler
 
alternateCenter - Variable in class loci.formats.in.LIFReader
 
altPlanes - Variable in class loci.formats.in.NativeQTReader
Number of frames that use the alternate codec.
AmiraParameters - Class in loci.formats.tools
AmiraParameters handles parsing and writing of AmiraMesh headers.
AmiraParameters(String) - Constructor for class loci.formats.tools.AmiraParameters
 
AmiraParameters(RandomAccessInputStream) - Constructor for class loci.formats.tools.AmiraParameters
 
AmiraReader - Class in loci.formats.in
This is a file format reader for AmiraMesh data.
AmiraReader() - Constructor for class loci.formats.in.AmiraReader
 
AmiraReader.ASCII - Class in loci.formats.in
This class provides a not-quite-efficient, but simple reader for planes stored in ASCII-encoded numbers.
AmiraReader.HxRLE - Class in loci.formats.in
This is the reader for RLE-compressed AmiraMeshes.
AmiraReader.HxZip - Class in loci.formats.in
This is the reader for GZip-compressed AmiraMeshes.
AmiraReader.PlaneReader - Interface in loci.formats.in
This is the common interface for all formats, compressed or not.
amplificationGain - Variable in class loci.formats.in.ZeissLSMReader.DetectionChannel
 
AnalysisFile() - Constructor for class loci.formats.in.MIASReader.AnalysisFile
 
analysisFiles - Variable in class loci.formats.in.MIASReader
 
AnalyzeReader - Class in loci.formats.in
AnalyzeReader is the file format reader for Analyze 7.5 files.
AnalyzeReader() - Constructor for class loci.formats.in.AnalyzeReader
Constructs a new Analyze reader.
and(int) - Method in class loci.plugins.util.RecordedImageProcessor
 
ANDOR_MAGIC_STRING - Static variable in class loci.formats.in.FluoviewReader
 
ANDOR_SHIFT_SPEED - Static variable in class loci.formats.in.CellSensReader
 
ANGLE - Static variable in class loci.formats.in.ZeissLSMReader
 
angle - Variable in class loci.formats.in.ZeissTIFFHandler.Scaling.Dimension
 
angles - Variable in class loci.formats.in.ZeissCZIReader
 
anim - Variable in class loci.formats.gui.ImageViewer
 
anim - Variable in class loci.plugins.util.DataBrowser
 
animate - Variable in class loci.plugins.util.DataBrowser
 
ANIMATION_KEY - Static variable in class loci.formats.gui.ImageViewer
 
ANN_BOOLEAN_VALUE - Static variable in class loci.formats.in.FakeReader
 
ANN_COMMENT_VALUE - Static variable in class loci.formats.in.FakeReader
 
ANN_DOUBLE_VALUE - Static variable in class loci.formats.in.FakeReader
 
ANN_LONG_VALUE - Static variable in class loci.formats.in.FakeReader
 
ANN_TAG_VALUE - Static variable in class loci.formats.in.FakeReader
 
ANN_TERM_VALUE - Static variable in class loci.formats.in.FakeReader
 
ANN_TIME_VALUE - Static variable in class loci.formats.in.FakeReader
 
ANN_XML_VALUE_END - Static variable in class loci.formats.in.FakeReader
 
ANN_XML_VALUE_START - Static variable in class loci.formats.in.FakeReader
 
annBool - Variable in class loci.formats.in.FakeReader
 
annComment - Variable in class loci.formats.in.FakeReader
 
annDouble - Variable in class loci.formats.in.FakeReader
 
annLong - Variable in class loci.formats.in.FakeReader
 
annMap - Variable in class loci.formats.in.FakeReader
 
ANNOTATION_NAMESPACE - Static variable in class loci.formats.in.FakeReader
 
ANNOTATION_PREFIX - Static variable in class loci.formats.in.FakeReader
 
ANNOTATION_SUFFIX - Static variable in class loci.formats.in.VectraReader
 
annotationBoolCount - Variable in class loci.formats.in.FakeReader
 
annotationCommentCount - Variable in class loci.formats.in.FakeReader
 
annotationCount - Variable in class loci.formats.in.FakeReader
 
annotationDoubleCount - Variable in class loci.formats.in.FakeReader
 
annotationLongCount - Variable in class loci.formats.in.FakeReader
 
annotationMapCount - Variable in class loci.formats.in.FakeReader
 
annotationTagCount - Variable in class loci.formats.in.FakeReader
 
annotationTermCount - Variable in class loci.formats.in.FakeReader
 
annotationTimeCount - Variable in class loci.formats.in.FakeReader
 
annotationXmlCount - Variable in class loci.formats.in.FakeReader
 
annTag - Variable in class loci.formats.in.FakeReader
 
annTerm - Variable in class loci.formats.in.FakeReader
 
annTime - Variable in class loci.formats.in.FakeReader
 
annXml - Variable in class loci.formats.in.FakeReader
 
ANO_SUFFIX - Static variable in class loci.formats.in.PerkinElmerReader
 
APERIO_IMAGE_DESCRIPTION_PREFIX - Static variable in class loci.formats.in.SVSReader
TIFF image description prefix for Aperio SVS files.
APERTURE_VALUE - Static variable in class loci.formats.tiff.IFD
 
APLReader - Class in loci.formats.in
APLReader is the file format reader for Olympus APL files.
APLReader() - Constructor for class loci.formats.in.APLReader
Constructs a new APL reader.
APNGReader - Class in loci.formats.in
APNGReader is the file format reader for Animated Portable Network Graphics (APNG) images.
APNGReader() - Constructor for class loci.formats.in.APNGReader
Constructs a new APNGReader.
APNGReader.PNGBlock - Class in loci.formats.in
 
APNGReader.PNGInputStream - Class in loci.formats.in
InputStream implementation that stitches together IDAT blocks into a seamless zlib stream.
APNGWriter - Class in loci.formats.out
APNGWriter is the file format writer for PNG and APNG files.
APNGWriter() - Constructor for class loci.formats.out.APNGWriter
 
append(ClassList<T>) - Method in class loci.formats.ClassList
Appends a class list which must be assignable to the base class
append(List<Class<? extends T>>) - Method in class loci.formats.ClassList
Appends a list of classes which must be assignable to the base class
append(ILoggingEvent) - Method in class loci.plugins.util.IJStatusEchoer
 
appendHexValue(StringBuilder, String, int) - Method in class loci.formats.in.BaseZeissReader.Shape
 
appendServerMap(String, String) - Static method in class loci.formats.in.FlexReader
Add the path 'realName' to the mapping for the server named 'alias'.
appendValue(StringBuilder, String, Object) - Method in class loci.formats.in.BaseZeissReader.Shape
 
applyCalibration(ImagePlus) - Method in class loci.plugins.in.Calibrator
Applies spatial calibrations to an image stack.
applyColors(List<ImagePlus>) - Method in class loci.plugins.in.Colorizer
 
applyColors(List<ImagePlus>) - Method in class loci.plugins.in.ImagePlusReader
 
applyDisplayRanges(ImagePlus, int) - Method in class loci.plugins.in.Colorizer
 
applyMatrix() - Method in class loci.formats.in.OperettaReader.Plane
Applies the orientationMatrix to positionX, positionY, and positionZ.
applyMethodStack(List<RecordedImageProcessor.MethodEntry>) - Method in class loci.plugins.util.RecordedImageProcessor
 
applyTable(int[]) - Method in class loci.plugins.util.RecordedImageProcessor
 
ARCHIVE - Static variable in class loci.formats.in.FlexReader
 
AreaInfo() - Constructor for class loci.formats.in.CellVoyagerReader.AreaInfo
 
AreaOfInterest() - Constructor for class loci.formats.in.VentanaReader.AreaOfInterest
 
areas - Variable in class loci.formats.in.CellVoyagerReader.WellInfo
 
areas - Variable in class loci.formats.in.VentanaReader
 
ARFReader - Class in loci.formats.in
ARFReader is the file format reader for Axon Raw Format (ARF) files, produced by INDEC BioSystems's Imaging Workbench software.
ARFReader() - Constructor for class loci.formats.in.ARFReader
Constructs a new ARF reader.
arg - Variable in class loci.plugins.LociExporter
Argument passed to setup method.
arg - Variable in class loci.plugins.Slicer
Plugin options.
args - Static variable in class loci.plugins.shortcut.ShortcutPanel
Details for installed plugins.
args - Variable in class loci.plugins.util.RecordedImageProcessor.MethodEntry
 
ARRAY - Static variable in class loci.formats.in.GatanReader
Data types.
arrayToString(Array) - Method in class loci.formats.services.NetCDFServiceImpl
 
ARROW - Static variable in class loci.formats.in.FV1000Reader
 
ARROW - Static variable in class loci.formats.in.LeicaHandler.ROI
 
ARROW - Static variable in class loci.formats.in.LIFReader.ROI
 
ARTIST - Static variable in class loci.formats.tiff.IFD
 
AS - Static variable in class loci.formats.in.DicomReader
 
ascii - Variable in class loci.formats.in.AmiraReader
 
ASCII(int, int) - Constructor for class loci.formats.in.AmiraReader.ASCII
 
ascii - Variable in class loci.formats.tools.AmiraParameters
 
AsciiImage - Class in loci.formats.tools
A utility class for outputting a BufferedImage as ASCII text.
AsciiImage(BufferedImage) - Constructor for class loci.formats.tools.AsciiImage
 
asMap() - Method in class loci.formats.in.DeltavisionReader.DVExtHdrFields
 
asRetrieve(MetadataStore) - Method in interface loci.formats.services.OMEXMLService
Gets the given MetadataStore object as a MetadataRetrieve.
asRetrieve(MetadataStore) - Method in class loci.formats.services.OMEXMLServiceImpl
 
assertId(String, boolean, int) - Static method in class loci.formats.FormatTools
Asserts that the current file is either null, or not, according to the given flag.
assertStep(ImportStep) - Method in class loci.plugins.in.ImportProcess
 
assignPlaneIndices() - Method in class loci.formats.in.ZeissCZIReader
 
assignValues(double[]) - Method in class loci.formats.in.TextReader
Assigns values from the given row into the data array.
asStore(MetadataRetrieve) - Method in interface loci.formats.services.OMEXMLService
Gets the given MetadataRetrieve object as a MetadataStore.
asStore(MetadataRetrieve) - Method in class loci.formats.services.OMEXMLServiceImpl
 
ASTRONOMY_DOMAIN - Static variable in class loci.formats.FormatTools
Identifies the astronomy domain.
AT - Static variable in class loci.formats.in.DicomReader
 
attachCompanionFiles() - Method in class loci.formats.in.DicomReader
DICOM datasets produced by: http://www.ct-imaging.de/index.php/en/ct-systeme-e/mikro-ct-e.html contain a bunch of extra metadata and log files.
attachListeners(List<TextField>, List<Panel>) - Method in class loci.plugins.in.ColorDialog
 
Attachment(String, long) - Constructor for class loci.formats.in.ZeissCZIReader.Attachment
 
attachment - Variable in class loci.formats.in.ZeissCZIReader.Attachment
 
attachment - Variable in class loci.formats.in.ZeissCZIReader.Metadata
 
attachmentData - Variable in class loci.formats.in.ZeissCZIReader.Attachment
 
AttachmentDirectory() - Constructor for class loci.formats.in.ZeissCZIReader.AttachmentDirectory
 
attachmentDirectoryPosition - Variable in class loci.formats.in.ZeissCZIReader.FileHeader
 
AttachmentEntry(RandomAccessInputStream) - Constructor for class loci.formats.in.ZeissCZIReader.AttachmentEntry
 
attachmentSize - Variable in class loci.formats.in.ZeissCZIReader.SubBlock
 
attenuation - Variable in class loci.formats.in.ZeissLSMReader.IlluminationChannel
 
attr(Element, String) - Method in class loci.formats.in.PrairieMetadata
Gets the attribute value with the given name, or null if not defined.
ATTR_NAME_STYLE_END - Static variable in class loci.formats.gui.XMLCellRenderer
 
ATTR_NAME_STYLE_START - Static variable in class loci.formats.gui.XMLCellRenderer
 
ATTR_VALUE_STYLE_END - Static variable in class loci.formats.gui.XMLCellRenderer
 
ATTR_VALUE_STYLE_START - Static variable in class loci.formats.gui.XMLCellRenderer
 
attributeList - Variable in class loci.formats.services.NetCDFServiceImpl
 
AUTOEXPOSURE - Static variable in class loci.formats.in.CellSensReader
 
autoscale(BufferedImage) - Static method in class loci.formats.gui.AWTImageTools
Perform autoscaling on the given BufferedImage.
autoscale(BufferedImage, int, int) - Static method in class loci.formats.gui.AWTImageTools
Perform autoscaling on the given BufferedImage; map min to 0 and max to 255.
autoscale(byte[], int, int, int, boolean) - Static method in class loci.formats.ImageTools
Perform autoscaling on the given byte array; map min to 0 and max to 255.
autoscaleBox - Variable in class loci.plugins.in.MainDialog
 
autoThreshold() - Method in class loci.plugins.util.RecordedImageProcessor
 
autoUpdate - Variable in class loci.formats.cache.Cache
Whether the cache should automatically update when a parameter changes.
available() - Method in class loci.formats.in.APNGReader.PNGInputStream
 
availMem - Variable in class loci.plugins.in.MemoryDialog
Remaining memory for the JVM.
AVERAGE - Static variable in class loci.formats.in.APNGReader
 
AVERAGING - Static variable in class loci.formats.in.CellSensReader
 
AVI_MAGIC_STRING - Static variable in class loci.formats.in.AVIReader
 
AVIReader - Class in loci.formats.in
AVIReader is the file format reader for AVI files.
AVIReader() - Constructor for class loci.formats.in.AVIReader
Constructs a new AVI reader.
AVIWriter - Class in loci.formats.out
AVIWriter is the file format writer for AVI files.
AVIWriter() - Constructor for class loci.formats.out.AVIWriter
 
AWTImageTools - Class in loci.formats.gui
A utility class with convenience methods for manipulating images in BufferedImage form.
AWTImageTools() - Constructor for class loci.formats.gui.AWTImageTools
 
axis - Variable in class loci.formats.gui.CacheIndicator
 
AxisGuesser - Class in loci.formats
AxisGuesser guesses which blocks in a file pattern correspond to which dimensional axes (Z, T, C or S), potentially recommending an adjustment in dimension order within the files, depending on the confidence of each guess.
AxisGuesser(FilePattern, String, int, int, int, boolean) - Constructor for class loci.formats.AxisGuesser
Guesses dimensional axis assignments corresponding to the given file pattern, using the specified dimensional information from within each file as a guide.
axisTypes - Variable in class loci.formats.AxisGuesser
Guessed axis types.

B

b(String) - Method in class loci.formats.in.PrairieMetadata
Converts the given string to a boolean.
b - Variable in class loci.formats.in.VentanaReader.Overlap
 
BACKGROUND_TABLE - Static variable in class loci.formats.in.LiFlimReader
 
backgroundC - Variable in class loci.formats.in.LiFlimReader
 
backgroundColor - Variable in class loci.formats.in.CellSensReader
 
backgroundDatatype - Variable in class loci.formats.in.LiFlimReader
 
backgroundF - Variable in class loci.formats.in.LiFlimReader
 
backgroundP - Variable in class loci.formats.in.LiFlimReader
 
backgroundT - Variable in class loci.formats.in.LiFlimReader
 
backgroundX - Variable in class loci.formats.in.LiFlimReader
 
backgroundY - Variable in class loci.formats.in.LiFlimReader
 
backgroundZ - Variable in class loci.formats.in.LiFlimReader
 
backupHandler - Variable in class loci.formats.in.NativeND2Reader
 
BACKWARD_ORDER - Static variable in interface loci.formats.cache.ICacheStrategy
 
backwardsStageX - Variable in class loci.formats.in.DeltavisionReader
Whether or not the stage moved backwards.
backwardsStageY - Variable in class loci.formats.in.DeltavisionReader
 
bandUsed - Variable in class loci.formats.in.NDPISReader
 
bankData - Variable in class loci.formats.gui.SignedByteBuffer
 
bankData - Variable in class loci.formats.gui.UnsignedIntBuffer
 
barcode - Variable in class loci.formats.in.LeicaSCNReader.ImageCollection
 
barrierFilter - Variable in class loci.formats.in.FV1000Reader.ChannelData
 
base - Variable in class loci.formats.ClassList
Base class to which all classes are assignable.
Base64Codec - Class in loci.formats.codec
Implements encoding (compress) and decoding (decompress) methods for Base64.
Base64Codec() - Constructor for class loci.formats.codec.Base64Codec
 
BASE_OFFSET - Static variable in class loci.formats.in.BioRadGelReader
 
BaseCodec - Class in loci.formats.codec
BaseCodec contains default implementation and testing for classes implementing the Codec interface, and acts as a base class for any of the compression classes.
BaseCodec() - Constructor for class loci.formats.codec.BaseCodec
 
basedir - Variable in class loci.formats.in.ZeissTIFFReader.TIFFInfo
 
BASELINE_CLAMP - Static variable in class loci.formats.in.FluoviewReader
 
BASELINE_OFFSET - Static variable in class loci.formats.in.FluoviewReader
 
BASELINE_OFFSET_CLAMP - Static variable in class loci.formats.in.CellSensReader
 
BaseMetadata - Interface in loci.formats.meta
 
baseName - Variable in class loci.formats.in.OIRReader
 
basename - Variable in class loci.formats.in.ZeissTIFFHandler.Plane
 
baseReader - Variable in class loci.plugins.in.ImportProcess
 
baseTiff - Variable in class loci.formats.in.MicromanagerReader.Position
 
BaseTiffReader - Class in loci.formats.in
BaseTiffReader is the superclass for file format readers compatible with or derived from the TIFF 6.0 file format.
BaseTiffReader(String, String) - Constructor for class loci.formats.in.BaseTiffReader
Constructs a new BaseTiffReader.
BaseTiffReader(String, String[]) - Constructor for class loci.formats.in.BaseTiffReader
Constructs a new BaseTiffReader.
baseX - Variable in class loci.formats.in.VentanaReader.TIFFTile
 
baseY - Variable in class loci.formats.in.VentanaReader.TIFFTile
 
BaseZeissReader - Class in loci.formats.in
BaseZeissReader contains common functionality required by readers for Zeiss AxioVision formats.
BaseZeissReader(String, String) - Constructor for class loci.formats.in.BaseZeissReader
Constructs a new ZeissZVI reader.
BaseZeissReader(String, String[]) - Constructor for class loci.formats.in.BaseZeissReader
Constructs a new ZeissZVI reader.
BaseZeissReader.Charset - Enum in loci.formats.in
 
BaseZeissReader.Context - Enum in loci.formats.in
 
BaseZeissReader.DrawStyle - Enum in loci.formats.in
Line drawing styles.
BaseZeissReader.FeatureType - Enum in loci.formats.in
Feature types.
BaseZeissReader.FillStyle - Enum in loci.formats.in
Fill styles.
BaseZeissReader.Layer - Class in loci.formats.in
Layer class representing an AxioVision layer; used to contain a collection of shapes.
BaseZeissReader.LineEndPositions - Enum in loci.formats.in
 
BaseZeissReader.LineEndStyle - Enum in loci.formats.in
Line ending styles.
BaseZeissReader.PointStyle - Enum in loci.formats.in
Point styles.
BaseZeissReader.Shape - Class in loci.formats.in
Shape class representing the metadata within an AxioVision Shape ROI
BaseZeissReader.Tag - Class in loci.formats.in
Content of a single tag from a Tags block.
BaseZeissReader.TextAlignment - Enum in loci.formats.in
 
bayerPattern - Variable in class loci.formats.in.MRWReader
 
bbox - Variable in class loci.formats.in.BDVReader
 
BBOX - Static variable in class loci.formats.in.BDVReader.H5Constants
 
bbox - Variable in class loci.formats.in.CellH5Reader
 
BBOX - Static variable in class loci.formats.in.CellH5Reader.CellH5Constants
 
bBox - Variable in class loci.formats.services.WlzServiceImpl
 
BDReader - Class in loci.formats.in
BDReader is the file format reader for BD Pathway datasets.
BDReader() - Constructor for class loci.formats.in.BDReader
Constructs a new ScanR reader.
BDV_MAGIC_STRING - Static variable in class loci.formats.in.BDVReader
 
BDVReader - Class in loci.formats.in
Reader for BDV files.
BDVReader() - Constructor for class loci.formats.in.BDVReader
Constructs a new BDV reader.
BDVReader.BDVXMLHandler - Class in loci.formats.in
 
BDVReader.H5Constants - Class in loci.formats.in
 
BDVReader.H5Coordinate - Class in loci.formats.in
 
bdvxml - Variable in class loci.formats.in.BDVReader
 
BDVXMLHandler() - Constructor for class loci.formats.in.BDVReader.BDVXMLHandler
 
BEAM_SPLITTER_FILTER - Static variable in class loci.formats.in.ZeissLSMReader
 
BEAM_SPLITTER_FILTER_SET - Static variable in class loci.formats.in.ZeissLSMReader
 
BeamSplitter() - Constructor for class loci.formats.in.ZeissLSMReader.BeamSplitter
 
begin - Variable in class loci.formats.FilePatternBlock
 
BEZIER_WITH_ARROW - Static variable in class loci.formats.in.ZeissLSMReader
 
BF - Class in loci.plugins
Miscellaneous plugins utility methods.
BF() - Constructor for class loci.plugins.BF
 
BFVirtualStack - Class in loci.plugins.util
Subclass of VirtualStack that uses Bio-Formats to read planes on demand.
BFVirtualStack(String, IFormatReader, boolean, boolean, boolean) - Constructor for class loci.plugins.util.BFVirtualStack
 
BGR - Static variable in class loci.formats.in.CellSensReader
 
BGR_24 - Static variable in class loci.formats.in.ZeissCZIReader
 
BGR_24 - Static variable in class loci.formats.services.JPEGXRServiceImpl
 
BGR_32 - Static variable in class loci.formats.services.JPEGXRServiceImpl
 
BGR_48 - Static variable in class loci.formats.in.ZeissCZIReader
 
BGR_FLOAT - Static variable in class loci.formats.in.ZeissCZIReader
 
BGRA_32 - Static variable in class loci.formats.services.JPEGXRServiceImpl
 
BGRA_8 - Static variable in class loci.formats.in.ZeissCZIReader
 
bgrToRgb(byte[], boolean, int, int) - Static method in class loci.formats.ImageTools
 
BH_HEADER_CHKSUM - Static variable in class loci.formats.in.SDTInfo
 
BH_HEADER_NOT_VALID - Static variable in class loci.formats.in.SDTInfo
 
BH_HEADER_VALID - Static variable in class loci.formats.in.SDTInfo
 
BIFormatReader - Class in loci.formats.in
BIFormatReader is the superclass for file format readers that use java.awt.image.BufferedImage as the native data type.
BIFormatReader(String, String) - Constructor for class loci.formats.in.BIFormatReader
Constructs a new BIFormatReader.
BIFormatReader(String, String[]) - Constructor for class loci.formats.in.BIFormatReader
Constructs a new BIFormatReader.
BIG - Static variable in class loci.formats.tiff.TiffConstants
 
BIG_TIFF - Static variable in class loci.formats.tiff.IFD
 
BIG_TIFF_BYTES_PER_ENTRY - Static variable in class loci.formats.tiff.TiffConstants
The number of bytes in each IFD entry of a BigTIFF file.
BIG_TIFF_CUTOFF - Static variable in class loci.formats.out.TiffWriter
Number of bytes at which to automatically switch to BigTIFF This is approximately 3.9 GB instead of 4 GB, to allow space for the IFDs.
BIG_TIFF_MAGIC_NUMBER - Static variable in class loci.formats.tiff.TiffConstants
 
BIG_TIFF_SUFFIXES - Static variable in class loci.formats.out.TiffWriter
 
bigEndianTransferSyntax - Variable in class loci.formats.in.DicomReader
 
bigTiff - Variable in class loci.formats.tiff.TiffParser
Whether or not the TIFF file contains BigTIFF data.
bigTiff - Variable in class loci.formats.tiff.TiffSaver
Whether or not to write BigTIFF data.
bin - Variable in class loci.formats.in.InCellReader
 
binary - Variable in class loci.formats.in.EPSReader
Flag indicating binary data.
BINARY_SETUP - Static variable in class loci.formats.in.SDTInfo
 
binData - Variable in class loci.formats.in.OMEXMLReader
 
BinData(int, int) - Constructor for class loci.formats.in.OMEXMLReader.BinData
 
binDataOffsets - Variable in class loci.formats.in.OMEXMLReader
 
binning - Variable in class loci.formats.in.BDReader
 
binning - Variable in class loci.formats.in.BioRadSCNReader
 
binning - Variable in class loci.formats.in.CV7000Reader.Channel
 
binning - Variable in class loci.formats.in.MetamorphHandler
 
binning - Variable in class loci.formats.in.MetamorphReader
 
binning - Variable in class loci.formats.in.MicromanagerReader.Position
 
binning - Variable in class loci.formats.in.ND2Handler
 
binning - Variable in class loci.formats.in.PCIReader
 
binning - Variable in class loci.formats.in.SimplePCITiffReader
 
binning - Variable in class loci.formats.in.ZeissLSMReader
 
binning - Variable in class loci.formats.in.ZeissLSMReader.Recording
 
binnings - Variable in class loci.formats.in.FlexReader
 
binnings - Variable in class loci.formats.in.ZeissCZIReader
 
binningX - Variable in class loci.formats.in.CellSensReader.Pyramid
 
binningY - Variable in class loci.formats.in.CellSensReader.Pyramid
 
binSize - Variable in class loci.formats.in.SPCReader
 
binX - Variable in class loci.formats.in.FlexReader
Camera binning values.
binX - Variable in class loci.formats.in.IvisionReader
 
binY - Variable in class loci.formats.in.FlexReader
Camera binning values.
binY - Variable in class loci.formats.in.IvisionReader
 
BioFormatsExtensionPrinter - Class in loci.formats.tools
This class is used to generate a text file containing all of the image file extensions supported by Bio-Formats.
BioFormatsExtensionPrinter() - Constructor for class loci.formats.tools.BioFormatsExtensionPrinter
 
BioRadGelReader - Class in loci.formats.in
BioRadGelReader is the file format reader for Bio-Rad gel files.
BioRadGelReader() - Constructor for class loci.formats.in.BioRadGelReader
Constructs a new Bio-Rad gel reader.
BioRadHandler() - Constructor for class loci.formats.in.BioRadReader.BioRadHandler
 
BioRadReader - Class in loci.formats.in
BioRadReader is the file format reader for Bio-Rad PIC files.
BioRadReader() - Constructor for class loci.formats.in.BioRadReader
Constructs a new BioRadReader.
BioRadReader.BioRadHandler - Class in loci.formats.in
SAX handler for parsing XML.
BioRadReader.Note - Class in loci.formats.in
 
BioRadSCNReader - Class in loci.formats.in
BioRadSCNReader is the reader for Bio-Rad .scn files
BioRadSCNReader() - Constructor for class loci.formats.in.BioRadSCNReader
Constructs a new Bio-Rad .scn reader.
BioRadSCNReader.SCNHandler - Class in loci.formats.in
 
biReader - Variable in class loci.formats.gui.DataConverter
 
BIT - Static variable in class loci.formats.FormatTools
Identifies the BIT data type used to store pixel values.
BIT_DEPTH - Static variable in class loci.formats.in.CellSensReader
 
BitBuffer - Class in loci.formats.codec
Deprecated.
Use loci.common.RandomAccessInputStream instead
BitBuffer(byte[]) - Constructor for class loci.formats.codec.BitBuffer
Deprecated.
Default constructor.
bitDepth - Variable in class loci.formats.in.CellSensReader.Pyramid
 
BITMASK_COMPRESSION - Static variable in class loci.formats.in.FlowSightReader
 
bits - Variable in class loci.formats.in.BrukerReader
 
bits - Variable in class loci.formats.in.TargaReader
 
BITS_ALLOCATED - Static variable in class loci.formats.in.DicomReader
 
BITS_PER_SAMPLE - Static variable in class loci.formats.tiff.IFD
 
bitsPerPixel - Variable in class loci.formats.CoreMetadata
Number of valid bits per pixel.
bitsPerPixel - Variable in class loci.formats.in.DicomReader
Bits per pixel.
bitsPerPixel - Variable in class loci.formats.in.NativeQTReader
Pixel depth.
bitsPerSample - Variable in class loci.formats.codec.CodecOptions
Number of bits per channel.
BitWriter - Class in loci.formats.codec
Deprecated.
Use loci.common.RandomAccessOutputStream instead
BitWriter() - Constructor for class loci.formats.codec.BitWriter
Deprecated.
Constructs a new bit writer.
BitWriter(int) - Constructor for class loci.formats.codec.BitWriter
Deprecated.
Constructs a new bit writer with the given initial buffer size.
biWriter - Variable in class loci.formats.gui.DataConverter
 
bizarreMultichannelAcquisition - Variable in class loci.formats.in.MetamorphReader
 
blank(byte[]) - Method in class loci.formats.in.PrairieReader
Blanks out and returns the given buffer.
blankImage(int, int, int, int) - Static method in class loci.formats.gui.AWTImageTools
Creates a blank image with the given dimensions and transfer type.
blankThumbBytes - Variable in class loci.formats.FileStitcher.ExternalSeries
 
block - Variable in class loci.formats.FilePatternBlock
String representation of this block.
BLOCK_END - Static variable in class loci.formats.FilePatternBlock
Identifies the end of a block.
BLOCK_START - Static variable in class loci.formats.FilePatternBlock
Identifies the start of a block.
blockData - Variable in class loci.formats.in.ZeissLSMReader.SubBlock
 
blockLength - Variable in class loci.formats.in.APNGReader.PNGInputStream
 
blockLength - Variable in class loci.formats.in.PQBinReader
No of timeBins pre-loaded as a block
blockLength - Variable in class loci.formats.in.SDTInfo
reserved2 now contains block (set) length.
blockLength - Variable in class loci.formats.in.SDTReader
No of timeBins pre-loaded as a block
blockNo - Variable in class loci.formats.in.SDTInfo
Number of the block in the file.
blockOffsets - Variable in class loci.formats.in.KLBReader
 
blockPointer - Variable in class loci.formats.in.APNGReader.PNGInputStream
 
blocks - Variable in class loci.formats.FilePattern
List of pattern blocks for this file pattern.
blocks - Variable in class loci.formats.in.APNGReader
 
blockSize - Variable in class loci.formats.in.GIFReader
Block size.
blockSize - Variable in class loci.formats.in.VolocityReader.Stack
 
blocksPerPlane - Variable in class loci.formats.in.KLBReader
 
blocksPerPlane - Variable in class loci.formats.in.OIRReader
 
blockType - Variable in class loci.formats.in.APNGReader.PNGInputStream
 
blockType - Variable in class loci.formats.in.SDTInfo
See blockType defines below.
BLUE_GAIN - Static variable in class loci.formats.in.CellSensReader
 
BLUE_MIN - Static variable in class loci.plugins.in.Colorizer
 
BLUE_MULTIPLIER - Static variable in class loci.formats.in.NDPIReader
 
BLUE_OFFSET - Static variable in class loci.formats.in.CellSensReader
 
BLUE_TO_GREEN_MIN - Static variable in class loci.plugins.in.Colorizer
 
blueGain - Variable in class loci.formats.in.CellSensReader.Pyramid
 
blueOffset - Variable in class loci.formats.in.CellSensReader.Pyramid
 
blueOffset - Static variable in class org.libjpegturbo.turbojpeg.TJ
 
blueShort - Variable in class loci.formats.gui.Index16ColorModel
Lookup tables.
BMP - Static variable in class loci.formats.in.CellSensReader
 
BMP_MAGIC_STRING - Static variable in class loci.formats.in.BMPReader
 
bmpBitsPerPixel - Variable in class loci.formats.in.AVIReader
 
bmpColorsUsed - Variable in class loci.formats.in.AVIReader
 
bmpCompression - Variable in class loci.formats.in.AVIReader
 
BMPReader - Class in loci.formats.in
BMPReader is the file format reader for Microsoft Bitmap (BMP) files.
BMPReader() - Constructor for class loci.formats.in.BMPReader
Constructs a new BMP reader.
bmpScanLineSize - Variable in class loci.formats.in.AVIReader
 
bmpWidth - Variable in class loci.formats.in.AVIReader
 
bold - Variable in class loci.formats.in.BaseZeissReader.Shape
 
BOOLEAN - Static variable in class loci.formats.in.CellSensReader
 
BooleanIM3Record(String, int, long, int) - Constructor for class loci.formats.in.IM3Reader.BooleanIM3Record
 
BooleanOption - Class in loci.plugins.prefs
A boolean option for one of the plugins.
BooleanOption(HashMap<String, String>) - Constructor for class loci.plugins.prefs.BooleanOption
Constructs a boolean option with the parameters from the given map.
BooleanOption(String, boolean, String, String, boolean) - Constructor for class loci.plugins.prefs.BooleanOption
Constructs a boolean option with the given parameters.
BORDER - Static variable in class loci.plugins.shortcut.ShortcutPanel
Number of pixels for window border.
bordL - Variable in class loci.formats.in.SDTInfo
 
bordU - Variable in class loci.formats.in.SDTInfo
 
boundingBox - Variable in class loci.formats.in.VentanaReader.AreaOfInterest
 
boundValues - Variable in class loci.formats.services.MDBServiceImpl
 
BOX_SIZE - Static variable in class loci.formats.in.FakeReader
 
boxes - Variable in class loci.plugins.in.SeriesDialog
 
bpp - Variable in class loci.formats.in.BaseZeissReader
Number of bytes per pixel.
bpp - Variable in class loci.formats.in.BMPReader
Number of bits per pixel.
bpp - Variable in class loci.formats.in.MIASReader
 
bpp - Variable in class loci.formats.in.SPCReader
 
bpp - Variable in class loci.formats.out.CellH5Writer
 
BRIGHT_FIELD - Static variable in class loci.formats.in.LegacyND2Reader
 
BRIGHTNESS - Static variable in class loci.formats.in.CellSensReader
 
BRIGHTNESS_VALUE - Static variable in class loci.formats.tiff.IFD
 
brokenNotes - Variable in class loci.formats.in.BioRadReader
 
BrowserOptionsWindow - Class in loci.plugins.util
Extension of JFrame that allows the user to adjust caching settings.
BrowserOptionsWindow(String, Cache, String[]) - Constructor for class loci.plugins.util.BrowserOptionsWindow
 
BrukerReader - Class in loci.formats.in
BrukerReader is the file format reader for Bruker MRI files.
BrukerReader() - Constructor for class loci.formats.in.BrukerReader
Constructs a new Bruker reader.
btsType - Variable in class loci.formats.in.CV7000Reader.MeasurementDataHandler
 
buffer - Variable in class loci.formats.codec.BitBuffer
Deprecated.
 
