4.1 (2009 October 21): * Fixed many bugs in most file format readers * Significantly improved confocal and HCS metadata parsing * Improved C++ bindings * Eliminated references to Java AWT classes in core Bio-Formats packages * Added support for reading Flex datasets from multiple servers * Improved OME-XML generation; generated OME-XML is now valid * Added support for Olympus ScanR data * Added OSGi information to JARs * Added support for Amira Mesh files * Added support for LI-FLIM files * Added more informative exceptions * Added support for various types of ICS lifetime data * Added support for Nikon EZ-C1 TIFFs * Added support for Maia Scientific MIAS data 4.0.1 (2009 June 1): * Lots of bug fixes in most format readers and writers * Added support for Analyze 7.1 files * Added support for Nifti files * Added support for Cellomics .c01 files * Refactored ImageJ plugins * Bio-Formats, the common package, and the ImageJ plugins now require Java 1.5 * Eliminated native library dependency for reading lossless JPEGs * Changed license from GPL v3 or later to GPL v2 or later * Updated Olympus FV1000, Zeiss LSM, Zeiss ZVI and Nikon ND2 readers to parse ROI data * Added option to ImageJ plugin for displaying ROIs parsed from the chosen dataset * Fixed BufferedImage construction for signed data and unsigned int data 4.0.0 (2009 March 3): * Improved OME data model population for Olympus FV1000, Nikon ND2, Metamorph STK, Leica LEI, Leica LIF, InCell 1000 and MicroManager * Added TestNG tests for format writers * Added option to ImageJ plugin to specify custom colors when customizing channels * Added ability to upgrade the ImageJ plugin from within ImageJ * Fixed bugs in Nikon ND2, Leica LIF, BioRad PIC, TIFF, PSD, and OME-TIFF * Fixed bugs in Data Browser and Exporter plugins * Added support for Axon Raw Format (ARF), courtesy of Johannes Schindelin * Added preliminary support for IPLab-Mac file format 2008 December 29: * Improved metadata support for Deltavision, Zeiss LSM, MicroManager, and Leica LEI * Restructured code base/build system to be component-driven * Added support for JPEG and JPEG-2000 codecs within TIFF, OME-TIFF and OME-XML * Added support for 16-bit compressed Flex files * Added support for writing JPEG-2000 files * Added support for Minolta MRW format * Added support for the 2008-09 release of OME-XML * Removed dependency on JMagick * Re-added caching support to data browser plugin * Updated loci.formats.Codec API to be more user-friendly * Expanded loci.formats.MetadataStore API to better represent the OME-XML model * Improved support for Nikon NEF * Improved support for TillVision files * Improved ImageJ import options dialog * Fixed bugs with Zeiss LSM files larger than 4 GB * Fixed minor bugs in most readers * Fixed bugs with exporting from an Image5D window * Fixed several problems with virtual stacks in ImageJ 2008 August 30: * Fixed bugs in many file format readers * Fixed several bugs with swapping dimensions * Added support for Olympus CellR/APL files * Added support for MINC MRI files * Added support for Aperio SVS files compressed with JPEG 2000 * Added support for writing OME-XML files * Added support for writing APNG files * Added faster LZW codec * Added drag and drop support to ImageJ shortcut window * Re-integrated caching into the data browser plugin 2008 July 1: * Fixed bugs in most file format readers * Fixed bugs in OME and OMERO download functionality * Fixed bugs in OME server-side import * Improved metadata storage/retrieval when uploading to and downloading from the OME Perl server * Improved Bio-Formats ImageJ macro extensions * Major updates to MetadataStore API * Updated OME-XML generation to use 2008-02 schema by default * Addressed time and memory performance issues in many readers * Changed license from LGPL to GPL * Added support for the FEI file format * Added support for uncompressed Hamamatsu Aquacosmos NAF files * Added support for Animated PNG files * Added several new options to Bio-Formats ImageJ plugin * Added support for writing