## Uses of Class
loci.formats.FormatException

- Packages that use FormatException
  Package | Description
  --- | ---
  loci.formats | Bio-Formats: a library for reading and writing popular microscopy file formats.
  loci.formats.cache | Package containing Bio-Formats caching logic, for managing subsets of large collections of image planes in memory.
  loci.formats.codec |
  loci.formats.dicom |
  loci.formats.gui | Package containing Bio-Formats graphical user interface code.
  loci.formats.in | Package containing Bio-Formats file format readers.
  loci.formats.in.LeicaMicrosystemsMetadata |
  loci.formats.out | Package containing Bio-Formats file format writers.
  loci.formats.services |
  loci.formats.tiff | Package containing Bio-Formats TIFF code of general utility.
  loci.formats.tools | Package containing utility methods corresponding to the Bio-Formats command line tools.
  loci.plugins | Bio-Formats Plugins: a collection of plugins for ImageJ, including the Bio-Formats Importer, Bio-Formats Exporter, Bio-Formats Macro Extensions, Data Browser and Stack Slicer.
  loci.plugins.in | Bio-Formats Importer plugin for ImageJ.
  loci.plugins.macro | Bio-Formats Macro Extensions plugin for ImageJ.
  loci.plugins.util | Utility classes and methods for the Bio-Formats plugins for ImageJ.

- - ### Uses of FormatException in loci.formats

    Subclasses of FormatException in loci.formats
    Modifier and Type | Class and Description
    --- | ---
    `class` | `MissingLibraryException` MissingLibraryException is the exception thrown when a particular data stream or filename requires a library that is not present on the system.
    `class` | `UnknownFormatException` UnknownFormatException is the exception thrown when the format of a particular data stream or filename cannot be recognized or is unsupported.
    `class` | `UnsupportedCompressionException` UnsupportedCompressionException is the exception thrown when the compression scheme used in a particular file or stream is unsupported.