BUFFER_SIZE - Static variable in class loci.formats.in.NativeND2Reader
 
BUFFER_SIZE - Static variable in class loci.formats.in.OIRReader
 
BUFFER_SIZE - Static variable in class loci.formats.in.ZeissCZIReader
 
BufferedImageReader - Class in loci.formats.gui
A reader wrapper for reading image planes as BufferedImage objects.
BufferedImageReader() - Constructor for class loci.formats.gui.BufferedImageReader
Constructs a BufferedImageReader around a new image reader.
BufferedImageReader(IFormatReader) - Constructor for class loci.formats.gui.BufferedImageReader
Constructs a BufferedImageReader with the given reader.
BufferedImageSource - Class in loci.formats.gui
Retrieves BufferedImages from a data source using Bio-Formats.
BufferedImageSource(IFormatReader) - Constructor for class loci.formats.gui.BufferedImageSource
 
BufferedImageWriter - Class in loci.formats.gui
A writer wrapper for writing image planes from BufferedImage objects.
BufferedImageWriter() - Constructor for class loci.formats.gui.BufferedImageWriter
Constructs a BufferedImageWriter around a new image writer.
BufferedImageWriter(IFormatWriter) - Constructor for class loci.formats.gui.BufferedImageWriter
Constructs a BufferedImageWriter with the given writer.
bufLength - Variable in class loci.formats.in.SPCReader
 
bufSize(int, int, int) - Static method in class org.libjpegturbo.turbojpeg.TJ
Returns the maximum size of the buffer (in bytes) required to hold a JPEG image with the given width and height, and level of chrominance subsampling.
bufSizeYUV(int, int, int) - Static method in class org.libjpegturbo.turbojpeg.TJ
Returns the size of the buffer (in bytes) required to hold a YUV planar image with the given width, height, and level of chrominance subsampling.
BUILDER - Static variable in class loci.formats.meta.OriginalMetadataAnnotation
 
buildExtensions() - Method in class loci.plugins.macro.MacroFunctions
Builds the list of extensions, using reflection, from public methods of this class.
buildFileChooser(IFormatHandler) - Static method in class loci.formats.gui.GUITools
Constructs a file chooser for the given file format handler.
buildFileChooser(IFormatHandler, boolean) - Static method in class loci.formats.gui.GUITools
Constructs a file chooser for the given file format handler.
buildFileChooser(FileFilter[]) - Static method in class loci.formats.gui.GUITools
Builds a file chooser with the given file filters, as well as an "All supported file types" combo filter.
buildFileChooser(FileFilter[], boolean) - Static method in class loci.formats.gui.GUITools
Builds a file chooser with the given file filters, as well as an "All supported file types" combo filter, if one is not already specified.
buildFileFilters(IFormatHandler) - Static method in class loci.formats.gui.GUITools
Constructs a list of file filters for the given file format handler.
buildFiles(String, int, List<String>) - Method in class loci.formats.FilePattern
 
buildTIFFList(int) - Method in class loci.formats.in.MicromanagerReader
 
buildTIFFList(int, String) - Method in class loci.formats.in.MicromanagerReader
Populate the list of TIFF files using the given file name as a pattern.
buildTypes() - Static method in class loci.formats.in.DicomReader
Assemble the data dictionary.
BurleighReader - Class in loci.formats.in
BurleighReader is the file format reader for Burleigh .img files.
BurleighReader() - Constructor for class loci.formats.in.BurleighReader
Constructs a new Burleigh reader.
BYTE - Static variable in class loci.formats.in.GatanReader
 
BYTE_COUNT_HIGH_BYTES - Static variable in class loci.formats.in.NDPIReader
 
BYTE_COUNT_OFFSET - Static variable in class loci.formats.out.QTWriter
Seek to this offset to update the total number of pixel bytes.
ByteArraySource - Class in loci.formats.cache
Retrieves byte arrays from a data source (e.g., a file) using Bio-Formats.
ByteArraySource(IFormatReader) - Constructor for class loci.formats.cache.ByteArraySource
Constructs a byte array source from the given Bio-Formats reader.
ByteArraySource(String) - Constructor for class loci.formats.cache.ByteArraySource
Constructs a byte array source that draws from the given file.
byteOrder - Variable in class org.libjpegturbo.turbojpeg.TJCompressor
 
byteOrder - Variable in class org.libjpegturbo.turbojpeg.TJDecompressor
 
bytes - Variable in class loci.formats.tiff.TiffSaver
Output bytes.
BYTES_PER_ENTRY - Static variable in class loci.formats.tiff.TiffConstants
The number of bytes in each IFD entry.
bytesFromReader(IFormatReader) - Method in class loci.formats.Memoizer.RandomAccessDeser
 
bytesPerAxis - Variable in class loci.formats.in.LeicaHandler
 
bytesPerElement - Variable in enum loci.formats.tiff.IFDType
Number of bytes per element of this type.
bytesPerLine - Variable in class loci.formats.in.PCXReader
Number of bytes per scan line - may be different than image width.
bytesPerPixel - Variable in class loci.formats.in.AmiraReader.ASCII
 
bytesPerPixel - Variable in class loci.formats.in.OpenlabRawReader
Number of bytes per pixel.
bytesPerPixel - Variable in class loci.formats.out.AVIWriter
 
bytesPerPlane - Variable in class loci.formats.in.AVIReader
 
bytesPerSample - Variable in class loci.formats.in.OBFReader.Stack
 
byteValue() - Method in class loci.formats.tiff.TiffRational
Returns the value of the specified number as a byte.
ByteVector - Class in loci.formats.codec
A growable array of bytes.
ByteVector() - Constructor for class loci.formats.codec.ByteVector
 
ByteVector(int) - Constructor for class loci.formats.codec.ByteVector
 
ByteVector(byte[]) - Constructor for class loci.formats.codec.ByteVector
 

C

C - Static variable in class loci.formats.in.CellSensReader
 
c - Variable in class loci.formats.in.LeicaSCNReader.Dimension
 
c - Variable in class loci.formats.in.MicromanagerReader.Index
 
c - Variable in class loci.formats.in.OperettaReader.Plane
 
c - Variable in class loci.formats.tools.AmiraParameters
 
C01_MAGIC_BYTES - Static variable in class loci.formats.in.CellomicsReader
 
C_AXIS - Static variable in class loci.formats.AxisGuesser
Axis type for channels.
C_KEY - Static variable in class loci.formats.in.LiFlimReader
 
C_PREFIXES - Static variable in class loci.formats.AxisGuesser
Prefixes indicating channel dimension.
C_STRING - Static variable in class loci.formats.in.SDTInfo
 
Cache - Class in loci.formats.cache
Cache provides a means of managing subsets of large collections of image planes in memory.
Cache(ICacheStrategy, ICacheSource, boolean) - Constructor for class loci.formats.cache.Cache
Constructs an object cache with the given cache strategy and source.
cache - Variable in class loci.formats.cache.Cache
Master array containing cached objects.
cache - Variable in class loci.formats.cache.CacheUpdater
 
cache - Variable in class loci.formats.gui.CacheComponent
The cache that this component controls.
cache - Variable in class loci.formats.gui.CacheIndicator
 
cache - Variable in class loci.plugins.util.BFVirtualStack
 
CacheComponent - Class in loci.formats.gui
GUI component for managing a cache.
CacheComponent(Cache, String[]) - Constructor for class loci.formats.gui.CacheComponent
Creates a cache GUI component.
CacheComponent(Cache, String[], String) - Constructor for class loci.formats.gui.CacheComponent
Creates a cache GUI component with the ability to change between the various source types (mainly for debugging purposes).
CacheConsole - Class in loci.formats.tools
CacheConsole provides an interactive interpreter for testing the Bio-Formats caching implementation.
CacheConsole() - Constructor for class loci.formats.tools.CacheConsole
 
cachedTileBuffer - Variable in class loci.formats.in.MIASReader
Cached tile buffer to avoid re-allocations when reading tiles.
cachedTileBuffer - Variable in class loci.formats.tiff.TiffParser
Cached tile buffer to avoid re-allocations when reading tiles.
CacheEvent - Class in loci.formats.cache
A event indicating a cache update.
CacheEvent(Object, int) - Constructor for class loci.formats.cache.CacheEvent
Constructs a cache event.
CacheEvent(Object, int, int) - Constructor for class loci.formats.cache.CacheEvent
Constructs a cache event.
CacheException - Exception in loci.formats.cache
CacheException is the exception thrown when something goes wrong performing a cache operation.
CacheException() - Constructor for exception loci.formats.cache.CacheException
 
CacheException(String) - Constructor for exception loci.formats.cache.CacheException
 
CacheException(String, Throwable) - Constructor for exception loci.formats.cache.CacheException
 
CacheException(Throwable) - Constructor for exception loci.formats.cache.CacheException
 
CacheIndicator - Class in loci.formats.gui
Indicator GUI component showing which planes are currently in the cache for a given dimensional axis at a particular dimensional position.
CacheIndicator(Cache, int) - Constructor for class loci.formats.gui.CacheIndicator
Creates a new cache indicator for the given cache.
CacheIndicator(Cache, int, Component, int, int) - Constructor for class loci.formats.gui.CacheIndicator
Creates a new cache indicator.
CacheListener - Interface in loci.formats.cache
A listener for cache updates.
CacheReporter - Interface in loci.formats.cache
Interface for components capable of reporting cache updates.
CacheSource - Class in loci.formats.cache
Superclass of cache sources that retrieve image planes from a data source (e.g., a file) using Bio-Formats.
CacheSource(IFormatReader) - Constructor for class loci.formats.cache.CacheSource
Constructs a cache source from the given Bio-Formats reader.
CacheSource(String) - Constructor for class loci.formats.cache.CacheSource
Constructs a cache source that draws from the given file.
CacheStrategy - Class in loci.formats.cache
Superclass of cache strategies.
CacheStrategy(int[]) - Constructor for class loci.formats.cache.CacheStrategy
Constructs a cache strategy.
cacheUpdated(CacheEvent) - Method in interface loci.formats.cache.CacheListener
Called when cache is updated.
cacheUpdated(CacheEvent) - Method in class loci.formats.gui.CacheComponent
Updates GUI to match latest cache state.
cacheUpdated(CacheEvent) - Method in class loci.formats.gui.CacheIndicator
 
CacheUpdater - Class in loci.formats.cache
Thread responsible for updating the cache (loading and dropping planes) in the background.
CacheUpdater(Cache) - Constructor for class loci.formats.cache.CacheUpdater
 
calcPhotons - Variable in class loci.formats.in.SDTInfo
No of photons.
calculateDimensions() - Method in class loci.formats.in.ZeissCZIReader
 
calculateDimensions(int, boolean) - Method in class loci.formats.in.ZeissCZIReader
 
CALIBRATION - Static variable in class loci.formats.in.OpenlabReader
 
calibrationTable - Variable in class loci.plugins.util.BFVirtualStack
 
calibrationUnit - Variable in class loci.formats.in.TiffReader
 
Calibrator - Class in loci.plugins.in
Logic for calibrating images.
Calibrator(ImportProcess) - Constructor for class loci.plugins.in.Calibrator
 
callDeferredSetters(ReaderWrapper) - Method in class loci.formats.WrappedReader
A helper may not exist before initFile() is called.
callLegacyReader() - Method in class loci.formats.DelegateReader
 
CAMERA_GAIN - Static variable in class loci.formats.in.CellSensReader
 
CAMERA_GAMMA - Static variable in class loci.formats.in.CellSensReader
 
CAMERA_OFFSET - Static variable in class loci.formats.in.CellSensReader
 
CAMERA_SERIAL_SETTING - Static variable in class loci.formats.in.FluoviewReader
 
cameraIDs - Variable in class loci.formats.in.FlexReader
 
cameraMode - Variable in class loci.formats.in.MicromanagerReader.Position
 
cameraModel - Variable in class loci.formats.in.ND2Handler
 
cameraName - Variable in class loci.formats.in.SimplePCITiffReader
 
cameraName - Variable in class loci.formats.in.SISReader
 
cameraNumber - Variable in class loci.formats.in.CV7000Reader.Channel
 
cameraRef - Variable in class loci.formats.in.MicromanagerReader.Position
 
cameraRefs - Variable in class loci.formats.in.FlexReader
 
cameraType - Variable in class loci.formats.in.SimplePCITiffReader
 
CAN_GROUP - Static variable in class loci.formats.FormatTools
 
CAN_GROUP - Static variable in interface loci.formats.IFormatReader
 
canAdjustDimensions - Variable in class loci.formats.in.ND2Handler
 
cancel - Variable in class loci.plugins.in.ImportProcess
Whether the process has been canceled.
cancel() - Method in class loci.plugins.in.ImportProcess
Cancels the import process.
canceled - Variable in class loci.plugins.LociImporter
Flag indicating whether last operation was canceled.
canceled - Variable in class loci.plugins.Slicer
Flag indicating whether last operation was canceled.
canceled - Variable in class loci.plugins.Updater
Flag indicating whether last operation was canceled.
canChangePattern() - Method in class loci.formats.FileStitcher
 
canClose - Variable in class loci.formats.tiff.TiffParser
 
canCloseReader - Variable in class loci.formats.gui.ImageViewer
 
canDetectBigTiff - Variable in class loci.formats.out.TiffWriter
Whether or not BigTIFF can be used automatically.
canDoQT() - Method in class loci.formats.gui.LegacyQTTools
Whether QuickTime is available to this JVM.
canDoStacks() - Method in class loci.formats.FormatWriter
 
canDoStacks() - Method in interface loci.formats.IFormatWriter
Reports whether the writer can save multiple images to a single file.
canDoStacks() - Method in class loci.formats.ImageWriter
 
canDoStacks() - Method in class loci.formats.out.APNGWriter
 
canDoStacks() - Method in class loci.formats.out.AVIWriter
 
canDoStacks() - Method in class loci.formats.out.CellH5Writer
 
canDoStacks() - Method in class loci.formats.out.ICSWriter
 
canDoStacks() - Method in class loci.formats.out.JavaWriter
 
canDoStacks() - Method in class loci.formats.out.JPEG2000Writer
Overridden to indicate that stacks are not supported.
canDoStacks() - Method in class loci.formats.out.LegacyQTWriter
 
canDoStacks() - Method in class loci.formats.out.OMEXMLWriter
 
canDoStacks() - Method in class loci.formats.out.QTWriter
 
canDoStacks() - Method in class loci.formats.out.TiffWriter
 
canDoStacks() - Method in class loci.formats.out.V3DrawWriter
 
canDoStacks() - Method in class loci.formats.out.WlzWriter
 
canDoStacks() - Method in class loci.formats.WriterWrapper
 
canDoUpgradeCheck() - Method in class loci.formats.UpgradeChecker
Return whether or not we are ever allowed to perform an upgrade check.
canImport(JComponent, DataFlavor[]) - Method in class loci.plugins.shortcut.ShortcutTransferHandler
 
canLookForND - Variable in class loci.formats.in.MetamorphReader
 
canMerge() - Method in class loci.formats.ChannelMerger
Determines whether the channels in the file can be merged.
CANNOT_GROUP - Static variable in class loci.formats.FormatTools
 
CANNOT_GROUP - Static variable in interface loci.formats.IFormatReader
 
CANON_TAG - Static variable in class loci.formats.in.DNGReader
 
CanonRawReader - Class in loci.formats.in
CanonRawReader is the file format reader for Canon RAW files.
CanonRawReader() - Constructor for class loci.formats.in.CanonRawReader
Constructs a new Canon RAW reader.
canParse - Variable in class loci.formats.in.LeicaHandler
 
canReadAttachments() - Method in class loci.formats.in.ZeissCZIReader
 
canSeparateSeries - Variable in class loci.formats.in.MinimalTiffReader
Whether or not IFDs with different dimensions can be split into separate series.
canUseBankDataDirectly(WritableRaster, int, Class<? extends DataBuffer>) - Static method in class loci.formats.gui.AWTImageTools
Whether we can return the data buffer's bank data without performing any copy or conversion operations.
canUsePrevious - Variable in class loci.formats.in.NativeQTReader
Flag indicating whether we can safely use prevPixels.
CANVAS_COLOR_1 - Static variable in class loci.formats.in.CellSensReader
 
CANVAS_COLOR_2 - Static variable in class loci.formats.in.CellSensReader
 
CAPTURE_EDITOR_DATA - Static variable in class loci.formats.in.NikonReader
 
CAPTURE_MODE - Static variable in class loci.formats.in.NDPIReader
 
cast(Class<?>) - Method in class loci.formats.ClassList
Cast the given class to something that extends the base class.
category - Variable in class loci.formats.in.BaseZeissReader.Tag
 
category - Variable in class loci.formats.in.ZeissTIFFHandler.Scaling
 
category - Variable in class loci.formats.in.ZeissTIFFHandler.Tag
 
cBegin - Variable in class loci.plugins.in.ImporterOptions
 
CCD_SENSITIVITY - Static variable in class loci.formats.in.CellSensReader
 
cChoice - Variable in class loci.formats.gui.DataConverter
 
cChoice - Variable in class loci.plugins.in.SwapDialog
 
cdata - Variable in class loci.formats.in.LeicaSCNReader.LeicaSCNHandler
 
cdata - Variable in class loci.formats.in.ZeissTIFFHandler
 
CELL_LENGTH - Static variable in class loci.formats.tiff.IFD
 
CELL_WIDTH - Static variable in class loci.formats.tiff.IFD
 
CellH5Constants() - Constructor for class loci.formats.in.CellH5Reader.CellH5Constants
 
CellH5Coordinate(String, String, String) - Constructor for class loci.formats.in.CellH5Reader.CellH5Coordinate
 
CellH5PathsToImageData - Variable in class loci.formats.in.CellH5Reader
 
CellH5PositionList - Variable in class loci.formats.in.CellH5Reader
 
CellH5Reader - Class in loci.formats.in
Reader for CellH5 (HDF) files.
CellH5Reader() - Constructor for class loci.formats.in.CellH5Reader
Constructs a new CellH5 HDF reader.
CellH5Reader.CellH5Constants - Class in loci.formats.in
 
CellH5Reader.CellH5Coordinate - Class in loci.formats.in
 
CellH5Writer - Class in loci.formats.out
CellH5Writer is the file format writer for CellH5 format.
CellH5Writer() - Constructor for class loci.formats.out.CellH5Writer
 
CellH5Writer(String, String[]) - Constructor for class loci.formats.out.CellH5Writer
 
cellObjectNames - Variable in class loci.formats.in.BDVReader
 
cellObjectNames - Variable in class loci.formats.in.CellH5Reader
 
cellomicsPattern - Variable in class loci.formats.in.CellomicsReader
 
CellomicsReader - Class in loci.formats.in
Reader for Cellomics C01 files.
CellomicsReader() - Constructor for class loci.formats.in.CellomicsReader
Constructs a new Cellomics reader.
CellomicsReader.ChannelFile - Class in loci.formats.in
 
CellSensReader - Class in loci.formats.in
CellSensReader is the file format reader for cellSens .vsi files.
CellSensReader() - Constructor for class loci.formats.in.CellSensReader
Constructs a new cellSens reader.
CellSensReader.Pyramid - Class in loci.formats.in
 
CellSensReader.TileCoordinate - Class in loci.formats.in
 
CellSensWidgets - Class in loci.plugins.config
Custom widgets for configuring Bio-Formats CellSens .vsi support.
CellSensWidgets() - Constructor for class loci.plugins.config.CellSensWidgets
 
CellVoyagerReader - Class in loci.formats.in
A bioformat reader for the Yokagawa Cellvoyager CV1000 automated microscope ( http://www.yokogawa.com/scanner/products/cv1000e.htm).
CellVoyagerReader() - Constructor for class loci.formats.in.CellVoyagerReader
 
CellVoyagerReader.AreaInfo - Class in loci.formats.in
 
CellVoyagerReader.ChannelInfo - Class in loci.formats.in
 
CellVoyagerReader.FieldInfo - Class in loci.formats.in
 
CellVoyagerReader.WellInfo - Class in loci.formats.in
 
CellWorxReader - Class in loci.formats.in
CellWorxReader is the file format reader for CellWorx .pnl files.
CellWorxReader() - Constructor for class loci.formats.in.CellWorxReader
Constructs a new CellWorx reader.
cEnd - Variable in class loci.plugins.in.ImporterOptions
 
CENTERED_ORDER - Static variable in interface loci.formats.cache.ICacheStrategy
 
centerPixelValue - Variable in class loci.formats.in.DicomReader
 
centerX - Variable in class loci.formats.in.CellVoyagerReader.WellInfo
 
centerY - Variable in class loci.formats.in.CellVoyagerReader.WellInfo
 
certain - Variable in class loci.formats.AxisGuesser
Whether the guesser is confident that all axis types are correct.
certain - Variable in class loci.formats.in.OMETiffReader.OMETiffPlane
Certainty flag, for dealing with unspecified NumPlanes.
cf - Variable in class org.libjpegturbo.turbojpeg.TJTransform
Custom filter instance
CFA_PATTERN - Static variable in class loci.formats.tiff.IFD
 
cfaPattern - Variable in class loci.formats.in.DNGReader
 
cfaPattern - Variable in class loci.formats.in.NikonReader
 
cfdHF - Variable in class loci.formats.in.SDTInfo
 
cfdLH - Variable in class loci.formats.in.SDTInfo
 
cfdLL - Variable in class loci.formats.in.SDTInfo
 
cfdZC - Variable in class loci.formats.in.SDTInfo
 
CFG_SUFFIX - Static variable in class loci.formats.in.PerkinElmerReader
 
CFG_SUFFIX - Static variable in class loci.formats.in.PrairieReader
 
cfgFile - Variable in class loci.formats.in.PrairieReader
The associated XML files.
CHAINED_LAYERS - Static variable in class loci.formats.in.CellSensReader
 
chan - Variable in class loci.formats.in.SDTInfo
Routing channel number.
CHANDESC - Static variable in class loci.formats.in.LeicaReader
 
changedUpdate(DocumentEvent) - Method in class loci.plugins.config.FlexWidgets
 
changeOutputFile(String) - Method in class loci.formats.FormatWriter
 
changeOutputFile(String) - Method in interface loci.formats.IFormatWriter
Switch the output file for the current dataset.
changeOutputFile(String) - Method in class loci.formats.ImageWriter
 
changeOutputFile(String) - Method in class loci.formats.WriterWrapper
 
chanMax - Variable in class loci.formats.MinMaxCalculator
Max values for each channel.
chanMin - Variable in class loci.formats.MinMaxCalculator
Min values for each channel.
CHANNEL - Static variable in class loci.formats.FormatTools
Identifies the Channel dimensional type, representing a generic channel dimension.
channel - Variable in class loci.formats.in.CellomicsReader.ChannelFile
 
channel - Variable in class loci.formats.in.ColumbusReader.Plane
 
Channel() - Constructor for class loci.formats.in.CV7000Reader.Channel
 
channel - Variable in class loci.formats.in.CV7000Reader.Plane
 
Channel() - Constructor for class loci.formats.in.LeicaHandler.Channel
 
channel - Variable in class loci.formats.in.LeicaHandler.Detector
 
channel - Variable in class loci.formats.in.LeicaHandler.MultiBand
 
Channel() - Constructor for class loci.formats.in.OIRReader.Channel
 
channel - Variable in class loci.formats.in.PrairieMetadata.PFile
channel of this <File>.
channel - Variable in class loci.formats.in.SPCReader
 
Channel() - Constructor for class loci.formats.in.ZeissCZIReader.Channel
 
CHANNEL_ACQUIRE - Static variable in class loci.formats.in.ZeissLSMReader
 
CHANNEL_AMPLIFIER_GAIN - Static variable in class loci.formats.in.ZeissLSMReader
 
CHANNEL_CONTRAST_BRIGHTNESS - Static variable in class loci.formats.in.CellSensReader
 
CHANNEL_COUNT_TAG - Static variable in class loci.formats.in.FlowSightReader
 
CHANNEL_DESCS_TAG - Static variable in class loci.formats.in.FlowSightReader
 
CHANNEL_DETECTOR_GAIN - Static variable in class loci.formats.in.ZeissLSMReader
 
CHANNEL_DIM - Static variable in class loci.formats.in.CellSensReader
 
CHANNEL_FILTER - Static variable in class loci.formats.in.ZeissLSMReader
 
CHANNEL_FILTER_SET - Static variable in class loci.formats.in.ZeissLSMReader
 
CHANNEL_GAMMA_CORRECTION - Static variable in class loci.formats.in.CellSensReader
 
CHANNEL_INFO_PROPERTIES - Static variable in class loci.formats.in.CellSensReader
 
CHANNEL_NAME - Static variable in class loci.formats.FormatTools
 
CHANNEL_NAME - Static variable in class loci.formats.in.CellSensReader
 
CHANNEL_NAME - Static variable in class loci.formats.in.ZeissLSMReader
 
CHANNEL_NAMES_TAG - Static variable in class loci.formats.in.FlowSightReader
 
CHANNEL_NUM - Static variable in class loci.formats.FormatTools
 
CHANNEL_OVERFLOW - Static variable in class loci.formats.in.CellSensReader
 
CHANNEL_PINHOLE_DIAMETER - Static variable in class loci.formats.in.ZeissLSMReader
 
CHANNEL_PREFIX - Static variable in class loci.formats.in.KLBReader
Prefixes indicating dimensions and projections
CHANNEL_PRIORITIES - Static variable in class loci.formats.in.LIFReader
 
CHANNEL_PROPERTIES - Static variable in class loci.formats.in.CellSensReader
 
CHANNEL_TAG - Static variable in class loci.formats.in.SlidebookTiffReader
 
CHANNEL_TRANSPARENCY_VALUE - Static variable in class loci.formats.in.CellSensReader
 
CHANNEL_VISIBLE - Static variable in class loci.formats.in.CellSensReader
 
channelColor - Variable in class loci.formats.in.ColumbusReader.Plane
 
channelColor - Variable in class loci.formats.in.LeicaReader
 
channelColor - Variable in class loci.formats.in.ZeissLSMReader
 
channelColors - Variable in class loci.formats.in.BaseZeissReader
 
channelColors - Variable in class loci.formats.in.ImprovisionTiffReader
 
channelColors - Variable in class loci.formats.in.MicromanagerReader.Position
 
channelColors - Variable in class loci.formats.in.NativeND2Reader
 
channelCount - Variable in class loci.formats.in.CellSensReader
 
ChannelData() - Constructor for class loci.formats.in.FV1000Reader.ChannelData
 
channelDescs - Variable in class loci.formats.in.FlowSightReader
 
ChannelFile(String, int, int, int, int) - Constructor for class loci.formats.in.CellomicsReader.ChannelFile
 
ChannelFiller - Class in loci.formats
For indexed color data representing true color, factors out the indices, replacing them with the color table values directly.
ChannelFiller() - Constructor for class loci.formats.ChannelFiller
Constructs a ChannelFiller around a new image reader.
ChannelFiller(IFormatReader) - Constructor for class loci.formats.ChannelFiller
Constructs a ChannelFiller with a given reader.
channelFiller - Variable in class loci.plugins.in.ImportProcess
 
channelId - Variable in class loci.formats.in.OIRReader.Detector
 
channelIDs - Variable in class loci.formats.in.IonpathMIBITiffReader
 
channelIndex - Variable in class loci.formats.in.CV7000Reader.Plane
 
channelIndexes - Variable in class loci.formats.in.BDVReader
 
channelIndices - Variable in class loci.formats.in.BaseZeissReader
 
ChannelInfo() - Constructor for class loci.formats.in.CellVoyagerReader.ChannelInfo
 
channelInfos - Variable in class loci.formats.in.CellVoyagerReader
 
channelLengths - Variable in class loci.formats.in.ICSReader
The length of each channel axis.
channelMap - Variable in class loci.formats.in.CV7000Reader.MeasurementDataHandler
 
channelMax - Variable in class loci.formats.in.ImarisHDFReader
 
ChannelMerger - Class in loci.formats
Logic to automatically merge channels in a file.
ChannelMerger() - Constructor for class loci.formats.ChannelMerger
Constructs a ChannelMerger around a new image reader.
ChannelMerger(IFormatReader) - Constructor for class loci.formats.ChannelMerger
Constructs a ChannelMerger with the given reader.
channelMin - Variable in class loci.formats.in.ImarisHDFReader
 
channelName - Variable in class loci.formats.in.BaseZeissReader
 
channelName - Variable in class loci.formats.in.ColumbusReader.Plane
 
channelName - Variable in class loci.formats.in.ImarisHDFReader
 
channelName - Variable in class loci.formats.in.MetamorphHandler
 
channelName - Variable in class loci.formats.in.OpenlabReader.PlaneInfo
 
channelName - Variable in class loci.formats.in.OperettaReader.Plane
 
channelName - Variable in class loci.formats.in.PrairieMetadata.PFile
channelName attribute of this <File>.
channelName - Variable in class loci.formats.in.SISReader
 
channelName - Variable in class loci.formats.in.ZeissLSMReader.DetectionChannel
 
channelNames - Variable in class loci.formats.in.BDReader
 
channelNames - Variable in class loci.formats.in.CellSensReader.Pyramid
 
channelNames - Variable in class loci.formats.in.FlexReader
 
channelNames - Variable in class loci.formats.in.FlowSightReader
 
channelNames - Variable in class loci.formats.in.FluoviewReader
 
channelNames - Variable in class loci.formats.in.InCellReader
 
channelNames - Variable in class loci.formats.in.IonpathMIBITiffReader
 
channelNames - Variable in class loci.formats.in.LeicaReader
 
channelNames - Variable in class loci.formats.in.LIFReader
 
channelNames - Variable in class loci.formats.in.MetamorphHandler
 
channelNames - Variable in class loci.formats.in.ND2Handler
 
channelNames - Variable in class loci.formats.in.ScanrReader
 
channelNames - Variable in class loci.formats.in.SlidebookTiffReader
 
channelNames - Variable in class loci.formats.in.VolocityReader.Stack
 
channelNames - Variable in class loci.formats.in.ZeissLSMReader
 
channelNumber - Variable in class loci.formats.in.CellVoyagerReader.ChannelInfo
 
channelNumber - Variable in class loci.plugins.util.RecordedImageProcessor
 
channelOrder - Variable in class loci.formats.in.PhotoshopTiffReader
 
channels - Variable in class loci.formats.codec.CodecOptions
Number of channels.
channels - Variable in class loci.formats.in.CV7000Reader
 
channels - Variable in class loci.formats.in.FV1000Reader
 
channels - Variable in class loci.formats.in.KLBReader
 
channels - Variable in class loci.formats.in.LeicaHandler
 
channels - Variable in class loci.formats.in.LiFlimReader
 
channels - Variable in class loci.formats.in.MicromanagerReader.Position
 
channels - Variable in class loci.formats.in.OIRReader
 
channels - Variable in class loci.formats.in.PrairieReader
List of active channels.
channels - Variable in class loci.formats.in.SDTInfo
 
channels - Variable in class loci.formats.in.SDTReader
Number of spectral channels.
channels - Variable in class loci.formats.in.TextReader
List of channel labels.
channels - Variable in class loci.formats.in.ZeissCZIReader
 
ChannelSeparator - Class in loci.formats
Logic to automatically separate the channels in a file.
ChannelSeparator() - Constructor for class loci.formats.ChannelSeparator
Constructs a ChannelSeparator around a new image reader.
ChannelSeparator(IFormatReader) - Constructor for class loci.formats.ChannelSeparator
Constructs a ChannelSeparator with the given reader.
channelSeparator - Variable in class loci.plugins.in.ImportProcess
 
channelsPerTimepoint - Variable in class loci.formats.in.InCellReader
 
channelType - Variable in class loci.formats.in.OperettaReader.Plane
 
channelTypes - Variable in class loci.formats.in.ICSReader
The type of each channel axis.
channelWavelengths - Variable in class loci.formats.in.CellSensReader.Pyramid
 
