## Uses of Interface
loci.formats.IFormatReader

- Packages that use IFormatReader
  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.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.tools | Package containing utility methods corresponding to the Bio-Formats command line tools.
  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 IFormatReader in loci.formats

    Classes in loci.formats that implement IFormatReader
    Modifier and Type | Class and Description
    --- | ---
    `class` | `ChannelFiller` For indexed color data representing true color, factors out the indices, replacing them with the color table values directly.
    `class` | `ChannelMerger` Logic to automatically merge channels in a file.
    `class` | `ChannelSeparator` Logic to automatically separate the channels in a file.
    `class` | `DelegateReader` DelegateReader is a file format reader that selects which reader to use for a format if there are two readers which handle the same format.
    `class` | `DimensionSwapper` Handles swapping the dimension order of an image series.
    `class` | `FileStitcher` Logic to stitch together files with similar names.
    `class` | `FormatReader` Abstract superclass of all biological file format readers.
    `class` | `ImageReader` ImageReader is the master file format reader for all supported formats.
    `class` | `Memoizer` `ReaderWrapper` implementation which caches the state of the delegate (including and other `ReaderWrapper` instances) after `Memoizer.setId(String)` has been called.
    `class` | `MinMaxCalculator` Logic to compute minimum and maximum values for each channel.
    `class` | `ReaderWrapper` Abstract superclass of reader logic that wraps other readers.
    `class` | `SubResolutionFormatReader` Abstract superclass of all biological file format readers that can handle image pyramids.
    `class` | `TileStitcher`
    `class` | `WrappedReader` Helper class for readers which wrap other readers.

    Fields in loci.formats declared as IFormatReader
    Modifier and Type | Field and Description
    --- | ---
    `protected IFormatReader` | DelegateReader.`legacyReader` Legacy reader.
    `protected IFormatReader` | DelegateReader.`nativeReader` Native reader.
    `protected IFormatReader` | ReaderWrapper.`reader` FormatReader used to read the file.
    `private IFormatReader[]` | ImageReader.`readers` List of supported file format readers.

    Fields in loci.formats with type parameters of type IFormatReader
    Modifier and Type | Field and Description
    --- | ---
    `private ClassList<IFormatReader>` | FileStitcher.`classList`
    `private static ClassList<IFormatReader>` | ImageReader.`defaultClasses` Default list of reader classes, for use with noargs constructor.

    Methods in loci.formats that return IFormatReader
    Modifier and Type | Method and Description
    --- | ---
    `IFormatReader` | FileStitcher.`getReader()` Gets the wrapped reader prototype.
    `IFormatReader` | ReaderWrapper.`getReader()` Gets the wrapped reader.
    `IFormatReader` | ImageReader.`getReader()` Gets the reader used to open the current file.
    `IFormatReader` | ImageReader.`getReader(java.lang.Class<? extends IFormatReader> c)` Gets the file format reader instance matching the given class.
    `static IFormatReader` | FormatTools.`getReader(IFormatReader r, java.lang.Class<? extends IFormatReader> c)` Recursively look for the first underlying reader that is an instance of the given class.
    `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.
    `IFormatReader[]` | ImageReader.`getReaders()` Gets all constituent file format readers.
    `IFormatReader[]` | FileStitcher.`getUnderlyingReaders()`
    `IFormatReader[]` | WrappedReader.`getUnderlyingReaders()`
    `IFormatReader[]` | ReaderWrapper.`getUnderlyingReaders()`
    `IFormatReader[]` | ImageReader.`getUnderlyingReaders()`
    `IFormatReader[]` | IFormatReader.`getUnderlyingReaders()` Retrieves all underlying readers.
    `IFormatReader[]` | FormatReader.`getUnderlyingReaders()`
    `protected IFormatReader` | Memoizer.`handleMetadataStore(IFormatReader memo)` Return the `IFormatReader` instance that is passed in or null if it has been invalidated, which will include the instance being closed.
    `IFormatReader` | Memoizer.`loadMemo()` Load a memo file if possible, returning a null if not.
    `IFormatReader` | Memoizer.Deser.`loadReader()`
    `IFormatReader` | Memoizer.KryoDeser.`loadReader()`
    `IFormatReader` | Memoizer.RandomAccessDeser.`loadReader()`
    `protected abstract IFormatReader` | Memoizer.RandomAccessDeser.`readerFromBytes(java.lang.Class<IFormatReader> c, byte[] rArr)`
    `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.
    `IFormatReader` | ReaderWrapper.`unwrap(java.lang.String id)` Unwraps nested wrapped readers until the core reader (i.e., not a `ReaderWrapper` or `ImageReader`) is found.