    Methods in loci.formats that throw FormatException
    Modifier and Type | Method and Description
    --- | ---
    `static boolean` | FormatTools.`canUsePrecompressedTiles(IFormatReader reader, IFormatWriter writer, int series, int resolution)` Compare the given reader and writer at the specified series and resolution to see if pre-compressed tiles can be transferred directly from the reader to the writer.
    `void` | WriterWrapper.`changeOutputFile(java.lang.String id)`
    `void` | ImageWriter.`changeOutputFile(java.lang.String id)`
    `void` | IFormatWriter.`changeOutputFile(java.lang.String id)` Switch the output file for the current dataset.
    `void` | FormatWriter.`changeOutputFile(java.lang.String id)`
    `static void` | FormatTools.`checkBufferSize(IFormatReader r, int len)`
    `static void` | FormatTools.`checkBufferSize(IFormatReader r, int len, int w, int h)` Checks that the given buffer size is large enough to hold a w * h image as returned by the given reader.
    `protected void` | FormatWriter.`checkParams(int no, byte[] buf, int x, int y, int w, int h)` Ensure that the arguments that are being passed to saveBytes(...) are valid.
    `static void` | FormatTools.`checkPlaneNumber(IFormatReader r, int no)` Checks that the given plane number is valid for the given reader.
    `static void` | FormatTools.`checkPlaneParameters(IFormatReader r, int no, int bufLength, int x, int y, int w, int h)` Convenience method for checking that the plane number, tile size and buffer sizes are all valid for the given reader.
    `static void` | FormatTools.`checkTileSize(IFormatReader r, int x, int y, int w, int h)` Checks that the given tile size is valid for the given reader.
    `protected void` | FileStitcher.`computeAxisLengths()` Computes axis length arrays, and total axis lengths.
    `protected int[]` | FileStitcher.`computeIndices(int no)` Gets the file index, and image index into that file, corresponding to the given global image index.
    `static void` | FormatTools.`convert(IFormatReader input, IFormatWriter output, java.lang.String outputFile)` Convenience method for writing all of the images and metadata obtained from the specified IFormatReader into the specified IFormatWriter.
    `static void` | FormatTools.`convert(java.lang.String input, java.lang.String output)` Convenience method for converting the specified input file to the specified output file.
    `ReaderWrapper` | ReaderWrapper.`duplicate(java.lang.Class<? extends IFormatReader> imageReaderClass)` Performs a deep copy of the reader, including nested wrapped readers.
    `WriterWrapper` | WriterWrapper.`duplicate(java.lang.Class<? extends IFormatWriter> imageWriterClass)` Performs a deep copy of the writer, including nested wrapped writers.
    `private ReaderWrapper` | ReaderWrapper.`duplicateRecurse(java.lang.Class<? extends IFormatReader> imageReaderClass)`
    `private WriterWrapper` | WriterWrapper.`duplicateRecurse(java.lang.Class<? extends IFormatWriter> imageWriterClass)`
    `int` | ReaderWrapper.`fileGroupOption(java.lang.String id)`
    `int` | ImageReader.`fileGroupOption(java.lang.String id)`
    `int` | IFormatReader.`fileGroupOption(java.lang.String id)` Returns an indication of whether the files in a multi-file dataset can be handled individually.
    `int` | FormatReader.`fileGroupOption(java.lang.String id)`
    `short[][]` | FileStitcher.`get16BitLookupTable()`
    `short[][]` | ChannelFiller.`get16BitLookupTable()`
    `short[][]` | WrappedReader.`get16BitLookupTable()`
    `short[][]` | ReaderWrapper.`get16BitLookupTable()`
    `short[][]` | ImageReader.`get16BitLookupTable()`
    `short[][]` | IFormatReader.`get16BitLookupTable()` Gets the 16-bit color lookup table associated with the most recently opened image.
    `short[][]` | FormatReader.`get16BitLookupTable()`
    `short[][]` | DelegateReader.`get16BitLookupTable()`
    `byte[][]` | FileStitcher.`get8BitLookupTable()`
    `byte[][]` | ChannelFiller.`get8BitLookupTable()`
    `byte[][]` | WrappedReader.`get8BitLookupTable()`
    `byte[][]` | ReaderWrapper.`get8BitLookupTable()`
    `byte[][]` | ImageReader.`get8BitLookupTable()`
    `byte[][]` | IFormatReader.`get8BitLookupTable()` Gets the 8-bit color lookup table associated with the most recently opened image.
    `byte[][]` | FormatReader.`get8BitLookupTable()`
    `byte[][]` | DelegateReader.`get8BitLookupTable()`
    `static ome.xml.model.enums.AcquisitionMode` | MetadataTools.`getAcquisitionMode(java.lang.String value)` Retrieves an `AcquisitionMode` enumeration value for the given String.
    `protected ome.xml.model.enums.AcquisitionMode` | FormatReader.`getAcquisitionMode(java.lang.String value)` Deprecated. Use `MetadataTools.getAcquisitionMode(String)`.
    `int` | FileStitcher.`getAdjustedIndex(int no)` Gets the local reader index for use with the given image plane.
    `static ome.xml.model.enums.ArcType` | MetadataTools.`getArcType(java.lang.String value)` Retrieves an `ArcType` enumeration value for the given String.
    `protected ome.xml.model.enums.ArcType` | FormatReader.`getArcType(java.lang.String value)` Deprecated. Use `MetadataTools.getArcType(String)`.
    `static ome.xml.model.enums.Binning` | MetadataTools.`getBinning(java.lang.String value)` Retrieves an `Binning` enumeration value for the given String.
    `protected ome.xml.model.enums.Binning` | FormatReader.`getBinning(java.lang.String value)` Deprecated. Use `MetadataTools.getBinning(String)`.
    `java.lang.Double` | MinMaxCalculator.`getChannelGlobalMaximum(int theC)` Retrieves a specified channel's global maximum.
    `java.lang.Double` | MinMaxCalculator.`getChannelGlobalMinimum(int theC)` Retrieves a specified channel's global minimum.
    `java.lang.Double` | MinMaxCalculator.`getChannelKnownMaximum(int theC)` Retrieves the specified channel's maximum based on the images that have been read.
    `java.lang.Double` | MinMaxCalculator.`getChannelKnownMinimum(int theC)` Retrieves the specified channel's minimum based on the images that have been read.
    `static ome.xml.model.enums.Compression` | MetadataTools.`getCompression(java.lang.String value)` Retrieves an `Compression` enumeration value for the given String.
    `protected ome.xml.model.enums.Compression` | FormatReader.`getCompression(java.lang.String value)` Deprecated. Use `MetadataTools.getCompression(String)`.
    `static ome.xml.model.enums.ContrastMethod` | MetadataTools.`getContrastMethod(java.lang.String value)` Retrieves an `ContrastMethod` enumeration value for the given String.
    `protected ome.xml.model.enums.ContrastMethod` | FormatReader.`getContrastMethod(java.lang.String value)` Deprecated. Use `MetadataTools.getContrastMethod(String)`.
    `static ome.xml.model.enums.Correction` | MetadataTools.`getCorrection(java.lang.String value)` Retrieves an `Correction` enumeration value for the given String.
    `protected ome.xml.model.enums.Correction` | FormatReader.`getCorrection(java.lang.String value)` Deprecated. Use `MetadataTools.getCorrection(String)`.
    `static ome.xml.model.enums.DetectorType` | MetadataTools.`getDetectorType(java.lang.String value)` Retrieves an `DetectorType` enumeration value for the given String.
    `protected ome.xml.model.enums.DetectorType` | FormatReader.`getDetectorType(java.lang.String value)` Deprecated. Use `MetadataTools.getDetectorType(String)`.
    `static ome.xml.model.enums.DimensionOrder` | MetadataTools.`getDimensionOrder(java.lang.String value)` Retrieves an `DimensionOrder` enumeration value for the given String.
    `protected ome.xml.model.enums.DimensionOrder` | FormatReader.`getDimensionOrder(java.lang.String value)` Deprecated. Use `MetadataTools.getDimensionOrder(String)`.
    `static ome.xml.model.enums.ExperimentType` | MetadataTools.`getExperimentType(java.lang.String value)` Retrieves an `ExperimentType` enumeration value for the given String.
    `protected ome.xml.model.enums.ExperimentType` | FormatReader.`getExperimentType(java.lang.String value)` Deprecated. Use `MetadataTools.getExperimentType(String)`.
    `static ome.xml.model.enums.FilamentType` | MetadataTools.`getFilamentType(java.lang.String value)` Retrieves an `FilamentType` enumeration value for the given String.
    `protected ome.xml.model.enums.FilamentType` | FormatReader.`getFilamentType(java.lang.String value)` Deprecated. Use `MetadataTools.getFilamentType(String)`.
    `static java.lang.String` | FormatTools.`getFilename(int series, int image, IFormatReader r, java.lang.String pattern)`
    `static java.lang.String` | FormatTools.`getFilename(int series, int image, IFormatReader r, java.lang.String pattern, boolean padded)`
    `static java.lang.String` | FormatTools.`getFilename(int series, int image, MetadataRetrieve retrieve, java.lang.String pattern, boolean padded)`
    `static java.lang.String[]` | FormatTools.`getFilenames(java.lang.String pattern, IFormatReader r)`
    `static ome.xml.model.enums.FillRule` | MetadataTools.`getFillRule(java.lang.String value)` Retrieves an `FillRule` enumeration value for the given String.
    `protected ome.xml.model.enums.FillRule` | FormatReader.`getFillRule(java.lang.String value)` Deprecated. Use `MetadataTools.getFillRule(String)`.
    `static ome.xml.model.enums.FilterType` | MetadataTools.`getFilterType(java.lang.String value)` Retrieves an `FilterType` enumeration value for the given String.
    `protected ome.xml.model.enums.FilterType` | FormatReader.`getFilterType(java.lang.String value)` Deprecated. Use `MetadataTools.getFilterType(String)`.
    `static ome.xml.model.enums.FontFamily` | MetadataTools.`getFontFamily(java.lang.String value)` Retrieves an `FontFamily` enumeration value for the given String.
    `protected ome.xml.model.enums.FontFamily` | FormatReader.`getFontFamily(java.lang.String value)` Deprecated. Use `MetadataTools.getFontFamily(String)`.
    `static ome.xml.model.enums.FontStyle` | MetadataTools.`getFontStyle(java.lang.String value)` Retrieves an `FontStyle` enumeration value for the given String.
    `protected ome.xml.model.enums.FontStyle` | FormatReader.`getFontStyle(java.lang.String value)` Deprecated. Use `MetadataTools.getFontStyle(String)`.
    `java.lang.String` | ImageWriter.`getFormat(java.lang.String id)` Gets a string describing the file format for the given file.
    `java.lang.String` | ImageReader.`getFormat(java.lang.String id)` Gets a string describing the file format for the given file.
    `static ome.xml.model.enums.IlluminationType` | MetadataTools.`getIlluminationType(java.lang.String value)` Retrieves an `IlluminationType` enumeration value for the given String.
    `protected ome.xml.model.enums.IlluminationType` | FormatReader.`getIlluminationType(java.lang.String value)` Deprecated. Use `MetadataTools.getIlluminationType(String)`.
    `static int` | FormatTools.`getImagesPerFile(java.lang.String pattern, IFormatReader r)`
    `static ome.xml.model.enums.Immersion` | MetadataTools.`getImmersion(java.lang.String value)` Retrieves an `Immersion` enumeration value for the given String.
    `protected ome.xml.model.enums.Immersion` | FormatReader.`getImmersion(java.lang.String value)` Deprecated. Use `MetadataTools.getImmersion(String)`.
    `static ome.xml.model.enums.LaserMedium` | MetadataTools.`getLaserMedium(java.lang.String value)` Retrieves an `LaserMedium` enumeration value for the given String.
    `protected ome.xml.model.enums.LaserMedium` | FormatReader.`getLaserMedium(java.lang.String value)` Deprecated. Use `MetadataTools.getLaserMedium(String)`.
    `static ome.xml.model.enums.LaserType` | MetadataTools.`getLaserType(java.lang.String value)` Retrieves an `LaserType` enumeration value for the given String.
    `protected ome.xml.model.enums.LaserType` | FormatReader.`getLaserType(java.lang.String value)` Deprecated. Use `MetadataTools.getLaserType(String)`.
    `private int` | ChannelFiller.`getLookupTableComponentCount()` Gets the number of color components in the lookup table.
    `static ome.xml.model.enums.Marker` | MetadataTools.`getMarker(java.lang.String value)` Retrieves an `Marker` enumeration value for the given String.
    `protected ome.xml.model.enums.Marker` | FormatReader.`getMarker(java.lang.String value)` Deprecated. Use `MetadataTools.getMarker(String)`.
    `static ome.xml.model.enums.Medium` | MetadataTools.`getMedium(java.lang.String value)` Retrieves an `Medium` enumeration value for the given String.
    `protected ome.xml.model.enums.Medium` | FormatReader.`getMedium(java.lang.String value)` Deprecated. Use `MetadataTools.getMedium(String)`.
    `static ome.xml.model.enums.MicrobeamManipulationType` | MetadataTools.`getMicrobeamManipulationType(java.lang.String value)` Retrieves an `MicrobeamManipulationType` enumeration value for the given String.
    `protected ome.xml.model.enums.MicrobeamManipulationType` | FormatReader.`getMicrobeamManipulationType(java.lang.String value)` Deprecated. Use `MetadataTools.getMicrobeamManipulationType(String)`.
    `static ome.xml.model.enums.MicroscopeType` | MetadataTools.`getMicroscopeType(java.lang.String value)` Retrieves an `MicroscopeType` enumeration value for the given String.
    `protected ome.xml.model.enums.MicroscopeType` | FormatReader.`getMicroscopeType(java.lang.String value)` Deprecated. Use `MetadataTools.getMicroscopeType(String)`.
    `static ome.xml.model.enums.NamingConvention` | MetadataTools.`getNamingConvention(java.lang.String value)` Retrieves an `NamingConvention` enumeration value for the given String.
    `protected ome.xml.model.enums.NamingConvention` | FormatReader.`getNamingConvention(java.lang.String value)` Deprecated. Use `MetadataTools.getNamingConvention(String)`.
    `int` | ChannelMerger.`getOriginalIndex(int no)` Returns the image number in the original dataset that corresponds to the given image number.
    `static ome.xml.model.enums.PixelType` | MetadataTools.`getPixelType(java.lang.String value)` Retrieves an `PixelType` enumeration value for the given String.
    `protected ome.xml.model.enums.PixelType` | FormatReader.`getPixelType(java.lang.String value)` Deprecated. Use `MetadataTools.getPixelType(String)`.
    `java.lang.Double[]` | MinMaxCalculator.`getPlaneMaximum(int no)` Retrieves the maximum pixel value for the specified plane.
    `java.lang.Double[]` | MinMaxCalculator.`getPlaneMinimum(int no)` Retrieves the minimum pixel value for the specified plane.
    `java.lang.String[]` | WrappedReader.`getPossibleDomains(java.lang.String id)`
    `java.lang.String[]` | ReaderWrapper.`getPossibleDomains(java.lang.String id)`
    `java.lang.String[]` | ImageReader.`getPossibleDomains(java.lang.String id)`
    `java.lang.String[]` | IFormatReader.`getPossibleDomains(java.lang.String id)` Returns a list of scientific domains in which this format is used.
    `java.lang.String[]` | FormatReader.`getPossibleDomains(java.lang.String id)`
    `static ome.xml.model.enums.Pulse` | MetadataTools.`getPulse(java.lang.String value)` Retrieves an `Pulse` enumeration value for the given String.
    `protected ome.xml.model.enums.Pulse` | FormatReader.`getPulse(java.lang.String value)` Deprecated. Use `MetadataTools.getPulse(String)`.
    `IFormatReader` | FileStitcher.`getReader(int no)` Gets the reader appropriate for use with the given image plane.
    `IFormatReader` | ImageReader.`getReader(java.lang.String id)` Gets the reader used to open the given file.
    `static int` | FormatTools.`getReorderedIndex(IFormatReader reader, java.lang.String newOrder, int newIndex)` Converts index from the given dimension order to the reader's native one.
    `int` | FileStitcher.`getRequiredDirectories(java.lang.String[] files)`
    `int` | ReaderWrapper.`getRequiredDirectories(java.lang.String[] files)`
    `int` | ImageReader.`getRequiredDirectories(java.lang.String[] files)`
    `int` | IFormatReader.`getRequiredDirectories(java.lang.String[] files)` Returns the number of parent directories that are important when processing the given list of files.
    `int` | FormatReader.`getRequiredDirectories(java.lang.String[] files)`
    `protected int` | FormatWriter.`getSizeX()`
    `protected int` | FormatWriter.`getSizeY()`
    `Codec` | TileStitcher.`getTileCodec(int no)`
    `Codec` | FileStitcher.`getTileCodec(int no)`
    `Codec` | DimensionSwapper.`getTileCodec(int no)`
    `Codec` | ChannelSeparator.`getTileCodec(int no)`
    `Codec` | ChannelMerger.`getTileCodec(int no)`
    `Codec` | ChannelFiller.`getTileCodec(int no)`
    `Codec` | ReaderWrapper.`getTileCodec(int no)`
    `Codec` | ImageReader.`getTileCodec(int no)`
    `default Codec` | ICompressedTileReader.`getTileCodec(int no)` Retrieve a codec that can be used to decompress compressed tiles.
    `CodecOptions` | TileStitcher.`getTileCodecOptions(int no, int x, int y)`
    `CodecOptions` | FileStitcher.`getTileCodecOptions(int no, int x, int y)`
    `CodecOptions` | DimensionSwapper.`getTileCodecOptions(int no, int x, int y)`
    `CodecOptions` | ChannelSeparator.`getTileCodecOptions(int no, int x, int y)`
    `CodecOptions` | ChannelMerger.`getTileCodecOptions(int no, int x, int y)`
    `CodecOptions` | ChannelFiller.`getTileCodecOptions(int no, int x, int y)`
    `CodecOptions` | ReaderWrapper.`getTileCodecOptions(int no, int x, int y)`
    `CodecOptions` | ImageReader.`getTileCodecOptions(int no, int x, int y)`
    `default CodecOptions` | ICompressedTileReader.`getTileCodecOptions(int no, int x, int y)` Retrieve codec options that can be used to decompressed the specified tile.
    `int` | WriterWrapper.`getTileSizeX()`
    `int` | ImageWriter.`getTileSizeX()`
    `int` | IFormatWriter.`getTileSizeX()` Retrieves the current tile width Defaults to 0 if not supported
    `int` | FormatWriter.`getTileSizeX()`
    `int` | WriterWrapper.`getTileSizeY()`
    `int` | ImageWriter.`getTileSizeY()`
    `int` | IFormatWriter.`getTileSizeY()` Retrieves the current tile height Defaults to 0 if not supported
    `int` | FormatWriter.`getTileSizeY()`
    `IFormatWriter` | ImageWriter.`getWriter(java.lang.String id)` Gets the writer used to save the given file.
    `protected void` | FileStitcher.`initFile(java.lang.String id)` Initializes the given file or file pattern.
    `protected void` | SubResolutionFormatReader.`initFile(java.lang.String id)` Initializes the given file (parsing header information, etc.).
    `protected void` | FormatReader.`initFile(java.lang.String id)` Initializes the given file (parsing header information, etc.).
    `protected void` | MinMaxCalculator.`initMinMax()` Ensures internal min/max variables are initialized properly.
    `protected boolean` | FormatWriter.`isFullPlane(int x, int y, int w, int h)` Returns true if the given rectangle coordinates correspond to a full image in the given series.
    `boolean` | MinMaxCalculator.`isMinMaxPopulated()` Returns true if the values returned by getChannelGlobalMinimum/Maximum can be trusted.
    `boolean` | WrappedReader.`isSingleFile(java.lang.String id)`
    `boolean` | ReaderWrapper.`isSingleFile(java.lang.String id)`
    `boolean` | ImageReader.`isSingleFile(java.lang.String id)`
    `boolean` | IFormatReader.`isSingleFile(java.lang.String id)` Returns true if the named file is expected to be the only file in the dataset.
    `boolean` | FormatReader.`isSingleFile(java.lang.String id)`
    `IFormatReader` | Memoizer.`loadMemo()` Load a memo file if possible, returning a null if not.
    `byte[]` | TileStitcher.`openBytes(int no)`
    `byte[]` | MinMaxCalculator.`openBytes(int no)`
    `byte[]` | FileStitcher.`openBytes(int no)`
    `byte[]` | DimensionSwapper.`openBytes(int no)`
    `byte[]` | ChannelSeparator.`openBytes(int no)`
    `byte[]` | ChannelMerger.`openBytes(int no)`
    `byte[]` | ChannelFiller.`openBytes(int no)`
    `byte[]` | WrappedReader.`openBytes(int no)`
    `byte[]` | ReaderWrapper.`openBytes(int no)`
    `byte[]` | ImageReader.`openBytes(int no)`
    `byte[]` | IFormatReader.`openBytes(int no)` Obtains the specified image plane from the current file as a byte array.
    `byte[]` | FormatReader.`openBytes(int no)`
    `byte[]` | TileStitcher.`openBytes(int no, byte[] buf)`
    `byte[]` | MinMaxCalculator.`openBytes(int no, byte[] buf)`
    `byte[]` | FileStitcher.`openBytes(int no, byte[] buf)`
    `byte[]` | DimensionSwapper.`openBytes(int no, byte[] buf)`
    `byte[]` | ChannelSeparator.`openBytes(int no, byte[] buf)`
    `byte[]` | ChannelMerger.`openBytes(int no, byte[] buf)`
    `byte[]` | ChannelFiller.`openBytes(int no, byte[] buf)`
    `byte[]` | WrappedReader.`openBytes(int no, byte[] buf)`
    `byte[]` | ReaderWrapper.`openBytes(int no, byte[] buf)`
    `byte[]` | ImageReader.`openBytes(int no, byte[] buf)`
    `byte[]` | IFormatReader.`openBytes(int no, byte[] buf)` Obtains the specified image plane from the current file into a pre-allocated byte array of (sizeX * sizeY * bytesPerPixel * RGB channel count).
    `byte[]` | FormatReader.`openBytes(int no, byte[] buf)`
    `byte[]` | TileStitcher.`openBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `byte[]` | MinMaxCalculator.`openBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `byte[]` | FileStitcher.`openBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `byte[]` | DimensionSwapper.`openBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `byte[]` | ChannelSeparator.`openBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `byte[]` | ChannelMerger.`openBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `byte[]` | ChannelFiller.`openBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `byte[]` | WrappedReader.`openBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `byte[]` | ReaderWrapper.`openBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `byte[]` | ImageReader.`openBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `byte[]` | IFormatReader.`openBytes(int no, byte[] buf, int x, int y, int w, int h)` Obtains a sub-image of the specified image plane into a pre-allocated byte array.
    `abstract byte[]` | FormatReader.`openBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `byte[]` | DelegateReader.`openBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `byte[]` | TileStitcher.`openBytes(int no, int x, int y, int w, int h)`
    `byte[]` | MinMaxCalculator.`openBytes(int no, int x, int y, int w, int h)`
    `byte[]` | FileStitcher.`openBytes(int no, int x, int y, int w, int h)`
    `byte[]` | DimensionSwapper.`openBytes(int no, int x, int y, int w, int h)`
    `byte[]` | ChannelSeparator.`openBytes(int no, int x, int y, int w, int h)`
    `byte[]` | ChannelMerger.`openBytes(int no, int x, int y, int w, int h)`
    `byte[]` | ChannelFiller.`openBytes(int no, int x, int y, int w, int h)`
    `byte[]` | WrappedReader.`openBytes(int no, int x, int y, int w, int h)`
    `byte[]` | ReaderWrapper.`openBytes(int no, int x, int y, int w, int h)`
    `byte[]` | ImageReader.`openBytes(int no, int x, int y, int w, int h)`
    `byte[]` | IFormatReader.`openBytes(int no, int x, int y, int w, int h)` Obtains a sub-image of the specified image plane, whose upper-left corner is given by (x, y).
    `byte[]` | FormatReader.`openBytes(int no, int x, int y, int w, int h)`
    `byte[]` | TileStitcher.`openCompressedBytes(int no, byte[] buf, int x, int y)`
    `byte[]` | FileStitcher.`openCompressedBytes(int no, byte[] buf, int x, int y)`
    `byte[]` | DimensionSwapper.`openCompressedBytes(int no, byte[] buf, int x, int y)`
    `byte[]` | ChannelSeparator.`openCompressedBytes(int no, byte[] buf, int x, int y)`
    `byte[]` | ChannelMerger.`openCompressedBytes(int no, byte[] buf, int x, int y)`
    `byte[]` | ChannelFiller.`openCompressedBytes(int no, byte[] buf, int x, int y)`
    `byte[]` | ReaderWrapper.`openCompressedBytes(int no, byte[] buf, int x, int y)`
    `byte[]` | ImageReader.`openCompressedBytes(int no, byte[] buf, int x, int y)`
    `default byte[]` | ICompressedTileReader.`openCompressedBytes(int no, byte[] buf, int x, int y)` Retrieve the specified tile without performing any decompression.
    `byte[]` | TileStitcher.`openCompressedBytes(int no, int x, int y)`
    `byte[]` | FileStitcher.`openCompressedBytes(int no, int x, int y)`
    `byte[]` | DimensionSwapper.`openCompressedBytes(int no, int x, int y)`
    `byte[]` | ChannelSeparator.`openCompressedBytes(int no, int x, int y)`
    `byte[]` | ChannelMerger.`openCompressedBytes(int no, int x, int y)`
    `byte[]` | ChannelFiller.`openCompressedBytes(int no, int x, int y)`
    `byte[]` | ReaderWrapper.`openCompressedBytes(int no, int x, int y)`
    `byte[]` | ImageReader.`openCompressedBytes(int no, int x, int y)`
    `default byte[]` | ICompressedTileReader.`openCompressedBytes(int no, int x, int y)` Retrieve the specified tile without performing any decompression.
    `java.lang.Object` | FileStitcher.`openPlane(int no, int x, int y, int w, int h)`
    `java.lang.Object` | WrappedReader.`openPlane(int no, int x, int y, int w, int h)`
    `java.lang.Object` | ReaderWrapper.`openPlane(int no, int x, int y, int w, int h)`
    `java.lang.Object` | ImageReader.`openPlane(int no, int x, int y, int w, int h)`
    `java.lang.Object` | IFormatReader.`openPlane(int no, int x, int y, int w, int h)` Obtains the specified image plane (or sub-image thereof) in the reader's native data structure.
    `java.lang.Object` | FormatReader.`openPlane(int no, int x, int y, int w, int h)`
    `static byte[]` | FormatTools.`openThumbBytes(IFormatReader reader, int no)` Default implementation for `IFormatReader.openThumbBytes(int)`.
    `byte[]` | FileStitcher.`openThumbBytes(int no)`
    `byte[]` | DimensionSwapper.`openThumbBytes(int no)`
    `byte[]` | ChannelSeparator.`openThumbBytes(int no)`
    `byte[]` | WrappedReader.`openThumbBytes(int no)`
    `byte[]` | ReaderWrapper.`openThumbBytes(int no)`
    `byte[]` | ImageReader.`openThumbBytes(int no)`
    `byte[]` | IFormatReader.`openThumbBytes(int no)` Obtains a thumbnail for the specified image plane from the current file, as a byte array.
    `byte[]` | FormatReader.`openThumbBytes(int no)`
    `static int` | FormatTools.`pixelTypeFromBytes(int bytes, boolean signed, boolean fp)` Returns an appropriate pixel type given the number of bytes per pixel.
    `void` | WriterWrapper.`saveBytes(int no, byte[] buf)`
    `void` | ImageWriter.`saveBytes(int no, byte[] buf)`
    `void` | IFormatWriter.`saveBytes(int no, byte[] buf)` Saves the given image to the current series in the current file.
    `void` | FormatWriter.`saveBytes(int no, byte[] buf)`
    `void` | WriterWrapper.`saveBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `void` | ImageWriter.`saveBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `void` | IFormatWriter.`saveBytes(int no, byte[] buf, int x, int y, int w, int h)` Saves the given image tile to the current series in the current file.
    `void` | WriterWrapper.`saveBytes(int no, byte[] buf, loci.common.Region tile)`
    `void` | ImageWriter.`saveBytes(int no, byte[] buf, loci.common.Region tile)`
    `void` | IFormatWriter.`saveBytes(int no, byte[] buf, loci.common.Region tile)` Saves the given image tile to the current series in the current file.
    `void` | FormatWriter.`saveBytes(int no, byte[] buf, loci.common.Region tile)`
    `void` | WriterWrapper.`saveCompressedBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `void` | ImageWriter.`saveCompressedBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `default void` | ICompressedTileWriter.`saveCompressedBytes(int no, byte[] buf, int x, int y, int w, int h)` Save a compressed tile to the current output file.
    `void` | WriterWrapper.`savePlane(int no, java.lang.Object plane)`
    `void` | ImageWriter.`savePlane(int no, java.lang.Object plane)`
    `void` | IFormatWriter.`savePlane(int no, java.lang.Object plane)` Saves the given image plane to the current series in the current file.
    `void` | FormatWriter.`savePlane(int no, java.lang.Object plane)`
    `void` | WriterWrapper.`savePlane(int no, java.lang.Object plane, int x, int y, int w, int h)`
    `void` | ImageWriter.`savePlane(int no, java.lang.Object plane, int x, int y, int w, int h)`
    `void` | IFormatWriter.`savePlane(int no, java.lang.Object plane, int x, int y, int w, int h)` Saves the given image plane to the current series in the current file.
    `void` | FormatWriter.`savePlane(int no, java.lang.Object plane, int x, int y, int w, int h)`
    `void` | WriterWrapper.`savePlane(int no, java.lang.Object plane, loci.common.Region tile)`
    `void` | ImageWriter.`savePlane(int no, java.lang.Object plane, loci.common.Region tile)`
    `void` | IFormatWriter.`savePlane(int no, java.lang.Object plane, loci.common.Region tile)` Saves the given image plane to the current series in the current file.
    `void` | FormatWriter.`savePlane(int no, java.lang.Object plane, loci.common.Region tile)`
    `void` | FileStitcher.`setAxisTypes(int[] axes)` Sets the axis type for each dimensional block.
    `void` | WriterWrapper.`setCompression(java.lang.String compress)`
    `void` | ImageWriter.`setCompression(java.lang.String compress)`
    `void` | IFormatWriter.`setCompression(java.lang.String compress)` Sets the current compression type.
    `void` | FormatWriter.`setCompression(java.lang.String compress)`
    `void` | TileStitcher.`setId(java.lang.String id)`
    `void` | Memoizer.`setId(java.lang.String id)`
    `void` | FileStitcher.`setId(java.lang.String id)`
    `void` | DimensionSwapper.`setId(java.lang.String id)`
    `void` | ChannelSeparator.`setId(java.lang.String id)`
    `void` | ChannelMerger.`setId(java.lang.String id)`
    `void` | ChannelFiller.`setId(java.lang.String id)`
    `void` | WriterWrapper.`setId(java.lang.String id)`
    `void` | ReaderWrapper.`setId(java.lang.String id)`
    `void` | ImageWriter.`setId(java.lang.String id)`
    `void` | ImageReader.`setId(java.lang.String id)`
    `void` | IFormatHandler.`setId(java.lang.String id)` Sets the current file name.
    `void` | FormatWriter.`setId(java.lang.String id)` Initializes a writer from the input file name.
    `void` | FormatReader.`setId(java.lang.String id)` Initialize a reader from the input file name.
    `void` | DelegateReader.`setId(java.lang.String id)`
    `void` | WriterWrapper.`setSeries(int series)`
    `void` | ImageWriter.`setSeries(int series)`
    `void` | IFormatWriter.`setSeries(int series)` Sets the current series.
    `void` | FormatWriter.`setSeries(int series)`
    `int` | WriterWrapper.`setTileSizeX(int tileSize)`
    `int` | ImageWriter.`setTileSizeX(int tileSize)`
    `int` | IFormatWriter.`setTileSizeX(int tileSize)` Will attempt to set the tile width to the desired value and return the actual value which will be used
    `int` | FormatWriter.`setTileSizeX(int tileSize)`
    `int` | WriterWrapper.`setTileSizeY(int tileSize)`
    `int` | ImageWriter.`setTileSizeY(int tileSize)`
    `int` | IFormatWriter.`setTileSizeY(int tileSize)` Will attempt to set the tile height to the desired value and return the actual value which will be used
    `int` | FormatWriter.`setTileSizeY(int tileSize)`
    `IFormatWriter` | WriterWrapper.`unwrap()` Unwraps nested wrapped writers until the core writer (i.e., not a `WriterWrapper` or `ImageWriter`) is found.
    `IFormatReader` | ReaderWrapper.`unwrap()` Unwraps nested wrapped readers until the core reader (i.e., not a `ReaderWrapper` or `ImageReader`) is found.
    `IFormatReader` | ReaderWrapper.`unwrap(java.lang.Class<? extends IFormatReader> readerClass, java.lang.String id)` Unwraps nested wrapped readers until the given reader class is found.
    `IFormatWriter` | WriterWrapper.`unwrap(java.lang.Class<? extends IFormatWriter> writerClass, java.lang.String id)` Unwraps nested wrapped writers until the given writer class is found.
    `IFormatWriter` | WriterWrapper.`unwrap(java.lang.String id)` Unwraps nested wrapped writers until the core writer (i.e., not a `WriterWrapper` or `ImageWriter`) is found.
    `IFormatReader` | ReaderWrapper.`unwrap(java.lang.String id)` Unwraps nested wrapped readers until the core reader (i.e., not a `ReaderWrapper` or `ImageReader`) is found.
    `protected void` | MinMaxCalculator.`updateMinMax(int no, byte[] buf, int len)` Updates min/max values based on the given byte array.
    `static void` | MetadataTools.`verifyMinimumPopulated(MetadataRetrieve src)` Checks whether the given metadata object has the minimum metadata populated to successfully describe an Image.
    `static void` | MetadataTools.`verifyMinimumPopulated(MetadataRetrieve src, int n)` Checks whether the given metadata object has the minimum metadata populated to successfully describe the nth Image.

