Version history =============== 5.1.10 (2016 May 9) ------------------- Java bug fixes: * fixed warnings being thrown for ImageJ and other non-FIJI users on Windows (these warnings were triggered by the removal of the 3i Slidebook DLLs from the source code repository in Bio-Formats 5.1.9 and should now only be triggered when opening Slidebook files without the update site enabled - http://www.openmicroscopy.org/info/slidebook) * a fix in the ImageJ plugin for files grouped using the "Dimensions" option * a fix for writing TIFF files in tiles 5.1.9 (2016 April 14) --------------------- * Java bug fixes, including: - SDT - fixed width padding calculation for single-pixel image - Deltavision - fixed the parsing of the new date format - added support for parsing and storing the working distance in native units - Micromanager - cleaned up JSON metadata parsing - Olympus Fluoview - fixed null pointer exceptions while parsing metadata - Leica LIF - fixed large multi-tiled files from having incorrect plane offsets after the 2GB mark - EM formats (MRC and Spider) - added native length support for EM readers - Gatan - fixed erroneous metadata parsing - added support for parsing and storing the physical sizes in native units - OME-TIFF - improved handling of OME-TIFF multi-file fileset’s with partial metadata blocks - Nikon ND2 - fixed the parsing of emission wavelength - Olympus CellR (APL) - fixed multiple parsing issues with the mtb file - SlideBook - removed slidebook dlls from Bio-Formats repository - http://www.openmicroscopy.org/info/slidebook - Zeiss CZI - fixed parsing of files with multiple mosaics and positions * Documentation updates, including: - improved documentation for the export of BigTIFFs in ImageJ * C++: - no changes. 5.1.8 (2016 February 15) ------------------------ * Java bug fixes, including: - FEI TIFF - fixed stage position parsing and whitespace handling (thanks to Antoine Vandecreme) - Pyramid TIFF - fixed tile reading when a cache (.bfmemo) file is present - MicroManager - updated to parse JSON data from tags 50839 and 51123 - fixed to detect :file:`*_metadata.txt` files in addition to :file:`metadata.txt` files - fixed to handle datasets with each stack in a single file - OME-XML - updated to make .ome.xml an official extension - OME-TIFF - fixed to ignore invalid BinaryOnly elements - TIFF - fixed caching of BigTIFF files - Slidebook - fixed handling of montages in Slidebook6Reader (thanks to Richard Myers) - Performance improvement for writing files to disk (thanks to Stephane Dallongeville) - Build system - fixed Maven POMs to reduce calls to artifacts.openmicroscopy.org - fixed bioformats_package.jar to include the loci.formats.tools package * Documentation updates, including: - updated format pages to include links to example data - clarified description of Qu for MATLAB (thanks to Carnë Draug) - added installation instructions for Octave (thanks to Carnë Draug) * C++: - Bugfixes to the OME-TIFF writer to correct use of the metadata store with multiple series - Ensure file and writer state consistency upon close failure 5.1.7 (2015 December 7) ----------------------- * Java bug fixes, including: - Prevent physical pixel sizes from being rounded to 0, for all formats - Metamorph - fixed calculation of Z step size - fixed detection of post-processed dual camera acquisitions (thanks to Mark Kittisopikul) - OME-XML - fixed XML validation when an 'xmlns' value is not present (thanks to Bjoern Thiel) - MINC - fixed endianness of image data - Andor/Fluoview TIFF - fixed calculation of Z step size - MATLAB - improved performance by reducing static classpath checks (thanks to Mark Kittisopikul) - Gatan - fixed physical size parsing in non-English locales - Automated testing - fixed handling of non-default physical size and plane position units * Documentation updates, including: - updated MapAnnotation example to show linkage of annotations to images * C++: - no changes, released to keep version numbers in sync with Bio-Formats Java 5.1.6 (2015 November 16) ------------------------ * Java bug fixes, including: - Updated to use native units for following formats: - IMOD - Analyze - Unisoku - Olympus CellR (APL) - Metamorph TIFF - fixed handling of multi-line descriptions - added support for dual camera acquisitions - Zeiss LMS - fixed exception in type detection - Zeiss CZI - fixed detection of line scan Airyscan data - Slidebook - fixed calculation of physical Z size - ImageJ plugins - fixed handling of non-default units - fixed setting of preferences via macros - Automated testing - fixed handling of non-default units for physical sizes and timings * C++ changes, including: - allow relocatable installation on Windows - reduce time required for debug builds * Documentation