Index (Bio-Formats API)

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

A

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
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(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
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.PerkinElmerReader: List of all files to open
allFiles - Variable in class loci.formats.in.SPCReader: List of all files to open
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
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
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
areas - Variable in class loci.formats.in.CellVoyagerReader.WellInfo
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.
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
backwardsStage - Variable in class loci.formats.in.DeltavisionReader: Whether or not the stage moved backwards.
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.
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.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.
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_48 - Static variable in class loci.formats.in.ZeissCZIReader
BGR_FLOAT - Static variable in class loci.formats.in.ZeissCZIReader
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.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.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.
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.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_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
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.
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_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.in.OBFReader.Frame
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
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
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
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
canCloseReader - Variable in class loci.formats.gui.ImageViewer
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
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
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.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.
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.ColumbusReader.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(int) - Constructor for class loci.formats.in.ZeissTIFFReader.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_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.NativeND2Reader
ChannelData() - Constructor for class loci.formats.in.FV1000Reader.ChannelData
channelDescs - Variable in class loci.formats.in.FlowSightReader
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
channelIndices - Variable in class loci.formats.in.BaseZeissReader
ChannelInfo() - Constructor for class loci.formats.in.CellVoyagerReader.ChannelInfo
channelInfos - Variable in class loci.formats.in.CellVoyagerReader
channelLengths - Variable in class loci.formats.in.ICSReader: The length of each channel axis.
channelMax - Variable in class loci.formats.in.ImarisHDFReader
ChannelMerger - Class in loci.formats: Logic to automatically merge channels in a file.
ChannelMerger() - Constructor for class loci.formats.ChannelMerger: Constructs a ChannelMerger around a new image reader.
ChannelMerger(IFormatReader) - Constructor for class loci.formats.ChannelMerger: Constructs a ChannelMerger with the given reader.
channelMin - Variable in class loci.formats.in.ImarisHDFReader
channelName - Variable in class loci.formats.in.BaseZeissReader
channelName - Variable in class loci.formats.in.ColumbusReader.Plane
channelName - Variable in class loci.formats.in.ImarisHDFReader
channelName - Variable in class loci.formats.in.MetamorphHandler
channelName - Variable in class loci.formats.in.OpenlabReader.PlaneInfo
channelName - Variable in class loci.formats.in.OperettaReader.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.FV1000Reader
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
channels - Variable in class loci.formats.in.ZeissTIFFReader
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
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.BioRadSCNReader.SCNHandler
characters(char[], int, int) - Method in class loci.formats.in.ColumbusReader.MeasurementHandler
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.
checkHeader() - Method in class loci.formats.tiff.TiffParser: Checks the TIFF header.
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.
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.
ChunkMapEntry() - Constructor for class loci.formats.in.NativeND2Reader.ChunkMapEntry
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.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.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
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(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.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.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.FilePatternReader
close() - Method in class loci.formats.in.FilePatternReader
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.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.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.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.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.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() - Method in class loci.formats.tiff.OnDemandLongArray
close() - Method in class loci.formats.tiff.TiffSaver: Closes the output stream if not null.
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.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.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.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.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_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
compare(Object, Object) - Method in class loci.formats.cache.CacheStrategy: Default comparator orders dimensional positions based on distance from the current position, taking into account axis priorities and planar ordering.
compare(String, String) - Method in class loci.formats.in.MetamorphTiffReader.NumericComparator
compareTo(Object) - Method in class loci.formats.gui.ComboFileFilter: Compares two FileFilter objects alphanumerically.
compareTo(Object) - Method in class loci.formats.gui.ExtensionFileFilter: Compares two FileFilter objects alphanumerically.
compareTo(Object) - Method in class loci.formats.gui.FormatFileFilter: Compares two FileFilter objects alphanumerically.
compareTo(Object) - Method in class loci.formats.gui.NoExtensionFileFilter: Compares two FileFilter objects alphanumerically.
compareTo(Object) - Method in class loci.formats.tiff.TiffIFDEntry
compareTo(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_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.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
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
compressionTypes - Variable in class loci.formats.FormatWriter: Available compression types.
compressionTypes - Variable in class loci.formats.ImageWriter: Compression types for all file format writers.