CHAR - Static variable in class loci.formats.in.CellSensReader
 
CHAR - Static variable in class loci.formats.in.GatanReader
 
characters(char[], int, int) - Method in class loci.formats.in.AFIReader.AFIHandler
 
characters(char[], int, int) - Method in class loci.formats.in.BDVReader.BDVXMLHandler
 
characters(char[], int, int) - Method in class loci.formats.in.BioRadSCNReader.SCNHandler
 
characters(char[], int, int) - Method in class loci.formats.in.ColumbusReader.MeasurementHandler
 
characters(char[], int, int) - Method in class loci.formats.in.CV7000Reader.MeasurementDataHandler
 
characters(char[], int, int) - Method in class loci.formats.in.CV7000Reader.MeasurementSettingsHandler
 
characters(char[], int, int) - Method in class loci.formats.in.FEITiffReader.FEIHandler
 
characters(char[], int, int) - Method in class loci.formats.in.FlexReader.FlexHandler
 
characters(char[], int, int) - Method in class loci.formats.in.ImaconReader.ImaconHandler
 
characters(char[], int, int) - Method in class loci.formats.in.InCellReader.InCellHandler
 
characters(char[], int, int) - Method in class loci.formats.in.IvisionReader.IvisionHandler
 
characters(char[], int, int) - Method in class loci.formats.in.LeicaSCNReader.LeicaSCNHandler
 
characters(char[], int, int) - Method in class loci.formats.in.OMEXMLReader.OMEXMLHandler
 
characters(char[], int, int) - Method in class loci.formats.in.OperettaReader.OperettaHandler
 
characters(char[], int, int) - Method in class loci.formats.in.ScanrReader.ScanrHandler
 
characters(char[], int, int) - Method in class loci.formats.in.ZeissTIFFHandler
 
characters(char[], int, int) - Method in class loci.formats.out.OMEXMLWriter.OMEHandler
 
charData - Variable in class loci.formats.in.FlexReader.FlexHandler
 
CHARS - Static variable in class loci.formats.tools.AsciiImage
 
Charset(int, String) - Constructor for enum loci.formats.in.BaseZeissReader.Charset
 
charset - Variable in class loci.formats.in.BaseZeissReader.Shape
 
CHECK - Static variable in class loci.formats.in.ZeissLMSReader
 
checkBufferSize(IFormatReader, int) - Static method in class loci.formats.FormatTools
 
checkBufferSize(IFormatReader, int, int, int) - Static method in class loci.formats.FormatTools
Checks that the given buffer size is large enough to hold a w * h image as returned by the given reader.
checkClass(String) - Static method in class loci.plugins.util.LibraryChecker
Checks whether the given class is available.
checkClassDependency(Class<? extends Object>) - Method in class loci.formats.services.WlzServiceImpl
 
checkCommentImageJ(String) - Method in class loci.formats.in.TiffReader
 
checkCommentMetamorph(String) - Method in class loci.formats.in.TiffReader
 
checkElement(Element, String) - Method in class loci.formats.in.PrairieMetadata
Checks that the given element has the specified name.
checkFlip(boolean, Length) - Method in class loci.formats.in.LIFReader
 
checkHeader() - Method in class loci.formats.tiff.TiffParser
Checks the TIFF header.
checkImageIndex(int) - Method in class loci.formats.ome.OMEPyramidStore
Verify that the given index is non-negative and less than the Image count.
checkImageJ() - Static method in class loci.plugins.util.LibraryChecker
Checks whether ImageJ is new enough for the Bio-Formats plugins.
checkImageJ(String, String) - Static method in class loci.plugins.util.LibraryChecker
Returns true the current ImageJ version is greater than or equal to the specified version.
checkImageJ(String, String, String) - Static method in class loci.plugins.util.LibraryChecker
Returns true the current ImageJ version is greater than or equal to the specified version.
checkJava() - Static method in class loci.plugins.util.LibraryChecker
Checks for a new enough version of the Java Runtime Environment.
checkKey(String, String) - Method in class loci.formats.in.MetamorphHandler
Check if the value needs to be saved.
checkKey(String, String) - Method in class loci.plugins.in.ImporterOptions
Tests whether the given boolean key is set in the specified options.
checkLatest(String, String) - Static method in class loci.plugins.config.InstallWizard
 
checkLibrary(LibraryChecker.Library, HashSet<String>) - Static method in class loci.plugins.util.LibraryChecker
Checks for a required library.
checkLibrary(String, String, HashSet<String>) - Static method in class loci.plugins.util.LibraryChecker
Checks whether the given class is available; if not, adds the specified JAR file name to the hash set (presumably to report it missing to the user).
checkMissing(HashSet<String>) - Static method in class loci.plugins.util.LibraryChecker
Reports missing libraries in the given hash set to the user.
checkObsoleteOptions() - Method in class loci.plugins.in.ImporterOptions
Handles obsolete macro keys, for backward compatibility.
checkPALM(String) - Method in class loci.formats.in.ZeissCZIReader
 
checkParams(int, byte[], int, int, int, int) - Method in class loci.formats.FormatWriter
Ensure that the arguments that are being passed to saveBytes(...) are valid.
checkParams - Variable in class loci.formats.out.TiffWriter
Whether or not to check the parameters passed to saveBytes.
checkPerformed - Static variable in class loci.plugins.in.UpgradeDialog
Whether an upgrade check has already been performed this session.
checkPlaneNumber(IFormatReader, int) - Static method in class loci.formats.FormatTools
Checks that the given plane number is valid for the given reader.
checkPlaneParameters(IFormatReader, int, int, int, int, int, int) - Static method in class loci.formats.FormatTools
Convenience method for checking that the plane number, tile size and buffer sizes are all valid for the given reader.
checkPoints(int) - Method in enum loci.formats.in.BaseZeissReader.FeatureType
 
checkQTLibrary() - Method in class loci.formats.gui.LegacyQTTools
Checks whether QTJava is available, throwing an exception if not.
checkResolutionIndex(int, int) - Method in class loci.formats.ome.OMEPyramidStore
Verify that the given image and resolution indices are valid.
checkSuffix(String, String) - Static method in class loci.formats.FormatHandler
Performs suffix matching for the given filename.
checkSuffix(String, String[]) - Static method in class loci.formats.FormatHandler
Performs suffix matching for the given filename.
checkTileSize(IFormatReader, int, int, int, int) - Static method in class loci.formats.FormatTools
Checks that the given tile size is valid for the given reader.
checkTime(long, int, long, long) - Method in class loci.formats.in.TextReader
 
checkUnit(String, String...) - Method in class loci.formats.in.ICSReader
Verifies that a unit matches the expected value.
CHIP_SIZE_X - Static variable in class loci.formats.in.FluoviewReader
 
CHIP_SIZE_Y - Static variable in class loci.formats.in.FluoviewReader
 
chksum - Variable in class loci.formats.in.SDTInfo
 
CHUNK_SIZE - Static variable in class loci.formats.UpgradeChecker
Number of bytes to read from the CI server at a time.
chunkFilePositions - Variable in class loci.formats.in.OBFReader.Stack
 
chunkFileStart - Variable in class loci.formats.in.OBFReader.State
 
chunkLogicalPositions - Variable in class loci.formats.in.OBFReader.Stack
 
chunkLogicalStart - Variable in class loci.formats.in.OBFReader.State
 
ChunkMapEntry() - Constructor for class loci.formats.in.NativeND2Reader.ChunkMapEntry
 
chunkSize - Variable in class loci.formats.in.OBFReader.State
 
chunkSizes - Variable in class loci.formats.in.NativeQTReader
Number of bytes in each plane.
CI_SERVER - Static variable in class loci.formats.UpgradeChecker
Location of the OME continuous integration server.
cIndex - Variable in class loci.formats.in.BaseZeissReader
 
cIndex - Variable in class loci.plugins.util.DataBrowser
 
CIRCLE - Static variable in class loci.formats.in.FV1000Reader
 
CIRCLE - Static variable in class loci.formats.in.ZeissLSMReader
 
CIRCLE_3POINT - Static variable in class loci.formats.in.ZeissLSMReader
 
cLabel - Variable in class loci.formats.gui.DataConverter
 
CLASS_IMAGE_5D - Static variable in class loci.plugins.in.ImporterOptions
 
CLASS_LABELS - Static variable in class loci.formats.in.BDVReader.H5Constants
 
CLASS_LABELS - Static variable in class loci.formats.in.CellH5Reader.CellH5Constants
 
CLASS_VIEW_5D - Static variable in class loci.plugins.in.ImporterOptions
 
classes - Variable in class loci.formats.ClassList
List of classes.
classes - Variable in class loci.formats.in.BDVReader
 
classes - Variable in class loci.formats.in.CellH5Reader
 
ClassList<T> - Class in loci.formats
ClassList is a list of classes for use with ImageReader or ImageWriter, parsed from a configuration file such as readers.txt or writers.txt.
ClassList(Class<T>) - Constructor for class loci.formats.ClassList
Constructs a list of classes, initially empty.
ClassList(String, Class<T>) - Constructor for class loci.formats.ClassList
Constructs a list of classes from the given configuration file.
ClassList(String, Class<T>, Class<?>) - Constructor for class loci.formats.ClassList
Constructs a list of classes from the given configuration file.
classList - Variable in class loci.formats.FileStitcher
 
cleanup() - Method in class loci.formats.Memoizer
 
clear() - Method in class loci.formats.codec.ByteVector
 
clear() - Method in class loci.formats.MetadataList
Clear the array.
clear(int) - Method in class loci.formats.MetadataList
Clear the specified primary array element.
clearSeries() - Method in class loci.plugins.in.ImporterOptions
 
clearXML() - Method in class loci.formats.in.ZeissCZIReader.Metadata
 
cLengths - Variable in class loci.plugins.util.DataBrowser
 
CLIPPING - Static variable in class loci.formats.in.CellSensReader
 
CLIPPING_MAGIC_STRING - Static variable in class loci.formats.in.VolocityClippingReader
 
CLIPPING_STATE - Static variable in class loci.formats.in.CellSensReader
 
clippingData - Variable in class loci.formats.in.VolocityReader.Stack
 
CLOCKWISE - Static variable in class loci.formats.in.FluoviewReader
 
clone() - Method in class loci.formats.CoreMetadata
 
clone(IFormatReader, int) - Method in class loci.formats.CoreMetadata
 
clone() - Method in class loci.formats.SwappableMetadata
 
clone(IFormatReader, int) - Method in class loci.formats.SwappableMetadata
 
close(boolean) - Method in class loci.formats.ChannelSeparator
 
close() - Method in class loci.formats.codec.JPEGTileDecoder
 
close(boolean) - Method in class loci.formats.DelegateReader
 
close() - Method in class loci.formats.FileStitcher
 
close(boolean) - Method in class loci.formats.FileStitcher
 
close() - Method in class loci.formats.FileStitcher.ExternalSeries
 
close(boolean) - Method in class loci.formats.FileStitcher.ExternalSeries
 
close(boolean) - Method in class loci.formats.FormatReader
 
close() - Method in class loci.formats.FormatReader
 
close() - Method in class loci.formats.FormatWriter
 
close() - Method in class loci.formats.gui.PreviewPane
Closes the underlying image reader.
close(boolean) - Method in interface loci.formats.IFormatReader
Closes the currently open file.
close(boolean) - Method in class loci.formats.ImageReader
 
close() - Method in class loci.formats.ImageReader
 
close() - Method in class loci.formats.ImageWriter
 
close(boolean) - Method in class loci.formats.in.AFIReader
 
close(boolean) - Method in class loci.formats.in.AIMReader
 
close(boolean) - Method in class loci.formats.in.AliconaReader
 
close(boolean) - Method in class loci.formats.in.AmiraReader
 
close(boolean) - Method in class loci.formats.in.AnalyzeReader
 
close(boolean) - Method in class loci.formats.in.APLReader
 
close(boolean) - Method in class loci.formats.in.APNGReader
 
close(boolean) - Method in class loci.formats.in.AVIReader
 
close(boolean) - Method in class loci.formats.in.BaseZeissReader
 
close(boolean) - Method in class loci.formats.in.BDReader
 
close(boolean) - Method in class loci.formats.in.BDVReader
 
close(boolean) - Method in class loci.formats.in.BioRadReader
 
close(boolean) - Method in class loci.formats.in.BioRadSCNReader
 
close(boolean) - Method in class loci.formats.in.BMPReader
 
close(boolean) - Method in class loci.formats.in.BrukerReader
 
close(boolean) - Method in class loci.formats.in.BurleighReader
 
close(boolean) - Method in class loci.formats.in.CanonRawReader
 
close(boolean) - Method in class loci.formats.in.CellH5Reader
 
close(boolean) - Method in class loci.formats.in.CellomicsReader
 
close(boolean) - Method in class loci.formats.in.CellSensReader
 
close(boolean) - Method in class loci.formats.in.CellWorxReader
 
close(boolean) - Method in class loci.formats.in.ColumbusReader
 
close(boolean) - Method in class loci.formats.in.CV7000Reader
 
close(boolean) - Method in class loci.formats.in.DeltavisionReader
 
close(boolean) - Method in class loci.formats.in.DicomReader
 
close(boolean) - Method in class loci.formats.in.DNGReader
 
close(boolean) - Method in class loci.formats.in.EPSReader
 
close(boolean) - Method in class loci.formats.in.FakeReader
 
close(boolean) - Method in class loci.formats.in.FEIReader
 
close(boolean) - Method in class loci.formats.in.FEITiffReader
 
close(boolean) - Method in class loci.formats.in.FitsReader
 
close(boolean) - Method in class loci.formats.in.FlexReader
 
close(boolean) - Method in class loci.formats.in.FlowSightReader
 
close(boolean) - Method in class loci.formats.in.FluoviewReader
 
close(boolean) - Method in class loci.formats.in.FujiReader
 
close(boolean) - Method in class loci.formats.in.FV1000Reader
 
close(boolean) - Method in class loci.formats.in.GatanDM2Reader
 
close(boolean) - Method in class loci.formats.in.GatanReader
 
close(boolean) - Method in class loci.formats.in.GIFReader
 
close(boolean) - Method in class loci.formats.in.HamamatsuVMSReader
 
close(boolean) - Method in class loci.formats.in.HitachiReader
 
close(boolean) - Method in class loci.formats.in.HRDGDFReader
 
close(boolean) - Method in class loci.formats.in.ICSReader
 
close(boolean) - Method in class loci.formats.in.IM3Reader
 
close(boolean) - Method in class loci.formats.in.ImaconReader
 
close(boolean) - Method in class loci.formats.in.ImageIOReader
 
close(boolean) - Method in class loci.formats.in.ImagicReader
 
close(boolean) - Method in class loci.formats.in.ImarisHDFReader
 
close(boolean) - Method in class loci.formats.in.ImarisReader
 
close(boolean) - Method in class loci.formats.in.IMODReader
 
close(boolean) - Method in class loci.formats.in.ImprovisionTiffReader
 
close(boolean) - Method in class loci.formats.in.ImspectorReader
 
close(boolean) - Method in class loci.formats.in.InCell3000Reader
 
close(boolean) - Method in class loci.formats.in.InCellReader
 
close(boolean) - Method in class loci.formats.in.InveonReader
 
close(boolean) - Method in class loci.formats.in.IonpathMIBITiffReader
 
close(boolean) - Method in class loci.formats.in.IPLabReader
 
close(boolean) - Method in class loci.formats.in.IPWReader
 
close(boolean) - Method in class loci.formats.in.IvisionReader
 
close(boolean) - Method in class loci.formats.in.JEOLReader
 
close(boolean) - Method in class loci.formats.in.JPEG2000Reader
 
close(boolean) - Method in class loci.formats.in.JPEGReader
 
close(boolean) - Method in class loci.formats.in.JPXReader
 
close(boolean) - Method in class loci.formats.in.KhorosReader
 
close(boolean) - Method in class loci.formats.in.KLBReader
 
close(boolean) - Method in class loci.formats.in.KodakReader
 
close(boolean) - Method in class loci.formats.in.L2DReader
 
close(boolean) - Method in class loci.formats.in.LegacyQTReader
 
close(boolean) - Method in class loci.formats.in.LeicaReader
 
close(boolean) - Method in class loci.formats.in.LeicaSCNReader
 
close(boolean) - Method in class loci.formats.in.LiFlimReader
 
close(boolean) - Method in class loci.formats.in.LIFReader
 
close(boolean) - Method in class loci.formats.in.LIMReader
 
close(boolean) - Method in class loci.formats.in.MetamorphReader
 
close(boolean) - Method in class loci.formats.in.MetamorphTiffReader
 
close(boolean) - Method in class loci.formats.in.MIASReader
 
close(boolean) - Method in class loci.formats.in.MicroCTReader
 
close(boolean) - Method in class loci.formats.in.MicromanagerReader
 
close(boolean) - Method in class loci.formats.in.MINCReader
 
close(boolean) - Method in class loci.formats.in.MinimalTiffReader
 
close(boolean) - Method in class loci.formats.in.MNGReader
 
close(boolean) - Method in class loci.formats.in.MolecularImagingReader
 
close(boolean) - Method in class loci.formats.in.MRCReader
 
close(boolean) - Method in class loci.formats.in.MRWReader
 
close(boolean) - Method in class loci.formats.in.NAFReader
 
close(boolean) - Method in class loci.formats.in.NativeND2Reader
 
close(boolean) - Method in class loci.formats.in.NativeQTReader
 
close(boolean) - Method in class loci.formats.in.NDPIReader
 
close(boolean) - Method in class loci.formats.in.NDPISReader
 
close(boolean) - Method in class loci.formats.in.NiftiReader
 
close(boolean) - Method in class loci.formats.in.NikonElementsTiffReader
 
close(boolean) - Method in class loci.formats.in.NikonReader
 
close(boolean) - Method in class loci.formats.in.NikonTiffReader
 
close(boolean) - Method in class loci.formats.in.NRRDReader
 
close(boolean) - Method in class loci.formats.in.OBFReader
 
close(boolean) - Method in class loci.formats.in.OIRReader
 
close(boolean) - Method in class loci.formats.in.OMETiffReader
 
close(boolean) - Method in class loci.formats.in.OMEXMLReader
 
close(boolean) - Method in class loci.formats.in.OpenlabRawReader
 
close(boolean) - Method in class loci.formats.in.OpenlabReader
 
close(boolean) - Method in class loci.formats.in.OperettaReader
 
close(boolean) - Method in class loci.formats.in.PCIReader
 
close(boolean) - Method in class loci.formats.in.PCORAWReader
 
close(boolean) - Method in class loci.formats.in.PCXReader
 
close(boolean) - Method in class loci.formats.in.PDSReader
 
close(boolean) - Method in class loci.formats.in.PerkinElmerReader
 
close(boolean) - Method in class loci.formats.in.PGMReader
 
close(boolean) - Method in class loci.formats.in.PhotoshopTiffReader
 
close(boolean) - Method in class loci.formats.in.PictReader
 
close(boolean) - Method in class loci.formats.in.PQBinReader
 
close(boolean) - Method in class loci.formats.in.PrairieReader
 
close(boolean) - Method in class loci.formats.in.PSDReader
 
close(boolean) - Method in class loci.formats.in.QuesantReader
 
close(boolean) - Method in class loci.formats.in.RHKReader
 
close(boolean) - Method in class loci.formats.in.SBIGReader
 
close(boolean) - Method in class loci.formats.in.ScanrReader
 
close(boolean) - Method in class loci.formats.in.SDTReader
 
close(boolean) - Method in class loci.formats.in.SEQReader
 
close(boolean) - Method in class loci.formats.in.SIFReader
 
close(boolean) - Method in class loci.formats.in.SimplePCITiffReader
 
close(boolean) - Method in class loci.formats.in.SISReader
 
close(boolean) - Method in class loci.formats.in.SlidebookReader
 
close(boolean) - Method in class loci.formats.in.SlidebookTiffReader
 
close(boolean) - Method in class loci.formats.in.SPCReader
 
close(boolean) - Method in class loci.formats.in.SPEReader
 
close(boolean) - Method in class loci.formats.in.SpiderReader
 
close(boolean) - Method in class loci.formats.in.SVSReader
 
close(boolean) - Method in class loci.formats.in.TargaReader
 
close(boolean) - Method in class loci.formats.in.TCSReader
 
close(boolean) - Method in class loci.formats.in.TextReader
 
close(boolean) - Method in class loci.formats.in.TiffReader
 
close(boolean) - Method in class loci.formats.in.TileJPEGReader
 
close(boolean) - Method in class loci.formats.in.TillVisionReader
 
close(boolean) - Method in class loci.formats.in.TopometrixReader
 
close(boolean) - Method in class loci.formats.in.TrestleReader
 
close(boolean) - Method in class loci.formats.in.UBMReader
 
close(boolean) - Method in class loci.formats.in.UnisokuReader
 
close(boolean) - Method in class loci.formats.in.VarianFDFReader
 
close(boolean) - Method in class loci.formats.in.VectraReader
 
close(boolean) - Method in class loci.formats.in.VeecoReader
 
close(boolean) - Method in class loci.formats.in.VentanaReader
 
close(boolean) - Method in class loci.formats.in.VisitechReader
 
close(boolean) - Method in class loci.formats.in.VolocityClippingReader
 
close(boolean) - Method in class loci.formats.in.VolocityReader
 
close(boolean) - Method in class loci.formats.in.WlzReader
 
close(boolean) - Method in class loci.formats.in.ZeissCZIReader
 
close() - Method in class loci.formats.in.ZeissCZIReader.Segment
 
close(boolean) - Method in class loci.formats.in.ZeissLMSReader
 
close(boolean) - Method in class loci.formats.in.ZeissLSMReader
 
close(boolean) - Method in class loci.formats.in.ZeissTIFFReader
 
close(boolean) - Method in class loci.formats.in.ZeissZVIReader
 
close(boolean) - Method in class loci.formats.in.ZipReader
 
close() - Method in class loci.formats.Memoizer
 
close(boolean) - Method in class loci.formats.Memoizer
 
close() - Method in interface loci.formats.Memoizer.Deser
 
close() - Method in class loci.formats.Memoizer.KryoDeser
 
close(boolean) - Method in class loci.formats.MinMaxCalculator
 
close() - Method in class loci.formats.out.APNGWriter
 
close() - Method in class loci.formats.out.AVIWriter
 
close() - Method in class loci.formats.out.CellH5Writer
 
close() - Method in class loci.formats.out.ICSWriter
 
close() - Method in class loci.formats.out.JavaWriter
 
close() - Method in class loci.formats.out.LegacyQTWriter
 
close() - Method in class loci.formats.out.OMETiffWriter
 
close() - Method in class loci.formats.out.OMEXMLWriter
 
close() - Method in class loci.formats.out.PyramidOMETiffWriter
 
close() - Method in class loci.formats.out.QTWriter
 
close() - Method in class loci.formats.out.TiffWriter
 
close() - Method in class loci.formats.out.V3DrawWriter
 
close() - Method in class loci.formats.out.WlzWriter
 
close(boolean) - Method in class loci.formats.ReaderWrapper
 
close() - Method in class loci.formats.ReaderWrapper
 
close() - Method in interface loci.formats.services.EXIFService
 
close() - Method in class loci.formats.services.EXIFServiceImpl
 
close() - Method in interface loci.formats.services.JHDFService
Closes and resets the service.
close() - Method in class loci.formats.services.JHDFServiceImpl
 
close() - Method in interface loci.formats.services.JPEGTurboService
 
close() - Method in class loci.formats.services.JPEGTurboServiceImpl
 
close() - Method in interface loci.formats.services.MDBService
Close the currently initialized file.
close() - Method in class loci.formats.services.MDBServiceImpl
 
close() - Method in interface loci.formats.services.MetakitService
 
close() - Method in class loci.formats.services.MetakitServiceImpl
 
close() - Method in interface loci.formats.services.NetCDFService
Closes and resets the service.
close() - Method in class loci.formats.services.NetCDFServiceImpl
 
close() - Method in interface loci.formats.services.POIService
Close the current POI file system.
close() - Method in class loci.formats.services.POIServiceImpl
 
close() - Method in interface loci.formats.services.WlzService
Closes the file.
close() - Method in class loci.formats.services.WlzServiceImpl
 
close(boolean) - Method in class loci.formats.SubResolutionFormatReader
 
close() - Method in class loci.formats.tiff.OnDemandLongArray
 
close() - Method in class loci.formats.tiff.TiffParser
Close the underlying stream, if this TiffParser was constructed with a file path.
close() - Method in class loci.formats.tiff.TiffSaver
Closes the output stream if not null.
close(boolean) - Method in class loci.formats.WrappedReader
 
close() - Method in class loci.formats.WrappedReader
 
close() - Method in class loci.formats.WriterWrapper
 
close() - Method in class loci.plugins.config.TextAreaWriter
Closing a TextAreaWriter does nothing.
close() - Method in class loci.plugins.macro.LociFunctions
 
close() - Method in class loci.plugins.util.VirtualImagePlus
 
close() - Method in class loci.plugins.util.VirtualReader
 
close() - Method in class org.libjpegturbo.turbojpeg.TJCompressor
Free the native structures associated with this compressor instance.
close() - Method in class org.libjpegturbo.turbojpeg.TJDecompressor
Free the native structures associated with this decompressor instance.
CLOSED_ARROW - Static variable in class loci.formats.in.ZeissLSMReader
 
CLOSED_BEZIER - Static variable in class loci.formats.in.ZeissLSMReader
 
CLOSED_POLYLINE - Static variable in class loci.formats.in.ZeissLSMReader
 
closeFileOnly() - Method in class loci.plugins.macro.LociFunctions
 
cm - Variable in class loci.formats.FormatWriter
Default color model.
cNames - Variable in class loci.formats.in.ImprovisionTiffReader
 
co2Percent - Variable in class loci.formats.in.ZeissCZIReader
 
COARSE_FRAME_IFD - Static variable in class loci.formats.in.CellSensReader
 
COARSE_PYRAMID_LEVEL - Static variable in class loci.formats.in.CellSensReader
 
code - Variable in enum loci.formats.codec.CompressionType
Code for the compression.
code - Variable in enum loci.formats.codec.JPEG2000BoxType
Code for the box type.
code - Variable in enum loci.formats.codec.JPEG2000SegmentMarker
Code for the segment marker.
code - Variable in class loci.formats.in.FV1000Reader
 
code - Variable in enum loci.formats.tiff.IFDType
Code for the IFD type in the actual TIFF file.
code - Variable in enum loci.formats.tiff.PhotoInterp
Code for the IFD type in the actual TIFF file.
code - Variable in enum loci.formats.tiff.TiffCompression
Code for the TIFF compression in the actual TIFF file.
codeBlockSize - Variable in class loci.formats.codec.JPEG2000CodecOptions
The maximum code-block size to use per tile-component as it would be provided to: J2KImageWriteParam.setCodeBlockSize(int[]) (WRITE).
Codec - Interface in loci.formats.codec
This class is an interface for any kind of compression or decompression.
codec - Variable in class loci.formats.codec.WrappedCodec
 
codec - Variable in class loci.formats.gui.DataConverter
 
codec - Variable in class loci.formats.in.NativeND2Reader
Codec to use when decompressing pixel data.
codec - Variable in class loci.formats.in.NativeQTReader
Video codec used by this movie.
codec - Variable in class loci.formats.out.LegacyQTWriter
The codec to use.
codec - Variable in class loci.formats.out.QTWriter
The codec to use.
codec - Variable in enum loci.formats.tiff.TiffCompression
TIFF compression codec.
CODEC_ANIMATION - Static variable in class loci.formats.out.QTWriter
Value indicating Animation codec.
CODEC_CINEPAK - Static variable in class loci.formats.out.QTWriter
Value indicating Cinepak codec.
CODEC_H_263 - Static variable in class loci.formats.out.QTWriter
Value indicating H.263 codec.
CODEC_MOTION_JPEG_B - Static variable in class loci.formats.out.QTWriter
Value indicating Motion JPEG-B codec.
CODEC_MPEG_4 - Static variable in class loci.formats.out.QTWriter
Value indicating MPEG-4 codec.
CODEC_RAW - Static variable in class loci.formats.out.QTWriter
Value indicating Raw codec.
CODEC_SORENSON - Static variable in class loci.formats.out.QTWriter
Value indicating Sorenson codec.
CODEC_SORENSON_3 - Static variable in class loci.formats.out.QTWriter
Value indicating Sorenson 3 codec.
codecName - Variable in enum loci.formats.tiff.TiffCompression
Name of the TIFF compression codec.
CodecOptions - Class in loci.formats.codec
Options for compressing and decompressing data.
CodecOptions() - Constructor for class loci.formats.codec.CodecOptions
Construct a new CodecOptions.
CodecOptions(CodecOptions) - Constructor for class loci.formats.codec.CodecOptions
Construct a new CodecOptions using the given CodecOptions.
codecOptions - Variable in class loci.formats.tiff.TiffParser
Codec options to be used when decoding compressed pixel data.
codestreamOffset - Variable in class loci.formats.in.JPEG2000MetadataParser
Offset to first contiguous codestream.
codestreamPixelType - Variable in class loci.formats.in.JPEG2000MetadataParser
Pixel type as specified in the JPEG 2000 codestream..
codestreamSizeC - Variable in class loci.formats.in.JPEG2000MetadataParser
Number of channels the image as specified in the JPEG 2000 codestream.
codestreamSizeX - Variable in class loci.formats.in.JPEG2000MetadataParser
Width of the image as specified in the JPEG 2000 codestream.
codestreamSizeY - Variable in class loci.formats.in.JPEG2000MetadataParser
Height of the image as specified in the JPEG 2000 codestream.
col - Variable in class loci.formats.in.CellomicsReader.ChannelFile
 
col - Variable in class loci.formats.in.CellVoyagerReader.WellInfo
 
col - Variable in class loci.formats.in.ColumbusReader.Plane
 
col - Variable in class loci.formats.in.OperettaReader.Plane
 
col - Variable in class loci.formats.in.ZeissCZIReader.SubBlock
 
colCount - Variable in class loci.formats.in.BaseZeissReader
 
collection - Variable in class loci.formats.in.LeicaHandler
 
collection - Variable in class loci.formats.in.LeicaSCNReader.LeicaSCNHandler
 
COLLECTION_VOLUME - Static variable in class loci.formats.in.CellSensReader
 
colName - Variable in class loci.formats.in.InCellReader
 
color - Variable in class loci.formats.in.CellVoyagerReader.ChannelInfo
 
color - Variable in class loci.formats.in.CV7000Reader.Channel
 
color - Variable in class loci.formats.in.LeicaHandler.ROI
 
color - Variable in class loci.formats.in.LIFReader.ROI
 
color - Variable in class loci.formats.in.OIRReader.Channel
 
color - Variable in class loci.formats.in.ZeissCZIReader.Channel
 
color16 - Variable in class loci.formats.in.IvisionReader
 
COLOR_BAR - Static variable in class loci.formats.in.FV1000Reader
 
COLOR_MAP - Static variable in class loci.formats.in.CanonRawReader
 
COLOR_MAP - Static variable in class loci.formats.in.DNGReader
 
COLOR_MAP - Static variable in class loci.formats.in.NikonReader
 
COLOR_MAP - Static variable in class loci.formats.tiff.IFD
 
COLOR_MAP_1 - Static variable in class loci.formats.in.MRWReader
 
COLOR_MAP_2 - Static variable in class loci.formats.in.MRWReader
 
COLOR_MODE - Static variable in class loci.formats.in.NikonReader
 
COLOR_MODE_COLORIZED - Static variable in class loci.plugins.in.ImporterOptions
 
COLOR_MODE_COMPOSITE - Static variable in class loci.plugins.in.ImporterOptions
 
COLOR_MODE_CUSTOM - Static variable in class loci.plugins.in.ImporterOptions
 
COLOR_MODE_DEFAULT - Static variable in class loci.plugins.in.ImporterOptions
 
COLOR_MODE_GRAYSCALE - Static variable in class loci.plugins.in.ImporterOptions
 
COLOR_SPACE - Static variable in class loci.formats.in.CellSensReader
 
COLOR_SPACE - Static variable in class loci.formats.tiff.IFD
 
ColorDialog - Class in loci.plugins.in
Bio-Formats Importer custom color chooser dialog box.
ColorDialog(ImportProcess) - Constructor for class loci.plugins.in.ColorDialog
 
colorize - Variable in class loci.plugins.util.BFVirtualStack
 
Colorizer - Class in loci.plugins.in
Logic for colorizing images.
Colorizer(ImportProcess) - Constructor for class loci.plugins.in.Colorizer
 
colorMap - Variable in class loci.formats.in.TargaReader
 
colorModeChoice - Variable in class loci.plugins.in.MainDialog
 
colorModel - Variable in class loci.formats.codec.CodecOptions
Color model to use when constructing an image (WRITE).
COLORS - Variable in class loci.formats.in.BDVReader
 
COLORS - Variable in class loci.formats.in.CellH5Reader
 
colors - Variable in class loci.formats.in.ImarisHDFReader
 
colors - Variable in class loci.formats.in.IMODReader
 
colors - Variable in class loci.formats.in.NativeND2Reader
 
colors - Variable in class loci.formats.in.ND2Handler
 
COLORSPACE - Static variable in class loci.formats.in.CellSensReader
 
colorTables - Variable in class loci.formats.in.GIFReader
 
cols - Variable in class loci.formats.in.CellSensReader
 
colT - Variable in class loci.formats.in.SDTInfo
 
ColumbusReader - Class in loci.formats.in
ColumbusReader is the file format reader for screens exported from PerkinElmer Columbus.
ColumbusReader() - Constructor for class loci.formats.in.ColumbusReader
Constructs a new Columbus reader.
ColumbusReader.MeasurementHandler - Class in loci.formats.in
 
