All Classes and Interfaces
Class
Description
AmiraParameters handles parsing and writing of AmiraMesh headers.
APNGReader is the file format reader for
Animated Portable Network Graphics (APNG) images.
APNGWriter is the file format writer for PNG and APNG files.
A utility class for outputting a BufferedImage as ASCII text.
AVIReader is the file format reader for AVI files.
AVIWriter is the file format writer for AVI files.
A utility class with convenience methods for manipulating images
in
BufferedImage form.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.
Implements encoding (compress) and decoding (decompress) methods
for Base64.
BaseCodec contains default implementation and testing for classes
implementing the Codec interface, and acts as a base class for any
of the compression classes.
BaseTiffReader is the superclass for file format readers compatible with
or derived from the TIFF 6.0 file format.
Reader for BDV files.
BIFormatReader is the superclass for file format readers
that use java.awt.image.BufferedImage as the native data type.
This class is used to generate a text file containing all of the
image file extensions supported by Bio-Formats.
Deprecated.
Use loci.common.RandomAccessInputStream instead
Deprecated.
Use loci.common.RandomAccessOutputStream instead
BMPReader is the file format reader for Microsoft Bitmap (BMP) files.
A reader wrapper for reading image planes as BufferedImage objects.
Retrieves BufferedImages from a data source using Bio-Formats.
A writer wrapper for writing image planes from BufferedImage objects.
Retrieves byte arrays from a data source
(e.g., a file) using Bio-Formats.
A growable array of bytes.
Cache provides a means of managing subsets of large collections of image
planes in memory.
GUI component for managing a cache.
CacheConsole provides an interactive interpreter for
testing the Bio-Formats caching implementation.
A event indicating a cache update.
CacheException is the exception thrown when something
goes wrong performing a cache operation.
Indicator GUI component showing which planes are currently in the cache
for a given dimensional axis at a particular dimensional position.
A listener for cache updates.
Interface for components capable of reporting cache updates.
Superclass of cache sources that retrieve image planes
from a data source (e.g., a file) using Bio-Formats.
Superclass of cache strategies.
Thread responsible for updating the cache
(loading and dropping planes) in the background.
Reader for CellH5 (HDF) files.
CellH5Writer is the file format writer for CellH5 format.
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.
A file filter that recognizes files from a union of other filters.
An enumeration of compression types.
A crosshair strategy caches planes extending from the the current
dimensional position along each individual axis, but not combinations of
axes.
A utility for reorganizing and converting QuickTime movies,
TIFF series and other 4D datasets.
Describes a DICOM attribute (integer tag, associated description, and expected VR).
Structure containing metadata for one DICOM file (instance).
Provide DICOM tags from a file containing JSON.
DicomReader is the file format reader for DICOM files.
Represents a complete DICOM tag, including the dictionary attribute,
actual VR, value, and any "child" tags (in the case of a sequence).
Represents a tile stored in a DICOM file.
Enumeration of valid DICOM value representations (VRs).
DicomWriter is the file format writer for DICOM files.
Handles swapping the dimension order of an image series.
Provides a GUI for editing TIFF file comments.
Reader is the file format reader for Encapsulated PostScript (EPS) files.
EPSWriter is the file format writer for Encapsulated PostScript (EPS) files.
A file filter based on file extensions, for use with a JFileChooser.
Generates fake image structures.
FakeReader is the file format reader for faking input data.
Represents a collection of files meant to be part of the same
data series.
FilePatternBlock represents a single block in a
FilePattern.Logic to stitch together files with similar names.
FitsReader is the file format reader for
Flexible Image Transport System (FITS) images.
A file filter for a biological file format, for use with a JFileChooser.
GIFReader is the file format reader for Graphics Interchange Format
(GIF) files.
A utility class for working with graphical user interfaces.
This class implements Huffman decoding.
Options for compressing and decompressing Huffman data.
Interface for cache sources.
Interface for cache strategies.
ICSReader is the file format reader for ICS (Image Cytometry Standard)
files.
ICSWriter is the file format writer for ICS files.
Data structure for working with TIFF Image File Directories (IFDs).
Data structure for working with a list of TIFF
IFDs.An enumeration of IFD types.
Exception thrown when
FilePatternBlock encounters an
invalid pattern.A record containing boolean values
ImageIOReader is the superclass for file format readers
that use the javax.imageio package.
ImageIOWriter is the superclass for file format writers that use the
javax.imageio library.
A utility class with convenience methods for manipulating images
in primitive array form.
ImageViewer is a simple viewer/converter
for the Bio-Formats image formats.
ColorModel that handles 16 bits per channel lookup tables.
Interface used to provide DICOM tags.
Interface defining methods for reading data using JAI Image I/O.
Implementation of JAIIIOService for reading and writing JPEG-2000 data.
JavaWriter is the file format writer for Java source code.
Utility class for working with NetCDF/HDF files.