    Methods in loci.formats that return types with arguments of type IFormatReader
    Modifier and Type | Method and Description
    --- | ---
    `static ClassList<IFormatReader>` | ImageReader.`getDefaultReaderClasses()`

    Methods in loci.formats with parameters of type IFormatReader
    Modifier and Type | Method and Description
    --- | ---
    `protected abstract byte[]` | Memoizer.RandomAccessDeser.`bytesFromReader(IFormatReader reader)`
    `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.
    `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.
    `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.
    `CoreMetadata` | SwappableMetadata.`clone(IFormatReader r, int coreIndex)`
    `CoreMetadata` | CoreMetadata.`clone(IFormatReader r, int coreIndex)`
    `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 boolean` | FormatTools.`equalReaders(IFormatReader a, IFormatReader b)` Check if the two given readers are equal.
    `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.`getFilenames(java.lang.String pattern, IFormatReader r)`
    `static int` | FormatTools.`getImagesPerFile(java.lang.String pattern, IFormatReader r)`
    `static int` | FormatTools.`getIndex(IFormatReader reader, int z, int c, int t)` Gets the rasterized index corresponding to the given Z, C and T coordinates (real sizes).
    `static int` | FormatTools.`getIndex(IFormatReader reader, int z, int c, int t, int moduloZ, int moduloC, int moduloT)` Gets the rasterized index corresponding to the given Z, C, T, ModuloZ, ModuloC and ModuloT coordinates (effective sizes).
    `static int` | FormatTools.`getPlaneSize(IFormatReader r)` Returns the size in bytes of a single plane.
    `static int` | FormatTools.`getPlaneSize(IFormatReader r, int w, int h)` Returns the size in bytes of a w * h tile.
    `static IFormatReader` | FormatTools.`getReader(IFormatReader r, java.lang.Class<? extends IFormatReader> c)` Recursively look for the first underlying reader that is an instance of the given class.
    `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.
    `static int[]` | FormatTools.`getZCTCoords(IFormatReader reader, int index)` Gets the Z, C and T coordinates corresponding to the given rasterized index value (real sizes).
    `static int[]` | FormatTools.`getZCTModuloCoords(IFormatReader reader, int index)` Gets the Z, C, T, ModuloZ, ModuloC and ModuloZ coordinates corresponding to the given rasterized index value (effective sizes).
    `protected IFormatReader` | Memoizer.`handleMetadataStore(IFormatReader memo)` Return the `IFormatReader` instance that is passed in or null if it has been invalidated, which will include the instance being closed.
    `static boolean` | FormatTools.`isFloatingPoint(IFormatReader reader)` Determines whether the given reader represents any floating point data.
    `private boolean` | ImageReader.`isThisType(IFormatReader reader, byte[] block)`
    `private boolean` | ImageReader.`isThisType(IFormatReader reader, loci.common.RandomAccessInputStream rais)`
    `private boolean` | ImageReader.`isThisType(IFormatReader reader, java.lang.String name, boolean allowOpen)`
    `private void` | ImageReader.`logIsThisTypeError(IFormatReader reader, java.lang.Exception e)`
    `static ChannelFiller` | ChannelFiller.`makeChannelFiller(IFormatReader r)` Converts the given reader into a ChannelFiller, wrapping if needed.
    `static ChannelMerger` | ChannelMerger.`makeChannelMerger(IFormatReader r)` Converts the given reader into a ChannelMerger, wrapping if needed.
    `static ChannelSeparator` | ChannelSeparator.`makeChannelSeparator(IFormatReader r)` Converts the given reader into a ChannelSeparator, wrapping if needed.
    `static DimensionSwapper` | DimensionSwapper.`makeDimensionSwapper(IFormatReader r)` Converts the given reader into a DimensionSwapper, wrapping if needed.
    `static MinMaxCalculator` | MinMaxCalculator.`makeMinMaxCalculator(IFormatReader r)` Converts the given reader into a MinMaxCalculator, wrapping if needed.
    `static TileStitcher` | TileStitcher.`makeTileStitcher(IFormatReader r)` Converts the given reader into a TileStitcher, wrapping if needed.
    `static byte[]` | FormatTools.`openThumbBytes(IFormatReader reader, int no)` Default implementation for `openThumbBytes(int)`.
    `static void` | MetadataTools.`populatePixels(MetadataStore store, IFormatReader r)` Populates the Pixels element of the given metadata store, using core metadata from the given reader.
    `static void` | MetadataTools.`populatePixels(MetadataStore store, IFormatReader r, boolean doPlane)` Populates the Pixels element of the given metadata store, using core metadata from the given reader.
    `static void` | MetadataTools.`populatePixels(MetadataStore store, IFormatReader r, boolean doPlane, boolean doImageName)` Populates the Pixels element of the given metadata store, using core metadata from the given reader.
    `static void` | MetadataTools.`populatePixelsOnly(MetadataStore store, IFormatReader r)`
    `void` | Memoizer.Deser.`saveReader(IFormatReader reader)`
    `void` | Memoizer.KryoDeser.`saveReader(IFormatReader reader)`
    `void` | Memoizer.RandomAccessDeser.`saveReader(IFormatReader reader)`