ColumbusReader.Plane - Class in loci.formats.in
 
column - Variable in class loci.formats.in.CV7000Reader.Plane
 
column - Variable in class loci.formats.in.FlexReader.FlexFile
 
column - Variable in class loci.formats.in.OMEXMLReader.BinData
 
column - Variable in class loci.formats.tools.AmiraParameters
 
COLUMNS - Static variable in class loci.formats.gui.DataConverter
 
COLUMNS - Static variable in class loci.formats.in.DicomReader
 
ComboFileFilter - Class in loci.formats.gui
A file filter that recognizes files from a union of other filters.
ComboFileFilter(FileFilter[], String) - Constructor for class loci.formats.gui.ComboFileFilter
Constructs a new filter from a list of other filters.
comment - Variable in class loci.formats.in.FluoviewReader
 
comment - Variable in class loci.formats.in.MicromanagerReader.Position
 
comment - Variable in class loci.formats.in.QuesantReader
 
comment - Variable in class loci.formats.in.SVSCoreMetadata
 
COMMENT_STYLE_END - Static variable in class loci.formats.gui.XMLCellRenderer
 
COMMENT_STYLE_START - Static variable in class loci.formats.gui.XMLCellRenderer
 
comments - Variable in class loci.formats.in.JPEG2000MetadataParser
List of comments stored in the file.
comments - Variable in class loci.formats.in.SVSReader
 
comp - Variable in class loci.formats.gui.CacheIndicator
 
COMPANION_KEY - Static variable in class loci.formats.out.OMETiffWriter
 
COMPANION_SUFFIXES - Static variable in class loci.formats.in.TiffReader
 
companionFile - Variable in class loci.formats.in.TiffReader
 
companionFiles - Variable in class loci.formats.in.DicomReader
 
comparator - Static variable in class loci.formats.CoreMetadataList
 
compare(Object, Object) - Method in class loci.formats.cache.CacheStrategy
Default comparator orders dimensional positions based on distance from the current position, taking into account axis priorities and planar ordering.
compare(String, String) - Method in class loci.formats.in.MetamorphTiffReader.NumericComparator
 
compareTo(Object) - Method in class loci.formats.gui.ComboFileFilter
Compares two FileFilter objects alphanumerically.
compareTo(Object) - Method in class loci.formats.gui.ExtensionFileFilter
Compares two FileFilter objects alphanumerically.
compareTo(Object) - Method in class loci.formats.gui.FormatFileFilter
Compares two FileFilter objects alphanumerically.
compareTo(Object) - Method in class loci.formats.gui.NoExtensionFileFilter
Compares two FileFilter objects alphanumerically.
compareTo(VentanaReader.Overlap) - Method in class loci.formats.in.VentanaReader.Overlap
 
compareTo(Object) - Method in class loci.formats.tiff.TiffIFDEntry
 
compareTo(TiffRational) - Method in class loci.formats.tiff.TiffRational
Compares this object with the specified object for order.
compareTo(Object) - Method in class loci.plugins.config.FormatEntry
 
compareTo(Object) - Method in class loci.plugins.config.LibraryEntry
 
compareTo(ThumbLoader.SeriesInfo) - Method in class loci.plugins.in.ThumbLoader.SeriesInfo
 
compareTokens(String[], int, String[], int) - Method in class loci.formats.in.ICSReader
 
COMPLEX - Static variable in class loci.formats.in.CellSensReader
 
COMPLEX - Static variable in class loci.formats.in.ZeissCZIReader
 
COMPLEX_FLOAT - Static variable in class loci.formats.in.ZeissCZIReader
 
COMPONENT_HEIGHT - Static variable in class loci.formats.gui.CacheIndicator
 
COMPONENT_WIDTH - Static variable in class loci.formats.gui.CacheIndicator
 
COMPONENTS_CONFIGURATION - Static variable in class loci.formats.tiff.IFD
 
compress(byte[][], CodecOptions) - Method in class loci.formats.codec.BaseCodec
2D data block encoding default implementation.
compress(byte[], CodecOptions) - Method in interface loci.formats.codec.Codec
Compresses a block of data.
compress(byte[][], CodecOptions) - Method in interface loci.formats.codec.Codec
Compresses a block of data.
compress(byte[], CodecOptions) - Method in class loci.formats.codec.JPEGXRCodec
 
compress(byte[], CodecOptions) - Method in class loci.formats.codec.NikonCodec
 
compress(byte[], CodecOptions) - Method in class loci.formats.codec.TargaRLECodec
 
compress(byte[], CodecOptions) - Method in class loci.formats.codec.WrappedCodec
 
compress(byte[][], CodecOptions) - Method in class loci.formats.codec.WrappedCodec
 
compress(byte[]) - Method in class loci.formats.out.OMEXMLWriter
Compress the given byte array using the current codec.
compress(byte[], CodecOptions) - Method in enum loci.formats.tiff.TiffCompression
Encodes a strip of data.
compress(byte[], int) - Method in class org.libjpegturbo.turbojpeg.TJCompressor
Compress the uncompressed source image associated with this compressor instance and output a JPEG image to the given destination buffer.
compress(int) - Method in class org.libjpegturbo.turbojpeg.TJCompressor
Compress the uncompressed source image associated with this compressor instance and return a buffer containing a JPEG image.
compress(BufferedImage, byte[], int) - Method in class org.libjpegturbo.turbojpeg.TJCompressor
Compress the uncompressed source image stored in srcImage and output a JPEG image to the given destination buffer.
compress(BufferedImage, int) - Method in class org.libjpegturbo.turbojpeg.TJCompressor
Compress the uncompressed source image stored in srcImage and return a buffer containing a JPEG image.
compress(byte[], int, int, int, int, byte[], int, int, int) - Method in class org.libjpegturbo.turbojpeg.TJCompressor
 
compress(int[], int, int, int, int, byte[], int, int, int) - Method in class org.libjpegturbo.turbojpeg.TJCompressor
 
compressBuffer(int, byte[], int, int, int, int) - Method in class loci.formats.out.JPEG2000Writer
Compresses the buffer.
compressed - Variable in class loci.formats.in.NAFReader
 
compressed - Variable in class loci.formats.in.OpenlabReader.PlaneInfo
 
compressed - Variable in class loci.formats.in.PSDReader
 
compressed - Variable in class loci.formats.in.SBIGReader
 
compressed - Variable in class loci.formats.in.TargaReader
 
COMPRESSED_BITS_PER_PIXEL - Static variable in class loci.formats.tiff.IFD
 
compressedSize - Variable in class loci.formats.in.AmiraReader.HxRLE
 
compressedSize - Variable in class loci.formats.in.AmiraReader.HxZip
 
compressedSize - Variable in class org.libjpegturbo.turbojpeg.TJCompressor
 
compression - Variable in enum loci.formats.codec.CompressionType
The compression used.
compression - Variable in class loci.formats.FormatWriter
Current compression type.
compression - Variable in class loci.formats.in.AmiraReader
 
compression - Variable in class loci.formats.in.APNGReader
 
compression - Variable in class loci.formats.in.BMPReader
Compression type
compression - Variable in class loci.formats.in.LiFlimReader
 
compression - Variable in class loci.formats.in.OBFReader.Stack
 
compression - Variable in class loci.formats.in.OMEXMLReader
 
compression - Variable in class loci.formats.in.PhotoshopTiffReader
 
compression - Variable in class loci.formats.in.ZeissCZIReader.DirectoryEntry
 
COMPRESSION - Static variable in class loci.formats.tiff.IFD
 
COMPRESSION_BZIP2 - Static variable in class loci.formats.in.KLBReader
 
COMPRESSION_GZIP - Static variable in class loci.formats.in.LiFlimReader
 
COMPRESSION_J2K - Static variable in class loci.formats.out.TiffWriter
 
COMPRESSION_J2K_LOSSY - Static variable in class loci.formats.out.TiffWriter
 
COMPRESSION_JPEG - Static variable in class loci.formats.out.TiffWriter
 
COMPRESSION_KEY - Static variable in class loci.formats.in.LiFlimReader
 
COMPRESSION_LZW - Static variable in class loci.formats.out.TiffWriter
 
COMPRESSION_NONE - Static variable in class loci.formats.in.KLBReader
 
COMPRESSION_NONE - Static variable in class loci.formats.in.LiFlimReader
 
COMPRESSION_SUFFIXES - Static variable in class loci.formats.FormatHandler
Suffixes for supported compression types.
COMPRESSION_UNCOMPRESSED - Static variable in class loci.formats.out.TiffWriter
 
COMPRESSION_ZLIB - Static variable in class loci.formats.in.KLBReader
 
COMPRESSION_ZLIB - Static variable in class loci.formats.out.TiffWriter
 
CompressionType - Enum in loci.formats.codec
An enumeration of compression types.
CompressionType(int, String) - Constructor for enum loci.formats.codec.CompressionType
Default constructor.
compressionType - Variable in class loci.formats.in.CellSensReader
 
compressionType - Variable in class loci.formats.in.KLBReader
 
compressionTypes - Variable in class loci.formats.FormatWriter
Available compression types.
computeAxisLengths() - Method in class loci.formats.FileStitcher
Computes axis length arrays, and total axis lengths.
computeIndices(int) - Method in class loci.formats.FileStitcher
Gets the file index, and image index into that file, corresponding to the given global image index.
computeNameAndLocation() - Method in class loci.plugins.in.ImportProcess
Initializes the idName and idLoc derived values.
computePhysicalSize(int, String, String) - Method in class loci.formats.in.VarianFDFReader
Return the physical size of a pixel, in microns, along an arbitrary axis based on the supplied physical and pixel lengths of the axis.
computeSeriesLabels(IFormatReader) - Method in class loci.plugins.in.ImportProcess
 
computeSizeT(int) - Method in class loci.formats.in.PrairieReader
Scans the parsed metadata to determine the number of actual time points versus the number of actual stage positions.
computeVariableTimeInterval(IMetadata, int) - Method in class loci.plugins.in.Calibrator
 
concatenate(List<ImagePlus>) - Method in class loci.plugins.in.Concatenator
Concatenates the list of images as appropriate.
concatenate(List<ImagePlus>) - Method in class loci.plugins.in.ImagePlusReader
 
concatenateBox - Variable in class loci.plugins.in.MainDialog
 
concatenateTokens(String[], int, int) - Method in class loci.formats.in.ICSReader
 
Concatenator - Class in loci.plugins.in
Logic for concatenating multiple images together.
Concatenator() - Constructor for class loci.plugins.in.Concatenator
 
confidence - Variable in class loci.formats.in.VentanaReader.Overlap
 
config - Variable in class loci.formats.in.PrairieMetadata
Key/value pairs from CFG and/or ENV files.
ConfigWindow - Class in loci.plugins.config
A window for managing configuration of the Bio-Formats plugins.
ConfigWindow() - Constructor for class loci.plugins.config.ConfigWindow
 
constructDialog() - Method in class loci.plugins.in.ColorDialog
 
constructDialog() - Method in class loci.plugins.in.CropDialog
 
constructDialog() - Method in class loci.plugins.in.FilePatternDialog
 
constructDialog() - Method in class loci.plugins.in.IdDialog
 
constructDialog() - Method in class loci.plugins.in.ImporterDialog
 
constructDialog() - Method in class loci.plugins.in.LocationDialog
 
constructDialog() - Method in class loci.plugins.in.MainDialog
 
constructDialog() - Method in class loci.plugins.in.MemoryDialog
 
constructDialog() - Method in class loci.plugins.in.RangeDialog
 
constructDialog() - Method in class loci.plugins.in.SeriesDialog
 
constructDialog() - Method in class loci.plugins.in.SwapDialog
 
constructDialog() - Method in class loci.plugins.in.UpgradeDialog
 
constructImage(int, int, int, int, boolean, boolean, DataBuffer) - Static method in class loci.formats.gui.AWTImageTools
Creates an image with the given DataBuffer.
constructImage(int, int, int, int, boolean, boolean, DataBuffer, ColorModel) - Static method in class loci.formats.gui.AWTImageTools
Creates an image with the given DataBuffer.
constructImageTitle(IFormatReader, String, String, boolean) - Method in class loci.plugins.in.ImagePlusReader
 
constructLoader() - Static method in class loci.formats.gui.LegacyQTTools
 
constructSliceLabel(int, IFormatReader, IMetadata, int, int, int, int) - Method in class loci.plugins.in.ImagePlusReader
 
CONTAINER_TYPES - Static variable in class loci.formats.in.NativeQTReader
List of identifiers for each container atom.
ContainerRecord(String, int, long, int) - Constructor for class loci.formats.in.IM3Reader.ContainerRecord
 
contentFileType - Variable in class loci.formats.in.ZeissCZIReader.AttachmentEntry
 
contentGUID - Variable in class loci.formats.in.ZeissCZIReader.AttachmentEntry
 
Context() - Constructor for enum loci.formats.in.BaseZeissReader.Context
 
context - Variable in class loci.formats.in.BaseZeissReader.Tag
 
CONTRAST - Static variable in class loci.formats.in.CellSensReader
 
CONTRAST - Static variable in class loci.formats.tiff.IFD
 
CONTRAST_BRIGHTNESS - Static variable in class loci.formats.in.CellSensReader
 
CONTRAST_TARGET - Static variable in class loci.formats.in.CellSensReader
 
convert(String, String) - Static method in class loci.formats.FormatTools
Convenience method for converting the specified input file to the specified output file.
convert(IFormatReader, IFormatWriter, String) - Static method in class loci.formats.FormatTools
Convenience method for writing all of the images and metadata obtained from the specified IFormatReader into the specified IFormatWriter.
convert - Variable in class loci.formats.gui.DataConverter
 
convert12to16(byte[]) - Static method in class loci.formats.in.LiFlimReader
 
convertMetadata(MetadataRetrieve, MetadataStore) - Static method in class loci.formats.meta.MetadataConverter
Deprecated.
Copies information from a metadata retrieval object (source) into a metadata store (destination).
convertMetadata(String, MetadataStore) - Method in interface loci.formats.services.OMEXMLService
Converts information from an OME-XML string (source) into a metadata store (destination).
convertMetadata(MetadataRetrieve, MetadataStore) - Method in interface loci.formats.services.OMEXMLService
Copies information from a metadata retrieval object (source) into a metadata store (destination).
convertMetadata(String, MetadataStore) - Method in class loci.formats.services.OMEXMLServiceImpl
 
convertMetadata(MetadataRetrieve, MetadataStore) - Method in class loci.formats.services.OMEXMLServiceImpl
 
convertPixelType(int) - Method in class loci.formats.in.CellSensReader
 
convertPixelType(int) - Method in class loci.formats.in.JPEG2000MetadataParser
 
convertPixelType(CoreMetadata, int) - Method in class loci.formats.in.KLBReader
 
convertPixelType(int) - Method in class loci.formats.in.TillVisionReader
 
convertPixelType(int) - Method in class loci.formats.in.ZeissCZIReader
 
convertPixelType(CoreMetadata, int) - Method in class loci.formats.in.ZeissCZIReader
 
convertRenderedImage(RenderedImage) - Static method in class loci.formats.gui.AWTImageTools
Converts a java.awt.image.RenderedImage into a java.awt.image.BufferedImage.
convertTo8Bit(short[][]) - Method in class loci.plugins.util.ImageProcessorReader
 
convertToByte(boolean) - Method in class loci.plugins.util.RecordedImageProcessor
 
convertToFloat() - Method in class loci.plugins.util.RecordedImageProcessor
 
convertToRGB() - Method in class loci.plugins.util.RecordedImageProcessor
 
convertToShort(boolean) - Method in class loci.plugins.util.RecordedImageProcessor
 
convertUnits(String) - Method in class loci.formats.in.GatanReader
 
convertUnits(int) - Method in class loci.formats.in.IMODReader
 
convolve(float[], int, int) - Method in class loci.plugins.util.RecordedImageProcessor
 
convolve3x3(int[]) - Method in class loci.plugins.util.RecordedImageProcessor
 
COOKIE - Static variable in class loci.formats.in.IM3Reader
First 4 bytes of file is "1985"
COOLING_ON - Static variable in class loci.formats.in.CellSensReader
 
coordinate - Variable in class loci.formats.in.CellSensReader.TileCoordinate
 
Coordinate(int, int, int) - Constructor for class loci.formats.in.ZeissCZIReader.Coordinate
 
coordinates - Variable in class loci.formats.in.BaseZeissReader
 
copyBits(ImageProcessor, int, int, int) - Method in class loci.plugins.util.RecordedImageProcessor
 
copyOptions(CodecOptions, CodecOptions) - Static method in class loci.formats.codec.WrappedCodec
 
copyPixels(int, int, int, int, int, int, byte[], byte[], boolean) - Method in class loci.formats.in.NativeND2Reader
 
COPYRIGHT - Static variable in class loci.formats.tiff.IFD
 
copyScaled(BufferedImage, BufferedImage, Object) - Static method in class loci.formats.gui.AWTImageTools
Copies the source image into the target, applying scaling.
core - Variable in class loci.formats.DimensionSwapper
Core metadata associated with this dimension swapper.
core - Variable in class loci.formats.FileStitcher
Core metadata.
core - Variable in class loci.formats.FormatReader
Core metadata values.
core - Variable in class loci.formats.in.LeicaHandler
 
core - Variable in class loci.formats.in.ND2Handler
 
core - Variable in class loci.formats.in.VolocityReader.Stack
 
core - Variable in class loci.formats.SubResolutionFormatReader
List of CoreMetadata objects for each series and resolution.
coreIndex - Variable in class loci.formats.FileStitcher
The number of the current series.
coreIndex - Variable in class loci.formats.FormatReader
The number of the current series.
coreIndex - Variable in class loci.formats.in.ZeissCZIReader.SubBlock
 
coreIndexToSeries(int) - Method in class loci.formats.FileStitcher
 
coreIndexToSeries(int) - Method in class loci.formats.FormatReader
 
coreIndexToSeries(int) - Method in interface loci.formats.IFormatReader
Deprecated.
This method is no longer required for sub-resolution support.
coreIndexToSeries(int) - Method in class loci.formats.ImageReader
 
coreIndexToSeries(int) - Method in class loci.formats.ReaderWrapper
 
coreIndexToSeries(int) - Method in class loci.formats.SubResolutionFormatReader
 
coreIndexToSeries(int) - Method in class loci.formats.WrappedReader
 
CoreMetadata - Class in loci.formats
Encompasses core metadata values.
CoreMetadata() - Constructor for class loci.formats.CoreMetadata
 
CoreMetadata(IFormatReader, int) - Constructor for class loci.formats.CoreMetadata
 
CoreMetadata(CoreMetadata) - Constructor for class loci.formats.CoreMetadata
 
coreMetaData - Static variable in class loci.formats.in.SPEReader
 
CoreMetadataList - Class in loci.formats
 
CoreMetadataList() - Constructor for class loci.formats.CoreMetadataList
 
CoreMetadataList(CoreMetadataList) - Constructor for class loci.formats.CoreMetadataList
 
CoreMetadataList(int) - Constructor for class loci.formats.CoreMetadataList
Construct a list containing a specified number of primary elements.
CoreMetadataList(int, int) - Constructor for class loci.formats.CoreMetadataList
Construct a list containing a specified number of primary elements and a fixed number of secondary elements.
CoreMetadataList(int[]) - Constructor for class loci.formats.CoreMetadataList
Construct a list containing a specified number of primary and secondary elements.
CoreMetadataList(List<CoreMetadata>) - Constructor for class loci.formats.CoreMetadataList
 
correction - Variable in class loci.formats.in.ND2Handler
 
correction - Variable in class loci.formats.in.NikonTiffReader
 
correction - Variable in class loci.formats.in.ZeissLSMReader.Recording
 
correctionCollar - Variable in class loci.formats.in.ZeissCZIReader
 
correctionFile - Variable in class loci.formats.in.CV7000Reader.Channel
 
corrections - Variable in class loci.formats.in.LIFReader
 
correctUnits(Double, String) - Method in class loci.formats.in.ColumbusReader
 
cortime - Variable in class loci.formats.in.SDTInfo
Correlation time [ms].
count - Variable in class loci.formats.in.LeicaHandler
 
count() - Method in class loci.formats.in.LeicaSCNReader.LeicaSCNHandler
 
count - Variable in class loci.formats.in.ZeissTIFFHandler.TagSet
 
COUNTER_CLOCKWISE - Static variable in class loci.formats.in.FluoviewReader
 
countImages() - Method in class loci.formats.in.BaseZeissReader
 
countImages() - Method in class loci.formats.in.ZeissTIFFReader
 
countImages() - Method in class loci.formats.in.ZeissZVIReader
 
crc(byte[]) - Method in class loci.formats.out.APNGWriter
 
crc(byte[], int, int) - Method in class loci.formats.out.APNGWriter
 
createAngle(Double, Unit<Angle>) - Static method in class loci.formats.FormatTools
 
createAngle(Integer, Unit<Angle>) - Static method in class loci.formats.FormatTools
 
createAngle(T, Unit<Angle>) - Static method in class loci.formats.FormatTools
 
createBaseReader() - Method in class loci.plugins.in.ImportProcess
Initializes an IFormatReader according to the current configuration.
createChannelPriorities() - Static method in class loci.formats.in.LIFReader
 
createCodec(boolean) - Method in class loci.formats.in.NativeND2Reader
 
createColorModel() - Method in class loci.plugins.util.ImageProcessorReader
 
createCompatibleWritableRaster(int, int) - Method in class loci.formats.gui.Index16ColorModel
 
createCompatibleWritableRaster(int, int) - Method in class loci.formats.gui.SignedColorModel
 
createCompatibleWritableRaster(int, int) - Method in class loci.formats.gui.UnsignedIntColorModel
 
created - Variable in class loci.formats.out.QTWriter
Time the file was created.
createElectricPotential(Double, Unit<ElectricPotential>) - Static method in class loci.formats.FormatTools
 
createElectricPotential(Integer, Unit<ElectricPotential>) - Static method in class loci.formats.FormatTools
 
createElectricPotential(T, Unit<ElectricPotential>) - Static method in class loci.formats.FormatTools
 
createFileInfo() - Method in class loci.plugins.in.ImagePlusReader
 
createFrequency(Double, Unit<Frequency>) - Static method in class loci.formats.FormatTools
 
createFrequency(Integer, Unit<Frequency>) - Static method in class loci.formats.FormatTools
 
createFrequency(T, Unit<Frequency>) - Static method in class loci.formats.FormatTools
 
createGroup(String) - Method in interface loci.formats.services.JHDFService
Writes an array as sub-slice into an existing HDF5 dataset
createGroup(String) - Method in class loci.formats.services.JHDFServiceImpl
 
createImage(String, List<ImageProcessor>) - Static method in class loci.plugins.in.ImagePlusReader
Creates an ImagePlus from the given image processors.
createImage(String, ImageStack, List<LUT>) - Static method in class loci.plugins.in.ImagePlusReader
Creates an ImagePlus from the given image stack.
createImage() - Method in class loci.plugins.util.RecordedImageProcessor
 
createIndexMap(int) - Method in class loci.formats.in.FakeReader
Creates a mapping between indices and color values.
createInputStream() - Method in class loci.formats.out.TiffWriter
 
createKeys() - Static method in class loci.formats.in.ZeissLSMReader
 
createLength(Double, Unit<Length>) - Static method in class loci.formats.FormatTools
 
createLength(Integer, Unit<Length>) - Static method in class loci.formats.FormatTools
 
createLength(T, Unit<Length>) - Static method in class loci.formats.FormatTools
 
createLSID(String, int...) - Static method in class loci.formats.MetadataTools
Constructs an LSID, given the object type and indices.
createMetadata(String, CoreMetadata) - Method in class loci.formats.tools.MakeTestOmeTiff
 
createModulo(OMEXMLMetadata, Modulo, StructuredAnnotations, Image, int, int, int) - Method in class loci.formats.services.OMEXMLServiceImpl
Create a ModuloAlong* annotation corresponding to the given Modulo.
createOMEXMLMetadata() - Static method in class loci.formats.MetadataTools
Creates an OME-XML metadata object using reflection, to avoid direct dependencies on the optional loci.formats.ome package.
createOMEXMLMetadata() - Method in interface loci.formats.services.OMEXMLService
Creates an OME-XML metadata object using reflection, to avoid direct dependencies on the optional loci.formats.ome package.
createOMEXMLMetadata(String) - Method in interface loci.formats.services.OMEXMLService
Creates an OME-XML metadata object using reflection, to avoid direct dependencies on the optional loci.formats.ome package, wrapping a DOM representation of the given OME-XML string.
createOMEXMLMetadata(String, String) - Method in interface loci.formats.services.OMEXMLService
Creates an OME-XML metadata object using reflection, to avoid direct dependencies on the optional loci.formats.ome package, wrapping a DOM representation of the given OME-XML string.
createOMEXMLMetadata() - Method in class loci.formats.services.OMEXMLServiceImpl
 
createOMEXMLMetadata(String) - Method in class loci.formats.services.OMEXMLServiceImpl
 
createOMEXMLMetadata(String, String) - Method in class loci.formats.services.OMEXMLServiceImpl
 
createOMEXMLRoot(String) - Method in interface loci.formats.services.OMEXMLService
Constructs an OME root node.
createOMEXMLRoot(String) - Method in class loci.formats.services.OMEXMLServiceImpl
 
createOutputStream() - Method in class loci.formats.FormatWriter
Create an output stream for the current file path.
createPlane(String, CoreMetadata, int) - Method in class loci.formats.tools.MakeTestOmeTiff
 
createPower(Double, Unit<Power>) - Static method in class loci.formats.FormatTools
 
createPower(Integer, Unit<Power>) - Static method in class loci.formats.FormatTools
 
createPower(T, Unit<Power>) - Static method in class loci.formats.FormatTools
 
createPressure(Double, Unit<Pressure>) - Static method in class loci.formats.FormatTools
 
createPressure(Integer, Unit<Pressure>) - Static method in class loci.formats.FormatTools
 
createPressure(T, Unit<Pressure>) - Static method in class loci.formats.FormatTools
 
createProcessor(int, int) - Method in class loci.plugins.util.RecordedImageProcessor
 
createROI(MetadataStore, int) - Method in class loci.formats.in.GatanReader
Create an empty ROI and link it to the Image.
createRoot(String) - Method in class loci.formats.services.OMEXMLServiceImpl
Constructs an OME root node.
createStack(List<ImageProcessor>, List<String>, List<LUT>) - Static method in class loci.plugins.in.ImagePlusReader
Creates an image stack from the given image processors.
createSwatch(Color) - Method in class loci.plugins.in.ColorDialog
 
createTemperature(Double, Unit<Temperature>) - Static method in class loci.formats.FormatTools
 
createTemperature(Integer, Unit<Temperature>) - Static method in class loci.formats.FormatTools
 
createTemperature(T, Unit<Temperature>) - Static method in class loci.formats.FormatTools
 
createTiffSaver() - Method in class loci.formats.out.TiffWriter
 
createTime(Double, Unit<Time>) - Static method in class loci.formats.FormatTools
 
createTime(Integer, Unit<Time>) - Static method in class loci.formats.FormatTools
 
createTime(T, Unit<Time>) - Static method in class loci.formats.FormatTools
 
createVirtualStack(ImportProcess, int, List<LUT>) - Method in class loci.plugins.in.ImagePlusReader
 
createWriter(String, CoreMetadata, String) - Method in class loci.formats.tools.MakeTestOmeTiff
 
CREATION_TIME - Static variable in class loci.formats.in.CellSensReader
 
creationDate - Variable in class loci.formats.in.FV1000Reader
 
creationDate - Variable in class loci.formats.in.ImaconReader
 
creationDate - Variable in class loci.formats.in.InCellReader
 
creationDate - Variable in class loci.formats.in.IvisionReader
 
creationDate - Variable in class loci.formats.in.LeicaSCNReader.Image
 
creationDate - Variable in class loci.formats.in.PCIReader
 
CREATOR - Static variable in class loci.formats.FormatTools
Value to use when setting creator/software fields in exported files.
CREATOR_TAG - Static variable in class loci.formats.in.ImaconReader
 
crop() - Method in class loci.plugins.util.RecordedImageProcessor
 
cropBox - Variable in class loci.plugins.in.MainDialog
 
CropDialog - Class in loci.plugins.in
Bio-Formats Importer crop options dialog box.
CropDialog(ImportProcess) - Constructor for class loci.plugins.in.CropDialog
Creates a crop options dialog for the Bio-Formats Importer.
cropRegion - Variable in class loci.plugins.in.ImporterOptions
 
crossChan - Variable in class loci.formats.in.SDTInfo
Cross FCS routing channel number when chan = crossChan and mod == crossMod - Auto FCS otherwise - Cross FCS.
CrosshairStrategy - Class in loci.formats.cache
A crosshair strategy caches planes extending from the the current dimensional position along each individual axis, but not combinations of axes.
CrosshairStrategy(int[]) - Constructor for class loci.formats.cache.CrosshairStrategy
Constructs a crosshair strategy.
crossMod - Variable in class loci.formats.in.SDTInfo
Cross FCS module number.
crossMtResol - Variable in class loci.formats.in.SDTInfo
Macro time clock of cross FCS module in 0.1 ns units.
CS - Static variable in class loci.formats.in.DicomReader
 
CS_2C - Static variable in class loci.formats.gui.TwoChannelColorSpace
 
cScroll - Variable in class loci.plugins.util.DataBrowser
 
cSlider - Variable in class loci.formats.gui.ImageViewer
 
cSliders - Variable in class loci.plugins.util.DataBrowser
 
cStep - Variable in class loci.plugins.in.ImporterOptions
 
CSV_SUFFIX - Static variable in class loci.formats.in.PerkinElmerReader
 
curCycle - Variable in class loci.formats.in.SDTInfo
Current cycle (accumulation cycle in FLOW mode) - (if multi-cycle measurement).
curPage - Variable in class loci.formats.in.SDTInfo
Current measured page.
current - Variable in class loci.formats.ImageReader
Current form index.
current - Variable in class loci.formats.ImageWriter
Current form index.
current_layer - Variable in class loci.formats.in.ZeissTIFFHandler
 
current_scaling - Variable in class loci.formats.in.ZeissTIFFHandler
 
current_shape - Variable in class loci.formats.in.ZeissTIFFHandler
 
current_tag - Variable in class loci.formats.in.ZeissTIFFHandler
 
current_tagset - Variable in class loci.formats.in.ZeissTIFFHandler
 
currentBlock - Variable in class loci.formats.in.APNGReader.PNGInputStream
 
currentBlock - Variable in class loci.formats.in.PQBinReader
Block of time bins currently stored for faster loading.
currentBlock - Variable in class loci.formats.in.SDTReader
Block of time bins currently stored for faster loading.
currentChannel - Variable in class loci.formats.in.CV7000Reader.MeasurementSettingsHandler
 
currentChunk - Variable in class loci.formats.in.OBFReader.State
 
currentCol - Variable in class loci.formats.in.InCellReader.InCellHandler
 
currentElement - Variable in class loci.formats.in.AFIReader.AFIHandler
 
currentElement - Variable in class loci.formats.in.IvisionReader.IvisionHandler
 
currentField - Variable in class loci.formats.in.CV7000Reader.MeasurementDataHandler
 
currentField - Variable in class loci.formats.in.InCellReader.InCellHandler
 
currentFile - Variable in class loci.formats.services.JHDFServiceImpl
 
currentFile - Variable in class loci.formats.services.NetCDFServiceImpl
 
currentFragment - Variable in class loci.formats.out.OMEXMLWriter
 
currentFrame - Variable in class loci.formats.in.SPCReader
 
currentIcsId - Variable in class loci.formats.in.ICSReader
Current filename.
currentId - Variable in class loci.formats.FormatHandler
Name of current file.
currentId - Variable in class loci.formats.ImageReader
Name of current file.
currentId - Variable in class loci.formats.ImageWriter
Name of current file.
currentIdsId - Variable in class loci.formats.in.ICSReader
 
currentImage - Variable in class loci.formats.in.InCellReader.InCellHandler
 
currentImage - Variable in class loci.formats.in.LeicaSCNReader.LeicaSCNHandler
 
currentImageFile - Variable in class loci.formats.in.InCellReader.MinimalInCellHandler
 
currentLine - Variable in class loci.formats.in.SPCReader
 
currentName - Variable in class loci.formats.in.ColumbusReader.MeasurementHandler
 
currentName - Variable in class loci.formats.in.OperettaReader.OperettaHandler
 
currentNo - Variable in class loci.formats.in.AmiraReader.HxRLE
 
currentNo - Variable in class loci.formats.in.AmiraReader.HxZip
 
currentPixel - Variable in class loci.formats.in.SPCReader
 
currentPlane - Variable in class loci.formats.in.InCellReader.InCellHandler
 
currentPlane - Variable in class loci.formats.in.ZeissZVIReader
 
currentPlaneIndex - Variable in class loci.formats.in.ZeissZVIReader
 
currentPos - Variable in class loci.formats.cache.Cache
Current dimensional position.
currentProcessor - Variable in class loci.plugins.util.BFVirtualStack
 
currentQName - Variable in class loci.formats.in.BDVReader.BDVXMLHandler
 
currentQName - Variable in class loci.formats.in.InCellReader.InCellHandler
 
currentQName - Variable in class loci.formats.in.OMEXMLReader.OMEXMLHandler
 
currentRow - Variable in class loci.formats.in.InCellReader.InCellHandler
 
currentSetupIndex - Variable in class loci.formats.in.BDVReader.BDVXMLHandler
 
currentSlice - Variable in class loci.plugins.util.BFVirtualStack
 
currentThumbnail - Variable in class loci.formats.in.InCellReader.MinimalInCellHandler
 
currentValue - Variable in class loci.formats.in.ColumbusReader.MeasurementHandler
 
currentValue - Variable in class loci.formats.in.CV7000Reader.MeasurementDataHandler
 
currentValue - Variable in class loci.formats.in.CV7000Reader.MeasurementSettingsHandler
 
currentValue - Variable in class loci.formats.in.OperettaReader.OperettaHandler
 
currentValue - Variable in class loci.formats.in.ScanrReader.ScanrHandler
 
curStep - Variable in class loci.formats.in.SDTInfo
Current step (if multi-step measurement).
curve - Variable in class loci.formats.codec.NikonCodecOptions
 
