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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 -
  • 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
    • 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 *_metadata.txt files in addition to 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
      • fixed bioformats_package.jar to include the 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 native C++ implementation

  • Improved support for opening and saving ROI data with ImageJ

  • Added support for CellH5 data (thanks to Christophe Sommer)

  • Added support for Perkin Elmer Nuance data (thanks to Lee Kamentsky)

  • Added support for Amnis FlowSight data (thanks to Lee Kamentsky and Sebastien Simard)

  • Added support for Veeco AFM data

  • Added support for Zeiss .lms data (not to be confused with .lsm)

  • Added support for I2I data

  • Added support for writing Vaa3D data (thanks to Brian Long)

  • Updated to 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)
      • 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 command line documentation

5.0.0-RC1 (2013 Dec 19)

5.0.0-beta1 (2013 June 20)

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:

  • 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 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