    Constructors in loci.formats that throw FormatException
    Constructor and Description
    `ExternalSeries(FilePattern pattern)`

  - ### Uses of FormatException in loci.formats.cache

    Subclasses of FormatException in loci.formats.cache
    Modifier and Type | Class and Description
    --- | ---
    `class` | `CacheException` CacheException is the exception thrown when something goes wrong performing a cache operation.

  - ### Uses of FormatException in loci.formats.codec

    Methods in loci.formats.codec that return FormatException
    Modifier and Type | Method and Description
    --- | ---
    `(package private) static FormatException` | WrappedCodec.`unwrapCodecException(ome.codecs.CodecException e)`

    Methods in loci.formats.codec that throw FormatException
    Modifier and Type | Method and Description
    --- | ---
    `byte[]` | WrappedCodec.`compress(byte[][] data, CodecOptions options)`
    `byte[]` | BaseCodec.`compress(byte[][] data, CodecOptions options)` 2D data block encoding default implementation.
    `byte[]` | Codec.`compress(byte[][] data, CodecOptions options)` Compresses a block of data.
    `byte[]` | WrappedCodec.`compress(byte[] data, CodecOptions options)`
    `byte[]` | TargaRLECodec.`compress(byte[] data, CodecOptions options)`
    `byte[]` | NikonCodec.`compress(byte[] data, CodecOptions options)`
    `byte[]` | JPEGXRCodec.`compress(byte[] data, CodecOptions options)`
    `byte[]` | Codec.`compress(byte[] data, CodecOptions options)` Compresses a block of data.
    `private static void` | WrappedCodec.`copyOptions(CodecOptions src, ome.codecs.CodecOptions dest)`
    `byte[]` | WrappedCodec.`decompress(byte[] data)`
    `byte[]` | BaseCodec.`decompress(byte[] data)`
    `byte[]` | Codec.`decompress(byte[] data)` Decompresses a block of data.
    `byte[]` | WrappedCodec.`decompress(byte[][] data)`
    `byte[]` | BaseCodec.`decompress(byte[][] data)`
    `byte[]` | Codec.`decompress(byte[][] data)` Decompresses a block of data.
    `byte[]` | WrappedCodec.`decompress(byte[][] data, CodecOptions options)`
    `byte[]` | BaseCodec.`decompress(byte[][] data, CodecOptions options)` 2D data block decoding default implementation.
    `byte[]` | Codec.`decompress(byte[][] data, CodecOptions options)` Decompresses a block of data.
    `byte[]` | WrappedCodec.`decompress(byte[] data, CodecOptions options)`
    `byte[]` | JPEGXRCodec.`decompress(byte[] buf, CodecOptions options)` The CodecOptions parameter should have the following fields set: `maxBytes` `interleaved` `bitsPerSample` `littleEndian` `width` `height`
    `byte[]` | BaseCodec.`decompress(byte[] data, CodecOptions options)`
    `byte[]` | Codec.`decompress(byte[] data, CodecOptions options)` Decompresses a block of data.
    `byte[]` | ZstdCodec.`decompress(byte[] data, int pointer, int length)`
    `byte[]` | WrappedCodec.`decompress(loci.common.RandomAccessInputStream in, CodecOptions options)`
    `byte[]` | TargaRLECodec.`decompress(loci.common.RandomAccessInputStream in, CodecOptions options)` The CodecOptions parameter should have the following fields set: `maxBytes` `CodecOptions.bitsPerSample`
    `byte[]` | NikonCodec.`decompress(loci.common.RandomAccessInputStream in, CodecOptions options)` The CodecOptions parameter must be an instance of `NikonCodecOptions`, and should have the following fields set: `lossless` `vPredictor` `curve` `split` `bitsPerSample` `maxBytes` `width` `height`
    `byte[]` | JPEGXRCodec.`decompress(loci.common.RandomAccessInputStream in, CodecOptions options)`
    `abstract byte[]` | BaseCodec.`decompress(loci.common.RandomAccessInputStream in, CodecOptions options)`
    `byte[]` | Codec.`decompress(loci.common.RandomAccessInputStream in, CodecOptions options)` Decompresses data from the given RandomAccessInputStream.
    `protected static ome.codecs.CodecOptions` | WrappedCodec.`getOptions(CodecOptions options)`
    `int` | HuffmanCodec.`getSample(BitBuffer bb, CodecOptions options)` Deprecated.
    `int` | HuffmanCodec.`getSample(loci.common.RandomAccessInputStream bb, CodecOptions options)`
    `private void` | JPEGXRCodec.`initialize()` Initializes the JPEG-XR dependency service.
    `void` | BaseCodec.`test()` Main testing method default implementation.

  - ### Uses of FormatException in loci.formats.dicom

    Methods in loci.formats.dicom that throw FormatException
    Modifier and Type | Method and Description
    --- | ---
    `private int` | DicomTag.`getNextTag(loci.common.RandomAccessInputStream in)` Get the next 4 byte DICOM tag from the given input stream.

    Constructors in loci.formats.dicom that throw FormatException
    Constructor and Description
    `DicomFileInfo(java.lang.String filePath)` Construct an object from the given file.
    `DicomTag(loci.common.RandomAccessInputStream in, boolean bigEndian, long location, boolean oddLocations)` Read a complete tag and value from the given input stream.
    `DicomTag(loci.common.RandomAccessInputStream in, boolean bigEndian, long location, boolean oddLocations, boolean readValue)` Read a complete tag and optionally a value from the given input stream.

  - ### Uses of FormatException in loci.formats.gui

    Methods in loci.formats.gui that throw FormatException
    Modifier and Type | Method and Description
    --- | ---
    `static java.awt.image.BufferedImage` | AWTImageTools.`makeImage(byte[] data, boolean interleaved, MetadataRetrieve meta, int series)` Creates an image from the given raw byte array, obtaining the dimensional parameters from the specified metadata object.
    `static java.awt.image.BufferedImage` | AWTImageTools.`openImage(byte[] buf, IFormatReader r, int w, int h)` Creates an image from the given byte array, using the given IFormatReader to retrieve additional information.
    `static java.awt.image.BufferedImage` | AWTImageTools.`openImage(byte[] buf, IFormatReader r, int w, int h, boolean normal)` Creates an image from the given byte array, using the given IFormatReader to retrieve additional information.
    `java.awt.image.BufferedImage` | BufferedImageReader.`openImage(int no)` Obtains the specified image from the current file.
    `java.awt.image.BufferedImage` | BufferedImageReader.`openImage(int no, int x, int y, int w, int h)` Obtains a sub-image of the specified image, whose upper-left corner is given by (x, y).
    `java.awt.image.BufferedImage` | BufferedImageReader.`openThumbImage(int no)` Obtains a thumbnail for the specified image from the current file.
    `void` | BufferedImageWriter.`saveImage(int no, java.awt.image.BufferedImage image)` Saves the given BufferedImage to the current file.
    `void` | BufferedImageWriter.`saveImage(int no, java.awt.image.BufferedImage image, int x, int y, int w, int h)` Saves the given BufferedImage to the current file.