CURVE - Static variable in class loci.formats.in.NikonReader
 
curve - Variable in class loci.formats.in.NikonReader
 
CUSTOM_BITS - Static variable in class loci.formats.in.SimplePCITiffReader
 
CUSTOM_GRAYSCALE - Static variable in class loci.formats.in.CellSensReader
 
CUSTOM_RENDERED - Static variable in class loci.formats.tiff.IFD
 
customColors - Variable in class loci.plugins.in.ImporterOptions
 
customFilter(ShortBuffer, Rectangle, Rectangle, int, int, TJTransform) - Method in interface org.libjpegturbo.turbojpeg.TJCustomFilter
A callback function that can be used to modify the DCT coefficients after they are losslessly transformed but before they are transcoded to a new JPEG file.
cutIn - Variable in class loci.formats.in.LeicaHandler.MultiBand
 
cutInPopulated - Variable in class loci.formats.in.LeicaReader
 
cutIns - Variable in class loci.formats.in.LIFReader
 
cutOut - Variable in class loci.formats.in.LeicaHandler.MultiBand
 
cutOutPopulated - Variable in class loci.formats.in.LeicaReader
 
cutOuts - Variable in class loci.formats.in.LIFReader
 
CV7000Reader - Class in loci.formats.in
 
CV7000Reader() - Constructor for class loci.formats.in.CV7000Reader
Constructs a new Yokogawa CV7000 reader.
CV7000Reader.Channel - Class in loci.formats.in
 
CV7000Reader.LightSource - Class in loci.formats.in
 
CV7000Reader.MeasurementDataHandler - Class in loci.formats.in
 
CV7000Reader.MeasurementDetailHandler - Class in loci.formats.in
 
CV7000Reader.MeasurementSettingsHandler - Class in loci.formats.in
 
CV7000Reader.MinMax - Class in loci.formats.in
 
CV7000Reader.Plane - Class in loci.formats.in
 
CV7000Reader.WPIHandler - Class in loci.formats.in
 
cycle - Variable in class loci.formats.in.PrairieMetadata.Sequence
cycle of this <Sequence>.
cycleMax - Variable in class loci.formats.in.PrairieMetadata
Maximum cycle value.
cycleMin - Variable in class loci.formats.in.PrairieMetadata
Minimum cycle value.
cycles - Variable in class loci.formats.in.SDTInfo
Cycles (accumulation cycles in FLOW mode).
CYTELL_MAGIC_STRING - Static variable in class loci.formats.in.InCellReader
 
CZI_MAGIC_STRING - Static variable in class loci.formats.in.ZeissCZIReader
 

D

d(String) - Method in class loci.formats.in.PrairieMetadata
Converts the given string to a Double, or null if incompatible.
DA - Static variable in class loci.formats.in.DicomReader
 
DAILY - Static variable in class loci.plugins.Updater
 
DAILY_BUILD - Static variable in class loci.formats.UpgradeChecker
Location of the JAR artifacts for Bio-Formats' daily build.
DarkImage - Variable in class loci.formats.in.LiFlimReader
 
DarkImage_KEY - Static variable in class loci.formats.in.LiFlimReader
 
data - Variable in class loci.formats.in.ICSReader
Image data.
data - Variable in class loci.formats.in.IM3Reader
 
data - Variable in class loci.formats.in.TextReader
Because we have no way of indexing into the text file efficiently in general, we cheat and store the entire file's data in a giant array.
data - Variable in class loci.formats.MetadataList
 
DATA_CHANNEL_ACQUIRE - Static variable in class loci.formats.in.ZeissLSMReader
 
DATA_CHANNEL_NAME - Static variable in class loci.formats.in.ZeissLSMReader
 
DATA_DIR - Static variable in class loci.formats.in.VolocityReader
 
DATA_IDENTIFIER - Static variable in class loci.formats.in.SDTInfo
For normal .sdt files (setup + data).
DATA_SIGNATURE - Static variable in class loci.formats.out.AVIWriter
 
dataBlockLength - Variable in class loci.formats.in.SDTInfo
 
dataBlockOffs - Variable in class loci.formats.in.SDTInfo
Offset of the first data block.
DataBrowser - Class in loci.plugins.util
Extension of StackWindow with additional UI trimmings for animation, virtual stack caching options, metadata, and general beautification.
DataBrowser(ImagePlus) - Constructor for class loci.plugins.util.DataBrowser
 
DataBrowser(ImagePlus, ImageCanvas, String[], int[]) - Constructor for class loci.plugins.util.DataBrowser
 
DataBrowser(ImagePlus, ImageCanvas, String[], int[], XMLWindow) - Constructor for class loci.plugins.util.DataBrowser
 
DataChannel() - Constructor for class loci.formats.in.ZeissLSMReader.DataChannel
 
DataConverter - Class in loci.formats.gui
A utility for reorganizing and converting QuickTime movies, TIFF series and other 4D datasets.
DataConverter() - Constructor for class loci.formats.gui.DataConverter
 
DataConverter.RowPanel - Class in loci.formats.gui
 
dataFile - Variable in class loci.formats.in.NRRDReader
Name of data file, if the current extension is 'nhdr'.
dataId - Variable in class loci.formats.in.OIRReader.Laser
 
dataOffs - Variable in class loci.formats.in.SDTInfo
Offset of the data block from the beginning of the file.
dataOffset - Variable in class loci.formats.in.LiFlimReader
Offset to start of pixel data.
dataOffset - Variable in class loci.formats.in.ZeissCZIReader.Attachment
 
dataOffset - Variable in class loci.formats.in.ZeissCZIReader.SubBlock
 
dataPointers - Variable in class loci.formats.in.InveonReader
 
datasetDescription - Variable in class loci.formats.FormatReader
Short description of the structure of the dataset.
dataSets - Variable in class loci.formats.in.IM3Reader
 
dataSize - Variable in class loci.formats.in.MRWReader
 
dataSize - Variable in class loci.formats.in.ZeissCZIReader.Attachment
 
dataSize - Variable in class loci.formats.in.ZeissCZIReader.SubBlock
 
dataStore - Variable in class loci.formats.in.PQBinReader
 
dataStore - Variable in class loci.formats.in.SDTReader
 
datatype - Variable in class loci.formats.in.LiFlimReader
 
DATATYPE_INT16 - Static variable in class loci.formats.in.LiFlimReader
 
DATATYPE_INT32 - Static variable in class loci.formats.in.LiFlimReader
 
DATATYPE_INT8 - Static variable in class loci.formats.in.LiFlimReader
 
DATATYPE_KEY - Static variable in class loci.formats.in.LiFlimReader
 
DATATYPE_REAL32 - Static variable in class loci.formats.in.LiFlimReader
 
DATATYPE_REAL64 - Static variable in class loci.formats.in.LiFlimReader
 
DATATYPE_UINT12 - Static variable in class loci.formats.in.LiFlimReader
 
DATATYPE_UINT16 - Static variable in class loci.formats.in.LiFlimReader
 
DATATYPE_UINT32 - Static variable in class loci.formats.in.LiFlimReader
 
DATATYPE_UINT8 - Static variable in class loci.formats.in.LiFlimReader
 
DATE - Static variable in class loci.formats.FormatTools
Date on which this release was built.
DATE - Static variable in class loci.formats.in.CellSensReader
 
date - Variable in class loci.formats.in.DicomReader
 
date - Variable in class loci.formats.in.FEITiffReader
 
date - Variable in class loci.formats.in.FluoviewReader
 
date - Variable in class loci.formats.in.LEOReader
 
date - Variable in class loci.formats.in.MetamorphHandler
 
date - Variable in class loci.formats.in.MicroCTReader
 
date - Variable in class loci.formats.in.ND2Handler
 
date - Variable in class loci.formats.in.PrairieMetadata
The date of the acquisition.
date - Variable in class loci.formats.in.QuesantReader
 
date - Variable in class loci.formats.in.SDTInfo
Date of creation.
date - Variable in class loci.formats.in.SimplePCITiffReader
 
date - Variable in class loci.formats.in.SVSReader
 
DATE_FORMAT - Static variable in class loci.formats.in.BrukerReader
 
DATE_FORMAT - Static variable in class loci.formats.in.CellWorxReader
 
DATE_FORMAT - Static variable in class loci.formats.in.DeltavisionReader
Deprecated.
DATE_FORMAT - Static variable in class loci.formats.in.FEITiffReader
 
DATE_FORMAT - Static variable in class loci.formats.in.FluoviewReader
Date format
DATE_FORMAT - Static variable in class loci.formats.in.FujiReader
 
DATE_FORMAT - Static variable in class loci.formats.in.FV1000Reader
 
DATE_FORMAT - Static variable in class loci.formats.in.GelReader
 
DATE_FORMAT - Static variable in class loci.formats.in.HitachiReader
 
DATE_FORMAT - Static variable in class loci.formats.in.IvisionReader
 
DATE_FORMAT - Static variable in class loci.formats.in.KodakReader
 
DATE_FORMAT - Static variable in class loci.formats.in.L2DReader
 
DATE_FORMAT - Static variable in class loci.formats.in.LeicaReader
Format for dates.
DATE_FORMAT - Static variable in class loci.formats.in.MetamorphTiffReader
 
DATE_FORMAT - Static variable in class loci.formats.in.MicroCTReader
 
DATE_FORMAT - Static variable in class loci.formats.in.MicromanagerReader
 
DATE_FORMAT - Static variable in class loci.formats.in.MolecularImagingReader
 
DATE_FORMAT - Static variable in class loci.formats.in.ND2Handler
 
DATE_FORMAT - Static variable in class loci.formats.in.PDSReader
 
DATE_FORMAT - Static variable in class loci.formats.in.PerkinElmerReader
 
DATE_FORMAT - Static variable in class loci.formats.in.PrairieReader
 
DATE_FORMAT - Static variable in class loci.formats.in.SBIGReader
 
DATE_FORMAT - Static variable in class loci.formats.in.SimplePCITiffReader
 
DATE_FORMAT - Static variable in class loci.formats.in.SpiderReader
 
DATE_FORMAT - Static variable in class loci.formats.in.SVSReader
 
DATE_FORMAT - Static variable in class loci.formats.in.TCSReader
 
DATE_FORMATS - Static variable in class loci.formats.in.BaseTiffReader
 
DATE_FORMATS - Static variable in class loci.formats.in.DeltavisionReader
 
DATE_FORMATS - Static variable in class loci.formats.in.ICSReader
 
DATE_FORMATS - Static variable in class loci.formats.in.LEOReader
 
DATE_FORMATS - Static variable in class loci.formats.in.TillVisionReader
 
DATE_TIME - Static variable in class loci.formats.tiff.IFD
 
DATE_TIME_DIGITIZED - Static variable in class loci.formats.tiff.IFD
 
DATE_TIME_FORMAT - Static variable in class loci.formats.in.GelReader
 
DATE_TIME_ORIGINAL - Static variable in class loci.formats.tiff.IFD
 
dates - Variable in class loci.formats.in.TillVisionReader
 
datestamp - Variable in class loci.formats.in.TCSReader
 
datFile - Variable in class loci.formats.in.InveonReader
 
datFile - Variable in class loci.formats.in.UnisokuReader
 
dBlock - Variable in class loci.formats.in.GIFReader
Current data block.
deadTimeComp - Variable in class loci.formats.in.SDTInfo
 
debug(String) - Static method in class loci.plugins.BF
 
decode(APNGReader.PNGInputStream) - Method in class loci.formats.in.APNGReader
 
decode(APNGReader.PNGInputStream, int, int) - Method in class loci.formats.in.APNGReader
 
decode12BitCamera(byte[], int) - Method in class loci.formats.in.ZeissCZIReader
 
decodeDate(int) - Static method in class loci.formats.in.MetamorphReader
Converts a Julian date value into a human-readable string.
decodeImageData() - Method in class loci.formats.in.GIFReader
Decodes LZW image data into a pixel array.
decoder - Variable in class loci.formats.codec.JPEGTileDecoder
 
decodeTile(int, int, int) - Method in class loci.formats.in.CellSensReader
 
decodeTime(int) - Static method in class loci.formats.in.MetamorphReader
Converts a time value in milliseconds into a human-readable string.
decodeToMemoryGray16(short[], int, int, int, int, int, int, int, int, int, int) - Method in interface loci.formats.services.LuraWaveService
Wraps lwfDecoder.decodeToMemoryGray16(short[], int, int, int, int, int, int, int, int, int, int).
decodeToMemoryGray16(short[], int, int, int, int, int, int, int, int, int, int) - Method in class loci.formats.services.LuraWaveServiceImpl
 
decodeToMemoryGray8(byte[], int, int, int) - Method in interface loci.formats.services.LuraWaveService
Wraps lwfDecoder.decodeToMemoryGray8(byte[], int, int, int).
decodeToMemoryGray8(byte[], int, int, int) - Method in class loci.formats.services.LuraWaveServiceImpl
 
decompress(byte[]) - Method in class loci.formats.codec.BaseCodec
 
decompress(byte[][]) - Method in class loci.formats.codec.BaseCodec
 
decompress(byte[], CodecOptions) - Method in class loci.formats.codec.BaseCodec
 
decompress(RandomAccessInputStream, CodecOptions) - Method in class loci.formats.codec.BaseCodec
 
decompress(byte[][], CodecOptions) - Method in class loci.formats.codec.BaseCodec
2D data block decoding default implementation.
decompress(byte[], CodecOptions) - Method in interface loci.formats.codec.Codec
Decompresses a block of data.
decompress(byte[][], CodecOptions) - Method in interface loci.formats.codec.Codec
Decompresses a block of data.
decompress(byte[]) - Method in interface loci.formats.codec.Codec
Decompresses a block of data.
decompress(byte[][]) - Method in interface loci.formats.codec.Codec
Decompresses a block of data.
decompress(RandomAccessInputStream, CodecOptions) - Method in interface loci.formats.codec.Codec
Decompresses data from the given RandomAccessInputStream.
decompress(RandomAccessInputStream, CodecOptions) - Method in class loci.formats.codec.JPEGXRCodec
 
decompress(byte[], CodecOptions) - Method in class loci.formats.codec.JPEGXRCodec
The CodecOptions parameter should have the following fields set: maxBytes interleaved bitsPerSample littleEndian width height
decompress(RandomAccessInputStream, CodecOptions) - Method in class loci.formats.codec.NikonCodec
The CodecOptions parameter must be an instance of NikonCodecOptions, and should have the following fields set: lossless vPredictor curve split bitsPerSample maxBytes width height
decompress(RandomAccessInputStream, CodecOptions) - Method in class loci.formats.codec.TargaRLECodec
The CodecOptions parameter should have the following fields set: maxBytes CodecOptions.bitsPerSample
decompress(byte[], CodecOptions) - Method in class loci.formats.codec.WrappedCodec
 
decompress(byte[][], CodecOptions) - Method in class loci.formats.codec.WrappedCodec
 
decompress(byte[]) - Method in class loci.formats.codec.WrappedCodec
 
decompress(byte[][]) - Method in class loci.formats.codec.WrappedCodec
 
decompress(RandomAccessInputStream, CodecOptions) - Method in class loci.formats.codec.WrappedCodec
 
decompress(byte[]) - Method in interface loci.formats.services.JPEGXRService
Decompress the given JPEG-XR compressed byte array and return as a byte array.
decompress(byte[]) - Method in class loci.formats.services.JPEGXRServiceImpl
 
decompress(byte[], CodecOptions) - Method in enum loci.formats.tiff.TiffCompression
Decodes a strip of data.
decompress(byte[], int, int, int, int, int) - Method in class org.libjpegturbo.turbojpeg.TJDecompressor
Decompress the JPEG source image associated with this decompressor instance and output a decompressed image to the given destination buffer.
decompress(int, int, int, int, int) - Method in class org.libjpegturbo.turbojpeg.TJDecompressor
Decompress the JPEG source image associated with this decompressor instance and return a buffer containing the decompressed image.
decompress(BufferedImage, int) - Method in class org.libjpegturbo.turbojpeg.TJDecompressor
Decompress the JPEG source image associated with this decompressor instance and output a decompressed image to the given BufferedImage instance.
decompress(int, int, int, int) - Method in class org.libjpegturbo.turbojpeg.TJDecompressor
Decompress the JPEG source image associated with this decompressor instance and return a BufferedImage instance containing the decompressed image.
decompress(byte[], int, byte[], int, int, int, int, int) - Method in class org.libjpegturbo.turbojpeg.TJDecompressor
 
decompress(byte[], int, int[], int, int, int, int, int) - Method in class org.libjpegturbo.turbojpeg.TJDecompressor
 
decompressHeader(byte[], int) - Method in class org.libjpegturbo.turbojpeg.TJDecompressor
 
decompressor - Variable in class loci.formats.in.AmiraReader.HxZip
 
decompressToYUV(byte[], int) - Method in class org.libjpegturbo.turbojpeg.TJDecompressor
Decompress the JPEG source image associated with this decompressor instance and output a YUV planar image to the given destination buffer.
decompressToYUV(int) - Method in class org.libjpegturbo.turbojpeg.TJDecompressor
Decompress the JPEG source image associated with this decompressor instance and return a buffer containing a YUV planar image.
decompressToYUV(byte[], int, byte[], int) - Method in class org.libjpegturbo.turbojpeg.TJDecompressor
 
deconvolutionLogFile - Variable in class loci.formats.in.DeltavisionReader
 
DEEP_GREY_10 - Static variable in class loci.formats.in.OpenlabReader
 
DEEP_GREY_11 - Static variable in class loci.formats.in.OpenlabReader
 
DEEP_GREY_12 - Static variable in class loci.formats.in.OpenlabReader
 
DEEP_GREY_13 - Static variable in class loci.formats.in.OpenlabReader
 
DEEP_GREY_14 - Static variable in class loci.formats.in.OpenlabReader
 
DEEP_GREY_15 - Static variable in class loci.formats.in.OpenlabReader
 
DEEP_GREY_16 - Static variable in class loci.formats.in.OpenlabReader
 
DEEP_GREY_9 - Static variable in class loci.formats.in.OpenlabReader
 
DEFAULT_BACKGROUND_COLOR - Static variable in class loci.formats.in.CellSensReader
 
DEFAULT_CALLER - Static variable in class loci.formats.UpgradeChecker
Value of "bioformats.caller" for Bio-Formats utilities.
DEFAULT_COLORS - Static variable in class loci.plugins.in.ImporterOptions
Default custom colors for each channel.
DEFAULT_DIMENSION_ORDER - Static variable in class loci.formats.in.FakeReader
 
DEFAULT_GAMMA - Static variable in class loci.formats.in.NDPIReader
 
DEFAULT_IMAGE - Static variable in class loci.formats.in.CellSensReader
 
DEFAULT_LINEARIZATION_TABLE - Static variable in class loci.formats.codec.NikonCodec
 
DEFAULT_MINIMUM_ELAPSED - Static variable in class loci.formats.Memoizer
Default value for Memoizer.minimumElapsed if none is provided in the constructor.
DEFAULT_PIXEL_TYPE - Static variable in class loci.formats.in.FakeReader
 
DEFAULT_RANGE - Static variable in class loci.formats.cache.CacheStrategy
Default cache range.
DEFAULT_RESOLUTION_SCALE - Static variable in class loci.formats.in.FakeReader
 
DEFAULT_RGB_CHANNEL_COUNT - Static variable in class loci.formats.in.FakeReader
 
DEFAULT_SAMPLE_IFD - Static variable in class loci.formats.in.CellSensReader
 
DEFAULT_SERIES - Static variable in class loci.formats.in.KLBReader
 
DEFAULT_SIZE_C - Static variable in class loci.formats.in.FakeReader
 
DEFAULT_SIZE_T - Static variable in class loci.formats.in.FakeReader
 
DEFAULT_SIZE_X - Static variable in class loci.formats.in.FakeReader
 
DEFAULT_SIZE_Y - Static variable in class loci.formats.in.FakeReader
 
DEFAULT_SIZE_Z - Static variable in class loci.formats.in.FakeReader
 
defaultClasses - Static variable in class loci.formats.ImageReader
Default list of reader classes, for use with noargs constructor.
defaultClasses - Static variable in class loci.formats.ImageWriter
Default list of writer classes, for use with noargs constructor.
defaultDateEnabled - Static variable in class loci.formats.MetadataTools
 
defaultExposureTime - Variable in class loci.formats.in.CellSensReader.Pyramid
 
DefaultJPEGReader() - Constructor for class loci.formats.in.JPEGReader.DefaultJPEGReader
 
DefaultMetadataOptions - Class in loci.formats.in
Default implementation of MetadataOptions.
DefaultMetadataOptions() - Constructor for class loci.formats.in.DefaultMetadataOptions
Construct a new DefaultMetadataOptions.
DefaultMetadataOptions(MetadataLevel) - Constructor for class loci.formats.in.DefaultMetadataOptions
Construct a new DefaultMetadataOptions.
defaultMinMax(int) - Static method in class loci.formats.FormatTools
Get the default range for the specified pixel type.
defaultValue - Variable in class loci.plugins.prefs.BooleanOption
The option's default value.
defaultValue - Variable in class loci.plugins.prefs.DoubleOption
The option's default value.
defaultValue - Variable in class loci.plugins.prefs.StringOption
The option's default value.
defaultXMLSkip - Variable in class loci.formats.in.OIRReader
 
DEFINITION - Static variable in class loci.formats.in.BDVReader.H5Constants
 
DEFINITION - Static variable in class loci.formats.in.CellH5Reader.CellH5Constants
 
delegate - Variable in class loci.formats.in.SimplePCITiffReader
 
delegate - Variable in class loci.formats.services.LuraWaveServiceImpl
LuraWave decoder delegate.
DelegateReader - Class in loci.formats
DelegateReader is a file format reader that selects which reader to use for a format if there are two readers which handle the same format.
DelegateReader(String, String) - Constructor for class loci.formats.DelegateReader
Constructs a new delegate reader.
DelegateReader(String, String[]) - Constructor for class loci.formats.DelegateReader
Constructs a new delegate reader.
deleteQuietly(File) - Method in class loci.formats.Memoizer
Attempts to delete an existing file, logging at warn if the deletion returns false or at error if an exception is thrown.
DELIMITERS - Static variable in class loci.formats.in.ImarisHDFReader
 
deltaT - Variable in class loci.formats.in.ColumbusReader.Plane
 
deltaT - Variable in class loci.formats.in.FV1000Reader.PlaneData
 
deltaT - Variable in class loci.formats.in.InCellReader.Image
 
deltaT - Variable in class loci.formats.in.IvisionReader
 
deltaT - Variable in class loci.formats.in.NiftiReader
 
deltaT - Variable in class loci.formats.in.OperettaReader.Plane
 
deltaT - Variable in class loci.formats.in.ScanrReader
 
DeltavisionReader - Class in loci.formats.in
DeltavisionReader is the file format reader for Deltavision files.
DeltavisionReader() - Constructor for class loci.formats.in.DeltavisionReader
Constructs a new Deltavision reader.
DeltavisionReader.DVExtHdrFields - Class in loci.formats.in
This private class structure holds the details for the extended header.
denom - Variable in class loci.formats.tiff.TiffRational
Components of the rational's fractional representation.
denom - Variable in class org.libjpegturbo.turbojpeg.TJScalingFactor
Denominator
depth - Variable in class loci.formats.tools.AmiraParameters
 
desc - Variable in class loci.formats.gui.ComboFileFilter
Description.
desc - Variable in class loci.formats.gui.ExtensionFileFilter
Description.
desc - Variable in class loci.formats.gui.FormatFileFilter
Description.
description - Variable in class loci.formats.in.CV7000Reader.WPIHandler
 
description - Variable in class loci.formats.in.NiftiReader
 
description() - Method in interface loci.formats.in.PrairieMetadata.Value
 
description - Variable in class loci.formats.in.PrairieMetadata.ValueItem
 
description() - Method in class loci.formats.in.PrairieMetadata.ValueItem
 
description() - Method in class loci.formats.in.PrairieMetadata.ValueTable
 
description - Variable in class loci.formats.in.TiffReader
 
description - Variable in class loci.formats.in.VolocityReader.Stack
 
description - Variable in class loci.formats.in.ZeissCZIReader
 
description - Variable in class loci.formats.in.ZeissLSMReader.Recording
 
descriptions - Variable in class loci.formats.in.LIFReader
 
destroy() - Method in class org.libjpegturbo.turbojpeg.TJCompressor
 
destroy() - Method in class org.libjpegturbo.turbojpeg.TJDecompressor
 
detailPath - Variable in class loci.formats.in.CV7000Reader
 
details - Variable in class loci.formats.in.PerkinElmerReader
 
DetectionChannel() - Constructor for class loci.formats.in.ZeissLSMReader.DetectionChannel
 
detector - Variable in class loci.formats.in.LeicaHandler.Channel
 
Detector() - Constructor for class loci.formats.in.LeicaHandler.Detector
 
Detector() - Constructor for class loci.formats.in.LeicaReader.Detector
 
Detector() - Constructor for class loci.formats.in.OIRReader.Detector
 
detector - Variable in class loci.formats.in.VolocityReader.Stack
 
detectorChannel - Variable in class loci.formats.in.LeicaHandler
 
detectorGain - Variable in class loci.formats.in.BaseZeissReader
 
detectorID - Variable in class loci.formats.in.MicromanagerReader.Position
 
detectorIndexes - Variable in class loci.formats.in.LIFReader
 
detectorIndices - Variable in class loci.formats.in.LeicaHandler
 
detectorManufacturer - Variable in class loci.formats.in.FluoviewReader
 
detectorManufacturer - Variable in class loci.formats.in.MicromanagerReader.Position
 
detectorModel - Variable in class loci.formats.in.MicromanagerReader.Position
 
detectorModels - Variable in class loci.formats.in.LIFReader
 
detectorOffset - Variable in class loci.formats.in.BaseZeissReader
 
detectorOffset - Variable in class loci.formats.in.OpenlabReader
 
detectorOffsets - Variable in class loci.formats.in.LIFReader
 
detectorRefs - Variable in class loci.formats.in.ZeissCZIReader
 
detectors - Variable in class loci.formats.in.FEITiffReader
 
detectors - Variable in class loci.formats.in.LeicaHandler
 
detectors - Variable in class loci.formats.in.LeicaReader
 
detectors - Variable in class loci.formats.in.OIRReader
 
detType - Variable in class loci.formats.in.SDTInfo
Detector type (SPC-930 in camera mode).
DEVICE_ID - Static variable in class loci.formats.in.CellSensReader
 
DEVICE_MANUFACTURER - Static variable in class loci.formats.in.CellSensReader
 
DEVICE_NAME - Static variable in class loci.formats.in.CellSensReader
 
DEVICE_SUBTYPE - Static variable in class loci.formats.in.CellSensReader
 
deviceIDs - Variable in class loci.formats.in.CellSensReader.Pyramid
 
deviceManufacturers - Variable in class loci.formats.in.CellSensReader.Pyramid
 
deviceNames - Variable in class loci.formats.in.CellSensReader.Pyramid
 
deviceTypes - Variable in class loci.formats.in.CellSensReader.Pyramid
 
devModel - Variable in class loci.formats.in.LeicaSCNReader.Image
 
devVersion - Variable in class loci.formats.in.LeicaSCNReader.Image
 
dialog - Variable in class loci.plugins.in.ThumbLoader
 
dichroic - Variable in class loci.formats.in.FlexReader.FilterGroup
 
dichroicMap - Variable in class loci.formats.in.FlexReader
 
dichroicModels - Variable in class loci.formats.in.NikonTiffReader
 
DICOM_MAGIC_STRING - Static variable in class loci.formats.in.DicomReader
 
DICOM_SUFFIXES - Static variable in class loci.formats.in.DicomReader
 
DicomReader - Class in loci.formats.in
DicomReader is the file format reader for DICOM files.
DicomReader() - Constructor for class loci.formats.in.DicomReader
Constructs a new DICOM reader.
diff - Variable in class loci.formats.in.BioRadGelReader
 
difference(byte[], IFD) - Static method in enum loci.formats.tiff.TiffCompression
Performs in-place differencing according to the given predictor value.
DIGITAL_ZOOM_RATIO - Static variable in class loci.formats.tiff.IFD
 
digits(int) - Static method in class loci.plugins.in.ImporterMetadata
Computes the given value's number of digits.
dilate() - Method in class loci.plugins.util.RecordedImageProcessor
 
DIM_INDEX_1 - Static variable in class loci.formats.in.CellSensReader
 
DIM_INDEX_2 - Static variable in class loci.formats.in.CellSensReader
 
DIMDESCR - Static variable in class loci.formats.in.LeicaReader
 
Dimension(Attributes) - Constructor for class loci.formats.in.LeicaSCNReader.Dimension
 
dimension - Variable in class loci.formats.in.ZeissCZIReader.DimensionEntry
 
Dimension(Integer) - Constructor for class loci.formats.in.ZeissTIFFHandler.Scaling.Dimension
Constructor.
dimension - Variable in class loci.formats.in.ZeissTIFFHandler.Scaling.Dimension
 
DIMENSION_DESCRIPTION_VOLUME - Static variable in class loci.formats.in.CellSensReader
 
DIMENSION_INCREMENT_ID - Static variable in class loci.formats.in.CellSensReader
 
DIMENSION_MEANING - Static variable in class loci.formats.in.CellSensReader
 
DIMENSION_NAME - Static variable in class loci.formats.in.CellSensReader
 
DIMENSION_NAMES - Static variable in class loci.formats.in.LeicaReader
 
DIMENSION_SIZE - Static variable in class loci.formats.in.CellSensReader
 
DIMENSION_START_ID - Static variable in class loci.formats.in.CellSensReader
 
DIMENSION_VALUE_ID - Static variable in class loci.formats.in.CellSensReader
 
dimensionCount - Variable in class loci.formats.in.ZeissCZIReader.DirectoryEntry
 
dimensionEntries - Variable in class loci.formats.in.ZeissCZIReader.DirectoryEntry
 
DimensionEntry(RandomAccessInputStream) - Constructor for class loci.formats.in.ZeissCZIReader.DimensionEntry
 
dimensionLength - Variable in class loci.formats.out.ICSWriter
 
dimensionM - Variable in class loci.formats.in.ZeissLSMReader
 
dimensionOffset - Variable in class loci.formats.out.ICSWriter
 
dimensionOrder - Variable in class loci.formats.CoreMetadata
Order in which dimensions are stored.
dimensionOrder - Variable in class loci.formats.in.FluoviewReader
 
dimensionOrdering - Variable in class loci.formats.in.CellSensReader.Pyramid
 
dimensionP - Variable in class loci.formats.in.ZeissLSMReader
 
DIMENSIONS_STRING - Static variable in class loci.formats.in.KodakReader
 
DimensionSwapper - Class in loci.formats
Handles swapping the dimension order of an image series.
DimensionSwapper() - Constructor for class loci.formats.DimensionSwapper
Constructs a DimensionSwapper around a new image reader.
DimensionSwapper(IFormatReader) - Constructor for class loci.formats.DimensionSwapper
Constructs a DimensionSwapper with the given reader.
dimensionSwapper - Variable in class loci.plugins.in.ImportProcess
 
dimensionTag - Variable in class loci.formats.in.CellSensReader
 
dimOrder - Variable in class loci.formats.AxisGuesser
Original ordering of internal dimensional axes.
dims - Variable in class loci.formats.in.LeicaSCNReader.Pixels
 
dims - Variable in class loci.formats.in.ZeissTIFFHandler.Scaling
 
dims_blockSize - Variable in class loci.formats.in.KLBReader
 
dims_xyzct - Variable in class loci.formats.in.KLBReader
 
dir - Variable in class loci.formats.in.VolocityReader
 
direction - Variable in class loci.formats.in.VentanaReader.Overlap
 
Directory() - Constructor for class loci.formats.in.ZeissCZIReader.Directory
 
directory - Variable in class loci.formats.Memoizer
Directory where all memo files should be created.
directory - Variable in class loci.formats.services.EXIFServiceImpl
 
directoryCache - Variable in class loci.formats.in.ZeissTIFFReader
 
DirectoryEntry(RandomAccessInputStream) - Constructor for class loci.formats.in.ZeissCZIReader.DirectoryEntry
 
directoryEntry - Variable in class loci.formats.in.ZeissCZIReader.SubBlock
 
directoryList - Variable in class loci.formats.in.CellWorxReader
 
directoryPosition - Variable in class loci.formats.in.ZeissCZIReader.FileHeader
 
directoryRoot - Variable in class loci.formats.tools.FakeImage
 
dirty - Variable in class loci.formats.cache.CacheStrategy
Whether load order array needs to be recomputed before building the next load list.
DISPLAY_COLOR - Static variable in class loci.formats.in.CellSensReader
 
DISPLAY_CONTRAST_BRIGHTNESS - Static variable in class loci.formats.in.CellSensReader
 
DISPLAY_GAMMA_CORRECTION - Static variable in class loci.formats.in.CellSensReader
 
DISPLAY_LIMITS - Static variable in class loci.formats.in.CellSensReader
 
DISPLAY_LUT - Static variable in class loci.formats.in.CellSensReader
 
DISPLAY_MAPPING_VOLUME - Static variable in class loci.formats.in.CellSensReader
 
DISPLAY_PROCESSOR_TYPE - Static variable in class loci.formats.in.CellSensReader
 
DISPLAY_STACK_ID - Static variable in class loci.formats.in.CellSensReader
 
DISPLAY_STACK_INDEX - Static variable in class loci.formats.in.CellSensReader
 
DISPLAY_VISIBLE - Static variable in class loci.formats.in.CellSensReader
 
displayColor - Variable in class loci.formats.in.SVSReader
 
displayDataBrowser(ImagePlus) - Method in class loci.plugins.in.DisplayHandler
 
displayDialog(GenericDialog) - Method in class loci.plugins.in.IdDialog
Asks user whether Bio-Formats should automatically check for upgrades, and if so, checks for an upgrade and prompts user to install it.
displayDialog(GenericDialog) - Method in class loci.plugins.in.ImporterDialog
Displays the dialog, or grabs values from macro options.
displayDialog(GenericDialog) - Method in class loci.plugins.in.SeriesDialog
 
displayDialog(GenericDialog) - Method in class loci.plugins.in.UpgradeDialog
Asks user whether Bio-Formats should automatically check for upgrades, and if so, checks for an upgrade and prompts user to install it.
DISPLAYED_LUT_ID - Static variable in class loci.formats.in.CellSensReader
 