    Method parameters in loci.formats with type arguments of type IFormatReader
    Modifier and Type | Method and Description
    --- | ---
    `ReaderWrapper` | ReaderWrapper.`duplicate(java.lang.Class<? extends IFormatReader> imageReaderClass)` Performs a deep copy of the reader, including nested wrapped readers.
    `private ReaderWrapper` | ReaderWrapper.`duplicateRecurse(java.lang.Class<? extends IFormatReader> imageReaderClass)`
    `IFormatReader` | ImageReader.`getReader(java.lang.Class<? extends IFormatReader> c)` Gets the file format reader instance matching the given class.
    `static IFormatReader` | FormatTools.`getReader(IFormatReader r, java.lang.Class<? extends IFormatReader> c)` Recursively look for the first underlying reader that is an instance of the given class.
    `protected abstract IFormatReader` | Memoizer.RandomAccessDeser.`readerFromBytes(java.lang.Class<IFormatReader> c, byte[] rArr)`
    `void` | FileStitcher.`setReaderClassList(ClassList<IFormatReader> classList)` Set the ClassList object to use when constructing any helper readers.
    `IFormatReader` | ReaderWrapper.`unwrap(java.lang.Class<? extends IFormatReader> readerClass, java.lang.String id)` Unwraps nested wrapped readers until the given reader class is found.

    Constructors in loci.formats with parameters of type IFormatReader
    Constructor and Description
    `ChannelFiller(IFormatReader r)` Constructs a ChannelFiller with a given reader.
    `ChannelMerger(IFormatReader r)` Constructs a ChannelMerger with the given reader.
    `ChannelSeparator(IFormatReader r)` Constructs a ChannelSeparator with the given reader.
    `CoreMetadata(IFormatReader r, int coreIndex)`
    `DimensionSwapper(IFormatReader r)` Constructs a DimensionSwapper with the given reader.
    `FileStitcher(IFormatReader r)` Constructs a FileStitcher with the given reader.
    `FileStitcher(IFormatReader r, boolean patternIds)` Constructs a FileStitcher with the given reader.
    `Memoizer(IFormatReader r)` Constructs a memoizer around the given `IFormatReader` creating memo files under the same directory as the original file only if the call to `Memoizer.setId(java.lang.String)` takes longer than 100L in milliseconds.
    `Memoizer(IFormatReader r, java.io.File directory)` Constructs a memoizer around the given `IFormatReader` creating memo file under the `directory` argument including the full path of the original file only if the call to `Memoizer.setId(java.lang.String)` takes longer than 100L in milliseconds.
    `Memoizer(IFormatReader r, long minimumElapsed)` Constructs a memoizer around the given `IFormatReader` creating memo files under the same directory as the original file only if the call to `Memoizer.setId(java.lang.String)` takes longer than `minimumElapsed` in milliseconds.
    `Memoizer(IFormatReader r, long minimumElapsed, java.io.File directory)` Constructs a memoizer around the given `IFormatReader` creating memo files under the `directory` argument including the full path of the original file only if the call to `Memoizer.setId(java.lang.String)` takes longer than `minimumElapsed` in milliseconds.
    `MinMaxCalculator(IFormatReader r)` Constructs a MinMaxCalculator with the given reader.
    `ReaderWrapper(IFormatReader r)` Constructs a reader wrapper around the given reader.
    `SwappableMetadata(IFormatReader r, int seriesNo)`
    `TileStitcher(IFormatReader r)` Constructs a TileStitcher with the given reader.

    Constructor parameters in loci.formats with type arguments of type IFormatReader
    Constructor and Description
    `ImageReader(ClassList<IFormatReader> classList)` Constructs a new ImageReader from the given list of reader classes.

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

    Fields in loci.formats.cache declared as IFormatReader
    Modifier and Type | Field and Description
    --- | ---
    `protected IFormatReader` | CacheSource.`reader` Reader from which to draw image planes.

    Constructors in loci.formats.cache with parameters of type IFormatReader
    Constructor and Description
    `ByteArraySource(IFormatReader r)` Constructs a byte array source from the given Bio-Formats reader.
    `CacheSource(IFormatReader r)` Constructs a cache source from the given Bio-Formats reader.

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

    Classes in loci.formats.gui that implement IFormatReader
    Modifier and Type | Class and Description
    --- | ---
    `class` | `BufferedImageReader` A reader wrapper for reading image planes as BufferedImage objects.

    Fields in loci.formats.gui declared as IFormatReader
    Modifier and Type | Field and Description
    --- | ---
    `protected IFormatReader` | ImageViewer.`fileReader` Reader for files on disk.
    `protected IFormatReader` | ImageViewer.`in`
    `private IFormatReader` | FormatFileFilter.`reader` Associated file format reader.

    Methods in loci.formats.gui that return IFormatReader
    Modifier and Type | Method and Description
    --- | ---
    `IFormatReader` | FormatFileFilter.`getReader()` Returns the filter's reader.