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
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
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(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
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: Returns the series corresponding to the specified core index.
coreIndexToSeries(int) - Method in class loci.formats.ImageReader
coreIndexToSeries(int) - Method in class loci.formats.in.FilePatternReader
coreIndexToSeries(int) - Method in class loci.formats.ReaderWrapper
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
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
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
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
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.
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.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
currentInflatedFrame - Variable in class loci.formats.in.OBFReader
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
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.InCellReader.InCellHandler
currentQName - Variable in class loci.formats.in.OMEXMLReader.OMEXMLHandler
currentRow - Variable in class loci.formats.in.InCellReader.InCellHandler
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.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
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.
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_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_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.ND2Handler
date - Variable in class loci.formats.in.PrairieMetadata: The date of the acquisition.
date - Variable in class loci.formats.in.QuesantReader
date - Variable in class loci.formats.in.SDTInfo: Date of creation.
date - Variable in class loci.formats.in.SimplePCITiffReader
date - Variable in class loci.formats.in.SVSReader
DATE_FORMAT - Static variable in class loci.formats.in.BrukerReader
DATE_FORMAT - Static variable in class loci.formats.in.CellWorxReader
DATE_FORMAT - Static variable in class loci.formats.in.DeltavisionReader: Deprecated.
Use DeltavisionReader.DATE_FORMATS instead
DATE_FORMAT - Static variable in class loci.formats.in.FEITiffReader
DATE_FORMAT - Static variable in class loci.formats.in.FluoviewReader: Date format
DATE_FORMAT - Static variable in class loci.formats.in.FujiReader
DATE_FORMAT - Static variable in class loci.formats.in.FV1000Reader
DATE_FORMAT - Static variable in class loci.formats.in.GelReader
DATE_FORMAT - Static variable in class loci.formats.in.HitachiReader
DATE_FORMAT - Static variable in class loci.formats.in.IvisionReader
DATE_FORMAT - Static variable in class loci.formats.in.KodakReader
DATE_FORMAT - Static variable in class loci.formats.in.L2DReader
DATE_FORMAT - Static variable in class loci.formats.in.LeicaReader: Format for dates.
DATE_FORMAT - Static variable in class loci.formats.in.MetamorphTiffReader
DATE_FORMAT - Static variable in class loci.formats.in.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.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_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_RGB_CHANNEL_COUNT - Static variable in class loci.formats.in.FakeReader
DEFAULT_SAMPLE_IFD - Static variable in class loci.formats.in.CellSensReader
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.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.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
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
dir - Variable in class loci.formats.in.VolocityReader
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
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
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
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
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.ND2Handler
endDocument() - Method in class loci.formats.in.OMEXMLReader.OMEXMLHandler
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.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.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.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_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.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.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.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_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
extractCoreMetaData() - Method in class loci.formats.tools.AmiraParameters
extractTokensFromFakeSeries(String) - Method in class loci.formats.in.FakeReader
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.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.
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.ColumbusReader.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
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.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 int indicating that we cannot, must, or might group the files in a given dataset.
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.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.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.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.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
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.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.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
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
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.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
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
flattenedResolutions - Variable in class loci.formats.FormatReader: Whether or not resolutions are flattened.
flattenHashtables() - Method in class loci.formats.FormatReader: 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
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
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 .
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
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
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() - Constructor for class loci.formats.in.OBFReader.Frame
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
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.
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) - 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.ZeissCZIReader
get16BitLookupTable() - Method in class loci.formats.in.ZeissLSMReader
get16BitLookupTable() - Method in class loci.formats.in.ZipReader
get16BitLookupTable() - Method in class loci.formats.ReaderWrapper
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.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.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
getAbsoluteTime() - Method in class loci.formats.in.PrairieMetadata.Frame: Gets the absoluteTime associated with this Frame.
getAcquisitionMode(String) - Method in class loci.formats.FormatReader: 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: 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
getBinaryOnlyOMEXML(String, String, String) - Method in class loci.formats.out.OMETiffWriter
getBinning(String) - Method in class loci.formats.FormatReader: Retrieves an Binning enumeration value for the given String.
getBinning() - Method in class loci.formats.in.MetamorphHandler
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() - Method in class loci.formats.in.FilePatternReader
getBitsPerPixel(int) - Method in class loci.formats.in.OBFReader
getBitsPerPixel() - Method in class loci.formats.ReaderWrapper
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
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.