updates, including: - addition of "Multiple Images" column to the supported formats table - addition of a MapAnnotation example 5.1.5 (2015 October 12) ----------------------- * Java bug fixes, including: - ImageJ plugins - fixed use of "Group files..." and "Open files individually" options - fixed placement of ROIs - fixed size of the "About Plugins > Bio-Formats Plugins" window - xsd-fu (code generation) - removed OMERO-specific logic - Metamorph - fixed physical Z size calculation - Gatan DM3/DM4 - fixed physical pixel size parsing - BMP - added support for RLE compression - DICOM - updated to respect the WINDOW_CENTER tag - fixed image dimensions when multiple sets of width and height values are present - Fluoview and Andor TIFF - fixed physical Z size calculation - Imspector OBF - updated to parse OME-XML metadata (thanks to Bjoern Thiel) * C++ changes: - TIFF strip/tile row and column calulations corrected to compute the correct row and column count - Several compiler warnings removed (false positive warnings in third-party headers disabled, and additional warnings fixed) - It is now possible to build with Boost 1.59 and compile with a C++14 compiler * The source release is now provided in both tar.xz and zip formats * Documentation updates, including: - substantial updates to the format pages - improved linking of reader/writer classes to each format page - improved supported metadata pages for each format - updated format page formatting for clarity - added developer documentation for adding and modifying format pages 5.1.4 (2015 September 7) ------------------------ * Bug fixes, including: - Command line tools - fixed display of usage information - Automated testing - fixed problems with symlinked data on Windows - added unit tests for checking physical pixel size creation - Cellomics - fixed reading of sparse plates - SlideBook - fixed a few lingering issues with native library packaging - SimplePCI/HCImage TIFF - fixed bit depth parsing for files from newer versions of HCImage - SimplePCI/HCImage .cxd - fixed image dimensions to allow for extra padding bytes - Leica LIF - improved reading of image descriptions - ICS - fixed to use correct units for timestamps and physical pixel sizes - MicroManager - fixed to use correct units for timestamps - Gatan .dm3/.dm4 - fixed problems with reading double-precision metadata values - Hamamatsu NDPI - fixed reading of mask images - Leica .lei - fixed reading of bit depth and endianness for datasets that were modified after acquisition - FEI TIFF - updated to read metadata from files produced by FEI Titan systems - QuickTime - fixed to handle planes with no stored pixels - Leica .scn - fixed reading of files that contain fewer images than expected - Zeiss .czi - fixed channel colors when an alpha value is not recorded - fixed handling of pre-stitched image tiles - SDT - added support for Zip-compressed images - Nikon .nd2 - fixed to read image dimensions from new non-XML metadata - OME-XML - fixed writing of integer metadata values * Native C++ updates: - completed support for building on Windows * Documentation updates, including: - updated instructions for running automated data tests - clarified JVM versions currently supported 5.1.3 (2015 July 21) -------------------- * Native C++ updates: - Added cmake superbuild to build core dependencies (zlib, bzip2, png, icu, xerces, boost) - Progress on support for Windows * Bug fixes, including: - Fixed segfault in the `showinf` tool used with the C++ bindings - Allow reading from https URLs - ImageJ - improved performance of displaying ROIs - Command line tools - fixed bfconvert to correctly create datasets with multiple files - Metamorph - improved detection of time series - fixed .nd datasets with variable Z and T counts in each channel - fixed .nd datasets that contain invalid TIFF/STK files - fixed dimensions when the number of planes does not match the recorded Z, C, and T sizes - SlideBook - improved native library detection (thanks to Richard Myers) - JPEG - fixed decompression of lossless files with multiple channels (thanks to Aaron Avery) - Imspector OBF - updated to support version 2 files (thanks to Bjoern Thiel) - Imspector MSR - improved detection of Z stacks - PerkinElmer Opera Flex - improved handling of multiple acquisitions of the same plate - Zeiss CZI - fixed error when opening single-file datasets whose names contained "(" and ")" - TIFF - improved speed of reading files with many tiles - AVI - updated to read frame index (idx1) tables - Nikon ND2 - fixed channel counts for files with more than 3 channels - PNG - fixed decoding of interlaced images with a width or height that is not a multiple of 8 - PSD - improved reading of compressed images * Documentation improvements, including: - updated