Utility class for working with HDF files.
An enumeration of JPEG 2000 box types.
This class implements JPEG 2000 compression and decompression.
Options for compressing and decompressing JPEG-2000 data.
A parser for JPEG 2000 metadata.
JPEG2000Reader is the file format reader for JPEG-2000 images.
An enumeration of JPEG 2000 segment markers.
JPEG2000Writer is the file format writer for JPEG2000 files.
This class implements JPEG compression and decompression.
JPEGReader is the file format reader for JPEG images.
Based upon the NDPI to OME-TIFF converter by Matthias Baldauf:
http://matthias-baldauf.at/software/ndpi_converter/
JPEGWriter is the file format writer for JPEG files.
Interface defining methods for working with JPEG-XR data
Interface defining methods for working with JPEG-XR data
Reader for Keller Lab Block (KLB) files.
Decompresses lossless JPEG images.
This class implements LZO decompression.
This is an optimized LZW codec for use with TIFF files.
Creates sample OME-TIFF datasets according to the given parameters.
ReaderWrapper implementation which caches the state of the
delegate (including and other ReaderWrapper instances)
after Memoizer.setId(String) has been called.MicromanagerReader is the file format reader for Micro-Manager files.
MinimalTiffReader is the superclass for file format readers compatible with
or derived from the TIFF 6.0 file format.
Logic to compute minimum and maximum values for each channel.
Methods for compressing and decompressing QuickTime Motion JPEG-B data.
Options for compressing and decompressing MJPB data.
MNGReader is the file format reader for Multiple-image Network Graphics
(MNG) files.
Methods for compressing and decompressing data using Microsoft RLE.
Methods for compressing and decompressing data using Microsoft Video 1.
This class implements Nikon decompression.
Options for compressing and decompressing Nikon NEF data.
A file filter that selects files with no extension,
for use with a JFileChooser.
File format reader for NRRD files; see http://teem.sourceforge.net/nrrd.
NumberFilter is a helper filter for FilePattern.findPattern().
OBFReader is the file format reader for Imspector OBF files.
OMETiffReader is the file format reader for
OME-TIFF
files.
OMETiffWriter is the file format writer for OME-TIFF files.
OMEXMLReader is the file format reader for OME-XML files.
OMEXMLWriter is the file format writer for OME-XML files.
This class implements packbits decompression.
A codec which just returns the exact data it was given, performing no
compression or decompression.
PCXReader is the file format reader for PCX files (originally used by
PC Paintbrush; now used in Zeiss' LSM Image Browser).
PGMReader is the file format reader for Portable Gray Map (PGM) images.
Utility class for working with TIFF photometric interpretations.
PictReader is the file format reader for Apple PICT files.
PreviewPane is a panel for use as a JFileChooser accessory, displaying
a thumbnail for the selected image, loaded in a separate thread.
PyramidOMETiffWriter is the file format writer for pyramid OME-TIFF files.
QTReader is the file format reader for QuickTime movie files.
Methods for compressing and decompressing data using QuickTime RLE.
QTWriter is the file format writer for uncompressed QuickTime movie files.
A rectangle strategy caches planes extending from the the current
dimensional position along each axis and combination of axes.
Utility class helping with generating human-readable resource names
based on alphanumeric indexing.
Implements encoding and decoding methods for Apple RPZA.
DataBuffer that stores signed bytes.
ColorModel that handles 8, 16 and 32 bits per channel signed data.
DataBuffer that stores signed shorts.
Extends
CoreMetadata to include the notion of an "input order" for planes:
the input order being the order planes are stored on disk.This class implements Targa RLE decompression.
Reader for text files containing tables of data.
Utility class for performing compression operations with a TIFF file.
Generally useful TIFF-related constants.
TiffDelegateReader is a file format reader for TIFF files.
This class represents a single raw TIFF IFD entry.
TiffJAIReader is a file format reader for TIFF images.
Parses TIFF data from an input source.
A rational number (numerator over denominator).
TiffReader is the file format reader for regular TIFF files,
not of any specific TIFF variant.
Parses TIFF data from an input source.
TiffWriter is the file format writer for TIFF files.
Reader for decoding JPEG images using java.awt.Toolkit and TurboJPEG.
ColorSpace for 2-channel images.
DataBuffer that stores unsigned ints.
ColorModel that handles unsigned 32 bit data.
Utility that checks for a new stable version, and optionally installs
a new version of Bio-Formats ueber tools.
Class that allows checking for new versions of Bio-Formats, as well as
updating to the latest stable, daily, or trunk version.
V3DrawWriter writes images in the .v3draw format for rapid I/O in Vaa3D, an open-source 3D visualization and
analysis toolkit.
A tree cell renderer for displaying syntax highlighted XML in a JTree.
A window containing syntax highlighted XML as a tree.
Reader for Zip files.
This class implements ZLIB decompression.