Package loci.formats

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

See: Description

Interface Summary

Interface	Description
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.