  - ### Uses of FormatException in loci.formats.in

    Methods in loci.formats.in that throw FormatException
    Modifier and Type | Method and Description
    --- | ---
    `private void` | DCIMGReader.`addFileToList(java.lang.String file)`
    `private void` | DicomReader.`addFileToList(java.lang.String file, boolean checkSeries)` Determine if the given file belongs in the same dataset as this file.
    `private void` | FV1000Reader.`addPtyFiles()`
    `private void` | OMETiffReader.`addSubResolutions()`
    `private void` | LIFReader.`addUserCommentMeta(org.w3c.dom.Element imageNode, int image)`
    `static void` | FlexReader.`appendServerMap(java.lang.String alias, java.lang.String realName)` Add the path 'realName' to the mapping for the server named 'alias'.
    `private void` | MicromanagerReader.`buildTIFFList(int posIndex)`
    `private void` | DicomReader.`calculatePixelsOffsets(long baseOffset)` Calculate offsets to all pixel data (tiles or planes) in the file, starting from the given offset.
    `private void` | LOFReader.`checkForLofLayout(loci.common.RandomAccessInputStream in, java.lang.String filename)` Checks if file layout meets lof file specifications
    `private boolean` | ZeissCZIReader.`checkPALM(java.lang.String xml)`
    `private void` | ZeissCZIReader.`convertPixelType(CoreMetadata ms0, int pixelType)`
    `private void` | KLBReader.`convertPixelType(CoreMetadata ms0, int pixelType)`
    `private void` | ZeissCZIReader.`convertPixelType(int pixelType)`
    `private int` | TillVisionReader.`convertPixelType(int type)`
    `private int` | CellSensReader.`convertPixelType(int pixelType)`
    `private void` | TissueFAXSReader.`copyCorrectionImageToBuffer(TissueFAXSReader.ScanRegion region, loci.common.Region dest, int[] zct, byte[] buf)`
    `private void` | TissueFAXSReader.`copyRegionToBuffer(TissueFAXSReader.ScanRegion region, int level, loci.common.Region dest, int[] zct, byte[] buf)`
    `protected byte[]` | MinimalTiffReader.`copyTile(IFD ifd, byte[] buf, int x, int y)`
    `private DicomFileInfo` | DicomReader.`createFileInfo(java.lang.String file)` Construct a DicomFileInfo for the given file.
    `private byte[]` | APNGReader.`decode(APNGReader.PNGInputStream bytes)`
    `private byte[]` | APNGReader.`decode(APNGReader.PNGInputStream bytes, int width, int height)`
    `private byte[]` | CellSensReader.`decodeTile(int no, int row, int col)`
    `byte[]` | SlideBook7Reader.CCompressionBase.`DecompressBuffer(byte[] inBuffer)`
    `private boolean` | PictReader.`drivePictDecoder(int opcode)` Handles the opcodes in the PICT file.
    `protected ZeissTIFFReader.TIFFInfo` | ZeissTIFFReader.`evalFile(java.lang.String id)` Evaluate the metadata of a TIFF/XML file collection, and return this to the user.
    `private void` | PictReader.`expandPixels(int bitSize, byte[] ib, byte[] ob, int outLen)` Expand an array of bytes.
    `private java.lang.String` | BDVReader.`fetchXMLId()`
    `int` | ZeissTIFFReader.`fileGroupOption(java.lang.String id)`
    `int` | ZeissLSMReader.`fileGroupOption(java.lang.String id)`
    `int` | XLEFReader.`fileGroupOption(java.lang.String id)`
    `int` | VisitechReader.`fileGroupOption(java.lang.String id)`
    `int` | VentanaReader.`fileGroupOption(java.lang.String id)`
    `int` | TrestleReader.`fileGroupOption(java.lang.String id)`
    `int` | TillVisionReader.`fileGroupOption(java.lang.String id)`
    `int` | TecanReader.`fileGroupOption(java.lang.String id)`
    `int` | TCSReader.`fileGroupOption(java.lang.String id)`
    `int` | ScanrReader.`fileGroupOption(java.lang.String id)`
    `int` | SVSReader.`fileGroupOption(java.lang.String id)`
    `int` | SPCReader.`fileGroupOption(java.lang.String id)`
    `int` | PrairieReader.`fileGroupOption(java.lang.String id)`
    `int` | PerkinElmerReader.`fileGroupOption(java.lang.String id)`
    `int` | OperettaReader.`fileGroupOption(java.lang.String id)`
    `int` | OlympusTileReader.`fileGroupOption(java.lang.String id)`
    `int` | OIRReader.`fileGroupOption(java.lang.String id)`
    `int` | NiftiReader.`fileGroupOption(java.lang.String id)`
    `int` | NDPISReader.`fileGroupOption(java.lang.String id)`
    `int` | NDPIReader.`fileGroupOption(java.lang.String id)`
    `int` | MicroCTReader.`fileGroupOption(java.lang.String id)`
    `int` | MetamorphReader.`fileGroupOption(java.lang.String id)`
    `int` | MIASReader.`fileGroupOption(java.lang.String id)`
    `int` | LeicaReader.`fileGroupOption(java.lang.String id)`
    `int` | L2DReader.`fileGroupOption(java.lang.String id)`
    `int` | JDCEReader.`fileGroupOption(java.lang.String id)`
    `int` | InCellReader.`fileGroupOption(java.lang.String id)`
    `int` | ImagicReader.`fileGroupOption(java.lang.String id)`
    `int` | HitachiReader.`fileGroupOption(java.lang.String id)`
    `int` | FujiReader.`fileGroupOption(java.lang.String id)`
    `int` | FlexReader.`fileGroupOption(java.lang.String id)`
    `int` | FV1000Reader.`fileGroupOption(java.lang.String id)`
    `int` | DCIMGReader.`fileGroupOption(java.lang.String id)`
    `int` | ColumbusReader.`fileGroupOption(java.lang.String id)`
    `int` | CellomicsReader.`fileGroupOption(java.lang.String id)`
    `int` | CellWorxReader.`fileGroupOption(java.lang.String id)`
    `int` | CellVoyagerReader.`fileGroupOption(java.lang.String id)`
    `int` | CellSensReader.`fileGroupOption(java.lang.String id)`
    `int` | CV7000Reader.`fileGroupOption(java.lang.String id)`
    `int` | BrukerReader.`fileGroupOption(java.lang.String id)`
    `int` | BioRadReader.`fileGroupOption(java.lang.String id)`
    `int` | BDReader.`fileGroupOption(java.lang.String id)`
    `int` | AnalyzeReader.`fileGroupOption(java.lang.String id)`
    `int` | APLReader.`fileGroupOption(java.lang.String id)`
    `int` | AFIReader.`fileGroupOption(java.lang.String id)`
    `int` | NRRDReader.`fileGroupOption(java.lang.String id)`
    `int` | MicromanagerReader.`fileGroupOption(java.lang.String id)`
    `int` | KLBReader.`fileGroupOption(java.lang.String id)`
    `int` | ICSReader.`fileGroupOption(java.lang.String id)`
    `int` | DicomReader.`fileGroupOption(java.lang.String id)`
    `protected void` | ZeissZVIReader.`fillMetadataPass1(MetadataStore store)`
    `protected void` | ZeissTIFFReader.`fillMetadataPass1(MetadataStore store)`
    `protected void` | BaseZeissReader.`fillMetadataPass1(MetadataStore store)` Read and store basic dimensions in model
    `protected void` | ZeissTIFFReader.`fillMetadataPass2(MetadataStore store)`
    `protected void` | BaseZeissReader.`fillMetadataPass2(MetadataStore store)` Read and store basic dimensions in model
    `protected void` | ZeissZVIReader.`fillMetadataPass3(MetadataStore store)`
    `protected void` | BaseZeissReader.`fillMetadataPass3(MetadataStore store)` Read and store basic dimensions in model
    `protected void` | BaseZeissReader.`fillMetadataPass4(MetadataStore store)` Read and store basic dimensions in model
    `protected void` | ZeissZVIReader.`fillMetadataPass5(MetadataStore store)`
    `protected void` | ZeissTIFFReader.`fillMetadataPass5(MetadataStore store)`
    `protected void` | BaseZeissReader.`fillMetadataPass5(MetadataStore store)` Read and store basic dimensions in model
    `protected void` | BaseZeissReader.`fillMetadataPass6(MetadataStore store)` Read and store basic dimensions in model
    `protected void` | BaseZeissReader.`fillMetadataPass7(MetadataStore store)` Store basic dimensions in model
    `private java.lang.String` | LeicaReader.`findLEIFile(java.lang.String baseFile)` Find the .lei file that belongs to the same dataset as the given file.
    `private java.lang.String` | FV1000Reader.`findOIFFile(java.lang.String baseFile)`
    `protected void` | MetaxpressTiffReader.`findPixelsFiles()`
    `protected void` | CellWorxReader.`findPixelsFiles()`
    `short[][]` | ZeissLSMReader.`get16BitLookupTable()`
    `short[][]` | ZeissCZIReader.`get16BitLookupTable()`
    `short[][]` | VentanaReader.`get16BitLookupTable()`
    `short[][]` | TCSReader.`get16BitLookupTable()`
    `short[][]` | SlidebookTiffReader.`get16BitLookupTable()`
    `short[][]` | PerkinElmerReader.`get16BitLookupTable()`
    `short[][]` | PDSReader.`get16BitLookupTable()`
    `short[][]` | OIRReader.`get16BitLookupTable()`
    `short[][]` | MIASReader.`get16BitLookupTable()`
    `short[][]` | LeicaReader.`get16BitLookupTable()`
    `short[][]` | InCellReader.`get16BitLookupTable()`
    `short[][]` | ImprovisionTiffReader.`get16BitLookupTable()`
    `short[][]` | BaseZeissReader.`get16BitLookupTable()`
    `short[][]` | ZipReader.`get16BitLookupTable()`
    `short[][]` | OMETiffReader.`get16BitLookupTable()`
    `short[][]` | MinimalTiffReader.`get16BitLookupTable()`
    `short[][]` | FilePatternReader.`get16BitLookupTable()`
    `short[][]` | FakeReader.`get16BitLookupTable()`
    `byte[][]` | ZeissLSMReader.`get8BitLookupTable()`
    `byte[][]` | ZeissCZIReader.`get8BitLookupTable()`
    `byte[][]` | VentanaReader.`get8BitLookupTable()`
    `byte[][]` | TargaReader.`get8BitLookupTable()`
    `byte[][]` | TCSReader.`get8BitLookupTable()`
    `byte[][]` | SlidebookTiffReader.`get8BitLookupTable()`
    `byte[][]` | PerkinElmerReader.`get8BitLookupTable()`
    `byte[][]` | OIRReader.`get8BitLookupTable()`
    `byte[][]` | MIASReader.`get8BitLookupTable()`
    `byte[][]` | LeicaReader.`get8BitLookupTable()`
    `byte[][]` | KhorosReader.`get8BitLookupTable()`
    `byte[][]` | InCellReader.`get8BitLookupTable()`
    `byte[][]` | ImprovisionTiffReader.`get8BitLookupTable()`
    `byte[][]` | IPWReader.`get8BitLookupTable()`
    `byte[][]` | BaseZeissReader.`get8BitLookupTable()`
    `byte[][]` | ZipReader.`get8BitLookupTable()`
    `byte[][]` | PictReader.`get8BitLookupTable()`
    `byte[][]` | OMETiffReader.`get8BitLookupTable()`
    `byte[][]` | MinimalTiffReader.`get8BitLookupTable()`
    `byte[][]` | GIFReader.`get8BitLookupTable()`
    `byte[][]` | FilePatternReader.`get8BitLookupTable()`
    `byte[][]` | FakeReader.`get8BitLookupTable()`
    `byte[][]` | BMPReader.`get8BitLookupTable()`
    `protected ome.xml.model.enums.AcquisitionMode` | OperettaReader.`getAcquisitionMode(java.lang.String mode)` Deprecated.
    `private java.util.List<TissueFAXSReader.ScanRegion>` | TissueFAXSReader.`getAllRegions(int t)`
    `private int` | OBFReader.`getBitsPerPixel(int type)`
    `int` | SPEReader.SpeHeader.`getByte(SPEReader.SpeHeaderEntry entry)` Method used to retrieve data values for Byte entries into the SPE header table
    `private ome.xml.model.primitives.Color` | MIASReader.`getChannelColorFromFile(java.lang.String file)` Get the color associated with the given file's channel.
    `protected long` | MinimalTiffReader.`getCompressedByteCount(IFD ifd, int x, int y)`
    `private boolean` | OBFReader.`getCompression(int compression)`
    `private loci.common.RandomAccessInputStream` | ZeissLSMReader.`getCZTag(IFD ifd)`
    `private loci.common.RandomAccessInputStream` | CellomicsReader.`getDecompressedStream(java.lang.String filename)`
    `private int` | ZeissLSMReader.`getExtraSeries(java.lang.String file)`
    `private loci.common.RandomAccessInputStream` | FV1000Reader.`getFile(java.lang.String name)`
    `private java.lang.String` | SlidebookTiffReader.`getFirstChannel(java.lang.String path)`
    `private java.lang.Object` | CellH5Reader.`getImageData(int no, int y, int height)`
    `private java.lang.Object` | ImarisHDFReader.`getImageData(int no, int x, int y, int width, int height)` Retrieve an array corresponding to the specified image tile.
    `private java.lang.Object` | BDVReader.`getImageData(int no, int x, int y, int width, int height)`
    `private loci.common.IniList` | FV1000Reader.`getIniFile(java.lang.String filename)`
    `int` | SPEReader.SpeHeader.`getInt(SPEReader.SpeHeaderEntry entry)` Method used to retrieve data values for Integer entries into the SPE header table
    `int[]` | SPEReader.SpeHeader.`getIntArray(SPEReader.SpeHeaderEntry entry)` Method used to retrieve data values for Integer Array entries into the SPE header table
    `private long` | OBFReader.`getLength(long length)`
    `private int` | TissueFAXSReader.`getLevel()`
    `long` | SPEReader.SpeHeader.`getLong(SPEReader.SpeHeaderEntry entry)` Method used to retrieve data values for Long enteries into the SPE header table
    `long[]` | SPEReader.SpeHeader.`getLongArray(SPEReader.SpeHeaderEntry entry)` Method used to retrieve data values for Long Array entries into the SPE header table
    `(package private) byte[][]` | AmiraReader.`getLookupTable(java.util.Map materials)`
    `private long[]` | NDPIReader.`getMarkers(IFD ifd)` Get the array of restart markers (offsets) for the given IFD.
    `private java.lang.String` | ZeissLSMReader.`getMDBFile(java.lang.String id)`
    `private java.lang.String` | ZeissXRMReader.`getMetadataPixelType(int dataType)`
    `private org.w3c.dom.Element` | OlympusTileReader.`getMetadataRoot(java.lang.String xml)`
    `private org.w3c.dom.Element` | LIFReader.`getMetadataRoot(java.lang.String xml)`
    `int` | ZeissCZIReader.SubBlock.`getPhysicalHeight()`
    `int` | ZeissCZIReader.SubBlock.`getPhysicalWidth()`
    `private int` | ZeissXRMReader.`getPixelType(int dataType)` Convert an XRM data type to a Bio-Formats pixel type.
    `private int` | OBFReader.`getPixelType(int type)`
    `private int` | LiFlimReader.`getPixelTypeFromString(java.lang.String type)`
    `protected IFormatReader` | MetaxpressTiffReader.`getReader(java.lang.String file, boolean omexml)`
    `protected IFormatReader` | CellWorxReader.`getReader(java.lang.String file, boolean omexml)`
    `private TissueFAXSReader.ScanRegion` | TissueFAXSReader.`getRegion()`
    `private TissueFAXSReader.ScanRegion` | TissueFAXSReader.`getRegion(int t)`
    `int` | TecanReader.`getRequiredDirectories(java.lang.String[] files)`
    `int` | OperettaReader.`getRequiredDirectories(java.lang.String[] files)`
    `int` | MicroCTReader.`getRequiredDirectories(java.lang.String[] files)`
    `int` | MIASReader.`getRequiredDirectories(java.lang.String[] files)`
    `int` | ColumbusReader.`getRequiredDirectories(java.lang.String[] files)`
    `int` | CellVoyagerReader.`getRequiredDirectories(java.lang.String[] files)`
    `int` | CV7000Reader.`getRequiredDirectories(java.lang.String[] files)`
    `int` | BrukerReader.`getRequiredDirectories(java.lang.String[] files)`
    `int` | OMETiffReader.`getRequiredDirectories(java.lang.String[] files)`
    `int` | DicomReader.`getRequiredDirectories(java.lang.String[] files)`
    `SPEReader.SpeROI[]` | SPEReader.SpeHeader.`getROIs()` Method used to read and return meta data for upto 10 rectangular ROI's stored in the SPE header table
    `private java.lang.Object` | ImarisHDFReader.`getSampleData()`
    `int` | SPEReader.SpeHeader.`getShort(SPEReader.SpeHeaderEntry entry)` Method used to retrieve data values for Short entries into the SPE header table
    `int[]` | SPEReader.SpeHeader.`getShortArray(SPEReader.SpeHeaderEntry entry)` Method used to retrieve data values for Short Array entries into the SPE header table
    `int` | SPEReader.SpeHeader.`getStackSize()` Method used to determined the stack size of the SPE file.
    `java.lang.String` | SPEReader.SpeHeader.`getString(SPEReader.SpeHeaderEntry entry)` Method used to retrieve data values for String entries into the SPE header table
    `private java.lang.String[]` | MetaxpressTiffReader.`getTiffFiles(java.lang.String plateName, char rowLetter, int col, int channels, int nTimepoints, int zSteps)`
    `private void` | DicomReader.`getTile(DicomTile tile, byte[] buf, int x, int y, int w, int h)` Decompress pixel data associated with the given DicomTile.
    `private byte[]` | MIASReader.`getTile(int well, int no, int row, int col, loci.common.Region intersection)`
    `Codec` | SVSReader.`getTileCodec(int no)`
    `Codec` | NDPIReader.`getTileCodec(int no)`
    `Codec` | DicomReader.`getTileCodec(int no)`
    `CodecOptions` | SVSReader.`getTileCodecOptions(int no, int x, int y)`
    `CodecOptions` | NDPIReader.`getTileCodecOptions(int no, int x, int y)`
    `CodecOptions` | DicomReader.`getTileCodecOptions(int no, int x, int y)`
    `protected int` | MinimalTiffReader.`getTileIndex(IFD ifd, int x, int y)` Get the index of the tile corresponding to given IFD (plane) and tile XY indexes.
    `private java.lang.String` | SlidebookTiffReader.`getTimestamp(java.lang.String path)`
    `private long` | BDReader.`getTimestamp(java.lang.String file)`
    `private java.lang.String` | ImprovisionTiffReader.`getUUID(java.lang.String path)`
    `private void` | TCSReader.`groupFiles()`
    `private void` | FlexReader.`groupFiles(java.lang.String[] fileList, MetadataStore store)`
    `private void` | PictReader.`handleBitmap(int opcode)` Extract the image data in a PICT bitmap structure.
    `private void` | PictReader.`handlePixmap(int opcode)` Extracts the image data in a PICT pixmap structure.
    `private void` | PictReader.`handlePixmap(int pixelSize, int compCount)` Handles the unpacking of the image data.
    `private void` | FluoviewReader.`initAlternateMetadata()`
    `private void` | FluoviewReader.`initAlternateMetadataStore()`
    `private void` | LiFlimReader.`initCoreMetadata()`
    `protected void` | LeicaSCNReader.`initCoreMetadata(int series, int resolution)`
    `protected void` | DeltavisionReader.`initExtraMetadata()`
    `protected void` | ZeissZVIReader.`initFile(java.lang.String id)`
    `protected void` | ZeissXRMReader.`initFile(java.lang.String id)`
    `protected void` | ZeissTIFFReader.`initFile(java.lang.String id)`
    `protected void` | ZeissLSMReader.`initFile(java.lang.String id)`
    `void` | ZeissLMSReader.`initFile(java.lang.String id)`
    `protected void` | ZeissCZIReader.`initFile(java.lang.String id)`
    `protected void` | XLEFReader.`initFile(java.lang.String id)`
    `protected void` | WATOPReader.`initFile(java.lang.String id)`
    `protected void` | VolocityReader.`initFile(java.lang.String id)`
    `protected void` | VolocityClippingReader.`initFile(java.lang.String id)`
    `protected void` | VisitechReader.`initFile(java.lang.String id)`
    `protected void` | VeecoReader.`initFile(java.lang.String id)`
    `protected void` | VarianFDFReader.`initFile(java.lang.String id)`
    `protected void` | VGSAMReader.`initFile(java.lang.String id)`
    `protected void` | UnisokuReader.`initFile(java.lang.String id)`
    `protected void` | UBMReader.`initFile(java.lang.String id)`
    `protected void` | TrestleReader.`initFile(java.lang.String id)`
    `protected void` | TopometrixReader.`initFile(java.lang.String id)`
    `protected void` | TissueFAXSReader.`initFile(java.lang.String id)`
    `protected void` | TillVisionReader.`initFile(java.lang.String id)`
    `protected void` | TecanReader.`initFile(java.lang.String id)`
    `protected void` | TargaReader.`initFile(java.lang.String id)`
    `protected void` | TCSReader.`initFile(java.lang.String id)`
    `protected void` | SpiderReader.`initFile(java.lang.String id)`
    `protected void` | SlidebookReader.`initFile(java.lang.String id)`
    `protected void` | SeikoReader.`initFile(java.lang.String id)`
    `protected void` | ScanrReader.`initFile(java.lang.String id)`
    `protected void` | SPEReader.`initFile(java.lang.String id)`
    `protected void` | SPCReader.`initFile(java.lang.String id)`
    `protected void` | SMCameraReader.`initFile(java.lang.String id)`
    `protected void` | SIFReader.`initFile(java.lang.String id)`
    `protected void` | SEQReader.`initFile(java.lang.String id)`
    `protected void` | SDTReader.`initFile(java.lang.String id)`
    `protected void` | SBIGReader.`initFile(java.lang.String id)`
    `protected void` | RHKReader.`initFile(java.lang.String id)`
    `protected void` | QuesantReader.`initFile(java.lang.String id)`
    `protected void` | PrairieReader.`initFile(java.lang.String id)`
    `protected void` | PovrayReader.`initFile(java.lang.String id)`
    `protected void` | PhotoshopTiffReader.`initFile(java.lang.String id)`
    `protected void` | PerkinElmerReader.`initFile(java.lang.String id)`
    `protected void` | PSDReader.`initFile(java.lang.String id)`
    `protected void` | PQBinReader.`initFile(java.lang.String id)`
    `protected void` | PDSReader.`initFile(java.lang.String id)`
    `protected void` | PCORAWReader.`initFile(java.lang.String id)`
    `protected void` | PCIReader.`initFile(java.lang.String id)`
    `protected void` | OxfordInstrumentsReader.`initFile(java.lang.String id)`
    `protected void` | OperettaReader.`initFile(java.lang.String id)`
    `protected void` | OpenlabReader.`initFile(java.lang.String id)`
    `protected void` | OpenlabRawReader.`initFile(java.lang.String id)`
    `protected void` | OlympusTileReader.`initFile(java.lang.String id)`
    `protected void` | OIRReader.`initFile(java.lang.String id)`
    `protected void` | NikonReader.`initFile(java.lang.String id)`
    `protected void` | NiftiReader.`initFile(java.lang.String id)`
    `protected void` | NDPISReader.`initFile(java.lang.String id)`