    Methods in loci.formats.gui with parameters of type IFormatReader
    Modifier and Type | Method and Description
    --- | ---
    `static BufferedImageReader` | BufferedImageReader.`makeBufferedImageReader(IFormatReader r)` Converts the given reader into a BufferedImageReader, wrapping if needed.
    `protected void` | ImageViewer.`open(java.lang.String id, IFormatReader r)` Opens from the given data source using the specified reader in a separate thread.
    `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.
    `void` | ImageViewer.`setImages(IFormatReader reader, java.awt.image.BufferedImage[] img)` Sets the viewer to display the given images, obtaining corresponding core metadata from the specified format reader.

    Constructors in loci.formats.gui with parameters of type IFormatReader
    Constructor and Description
    `BufferedImageReader(IFormatReader r)` Constructs a BufferedImageReader with the given reader.
    `BufferedImageSource(IFormatReader reader)`
    `FormatFileFilter(IFormatReader reader)` Constructs a new filter that accepts files of the given reader's type.
    `FormatFileFilter(IFormatReader reader, boolean allowOpen)` Constructs a new filter that accepts files of the given reader's type, allowing the reader to open files only if the allowOpen flag is set.

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

    Classes in loci.formats.in that implement IFormatReader
    Modifier and Type | Class and Description
    --- | ---
    `class` | `AFIReader` AFIReader is the file format reader for Aperio AFI files.
    `class` | `AIMReader` AIMReader is the file format reader for .aim files.
    `class` | `AliconaReader` AliconaReader is the file format reader for Alicona AL3D files.
    `class` | `AmiraReader` This is a file format reader for AmiraMesh data.
    `class` | `AnalyzeReader` AnalyzeReader is the file format reader for Analyze 7.5 files.
    `class` | `APLReader` APLReader is the file format reader for Olympus APL files.
    `class` | `APNGReader` APNGReader is the file format reader for Animated Portable Network Graphics (APNG) images.
    `class` | `ARFReader` ARFReader is the file format reader for Axon Raw Format (ARF) files, produced by INDEC BioSystems's Imaging Workbench software.
    `class` | `AVIReader` AVIReader is the file format reader for AVI files.
    `class` | `BaseTiffReader` BaseTiffReader is the superclass for file format readers compatible with or derived from the TIFF 6.0 file format.
    `class` | `BaseZeissReader` BaseZeissReader contains common functionality required by readers for Zeiss AxioVision formats.
    `class` | `BDReader` BDReader is the file format reader for BD Pathway datasets.
    `class` | `BDVReader` Reader for BDV files.
    `class` | `BIFormatReader` BIFormatReader is the superclass for file format readers that use java.awt.image.BufferedImage as the native data type.
    `class` | `BioRadGelReader` BioRadGelReader is the file format reader for Bio-Rad gel files.
    `class` | `BioRadReader` BioRadReader is the file format reader for Bio-Rad PIC files.
    `class` | `BioRadSCNReader` BioRadSCNReader is the reader for Bio-Rad .scn files
    `class` | `BMPReader` BMPReader is the file format reader for Microsoft Bitmap (BMP) files.
    `class` | `BrukerReader` BrukerReader is the file format reader for Bruker MRI files.
    `class` | `BurleighReader` BurleighReader is the file format reader for Burleigh .img files.
    `class` | `CanonRawReader` CanonRawReader is the file format reader for Canon RAW files.
    `class` | `CellH5Reader` Reader for CellH5 (HDF) files.
    `class` | `CellomicsReader` Reader for Cellomics C01 files.
    `class` | `CellSensReader` CellSensReader is the file format reader for cellSens .vsi files.
    `class` | `CellVoyagerReader` A bioformat reader for the Yokagawa Cellvoyager CV1000 automated microscope ( http://www.yokogawa.com/scanner/products/cv1000e.htm).
    `class` | `CellWorxReader` CellWorxReader is the file format reader for CellWorx .pnl files.
    `class` | `ColumbusReader` ColumbusReader is the file format reader for screens exported from PerkinElmer Columbus.
    `class` | `CV7000Reader`
    `class` | `DCIMGReader` DCIMGReader reads Hamamatsu DCIMG files.
    `class` | `DeltavisionReader` DeltavisionReader is the file format reader for Deltavision files.
    `class` | `DicomReader` DicomReader is the file format reader for DICOM files.
    `class` | `DNGReader` DNGReader is the file format reader for Canon DNG (TIFF) files.
    `class` | `Ecat7Reader` Ecat7Reader is the file format reader for ECAT 7 files.
    `class` | `EPSReader` Reader is the file format reader for Encapsulated PostScript (EPS) files.
