# Package loci.formats

Bio-Formats: a library for reading and writing popular microscopy file formats.

See: Description

- Interface Summary
  Interface | Description
  --- | ---
  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 |

- Class Summary
  Class | 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<T> | 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 |
  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.
  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 | Logic to stitch together files with similar names.
  FormatHandler | Abstract superclass of all biological file format readers and writers.
  FormatReader | Abstract superclass of all biological file format readers.
  FormatTools | A utility class for format reader and writer implementations.
  FormatWriter | Abstract superclass of all biological file format writers.
  ImageReader | ImageReader is the master file format reader for all supported formats.
  ImageTools | A utility class with convenience methods for manipulating images in primitive array form.
  ImageWriter | ImageWriter is the master file format writer for all supported formats.
  Memoizer | `ReaderWrapper` implementation which caches the state of the delegate (including and other `ReaderWrapper` instances) after `Memoizer.setId(String)` has been called.
  Memoizer.KryoDeser |
  Memoizer.RandomAccessDeser | Helper implementation that can be used to implement `Memoizer.Deser` classes for libraries working solely with byte arrays.
  MetadataList<T> | A container of metadata for FormatReader and other reader implementations.
  MetadataTools | A utility class for working with metadata objects, including `MetadataStore`, `MetadataRetrieve`, and OME-XML strings.
  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.
  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.
  ResourceNamer | Utility class helping with generating human-readable resource names based on alphanumeric indexing.
  SubResolutionFormatReader | Abstract superclass of all biological file format readers that can handle image pyramids.
  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 |
  UpgradeChecker | Class that allows checking for new versions of Bio-Formats, as well as updating to the latest stable, daily, or trunk version.
  WrappedReader | Helper class for readers which wrap other readers.
  WriterWrapper | Abstract superclass of writer logic that wraps other writers.

- Exception Summary
  Exception | Description
  --- | ---
  FormatException | FormatException is the exception thrown when something goes wrong performing a file format operation.
  IllegalBlockException | Exception thrown when `FilePatternBlock` encounters an invalid pattern.
  MissingLibraryException | MissingLibraryException is the exception thrown when a particular data stream or filename requires a library that is not present on the system.
  UnknownFormatException | UnknownFormatException is the exception thrown when the format of a particular data stream or filename cannot be recognized or is unsupported.
  UnsupportedCompressionException | UnsupportedCompressionException is the exception thrown when the compression scheme used in a particular file or stream is unsupported.

## Package loci.formats Description

Bio-Formats: a library for reading and writing popular microscopy file formats.

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