getChannel(int) - Method in class loci.formats.in.ZeissTIFFReader
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.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: Retrieves an Compression enumeration value for the given String.
getCompression() - Method in class loci.formats.FormatWriter
getCompression() - Method in interface loci.formats.IFormatWriter: Gets the current compression type.
getCompression() - Method in class loci.formats.ImageWriter
getCompression(int) - Method in class loci.formats.in.OBFReader
getCompression() - 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: 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: Return the index into CoreMetadata of the current resolution/series.
getCoreIndex() - Method in class loci.formats.ImageReader
getCoreIndex() - Method in class loci.formats.in.FilePatternReader
getCoreIndex() - Method in class loci.formats.ReaderWrapper
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: Obtains the core metadata values for the current file.
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
getCorrection(String) - Method in class loci.formats.FormatReader: Retrieves an Correction enumeration value for the given String.
getCorrection() - Method in class loci.formats.in.ND2Handler
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
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.in.FilePatternReader
getDatasetStructureDescription() - Method in class loci.formats.ReaderWrapper
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: 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: Retrieves an DimensionOrder enumeration value for the given String.
getDimensionOrder() - Method in interface loci.formats.IFormatReader: Gets a five-character string representing the dimension order in which planes will be returned.
getDimensionOrder() - Method in class loci.formats.ImageReader
getDimensionOrder() - Method in class loci.formats.in.FilePatternReader
getDimensionOrder() - Method in class loci.formats.ReaderWrapper
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
getDocument() - Method in class loci.formats.gui.XMLWindow: Gets the XML document currently being displayed within the window.
getDocumentBytes(String) - Method in interface loci.formats.services.POIService: Retrieve all of the raw bytes that correspond to the given file name.
getDocumentBytes(String, int) - Method in interface loci.formats.services.POIService: Retrieve at most 'length' bytes that correspond to the given file name.
getDocumentBytes(String) - Method in class loci.formats.services.POIServiceImpl
getDocumentBytes(String, int) - Method in class loci.formats.services.POIServiceImpl
getDocumentList() - Method in interface loci.formats.services.POIService: Retrieve a list of all files in the current POI file system.
getDocumentList() - Method in class loci.formats.services.POIServiceImpl
getDocumentStream(String) - Method in interface loci.formats.services.POIService: Retrieve a RandomAccessInputStream corresponding to the given file name.
getDocumentStream(String) - Method in class loci.formats.services.POIServiceImpl
getDomains() - Method in class loci.formats.FormatReader
getDomains() - Method in interface loci.formats.IFormatReader: Returns the list of domains represented by the current file.
getDomains() - Method in class loci.formats.ImageReader
getDomains() - Method in class loci.formats.in.CellomicsReader
getDomains() - Method in class loci.formats.in.FilePatternReader
getDomains() - Method in class loci.formats.in.ICSReader
getDomains() - Method in class loci.formats.in.MetamorphTiffReader
getDomains() - Method in class loci.formats.in.NiftiReader
getDomains() - Method in class loci.formats.in.OMETiffReader
getDomains() - Method in class loci.formats.in.OMEXMLReader
getDomains() - Method in class loci.formats.ReaderWrapper
getDouble(String) - Method in class loci.formats.in.DynamicMetadataOptions: Get the value of property name as a Double.
getDouble(String, Double) - Method in class loci.formats.in.DynamicMetadataOptions: Get the value of property name as a Double.
getDoubles(BufferedImage) - Static method in class loci.formats.gui.AWTImageTools: Extracts pixel data as arrays of doubles, one per channel.
getDoubles(WritableRaster) - Static method in class loci.formats.gui.AWTImageTools: Extracts pixel data as arrays of doubles, one per channel.
getDoubles(WritableRaster, int, int, int, int) - Static method in class loci.formats.gui.AWTImageTools: Extracts pixel data as arrays of doubles, one per channel.