    `class` | `FakeReader` FakeReader is the file format reader for faking input data.
    `class` | `FEIReader` FEIReader is the file format reader for FEI and Philips .img files.
    `class` | `FEITiffReader` FEITiffReader is the file format reader for TIFF files produced by various FEI software.
    `class` | `FilePatternReader`
    `class` | `FitsReader` FitsReader is the file format reader for Flexible Image Transport System (FITS) images.
    `class` | `FlexReader` FlexReader is a file format reader for Evotec Flex files.
    `class` | `FlowSightReader`
    `class` | `FluoviewReader` FluoviewReader is the file format reader for Olympus Fluoview TIFF files AND Andor Bio-imaging Division (ABD) TIFF files.
    `class` | `FujiReader` FujiReader is the file format reader for Fuji LAS 3000 datasets.
    `class` | `FV1000Reader` FV1000Reader is the file format reader for Fluoview FV 1000 OIB and Fluoview FV 1000 OIF files.
    `class` | `GatanDM2Reader` GatanDM2Reader is the file format reader for Gatan .dm2 files.
    `class` | `GatanReader` GatanReader is the file format reader for Gatan files.
    `class` | `GelReader` GelReader is the file format reader for Molecular Dynamics GEL TIFF files.
    `class` | `GIFReader` GIFReader is the file format reader for Graphics Interchange Format (GIF) files.
    `class` | `HamamatsuVMSReader` HamamatsuVMSReader is the file format reader for Hamamatsu VMS datasets.
    `class` | `HISReader` HISReader is the file format reader for Hamamatsu .his files.
    `class` | `HitachiReader` HitachiReader is the file format reader for S-4800 files.
    `class` | `HRDGDFReader` HRDGDFReader is the file format reader for the Gridded Data Format used by NOAA's Hurricane Research Division.
    `class` | `I2IReader` I2IReader is the file format reader for I2I files.
    `class` | `ICSReader` ICSReader is the file format reader for ICS (Image Cytometry Standard) files.
    `class` | `IM3Reader`
    `class` | `ImaconReader` ImaconReader is the file format reader for Imacon .fff (TIFF) files.
    `class` | `ImageIOReader` ImageIOReader is the superclass for file format readers that use the javax.imageio package.
    `class` | `ImagicReader` ImagicReader is the file format reader for IMAGIC files.
    `class` | `ImarisHDFReader` Reader for Bitplane Imaris 5.5 (HDF) files.
    `class` | `ImarisReader` ImarisReader is the file format reader for Bitplane Imaris files.
    `class` | `ImarisTiffReader` ImarisTiffReader is the file format reader for Bitplane Imaris 3 files (TIFF variant).
    `class` | `IMODReader` Reader for IMOD binary files.
    `class` | `ImprovisionTiffReader` ImprovisionTiffReader is the file format reader for Improvision TIFF files.
    `class` | `ImspectorReader` ImspectorReader is the file format reader for Imspector .msr files.
    `class` | `InCell3000Reader` InCell3000Reader is the file format reader for InCell 3000.
    `class` | `InCellReader` InCellReader is the file format reader for InCell 1000/2000 datasets.
    `class` | `INRReader` INRReader is the file format reader for INR files.
    `class` | `InveonReader` InveonReader is the file format reader for Inveon files.
    `class` | `IonpathMIBITiffReader` IonpathMIBITiffReader is the file format reader for Ionpath MIBI TIFF files.
    `class` | `IPLabReader` IPLabReader is the file format reader for IPLab (.IPL) files.
    `class` | `IPWReader` IPWReader is the file format reader for Image-Pro Workspace (IPW) files.
    `class` | `IvisionReader` IvisionReader is the file format reader for IVision (.IPM) files.
    `class` | `JDCEReader` JDCEReader is the file format reader for Molecular Devices JDCE plates.
    `class` | `JEOLReader` JEOLReader is the file format reader for JEOL files.
    `class` | `JPEG2000Reader` JPEG2000Reader is the file format reader for JPEG-2000 images.
    `class` | `JPEGReader` JPEGReader is the file format reader for JPEG images.
    `static class` | `JPEGReader.DefaultJPEGReader`
    `class` | `JPKReader` JPKReader is the file format reader for JPK Instruments files.
    `class` | `JPXReader` JPXReader is the file format reader for JPX (3D JPEG-2000) images.
    `class` | `KhorosReader` Reader for Khoros XV files.
    `class` | `KLBReader` Reader for Keller Lab Block (KLB) files.
    `class` | `KodakReader` KodakReader is the file format reader for Kodak Molecular Imaging .bip files.
    `class` | `L2DReader` L2DReader is the file format reader for Li-Cor L2D datasets.
    `class` | `LeicaReader` LeicaReader is the file format reader for Leica files.
    `class` | `LeicaSCNReader` LeicaSCNReader is the file format reader for Leica SCN TIFF files.
    `class` | `LEOReader` LEOReader is the file format reader for LEO EM files.