DisplayHandler - Class in loci.plugins.in
Logic for displaying images and metadata onscreen using ImageJ.
DisplayHandler(ImportProcess) - Constructor for class loci.plugins.in.DisplayHandler
 
displayImage(ImagePlus) - Method in class loci.plugins.in.DisplayHandler
Displays the given image according to the configured options.
displayImage5D(ImagePlus) - Method in class loci.plugins.in.DisplayHandler
 
displayImages(ImagePlus[]) - Method in class loci.plugins.in.DisplayHandler
Displays the given images according to the configured options.
displayName - Variable in class loci.formats.in.OperettaReader.OperettaHandler
 
displayNormal(ImagePlus) - Method in class loci.plugins.in.DisplayHandler
Displays in a normal ImageJ window.
displayOMEXML() - Method in class loci.plugins.in.DisplayHandler
Displays OME-XML metadata in a tree in its own window.
displayOriginalMetadata() - Method in class loci.plugins.in.DisplayHandler
Displays standard metadata in a table in its own window.
displayROIs(ImagePlus[]) - Method in class loci.plugins.in.DisplayHandler
 
displayTag - Variable in class loci.formats.in.BaseZeissReader.Shape
 
displayUsage() - Method in class loci.formats.tools.MakeTestOmeTiff
 
displayView5D(ImagePlus) - Method in class loci.plugins.in.DisplayHandler
 
dispose() - Method in class loci.formats.gui.CacheComponent
 
dispose - Variable in class loci.formats.in.GIFReader
 
distance(int, int) - Method in class loci.formats.cache.CacheStrategy
Computes the distance from the given axis value to the axis center, taking into account the axis ordering scheme.
dither - Variable in class loci.formats.in.SDTInfo
 
DLL_DATA_IDENTIFIER - Static variable in class loci.formats.in.SDTInfo
For .sdt files created using DLL function SPC_save_data_to_sdtfile (no setup, only data).
DM2_MAGIC_BYTES - Static variable in class loci.formats.in.GatanDM2Reader
 
DM3_MAGIC_BYTES - Static variable in class loci.formats.in.GatanReader
 
DM4_MAGIC_BYTES - Static variable in class loci.formats.in.GatanReader
 
DNGReader - Class in loci.formats.in
DNGReader is the file format reader for Canon DNG (TIFF) files.
DNGReader() - Constructor for class loci.formats.in.DNGReader
Constructs a new DNG reader.
doc - Variable in class loci.formats.gui.XMLWindow
 
doCaching - Variable in class loci.formats.tiff.TiffParser
 
doChannels - Variable in class loci.formats.in.CellWorxReader
 
doCrop() - Method in class loci.plugins.in.ImporterOptions
 
DOCUMENT_AUTHOR - Static variable in class loci.formats.in.CellSensReader
 
DOCUMENT_COMPANY - Static variable in class loci.formats.in.CellSensReader
 
DOCUMENT_CREATOR_BUILD_NUMBER - Static variable in class loci.formats.in.CellSensReader
 
DOCUMENT_CREATOR_MAJOR_VERSION - Static variable in class loci.formats.in.CellSensReader
 
DOCUMENT_CREATOR_MINOR_VERSION - Static variable in class loci.formats.in.CellSensReader
 
DOCUMENT_CREATOR_NAME - Static variable in class loci.formats.in.CellSensReader
 
DOCUMENT_CREATOR_PACKAGE - Static variable in class loci.formats.in.CellSensReader
 
DOCUMENT_CREATOR_SUB_VERSION - Static variable in class loci.formats.in.CellSensReader
 
DOCUMENT_KEYS - Static variable in class loci.formats.in.ICSReader
 
DOCUMENT_NAME - Static variable in class loci.formats.in.CellSensReader
 
DOCUMENT_NAME - Static variable in class loci.formats.tiff.IFD
 
DOCUMENT_NOTE - Static variable in class loci.formats.in.CellSensReader
 
DOCUMENT_PRODUCT - Static variable in class loci.formats.in.CellSensReader
 
DOCUMENT_PRODUCT_NAME - Static variable in class loci.formats.in.CellSensReader
 
DOCUMENT_PRODUCT_VERSION - Static variable in class loci.formats.in.CellSensReader
 
DOCUMENT_PROPERTIES - Static variable in class loci.formats.in.CellSensReader
 
DOCUMENT_THUMB - Static variable in class loci.formats.in.CellSensReader
 
DOCUMENT_TIME - Static variable in class loci.formats.in.CellSensReader
 
DOCUMENT_TYPE_HINT - Static variable in class loci.formats.in.CellSensReader
 
documentUpdate() - Method in class loci.plugins.config.FlexWidgets
 
doFormatLayout(FormatEntry) - Method in class loci.plugins.config.ConfigWindow
 
doInPlaceCaching - Variable in class loci.formats.Memoizer
If true, then all memo files will be created in the same directory as the original file.
domains - Variable in class loci.formats.FormatReader
List of domains in which this format is used.
doMustGroup() - Method in class loci.plugins.in.ImporterOptions
 
doNotChangePattern - Variable in class loci.formats.FileStitcher
 
doRecording - Variable in class loci.plugins.util.RecordedImageProcessor
 
doStitchTiles() - Method in class loci.plugins.in.ImporterOptions
 
doT - Variable in class loci.formats.in.InCellReader.MinimalInCellHandler
 
DOT - Static variable in class loci.formats.ResourceNamer
 
DOT_RANGE - Static variable in class loci.formats.tiff.IFD
 
DOUBLE - Static variable in class loci.formats.FormatTools
Identifies the DOUBLE data type used to store pixel values.
DOUBLE - Static variable in class loci.formats.in.CellSensReader
 
DOUBLE - Static variable in class loci.formats.in.GatanReader
 
DOUBLE_2 - Static variable in class loci.formats.in.CellSensReader
 
DOUBLE_2_2 - Static variable in class loci.formats.in.CellSensReader
 
DOUBLE_3 - Static variable in class loci.formats.in.CellSensReader
 
DOUBLE_3_3 - Static variable in class loci.formats.in.CellSensReader
 
DOUBLE_4 - Static variable in class loci.formats.in.CellSensReader
 
DOUBLE_4_4 - Static variable in class loci.formats.in.CellSensReader
 
DOUBLE_ARRAY_2 - Static variable in class loci.formats.in.CellSensReader
 
DOUBLE_ARRAY_3 - Static variable in class loci.formats.in.CellSensReader
 
DOUBLE_INTERVAL - Static variable in class loci.formats.in.CellSensReader
 
DOUBLE_RECT - Static variable in class loci.formats.in.CellSensReader
 
doubleCapacity() - Method in class loci.formats.codec.ByteVector
 
DoubleOption - Class in loci.plugins.prefs
A double option for one of the plugins.
DoubleOption(HashMap<String, String>) - Constructor for class loci.plugins.prefs.DoubleOption
Constructs a double option with the parameters from the given map.
DoubleOption(String, boolean, String, String, double) - Constructor for class loci.plugins.prefs.DoubleOption
Constructs a double option with the given parameters.
doubleValue() - Method in class loci.formats.tiff.TiffRational
Returns the value of the specified number as a double.
doUpgradeCheck() - Method in class loci.plugins.in.ImporterOptions
 
download(URLConnection) - Static method in class loci.plugins.config.InstallWizard
 
download(URLConnection, File) - Static method in class loci.plugins.config.InstallWizard
 
doZ - Variable in class loci.formats.in.InCellReader.MinimalInCellHandler
 
DP80_FRAME_CENTERING - Static variable in class loci.formats.in.CellSensReader
 
drawColour - Variable in class loci.formats.in.BaseZeissReader.Shape
 
drawDot(int, int) - Method in class loci.plugins.util.RecordedImageProcessor
 
drawLine(int, int, int, int) - Method in class loci.plugins.util.RecordedImageProcessor
 
drawOval(int, int, int, int) - Method in class loci.plugins.util.RecordedImageProcessor
 
drawPixel(int, int) - Method in class loci.plugins.util.RecordedImageProcessor
 
drawPolygon(Polygon) - Method in class loci.plugins.util.RecordedImageProcessor
 
drawRect(int, int, int, int) - Method in class loci.plugins.util.RecordedImageProcessor
 
drawString(String) - Method in class loci.plugins.util.RecordedImageProcessor
 
drawString(String, int, int) - Method in class loci.plugins.util.RecordedImageProcessor
 
DrawStyle(int) - Constructor for enum loci.formats.in.BaseZeissReader.DrawStyle
 
drawStyle - Variable in class loci.formats.in.BaseZeissReader.Shape
 
DRI - Static variable in class loci.formats.services.JPEGTurboServiceImpl
 
drivePictDecoder(int) - Method in class loci.formats.in.PictReader
Handles the opcodes in the PICT file.
DS - Static variable in class loci.formats.in.DicomReader
 
DT - Static variable in class loci.formats.in.DicomReader
 
dualCamera - Variable in class loci.formats.in.MetamorphHandler
 
dualCamera - Variable in class loci.formats.in.MetamorphTiffReader
 
DUMMY_PIXEL - Static variable in class loci.formats.out.EPSWriter
 
DummyMetadata - Class in loci.formats.meta
 
DummyMetadata() - Constructor for class loci.formats.meta.DummyMetadata
 
dumpXML() - Method in class loci.formats.ome.OMEPyramidStore
 
duplicate(Class<? extends IFormatReader>) - Method in class loci.formats.ReaderWrapper
Performs a deep copy of the reader, including nested wrapped readers.
duplicate(Class<? extends IFormatWriter>) - Method in class loci.formats.WriterWrapper
Performs a deep copy of the writer, including nested wrapped writers.
duplicate() - Method in class loci.plugins.util.RecordedImageProcessor
 
duplicateRecurse(Class<? extends IFormatReader>) - Method in class loci.formats.ReaderWrapper
 
duplicateRecurse(Class<? extends IFormatWriter>) - Method in class loci.formats.WriterWrapper
 
DV_MAGIC_BYTES_1 - Static variable in class loci.formats.in.DeltavisionReader
 
DV_MAGIC_BYTES_2 - Static variable in class loci.formats.in.DeltavisionReader
 
DVExtHdrFields(RandomAccessInputStream) - Constructor for class loci.formats.in.DeltavisionReader.DVExtHdrFields
 
DWORD - Static variable in class loci.formats.in.CellSensReader
 
dyeName - Variable in class loci.formats.in.FV1000Reader.ChannelData
 
dyeName - Variable in class loci.formats.in.LeicaHandler.MultiBand
 
dyeNames - Variable in class loci.formats.in.SVSReader
 
dyes - Variable in class loci.formats.in.ND2Handler
 
DYNAMIC_PROPERTIES - Static variable in class loci.formats.in.CellSensReader
 
DynamicMetadataOptions - Class in loci.formats.in
Configuration object for readers and writers.
DynamicMetadataOptions() - Constructor for class loci.formats.in.DynamicMetadataOptions
Creates an options object with metadata level set to DynamicMetadataOptions.METADATA_LEVEL_DEFAULT and file validation set to DynamicMetadataOptions.READER_VALIDATE_DEFAULT.
DynamicMetadataOptions(MetadataLevel) - Constructor for class loci.formats.in.DynamicMetadataOptions
Creates an options object with metadata level set to the specified value and file validation set to DynamicMetadataOptions.READER_VALIDATE_DEFAULT

E

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

F

F_KEY - Static variable in class loci.formats.in.LiFlimReader
 
F_NUMBER - Static variable in class loci.formats.tiff.IFD
 
factor - Variable in class loci.formats.in.ZeissTIFFHandler.Scaling.Dimension
 
factors - Variable in class loci.formats.in.FlexReader.FlexFile
 
factors - Variable in class loci.formats.in.FlexReader.FlexHandler
 
factory - Variable in class loci.formats.FormatReader
 
FAIL_ON_MISSING_DEFAULT - Static variable in class loci.formats.in.CellSensReader
 
FAIL_ON_MISSING_KEY - Static variable in class loci.formats.in.CellSensReader
 
failOnMissingETS() - Method in class loci.formats.in.CellSensReader
 
FAKE_EXT - Static variable in class loci.formats.ResourceNamer
 
fakeBigTiff - Variable in class loci.formats.tiff.TiffParser
Whether or not 64-bit offsets are used for non-BigTIFF files.
FakeImage - Class in loci.formats.tools
Generates fake image structures.
FakeImage(Location) - Constructor for class loci.formats.tools.FakeImage
 
FakeReader - Class in loci.formats.in
FakeReader is the file format reader for faking input data.
FakeReader() - Constructor for class loci.formats.in.FakeReader
Constructs a new fake reader.
fakeSeries - Variable in class loci.formats.in.FakeReader
List of used files if the fake is a SPW structure
falseColor - Variable in class loci.formats.CoreMetadata
Indicates whether or not we can ignore the color map (if present).
FAN_SPEED - Static variable in class loci.formats.in.CellSensReader
 
fb - Variable in class loci.formats.in.BaseZeissReader.Shape
 
fcc - Variable in class loci.formats.in.AVIReader
 
FCS_DATA_IDENTIFIER - Static variable in class loci.formats.in.SDTInfo
For .sdt files created in FIFO mode (setup, data blocks = Decay, FCS, FIDA, FILDA & MCS curves for each used routing channel).
fcsDecayCalc - Variable in class loci.formats.in.SDTInfo
Bit 0 = 1 - decay curve calculated.
fcsPoints - Variable in class loci.formats.in.SDTInfo
No of FCS values.
fcsType - Variable in class loci.formats.in.SDTInfo
0 - linear FCS with log binning (100 bins/log) when bit 15 = 1 (0x8000) - Multi-Tau FCS where bits 14-0 = ktau parameter.
fctlCount - Variable in class loci.formats.in.APNGReader.PNGInputStream
 
FD - Static variable in class loci.formats.in.DicomReader
 
fdatValid - Variable in class loci.formats.in.APNGReader.PNGInputStream
 
FEATURE - Static variable in class loci.formats.in.BDVReader.H5Constants
 
FEATURE - Static variable in class loci.formats.in.CellH5Reader.CellH5Constants
 
FeatureType(int, int) - Constructor for enum loci.formats.in.BaseZeissReader.FeatureType
 
FEI_MAGIC_STRING - Static variable in class loci.formats.in.FEIReader
 
FEIHandler() - Constructor for class loci.formats.in.FEITiffReader.FEIHandler
 
FEIReader - Class in loci.formats.in
FEIReader is the file format reader for FEI and Philips .img files.
FEIReader() - Constructor for class loci.formats.in.FEIReader
Constructs a new FEI reader.
FEITiffReader - Class in loci.formats.in
FEITiffReader is the file format reader for TIFF files produced by various FEI software.
FEITiffReader() - Constructor for class loci.formats.in.FEITiffReader
 
FEITiffReader.FEIHandler - Class in loci.formats.in
 
fetchRow(MdbTableDef) - Method in class loci.formats.services.MDBServiceImpl
Fetches the next row from the table, ignoring potential parsing exceptions.
fetchXMLId() - Method in class loci.formats.in.BDVReader
 
fidaPoints - Variable in class loci.formats.in.SDTInfo
No of FIDA values.
fidaTime - Variable in class loci.formats.in.SDTInfo
Interval time [ms] for FIDA histogram.
field - Variable in class loci.formats.in.CellomicsReader.ChannelFile
 
field - Variable in class loci.formats.in.ColumbusReader.Plane
 
field - Variable in class loci.formats.in.CV7000Reader.Plane
 
field - Variable in class loci.formats.in.FlexReader.FlexFile
 
field - Variable in class loci.formats.in.OperettaReader.Plane
 
FIELD - Static variable in class loci.formats.ResourceNamer
 
FIELD_AUX_FLAGS - Static variable in class loci.formats.in.IM3Reader
 
FIELD_BAND_INDEX - Static variable in class loci.formats.in.IM3Reader
 
FIELD_BANDS - Static variable in class loci.formats.in.IM3Reader
 
FIELD_CLASS_ID - Static variable in class loci.formats.in.IM3Reader
 
FIELD_DATA - Static variable in class loci.formats.in.IM3Reader
 
FIELD_DATA_SET - Static variable in class loci.formats.in.IM3Reader
 
FIELD_EXPOSURE - Static variable in class loci.formats.in.IM3Reader
 
FIELD_FILE_VERSION - Static variable in class loci.formats.in.IM3Reader
 
FIELD_FILTER_PAIR - Static variable in class loci.formats.in.IM3Reader
 
FIELD_FIXED_FILTER - Static variable in class loci.formats.in.IM3Reader
 
FIELD_HOMOGENEOUS - Static variable in class loci.formats.in.IM3Reader
 
FIELD_INDEX - Static variable in class loci.formats.in.ND2Handler
 
FIELD_MAGNITUDES - Static variable in class loci.formats.in.IM3Reader
 
FIELD_MANUFACTURER - Static variable in class loci.formats.in.IM3Reader
 
FIELD_MILLIMETERS_PER_PIXEL - Static variable in class loci.formats.in.IM3Reader
 
FIELD_NAME - Static variable in class loci.formats.in.IM3Reader
 
FIELD_NUANCE_FLAGS - Static variable in class loci.formats.in.IM3Reader
 
FIELD_OBJECTIVE - Static variable in class loci.formats.in.IM3Reader
 
FIELD_PART_NUMBER - Static variable in class loci.formats.in.IM3Reader
 
FIELD_PROTOCOL - Static variable in class loci.formats.in.IM3Reader
 
FIELD_PROXY_PARENT_FILE_NAME - Static variable in class loci.formats.in.IM3Reader
 
FIELD_SAMPLE_ID - Static variable in class loci.formats.in.IM3Reader
 
FIELD_SHAPE - Static variable in class loci.formats.in.IM3Reader
 
FIELD_SOURCE_FILE_NAME - Static variable in class loci.formats.in.IM3Reader
 
FIELD_SPECTRA - Static variable in class loci.formats.in.IM3Reader
 
FIELD_SPECTRAL_BASIS_INFO - Static variable in class loci.formats.in.IM3Reader
 
FIELD_SPECTRAL_LIBRARY - Static variable in class loci.formats.in.IM3Reader
 
FIELD_SPECTRUM - Static variable in class loci.formats.in.IM3Reader
 
FIELD_THUMBNAIL - Static variable in class loci.formats.in.IM3Reader
 
FIELD_TIMESTAMP - Static variable in class loci.formats.in.IM3Reader
 
FIELD_TYPE - Static variable in class loci.formats.in.CellSensReader
 
FIELD_TYPE_ID - Static variable in class loci.formats.in.IM3Reader
 
FIELD_USER_COMMENTS - Static variable in class loci.formats.in.IM3Reader
 
FIELD_VALUES - Static variable in class loci.formats.in.IM3Reader
 
FIELD_WAVELENGTH - Static variable in class loci.formats.in.IM3Reader
 
FIELD_WAVELENGTHS - Static variable in class loci.formats.in.IM3Reader
 
fieldCol - Variable in class loci.formats.in.MetamorphTiffReader.Well
 
fieldCols - Variable in class loci.formats.in.BDReader
 
fieldColumnCount - Variable in class loci.formats.in.MetamorphTiffReader
 
fieldColumns - Variable in class loci.formats.in.ScanrReader
 
fieldCount - Variable in class loci.formats.in.CellWorxReader
 
fieldCount - Variable in class loci.formats.in.FlexReader
 
fieldCount - Variable in class loci.formats.in.InCellReader
 
fieldIndex - Variable in class loci.formats.in.FluoviewReader
 
fieldIndex - Variable in class loci.formats.in.NativeND2Reader
 
FieldInfo() - Constructor for class loci.formats.in.CellVoyagerReader.FieldInfo
 
fieldMap - Variable in class loci.formats.in.CellWorxReader
 
fieldOffsets - Variable in class loci.formats.in.FluoviewReader
 
fieldPositionX - Variable in class loci.formats.in.ScanrReader
 
fieldPositionY - Variable in class loci.formats.in.ScanrReader
 
fieldPosX - Variable in class loci.formats.in.LIFReader
 
fieldPosY - Variable in class loci.formats.in.LIFReader
 
fieldRow - Variable in class loci.formats.in.MetamorphTiffReader.Well
 
fieldRowCount - Variable in class loci.formats.in.MetamorphTiffReader
 
fieldRows - Variable in class loci.formats.in.BDReader
 
fieldRows - Variable in class loci.formats.in.ScanrReader
 
fields - Variable in class loci.formats.in.CellVoyagerReader.AreaInfo
 
fields - Variable in class loci.formats.in.CV7000Reader
 
fields - Variable in class loci.formats.in.FakeReader
 
fifoTyp - Variable in class loci.formats.in.SDTInfo
 
fildaPoints - Variable in class loci.formats.in.SDTInfo
No of FILDA values.
fildaTime - Variable in class loci.formats.in.SDTInfo
Interval time [ms] for FILDA histogram.
file - Variable in class loci.formats.in.ColumbusReader.Plane
 
file - Variable in class loci.formats.in.CV7000Reader.Plane
 
file - Variable in class loci.formats.in.FlexReader.FlexFile
 
file - Variable in class loci.formats.in.OIRReader.PixelBlock
 
file - Variable in class loci.formats.tools.EditTiffG
 
FILE_LENGTH - Static variable in class loci.formats.in.CanonRawReader
 
FILE_MAGIC_STRING - Static variable in class loci.formats.in.OBFReader
 
FILE_SOURCE - Static variable in class loci.formats.tiff.IFD
 
file_version - Variable in class loci.formats.in.OBFReader
 
fileBox - Variable in class loci.formats.tools.EditTiffG
 
fileGroupOption(String) - Method in class loci.formats.FormatReader
 
fileGroupOption(String) - Method in interface loci.formats.IFormatReader
Returns an indication of whether the files in a multi-file dataset can be handled individually.
fileGroupOption(String) - Method in class loci.formats.ImageReader
 
fileGroupOption(String) - Method in class loci.formats.in.AFIReader
 
fileGroupOption(String) - Method in class loci.formats.in.AnalyzeReader
 
fileGroupOption(String) - Method in class loci.formats.in.APLReader
 
fileGroupOption(String) - Method in class loci.formats.in.BDReader
 
fileGroupOption(String) - Method in class loci.formats.in.BioRadReader
 
fileGroupOption(String) - Method in class loci.formats.in.BrukerReader
 
fileGroupOption(String) - Method in class loci.formats.in.CellomicsReader
 
fileGroupOption(String) - Method in class loci.formats.in.CellSensReader
 
fileGroupOption(String) - Method in class loci.formats.in.CellVoyagerReader
 
fileGroupOption(String) - Method in class loci.formats.in.ColumbusReader
 
fileGroupOption(String) - Method in class loci.formats.in.CV7000Reader
 
fileGroupOption(String) - Method in class loci.formats.in.DicomReader
 
fileGroupOption(String) - Method in class loci.formats.in.FlexReader
 
fileGroupOption(String) - Method in class loci.formats.in.FujiReader
 
fileGroupOption(String) - Method in class loci.formats.in.FV1000Reader
 
fileGroupOption(String) - Method in class loci.formats.in.HitachiReader
 
fileGroupOption(String) - Method in class loci.formats.in.ICSReader
 
fileGroupOption(String) - Method in class loci.formats.in.ImagicReader
 
fileGroupOption(String) - Method in class loci.formats.in.InCellReader
 
fileGroupOption(String) - Method in class loci.formats.in.KLBReader
 
fileGroupOption(String) - Method in class loci.formats.in.L2DReader
 
fileGroupOption(String) - Method in class loci.formats.in.LeicaReader
 
fileGroupOption(String) - Method in class loci.formats.in.MetamorphReader
 
fileGroupOption(String) - Method in class loci.formats.in.MIASReader
 
fileGroupOption(String) - Method in class loci.formats.in.MicroCTReader
 
fileGroupOption(String) - Method in class loci.formats.in.MicromanagerReader
 
fileGroupOption(String) - Method in class loci.formats.in.NDPIReader
 
fileGroupOption(String) - Method in class loci.formats.in.NDPISReader
 
fileGroupOption(String) - Method in class loci.formats.in.NiftiReader
 
fileGroupOption(String) - Method in class loci.formats.in.NRRDReader
 
fileGroupOption(String) - Method in class loci.formats.in.OIRReader
 
fileGroupOption(String) - Method in class loci.formats.in.OMETiffReader
 
fileGroupOption(String) - Method in class loci.formats.in.OperettaReader
 
fileGroupOption(String) - Method in class loci.formats.in.PerkinElmerReader
 
fileGroupOption(String) - Method in class loci.formats.in.PrairieReader
 
fileGroupOption(String) - Method in class loci.formats.in.ScanrReader
 
fileGroupOption(String) - Method in class loci.formats.in.SPCReader
 
fileGroupOption(String) - Method in class loci.formats.in.SVSReader
 
fileGroupOption(String) - Method in class loci.formats.in.TCSReader
 
fileGroupOption(String) - Method in class loci.formats.in.TillVisionReader
 
fileGroupOption(String) - Method in class loci.formats.in.TrestleReader
 
fileGroupOption(String) - Method in class loci.formats.in.VentanaReader
 
fileGroupOption(String) - Method in class loci.formats.in.VisitechReader
 
fileGroupOption(String) - Method in class loci.formats.in.ZeissLSMReader
 
fileGroupOption(String) - Method in class loci.formats.in.ZeissTIFFReader
 
fileGroupOption(String) - Method in class loci.formats.ReaderWrapper
 
fileGroupOption(String, String[]) - Method in class loci.plugins.macro.LociFunctions
 
fileGUID - Variable in class loci.formats.in.ZeissCZIReader.FileHeader
 
FileHeader() - Constructor for class loci.formats.in.ZeissCZIReader.FileHeader
 
fileIndex - Variable in class loci.formats.in.ColumbusReader.Plane
 
FileInfo - Class in loci.formats
Encompasses basic metadata about a file.
FileInfo() - Constructor for class loci.formats.FileInfo
 
FILEINFO_STRING - Static variable in class loci.formats.in.KodakReader
 
fileLength - Variable in class loci.formats.in.LeicaReader
Length of each file name.
fileList - Variable in class loci.formats.in.DicomReader
 
filelist - Variable in class loci.formats.in.KLBReader
 
fileMap - Variable in class loci.formats.in.CellSensReader
 
filename - Variable in class loci.formats.FileInfo
Absolute path to this file.
filename - Variable in class loci.formats.gui.ImageViewer
 
filename - Variable in class loci.formats.in.CellomicsReader.ChannelFile
 
filename - Variable in class loci.formats.in.InCellReader.Image
 
filename - Variable in class loci.formats.in.MIASReader.AnalysisFile
 
filename - Variable in class loci.formats.in.OperettaReader.Plane
 
filename - Variable in class loci.formats.in.PrairieMetadata.PFile
filename attribute of this <File>.
filename - Variable in class loci.formats.in.ZeissCZIReader.Segment
 
filename - Variable in class loci.formats.in.ZeissTIFFReader.Plane
 
filename - Variable in class loci.formats.tiff.TiffSaver
Output filename.
fileNameMap - Variable in class loci.formats.in.MicromanagerReader.Position
 
filenames - Variable in class loci.formats.in.FV1000Reader
 
filePart - Variable in class loci.formats.in.ZeissCZIReader.AttachmentEntry
 
filePart - Variable in class loci.formats.in.ZeissCZIReader.DirectoryEntry
 
filePart - Variable in class loci.formats.in.ZeissCZIReader.FileHeader
 
filePath - Variable in class loci.formats.services.POIServiceImpl
 
FilePattern - Class in loci.formats
Represents a collection of files meant to be part of the same data series.
FilePattern(Location) - Constructor for class loci.formats.FilePattern
Creates a pattern object using the given file as a template.
FilePattern(String, String) - Constructor for class loci.formats.FilePattern
Creates a pattern object using the given filename and directory path as a template.
FilePattern(String) - Constructor for class loci.formats.FilePattern
Creates a pattern object for files with the given pattern string.
FilePatternBlock - Class in loci.formats
FilePatternBlock represents a single block in a FilePattern.
FilePatternBlock(String) - Constructor for class loci.formats.FilePatternBlock
Builds a FilePatternBlock from a block string.
FilePatternDialog - Class in loci.plugins.in
Bio-Formats Importer file pattern dialog box.
FilePatternDialog(ImportProcess) - Constructor for class loci.plugins.in.FilePatternDialog
Creates a file pattern dialog for the Bio-Formats Importer.
FilePatternReader - Class in loci.formats.in
 
FilePatternReader() - Constructor for class loci.formats.in.FilePatternReader
Constructs a new pattern reader.
filePosition - Variable in class loci.formats.in.ZeissCZIReader.AttachmentEntry
 
filePosition - Variable in class loci.formats.in.ZeissCZIReader.DirectoryEntry
 
fileReader - Variable in class loci.formats.gui.ImageViewer
Reader for files on disk.
files - Variable in class loci.formats.FilePattern
File listing for this file pattern.
files - Variable in class loci.formats.FileStitcher.ExternalSeries
 
files - Variable in class loci.formats.in.CellomicsReader
 
files - Variable in class loci.formats.in.HamamatsuVMSReader
 
files - Variable in class loci.formats.in.ImprovisionTiffReader
 
files - Variable in class loci.formats.in.LeicaReader
Array of image file names.
files - Variable in class loci.formats.in.MetamorphTiffReader
 
files - Variable in class loci.formats.in.PerkinElmerReader
List of files to open.
files - Variable in class loci.formats.in.PrairieMetadata.Frame
<File> elements beneath this <Frame>, keyed on each file's channel.
files - Variable in class loci.formats.in.SEQReader
 
files - Variable in class loci.formats.in.SlidebookTiffReader
 
files - Variable in class loci.formats.in.TrestleReader
 
files - Variable in class loci.formats.in.VarianFDFReader
 
files - Variable in class loci.formats.in.VisitechReader
Files in this dataset.
files - Variable in class loci.formats.in.ZeissZVIReader
 
files - Variable in class loci.formats.services.POIServiceImpl
 
fileSave - Variable in class loci.formats.gui.ImageViewer
 
fileSizes - Variable in class loci.formats.services.POIServiceImpl
 
FileStitcher - Class in loci.formats
Logic to stitch together files with similar names.
FileStitcher() - Constructor for class loci.formats.FileStitcher
Constructs a FileStitcher around a new image reader.
FileStitcher(boolean) - Constructor for class loci.formats.FileStitcher
Constructs a FileStitcher around a new image reader.
FileStitcher(IFormatReader) - Constructor for class loci.formats.FileStitcher
Constructs a FileStitcher with the given reader.
FileStitcher(IFormatReader, boolean) - Constructor for class loci.formats.FileStitcher
Constructs a FileStitcher with the given reader.
fileStitcher - Variable in class loci.plugins.in.ImportProcess
 
FileStitcher.ExternalSeries - Class in loci.formats
 
fileSystem - Variable in class loci.formats.services.POIServiceImpl
 
fileView - Variable in class loci.formats.gui.ImageViewer
 
fileWriter - Variable in class loci.formats.gui.ImageViewer
Writer for files on disk.
fill() - Method in class loci.plugins.util.RecordedImageProcessor
 
fill(ImageProcessor) - Method in class loci.plugins.util.RecordedImageProcessor
 
FILL_ORDER - Static variable in class loci.formats.tiff.IFD
 
fillAcquisitionDate(MetadataStore, String, int) - Method in class loci.formats.in.FakeReader
 
fillAnnotations(MetadataStore, int) - Method in class loci.formats.in.FakeReader
 
fillColour - Variable in class loci.formats.in.BaseZeissReader.Shape
 
filled - Variable in class loci.formats.ChannelFiller
Whether to fill in the indices.
fillExposureTime(MetadataStore) - Method in class loci.formats.in.FakeReader
 
fillInData() - Method in class loci.formats.in.ZeissCZIReader.Attachment
 
fillInData() - Method in class loci.formats.in.ZeissCZIReader.AttachmentDirectory
 
fillInData() - Method in class loci.formats.in.ZeissCZIReader.Directory
 
fillInData() - Method in class loci.formats.in.ZeissCZIReader.FileHeader
 
fillInData() - Method in class loci.formats.in.ZeissCZIReader.Metadata
 
fillInData() - Method in class loci.formats.in.ZeissCZIReader.Segment
 
fillInData() - Method in class loci.formats.in.ZeissCZIReader.SubBlock
 
fillInIFD(IFD) - Method in class loci.formats.tiff.TiffParser
Fill in IFD entries that are stored at an arbitrary offset.
fillMetadataPass1(MetadataStore) - Method in class loci.formats.in.BaseZeissReader
Read and store basic dimensions in model
fillMetadataPass1(MetadataStore) - Method in class loci.formats.in.ZeissTIFFReader
 
fillMetadataPass1(MetadataStore) - Method in class loci.formats.in.ZeissZVIReader
 
fillMetadataPass2(MetadataStore) - Method in class loci.formats.in.BaseZeissReader
Read and store basic dimensions in model
fillMetadataPass2(MetadataStore) - Method in class loci.formats.in.ZeissTIFFReader
 
fillMetadataPass3(MetadataStore) - Method in class loci.formats.in.BaseZeissReader
Read and store basic dimensions in model
fillMetadataPass3(MetadataStore) - Method in class loci.formats.in.ZeissZVIReader
 
fillMetadataPass4(MetadataStore) - Method in class loci.formats.in.BaseZeissReader
Read and store basic dimensions in model
fillMetadataPass5(MetadataStore) - Method in class loci.formats.in.BaseZeissReader
Read and store basic dimensions in model
fillMetadataPass5(MetadataStore) - Method in class loci.formats.in.ZeissTIFFReader
 
fillMetadataPass5(MetadataStore) - Method in class loci.formats.in.ZeissZVIReader
 
fillMetadataPass6(MetadataStore) - Method in class loci.formats.in.BaseZeissReader
Read and store basic dimensions in model
fillMetadataPass7(MetadataStore) - Method in class loci.formats.in.BaseZeissReader
Store basic dimensions in model
fillOval(int, int, int, int) - Method in class loci.plugins.util.RecordedImageProcessor
 
fillPhysicalSizes(MetadataStore) - Method in class loci.formats.in.FakeReader
 
fillPolygon(Polygon) - Method in class loci.plugins.util.RecordedImageProcessor
 
fillRegions(MetadataStore, int) - Method in class loci.formats.in.FakeReader
 
FillStyle(int) - Constructor for enum loci.formats.in.BaseZeissReader.FillStyle
 
fillStyle - Variable in class loci.formats.in.BaseZeissReader.Shape
 
filter - Variable in class loci.formats.in.ZeissLSMReader.BeamSplitter
 
filter - Variable in class loci.formats.in.ZeissLSMReader.DetectionChannel
 
filter(int) - Method in class loci.plugins.util.RecordedImageProcessor
 
FILTER_SET_NAME - Static variable in class loci.formats.in.NDPIReader
 
FilterGroup() - Constructor for class loci.formats.in.FlexReader.FilterGroup
 
filterMap - Variable in class loci.formats.in.FlexReader
 
filterMetadata - Variable in class loci.formats.FormatReader
Whether or not to filter out invalid metadata.
FilterMetadata - Class in loci.formats.meta
 
