# Uses of Package
loci.formats

- Packages that use loci.formats
  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.meta | Package containing core Bio-Formats metadata interfaces for the OME data model.
  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.

- Classes in loci.formats used by loci.formats
  Class and Description
  AxisGuesser AxisGuesser guesses which blocks in a file pattern correspond to which dimensional axes (Z, T, C or S), potentially recommending an adjustment in dimension order within the files, depending on the confidence of each guess.
  ChannelFiller For indexed color data representing true color, factors out the indices, replacing them with the color table values directly.
  ChannelMerger Logic to automatically merge channels in a file.
  ChannelSeparator Logic to automatically separate the channels in a file.
  ClassList ClassList is a list of classes for use with `ImageReader` or `ImageWriter`, parsed from a configuration file such as readers.txt or writers.txt.
  CoreMetadata Encompasses core metadata values.
  CoreMetadataList
  DimensionSwapper Handles swapping the dimension order of an image series.
  FileInfo Encompasses basic metadata about a file.
  FilePattern Represents a collection of files meant to be part of the same data series.
  FilePatternBlock FilePatternBlock represents a single block in a `FilePattern`.
  FileStitcher.ExternalSeries
  FormatException FormatException is the exception thrown when something goes wrong performing a file format operation.
  FormatHandler Abstract superclass of all biological file format readers and writers.
  FormatReader Abstract superclass of all biological file format readers.
  ICompressedTileReader Interface for reading pre-compressed image tiles.
  ICompressedTileWriter Interface for writing pre-compressed image tiles.
  IFormatHandler Interface for all biological file format readers and writers.
  IFormatReader Interface for all biological file format readers.
  IFormatWriter Interface for all biological file format writers.
  IMetadataConfigurable
  IPyramidHandler Interface for defining image pyramids.
  Memoizer.Deser
  MetadataList A container of metadata for FormatReader and other reader implementations.
  MinMaxCalculator Logic to compute minimum and maximum values for each channel.
  MissingLibraryException MissingLibraryException is the exception thrown when a particular data stream or filename requires a library that is not present on the system.
  Modulo Represents a subdimension of Z, C, or T as needed for supporting Modulo annotations.
  NumberFilter NumberFilter is a helper filter for FilePattern.findPattern().
  ReaderWrapper Abstract superclass of reader logic that wraps other readers.
  Resolution Represents a single subresolution in a pyramid.
  SwappableMetadata Extends `CoreMetadata` to include the notion of an "input order" for planes: the input order being the order planes are stored on disk.
  TileStitcher
  WriterWrapper Abstract superclass of writer logic that wraps other writers.

- Classes in loci.formats used by loci.formats.cache
  Class and Description
  FormatException FormatException is the exception thrown when something goes wrong performing a file format operation.
  IFormatReader Interface for all biological file format readers.

- Classes in loci.formats used by loci.formats.codec
  Class and Description
  FormatException FormatException is the exception thrown when something goes wrong performing a file format operation.

- Classes in loci.formats used by loci.formats.dicom
  Class and Description
  CoreMetadata Encompasses core metadata values.
  FormatException FormatException is the exception thrown when something goes wrong performing a file format operation.

- Classes in loci.formats used by loci.formats.gui
  Class and Description
  DimensionSwapper Handles swapping the dimension order of an image series.
  FileStitcher Logic to stitch together files with similar names.
  FormatException FormatException is the exception thrown when something goes wrong performing a file format operation.
  ICompressedTileReader Interface for reading pre-compressed image tiles.
  ICompressedTileWriter Interface for writing pre-compressed image tiles.
  IFormatHandler Interface for all biological file format readers and writers.
  IFormatReader Interface for all biological file format readers.
  IFormatWriter Interface for all biological file format writers.
  ImageWriter ImageWriter is the master file format writer for all supported formats.
  IMetadataConfigurable
  IPyramidHandler Interface for defining image pyramids.
  ReaderWrapper Abstract superclass of reader logic that wraps other readers.
  WriterWrapper Abstract superclass of writer logic that wraps other writers.