    `protected void` | NDPIReader.`initFile(java.lang.String id)`
    `protected void` | ND2Reader.`initFile(java.lang.String id)`
    `protected void` | NAFReader.`initFile(java.lang.String id)`
    `protected void` | MolecularImagingReader.`initFile(java.lang.String id)`
    `protected void` | MicroCTReader.`initFile(java.lang.String id)`
    `protected void` | MetamorphTiffReader.`initFile(java.lang.String id)`
    `protected void` | MetamorphReader.`initFile(java.lang.String id)`
    `protected void` | MRWReader.`initFile(java.lang.String id)`
    `void` | MRCReader.`initFile(java.lang.String id)`
    `protected void` | MINCReader.`initFile(java.lang.String id)`
    `protected void` | MIASReader.`initFile(java.lang.String id)`
    `protected void` | LiFlimReader.`initFile(java.lang.String id)`
    `protected void` | LeicaReader.`initFile(java.lang.String id)`
    `protected void` | LOFReader.`initFile(java.lang.String id)`
    `protected void` | LIMReader.`initFile(java.lang.String id)`
    `protected void` | LIFReader.`initFile(java.lang.String id)`
    `protected void` | L2DReader.`initFile(java.lang.String id)`
    `protected void` | KodakReader.`initFile(java.lang.String id)`
    `protected void` | KhorosReader.`initFile(java.lang.String id)`
    `protected void` | JPXReader.`initFile(java.lang.String id)`
    `protected void` | JEOLReader.`initFile(java.lang.String id)`
    `protected void` | JDCEReader.`initFile(java.lang.String id)`
    `protected void` | IvisionReader.`initFile(java.lang.String id)`
    `protected void` | InveonReader.`initFile(java.lang.String id)`
    `protected void` | InCellReader.`initFile(java.lang.String id)`
    `protected void` | InCell3000Reader.`initFile(java.lang.String id)`
    `protected void` | ImspectorReader.`initFile(java.lang.String id)`
    `protected void` | ImarisTiffReader.`initFile(java.lang.String id)`
    `protected void` | ImarisReader.`initFile(java.lang.String id)`
    `protected void` | ImarisHDFReader.`initFile(java.lang.String id)`
    `protected void` | ImagicReader.`initFile(java.lang.String id)`
    `protected void` | IPWReader.`initFile(java.lang.String id)`
    `protected void` | IPLabReader.`initFile(java.lang.String id)`
    `protected void` | INRReader.`initFile(java.lang.String id)`
    `protected void` | IMODReader.`initFile(java.lang.String id)`
    `void` | I2IReader.`initFile(java.lang.String id)`
    `protected void` | HitachiReader.`initFile(java.lang.String id)`
    `protected void` | HamamatsuVMSReader.`initFile(java.lang.String id)`
    `protected void` | HRDGDFReader.`initFile(java.lang.String id)`
    `protected void` | HISReader.`initFile(java.lang.String id)`
    `protected void` | GatanReader.`initFile(java.lang.String id)`
    `protected void` | GatanDM2Reader.`initFile(java.lang.String id)`
    `protected void` | FujiReader.`initFile(java.lang.String id)`
    `protected void` | FlexReader.`initFile(java.lang.String id)`
    `protected void` | FV1000Reader.`initFile(java.lang.String id)`
    `protected void` | FEIReader.`initFile(java.lang.String id)`
    `protected void` | Ecat7Reader.`initFile(java.lang.String id)`
    `protected void` | DeltavisionReader.`initFile(java.lang.String id)`
    `protected void` | DNGReader.`initFile(java.lang.String id)`
    `protected void` | DCIMGReader.`initFile(java.lang.String id)`
    `protected void` | ColumbusReader.`initFile(java.lang.String id)`
    `protected void` | CellomicsReader.`initFile(java.lang.String id)`
    `protected void` | CellWorxReader.`initFile(java.lang.String id)`
    `protected void` | CellVoyagerReader.`initFile(java.lang.String id)`
    `protected void` | CellSensReader.`initFile(java.lang.String id)`
    `protected void` | CanonRawReader.`initFile(java.lang.String id)`
    `protected void` | CV7000Reader.`initFile(java.lang.String id)`
    `protected void` | BurleighReader.`initFile(java.lang.String id)`
    `protected void` | BrukerReader.`initFile(java.lang.String id)`
    `protected void` | BioRadSCNReader.`initFile(java.lang.String id)`
    `protected void` | BioRadReader.`initFile(java.lang.String id)`
    `protected void` | BioRadGelReader.`initFile(java.lang.String id)`
    `protected void` | BDReader.`initFile(java.lang.String id)`
    `protected void` | AnalyzeReader.`initFile(java.lang.String id)`
    `protected void` | AmiraReader.`initFile(java.lang.String id)`
    `protected void` | AliconaReader.`initFile(java.lang.String id)`
    `protected void` | ARFReader.`initFile(java.lang.String id)`
    `protected void` | APLReader.`initFile(java.lang.String id)`
    `protected void` | AIMReader.`initFile(java.lang.String id)`
    `protected void` | AFIReader.`initFile(java.lang.String id)`
    `protected void` | ZipReader.`initFile(java.lang.String id)`
    `void` | TileJPEGReader.`initFile(java.lang.String id)`
    `protected void` | TiffJAIReader.`initFile(java.lang.String id)`
    `protected void` | TextReader.`initFile(java.lang.String id)`
    `protected void` | SlideBook7Reader.`initFile(java.lang.String id)`
    `protected void` | QTReader.`initFile(java.lang.String id)`
    `protected void` | PictReader.`initFile(java.lang.String id)`
    `protected void` | PGMReader.`initFile(java.lang.String id)`
    `protected void` | PCXReader.`initFile(java.lang.String id)`
    `protected void` | OMEXMLReader.`initFile(java.lang.String id)`
    `protected void` | OMETiffReader.`initFile(java.lang.String id)`
    `protected void` | OBFReader.`initFile(java.lang.String id)`
    `protected void` | NRRDReader.`initFile(java.lang.String id)`
    `protected void` | MinimalTiffReader.`initFile(java.lang.String id)`
    `void` | MicromanagerReader.`initFile(java.lang.String id)`
    `protected void` | MNGReader.`initFile(java.lang.String id)`
    `protected void` | KLBReader.`initFile(java.lang.String id)`
    `protected void` | JPEGReader.DefaultJPEGReader.`initFile(java.lang.String id)`
    `protected void` | JPEG2000Reader.`initFile(java.lang.String id)`
    `protected void` | ImageIOReader.`initFile(java.lang.String id)`
    `protected void` | IM3Reader.`initFile(java.lang.String id)`
    `protected void` | ICSReader.`initFile(java.lang.String id)`
    `protected void` | GIFReader.`initFile(java.lang.String id)`
    `protected void` | FlowSightReader.`initFile(java.lang.String id)`
    `protected void` | FitsReader.`initFile(java.lang.String id)`
    `protected void` | FilePatternReader.`initFile(java.lang.String id)`
    `protected void` | FakeReader.`initFile(java.lang.String id)`
    `protected void` | EPSReader.`initFile(java.lang.String id)`
    `protected void` | DicomReader.`initFile(java.lang.String id)`
    `protected void` | CellH5Reader.`initFile(java.lang.String id)`
    `protected void` | BaseTiffReader.`initFile(java.lang.String id)`
    `protected void` | BMPReader.`initFile(java.lang.String id)`
    `protected void` | BDVReader.`initFile(java.lang.String id)`
    `protected void` | AVIReader.`initFile(java.lang.String id)`
    `protected void` | APNGReader.`initFile(java.lang.String id)`
    `protected void` | BaseZeissReader.`initFileMain(java.lang.String id)`
    `private void` | FlexReader.`initFlexFile(java.lang.String id)`
    `private void` | OMETiffReader.`initializeReader(IFormatReader r, java.lang.String file)`
    `protected void` | ImageIOReader.`initImage()`
    `private void` | FlexReader.`initMeaFile(java.lang.String id)` Initialize the dataset from a .mea file.
    `protected void` | GelReader.`initMetadata()`
    `protected void` | BaseTiffReader.`initMetadata()` Populates the metadata hashtable and metadata store.
    `protected void` | ZeissLSMReader.`initMetadata(int series)`
    `private void` | LIFReader.`initMetadata(java.lang.String xml)` Parses a string of XML and puts the values in a Hashtable.
    `protected void` | VentanaReader.`initMetadataStore()`
    `protected void` | VectraReader.`initMetadataStore()`
    `protected void` | TrestleReader.`initMetadataStore()`
    `protected void` | SlidebookTiffReader.`initMetadataStore()`
    `protected void` | SimplePCITiffReader.`initMetadataStore()`
    `protected void` | SVSReader.`initMetadataStore()`
    `protected void` | SISReader.`initMetadataStore()`
    `protected void` | PyramidTiffReader.`initMetadataStore()`
    `protected void` | NikonTiffReader.`initMetadataStore()`
    `protected void` | NikonElementsTiffReader.`initMetadataStore()`
    `protected void` | NDPIReader.`initMetadataStore()`
    `protected void` | LeicaSCNReader.`initMetadataStore()`
    `protected void` | LEOReader.`initMetadataStore()`
    `protected void` | JPKReader.`initMetadataStore()`
    `protected void` | IonpathMIBITiffReader.`initMetadataStore()`
    `protected void` | ImprovisionTiffReader.`initMetadataStore()`
    `protected void` | ImaconReader.`initMetadataStore()`
    `protected void` | FluoviewReader.`initMetadataStore()`
    `protected void` | FEITiffReader.`initMetadataStore()`
    `protected void` | TiffReader.`initMetadataStore()`
    `protected void` | BaseTiffReader.`initMetadataStore()` Populates the metadata store using the data parsed in `BaseTiffReader.initStandardMetadata()` along with some further parsing done in the method itself.
    `protected void` | DeltavisionReader.`initPixels()`
    `private void` | ZeissZVIReader.`initPOIService()`
    `private void` | ZeissXRMReader.`initPOIService()`
    `private void` | PCIReader.`initPOIService()`
    `private void` | IPWReader.`initPOIService()`
    `private void` | FV1000Reader.`initPOIService()`
    `protected void` | CellWorxReader.`initReader(IFormatReader reader, java.lang.String file, boolean omexml)`
    `private void` | FlexReader.`initResFile(java.lang.String id)` Initialize the dataset from a .res file.
    `private long` | OBFReader.`initStack(long current)`
    `protected void` | VentanaReader.`initStandardMetadata()`
    `protected void` | VectraReader.`initStandardMetadata()`
    `protected void` | TrestleReader.`initStandardMetadata()`
    `protected void` | SlidebookTiffReader.`initStandardMetadata()`
    `protected void` | SimplePCITiffReader.`initStandardMetadata()`
    `protected void` | SVSReader.`initStandardMetadata()`
    `protected void` | SISReader.`initStandardMetadata()`
    `protected void` | SEQReader.`initStandardMetadata()`
    `protected void` | PyramidTiffReader.`initStandardMetadata()`
    `protected void` | NikonTiffReader.`initStandardMetadata()`
    `protected void` | NikonReader.`initStandardMetadata()`
    `protected void` | NikonElementsTiffReader.`initStandardMetadata()`
    `protected void` | NDPIReader.`initStandardMetadata()`
    `protected void` | MetamorphReader.`initStandardMetadata()`
    `protected void` | LeicaSCNReader.`initStandardMetadata()`
    `protected void` | LEOReader.`initStandardMetadata()`
    `protected void` | JPKReader.`initStandardMetadata()`
    `protected void` | IonpathMIBITiffReader.`initStandardMetadata()`
    `protected void` | ImprovisionTiffReader.`initStandardMetadata()`
    `protected void` | ImaconReader.`initStandardMetadata()`
    `protected void` | FluoviewReader.`initStandardMetadata()`
    `protected void` | FEITiffReader.`initStandardMetadata()`
    `protected void` | DNGReader.`initStandardMetadata()`
    `protected void` | TiffReader.`initStandardMetadata()`
    `protected void` | BaseTiffReader.`initStandardMetadata()` Parses standard metadata.
    `protected void` | ZeissZVIReader.`initVars(java.lang.String id)`
    `protected void` | ZeissTIFFReader.`initVars(java.lang.String id)`
    `protected void` | BaseZeissReader.`initVars(java.lang.String id)`
    `boolean` | ZeissTIFFReader.`isSingleFile(java.lang.String id)`
    `boolean` | ZeissLSMReader.`isSingleFile(java.lang.String id)`
    `boolean` | XLEFReader.`isSingleFile(java.lang.String id)`
    `boolean` | VisitechReader.`isSingleFile(java.lang.String id)`
    `boolean` | TillVisionReader.`isSingleFile(java.lang.String id)`
    `boolean` | TecanReader.`isSingleFile(java.lang.String id)`
    `boolean` | TCSReader.`isSingleFile(java.lang.String id)`
    `boolean` | ScanrReader.`isSingleFile(java.lang.String id)`
    `boolean` | SPCReader.`isSingleFile(java.lang.String id)`
    `boolean` | PrairieReader.`isSingleFile(java.lang.String id)`
    `boolean` | PerkinElmerReader.`isSingleFile(java.lang.String id)`
    `boolean` | OperettaReader.`isSingleFile(java.lang.String id)`
    `boolean` | OlympusTileReader.`isSingleFile(java.lang.String id)`
    `boolean` | OIRReader.`isSingleFile(java.lang.String id)`
    `boolean` | NiftiReader.`isSingleFile(java.lang.String id)`
    `boolean` | NDPISReader.`isSingleFile(java.lang.String id)`
    `boolean` | MicroCTReader.`isSingleFile(java.lang.String id)`
    `boolean` | MetamorphReader.`isSingleFile(java.lang.String id)`
    `boolean` | MIASReader.`isSingleFile(java.lang.String id)`
    `boolean` | LeicaReader.`isSingleFile(java.lang.String id)`
    `boolean` | L2DReader.`isSingleFile(java.lang.String id)`
    `boolean` | JDCEReader.`isSingleFile(java.lang.String id)`
    `boolean` | InCellReader.`isSingleFile(java.lang.String id)`
    `boolean` | ImagicReader.`isSingleFile(java.lang.String id)`
    `boolean` | HitachiReader.`isSingleFile(java.lang.String id)`
    `boolean` | FujiReader.`isSingleFile(java.lang.String id)`
    `boolean` | FlexReader.`isSingleFile(java.lang.String id)`
    `boolean` | FV1000Reader.`isSingleFile(java.lang.String id)`
    `boolean` | DeltavisionReader.`isSingleFile(java.lang.String id)`
    `boolean` | DCIMGReader.`isSingleFile(java.lang.String id)`
    `boolean` | ColumbusReader.`isSingleFile(java.lang.String id)`
    `boolean` | CellVoyagerReader.`isSingleFile(java.lang.String id)`
    `boolean` | CellSensReader.`isSingleFile(java.lang.String id)`
    `boolean` | CV7000Reader.`isSingleFile(java.lang.String id)`
    `boolean` | BrukerReader.`isSingleFile(java.lang.String id)`
    `boolean` | BioRadReader.`isSingleFile(java.lang.String id)`
    `boolean` | BDReader.`isSingleFile(java.lang.String id)`
    `boolean` | AnalyzeReader.`isSingleFile(java.lang.String id)`
    `boolean` | APLReader.`isSingleFile(java.lang.String id)`
    `boolean` | AFIReader.`isSingleFile(java.lang.String id)`
    `boolean` | SlideBook7Reader.`isSingleFile(java.lang.String id)`
    `boolean` | OMETiffReader.`isSingleFile(java.lang.String id)`
    `boolean` | NRRDReader.`isSingleFile(java.lang.String id)`
    `boolean` | MicromanagerReader.`isSingleFile(java.lang.String id)`
    `boolean` | ICSReader.`isSingleFile(java.lang.String id)`
    `boolean` | FilePatternReader.`isSingleFile(java.lang.String id)`
    `boolean` | FakeReader.`isSingleFile(java.lang.String id)`
    `void` | DynamicMetadataOptions.`loadOptions(java.lang.String optionsFile, java.util.ArrayList<java.lang.String> availableOptionKeys)`
    `private java.lang.String` | BDReader.`locateExperimentFile(java.lang.String id)`
    `private void` | DicomReader.`makeFileList()` Build a list of files that belong with the current file.
    `private java.lang.String` | FV1000Reader.`mapOIBFiles()`
    `static void` | FlexReader.`mapServersFromConfigurationFile(java.lang.String configFile)` Read a configuration file with lines of the form: <server alias>=<real server name> and call mapServer(String, String) accordingly.
    `private byte[]` | FlowSightReader.`openBitmaskBytes(IFD ifd, int imageWidth, int imageHeight)` Decode the whole IFD plane using bitmask compression
    `protected java.awt.image.BufferedImage` | TiffJAIReader.`openBufferedImage(int no)` Obtains a BufferedImage from the given data source using JAI.
    `byte[]` | ZeissZVIReader.`openBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `byte[]` | ZeissXRMReader.`openBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `byte[]` | ZeissTIFFReader.`openBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `byte[]` | ZeissLSMReader.`openBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `byte[]` | ZeissLMSReader.`openBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `byte[]` | ZeissCZIReader.`openBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `byte[]` | XLEFReader.`openBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `byte[]` | WATOPReader.`openBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `byte[]` | VolocityReader.`openBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `byte[]` | VolocityClippingReader.`openBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `byte[]` | VisitechReader.`openBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `byte[]` | VentanaReader.`openBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `byte[]` | VeecoReader.`openBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `byte[]` | VectraReader.`openBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `byte[]` | VarianFDFReader.`openBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `byte[]` | VGSAMReader.`openBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `byte[]` | UnisokuReader.`openBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `byte[]` | UBMReader.`openBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `byte[]` | TrestleReader.`openBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `byte[]` | TopometrixReader.`openBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `byte[]` | TissueFAXSReader.`openBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `byte[]` | TillVisionReader.`openBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `byte[]` | TecanReader.`openBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `byte[]` | TargaReader.`openBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `byte[]` | TCSReader.`openBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `byte[]` | SpiderReader.`openBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `byte[]` | SlidebookTiffReader.`openBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `byte[]` | SlidebookReader.`openBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `byte[]` | SimplePCITiffReader.`openBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `byte[]` | SeikoReader.`openBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `byte[]` | ScanrReader.`openBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `byte[]` | SVSReader.`openBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `byte[]` | SPEReader.`openBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `byte[]` | SPCReader.`openBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `byte[]` | SMCameraReader.`openBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `byte[]` | SIFReader.`openBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `byte[]` | SEQReader.`openBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `byte[]` | SDTReader.`openBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `byte[]` | SBIGReader.`openBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `byte[]` | RHKReader.`openBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `byte[]` | QuesantReader.`openBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `byte[]` | PyramidTiffReader.`openBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `byte[]` | PrairieReader.`openBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `byte[]` | PovrayReader.`openBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `byte[]` | PhotoshopTiffReader.`openBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `byte[]` | PerkinElmerReader.`openBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `byte[]` | PSDReader.`openBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `byte[]` | PQBinReader.`openBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `byte[]` | PDSReader.`openBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `byte[]` | PCORAWReader.`openBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `byte[]` | PCIReader.`openBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `byte[]` | OxfordInstrumentsReader.`openBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `byte[]` | OperettaReader.`openBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `byte[]` | OpenlabReader.`openBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `byte[]` | OpenlabRawReader.`openBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `byte[]` | OlympusTileReader.`openBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `byte[]` | OIRReader.`openBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `byte[]` | NikonReader.`openBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `byte[]` | NiftiReader.`openBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `byte[]` | NDPISReader.`openBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `byte[]` | NDPIReader.`openBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `byte[]` | ND2Reader.`openBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `byte[]` | NAFReader.`openBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `byte[]` | MolecularImagingReader.`openBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `byte[]` | MicroCTReader.`openBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `byte[]` | MetamorphTiffReader.`openBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `byte[]` | MetamorphReader.`openBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `byte[]` | MRWReader.`openBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `byte[]` | MRCReader.`openBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `byte[]` | MINCReader.`openBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `byte[]` | MIASReader.`openBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `byte[]` | LiFlimReader.`openBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `byte[]` | LeicaSCNReader.`openBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `byte[]` | LeicaReader.`openBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `byte[]` | LOFReader.`openBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `byte[]` | LIMReader.`openBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `byte[]` | LIFReader.`openBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `byte[]` | L2DReader.`openBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `byte[]` | KodakReader.`openBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `byte[]` | KhorosReader.`openBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `byte[]` | JPXReader.`openBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `byte[]` | JPKReader.`openBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `byte[]` | JEOLReader.`openBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `byte[]` | JDCEReader.`openBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `byte[]` | IvisionReader.`openBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `byte[]` | IonpathMIBITiffReader.`openBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `byte[]` | InveonReader.`openBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `byte[]` | InCellReader.`openBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `byte[]` | InCell3000Reader.`openBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `byte[]` | ImspectorReader.`openBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `byte[]` | ImprovisionTiffReader.`openBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `byte[]` | ImarisReader.`openBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `byte[]` | ImarisHDFReader.`openBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `byte[]` | ImagicReader.`openBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `byte[]` | ImaconReader.`openBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `byte[]` | IPWReader.`openBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `byte[]` | IPLabReader.`openBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `byte[]` | INRReader.`openBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `byte[]` | IMODReader.`openBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `byte[]` | I2IReader.`openBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `byte[]` | HitachiReader.`openBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `byte[]` | HamamatsuVMSReader.`openBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `byte[]` | HRDGDFReader.`openBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `byte[]` | HISReader.`openBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `byte[]` | GelReader.`openBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `byte[]` | GatanReader.`openBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `byte[]` | GatanDM2Reader.`openBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `byte[]` | FujiReader.`openBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `byte[]` | FluoviewReader.`openBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `byte[]` | FlexReader.`openBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `byte[]` | FV1000Reader.`openBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `byte[]` | FEIReader.`openBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `byte[]` | Ecat7Reader.`openBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `byte[]` | DeltavisionReader.`openBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `byte[]` | DNGReader.`openBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `byte[]` | DCIMGReader.`openBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `byte[]` | ColumbusReader.`openBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `byte[]` | CellomicsReader.`openBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `byte[]` | CellWorxReader.`openBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `byte[]` | CellVoyagerReader.`openBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `byte[]` | CellSensReader.`openBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `byte[]` | CanonRawReader.`openBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `byte[]` | CV7000Reader.`openBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `byte[]` | BurleighReader.`openBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `byte[]` | BrukerReader.`openBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `byte[]` | BioRadSCNReader.`openBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `byte[]` | BioRadReader.`openBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `byte[]` | BioRadGelReader.`openBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `byte[]` | BDReader.`openBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `byte[]` | AnalyzeReader.`openBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `byte[]` | AmiraReader.`openBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `byte[]` | AliconaReader.`openBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `byte[]` | ARFReader.`openBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `byte[]` | APLReader.`openBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `byte[]` | AIMReader.`openBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `byte[]` | AFIReader.`openBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `byte[]` | ZipReader.`openBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `byte[]` | TileJPEGReader.`openBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `byte[]` | TiffDelegateReader.`openBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `byte[]` | TextReader.`openBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `byte[]` | SlideBook7Reader.`openBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `byte[]` | QTReader.`openBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `byte[]` | PictReader.`openBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `byte[]` | PGMReader.`openBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `byte[]` | PCXReader.`openBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `byte[]` | OMEXMLReader.`openBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `byte[]` | OMETiffReader.`openBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `byte[]` | OBFReader.`openBytes(int no, byte[] buffer, int x, int y, int w, int h)`
    `byte[]` | NRRDReader.`openBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `byte[]` | MinimalTiffReader.`openBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `byte[]` | MicromanagerReader.`openBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `byte[]` | KLBReader.`openBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `byte[]` | JPEG2000Reader.`openBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `byte[]` | IM3Reader.`openBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `byte[]` | ICSReader.`openBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `byte[]` | GIFReader.`openBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `byte[]` | FlowSightReader.`openBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `byte[]` | FitsReader.`openBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `byte[]` | FakeReader.`openBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `byte[]` | EPSReader.`openBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `byte[]` | DicomReader.`openBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `byte[]` | CellH5Reader.`openBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `byte[]` | BMPReader.`openBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `byte[]` | BIFormatReader.`openBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `byte[]` | BDVReader.`openBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `byte[]` | AVIReader.`openBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `byte[]` | APNGReader.`openBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `byte[]` | XLEFReader.`openBytes(int no, int x, int y, int w, int h)`
    `private byte[]` | XLEFReader.`openBytesJpeg(int no, byte[] buf, int x, int y, int w, int h)` Gets bytes of jpeg images.
    `byte[]` | SVSReader.`openCompressedBytes(int no, byte[] buf, int x, int y)`
    `byte[]` | NDPIReader.`openCompressedBytes(int no, byte[] buf, int x, int y)`
    `byte[]` | DicomReader.`openCompressedBytes(int no, byte[] buf, int x, int y)`
    `byte[]` | SVSReader.`openCompressedBytes(int no, int x, int y)`
    `byte[]` | NDPIReader.`openCompressedBytes(int no, int x, int y)`
    `byte[]` | DicomReader.`openCompressedBytes(int no, int x, int y)`
    `private byte[]` | FlowSightReader.`openGreyscaleBytes(IFD ifd, int imageWidth, int imageHeight)` Decode the whole IFD plane using greyscale compression
    `java.lang.Object` | TiffJAIReader.`openPlane(int no, int x, int y, int w, int h)`
    `java.lang.Object` | TextReader.`openPlane(int no, int x, int y, int w, int h)`
    `java.lang.Object` | MNGReader.`openPlane(int no, int x, int y, int w, int h)`
    `java.lang.Object` | ImageIOReader.`openPlane(int no, int x, int y, int w, int h)`
    `byte[]` | VentanaReader.`openThumbBytes(int no)`
    `byte[]` | VectraReader.`openThumbBytes(int no)`
    `byte[]` | SVSReader.`openThumbBytes(int no)`
    `byte[]` | NDPIReader.`openThumbBytes(int no)`
    `byte[]` | LeicaSCNReader.`openThumbBytes(int no)`
    `byte[]` | CellSensReader.`openThumbBytes(int no)`
    `byte[]` | AFIReader.`openThumbBytes(int no)`
    `byte[]` | MinimalTiffReader.`openThumbBytes(int no)`
    `private void` | QTReader.`parse(int depth, long offset, long length)` Parse all of the atoms in the file.
    `private void` | TiffReader.`parseCommentImageJ(java.lang.String comment)`
    `private void` | DCIMGReader.`parseDCAMVersion0Footer(loci.common.RandomAccessInputStream stream)`
    `private void` | LeicaReader.`parseDimensionTag(int seriesIndex)`
    `private boolean` | CellSensReader.`parseETSFile(loci.common.RandomAccessInputStream etsFile, java.lang.String file, int s, boolean hasOrphanEtsFiles)`
    `private void` | VarianFDFReader.`parseFDF(java.lang.String file)`
    `private void` | MetamorphTiffReader.`parseFile(java.lang.String tiff, MetamorphHandler handler)`
    `private int` | TextReader.`parseFileHeader(java.util.List<java.lang.String> lines)` Parses the file looking for the file header.
    `private void` | FlexReader.`parseFlexFile(int currentWell, int wellRow, int wellCol, int field, boolean firstFile, MetadataStore store)` Parses XML metadata from the Flex file corresponding to the given well.
    `private void` | OIRReader.`parseFrameProperties(org.w3c.dom.Element root)`
    `protected void` | CellWorxReader.`parseHTD()`
    `private void` | OIRReader.`parseImageProperties(org.w3c.dom.Element root)`
    `private void` | ColumbusReader.`parseImageXML(java.lang.String filename, int externalTime)`
    `private void` | LeicaReader.`parseInstrumentData(MetadataStore store, int blockNum)`
    `private boolean` | DeltavisionReader.`parseLogFile(MetadataStore store)` Extract metadata from associated log file, if it exists.
    `private void` | OIRReader.`parseLUT(org.w3c.dom.Element root, java.lang.String uid)`
    `(package private) void` | BaseZeissReader.`parseMainTags(int image, MetadataStore store, java.util.ArrayList<BaseZeissReader.Tag> tags)`
    `void` | MIASReader.`parseMasks(MetadataStore overlayStore)` Parse masks into a separate overlay-specific MetadataStore.
    `private int` | MIASReader.`parseMasks(MetadataStore store, int series, int roi, java.lang.String overlayTiff)` Parse Mask ROIs from the given TIFF and place them in the given MetadataStore.
    `private java.lang.String[]` | ZeissLSMReader.`parseMDB(java.lang.String mdbFile)` Parse a .mdb file and return a list of referenced .lsm files.
    `private boolean` | BioRadReader.`parseNotes(MetadataStore store)`
    `private void` | ZeissCZIReader.`parseObjectives(org.w3c.dom.NodeList objectives)`
    `private void` | MicromanagerReader.`parsePosition(int posIndex)`
    `private void` | MicromanagerReader.`parsePosition(java.lang.String jsonData, int posIndex)`
    `private void` | PrairieReader.`parsePrairieMetadata()` This step parses the Prairie metadata files into the Prairie-specific metadata structure, `PrairieReader.meta`.
    `private int` | FV1000Reader.`parseROIFile(java.lang.String filename, MetadataStore store, int nextROI, int plane)`
    `private void` | TrestleReader.`parseROIs(MetadataStore store)`
    `private void` | CellH5Reader.`parseStructure()`
    `private void` | BDVReader.`parseStructure()`
    `private void` | ZeissZVIReader.`parseTags(int image, java.lang.String file, MetadataStore store)` Parse all of the tags in a stream.
    `private void` | GatanReader.`parseTags(int numTags, java.lang.String parent, java.lang.String indent)` Parses Gatan DM3 tags.
    `private void` | IPLabReader.`parseTags(MetadataStore store)`
    `private void` | OIRReader.`parseXML(loci.common.RandomAccessInputStream s, java.lang.String xml, long startFilePointer)`
    `private void` | PrairieReader.`populateCoreMetadata()` This step populates the `CoreMetadata` by extracting relevant values from the parsed `PrairieReader.meta` structure.
    `private void` | FlexReader.`populateCoreMetadata(int wellRow, int wellCol, int field, java.util.List<java.lang.String> imageNames)` Populate core metadata using the given list of image names.
    `private void` | SPEReader.`populateGlobalMetaData()` This function is used to populate values not contained in Core Meta Data to the Global Meta Data
    `boolean` | MIASReader.`populateMaskPixels(int imageIndex, int roiIndex, int shapeIndex, MetadataStore store)` Populate the MaskPixels.BinData attribute for the Mask identified by the given Image index, ROI index, and Shape index.
    `protected void` | CellWorxReader.`populateMetadata()`
    `private void` | MicromanagerReader.`populateMetadata()`
    `private void` | TillVisionReader.`populateMetadataStore()`
    `private void` | FlexReader.`populateMetadataStore(MetadataStore store)`
    `private void` | FV1000Reader.`populateMetadataStore(MetadataStore store, java.lang.String path)`
    `private void` | ND2Reader.`populateMetadataStore(ND2Handler handler)`
    `void` | MicromanagerReader.`populateMetadataStore(java.lang.String[] jsonData)`
    `protected void` | ZeissLSMReader.`populateMetadataStore(ZeissLSMReader.SubBlock block, MetadataStore store, int series)`
    `protected void` | RCPNLReader.`populateObjective(MetadataStore store, int lensID)`
    `protected void` | DeltavisionReader.`populateObjective(MetadataStore store, int lensID)` Populate an Objective based upon the lens ID.
    `private void` | PrairieReader.`populateOMEMetadata()` This step populates the OME `MetadataStore` by extracting relevant values from the parsed `PrairieReader.meta` structure.
    `private void` | NiftiReader.`populatePixelType(int dataType)`
    `private void` | SPEReader.`populateRoiMetaData(MetadataStore store)` Reads and populates ROI Meta Data values.
    `(package private) void` | AmiraReader.HxRLE.`read(byte[] buf, int len)`
    `byte[]` | AmiraReader.PlaneReader.`read(int no, byte[] buf)`
    `byte[]` | AmiraReader.ASCII.`read(int no, byte[] buf)`
    `byte[]` | AmiraReader.HxZip.`read(int no, byte[] buf)`
    `byte[]` | AmiraReader.HxRLE.`read(int no, byte[] buf)`
    `private void` | ZeissCZIReader.`readAttachments()`
    `private void` | AVIReader.`readChunk()`
    `byte[]` | SlideBook7Reader.CCompressionBase.`ReadData(loci.common.RandomAccessInputStream inStream, int inBlock)`
    `private void` | OBFReader.`readFlimFrame(OBFReader.Stack stack, int no, byte[] buffer, int x, int y, int w, int h)`
    `private void` | OBFReader.`readFromStack(OBFReader.Stack stack, byte[] buffer, int bufferOffset, int bytes)`
    `private void` | OBFReader.`readFromStackRaw(OBFReader.Stack stack, byte[] buffer, int bufferOffset, int bytes)`
    `private void` | KLBReader.`readHeader(CoreMetadata coreMeta)`
    `private void` | GIFReader.`readImageBlock()`
    `private void` | CellVoyagerReader.`readInfo(org.w3c.dom.Document msDocument, org.w3c.dom.Document omeDocument)`
    `private int[]` | GIFReader.`readLut(int size)` Read a color lookup table of the specified size.
    `private void` | OlympusTileReader.`readMetadata(java.lang.String xml)`
    `byte[]` | ZeissCZIReader.SubBlock.`readPixelData()`
    `byte[]` | ZeissCZIReader.SubBlock.`readPixelData(loci.common.RandomAccessInputStream s)`
    `byte[]` | ZeissCZIReader.SubBlock.`readPixelData(loci.common.RandomAccessInputStream s, loci.common.Region tile, byte[] buf)`
    `private void` | OIRReader.`readPixelsFile(java.lang.String file, loci.common.RandomAccessInputStream s)`
    `private void` | OBFReader.`readStackFrame(OBFReader.Stack stack, long sampleOffset, byte[] buffer, int bufferOffset, int w, int h)`
    `private void` | FluoviewReader.`readStamps()`
    `private void` | OpenlabReader.`readVariable()`
    `private void` | DeltavisionReader.`readWavelength(int channel, MetadataStore store)`
    `private void` | OIRReader.`readXMLBlock(java.lang.String file, loci.common.RandomAccessInputStream s)`
    `private void` | KLBReader.`reCalculateBlockOffsets(int no)`
    `private long` | OBFReader.`remainingBytesInChunk(OBFReader.Stack stack)`
    `private void` | NDPIReader.`resetStream(IFD ifd)`
    `private void` | DCIMGReader.`scanDirectory(loci.common.Location dir)`
    `private void` | DicomReader.`scanDirectory(loci.common.Location dir, boolean checkSeries)` Scan the given directory for files that belong to this dataset.
    `private static int[]` | FV1000Reader.`scanFormat(java.lang.String pattern, java.lang.String string)`
    `private void` | OBFReader.`seekToFrameStart(OBFReader.Stack stack, long sampleOffset)`
    `void` | MIASReader.`setAutomaticallyParseMasks(boolean parse)` Toggle whether or not Mask pixel data should be parsed in setId.
    `void` | TiffDelegateReader.`setId(java.lang.String id)`
    `void` | JPEGReader.`setId(java.lang.String id)`
    `void` | LOFReader.`setIdWithMetadata(java.lang.String id, XlifDocument xml)` Inits the LOFReader using passed xml (from XLIF) for metadata initiation, instead of reading the LOF's included xml
    `private void` | OMETiffReader.`setupService()`
    `private void` | OBFReader.`skipBytes(OBFReader.Stack stack, long byteCount)`
    `private void` | XLEFReader.`sortMultipleImagesReaders()` Sorts frames of all MultipleImagesReaders as per core dimension sizes and order
    `private IFD` | VentanaReader.`splitIFD(IFD ifd, int no)` Take the real IFD on disk and reshape it into something that represents only the given plane.
    `protected void` | BaseZeissReader.`storeROIs(MetadataStore store)` Store basic dimensions in model
    `private void` | OBFReader.`switchChunk(OBFReader.Stack stack, int chunkIndex)`
    `private void` | LIFReader.`translateAttachmentNodes(org.w3c.dom.Element imageNode, int image)`
    `private void` | LIFReader.`translateDetectors(org.w3c.dom.Element imageNode, int image)`
    `private void` | ZeissCZIReader.`translateDisplaySettings(org.w3c.dom.Element root)`
    `private void` | ZeissCZIReader.`translateExperiment(org.w3c.dom.Element root)`
    `private void` | LIFReader.`translateFilterSettings(org.w3c.dom.Element imageNode, int image)`
    `private void` | ZeissCZIReader.`translateHardwareSettings(org.w3c.dom.Element root)`
    `private void` | LIFReader.`translateImageNodes(org.w3c.dom.Element imageNode, int i)`
    `private void` | ZeissCZIReader.`translateInformation(org.w3c.dom.Element root)`
    `private void` | LIFReader.`translateLaserLines(org.w3c.dom.Element imageNode, int image)`
    `private void` | LIFReader.`translateMetadata(org.w3c.dom.Element root)`
    `private void` | ZeissCZIReader.`translateMetadata(java.lang.String xml)`
    `private void` | LIFReader.`translateROIs(org.w3c.dom.Element imageNode, int image)`
    `private void` | LIFReader.`translateScannerSettings(org.w3c.dom.Element imageNode, int image)`
    `private void` | LIFReader.`translateSingleROIs(org.w3c.dom.Element imageNode, int image)`
    `private void` | LIFReader.`translateTimestamps(org.w3c.dom.Element imageNode, int image)`
    `private byte[]` | QTReader.`uncompress(byte[] pixs, java.lang.String code)` Uncompresses an image plane according to the the codec identifier.
    `private byte[]` | AVIReader.`uncompress(int no, byte[] buf)`
    `private void` | APNGReader.`unfilter(byte[] filters, byte[] image, int width, int height)` See http://www.w3.org/TR/PNG/#9Filters.
    `private boolean` | NDPIReader.`useTiffParser(IFD ifd)`