instructions for writing a new file format reader - updated usage information for command line tools - new Javadocs for the `MetadataStore` and `MetadataRetrieve` interfaces 5.1.2 (2015 May 28) ------------------- * Added OME-TIFF writing support to the native C++ implementation * OME-TIFF export: switch to BigTIFF if .ome.tf2, .ome.tf8, or .ome.btf extensions are used * Improved MATLAB developer documentation * Added SlideBook reader that uses the SDK from 3I (thanks to Richard Myers and `3I - Intelligent Imaging Innovations `_) * Preliminary work to make MATLAB toolbox work with Octave * Many bug fixes, including: - ImageJ - fixed regression in getPlanePosition* macro extension methods - fixed display of composite color virtual stacks - Nikon ND2 - improved parsing of plane position and timestamp data - TIFF - reduced memory required to read color lookup tables - Zeiss LSM - improved parsing of 16-bit color lookup tables - Zeiss CZI - fixed ordering of original metadata table - fixed reading of large pre-stitched tiled images - AIM - fixed handling of truncated files - Metamorph/MetaXpress TIFF - improved UIC1 metadata tag parsing 5.1.1 (2015 April 28) --------------------- * Add TIFF writing support to the native C++ implementation * Fixed remaining functional differences between Windows and Mac/Linux * Improved performance of ImageJ plugin when working with ROIs * TIFF export: switch to BigTIFF if .tf2, .tf8, or .btf extensions are used * Many bug fixes, including: - fixed upgrade checking to more accurately report when a new version is available - Zeiss CZI - fixed ordering of multiposition data - improved support for RGB and fused images - Nikon ND2 - improved ordering of multiposition data - Leica LIF - improved metadata validity checks - improved excitation wavelength detection - Metamorph STK/TIFF - record lens numerical aperture - fixed millisecond values in timestamps - Gatan DM3 - correctly detect signed pixel data - Imaris HDF - fix channel count detection - ICS export - fix writing of files larger than 2GB 5.1.0 (2015 April 2) --------------------- * Improvements to performance with network file systems * Improvements to developer documentation * Initial version of :doc:`native C++ implementation ` * Improved support for opening and saving ROI data with ImageJ * Added support for :doc:`CellH5 ` data (thanks to Christophe Sommer) * Added support for :doc:`Perkin Elmer Nuance ` data (thanks to Lee Kamentsky) * Added support for :doc:`Amnis FlowSight ` data (thanks to Lee Kamentsky and Sebastien Simard) * Added support for :doc:`Veeco AFM ` data * Added support for :doc:`Zeiss .lms ` data (not to be confused with .lsm) * Added support for :doc:`I2I ` data * Added support for writing Vaa3D data (thanks to Brian Long) * Updated to :model_doc:`OME schema 2015-01 ` * Update RandomAccessInputStream and RandomAccessOutputStream to read and write bits * Many bug fixes, including: - Leica SCN - fix pixel data decompression - fix handling of files with multiple channels - parse magnification and physical pixel size data - Olympus/CellSens .vsi - more thorough parsing of metadata - improved reading of thumbnails and multi-resolution images - NDPI - fix reading of files larger than 4GB - parse magnification data - Zeiss CZI - improve parsing of plane position coordinates - Inveon - fix reading of files larger than 2 GB - Nikon ND2 - many improvements to dimension detection - many improvements to metadata parsing accuracy - update original metadata table to include PFS data - Gatan DM3 - fix encoding when parsing metadata - fix physical pixel size parsing - Metamorph - fix off-by-one in metadata parsing - fix number parsing to be independent of the system locale - JPEG - parse EXIF data, if present (thanks to Paul Van Schayck) - OME-XML/OME-TIFF - fix handling of missing image data - PrairieView - improved support for version 5.2 data (thanks to Curtis Rueden) - DICOM - fix dimensions for multi-file datasets - fix pixel data decoding for files with multiple images - PNG - reduce memory required to read large images - Imspector OBF - fix support for version 5 data (thanks to Bjoern Thiel) - PCORAW - fix reading of files larger than 4 GB - AIM - fix reading of files larger than 4 GB - MRC - add support for signed 8-bit data - Fix build errors in MIPAV plugin - ImageJ - fix export from a script/macro - fix windowless export - allow exporting from any open image window - allow the "Group files with similar names" and "Swap dimensions" options to be used from a script/macro - bfconvert - fix writing each channel, Z section, and/or timepoint to a separate file - add options for configuring the tile size to be used when saving images 5.0.8 (2015 February 10) ------------------------ * No changes - release