FilterMetadata(MetadataStore, boolean) - Constructor for class loci.formats.meta.FilterMetadata
 
filterModels - Variable in class loci.formats.in.LIFReader
 
filterModels - Variable in class loci.formats.in.NikonTiffReader
 
filterRefPopulated - Variable in class loci.formats.in.LeicaReader
 
filterSet - Variable in class loci.formats.in.FlexReader.FlexHandler
 
FILTERSET - Static variable in class loci.formats.in.LeicaReader
 
filterSet - Variable in class loci.formats.in.ZeissLSMReader.BeamSplitter
 
filterSet - Variable in class loci.formats.in.ZeissLSMReader.DetectionChannel
 
filterSetMap - Variable in class loci.formats.in.FlexReader
 
filterSetRef - Variable in class loci.formats.in.ZeissCZIReader.Channel
 
filterSets - Variable in class loci.formats.in.FlexReader
 
filts - Variable in class loci.formats.gui.ComboFileFilter
List of filters to be combined.
finalize() - Method in class org.libjpegturbo.turbojpeg.TJCompressor
 
finalize() - Method in class org.libjpegturbo.turbojpeg.TJDecompressor
 
find(String[]) - Method in class loci.formats.in.PrairieReader
Finds the first file with one of the given suffixes.
find(String, String) - Static method in class loci.plugins.Updater
 
findChildWithID(Node, String, String) - Method in class loci.formats.services.OMEXMLServiceImpl
Return the child node with specified value for the "ID" attribute.
findEdges() - Method in class loci.plugins.util.RecordedImageProcessor
 
findFiles(Location) - Method in class loci.formats.in.FlexReader
Search for files that correspond to the given file.
findFiles(Location, String[]) - Method in class loci.formats.in.FlexReader
 
findImages(RandomAccessInputStream) - Method in class loci.formats.in.TillVisionReader
 
findKeyValue(String[], String[][]) - Method in class loci.formats.in.ICSReader
 
findKeyValueForCategory(String[], String[][]) - Method in class loci.formats.in.ICSReader
 
findKeyValueOther(String[], String[][]) - Method in class loci.formats.in.ICSReader
 
findLEIFile(String) - Method in class loci.formats.in.LeicaReader
Find the .lei file that belongs to the same dataset as the given file.
findLogFiles() - Method in class loci.formats.in.DeltavisionReader
Find the log files.
findLogFiles() - Method in class loci.formats.in.FakeReader
 
findMetadataFiles() - Method in class loci.formats.in.PrairieReader
 
findNextBlock() - Method in class loci.formats.in.OpenlabReader
 
findNextOffset(RandomAccessInputStream) - Method in class loci.formats.in.TillVisionReader
 
findNextOffset(RandomAccessInputStream, byte[]) - Method in class loci.formats.in.TillVisionReader
 
findOffset() - Method in class loci.formats.in.ImspectorReader
Find the offset to the next block of pixel data.
findOffset(boolean) - Method in class loci.formats.in.ImspectorReader
 
findOIFFile(String) - Method in class loci.formats.in.FV1000Reader
 
findPattern(String) - Static method in class loci.formats.FilePattern
Identifies the group pattern from a given file within that group.
findPattern(Location) - Static method in class loci.formats.FilePattern
Identifies the group pattern from a given file within that group.
findPattern(File) - Static method in class loci.formats.FilePattern
Identifies the group pattern from a given file within that group.
findPattern(String, String) - Static method in class loci.formats.FilePattern
Identifies the group pattern from a given filename and directory.
findPattern(String, String, String[]) - Static method in class loci.formats.FilePattern
Identifies the group pattern from a given filename, directory and list of candidate filenames.
findPattern(String, String, String[], int[]) - Static method in class loci.formats.FilePattern
Identifies the group pattern from a given filename, directory and list of candidate filenames.
findPattern(String[]) - Static method in class loci.formats.FilePattern
Generate a pattern from a list of file names.
findPattern(String, String[], int, int, String) - Static method in class loci.formats.FilePattern
 
findPattern(String) - Method in class loci.formats.FileStitcher
 
findPatterns(String) - Method in class loci.formats.FileStitcher
Finds the file pattern for the given ID, based on the state of the file stitcher.
findPixelOffsets() - Method in class loci.formats.in.JPXReader
 
findPixelsOffset(int) - Method in class loci.formats.in.VisitechReader
 
findRootNode(Node) - Method in class loci.formats.services.OMEXMLServiceImpl
Return the absolute root node for the specified child node.
findSeriesPatterns(String) - Static method in class loci.formats.FilePattern
Works like FilePattern.findSeriesPatterns(String, String, String[]), but dir and nameList are inferred from the given file's absolute path.
findSeriesPatterns(String, String, String[]) - Static method in class loci.formats.FilePattern
Similar to FilePattern.findPattern(String, String, String[]), but this does not merge series indices into a pattern block.
findString(String) - Method in class loci.formats.in.KodakReader
 
findTIFFs() - Method in class loci.formats.in.MetamorphTiffReader
 
findXML(String) - Static method in class loci.formats.in.ColumbusReader
 
findZipEntries() - Method in class loci.formats.in.ZipReader
 
finish(ImportProcess) - Method in class loci.plugins.in.Importer
 
finishTime - Variable in class loci.formats.in.PerkinElmerReader
 
finishTiming() - Method in class loci.plugins.in.ImagePlusReader
 
FIRMWARE_VERSION - Static variable in class loci.formats.in.NDPIReader
 
FIRMWARE_VERSION - Static variable in class loci.formats.in.NikonReader
 
firstAvailable(int...) - Method in class loci.plugins.in.SwapDialog
 
firstDataStream - Variable in class loci.formats.tools.AmiraParameters
 
firstFile - Variable in class loci.formats.in.PrairieMetadata.Frame
The first actual <File> element for this <Frame>.
firstFrame - Variable in class loci.formats.in.PrairieMetadata.Sequence
The first actual <Frame> element for this <Sequence>.
firstIFD - Variable in class loci.formats.tiff.TiffParser
Cached first IFD in the current file.
firstIndex - Variable in class loci.formats.in.PerkinElmerReader.PixelsFile
 
firstSequence - Variable in class loci.formats.in.PrairieMetadata
The first actual <Sequence> element.
firstSeriesChannels - Variable in class loci.formats.in.MetamorphReader
 
firstStamp - Variable in class loci.formats.in.LeicaHandler
 
firstTimeLoop - Variable in class loci.formats.in.ND2Handler
 
firstTimepoint - Variable in class loci.formats.in.BDVReader
 
firstWellPlanes() - Method in class loci.formats.in.FlexReader
Returns the number of planes in the first well that has data.
fis - Variable in class loci.formats.Memoizer.KryoDeser
 
FitsReader - Class in loci.formats.in
FitsReader is the file format reader for Flexible Image Transport System (FITS) images.
FitsReader() - Constructor for class loci.formats.in.FitsReader
Constructs a new FitsReader.
fixed - Variable in class loci.formats.FilePatternBlock
Whether or not this is a fixed-width block.
FL - Static variable in class loci.formats.in.DicomReader
 
FLAG_ACCURATEDCT - Static variable in class org.libjpegturbo.turbojpeg.TJ
Use the most accurate DCT/IDCT algorithm available in the underlying codec.
FLAG_BOTTOMUP - Static variable in class org.libjpegturbo.turbojpeg.TJ
The uncompressed source/destination image is stored in bottom-up (Windows, OpenGL) order, not top-down (X11) order.
FLAG_FASTDCT - Static variable in class org.libjpegturbo.turbojpeg.TJ
Use the fastest DCT/IDCT algorithm available in the underlying codec.
FLAG_FASTUPSAMPLE - Static variable in class org.libjpegturbo.turbojpeg.TJ
When decompressing, use the fastest chrominance upsampling algorithm available in the underlying codec.
FLAG_FORCEMMX - Static variable in class org.libjpegturbo.turbojpeg.TJ
Turn off CPU auto-detection and force TurboJPEG to use MMX code (if the underlying codec supports it.)
FLAG_FORCESSE - Static variable in class org.libjpegturbo.turbojpeg.TJ
Turn off CPU auto-detection and force TurboJPEG to use SSE code (if the underlying codec supports it.)
FLAG_FORCESSE2 - Static variable in class org.libjpegturbo.turbojpeg.TJ
Turn off CPU auto-detection and force TurboJPEG to use SSE2 code (if the underlying codec supports it.)
FLAG_FORCESSE3 - Static variable in class org.libjpegturbo.turbojpeg.TJ
Turn off CPU auto-detection and force TurboJPEG to use SSE3 code (if the underlying codec supports it.)
flags - Variable in class loci.formats.in.BaseZeissReader.Layer
 
flags - Variable in class loci.formats.in.SDTInfo
Scan clocks bits 2-0 (frame, line, pixel), rates_read - bit 15.
FLASH - Static variable in class loci.formats.tiff.IFD
 
FLASH_COMPENSATION - Static variable in class loci.formats.in.NikonReader
 
FLASH_ENERGY - Static variable in class loci.formats.tiff.IFD
 
FLASH_MODE - Static variable in class loci.formats.in.NikonReader
 
FLASH_PIX_VERSION - Static variable in class loci.formats.tiff.IFD
 
FLASH_SETTING - Static variable in class loci.formats.in.NikonReader
 
FLASH_USED - Static variable in class loci.formats.in.NikonReader
 
flattenedIndex(int, int) - Method in class loci.formats.CoreMetadataList
 
flattenedIndexes(int) - Method in class loci.formats.CoreMetadataList
 
flattenedResolutions - Variable in class loci.formats.FormatReader
Whether or not resolutions are flattened.
flattenedSize() - Method in class loci.formats.CoreMetadataList
Get flattened size (all resolutions in all series)
flattenHashtables() - Method in class loci.formats.FormatReader
Call FormatReader.updateMetadataLists(Hashtable) on all metadata hashtables.
flattenHashtables() - Method in class loci.formats.SubResolutionFormatReader
Call FormatReader.updateMetadataLists(Hashtable) on all metadata hashtables.
flbckX - Variable in class loci.formats.in.SDTInfo
 
flbckY - Variable in class loci.formats.in.SDTInfo
 
FLEX - Static variable in class loci.formats.in.FlexReader
Custom IFD entry for Flex XML.
flex - Variable in class loci.formats.in.FlexReader.MeaHandler
 
FLEX_SUFFIX - Static variable in class loci.formats.in.FlexReader
 
FlexFile() - Constructor for class loci.formats.in.FlexReader.FlexFile
 
flexFiles - Variable in class loci.formats.in.FlexReader
 
FlexHandler(List<String>, List<String>, MetadataStore, boolean, int, int) - Constructor for class loci.formats.in.FlexReader.FlexHandler
 
FlexReader - Class in loci.formats.in
FlexReader is a file format reader for Evotec Flex files.
FlexReader() - Constructor for class loci.formats.in.FlexReader
Constructs a new Flex reader.
FlexReader.FilterGroup - Class in loci.formats.in
Stores a grouping of filters.
FlexReader.FlexFile - Class in loci.formats.in
 
FlexReader.FlexHandler - Class in loci.formats.in
SAX handler for parsing XML.
FlexReader.MeaHandler - Class in loci.formats.in
SAX handler for parsing XML from .mea files.
FlexReader.ResHandler - Class in loci.formats.in
SAX handler for parsing XML from .res files.
FlexWidgets - Class in loci.plugins.config
Custom widgets for configuring Bio-Formats Flex support.
FlexWidgets() - Constructor for class loci.plugins.config.FlexWidgets
 
FLIM_DOMAIN - Static variable in class loci.formats.FormatTools
Identifies the fluorescence-lifetime domain.
flip - Variable in class loci.formats.in.NativeQTReader
 
flipHorizontal() - Method in class loci.plugins.util.RecordedImageProcessor
 
flipVertical() - Method in class loci.plugins.util.RecordedImageProcessor
 
flipX - Variable in class loci.formats.in.LIFReader
 
flipY - Variable in class loci.formats.in.LIFReader
 
FLOAT - Static variable in class loci.formats.FormatTools
Identifies the FLOAT data type used to store pixel values.
FLOAT - Static variable in class loci.formats.in.CellSensReader
 
FLOAT - Static variable in class loci.formats.in.GatanReader
 
FLOAT - Static variable in class loci.formats.in.SPEReader
 
FLOAT32_TYPE - Static variable in class loci.formats.in.KLBReader
 
FLOAT64_TYPE - Static variable in class loci.formats.in.KLBReader
 
FloatIM3Record(String, int, long, int) - Constructor for class loci.formats.in.IM3Reader.FloatIM3Record
 
floatValue() - Method in class loci.formats.tiff.TiffRational
Returns the value of the specified number as a float.
FLOW_DATA_IDENTIFIER - Static variable in class loci.formats.in.SDTInfo
For .sdt files created automatically in Continuous Flow mode measurement (no setup, only data).
FlowSightReader - Class in loci.formats.in
 
FlowSightReader() - Constructor for class loci.formats.in.FlowSightReader
 
fluor - Variable in class loci.formats.in.ZeissCZIReader.Channel
 
FLUOVIEW_MAGIC_STRING - Static variable in class loci.formats.in.FluoviewReader
String identifying a Fluoview file.
FluoviewReader - Class in loci.formats.in
FluoviewReader is the file format reader for Olympus Fluoview TIFF files AND Andor Bio-imaging Division (ABD) TIFF files.
FluoviewReader() - Constructor for class loci.formats.in.FluoviewReader
Constructs a new Fluoview TIFF reader.
flush() - Method in class loci.plugins.config.TextAreaWriter
Flushing a TextAreaWriter does nothing .
flushBlockSize - Variable in class loci.formats.in.OBFReader.Stack
 
flushPoints - Variable in class loci.formats.in.OBFReader.Stack
 
fmt - Variable in class loci.formats.in.GelReader
 
fmt - Variable in class loci.formats.in.OpenlabReader
 
FOCAL_LENGTH - Static variable in class loci.formats.tiff.IFD
 
FOCAL_LENGTH_35MM_FILM - Static variable in class loci.formats.tiff.IFD
 
FOCAL_PLANE_RESOLUTION_UNIT - Static variable in class loci.formats.tiff.IFD
 
FOCAL_PLANE_X_RESOLUTION - Static variable in class loci.formats.tiff.IFD
 
FOCAL_PLANE_Y_RESOLUTION - Static variable in class loci.formats.tiff.IFD
 
FOCUS_IMAGE - Static variable in class loci.formats.in.CellSensReader
 
FOCUS_MODE - Static variable in class loci.formats.in.NikonReader
 
FOCUS_OFFSET - Static variable in class loci.formats.in.NDPIReader
 
FOCUS_POINT_REGIONS - Static variable in class loci.formats.in.NDPIReader
 
FOCUS_TIME - Static variable in class loci.formats.in.NDPIReader
 
focusGained(FocusEvent) - Method in class loci.plugins.in.MainDialog
Handles information pane updates when component focus changes.
focusLost(FocusEvent) - Method in class loci.plugins.in.MainDialog
 
font - Variable in class loci.formats.tools.MakeTestOmeTiff.TextLine
 
fontName - Variable in class loci.formats.in.BaseZeissReader.Shape
 
fontName - Variable in class loci.formats.in.LeicaHandler.ROI
 
fontName - Variable in class loci.formats.in.LIFReader.ROI
 
fontSize - Variable in class loci.formats.in.BaseZeissReader.Shape
 
fontSize - Variable in class loci.formats.in.GatanReader.ROIShape
 
fontSize - Variable in class loci.formats.in.LeicaHandler.ROI
 
fontSize - Variable in class loci.formats.in.LIFReader.ROI
 
fontWeight - Variable in class loci.formats.in.BaseZeissReader.Shape
 
FOOTER_SIZE - Static variable in class loci.formats.in.SIFReader
 
footerPointer - Variable in class loci.formats.out.APNGWriter
 
force - Variable in class loci.formats.gui.DataConverter
 
forceType - Variable in class loci.formats.gui.DataConverter
 
forkFile - Variable in class loci.formats.in.NativeQTReader
 
format - Variable in class loci.formats.FormatHandler
Name of this file format.
formatCompression(IFD) - Method in class loci.formats.out.TiffWriter
Sets the compression code for the specified IFD.
FormatEntry - Class in loci.plugins.config
A list entry for the configuration window's Formats tab.
FormatEntry(PrintWriter, Object) - Constructor for class loci.plugins.config.FormatEntry
 
FormatException - Exception in loci.formats
FormatException is the exception thrown when something goes wrong performing a file format operation.
FormatException() - Constructor for exception loci.formats.FormatException
 
FormatException(String) - Constructor for exception loci.formats.FormatException
 
FormatException(String, Throwable) - Constructor for exception loci.formats.FormatException
 
FormatException(Throwable) - Constructor for exception loci.formats.FormatException
 
FormatFileFilter - Class in loci.formats.gui
A file filter for a biological file format, for use with a JFileChooser.
FormatFileFilter(IFormatReader) - Constructor for class loci.formats.gui.FormatFileFilter
Constructs a new filter that accepts files of the given reader's type.
FormatFileFilter(IFormatReader, boolean) - Constructor for class loci.formats.gui.FormatFileFilter
Constructs a new filter that accepts files of the given reader's type, allowing the reader to open files only if the allowOpen flag is set.
FormatHandler - Class in loci.formats
Abstract superclass of all biological file format readers and writers.
FormatHandler(String, String) - Constructor for class loci.formats.FormatHandler
Constructs a format handler with the given name and default suffix.
FormatHandler(String, String[]) - Constructor for class loci.formats.FormatHandler
Constructs a format handler with the given name and default suffixes.
formatHex(int) - Method in class loci.formats.in.BaseZeissReader.Shape
 
formatInfo - Variable in class loci.plugins.config.ConfigWindow
 
formatLabel - Variable in class loci.formats.gui.PreviewPane
Labels containing thumbnail and dimensional information.
formatMetadata(String, String) - Static method in class loci.formats.in.IonpathMIBITiffReader
 
formatName - Variable in class loci.plugins.config.FormatEntry
 
FormatReader - Class in loci.formats
Abstract superclass of all biological file format readers.
FormatReader(String, String) - Constructor for class loci.formats.FormatReader
Constructs a format reader with the given name and default suffix.
FormatReader(String, String[]) - Constructor for class loci.formats.FormatReader
Constructs a format reader with the given name and default suffixes.
FORMATS - Static variable in class loci.formats.in.GelReader
 
formatsList - Variable in class loci.plugins.config.ConfigWindow
 
formatsListModel - Variable in class loci.plugins.config.ConfigWindow
 
formatTag(int) - Method in class loci.formats.in.DicomReader
 
formatText - Variable in class loci.formats.gui.PreviewPane
 
formatTip - Variable in class loci.formats.gui.PreviewPane
 
FormatTools - Class in loci.formats
A utility class for format reader and writer implementations.
FormatTools() - Constructor for class loci.formats.FormatTools
 
FormatWriter - Class in loci.formats
Abstract superclass of all biological file format writers.
FormatWriter(String, String) - Constructor for class loci.formats.FormatWriter
Constructs a format writer with the given name and default suffix.
FormatWriter(String, String[]) - Constructor for class loci.formats.FormatWriter
Constructs a format writer with the given name and default suffixes.
FORWARD_ORDER - Static variable in interface loci.formats.cache.ICacheStrategy
 
fos - Variable in class loci.formats.Memoizer.KryoDeser
 
found - Variable in class loci.formats.in.ZeissTIFFHandler.TagSet
 
foundChannelTag - Variable in class loci.formats.in.CellSensReader
 
foundMontage - Variable in class loci.formats.in.GatanReader
 
foundPlateLayout - Variable in class loci.formats.in.ScanrReader.ScanrHandler
 
foundPositions - Variable in class loci.formats.in.ScanrReader
 
fp - Variable in class loci.formats.AxisGuesser
File pattern identifying dimensional axis blocks.
fp - Variable in class loci.plugins.in.FilePatternDialog
 
fps - Variable in class loci.formats.FormatWriter
Frame rate to use when writing in frames per second, if applicable.
fps - Variable in class loci.formats.gui.DataConverter
 
fps - Variable in class loci.formats.gui.ImageViewer
 
fpsSpin - Variable in class loci.plugins.util.DataBrowser
 
Frame(PrairieMetadata.Sequence, Element) - Constructor for class loci.formats.in.PrairieMetadata.Frame
Creates a new frame by parsing the given <Frame> element.
frame - Variable in class loci.formats.in.PrairieMetadata.PFile
The <Frame> containing this <File>.
FRAME_OFFSET - Static variable in class loci.formats.out.AVIWriter
 
FRAME_OFFSET_2 - Static variable in class loci.formats.out.AVIWriter
 
FRAME_ORIGIN - Static variable in class loci.formats.in.CellSensReader
 
FRAME_PROPERTIES - Static variable in class loci.formats.in.CellSensReader
 
FRAME_SCALE - Static variable in class loci.formats.in.CellSensReader
 
FRAME_SIZE - Static variable in class loci.formats.in.CellSensReader
 
FRAME_TRANSFER - Static variable in class loci.formats.in.CellSensReader
 
FRAME_TYPE - Static variable in class loci.formats.in.CellSensReader
 
frameClockList - Variable in class loci.formats.in.SPCReader
 
frameCoordinates - Variable in class loci.formats.in.APNGReader
 
frameIndex(PrairieMetadata.Sequence, int, int, int) - Method in class loci.formats.in.PrairieReader
Gets the frame index associated with the given (Z, T) position of the specified series.
frames - Variable in class loci.formats.in.PrairieMetadata.Sequence
<Frame> elements beneath this <Sequence>, keyed on each frame's index.
framesAreTime - Variable in class loci.formats.in.PrairieReader
Whether a series uses Frames as time points rather than focal planes (i.e., sizeZ and sizeT values inverted).
frameValues - Variable in class loci.formats.in.PrairieMetadata.Frame
Table of key/value pairs for this <Frame>.
FREE_BYTE_COUNTS - Static variable in class loci.formats.tiff.IFD
 
FREE_LINE - Static variable in class loci.formats.in.FV1000Reader
 
FREE_OFFSETS - Static variable in class loci.formats.tiff.IFD
 
FREE_SHAPE - Static variable in class loci.formats.in.FV1000Reader
 
frequencies - Variable in class loci.formats.in.LiFlimReader
 
FREQUENCY - Static variable in class loci.formats.FormatTools
Identifies the Frequency dimensional type, representing a dimension consisting of frequencies.
fromCIEXYZ(float[]) - Method in class loci.formats.gui.TwoChannelColorSpace
 
fromRGB(float[]) - Method in class loci.formats.gui.TwoChannelColorSpace
 
FujiReader - Class in loci.formats.in
FujiReader is the file format reader for Fuji LAS 3000 datasets.
FujiReader() - Constructor for class loci.formats.in.FujiReader
Constructs a new Fuji reader.
fullImage - Variable in class loci.formats.in.MRWReader
 
FULLY_AUTO_FOCUS - Static variable in class loci.formats.in.NDPIReader
 
FV1000_MAGIC_STRING_1 - Static variable in class loci.formats.in.FV1000Reader
 
FV1000_MAGIC_STRING_2 - Static variable in class loci.formats.in.FV1000Reader
 
FV1000_SUFFIXES - Static variable in class loci.formats.in.FV1000Reader
 
FV1000Reader - Class in loci.formats.in
FV1000Reader is the file format reader for Fluoview FV 1000 OIB and Fluoview FV 1000 OIF files.
FV1000Reader() - Constructor for class loci.formats.in.FV1000Reader
Constructs a new FV1000 reader.
FV1000Reader.ChannelData - Class in loci.formats.in
 
FV1000Reader.PlaneData - Class in loci.formats.in
 

G

gain - Variable in class loci.formats.in.BDReader
 
gain - Variable in class loci.formats.in.BioRadReader
 
gain - Variable in class loci.formats.in.BioRadSCNReader
 
gain - Variable in class loci.formats.in.CellSensReader.Pyramid
 
gain - Variable in class loci.formats.in.FV1000Reader.ChannelData
 
gain - Variable in class loci.formats.in.ImarisHDFReader
 
gain - Variable in class loci.formats.in.InCellReader
 
gain - Variable in class loci.formats.in.IvisionReader
 
gain - Variable in class loci.formats.in.LeicaHandler.Channel
 
gain - Variable in class loci.formats.in.MetamorphHandler
 
gain - Variable in class loci.formats.in.MetamorphReader
 
gain - Variable in class loci.formats.in.MicromanagerReader.Position
 
gain - Variable in class loci.formats.in.ND2Handler
 
gain - Variable in class loci.formats.in.NikonTiffReader
 
gain - Variable in class loci.formats.in.OIRReader.Detector
 
gain - Variable in class loci.formats.in.OpenlabReader
 
gain - Variable in class loci.formats.in.ZeissCZIReader.Channel
 
gain - Variable in class loci.formats.in.ZeissCZIReader
 
gain - Variable in class loci.formats.in.ZeissLSMReader.DetectionChannel
 
GAIN_CONTROL - Static variable in class loci.formats.tiff.IFD
 
GAIN_UNIT - Static variable in class loci.formats.in.CellSensReader
 
gains - Variable in class loci.formats.in.FluoviewReader
 
gains - Variable in class loci.formats.in.LIFReader
 
gains - Variable in class loci.formats.in.ZeissCZIReader
 
gamma - Variable in class loci.formats.in.GatanReader
 
gamma(double) - Method in class loci.plugins.util.RecordedImageProcessor
 
GAMMA_CORRECTION - Static variable in class loci.formats.in.CellSensReader
 
GatanDM2Reader - Class in loci.formats.in
GatanDM2Reader is the file format reader for Gatan .dm2 files.
GatanDM2Reader() - Constructor for class loci.formats.in.GatanDM2Reader
Constructs a new Gatan .dm2 reader.
GatanReader - Class in loci.formats.in
GatanReader is the file format reader for Gatan files.
GatanReader() - Constructor for class loci.formats.in.GatanReader
Constructs a new Gatan reader.
GatanReader.ROIShape - Class in loci.formats.in
 
gct - Variable in class loci.formats.in.GIFReader
Global color table.
GEL_DOMAIN - Static variable in class loci.formats.FormatTools
Identifies the gel and blot imaging domain.
GelReader - Class in loci.formats.in
GelReader is the file format reader for Molecular Dynamics GEL TIFF files.
GelReader() - Constructor for class loci.formats.in.GelReader
Constructs a new GEL reader.
generateMemo(String) - Method in class loci.formats.Memoizer
Convenience method to generate (or regenerate) the memo file for a given file.
generateScreen(int, int, int, int, int) - Method in class loci.formats.tools.FakeImage
Creates a fake SPW file/directory structure.
get(int) - Method in class loci.formats.codec.ByteVector
 
get(int) - Static method in enum loci.formats.codec.CompressionType
Retrieves the compression by reverse lookup of its "code".
get(int) - Static method in enum loci.formats.codec.JPEG2000BoxType
Retrieves the box type by reverse lookup of its "code".
get(int) - Static method in enum loci.formats.codec.JPEG2000SegmentMarker
Retrieves the segment marker by reverse lookup of its "code".
get(int) - Static method in enum loci.formats.in.BaseZeissReader.Charset
 
get(int) - Static method in enum loci.formats.in.BaseZeissReader.DrawStyle
 
get(int) - Static method in enum loci.formats.in.BaseZeissReader.FeatureType
 
get(int) - Static method in enum loci.formats.in.BaseZeissReader.FillStyle
 
get(int) - Static method in enum loci.formats.in.BaseZeissReader.LineEndPositions
 
get(int) - Static method in enum loci.formats.in.BaseZeissReader.LineEndStyle
 
get(int) - Static method in enum loci.formats.in.BaseZeissReader.PointStyle
 
get(int) - Static method in enum loci.formats.in.BaseZeissReader.TextAlignment
 
get(String) - Method in class loci.formats.in.DynamicMetadataOptions
Get the value of property name.
get(String, String) - Method in class loci.formats.in.DynamicMetadataOptions
Get the value of property name.
get(Object) - Method in interface loci.formats.in.PrairieMetadata.Value
 
get(int) - Method in interface loci.formats.in.PrairieMetadata.Value
 
get(Object) - Method in class loci.formats.in.PrairieMetadata.ValueItem
 
get(int) - Method in class loci.formats.in.PrairieMetadata.ValueItem
 
get(int) - Method in class loci.formats.in.PrairieMetadata.ValueTable
 
get(int, int) - Method in class loci.formats.MetadataList
Get the array element for the specified indexes.
get(int) - Static method in enum loci.formats.tiff.IFDType
Retrieves a IFD type by reverse lookup of its "code".
get(int) - Method in class loci.formats.tiff.OnDemandLongArray
 
get(int) - Static method in enum loci.formats.tiff.PhotoInterp
Retrieves a photometric interpretation by reverse lookup of its "code".
get(int) - Static method in enum loci.formats.tiff.TiffCompression
Retrieves a TIFF compression instance by code.
get(List<T>, int, T) - Method in class loci.plugins.in.ImporterOptions
 
get(int) - Method in class loci.plugins.util.RecordedImageProcessor
 
get(int, int) - Method in class loci.plugins.util.RecordedImageProcessor
 
get16BitLookupTable() - Method in class loci.formats.ChannelFiller
 
get16BitLookupTable() - Method in class loci.formats.DelegateReader
 
get16BitLookupTable() - Method in class loci.formats.FileStitcher
 
get16BitLookupTable() - Method in class loci.formats.FormatReader
 
get16BitLookupTable() - Method in interface loci.formats.IFormatReader
Gets the 16-bit color lookup table associated with the most recently opened image.
get16BitLookupTable() - Method in class loci.formats.ImageReader
 
get16BitLookupTable() - Method in class loci.formats.in.BaseZeissReader
 
get16BitLookupTable() - Method in class loci.formats.in.DicomReader
 
get16BitLookupTable() - Method in class loci.formats.in.FakeReader
 
get16BitLookupTable() - Method in class loci.formats.in.FilePatternReader
 
get16BitLookupTable() - Method in class loci.formats.in.FV1000Reader
 
get16BitLookupTable() - Method in class loci.formats.in.ImarisHDFReader
 
get16BitLookupTable() - Method in class loci.formats.in.ImprovisionTiffReader
 
get16BitLookupTable() - Method in class loci.formats.in.InCellReader
 
get16BitLookupTable() - Method in class loci.formats.in.JPEG2000Reader
 
get16BitLookupTable() - Method in class loci.formats.in.JPXReader
 
get16BitLookupTable() - Method in class loci.formats.in.LeicaReader
 
get16BitLookupTable() - Method in class loci.formats.in.LIFReader
 
get16BitLookupTable() - Method in class loci.formats.in.MIASReader
 
get16BitLookupTable() - Method in class loci.formats.in.MinimalTiffReader
 
get16BitLookupTable() - Method in class loci.formats.in.NativeND2Reader
 
get16BitLookupTable() - Method in class loci.formats.in.OIRReader
 
get16BitLookupTable() - Method in class loci.formats.in.OMETiffReader
 
get16BitLookupTable() - Method in class loci.formats.in.PDSReader
 
get16BitLookupTable() - Method in class loci.formats.in.PerkinElmerReader
 
get16BitLookupTable() - Method in class loci.formats.in.SlidebookTiffReader
 
get16BitLookupTable() - Method in class loci.formats.in.TCSReader
 
get16BitLookupTable() - Method in class loci.formats.in.VentanaReader
 
get16BitLookupTable() - Method in class loci.formats.in.ZeissCZIReader
 
get16BitLookupTable() - Method in class loci.formats.in.ZeissLSMReader
 
get16BitLookupTable() - Method in class loci.formats.in.ZipReader
 
get16BitLookupTable() - Method in class loci.formats.ReaderWrapper
 
get16BitLookupTable() - Method in class loci.formats.WrappedReader
 
get8BitLookupTable() - Method in class loci.formats.ChannelFiller
 
get8BitLookupTable() - Method in class loci.formats.DelegateReader
 
get8BitLookupTable() - Method in class loci.formats.FileStitcher
 
get8BitLookupTable() - Method in class loci.formats.FormatReader
 
get8BitLookupTable(ColorModel) - Static method in class loci.formats.gui.AWTImageTools
Converts an IndexColorModel to a 2D byte array.
get8BitLookupTable() - Method in interface loci.formats.IFormatReader
Gets the 8-bit color lookup table associated with the most recently opened image.
get8BitLookupTable() - Method in class loci.formats.ImageReader
 