    `class` | `LiFlimReader` LiFlimReader is the file format reader for LI-FLIM files.
    `class` | `LIFReader` LIFReader is the file format reader for Leica LIF files.
    `class` | `LIMReader` LIMReader is the file format reader for Laboratory Imaging/Nikon LIM files.
    `class` | `LOFReader` LOFReader is the file format reader for Leica Microsystems' LOF files.
    `class` | `MetamorphReader` Reader is the file format reader for Metamorph STK files.
    `class` | `MetamorphTiffReader` MetamorphTiffReader is the file format reader for TIFF files produced by Metamorph software version 7.5 and above.
    `class` | `MetaxpressTiffReader` MetaxpressTiffReader is the file format reader for MetaXpress .htd + TIFF files.
    `class` | `MIASReader` MIASReader is the file format reader for Maia Scientific MIAS-2 datasets.
    `class` | `MicroCTReader` MicroCTReader is the file format reader for VFF files from a GE MicroCT scanner.
    `class` | `MicromanagerReader` MicromanagerReader is the file format reader for Micro-Manager files.
    `class` | `MikroscanTiffReader` MikroscanTiffReader is the file format reader for Mikroscan TIFF files.
    `class` | `MINCReader` MINCReader is the file format reader for MINC MRI files.
    `class` | `MinimalTiffReader` MinimalTiffReader is the superclass for file format readers compatible with or derived from the TIFF 6.0 file format.
    `class` | `MNGReader` MNGReader is the file format reader for Multiple-image Network Graphics (MNG) files.
    `class` | `MolecularImagingReader` MolecularImagingReader is the file format reader for Molecular Imaging files.
    `class` | `MRCReader` MRCReader is the file format reader for MRC files.
    `class` | `MRWReader` MRWReader is the file format reader for Minolta MRW files.
    `class` | `NAFReader` NAFReader is the file format reader for Hamamatsu Aquacosmos NAF files.
    `class` | `ND2Reader` ND2Reader is the file format reader for Nikon ND2 files.
    `class` | `NDPIReader` NDPIReader is the file format reader for Hamamatsu .ndpi files.
    `class` | `NDPISReader` NDPISReader is the file format reader for Hamamatsu .ndpis files.
    `class` | `NiftiReader` NiftiReader is the file format reader for NIfTI files.
    `class` | `NikonElementsTiffReader` NikonElementsTiffReader is the file format reader for TIFF files produced by Nikon Elements.
    `class` | `NikonReader` NikonReader is the file format reader for Nikon NEF (TIFF) files.
    `class` | `NikonTiffReader` NikonTiffReader is the file format reader for Nikon TIFF files.
    `class` | `NRRDReader` File format reader for NRRD files; see http://teem.sourceforge.net/nrrd.
    `class` | `OBFReader` OBFReader is the file format reader for Imspector OBF files.
    `class` | `OIRReader` OIRReader is the file format reader for Olympus .oir files.
    `class` | `OlympusTileReader` OlympusTileReader is the file format reader for Olympus .omp2info files.
    `class` | `OMETiffReader` OMETiffReader is the file format reader for OME-TIFF files.
    `class` | `OMEXMLReader` OMEXMLReader is the file format reader for OME-XML files.
    `class` | `OpenlabRawReader` OpenlabRawReader is the file format reader for Openlab RAW files.
    `class` | `OpenlabReader` OpenlabReader is the file format reader for Openlab LIFF files.
    `class` | `OperettaReader` OperettaReader is the file format reader for PerkinElmer Operetta data.
    `class` | `OxfordInstrumentsReader` OxfordInstrumentsReader is the file format reader for Oxford Instruments .top files.
    `class` | `PCIReader` PCIReader is the file format reader for SimplePCI (Compix) .cxd files.
    `class` | `PCORAWReader` PCORAWReader is the file format reader for PCORAW files.
    `class` | `PCXReader` PCXReader is the file format reader for PCX files (originally used by PC Paintbrush; now used in Zeiss' LSM Image Browser).
    `class` | `PDSReader` PDSReader is the file format reader for Perkin Elmer densitometer files.
    `class` | `PerkinElmerReader` PerkinElmerReader is the file format reader for PerkinElmer files.
    `class` | `PGMReader` PGMReader is the file format reader for Portable Gray Map (PGM) images.
    `class` | `PhotoshopTiffReader` PhotoshopTiffReader is the file format reader for Adobe Photoshop TIFF files.
    `class` | `PictReader` PictReader is the file format reader for Apple PICT files.
    `class` | `PovrayReader` PovrayReader is the file format reader for POV-Ray .df3 files.
    `class` | `PQBinReader` PQBinReader is the file format reader for PicoQuant .bin files.
    `class` | `PrairieReader` PrairieReader is the file format reader for Prairie Technologies' TIFF variant.
    `class` | `PSDReader` PSDReader is the file format reader for Photoshop PSD files.