to keep version numbers in sync with OMERO 5.0.7 (2015 February 5) ----------------------- * Several bug fixes, including: - ND filter parsing for DeltaVision - Timepoint count and original metadata parsing for Metamorph - Build issues when Genshi or Git are missing - LZW image decoding 5.0.6 (2014 November 11) ------------------------ * Several bug fixes, including: - Pixel sign for DICOM images - Image dimensions for Zeiss CZI and Nikon ND2 - Support for Leica LIF files produced by LAS AF 4.0 and later 5.0.5 (2014 September 23) ------------------------- * Documentation improvements * Support for non-spectral Prairie 5.2 datasets 5.0.4 (2014 September 3) ------------------------ * Fix compile and runtime errors under Java 1.8 * Improvements to Nikon .nd2 metadata parsing * Added support for PicoQuant .bin files (thanks to Ian Munro) 5.0.3 (2014 August 7) --------------------- * Many bug fixes for Nikon .nd2 files * Several other bug fixes, including: - LZW image decoding - Stage position parsing for Zeiss CZI - Exposure time units for ScanR - Physical pixel size units for DICOM - NDPI and Zeiss LSM files larger than 4GB - Z and T dimensions for InCell 6000 plates - Export of RGB images in ImageJ * Improved metadata saving in MATLAB functions 5.0.2 (2014 May 28) ------------------- * Many bug fixes for Zeiss .czi files * Several other bug fixes, including: - Gatan .dm3 units and step count parsing - Imspector .msr 5D image support - DICOM reading of nested tags * Update native-lib-loader version (to 2.0.1) * Updates and improvements to user documentation 5.0.1 (2014 Apr 7) ------------------ * Added image pyramid support for CellSens .vsi data * Several bug fixes, including: - Woolz import into OMERO - Cellomics file name parsing (thanks to Lee Kamentsky) - Olympus FV1000 timestamp support (thanks to Lewis Kraft and Patrick Riley) - (A)PNG large image support - Zeiss .czi dimension detection for SPIM datasets * Performance improvements for Becker & Hickl .sdt file reading (thanks to Ian Munro) * Performance improvements to directory listing over NFS * Update slf4j and logback versions (to 1.7.6 and 1.1.1 respectively) * Update jgoodies-forms version (to 1.7.2) 5.0.0 (2014 Feb 25) ------------------- * New bundled 'bioformats_package.jar' for ImageJ * Now uses logback as the slf4j binding by default * Updated component names, .jar file names, and Maven artifact names * Fixed support for Becker & Hickl .sdt files with multiple blocks * Fixed tiling support for TIFF, Hamamatsu .ndpi, JPEG, and Zeiss .czi files * Improved continuous integration testing * Updated :doc:`command line documentation ` 5.0.0-RC1 (2013 Dec 19) ----------------------- * Updated Maven build system and launched new Artifactory repository (http://artifacts.openmicroscopy.org) * Added support for: - :doc:`Bio-Rad SCN ` - :doc:`Yokogawa CellVoyager ` (thanks to Jean-Yves Tinevez) - :doc:`LaVision Imspector ` - :doc:`PCORAW ` - :doc:`Woolz ` (thanks to Bill Hill) * Added support for populating and parsing ModuloAlong{Z, C, T} annotations for FLIM/SPIM data * Updated netCDF and slf4j version requirements - netCDF 4.3.19 and slf4j 1.7.2 are now required * Updated and improved :doc:`MATLAB users ` and :doc:`developers ` documentation * Many bug fixes including for Nikon ND2, Zeiss CZI, and CellWorX formats 5.0.0-beta1 (2013 June 20) -------------------------- * Updated to :model_doc:`2013-06 OME-XML schema <>` * Improved the performance in tiled formats * Added caching of Reader metadata using http://code.google.com/p/kryo/ * Added support for: - :doc:`Aperio AFI ` - :doc:`Inveon ` - :doc:`MPI-BPC Imspector ` * Many bug fixes, including: - Add ZEN 2012/Lightsheet support to Zeiss CZI - Improved testing of autogenerated code - Moved OME-XML specification into Bio-Formats repository 4.4.10 (2014 Jan 15) -------------------- * Bug fixes including CellWorx, Metamorph and Zeiss CZI * Updates to MATLAB documentation 4.4.9 (2013 Oct 16) ------------------- * Many bug fixes including improvements to support for ND2 format * Java 1.6 is now the minimum supported version; Java 1.5 is no longer supported 4.4.8 (2013 May 2) ------------------ * No changes - release to keep version numbers in sync with OMERO 4.4.7 (2013 April 25) --------------------- * Many bug fixes to improve support for more than 20 formats * Improved export to multi-file datasets * Now uses slf4j for logging rather than using log4j directly, enabling other logging implementations to be used, for example when Bio-Formats is used as a component in other software using a different logging system. 