getDoubleValue(int) - Method in class loci.formats.in.ZeissLSMReader.SubBlock
getDT(int, int, int, int) - Method in class loci.formats.in.LegacyND2Reader
getDX(int, int, int, int) - Method in class loci.formats.in.LegacyND2Reader
getDY(int, int, int, int) - Method in class loci.formats.in.LegacyND2Reader
getDZ(int, int, int, int) - Method in class loci.formats.in.LegacyND2Reader
getEffectiveSeries(int) - Method in class loci.formats.in.ZeissLSMReader
getEffectiveSizeC() - Method in class loci.formats.FormatReader
getEffectiveSizeC() - Method in interface loci.formats.IFormatReader: Gets the effective size of the C dimension, guaranteeing that getEffectiveSizeC() * getSizeZ() * getSizeT() == getImageCount() regardless of the result of isRGB().
getEffectiveSizeC() - Method in class loci.formats.ImageReader
getEffectiveSizeC() - Method in class loci.formats.in.FilePatternReader
getEffectiveSizeC() - Method in class loci.formats.ReaderWrapper
getEffectiveSizeC(Double[]) - Method in class loci.plugins.macro.LociFunctions
getElem(int) - Method in class loci.formats.gui.SignedByteBuffer
getElem(int, int) - Method in class loci.formats.gui.SignedByteBuffer
getElem(int, int) - Method in class loci.formats.gui.SignedShortBuffer
getElem(int) - Method in class loci.formats.gui.UnsignedIntBuffer
getElem(int, int) - Method in class loci.formats.gui.UnsignedIntBuffer
getElemDouble(int) - Method in class loci.formats.gui.UnsignedIntBuffer
getElemDouble(int, int) - Method in class loci.formats.gui.UnsignedIntBuffer
getElements() - Method in class loci.formats.FilePattern: Gets individual elements for each pattern block.
getElements() - Method in class loci.formats.FilePatternBlock: Gets all block elements.
getElementSize(String) - Method in interface loci.formats.services.JHDFService: Retrieves the Element Size of a dataset in Byte.
getElementSize(String) - Method in class loci.formats.services.JHDFServiceImpl
getElemFloat(int) - Method in class loci.formats.gui.UnsignedIntBuffer
getElemFloat(int, int) - Method in class loci.formats.gui.UnsignedIntBuffer
getEmission() - Method in class loci.formats.in.SVSReader
getEmissionWavelength(Double) - Static method in class loci.formats.FormatTools
getEmissionWavelengths() - Method in class loci.formats.in.ND2Handler
getEndX() - Method in class loci.formats.in.SPEReader.SpeROI
getEndY() - Method in class loci.formats.in.SPEReader.SpeROI
getEntries(IRandomAccess) - Method in class loci.formats.in.IM3Reader.FloatIM3Record: Return all entries as an array
getEntry(IRandomAccess, int) - Method in class loci.formats.in.IM3Reader.BooleanIM3Record: Get the boolean value at the given index
getEntry(IRandomAccess, int) - Method in class loci.formats.in.IM3Reader.FloatIM3Record: Get the floating-point value at the given index
getEntry(IRandomAccess, int) - Method in class loci.formats.in.IM3Reader.IntIM3Record: Get the integer value at the given index
getEnum(String, T) - Method in class loci.formats.in.DynamicMetadataOptions: Get the value of property name as an enumerated type.
getErrorMessage() - Method in class loci.formats.FilePattern: Gets the file pattern error message, if any.
getExcitation() - Method in class loci.formats.in.SVSReader
getExcitationWavelength(Double) - Static method in class loci.formats.FormatTools
getExcitationWavelengths() - Method in class loci.formats.in.ND2Handler
getExifIFDs() - Method in class loci.formats.tiff.TiffParser: Returns EXIF IFDs.
getExifTagName(int) - Static method in class loci.formats.in.BaseTiffReader
getExperimenterName() - Method in class loci.formats.in.OperettaReader.OperettaHandler
getExperimentType(String) - Method in class loci.formats.FormatReader: Retrieves an ExperimentType enumeration value for the given String.
getExposures() - Method in class loci.formats.in.MetamorphHandler
getExposureTime() - Method in class loci.formats.in.SVSReader
getExposureTimes() - Method in class loci.formats.in.ND2Handler
getExtension() - Method in class loci.formats.gui.ExtensionFileFilter: Gets the filter's first valid extension.
getExtensionFunctions() - Method in class loci.plugins.macro.MacroFunctions
getExtensions() - Method in class loci.formats.gui.ExtensionFileFilter: Gets the filter's valid extensions.
