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.
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.
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.