- Classes in loci.formats used by loci.formats.in
  Class and Description
  ChannelSeparator Logic to automatically separate the channels in a file.
  CoreMetadata Encompasses core metadata values.
  CoreMetadataList
  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.
  FileStitcher Logic to stitch together files with similar names.
  FormatException FormatException is the exception thrown when something goes wrong performing a file format operation.
  FormatHandler Abstract superclass of all biological file format readers and writers.
  FormatReader Abstract superclass of all biological file format readers.
  ICompressedTileReader Interface for reading pre-compressed image tiles.
  IFormatHandler Interface for all biological file format readers and writers.
  IFormatReader Interface for all biological file format readers.
  ImageReader ImageReader is the master file format reader for all supported formats.
  IMetadataConfigurable
  IPyramidHandler Interface for defining image pyramids.
  MissingLibraryException MissingLibraryException is the exception thrown when a particular data stream or filename requires a library that is not present on the system.
  ReaderWrapper Abstract superclass of reader logic that wraps other readers.
  SubResolutionFormatReader Abstract superclass of all biological file format readers that can handle image pyramids.
  UnsupportedCompressionException UnsupportedCompressionException is the exception thrown when the compression scheme used in a particular file or stream is unsupported.
  WrappedReader Helper class for readers which wrap other readers.

- Classes in loci.formats used by loci.formats.in.LeicaMicrosystemsMetadata
  Class and Description
  CoreMetadata Encompasses core metadata values.
  FormatException FormatException is the exception thrown when something goes wrong performing a file format operation.
  FormatHandler Abstract superclass of all biological file format readers and writers.
  FormatReader Abstract superclass of all biological file format readers.
  ICompressedTileReader Interface for reading pre-compressed image tiles.
  IFormatHandler Interface for all biological file format readers and writers.
  IFormatReader Interface for all biological file format readers.
  IMetadataConfigurable
  IPyramidHandler Interface for defining image pyramids.

- Classes in loci.formats used by loci.formats.meta
  Class and Description
  Modulo Represents a subdimension of Z, C, or T as needed for supporting Modulo annotations.

- Classes in loci.formats used by loci.formats.out
  Class and Description
  FormatException FormatException is the exception thrown when something goes wrong performing a file format operation.
  FormatHandler Abstract superclass of all biological file format readers and writers.
  FormatWriter Abstract superclass of all biological file format writers.
  ICompressedTileWriter Interface for writing pre-compressed image tiles.
  IFormatHandler Interface for all biological file format readers and writers.
  IFormatWriter Interface for all biological file format writers.
  IMetadataConfigurable
  IPyramidHandler Interface for defining image pyramids.

- Classes in loci.formats used by loci.formats.services
  Class and Description
  CoreMetadata Encompasses core metadata values.
  FormatException FormatException is the exception thrown when something goes wrong performing a file format operation.
  Modulo Represents a subdimension of Z, C, or T as needed for supporting Modulo annotations.

- Classes in loci.formats used by loci.formats.tiff
  Class and Description
  FormatException FormatException is the exception thrown when something goes wrong performing a file format operation.

- Classes in loci.formats used by loci.formats.tools
  Class and Description
  CoreMetadata Encompasses core metadata values.
  FormatException FormatException is the exception thrown when something goes wrong performing a file format operation.
  IFormatReader Interface for all biological file format readers.
  ResourceNamer Utility class helping with generating human-readable resource names based on alphanumeric indexing.

- Classes in loci.formats used by loci.plugins
  Class and Description
  FormatException FormatException is the exception thrown when something goes wrong performing a file format operation.

- Classes in loci.formats used by loci.plugins.in
  Class and Description
  ChannelFiller For indexed color data representing true color, factors out the indices, replacing them with the color table values directly.
  ChannelSeparator Logic to automatically separate the channels in a file.
  DimensionSwapper Handles swapping the dimension order of an image series.
  FilePattern Represents a collection of files meant to be part of the same data series.
  FileStitcher Logic to stitch together files with similar names.
  FormatException FormatException is the exception thrown when something goes wrong performing a file format operation.
  IFormatReader Interface for all biological file format readers.
  ImageReader ImageReader is the master file format reader for all supported formats.
  MinMaxCalculator Logic to compute minimum and maximum values for each channel.
  Modulo Represents a subdimension of Z, C, or T as needed for supporting Modulo annotations.
  TileStitcher

- Classes in loci.formats used by loci.plugins.macro
  Class and Description
  FormatException FormatException is the exception thrown when something goes wrong performing a file format operation.
  IFormatReader Interface for all biological file format readers.

- Classes in loci.formats used by loci.plugins.util
  Class and Description
  FormatException FormatException is the exception thrown when something goes wrong performing a file format operation.
  ICompressedTileReader Interface for reading pre-compressed image tiles.
  IFormatHandler Interface for all biological file format readers and writers.
  IFormatReader Interface for all biological file format readers.
  ImageReader ImageReader is the master file format reader for all supported formats.
  IMetadataConfigurable
  IPyramidHandler Interface for defining image pyramids.
  ReaderWrapper Abstract superclass of reader logic that wraps other readers.

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