Interface for all biological file format readers and writers.
Interface for all biological file format readers.
Interface for all biological file format writers.
AxisGuesser guesses which blocks in a file pattern correspond to which dimensional axes (Z, T or C), 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 is a list of classes for use with ImageReader or ImageWriter, 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.
FilePattern is a collection of methods for handling file patterns, a way of succinctly representing a collection of files meant to be part of the same data series.
FilePatternBlock represents a single block in a
Logic to stitch together files with similar names.
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.
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.
Helper implementation that can be used to implement
Logic to compute minimum and maximum values for each channel.
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.
Utility class helping with generating human-readable resource names based on alphanumeric indexing.
Class that allows checking for new versions of Bio-Formats, as well as updating to the latest stable, daily, or trunk version.
Abstract superclass of writer logic that wraps other writers.
FormatException is the exception thrown when something goes wrong performing a file format operation.
MissingLibraryException is the exception thrown when a particular data stream or filename requires a library that is not present on the system.
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.
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