  - ### Uses of FormatException in loci.formats.in.LeicaMicrosystemsMetadata

    Methods in loci.formats.in.LeicaMicrosystemsMetadata that throw FormatException
    Modifier and Type | Method and Description
    --- | ---
    `private void` | LMSMetadataExtractor.`addUserCommentMeta(org.w3c.dom.Element imageNode, int image)` Extracts user comments and adds them to the reader's `CoreMetadata`
    `void` | MetadataStoreInitializer.`initMetadataStore()` Translates metadata information from the reader's `MetadataTempBuffer` and adds it to its `MetadataStore`
    `private void` | MultipleImagesReader.`initReaders(java.util.List<java.lang.String> ids)` Creates an internal reader for each image file
    `void` | MetadataStoreInitializer.`initStandDetails(int series)` Adds microscope and objective details from the reader's `MetadataTempBuffer` to its `MetadataStore`
    `byte[]` | MultipleImagesReader.`openBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `private void` | LMSMetadataExtractor.`setPixelType(int coreIndex)` Sets CoreMetadata.pixelType depending on extracted x bytesInc
    `void` | MultipleImagesReader.`swapDimensions()` Rearranges frame order from ZSTC order (used in XLIFs) to desired CoreMetadata.dimensionOrder
    `void` | LMSMetadataExtractor.`translateAttachmentNodes(org.w3c.dom.Element imageNode, int image)` Extracts information from dimension descriptions and writes it to reader's `MetadataTempBuffer`
    `void` | LMSMetadataExtractor.`translateChannelDescriptions(org.w3c.dom.Element imageNode, int coreIndex)` Extracts i.a.
    `void` | LMSMetadataExtractor.`translateDetectors(org.w3c.dom.Element imageNode, int image)` Extracts detector information and writes it to reader's `MetadataTempBuffer`
    `private void` | LMSMetadataExtractor.`translateDimensionDescriptions(org.w3c.dom.Element imageNode, int coreIndex)` Extracts information from dimension descriptions and writes it to reader's `CoreMetadata` and `MetadataTempBuffer`
    `void` | LMSMetadataExtractor.`translateFilterSettings(org.w3c.dom.Element imageNode, int image)` Extracts filter information and writes it to reader's `MetadataTempBuffer`
    `void` | LMSMetadataExtractor.`translateImage(org.w3c.dom.Element image, int i)` Extracts information from element node and writes it to reader's `CoreMetadata` and `MetadataTempBuffer`
    `void` | LMSMetadataExtractor.`translateLaserLines(org.w3c.dom.Element imageNode, int image)` Extracts laser information and writes it to reader's `MetadataTempBuffer`
    `void` | LMSMetadataExtractor.`translateMetadata(java.util.List<LMSImageXmlDocument> docs)` Extracts all information from Leica image xml Documents and writes it to reader's `CoreMetadata` and `MetadataTempBuffer`
    `void` | LMSFileReader.`translateMetadata(java.util.List<LMSImageXmlDocument> docs)` Extracts metadata from a list of Leica image XML Documents and writes them to the reader's CoreMetadata, `MetadataTempBuffer` and MetadataStore
    `void` | LMSFileReader.`translateMetadata(LMSImageXmlDocument doc)`
    `void` | LMSMetadataExtractor.`translateROIs(org.w3c.dom.Element imageNode, int image)` Extracts ROIs and writes them to reader's `MetadataTempBuffer`
    `void` | LMSMetadataExtractor.`translateScannerSettings(org.w3c.dom.Element imageNode, int image)` Extracts scanner information and writes it to reader's `CoreMetadata` and `MetadataTempBuffer`
    `void` | LMSMetadataExtractor.`translateSingleROIs(org.w3c.dom.Element imageNode, int image)` Extracts single ROIs and writes them to reader's `MetadataTempBuffer`
    `void` | LMSMetadataExtractor.`translateTimestamps(org.w3c.dom.Element imageNode, int image)` Extracts timestamps and writes them to reader's `MetadataTempBuffer`

    Constructors in loci.formats.in.LeicaMicrosystemsMetadata that throw FormatException
    Constructor and Description
    `MultipleImagesReader(XlifDocument xlif, int imageIndex)`

  - ### Uses of FormatException in loci.formats.out

    Methods in loci.formats.out that throw FormatException
    Modifier and Type | Method and Description
    --- | ---
    `private void` | DicomWriter.`checkPixelCount(boolean warn)`
    `private byte[]` | OMEXMLWriter.`compress(byte[] b)` Compress the given byte array using the current codec.
    `byte[]` | JPEG2000Writer.`compressBuffer(int no, byte[] buf, int x, int y, int w, int h)` Compresses the buffer.
    `private void` | TiffWriter.`formatCompression(IFD ifd)` Sets the compression code for the specified IFD.
    `private java.lang.String` | OMETiffWriter.`getBinaryOnlyOMEXML(java.lang.String file, java.lang.String companion, java.lang.String companionUUID)`
    `private java.lang.String` | OMETiffWriter.`getOMEXML(java.lang.String file)`
    `int` | TiffWriter.`getTileSizeX()`
    `int` | TiffWriter.`getTileSizeY()`
    `protected IFD` | TiffWriter.`makeIFD()`
    `protected IFD` | PyramidOMETiffWriter.`makeIFD()`
    `protected int` | TiffWriter.`prepareToWriteImage(int no, byte[] buf, IFD ifd, int x, int y, int w, int h)` Performs the preparation for work prior to the usage of the TIFF saver.
    `void` | CellH5Writer.`saveBytes(int no, byte[] buf)` Saves the given image to the specified (possibly already open) file.
    `void` | TiffWriter.`saveBytes(int no, byte[] buf, IFD ifd)` Saves the given image to the specified (possibly already open) file.
    `void` | TiffWriter.`saveBytes(int no, byte[] buf, IFD ifd, int x, int y, int w, int h)` Saves the given image to the specified series in the current file.
    `void` | PyramidOMETiffWriter.`saveBytes(int no, byte[] buf, IFD ifd, int x, int y, int w, int h)`
    `void` | OMETiffWriter.`saveBytes(int no, byte[] buf, IFD ifd, int x, int y, int w, int h)`
    `void` | V3DrawWriter.`saveBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `void` | TiffWriter.`saveBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `void` | QTWriter.`saveBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `void` | OMEXMLWriter.`saveBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `void` | OMETiffWriter.`saveBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `void` | JavaWriter.`saveBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `void` | JPEG2000Writer.`saveBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `void` | ImageIOWriter.`saveBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `void` | ICSWriter.`saveBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `void` | EPSWriter.`saveBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `void` | DicomWriter.`saveBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `void` | CellH5Writer.`saveBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `void` | AVIWriter.`saveBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `void` | APNGWriter.`saveBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `void` | TiffWriter.`saveCompressedBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `void` | OMETiffWriter.`saveCompressedBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `void` | DicomWriter.`saveCompressedBytes(int no, byte[] buf, int x, int y, int w, int h)`
    `void` | ImageIOWriter.`savePlane(int no, java.lang.Object plane, int x, int y, int w, int h)`
    `void` | V3DrawWriter.`setId(java.lang.String id)`
    `void` | TiffWriter.`setId(java.lang.String id)`
    `void` | QTWriter.`setId(java.lang.String id)`
    `void` | OMEXMLWriter.`setId(java.lang.String id)`
    `void` | OMETiffWriter.`setId(java.lang.String id)`
    `void` | JavaWriter.`setId(java.lang.String id)`
    `void` | ICSWriter.`setId(java.lang.String id)`
    `void` | DicomWriter.`setId(java.lang.String id)`
    `void` | CellH5Writer.`setId(java.lang.String id)`
    `void` | AVIWriter.`setId(java.lang.String id)`
    `void` | APNGWriter.`setId(java.lang.String id)`
    `void` | DicomWriter.`setSeries(int s)`
    `int` | TiffWriter.`setTileSizeX(int tileSize)`
    `int` | DicomWriter.`setTileSizeX(int tileSize)`
    `int` | TiffWriter.`setTileSizeY(int tileSize)`
    `int` | DicomWriter.`setTileSizeY(int tileSize)`
    `private void` | APNGWriter.`writePixels(java.lang.String chunk, byte[] stream, int x, int y, int width, int height)`