getExternalSeries() - Method in class loci.formats.FileStitcher
getExternalSeries(int) - Method in class loci.formats.FileStitcher
getExtraSeries(String) - Method in class loci.formats.in.ZeissLSMReader
getf(int) - Method in class loci.plugins.util.RecordedImageProcessor
getf(int, int) - Method in class loci.plugins.util.RecordedImageProcessor
getField(String) - Method in class loci.formats.in.CellomicsReader
getField(String) - Method in class loci.formats.in.FlexReader
getField(int) - Method in class loci.formats.in.FluoviewReader
getField(String) - Method in class loci.formats.in.MetamorphTiffReader
getFieldFromSeries(int) - Method in class loci.formats.in.InCellReader
getFieldIndex() - Method in class loci.formats.in.ND2Handler
getFieldName(int) - Static method in class loci.formats.tiff.IFD: This method uses reflection to scan the values of this class's static fields, returning the first matching field's name.
getFilamentType(String) - Method in class loci.formats.FormatReader: Retrieves an FilamentType enumeration value for the given String.
getFile(int, int) - Method in class loci.formats.in.CellWorxReader: Retrieve the .pnl file corresponding to the given series.
getFile(String) - Method in class loci.formats.in.DynamicMetadataOptions: Get the value of property name as a file object.
getFile(String, File) - Method in class loci.formats.in.DynamicMetadataOptions: Get the value of property name as a file object.
getFile(String) - Method in class loci.formats.in.FV1000Reader
getFile(int) - Method in class loci.formats.in.MicromanagerReader.Position
getFile(String, int, int, int, int, int) - Method in class loci.formats.in.MicromanagerReader.Position
getFile(int) - Method in class loci.formats.in.PerkinElmerReader
getFile(int) - Method in class loci.formats.in.PrairieMetadata.Frame: Gets the File with the given channel.
getFile(int, int, int) - Method in class loci.formats.in.PrairieMetadata: Gets the Frame at the given (cycle, index, channel).
getFile(int, int) - Method in class loci.formats.in.PrairieMetadata.Sequence: Gets the Frame at the given (cycle, index, channel).
getFile(Integer, Location) - Method in class loci.formats.in.VolocityReader
getFile() - Method in interface loci.formats.services.JHDFService: Retrieves the current initialized file path.
getFile() - Method in class loci.formats.services.JHDFServiceImpl
getFile() - Method in interface loci.formats.services.NetCDFService: Retrieves the current initialized file path.
getFile() - Method in class loci.formats.services.NetCDFServiceImpl
getFileHandle(String) - Method in class loci.formats.in.FlexReader
getFileIndex(int) - Method in class loci.formats.in.PerkinElmerReader
getFilename(int, int, IFormatReader, String) - Static method in class loci.formats.FormatTools
getFilename(int, int, IFormatReader, String, boolean) - Static method in class loci.formats.FormatTools
getFilename(int, int, MetadataRetrieve, String, boolean) - Static method in class loci.formats.FormatTools
getFilename(int, int) - Method in class loci.formats.in.BDReader
getFilename() - Method in class loci.formats.in.PrairieMetadata.PFile: Gets the filename associated with this File.
getFilenames(String, IFormatReader) - Static method in class loci.formats.FormatTools
getFilePattern() - Method in class loci.formats.AxisGuesser: Gets the file pattern.
getFilePattern() - Method in class loci.formats.FileStitcher.ExternalSeries
getFilePattern() - Method in class loci.formats.FileStitcher: Gets the file pattern object used to build the list of files.
getFiles() - Method in class loci.formats.FilePattern: Gets a listing of all files matching this file pattern.
getFiles() - Method in class loci.formats.FileStitcher.ExternalSeries
getFileSize(String) - Method in interface loci.formats.services.POIService: Retrieve the total number of bytes in the given file.
getFileSize(String) - Method in class loci.formats.services.POIServiceImpl
getFileStitcher() - Method in class loci.plugins.in.ImportProcess: Valid only after ImportStep.STACK.
getFileVersion(RandomAccessInputStream) - Method in class loci.formats.in.OBFReader
getFillRule(String) - Method in class loci.formats.FormatReader: Retrieves an FillRule enumeration value for the given String.
