Package loci.formats
package loci.formats
Bio-Formats: a library for reading and writing popular microscopy file
formats.
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ClassDescriptionAxisGuesser 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.For indexed color data representing true color, factors out the indices, replacing them with the color table values directly.Logic to automatically merge channels in a file.Logic to automatically separate the channels in a file.ClassList<T>ClassList is a list of classes for use with
ImageReaderorImageWriter, parsed from a configuration file such as readers.txt or writers.txt.Encompasses core metadata values.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.Handles swapping the dimension order of an image series.Encompasses basic metadata about a file.Represents a collection of files meant to be part of the same data series.FilePatternBlock represents a single block in aFilePattern.Logic to stitch together files with similar names.FormatException is the exception thrown when something goes wrong performing a file format operation.Abstract superclass of all biological file format readers and writers.Abstract superclass of all biological file format readers.A utility class for format reader and writer implementations.Abstract superclass of all biological file format writers.Interface for reading pre-compressed image tiles.Interface for writing pre-compressed image tiles.Interface for all biological file format readers and writers.Interface for all biological file format readers.Interface for all biological file format writers.Exception thrown whenFilePatternBlockencounters an invalid pattern.ImageReader is the master file format reader for all supported formats.A utility class with convenience methods for manipulating images in primitive array form.ImageWriter is the master file format writer for all supported formats.Interface for defining image pyramids.ReaderWrapperimplementation which caches the state of the delegate (including and otherReaderWrapperinstances) afterMemoizer.setId(String)has been called.Helper implementation that can be used to implementMemoizer.Deserclasses for libraries working solely with byte arrays.MetadataList<T>A container of metadata for FormatReader and other reader implementations.A utility class for working with metadata objects, includingMetadataStore,MetadataRetrieve, and OME-XML strings.Logic to compute minimum and maximum values for each channel.MissingLibraryException is the exception thrown when a particular data stream or filename requires a library that is not present on the system.Represents a subdimension of Z, C, or T as needed for supporting Modulo annotations.NumberFilter is a helper filter for FilePattern.findPattern().Abstract superclass of reader logic that wraps other readers.Represents a single subresolution in a pyramid.Utility class helping with generating human-readable resource names based on alphanumeric indexing.Abstract superclass of all biological file format readers that can handle image pyramids.ExtendsCoreMetadatato include the notion of an "input order" for planes: the input order being the order planes are stored on disk.UnknownFormatException is the exception thrown when the format of a particular data stream or filename cannot be recognized or is unsupported.UnsupportedCompressionException is the exception thrown when the compression scheme used in a particular file or stream is unsupported.Class that allows checking for new versions of Bio-Formats, as well as updating to the latest stable, daily, or trunk version.Helper class for readers which wrap other readers.Abstract superclass of writer logic that wraps other writers.