4.4.6 (2013 February 11) ------------------------ * Many bug fixes * Further documentation improvements 4.4.5 (2012 November 13) ------------------------ * Restructured and improved documentation * Many bug fixes, including: - File grouping in many multi-file formats - Maven build fixes - ITK plugin fixes 4.4.4 (2012 September 24) ------------------------- * Many bug fixes 4.4.2 (2012 August 22) ---------------------- * Security fix for OMERO plugins for ImageJ 4.4.1 (2012 July 20) -------------------- * Fix a bug that prevented BigTIFF files from being read * Fix a bug that prevented PerkinElmer .flex files from importing into OMERO 4.4.0 (2012 July 13) -------------------- * Many, many bug fixes * Added support for: - .nd2 files from Nikon Elements version 4 - PerkinElmer Operetta data - MJPEG-compressed AVIs - MicroManager datasets with multiple positions - Zeiss CZI data - IMOD data 4.3.3 (2011 October 18) ----------------------- * Many bug fixes, including: - Speed improvements to HCImage/SimplePCI and Zeiss ZVI files - Reduce memory required by Leica LIF reader - More accurately populate metadata for Prairie TIFF datasets - Various fixes to improve the security of the OMERO plugin for ImageJ - Better dimension detection for Bruker MRI datasets - Better thumbnail generation for histology (SVS, NDPI) datasets - Fix stage position parsing for Metamorph TIFF datasets - Correctly populate the channel name for PerkinElmer Flex files 4.3.2 (2011 September 15) ------------------------- * Many bug fixes, including: - Better support for Volocity datasets that contain compressed data - More accurate parsing of ICS metadata - More accurate parsing of cellSens .vsi files * Added support for a few new formats - .inr - Canon DNG - Hitachi S-4800 - Kodak .bip - JPX - Volocity Library Clipping (.acff) - Bruker MRI * Updated Zeiss LSM reader to parse application tags * Various performance improvements, particularly for reading/writing TIFFs * Updated OMERO ImageJ plugin to work with OMERO 4.3.x 4.3.1 (2011 July 8) ------------------- * Several bug fixes, including: - Fixes for multi-position DeltaVision files - Fixes for MicroManager 1.4 data - Fixes for 12 and 14-bit JPEG-2000 data - Various fixes for reading Volocity .mvd2 datasets * Added various options to the 'showinf' and 'bfconvert' command line tools * Added better tests for OME-XML backwards compatibility * Added the ability to roughly stitch tiles in a multi-position dataset 4.3.0 (2011 June 14) -------------------- * Many bug fixes, including: - Many fixes for reading and writing sub-images - Fixes for stage position parsing in the Zeiss formats - File type detection fixes * Updated JPEG-2000 reading and writing support to be more flexible * Added support for 9 new formats: - InCell 3000 - Trestle - Hamamatsu .ndpi - Hamamatsu VMS - SPIDER - Volocity .mvd2 - Olympus SIS TIFF - IMAGIC - cellSens VSI * Updated to 2011-06 OME-XML schema * Minor speed improvements in many formats * Switched version control system from SVN to Git * Moved all Trac tickets into the OME Trac: https://trac.openmicroscopy.org * Improvements to testing frameworks * Added Maven build system as an alternative to the existing Ant build system * Added pre-compiled C++ bindings to the download page 4.2.2 (2010 December 6) ----------------------- * Several bug fixes, notably: - Metadata parsing fixes for Zeiss LSM, Metamorph STK, and FV1000 - Prevented leaked file handles when exporting to TIFF/OME-TIFF - Fixed how BufferedImages are converted to byte arrays * Proper support for OME-XML XML annotations * Added support for SCANCO Medical .aim files * Minor improvements to ImageJ plugins * Added support for reading JPEG-compressed AVI files 4.2.1 (2010 November 12) ------------------------ * Many, many bug fixes * Added support for 7 new formats: - CellWorX .pnl - ECAT7 - Varian FDF - Perkin Elmer Densitometer - FEI TIFF - Compix/SimplePCI TIFF - Nikon Elements TIFF * Updated Zeiss LSM metadata parsing, with generous assistance from Zeiss, FMI, and MPI-CBG * Lots of work to ensure that converted OME-XML validates * Improved file stitching functionality; non-numerical file patterns and limited regular expression-style patterns are now supported 4.2.0 (2010 July 9) ------------------- * Fixed many, many bugs in all aspects of Bio-Formats * Reworked ImageJ plugins to be more user- and developer-friendly * Added many new unit tests * Added support for approximately 25 new file formats, primarily in the SPM domain * Rewrote underlying I/O infrastructure to be thread-safe and based on Java NIO * Rewrote OME-XML parsing/generation layer; OME-XML 2010-06 is now supported * Improved support for exporting large images * Improved support for exporting to multiple files * Updated logging infrastructure to use slf4j and log4j 4.1.1 (2009 December 3) ----------------------- * Fixed many bugs in popular file format readers 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