    `class` | `PyramidTiffReader` PyramidTiffReader is the file format reader for pyramid TIFFs.
    `class` | `QTReader` QTReader is the file format reader for QuickTime movie files.
    `class` | `QuesantReader` QuesantReader is the file format reader for Quesant .afm files.
    `class` | `RCPNLReader`
    `class` | `RHKReader` RHKReader is the file format reader for RHK Technologies files.
    `class` | `SBIGReader` SBIGReader is the file format reader for SBIG files.
    `class` | `ScanrReader` ScanrReader is the file format reader for Olympus ScanR datasets.
    `class` | `SDTReader` SDTReader is the file format reader for Becker & Hickl SPC-Image SDT files.
    `class` | `SeikoReader` SeikoReader is the file format reader for Seiko .xqd/.xqf files.
    `class` | `SEQReader` SEQReader is the file format reader for Image-Pro Sequence files.
    `class` | `SIFReader` SIFReader is the file format reader for Andor SIF files.
    `class` | `SimplePCITiffReader` SimplePCITiffReader is the file format reader for TIFF files produced by SimplePCI software.
    `class` | `SISReader` SISReader is the file format reader for Olympus Soft Imaging Solutions TIFF files.
    `class` | `SlideBook7Reader`
    `class` | `SlidebookReader` SlidebookReader is the file format reader for 3I Slidebook files.
    `class` | `SlidebookTiffReader`
    `class` | `SMCameraReader` SMCameraReader is the file format reader for SM camera files.
    `class` | `SPCReader` SPCReader is the file format reader for Becker & Hickl SPC-Image SPC FIFO files.
    `class` | `SPEReader` SPEReader is the file format reader for Princeton Instruments SPE .spe files.
    `class` | `SpiderReader` SpiderReader is the file format reader for SPIDER files.
    `class` | `SVSReader` SVSReader is the file format reader for Aperio SVS TIFF files.
    `class` | `TargaReader` File format reader for Truevision Targa files.
    `class` | `TCSReader` TCSReader is the file format reader for Leica TCS TIFF files and their companion XML file.
    `class` | `TecanReader`
    `class` | `TextReader` Reader for text files containing tables of data.
    `class` | `TiffDelegateReader` TiffDelegateReader is a file format reader for TIFF files.
    `class` | `TiffJAIReader` TiffJAIReader is a file format reader for TIFF images.
    `class` | `TiffReader` TiffReader is the file format reader for regular TIFF files, not of any specific TIFF variant.
    `class` | `TileJPEGReader` Reader for decoding JPEG images using java.awt.Toolkit and TurboJPEG.
    `class` | `TillVisionReader` TillVisionReader is the file format reader for TillVision files.
    `class` | `TissueFAXSReader` Reader for TissueFAXS format from TissueGnostics.
    `class` | `TopometrixReader` TopometrixReader is the file format reader for TopoMetrix .tfr, .ffr, .zfr, .zfp, and .2fl files.
    `class` | `TrestleReader` TrestleReader is the file format reader for Trestle slide datasets.
    `class` | `UBMReader` UBMReader is the file format reader for UBM .pr3 files.
    `class` | `UnisokuReader` UnisokuReader is the file format reader for Unisoku STM files.
    `class` | `VarianFDFReader` VarianFDFReader is the file format reader for Varian FDF files.
    `class` | `VectraReader` VectraReader is the reader for PerkinElmer Vectra QPTIFF data
    `class` | `VeecoReader` VeecoReader is the file format reader for Veeco HDF files.
    `class` | `VentanaReader` VentanaReader is the file format reader for Ventana .bif files.
    `class` | `VGSAMReader` VGSAMReader is the file format reader for VG SAM .dti files.
    `class` | `VisitechReader` VisitechReader is the file format reader for Visitech XYS files.
    `class` | `VolocityClippingReader` VolocityClippingReader is the file format reader for Volocity library clipping files.
    `class` | `VolocityReader` VolocityReader is the file format reader for Volocity library files.
    `class` | `WATOPReader` WATOPReader is the file format reader for WA Technology .wat files.
    `class` | `XLEFReader` XLEFReader is the file format reader for Leica Microsystems' XLEF files.
    `class` | `ZeissCZIReader` ZeissCZIReader is the file format reader for Zeiss .czi files.
    `class` | `ZeissLMSReader` Zeiss LMS reader for data from Zeiss CSM 700 systems.
    `class` | `ZeissLSMReader` ZeissLSMReader is the file format reader for Zeiss LSM files.
    `class` | `ZeissTIFFReader` ZeissTIFFReader is the file format reader for Zeiss AxioVision TIFF files and their companion XML file.
    `class` | `ZeissXRMReader` ZeissXRMReader is the file format reader for Zeiss X-Ray Microscopy .txm and .txrm files.
    `class` | `ZeissZVIReader` ZeissZVIReader is the file format reader for Zeiss ZVI files.
    `class` | `ZipReader` Reader for Zip files.