getFilter(String) - Method in class loci.formats.in.FV1000Reader.ChannelData
getFilters() - Method in class loci.formats.gui.ComboFileFilter: Gets the list of file filters forming this filter combination.
getFilterType(String) - Method in class loci.formats.FormatReader: Retrieves an FilterType enumeration value for the given String.
getFirst() - Method in class loci.formats.FilePattern: Gets the START element for all blocks.
getFirst() - Method in class loci.formats.FilePatternBlock: Gets the first element in a range block.
getFirstChannel(String) - Method in class loci.formats.in.SlidebookTiffReader
getFirstChild(Element, String) - Method in class loci.formats.in.OIRReader
getFirstChild(Element, String) - Method in class loci.formats.in.PrairieMetadata: Gets the first child element with the given name.
getFirstComment(int) - Method in class loci.formats.in.MetamorphReader: Returns the TIFF comment from the first IFD of the first STK file in the given series.
getFirstFile() - Method in class loci.formats.in.PrairieMetadata.Frame: Gets the first File of the Sequence.
getFirstFrame() - Method in class loci.formats.in.PrairieMetadata.Sequence: Gets the first Frame of the Sequence.
getFirstIFD() - Method in class loci.formats.tiff.TiffParser: Gets the first IFD within the TIFF file, or null if the input source is not a valid TIFF file.
getFirstIFDEntry(int) - Method in class loci.formats.tiff.TiffParser: Retrieve a given entry from the first IFD in the stream.
getFirstNode(Element, String) - Method in class loci.formats.in.ZeissCZIReader
getFirstNodeValue(Element, String) - Method in class loci.formats.in.ZeissCZIReader
getFirstOffset() - Method in class loci.formats.tiff.TiffParser: Gets offset to the first IFD, or -1 if stream is not TIFF.
getFirstSequence() - Method in class loci.formats.in.PrairieMetadata: Gets the first Sequence.
getFirstTimeInfo() - Method in class loci.plugins.in.ImporterOptions
getFixedHeader() - Method in class loci.formats.services.JPEGTurboServiceImpl
getFlexFiles() - Method in class loci.formats.in.FlexReader.MeaHandler
getFloat(String) - Method in class loci.formats.in.DynamicMetadataOptions: Get the value of property name as a Float.
getFloat(String, Float) - Method in class loci.formats.in.DynamicMetadataOptions: Get the value of property name as a Float.
getFloatArray() - Method in class loci.plugins.util.RecordedImageProcessor
getFloats(BufferedImage) - Static method in class loci.formats.gui.AWTImageTools: Extracts pixel data as arrays of floats, one per channel.
getFloats(WritableRaster) - Static method in class loci.formats.gui.AWTImageTools: Extracts pixel data as arrays of floats, one per channel.
getFloats(WritableRaster, int, int, int, int) - Static method in class loci.formats.gui.AWTImageTools: Extracts pixel data as arrays of floats, one per channel.
getFloatValue(int) - Method in class loci.formats.in.ZeissLSMReader.SubBlock
getFontFamily(String) - Method in class loci.formats.FormatReader: Retrieves an FontFamily enumeration value for the given String.
getFontMetrics() - Method in class loci.plugins.util.RecordedImageProcessor
getFontSize(Integer) - Static method in class loci.formats.FormatTools
getFontStyle(String) - Method in class loci.formats.FormatReader: Retrieves an FontStyle enumeration value for the given String.
getForceThumbnailsInfo() - Method in class loci.plugins.in.ImporterOptions
getFormat() - Method in class loci.formats.FormatHandler
getFormat() - Method in interface loci.formats.IFormatHandler: Gets the name of this file format.
getFormat(String) - Method in class loci.formats.ImageReader: Gets a string describing the file format for the given file.
getFormat() - Method in class loci.formats.ImageReader
getFormat(String) - Method in class loci.formats.ImageWriter: Gets a string describing the file format for the given file.
getFormat() - Method in class loci.formats.ImageWriter
getFormat() - Method in class loci.formats.ReaderWrapper
getFormat() - Method in class loci.formats.WriterWrapper
getFormat(String, String[]) - Method in class loci.plugins.macro.LociFunctions
getFrame(int, int) - Method in class loci.formats.in.PrairieMetadata: Gets the Frame at the given (cycle and index).