ICS files 2008 April 17: * Fixed bugs in Slidebook, ND2, FV1000 OIB/OIF, Perkin Elmer, TIFF, Prairie, Openlab, Zeiss LSM, MNG, Molecular Dynamics GEL, and OME-TIFF * Fixed bugs in OME and OMERO download functionality * Fixed bugs in OME server-side import * Fixed bugs in Data Browser * Added support for downloading from OMERO 2.3 servers * Added configuration plugin * Updates to MetadataStore API * Updates to OME-XML generation - 2007-06 schema used by default * Added support for Li-Cor L2D format * Major updates to TestNG testing framework * Added support for writing multi-series OME-TIFF files * Added support for writing BigTIFF files 2008 Feb 12: * Fixed bugs in QuickTime, SimplePCI and DICOM * Fixed a bug in channel splitting logic 2008 Feb 8: * Many critical bugfixes in format readers and ImageJ plugins * Newly reborn Data Browser for 5D image visualization + some combinations of import options do not work yet 2008 Feb 1: * Fixed bugs in Zeiss LSM, Metamorph STK, FV1000 OIB/OIF, Leica LEI, TIFF, Zeiss ZVI, ICS, Prairie, Openlab LIFF, Gatan, DICOM, QuickTime * Fixed bug in OME-TIFF writer * Major changes to MetadataStore API * Added support for JPEG-compressed TIFF files * Added basic support for Aperio SVS files + JPEG2000 compression is still not supported * Improved "crop on import" functionality * Improvements to bfconvert and bfview * Improved OME-XML population for several formats * Added support for JPEG2000-compressed DICOM files * EXIF data is now parsed from TIFF files 2007 Dec 28: * Fixed bugs in Leica LEI, Leica TCS, SDT, Leica LIF, Visitech, DICOM, Imaris 5.5 (HDF), and Slidebook readers * Better parsing of comments in TIFF files exported from ImageJ * Fixed problem with exporting 48-bit RGB data * Added logic to read multi-series datasets spread across multiple files * Improved channel merging in ImageJ - requires ImageJ 1.39l * Support for hyperstacks and virtual stacks in ImageJ - requires ImageJ 1.39l * Added API for reading directly from a byte array or InputStream * Metadata key/value pairs are now stored in ImageJ's "Info" property * Improved OMERO download plugin - it is now much faster * Added "open all series" option to ImageJ importer * ND2 reader based on Nikon's SDK now uses our own native bindings * Fixed metadata saving bug in ImageJ * Added sub-channel labels to ImageJ windows * Major updates to 4D Data Browser * Minor updates to automated testing suite 2007 Dec 1: * Updated OME plugin for ImageJ to support downloading from OMERO * Fixed bug with floating point TIFFs * Fixed bugs in Visitech, Zeiss LSM, Imaris 5.5 (HDF) * Added alternate ND2 reader that uses Nikon's native libraries * Fixed calibration and series name settings in importer * Added basic support for InCell 1000 datasets 2007 Nov 21: * Fixed bugs in ND2, Leica LIF, DICOM, Zeiss ZVI, Zeiss LSM, FV1000 OIB, FV1000 OIF, BMP, Evotec Flex, BioRad PIC, Slidebook, TIFF * Added new ImageJ plugins to slice stacks and do "smart" RGB merging * Added "windowless" importer plugin + uses import parameters from IJ_Prefs.txt, without prompting the user * Improved stack slicing and colorizing logic in importer plugin * Added support for DICOM files compressed with lossless JPEG + requires native libraries * Fixed bugs with signed pixel data * Added support for Imaris 5.5 (HDF) files * Added 4 channel merging to importer plugin * Added API methods for reading subimages * Major updates to the 4D Data Browser 2007 Oct 17: * Critical OME-TIFF bugfixes * Fixed bugs in Leica LIF, Zeiss ZVI, TIFF, DICOM, and AVI readers * Added support for JPEG-compressed ZVI images * Added support for BigTIFF * Added importer plugin option to open each plane in a new window * Added MS Video 1 codec for AVI 2007 Oct 1: * Added support for compressed DICOM images * Added support for uncompressed LIM files * Added support for Adobe Photoshop PSD files * Fixed bugs in DICOM, OME-TIFF, Leica LIF, Zeiss ZVI, Visitech, PerkinElmer and Metamorph * Improved indexed color support * Addressed several efficiency issues * Fixed how multiple