    Fields in loci.formats.in declared as IFormatReader
    Modifier and Type | Field and Description
    --- | ---
    `private IFormatReader` | OlympusTileReader.`helperReader`
    `private IFormatReader` | CellWorxReader.`lastReader`
    `IFormatReader` | OMETiffReader.OMETiffPlane.`reader` Reader to use for accessing this plane.

    Methods in loci.formats.in that return IFormatReader
    Modifier and Type | Method and Description
    --- | ---
    `protected IFormatReader` | MetaxpressTiffReader.`getReader(java.lang.String file, boolean omexml)`
    `protected IFormatReader` | CellWorxReader.`getReader(java.lang.String file, boolean omexml)`

    Methods in loci.formats.in with parameters of type IFormatReader
    Modifier and Type | Method and Description
    --- | ---
    `private void` | OMETiffReader.`initializeReader(IFormatReader r, java.lang.String file)`
    `protected void` | CellWorxReader.`initReader(IFormatReader reader, java.lang.String file, boolean omexml)`
    `private void` | OMETiffReader.`removeIFDComments(IFormatReader r)`

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

    Classes in loci.formats.in.LeicaMicrosystemsMetadata that implement IFormatReader
    Modifier and Type | Class and Description
    --- | ---
    `class` | `LMSFileReader` This class can be extended by readers of Leica Microsystems file formats that include LASX generated XML (e.g.
    `class` | `MultipleImagesReader` MultipleImagesReader presents a number of image files as one image reference

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

    Methods in loci.formats.tools with parameters of type IFormatReader
    Modifier and Type | Method and Description
    --- | ---
    `private static int[]` | CacheConsole.`getLengths(IFormatReader r)` Helper utility for constructing lengths array, used by main.

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

    Fields in loci.plugins.in declared as IFormatReader
    Modifier and Type | Field and Description
    --- | ---
    `private IFormatReader` | ImportProcess.`baseReader`

    Methods in loci.plugins.in that return IFormatReader
    Modifier and Type | Method and Description
    --- | ---
    `IFormatReader` | ImportProcess.`getBaseReader()` Valid only after `ImportStep.READER`.

    Methods in loci.plugins.in with parameters of type IFormatReader
    Modifier and Type | Method and Description
    --- | ---
    `private void` | ImportProcess.`computeSeriesLabels(IFormatReader r)`
    `private java.lang.String` | ImagePlusReader.`constructImageTitle(IFormatReader r, java.lang.String file, java.lang.String seriesName, boolean groupFiles)`
    `private java.lang.String` | ImagePlusReader.`constructSliceLabel(int ndx, IFormatReader r, IMetadata meta, int series, int zCount, int cCount, int tCount)`

    Constructors in loci.plugins.in with parameters of type IFormatReader
    Constructor and Description
    `ImporterMetadata(IFormatReader r, ImportProcess process, boolean usePrefix)`
    `ThumbLoader(IFormatReader ir, java.awt.Panel[] p, java.awt.Dialog dialog)` Constructs a new thumbnail loader.

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

    Methods in loci.plugins.macro with parameters of type IFormatReader
    Modifier and Type | Method and Description
    --- | ---
    `private static int` | LociFunctions.`getPlaneIndex(IFormatReader r, int no)` Finds the Plane index corresponding to the given image plane number.

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

    Classes in loci.plugins.util that implement IFormatReader
    Modifier and Type | Class and Description
    --- | ---
    `class` | `ImageProcessorReader` A low-level reader for `ImageProcessor` objects.
    `class` | `VirtualReader` TODO

    Fields in loci.plugins.util declared as IFormatReader
    Modifier and Type | Field and Description
    --- | ---
    `private IFormatReader` | VirtualImagePlus.`r`

    Methods in loci.plugins.util with parameters of type IFormatReader
    Modifier and Type | Method and Description
    --- | ---
    `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)`
    `static boolean` | LociPrefs.`isWindowless(IFormatReader r)` Gets whether windowless mode should be used when opening this reader's currently initialized dataset.
    `static ImageProcessorReader` | ImageProcessorReader.`makeImageProcessorReader(IFormatReader r)` Converts the given reader into a ImageProcessorReader, wrapping if needed.
    `void` | VirtualImagePlus.`setReader(IFormatReader r)`

    Method parameters in loci.plugins.util with type arguments of type IFormatReader
    Modifier and Type | Method and Description
    --- | ---
    `private static boolean` | LociPrefs.`getPref(java.lang.String pref, java.lang.Class<? extends IFormatReader> c, boolean defaultValue)`
    `static boolean` | LociPrefs.`isReaderEnabled(java.lang.Class<? extends IFormatReader> c)`

    Constructors in loci.plugins.util with parameters of type IFormatReader
    Constructor and Description
    `BFVirtualStack(java.lang.String path, IFormatReader r, boolean colorize, boolean merge, boolean record)`
    `ImageProcessorReader(IFormatReader r)` Constructs an ImageProcessorReader with the given reader.
    `ImageProcessorSource(IFormatReader reader)`
    `VirtualReader(IFormatReader r)`

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