get8BitLookupTable() - Method in class loci.formats.in.AmiraReader
 
get8BitLookupTable() - Method in class loci.formats.in.APNGReader
 
get8BitLookupTable() - Method in class loci.formats.in.AVIReader
 
get8BitLookupTable() - Method in class loci.formats.in.BaseZeissReader
 
get8BitLookupTable() - Method in class loci.formats.in.BDVReader
 
get8BitLookupTable() - Method in class loci.formats.in.BioRadReader
 
get8BitLookupTable() - Method in class loci.formats.in.BMPReader
 
get8BitLookupTable() - Method in class loci.formats.in.CellH5Reader
 
get8BitLookupTable() - Method in class loci.formats.in.DicomReader
 
get8BitLookupTable() - Method in class loci.formats.in.FakeReader
 
get8BitLookupTable() - Method in class loci.formats.in.FilePatternReader
 
get8BitLookupTable() - Method in class loci.formats.in.GIFReader
 
get8BitLookupTable() - Method in class loci.formats.in.ImarisHDFReader
 
get8BitLookupTable() - Method in class loci.formats.in.ImprovisionTiffReader
 
get8BitLookupTable() - Method in class loci.formats.in.InCellReader
 
get8BitLookupTable() - Method in class loci.formats.in.IPWReader
 
get8BitLookupTable() - Method in class loci.formats.in.JPEG2000Reader
 
get8BitLookupTable() - Method in class loci.formats.in.JPXReader
 
get8BitLookupTable() - Method in class loci.formats.in.KhorosReader
 
get8BitLookupTable() - Method in class loci.formats.in.LeicaReader
 
get8BitLookupTable() - Method in class loci.formats.in.LIFReader
 
get8BitLookupTable() - Method in class loci.formats.in.MIASReader
 
get8BitLookupTable() - Method in class loci.formats.in.MinimalTiffReader
 
get8BitLookupTable() - Method in class loci.formats.in.NativeND2Reader
 
get8BitLookupTable() - Method in class loci.formats.in.OIRReader
 
get8BitLookupTable() - Method in class loci.formats.in.OMETiffReader
 
get8BitLookupTable() - Method in class loci.formats.in.OpenlabReader
 
get8BitLookupTable() - Method in class loci.formats.in.PCXReader
 
get8BitLookupTable() - Method in class loci.formats.in.PerkinElmerReader
 
get8BitLookupTable() - Method in class loci.formats.in.PictReader
 
get8BitLookupTable() - Method in class loci.formats.in.PSDReader
 
get8BitLookupTable() - Method in class loci.formats.in.SlidebookTiffReader
 
get8BitLookupTable() - Method in class loci.formats.in.TargaReader
 
get8BitLookupTable() - Method in class loci.formats.in.TCSReader
 
get8BitLookupTable() - Method in class loci.formats.in.VentanaReader
 
get8BitLookupTable() - Method in class loci.formats.in.ZeissCZIReader
 
get8BitLookupTable() - Method in class loci.formats.in.ZeissLMSReader
 
get8BitLookupTable() - Method in class loci.formats.in.ZeissLSMReader
 
get8BitLookupTable() - Method in class loci.formats.in.ZipReader
 
get8BitLookupTable() - Method in class loci.formats.ReaderWrapper
 
get8BitLookupTable() - Method in class loci.formats.WrappedReader
 
getAbsoluteTime() - Method in class loci.formats.in.PrairieMetadata.Frame
Gets the absoluteTime associated with this Frame.
getAcquisitionMode(String) - Method in class loci.formats.FormatReader
getAcquisitionMode(String) - Method in class loci.formats.in.OperettaReader
 
getAcquisitionMode(String) - Static method in class loci.formats.MetadataTools
Retrieves an AcquisitionMode enumeration value for the given String.
getActiveChannels() - Method in class loci.formats.in.PrairieMetadata
Gets the list of active channel indices, in sorted order.
getAdjustedIndex(int) - Method in class loci.formats.FileStitcher
Gets the local reader index for use with the given image plane.
getAdjustedOrder() - Method in class loci.formats.AxisGuesser
Gets the adjusted dimension order.
getAdvancedSeriesUsedFiles(boolean) - Method in class loci.formats.FileStitcher
 
getAdvancedSeriesUsedFiles(boolean) - Method in class loci.formats.FormatReader
 
getAdvancedSeriesUsedFiles(boolean) - Method in interface loci.formats.IFormatReader
Returns an array of FileInfo objects representing the files needed to open the current series.
getAdvancedSeriesUsedFiles(boolean) - Method in class loci.formats.ImageReader
 
getAdvancedSeriesUsedFiles(boolean) - Method in class loci.formats.ReaderWrapper
 
getAdvancedUsedFiles(boolean) - Method in class loci.formats.FileStitcher
 
getAdvancedUsedFiles(boolean) - Method in class loci.formats.FormatReader
 
getAdvancedUsedFiles(boolean) - Method in interface loci.formats.IFormatReader
Returns an array of FileInfo objects representing the files needed to open this dataset.
getAdvancedUsedFiles(boolean) - Method in class loci.formats.ImageReader
 
getAdvancedUsedFiles(boolean) - Method in class loci.formats.ReaderWrapper
 
getAllChildren(Integer) - Method in class loci.formats.in.VolocityReader
 
getAllFiles(String) - Method in class loci.formats.FilePattern
 
getAlpha(int) - Method in class loci.formats.gui.Index16ColorModel
 
getAlpha(int) - Method in class loci.formats.gui.SignedColorModel
 
getAlpha(Object) - Method in class loci.formats.gui.SignedColorModel
 
getAlpha(int) - Method in class loci.formats.gui.UnsignedIntColorModel
 
getAlpha(Object) - Method in class loci.formats.gui.UnsignedIntColorModel
 
getAlphas() - Method in class loci.formats.gui.Index16ColorModel
Return the array of alpha color components.
getArcType(String) - Method in class loci.formats.FormatReader
getArcType(String) - Static method in class loci.formats.MetadataTools
Retrieves an ArcType enumeration value for the given String.
getArray(String, int[], int[]) - Method in interface loci.formats.services.NetCDFService
Retrieves an HDF path's values.
getArray(String, int[], int[]) - Method in class loci.formats.services.NetCDFServiceImpl
 
getAttributeList() - Method in interface loci.formats.services.NetCDFService
Retrieves an exhaustive list of the HDF paths for all attributes in the HDF document.
getAttributeList() - Method in class loci.formats.services.NetCDFServiceImpl
 
getAttributeValue(String) - Method in interface loci.formats.services.NetCDFService
Retrieves an attribute's value.
getAttributeValue(String) - Method in class loci.formats.services.NetCDFServiceImpl
 
getAutoscaleInfo() - Method in class loci.plugins.in.ImporterOptions
 
getAutoThreshold() - Method in class loci.plugins.util.RecordedImageProcessor
 
getAutoThreshold(int[]) - Method in class loci.plugins.util.RecordedImageProcessor
 
getAvailableMemory() - Method in class loci.plugins.in.MemoryDialog
 
getAxisCount(int) - Method in class loci.formats.AxisGuesser
Gets the number of axes in the pattern of the given type.
getAxisCountC() - Method in class loci.formats.AxisGuesser
Gets the number of C axes in the pattern.
getAxisCountS() - Method in class loci.formats.AxisGuesser
Gets the number of S axes in the pattern.
getAxisCountT() - Method in class loci.formats.AxisGuesser
Gets the number of T axes in the pattern.
getAxisCountZ() - Method in class loci.formats.AxisGuesser
Gets the number of Z axes in the pattern.
getAxisGuesser() - Method in class loci.formats.FileStitcher.ExternalSeries
 
getAxisGuesser() - Method in class loci.formats.FileStitcher
Gets the axis guesser object used to guess which dimensional axes are which.
getAxisType(String) - Static method in class loci.formats.AxisGuesser
Convert the given label to an axis type.
getAxisTypes() - Method in class loci.formats.AxisGuesser
Gets the guessed axis type for each dimensional block.
getAxisTypes() - Method in class loci.formats.FileStitcher
Gets the axis type for each dimensional block.
getBackgroundValue() - Method in class loci.plugins.util.RecordedImageProcessor
 
getBaseReader() - Method in class loci.plugins.in.ImportProcess
Valid only after ImportStep.READER.
getBestIndex(Color) - Method in class loci.plugins.util.RecordedImageProcessor
 
getBGRComponents(short[]) - Method in class loci.formats.services.JPEGXRServiceImpl
 
getBinaryOnlyOMEXML(String, String, String) - Method in class loci.formats.out.OMETiffWriter
 
getBinning(String) - Method in class loci.formats.FormatReader
getBinning() - Method in class loci.formats.in.MetamorphHandler
 
getBinning(String) - Static method in class loci.formats.MetadataTools
Retrieves an Binning enumeration value for the given String.
getBinnings() - Method in class loci.formats.in.ND2Handler
 
getBitDepth() - Method in class loci.formats.in.PrairieMetadata
Gets the bitDepth recorded in the configuration.
getBits(int) - Method in class loci.formats.codec.BitBuffer
Deprecated.
Returns an int value representing the value of the bits read from the byte array, from the current position.
getBitsPerPixel() - Method in class loci.formats.FileStitcher
 
getBitsPerPixel() - Method in class loci.formats.FormatReader
 
getBitsPerPixel() - Method in interface loci.formats.IFormatReader
Gets the number of valid bits per pixel.
getBitsPerPixel() - Method in class loci.formats.ImageReader
 
getBitsPerPixel(int) - Method in class loci.formats.in.OBFReader
 
getBitsPerPixel() - Method in class loci.formats.ReaderWrapper
 
getBitsPerPixel() - Method in class loci.formats.WrappedReader
 
getBitsPerSample(int) - Method in class loci.formats.in.NDPIReader
Get the number of bits per sample associated with the given capture mode.
getBitsPerSample() - Method in class loci.formats.tiff.IFD
Retrieves the image's bits per sample (TIFF tag BitsPerSample) from a given TIFF IFD.
getBlankThumbBytes() - Method in class loci.formats.FileStitcher.ExternalSeries
 
getBlock(int) - Method in class loci.formats.FilePattern
Gets the specified file pattern block (e.g., <0-9>).
getBlock() - Method in class loci.formats.FilePatternBlock
Gets the block string.
getBlock(String) - Method in class loci.formats.in.OIRReader
 
getBlock(int, String) - Method in class loci.formats.in.ScanrReader
 
getBlocks() - Method in class loci.formats.FilePattern
Gets all file pattern blocks.
getBlue(int) - Method in class loci.formats.gui.Index16ColorModel
 
getBlue(int) - Method in class loci.formats.gui.SignedColorModel
 
getBlue(Object) - Method in class loci.formats.gui.SignedColorModel
 
getBlue(int) - Method in class loci.formats.gui.UnsignedIntColorModel
 
getBlue(Object) - Method in class loci.formats.gui.UnsignedIntColorModel
 
getBlueOffset(int) - Static method in class org.libjpegturbo.turbojpeg.TJ
For the given pixel format, returns the number of bytes that the blue component is offset from the start of the pixel.
getBlues() - Method in class loci.formats.gui.Index16ColorModel
Return the array of blue color components.
getBoolean(String) - Method in class loci.formats.in.DynamicMetadataOptions
Get the value of property name as a Boolean.
getBoolean(String, Boolean) - Method in class loci.formats.in.DynamicMetadataOptions
Get the value of property name as a Boolean.
getBooleanOption(String) - Method in class loci.plugins.prefs.OptionsList
Gets the boolean option with the given key.
getBooleanValue(String) - Method in class loci.plugins.Slicer
Gets the value of the given macro key as a boolean.
getBounds(BigInteger[], boolean) - Static method in class loci.formats.FilePattern
Gets a string containing start, end and step values for a sorted list of numbers.
getBufferedImage() - Method in class loci.plugins.util.RecordedImageProcessor
 
getBuildDate(String[]) - Method in class loci.plugins.macro.LociFunctions
 
getByte(SPEReader.SpeHeaderEntry) - Method in class loci.formats.in.SPEReader.SpeHeader
Method used to retrieve data values for Byte entries into the SPE header table
getByte(int) - Method in class loci.formats.in.SPEReader.SpeHeader
Private method used to retrieve a Byte value from the SPE header
getByteBuffer() - Method in class loci.formats.codec.BitBuffer
Deprecated.
Return the backing byte array.
getBytes(BufferedImage) - Static method in class loci.formats.gui.AWTImageTools
Extracts pixel data as arrays of unsigned bytes, one per channel.
getBytes(WritableRaster) - Static method in class loci.formats.gui.AWTImageTools
Extracts pixel data as arrays of unsigned bytes, one per channel.
getBytes(WritableRaster, int, int, int, int) - Static method in class loci.formats.gui.AWTImageTools
Extracts pixel data as arrays of unsigned bytes, one per channel.
getBytes(BufferedImage, boolean) - Static method in class loci.formats.gui.AWTImageTools
Get the bytes from an image, merging the channels as necessary.
getBytesPerElement() - Method in enum loci.formats.tiff.IFDType
Retrieves the number of bytes per element.
getBytesPerPixel(int) - Static method in class loci.formats.FormatTools
Retrieves how many bytes per pixel the current plane or section has.
getBytesPerPixel(String) - Static method in class loci.formats.FormatTools
Retrieves the number of bytes per pixel in the current plane.
getBytesPerPixel(int) - Method in class loci.formats.in.LegacyND2Reader
 
getBytesPerSample() - Method in class loci.formats.tiff.IFD
Retrieves the image's bytes per sample (derived from tag BitsPerSample) from this IFD.
getC() - Method in class loci.formats.gui.ImageViewer
Gets the C value of the currently displayed image.
getCache() - Method in class loci.formats.gui.CacheComponent
 
getCache() - Method in class loci.plugins.util.BFVirtualStack
 
getCacheListeners() - Method in class loci.formats.cache.Cache
 
getCacheListeners() - Method in interface loci.formats.cache.CacheReporter
Gets a list of all registered status update listeners.
getCacheListeners() - Method in class loci.formats.cache.CacheStrategy
 
getCalibrationTable() - Method in class loci.plugins.util.RecordedImageProcessor
 
getCameraModel() - Method in class loci.formats.in.ND2Handler
 
getCaptureMode(int) - Method in class loci.formats.in.NDPIReader
Get the description of the given capture mode.
getCategory() - Method in class loci.formats.in.BaseZeissReader.Tag
 
getCBegin(int) - Method in class loci.plugins.in.ImporterOptions
 
getCBegin(int) - Method in class loci.plugins.in.ImportProcess
 
getCCount(int) - Method in class loci.plugins.in.ImportProcess
Valid only after ImportStep.SERIES.
getCEnd(int) - Method in class loci.plugins.in.ImporterOptions
 
getCEnd(int) - Method in class loci.plugins.in.ImportProcess
Valid only after ImportStep.STACK.
getChannel(String) - Method in class loci.formats.in.CellomicsReader
 
getChannel() - Method in class loci.formats.in.PrairieMetadata.PFile
Gets the channel associated with this File.
getChannelColor(int) - Method in class loci.formats.in.LIFReader
 
getChannelColorFromFile(String) - Method in class loci.formats.in.MIASReader
Get the color associated with the given file's channel.
getChannelColors() - Method in class loci.formats.in.ND2Handler
 
getChannelCount() - Method in class loci.formats.in.SDTReader
Gets the number of spectral channels.
getChannelDescriptionNodes(Element) - Method in class loci.formats.in.LIFReader
 
getChannelDimCount(Double[]) - Method in class loci.plugins.macro.LociFunctions
 
getChannelDimLength(Double, Double[]) - Method in class loci.plugins.macro.LociFunctions
 
getChannelDimType(Double, Double[]) - Method in class loci.plugins.macro.LociFunctions
 
getChannelFiller() - Method in class loci.plugins.in.ImportProcess
Valid only after ImportStep.STACK.
getChannelGlobalMaximum(int) - Method in class loci.formats.MinMaxCalculator
Retrieves a specified channel's global maximum.
getChannelGlobalMinimum(int) - Method in class loci.formats.MinMaxCalculator
Retrieves a specified channel's global minimum.
getChannelIndex(Element) - Method in class loci.formats.in.LIFReader
 
getChannelIndexOfCellObjectName(String) - Method in class loci.formats.in.BDVReader
 
getChannelIndexOfCellObjectName(String) - Method in class loci.formats.in.CellH5Reader
 
getChannelKnownMaximum(int) - Method in class loci.formats.MinMaxCalculator
Retrieves the specified channel's maximum based on the images that have been read.
getChannelKnownMinimum(int) - Method in class loci.formats.MinMaxCalculator
Retrieves the specified channel's minimum based on the images that have been read.
getChannelLabel(int) - Method in class loci.formats.in.TextReader
Gets the label for the given channel.
getChannelName(int, int, int, int) - Method in class loci.formats.in.LegacyND2Reader
 
getChannelName() - Method in class loci.formats.in.MetamorphHandler
 
getChannelName() - Method in class loci.formats.in.PrairieMetadata.PFile
Gets the channelName associated with this File.
getChannelNames() - Method in class loci.formats.in.MetamorphHandler
 
getChannelNames() - Method in class loci.formats.in.ND2Handler
 
getChannels(int) - Method in class loci.formats.in.LegacyND2Reader
 
getChannelSeparator() - Method in class loci.plugins.in.ImportProcess
Valid only after ImportStep.STACK.
getChar(int) - Method in class loci.formats.tools.AsciiImage
 
getCheckboxes(GenericDialog) - Static method in class loci.plugins.util.WindowTools
 
getChild(Element, String) - Static method in class loci.formats.in.CellVoyagerReader
 
getChild(Element, String[]) - Static method in class loci.formats.in.CellVoyagerReader
 
getChild() - Method in class loci.plugins.util.RecordedImageProcessor
 
getChildIndex(Integer, String) - Method in class loci.formats.in.VolocityReader
 
getChildNodes(Element) - Method in class loci.formats.in.OBFReader
 
getChildren(Element, String) - Static method in class loci.formats.in.CellVoyagerReader
 
getChildText(Element, String[]) - Static method in class loci.formats.in.CellVoyagerReader
 
getChildText(Element, String) - Static method in class loci.formats.in.CellVoyagerReader
 
getChoices(GenericDialog) - Static method in class loci.plugins.util.WindowTools
 
getClass(String) - Method in class loci.formats.in.DynamicMetadataOptions
Get the value of property name as a class.
getClass(String, Class<?>) - Method in class loci.formats.in.DynamicMetadataOptions
Get the value of property name as a class.
getClasses() - Method in class loci.formats.ClassList
Gets the list of classes as an array.
getCode() - Method in enum loci.formats.codec.CompressionType
Implemented as specified by the CodedEnum I/F.
getCode() - Method in enum loci.formats.codec.JPEG2000BoxType
Implemented as specified by the CodedEnum I/F.
getCode() - Method in enum loci.formats.codec.JPEG2000SegmentMarker
Implemented as specified by the CodedEnum I/F.
getCode() - Method in enum loci.formats.tiff.IFDType
 
getCode() - Method in enum loci.formats.tiff.PhotoInterp
 
getCode() - Method in enum loci.formats.tiff.TiffCompression
 
getCodecName(int) - Method in class loci.formats.in.AVIReader
 
getCodecName() - Method in enum loci.formats.tiff.TiffCompression
Retrieves the name of the TIFF compression codec.
getCodecOptions() - Method in class loci.formats.tiff.TiffParser
Retrieves the current set of codec options being used to decompress pixel data.
getCodestreamOffset() - Method in class loci.formats.in.JPEG2000MetadataParser
Retrieves the offset to the first contiguous codestream.
getCodestreamPixelType() - Method in class loci.formats.in.JPEG2000MetadataParser
Returns the pixel type as specified in the header.
getCodestreamSizeC() - Method in class loci.formats.in.JPEG2000MetadataParser
Returns the number of channels the image has as specified in the header.
getCodestreamSizeX() - Method in class loci.formats.in.JPEG2000MetadataParser
Returns the width of the image as specified in the header.
getCodestreamSizeY() - Method in class loci.formats.in.JPEG2000MetadataParser
Returns the height of the image as specified in the header.
getColorMap(IFD) - Method in class loci.formats.tiff.TiffParser
Retrieve the color map associated with the given IFD.
getColorMode() - Method in class loci.plugins.in.ImporterOptions
 
getColorModeInfo() - Method in class loci.plugins.in.ImporterOptions
 
getColorModel() - Method in class loci.formats.FormatWriter
 
getColorModel() - Method in interface loci.formats.IFormatWriter
Gets the color model.
getColorModel() - Method in class loci.formats.ImageWriter
 
getColorModel() - Method in class loci.formats.WriterWrapper
 
getColorModel() - Method in class loci.plugins.util.RecordedImageProcessor
 
getColorModes() - Method in class loci.plugins.in.ImporterOptions
 
getColorValue(TextField) - Method in class loci.plugins.in.ColorDialog
 
getColumn() - Method in class loci.formats.in.OMEXMLReader.BinData
 
getColumn(int, int, int[], int) - Method in class loci.plugins.util.RecordedImageProcessor
 
getColumNames(int) - Method in interface loci.formats.services.MetakitService
 
getColumNames(int) - Method in class loci.formats.services.MetakitServiceImpl
 
getColumnNames(String) - Method in interface loci.formats.services.MetakitService
 
getColumnNames(String) - Method in class loci.formats.services.MetakitServiceImpl
 
getColumnTypes(int) - Method in interface loci.formats.services.MetakitService
 
getColumnTypes(String) - Method in interface loci.formats.services.MetakitService
 
getColumnTypes(int) - Method in class loci.formats.services.MetakitServiceImpl
 
getColumnTypes(String) - Method in class loci.formats.services.MetakitServiceImpl
 
getComment(int, int) - Method in class loci.formats.in.MetamorphReader
 
getComment() - Method in class loci.formats.tiff.IFD
Convenience method for obtaining the ImageDescription from this IFD.
getComment() - Method in class loci.formats.tiff.TiffParser
Convenience method for obtaining a stream's first ImageDescription.
getComments() - Method in class loci.formats.in.JPEG2000MetadataParser
Retrieves the list of comments stored in the file.
getCompanion() - Method in class loci.formats.out.OMETiffWriter
 
getComponent(int, int) - Method in class loci.formats.gui.UnsignedIntColorModel
 
getCompressedSize() - Method in class org.libjpegturbo.turbojpeg.TJCompressor
Returns the size of the image (in bytes) generated by the most recent compress/encode operation.
getCompression() - Method in enum loci.formats.codec.CompressionType
Returns the compression.
getCompression(String) - Method in class loci.formats.FormatReader
getCompression() - Method in class loci.formats.FormatWriter
 
getCompression() - Method in interface loci.formats.IFormatWriter
Gets the current compression type.
getCompression() - Method in class loci.formats.ImageWriter
 
getCompression(int) - Method in class loci.formats.in.OBFReader
 
getCompression(String) - Static method in class loci.formats.MetadataTools
Retrieves an Compression enumeration value for the given String.
getCompression() - Method in class loci.formats.tiff.IFD
Retrieves the image's compression type (TIFF tag Compression) from this IFD.
getCompression() - Method in class loci.formats.WriterWrapper
 
getCompressionCodecOptions(IFD) - Method in enum loci.formats.tiff.TiffCompression
Creates a set of codec options for compression.
getCompressionCodecOptions(IFD, CodecOptions) - Method in enum loci.formats.tiff.TiffCompression
Creates a set of codec options for compression.
getCompressionMap() - Static method in enum loci.formats.tiff.TiffCompression
 
getCompressionTypes() - Method in class loci.formats.FormatWriter
 
getCompressionTypes() - Method in interface loci.formats.IFormatWriter
Gets the available compression types.
getCompressionTypes() - Method in class loci.formats.ImageWriter
 
getCompressionTypes() - Method in class loci.formats.WriterWrapper
 
getConcatenateInfo() - Method in class loci.plugins.in.ImporterOptions
 
getConfig(String) - Method in class loci.formats.in.PrairieMetadata
Gets the value of the given configuration key.
getConfig() - Method in class loci.formats.in.PrairieMetadata
Gets the map of configuration key/value pairs.
getConstraintsForCell(int, int, Container, int) - Static method in class loci.plugins.config.SpringUtilities
 
getContrastMethod(String) - Method in class loci.formats.FormatReader
getContrastMethod(String) - Static method in class loci.formats.MetadataTools
Retrieves an ContrastMethod enumeration value for the given String.
getCoreIndex() - Method in class loci.formats.FileStitcher
 
getCoreIndex() - Method in class loci.formats.FormatReader
 
getCoreIndex() - Method in interface loci.formats.IFormatReader
Deprecated.
This method is no longer required for sub-resolution support.
getCoreIndex() - Method in class loci.formats.ImageReader
 
getCoreIndex() - Method in class loci.formats.ReaderWrapper
 
getCoreIndex() - Method in class loci.formats.SubResolutionFormatReader
 
getCoreIndex() - Method in class loci.formats.WrappedReader
 
getCoreMetadataList() - Method in class loci.formats.DimensionSwapper
 
getCoreMetadataList() - Method in class loci.formats.FileStitcher
 
getCoreMetadataList() - Method in class loci.formats.FormatReader
 
getCoreMetadataList() - Method in interface loci.formats.IFormatReader
Deprecated.
Reader internals should not be accessed by reader users
getCoreMetadataList() - Method in class loci.formats.ImageReader
 
getCoreMetadataList() - Method in class loci.formats.in.FilePatternReader
 
getCoreMetadataList() - Method in class loci.formats.in.LeicaHandler
 
getCoreMetadataList() - Method in class loci.formats.in.ND2Handler
 
getCoreMetadataList() - Method in class loci.formats.ReaderWrapper
 
getCoreMetadataList() - Method in class loci.formats.SubResolutionFormatReader
 
getCoreMetadataList() - Method in class loci.formats.WrappedReader
 
getCorrection(String) - Method in class loci.formats.FormatReader
getCorrection() - Method in class loci.formats.in.ND2Handler
 
getCorrection(String) - Static method in class loci.formats.MetadataTools
Retrieves an Correction enumeration value for the given String.
getCount() - Method in class loci.formats.FilePattern
Gets the number of elements for each pattern block.
getCreationDate() - Method in interface loci.formats.services.EXIFService
 
getCreationDate() - Method in class loci.formats.services.EXIFServiceImpl
 
getCropInfo() - Method in class loci.plugins.in.ImporterOptions
 
getCropRegion(int) - Method in class loci.plugins.in.ImporterOptions
 
getCropRegion(int) - Method in class loci.plugins.in.ImportProcess
Valid only after ImportStep.STACK.
getCStep(int) - Method in class loci.plugins.in.ImporterOptions
 
getCStep(int) - Method in class loci.plugins.in.ImportProcess
 
getCurrentColorModel() - Method in class loci.plugins.util.RecordedImageProcessor
 
getCurrentCore() - Method in class loci.formats.FormatReader
Get the CoreMetadata corresponding to the current series and resolution
getCurrentCore() - Method in class loci.formats.SubResolutionFormatReader
Get the CoreMetadata corresponding to the current series and resolution
getCurrentFile() - Method in class loci.formats.FormatReader
 
getCurrentFile() - Method in interface loci.formats.IFormatReader
Returns the current file.
getCurrentFile() - Method in class loci.formats.ImageReader
 
getCurrentFile() - Method in class loci.formats.ReaderWrapper
 
getCurrentFile() - Method in class loci.plugins.in.ImportProcess
Valid only after ImportStep.STACK.
getCurrentFile(String[]) - Method in class loci.plugins.macro.LociFunctions
 
getCurrentPos() - Method in class loci.formats.cache.Cache
Gets the current dimensional position.
getCustomColor(int, int) - Method in class loci.plugins.in.ImporterOptions
 
getCustomColorKey(int, int) - Method in class loci.plugins.in.ImporterOptions
 
getCutIn(Double) - Static method in class loci.formats.FormatTools
 
getCutOut(Double) - Static method in class loci.formats.FormatTools
 
getCycle() - Method in class loci.formats.in.PrairieMetadata.Sequence
Gets the cycle associated with this Sequence.
getCycleCount() - Method in class loci.formats.in.PrairieMetadata
Gets the number of recorded cycles.
getCycleMax() - Method in class loci.formats.in.PrairieMetadata
Gets the maximum cycle value.
getCycleMin() - Method in class loci.formats.in.PrairieMetadata
Gets the minimum cycle value.
getCZTag(IFD) - Method in class loci.formats.in.ZeissLSMReader
 
getData() - Method in class loci.formats.gui.SignedByteBuffer
 
getData(int) - Method in class loci.formats.gui.SignedByteBuffer
 
getData() - Method in class loci.formats.gui.SignedShortBuffer
 
getData(int) - Method in class loci.formats.gui.SignedShortBuffer
 
getData() - Method in class loci.formats.gui.UnsignedIntBuffer
 
getData(int) - Method in class loci.formats.gui.UnsignedIntBuffer
 
getDataElements(int, Object) - Method in class loci.formats.gui.Index16ColorModel
 
getDataElements(int, Object) - Method in class loci.formats.gui.SignedColorModel
 
getDataElements(int, Object) - Method in class loci.formats.gui.UnsignedIntColorModel
 
getDatasetStructureDescription() - Method in class loci.formats.FormatReader
 
getDatasetStructureDescription() - Method in interface loci.formats.IFormatReader
Returns a short description of the dataset structure.
getDatasetStructureDescription() - Method in class loci.formats.ImageReader
 
getDatasetStructureDescription() - Method in class loci.formats.ReaderWrapper
 
getDatasetStructureDescription() - Method in class loci.formats.WrappedReader
 
getDate() - Method in class loci.formats.in.MetamorphHandler
 
getDate() - Method in class loci.formats.in.ND2Handler
 
getDate() - Method in class loci.formats.in.PrairieMetadata
Gets the date of the acquisition.
getDatestamp() - Method in class loci.formats.in.SVSReader
 
getDecompressedStream(String) - Method in class loci.formats.in.CellomicsReader
 
getDefault() - Method in class loci.plugins.prefs.BooleanOption
Gets the default value of the option.
getDefault() - Method in class loci.plugins.prefs.DoubleOption
Gets the default value of the option.
getDefault() - Method in class loci.plugins.prefs.StringOption
Gets the default value of the option.
getDefaultColorModel() - Method in class loci.plugins.util.RecordedImageProcessor
 
getDefaultConfiguration() - Static method in class loci.formats.gui.AWTImageTools
Gets the default graphics configuration for the environment.
getDefaultCustomColor(int) - Method in class loci.plugins.in.ImporterOptions
 
getDefaultOptions() - Static method in class loci.formats.codec.CodecOptions
Return CodecOptions with reasonable default values.
getDefaultOptions() - Static method in class loci.formats.codec.JPEG2000CodecOptions
Return JPEG2000CodecOptions with reasonable default values.
getDefaultOptions(CodecOptions) - Static method in class loci.formats.codec.JPEG2000CodecOptions
Return JPEG2000CodecOptions using the given CodecOptions as the default.
getDefaultReaderClasses() - Static method in class loci.formats.ImageReader
 
getDefaultValue(String) - Method in class loci.plugins.prefs.OptionsList
Gets the default value of the string option with the given key.
getDefaultWriterClasses() - Static method in class loci.formats.ImageWriter
 
getDenom() - Method in class org.libjpegturbo.turbojpeg.TJScalingFactor
Returns denominator
getDenominator() - Method in class loci.formats.tiff.TiffRational
Gets this number's denominator.
getDescription() - Method in class loci.formats.gui.ComboFileFilter
Returns the filter's description.
getDescription() - Method in class loci.formats.gui.ExtensionFileFilter
Gets the filter's description.
getDescription() - Method in class loci.formats.gui.FormatFileFilter
Gets the filter's description.
getDescription() - Method in class loci.formats.gui.NoExtensionFileFilter
Gets the filter's description.
getDeser() - Method in class loci.formats.Memoizer
Returns a configured Kryo instance.
getDetectorType(String) - Method in class loci.formats.FormatReader
getDetectorType(String) - Static method in class loci.formats.MetadataTools
Retrieves an DetectorType enumeration value for the given String.
getDeviceSubtype(String) - Method in class loci.formats.in.CellSensReader
 
getDimension(RandomAccessInputStream) - Method in class loci.formats.in.I2IReader
 
getDimension(String) - Method in class loci.formats.in.ZeissTIFFHandler.Scaling
Get a dimension by its index.
getDimension(String) - Method in interface loci.formats.services.NetCDFService
Retrieves the length of a dimension.
getDimension(String) - Method in class loci.formats.services.NetCDFServiceImpl
 
getDimensionDescriptionNodes(Element) - Method in class loci.formats.in.LIFReader
 
getDimensionOrder() - Method in class loci.formats.ChannelMerger
 
getDimensionOrder() - Method in class loci.formats.ChannelSeparator
 
getDimensionOrder() - Method in class loci.formats.DimensionSwapper
 
getDimensionOrder() - Method in class loci.formats.FileStitcher
 
getDimensionOrder() - Method in class loci.formats.FormatReader
 
getDimensionOrder(String) - Method in class loci.formats.FormatReader
getDimensionOrder() - Method in interface loci.formats.IFormatReader
Gets a five-character string representing the dimension order in which planes will be returned.
getDimensionOrder() - Method in class loci.formats.ImageReader
 
getDimensionOrder(String) - Static method in class loci.formats.MetadataTools
Retrieves an DimensionOrder enumeration value for the given String.
getDimensionOrder() - Method in class loci.formats.ReaderWrapper
 
getDimensionOrder() - Method in class loci.formats.WrappedReader
 
getDimensionOrder(String[]) - Method in class loci.plugins.macro.LociFunctions
 
getDimensionSwapper() - Method in class loci.plugins.in.ImportProcess
Valid only after ImportStep.STACK.
getDirectory(String) - Method in class loci.formats.services.NetCDFServiceImpl
 
getDisplayColor() - Method in class loci.formats.in.SVSReader
 
getDocument() - Method in class loci.formats.gui.XMLWindow
Gets the XML document currently being displayed within the window.
getDocumentBytes(String) - Method in interface l