series are handled in 4D data browser * Added option to reorder stacks in importer plugin * Added option to turn off autoscaling in importer plugin * Additional metadata convenience methods 2007 Sept 11: * Major improvements to ND2 support; lossless compression now supported * Support for indexed color images * Added support for Simple-PCI .cxd files * Command-line OME-XML validation * Bugfixes in most readers, especially Zeiss ZVI, Metamorph, PerkinElmer and Leica LEI * Initial version of Bio-Formats macro extensions for ImageJ 2007 Aug 1: * Added support for latest version of Leica LIF * Fixed several issues with Leica LIF, Zeiss ZVI * Better metadata mapping for Zeiss ZVI * Added OME-TIFF writer * Added MetadataRetrieve API for retrieving data from a MetadataStore * Miscellaneous bugfixes 2007 July 16: * Fixed several issues with ImageJ plugins * Better support for Improvision and Leica TCS TIFF files * Minor improvements to Leica LIF, ICS, QuickTime and Zeiss ZVI readers * Added searchable metadata window to ImageJ importer 2007 July 2: * Fixed issues with ND2, Openlab LIFF and Slidebook * Added support for Visitech XYS * Added composite stack support to ImageJ importer 2007 June 18: * Fixed issues with ICS, ND2, MicroManager, Leica LEI, and FV1000 OIF * Added support for large (> 2 GB) ND2 files * Added support for new version of ND2 * Minor enhancements to ImageJ importer * Implemented more flexible logging * Updated automated testing framework to use TestNG * Added package for caching images produced by Bio-Formats 2007 June 6: * Fixed OME upload/download bugs * Fixed issues with ND2, EPS, Leica LIF, and OIF * Added support for Khoros XV * Minor improvements to the importer 2007 May 24: * Better Slidebook support * Added support for Quicktime RPZA * Better Leica LIF metadata parsing * Added support for BioRad PIC companion files * Added support for bzip2-compressed files * Improved ImageJ plugins * Native support for FITS and PGM 2007 May 2: * Added support for NRRD * Added support for Evotec Flex (requires LuraWave Java SDK with license code) * Added support for gzip-compressed files * Added support for compressed QuickTime headers * Fixed QuickTime Motion JPEG-B support * Fixed some memory issues (repeated small array allocations) * Fixed issues reading large (> 2 GB) files * Removed "ignore color table" logic, and replaced with Leica-specific solution * Added status event reporting to readers * Added API to toggle metadata collection * Support for multiple dimensions rasterized into channels * Deprecated reader and writer methods that accept the 'id' parameter * Deprecated IFormatWriter.save in favor of saveImage and saveBytes * Moved dimension swapping and min/max calculation logic to delegates * Separate GUI logic into isolated loci.formats.gui package * Miscellaneous bugfixes and tweaks in most readers and writers * Many other bugfixes and improvements 2007 Mar 16: * Fixed calibration bugs in importer plugin * Enhanced metadata support for additional formats * Fixed LSM bug 2007 Mar 7: * Added support for Micro-Manager file format * Fixed several bugs -- Leica LIF, Leica LEI, ICS, ND2, and others * Enhanced metadata support for several formats * Load series preview thumbnails in the background * Better implementation of openBytes(String, int, byte[]) for most readers * Expanded unit testing framework 2007 Feb 28: * Better series preview thumbnails * Fixed bugs with multi-channel Leica LEI * Fixed bugs with "ignore color tables" option in ImageJ plugin 2007 Feb 26: * Many bugfixes: Leica LEI, ICS, FV1000 OIB, OME-XML and others * Better metadata parsing for BioRad PIC files * Enhanced API for calculating channel minimum and maximum values * Expanded MetadataStore API to include more semantic types * Added thumbnails to series chooser in ImageJ plugin * Fixed plugins that upload and download from an OME server 2007 Feb 7: * Added plugin for downloading images from OME server * Improved HTTP import functionality * Added metadata filtering -- unreadable metadata is