  - ### Uses of FormatException in loci.formats.services

    Methods in loci.formats.services that throw FormatException
    Modifier and Type | Method and Description
    --- | ---
    `byte[]` | JPEGXRServiceImpl.`decompress(byte[] compressed)`
    `byte[]` | JPEGXRService.`decompress(byte[] compressed)` Decompress the given JPEG-XR compressed byte array and return as a byte array.
    `private short[]` | JPEGXRServiceImpl.`getPixelFormat(byte[] stream)`

  - ### Uses of FormatException in loci.formats.tiff

    Methods in loci.formats.tiff that throw FormatException
    Modifier and Type | Method and Description
    --- | ---
    `byte[]` | TiffCompression.`compress(byte[] input, CodecOptions options)` Encodes a strip of data.
    `byte[]` | TiffCompression.`decompress(byte[] input, CodecOptions options)` Decodes a strip of data.
    `static void` | TiffCompression.`difference(byte[] input, IFD ifd)` Performs in-place differencing according to the given predictor value.
    `int[]` | IFD.`getBitsPerSample()` Retrieves the image's bits per sample (TIFF tag BitsPerSample) from a given TIFF IFD.
    `long` | IFD.`getByteCount(boolean bigTiff)` Get the maximum number of bytes needed to represent this IFD.
    `int[]` | IFD.`getBytesPerSample()` Retrieves the image's bytes per sample (derived from tag BitsPerSample) from this IFD.
    `TiffCompression` | IFD.`getCompression()` Retrieves the image's compression type (TIFF tag Compression) from this IFD.
    `CodecOptions` | TiffCompression.`getCompressionCodecOptions(IFD ifd)` Creates a set of codec options for compression.
    `CodecOptions` | TiffCompression.`getCompressionCodecOptions(IFD ifd, CodecOptions opt)` Creates a set of codec options for compression.
    `IFDList` | TiffParser.`getExifIFDs()` Returns EXIF IFDs.
    `int[]` | IFD.`getIFDIntArray(int tag)` Gets the given directory entry values in int format from this IFD, performing some error checking.
    `int` | IFD.`getIFDIntValue(int tag, int defaultValue)` Gets the given directory entry value in int format from this IFD, performing some error checking.
    `long[]` | IFD.`getIFDLongArray(int tag)` Gets the given directory entry values in long format from this IFD, performing some error checking.
    `long` | IFD.`getIFDLongValue(int tag, long defaultValue)` Gets the given directory entry value in long format from this IFD, performing some error checking.
    `TiffRational` | IFD.`getIFDRationalValue(int tag)` Gets the given directory entry value in rational format from this IFD, performing some error checking.
    `short[]` | IFD.`getIFDShortArray(int tag)` Gets the given directory entry values in short format from this IFD, performing some error checking.
    `java.lang.String` | IFD.`getIFDStringValue(int tag)` Gets the given directory entry value as a string from this IFD, performing some error checking.
    `java.lang.Object` | IFD.`getIFDValue(int tag, java.lang.Class checkClass)` Gets the given directory entry value from this IFD, performing some error checking.
    `long` | IFD.`getImageLength()` Retrieves the image's length (TIFF tag ImageLength) from a given TIFF IFD.
    `long` | IFD.`getImageWidth()` Retrieves the image's width (TIFF tag ImageWidth) from a given TIFF IFD.
    `OnDemandLongArray` | IFD.`getOnDemandStripOffsets()`
    `PhotoInterp` | IFD.`getPhotometricInterpretation()` Retrieves the image's photometric interpretation (TIFF tag PhotometricInterpretation) from this IFD.
    `int` | IFD.`getPixelType()` Retrieves the image's pixel type based on the BitsPerSample tag.
    `int` | IFD.`getPlanarConfiguration()` Retrieves the image's planar configuration (TIFF tag PlanarConfiguration) from this IFD.
    `long[]` | IFD.`getRowsPerStrip()` Retrieves the number of rows per strip for image (TIFF tag RowsPerStrip) from this IFD.
    `byte[]` | TiffParser.`getSamples(IFD ifd, byte[] buf)`
    `byte[]` | TiffParser.`getSamples(IFD ifd, byte[] buf, int x, int y, long width, long height)`
    `byte[]` | TiffParser.`getSamples(IFD ifd, byte[] buf, int x, int y, long width, long height, int overlapX, int overlapY)`
    `int` | IFD.`getSamplesPerPixel()` Retrieves the number of samples per pixel for the image (TIFF tag SamplesPerPixel) from this IFD.
    `long[]` | IFD.`getStripByteCounts()` Retrieves strip byte counts for the image (TIFF tag StripByteCounts) from this IFD.
    `long[]` | IFD.`getStripOffsets()` Retrieves the strip offsets for the image (TIFF tag StripOffsets) from this IFD.
    `byte[]` | TiffParser.`getTile(IFD ifd, byte[] buf, int row, int col)`
    `long` | IFD.`getTileLength()` Returns the length of an image tile.
    `long` | IFD.`getTilesPerColumn()` Returns the number of image tiles per column.
    `long` | IFD.`getTilesPerRow()` Returns the number of image tiles per row.
    `long` | IFD.`getTileWidth()` Returns the width of an image tile.
    `static IFDType` | IFDType.`getType(java.lang.Object value, boolean bigTiff)` Get the type corresponding to the given value.
    `double` | IFD.`getXResolution()` Retrieve the X resolution (TIFF tag XResolution) from this IFD.
    `double` | IFD.`getYResolution()` Retrieve the Y resolution (TIFF tag YResolution) from this IFD.
    `boolean` | IFD.`isBigTiff()` Gets whether this is a BigTIFF IFD.
    `boolean` | IFD.`isLittleEndian()` Gets whether the TIFF information in this IFD is little-endian.
    `boolean` | IFD.`isTiled()`
    `void` | TiffSaver.`overwriteComment(loci.common.RandomAccessInputStream in, java.lang.Object value)` Convenience method for overwriting a file's first ImageDescription.
    `void` | TiffSaver.`overwriteIFDOffset(loci.common.RandomAccessInputStream raf, long offset, long nextPointer)`
    `void` | TiffSaver.`overwriteIFDValue(loci.common.RandomAccessInputStream raf, int ifd, int tag, java.lang.Object value)` Surgically overwrites an existing IFD value with the given one.
    `void` | TiffSaver.`overwriteIFDValue(loci.common.RandomAccessInputStream raf, long ifdOffset, int tag, java.lang.Object value)` Surgically overwrites an existing IFD value with the given one.
    `void` | TiffSaver.`overwriteIFDValue(loci.common.RandomAccessInputStream raf, long ifdOffset, int tag, java.lang.Object value, boolean skipHeaderCheck)` Surgically overwrites an existing IFD value with the given one.
    `void` | TiffSaver.`overwriteLastIFDOffset(loci.common.RandomAccessInputStream raf)`
    `static void` | TiffCompression.`undifference(byte[] input, IFD ifd)` Undoes in-place differencing according to the given predictor value.
    `static void` | TiffParser.`unpackBytes(byte[] samples, int startIndex, byte[] bytes, IFD ifd)` Extracts pixel information from the given byte array according to the bits per sample, photometric interpretation and color map IFD directory entry values, and the specified byte ordering.
    `void` | TiffSaver.`writeIFD(IFD ifd, long nextOffset)` Write the given IFD to the open stream.
    `void` | TiffSaver.`writeIFD(IFD ifd, long nextOffset, boolean calculateOffset)` Write the given IFD to the open stream.
    `private void` | TiffSaver.`writeIFDStrips(IFD ifd, int no, byte[][] strips, int nChannels, boolean last, int x, int y, long defaultByteCount)`
    `void` | TiffSaver.`writeIFDValue(loci.common.RandomAccessOutputStream extraOut, long offset, int tag, java.lang.Object value)` Writes the given IFD value to the given output object.
    `void` | TiffSaver.`writeImage(byte[][] buf, IFDList ifds, int pixelType)`
    `void` | TiffSaver.`writeImage(byte[] buf, IFD ifd, int no, int pixelType, boolean last)`
    `void` | TiffSaver.`writeImage(byte[] buf, IFD ifd, int no, int pixelType, int x, int y, int w, int h, boolean last)` Writes to any rectangle from the passed block.
    `void` | TiffSaver.`writeImage(byte[] buf, IFD ifd, int no, int pixelType, int x, int y, int w, int h, boolean last, java.lang.Integer nChannels, boolean copyDirectly)`
    `void` | TiffSaver.`writeImageIFD(IFD ifd, int no, byte[][] strips, int nChannels, boolean last, int x, int y)` Performs the actual work of dealing with IFD data and writing it to the TIFF for a given image or sub-image.

  - ### Uses of FormatException in loci.formats.tools

    Methods in loci.formats.tools that throw FormatException
    Modifier and Type | Method and Description
    --- | ---
    `private OMETiffWriter` | MakeTestOmeTiff.`createWriter(java.lang.String name, CoreMetadata info, java.lang.String id)`
    `static java.lang.String` | AmiraParameters.`entryToString(java.lang.Object object, java.lang.String indent)`
    `protected void` | AmiraParameters.`extractCoreMetaData()`
    `static void` | MakeTestOmeTiff.`main(java.lang.String[] args)`
    `static void` | CacheConsole.`main(java.lang.String[] args)` Interactive interpreter for testing Bio-Formats caching implementation.
    `int` | MakeTestOmeTiff.`makeOmeTiff(java.lang.String... args)`
    `void` | MakeTestOmeTiff.`makeOmeTiff(java.lang.String name, CoreMetadata info)`
    `void` | MakeTestOmeTiff.`makeOmeTiffExtensions(java.lang.String... args)`
    `void` | MakeTestOmeTiff.`makeSamples()`
    `protected java.lang.Double[]` | AmiraParameters.`readDoubleArray(int count)`
    `protected void` | AmiraParameters.`readFile(loci.common.RandomAccessInputStream inputStream)`
    `protected void` | AmiraParameters.`readFile(java.lang.String path)`
    `protected java.lang.Integer[]` | AmiraParameters.`readIntArray()`
    `protected java.lang.Integer[]` | AmiraParameters.`readIntArray(int count)`
    `protected java.util.Map` | AmiraParameters.`readMap()`
    `protected java.lang.Number` | AmiraParameters.`readNumber()`
    `protected java.lang.Number[]` | AmiraParameters.`readNumberArray()`
    `protected java.lang.String` | AmiraParameters.`readQuotedString()`
    `protected void` | AmiraParameters.`readTopLevel()`
    `protected void` | AmiraParameters.`syntaxError(java.lang.String message)`
    `static java.lang.String` | AmiraParameters.`toString(java.util.Map map, java.lang.String indent)`
    `private void` | MakeTestOmeTiff.`writeData(java.lang.String name, CoreMetadata info, java.lang.String id, OMETiffWriter out)`

    Constructors in loci.formats.tools that throw FormatException
    Constructor and Description
    `AmiraParameters(loci.common.RandomAccessInputStream inputStream)`
    `AmiraParameters(java.lang.String path)`

  - ### Uses of FormatException in loci.plugins

    Methods in loci.plugins that throw FormatException
    Modifier and Type | Method and Description
    --- | ---
    `static ij.ImagePlus[]` | BF.`openImagePlus(ImporterOptions options)`
    `static ij.ImagePlus[]` | BF.`openImagePlus(java.lang.String path)`
    `static ij.ImagePlus[]` | BF.`openThumbImagePlus(ImporterOptions options)`
    `static ij.ImagePlus[]` | BF.`openThumbImagePlus(java.lang.String path)`

  - ### Uses of FormatException in loci.plugins.in

    Methods in loci.plugins.in that throw FormatException
    Modifier and Type | Method and Description
    --- | ---
    `private void` | ImportProcess.`createBaseReader()` Initializes an `IFormatReader` according to the current configuration.
    `private ij.ImageStack` | ImagePlusReader.`createVirtualStack(ImportProcess process, int s, java.util.List<ij.process.LUT> luts)`
    `XMLWindow` | DisplayHandler.`displayOMEXML()` Displays OME-XML metadata in a tree in its own window.
    `boolean` | ImportProcess.`execute()` Performs the import preparation process, notifying status listeners at each step.
    `private void` | ImportProcess.`initializeFile()` Performed following ImportStep.FILE notification.
    `private void` | ImportProcess.`initializeReader()` Performed following ImportStep.READER notification.
    `private void` | ImportProcess.`initializeStack()` Performed following ImportStep.STACK notification.
    `ij.ImagePlus[]` | ImagePlusReader.`openImagePlus()` Opens one or more `ImagePlus` objects corresponding to the reader's associated options.
    `ij.ImagePlus[]` | ImagePlusReader.`openThumbImagePlus()`
    `private ij.ImagePlus` | ImagePlusReader.`readImage(int s, boolean thumbnail)`
    `private java.util.List<ij.ImagePlus>` | ImagePlusReader.`readImages()`
    `private java.util.List<ij.ImagePlus>` | ImagePlusReader.`readImages(boolean thumbnail)`
    `ij.ImagePlus[]` | Importer.`readPixels(ImagePlusReader reader, ImporterOptions options, DisplayHandler displayHandler)`
    `private ij.ImageStack` | ImagePlusReader.`readPlanes(ImportProcess process, int s, java.util.List<ij.process.LUT> luts, boolean thumbnail)`
    `private java.util.List<ij.ImagePlus>` | ImagePlusReader.`readThumbImages()`
    `void` | Importer.`showDialogs(ImportProcess process)`

  - ### Uses of FormatException in loci.plugins.macro

    Methods in loci.plugins.macro that throw FormatException
    Modifier and Type | Method and Description
    --- | ---
    `void` | LociFunctions.`fileGroupOption(java.lang.String id, java.lang.String[] fileGroupOption)`
    `void` | LociFunctions.`getFormat(java.lang.String id, java.lang.String[] format)`
    `void` | LociFunctions.`openImage(java.lang.String title, java.lang.Double no)`
    `void` | LociFunctions.`openSubImage(java.lang.String title, java.lang.Double no, java.lang.Double x, java.lang.Double y, java.lang.Double w, java.lang.Double h)`
    `void` | LociFunctions.`openThumbImage(java.lang.String title, java.lang.Double no)`
    `void` | LociFunctions.`setId(java.lang.String id)`

  - ### Uses of FormatException in loci.plugins.util

    Methods in loci.plugins.util that throw FormatException
    Modifier and Type | Method and Description
    --- | ---
    `private ij.process.LUT` | ImageProcessorReader.`createColorModel()`
    `protected static int` | BFVirtualStack.`getHeight(IFormatReader r, java.lang.String path, int series)`
    `protected static int` | BFVirtualStack.`getWidth(IFormatReader r, java.lang.String path, int series)`
    `java.lang.Object` | ImageProcessorReader.`openPlane(int no, int x, int y, int w, int h)`
    `ij.process.ImageProcessor[]` | ImageProcessorReader.`openProcessors(int no)` Creates an ImageJ image processor object for the image plane at the given position.
    `ij.process.ImageProcessor[]` | ImageProcessorReader.`openProcessors(int no, int x, int y, int w, int h)` Returns an array of ImageProcessors that represent the given slice.
    `ij.process.ImageProcessor[]` | ImageProcessorReader.`openThumbProcessors(int no)`

    Constructors in loci.plugins.util that throw FormatException
    Constructor and Description
    `BFVirtualStack(java.lang.String path, IFormatReader r, boolean colorize, boolean merge, boolean record)`

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