getFrame() - Method in class loci.formats.in.PrairieMetadata.PFile: Gets the <Frame> containing this <File>.
getFrame(int) - Method in class loci.formats.in.PrairieMetadata.Sequence: Gets the Frame with the given index.
getFramesPerSecond() - Method in class loci.formats.FormatWriter
getFramesPerSecond() - Method in interface loci.formats.IFormatWriter: Gets the frames per second to use when writing.
getFramesPerSecond() - Method in class loci.formats.ImageWriter
getFramesPerSecond() - Method in class loci.formats.WriterWrapper
getGain() - Method in class loci.formats.in.MetamorphHandler
getGain(int) - Method in class loci.formats.in.PrairieMetadata.Frame: Gets the cth gain for this Frame.
getGains() - Method in class loci.formats.in.ND2Handler
getGlobalMeta(String) - Method in class loci.formats.FormatReader: Gets a value from the global metadata table.
getGlobalMetadata() - Method in class loci.formats.FormatReader
getGlobalMetadata() - Method in interface loci.formats.IFormatReader: Obtains the hashtable containing the metadata field/value pairs from the current file.
getGlobalMetadata() - Method in class loci.formats.ImageReader
getGlobalMetadata() - Method in class loci.formats.in.FilePatternReader
getGlobalMetadata() - Method in class loci.formats.in.LeicaHandler
getGlobalMetadata() - Method in class loci.formats.ReaderWrapper
getGrandchildren(Element, String) - Method in class loci.formats.in.ZeissCZIReader
getGrandchildren(Element, String, String) - Method in class loci.formats.in.ZeissCZIReader
getGreen(int) - Method in class loci.formats.gui.Index16ColorModel
getGreen(int) - Method in class loci.formats.gui.SignedColorModel
getGreen(Object) - Method in class loci.formats.gui.SignedColorModel
getGreen(int) - Method in class loci.formats.gui.UnsignedIntColorModel
getGreen(Object) - Method in class loci.formats.gui.UnsignedIntColorModel
getGreenOffset(int) - Static method in class org.libjpegturbo.turbojpeg.TJ: For the given pixel format, returns the number of bytes that the green component is offset from the start of the pixel.
getGreens() - Method in class loci.formats.gui.Index16ColorModel: Return the array of green color components.
getGroup(String) - Method in class loci.formats.services.NetCDFServiceImpl: Retrieves a group based on its fully qualified path.
getGroupFilesInfo() - Method in class loci.plugins.in.ImporterOptions
getGroupX() - Method in class loci.formats.in.SPEReader.SpeROI
getGroupY() - Method in class loci.formats.in.SPEReader.SpeROI
getHeader() - Method in class loci.formats.in.SPEReader.SpeHeader
getHeaderInfo(int, String) - Method in class loci.formats.in.DicomReader
getHeaderPixelType() - Method in class loci.formats.in.JPEG2000MetadataParser: Returns the pixel type as specified in the header.
getHeaderSize() - Method in class loci.formats.in.SPEReader.SpeHeader
getHeaderSizeC() - Method in class loci.formats.in.JPEG2000MetadataParser: Returns the number of channels the image has as specified in the header.
getHeaderSizeX() - Method in class loci.formats.in.JPEG2000MetadataParser: Returns the width of the image as specified in the header.
getHeaderSizeY() - Method in class loci.formats.in.JPEG2000MetadataParser: Returns the height of the image as specified in the header.
getHeight() - Method in class loci.formats.codec.JPEGTileDecoder
getHeight(int) - Method in class loci.formats.in.LegacyND2Reader
getHeight() - Method in interface loci.formats.services.LuraWaveService: Wraps lwfDecoder.getHeight()
getHeight() - Method in class loci.formats.services.LuraWaveServiceImpl
getHeight(IFormatReader, String, int) - Static method in class loci.plugins.util.BFVirtualStack
getHeight() - Method in class loci.plugins.util.BFVirtualStack
getHeight() - Method in class loci.plugins.util.RecordedImageProcessor
getHeight() - Method in class org.libjpegturbo.turbojpeg.TJDecompressor: Returns the height of the JPEG image associated with this decompressor instance.