no longer shown * Better metadata table for multi-series datasets * Added support for calibration information in Gatan DM3 * Eliminated need to install JAI Image I/O Tools to read ND2 files * Fixed ZVI bugs: metadata truncation, and other problems * Fixed bugs in Leica LIF: incorrect calibration, first series labeling * Fixed memory bug in Zeiss LSM * Many bugfixes: PerkinElmer, Deltavision, Leica LEI, LSM, ND2, and others * IFormatReader.close(boolean) method to close files temporarily * Replaced Compression utility class with extensible Compressor interface * Improved testing framework to use .bioformats configuration files 2007 Jan 5: * Added support for Prairie TIFF * Fixed bugs in Zeiss LSM, OIB, OIF, and ND2 * Improved API for writing files * Added feature to read files over HTTP * Fixed bugs in automated testing framework * Miscellaneous bugfixes 2006 Dec 22: * Expanded ImageJ plugin to optionally use Image5D or View5D * Improved support for ND2 and JPEG-2000 files * Added automated testing framework * Fixed bugs in Zeiss ZVI reader * Miscellaneous bugfixes 2006 Nov 30: * Added support for ND2/JPEG-2000 * Added support for MRC * Added support for MNG * Improved support for floating-point images * Fixed problem with 2-channel Leica LIF data * Minor tweaks and bugfixes in many readers * Improved file stitching logic * Allow ImageJ plugin to be called from a macro 2006 Nov 2: * Bugfixes and improvements for Leica LIF, Zeiss LSM, OIF and OIB * Colorize channels when they are split into separate windows * Fixed a bug with 4-channel datasets 2006 Oct 31: * Added support for Imaris 5 files * Added support for RGB ICS images 2006 Oct 30: * Added support for tiled TIFFs * Fixed bugs in ICS reader * Fixed importer plugin deadlock on some systems 2006 Oct 27: * Multi-series support for Slidebook * Added support for Alicona AL3D * Fixed plane ordering issue with FV1000 OIB * Enhanced dimension detection in FV1000 OIF * Added preliminary support for reading NEF images * Added option to ignore color tables * Fixed ImageJ GUI problems * Fixed spatial calibration problem in ImageJ * Fixed some lingering bugs in Zeiss ZVI support * Fixed bugs in OME-XML reader * Tweaked ICS floating-point logic * Fixed memory leaks in all readers * Better file stitching logic 2006 Oct 6: * Support for 3i SlideBook format (single series only for now) * Support for 16-bit RGB palette TIFF * Fixed bug preventing import of certain Metamorph STK files * Fixed some bugs in PerkinElmer UltraView support * Fixed some bugs in Leica LEI support * Fixed a bug in Zeiss ZVI support * Fixed bugs in Zeiss LSM support * Fixed a bug causing slow identification of Leica datasets * Fixed bugs in the channel merging logic * Fixed memory leak for OIB format * Better scaling of 48-bit RGB data to 24-bit RGB * Fixed duplicate channels bug in "open each channel in a separate window" * Fixed a bug preventing PICT import into ImageJ * Better integration with HandleExtraFileTypes * Better virtual stack support in Data Browser plugin * Fixed bug in native QuickTime random access * Keep aspect ratio for computed thumbnails * Much faster file stitching logic 2006 Sep 27: * PerkinElmer: support for PE UltraView * Openlab LIFF: support for Openlab v5 * Leica LEI: bugfixes, and support for multiple series * ZVI, OIB, IPW: more robust handling of these formats (eliminated custom OLE parsing logic in favor of Apache POI) * OIB: better metadata parsing (but maybe still not perfect?) * LSM: fixed a bug preventing import of certain LSMs * Metamorph STK: fixed a bug resulting in duplicate image planes * User interface: use of system look & feel for file chooser dialog when available * Better notification when JAR libraries are missing 2006 Sep 6: * Leica LIF: multiple distinct image series within a single file * Zeiss ZVI: fixes and improvements contributed by Michel Boudinot * Zeiss LSM: fixed bugs preventing the import of certain LSM files * TIFF: fixed a bug preventing import of TIFFs created with Bio-Rad software 2006 Mar 31: * First release