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 *_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 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 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)

  • 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 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:

  • Bio-Rad SCN
  • Yokogawa CellVoyager (thanks to Jean-Yves Tinevez)
  • LaVision Imspector
  • PCORAW
  • 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 MATLAB users and developers documentation

• Many bug fixes including for Nikon ND2, Zeiss CZI, and CellWorX formats

5.0.0-beta1 (2013 June 20)

• Updated to 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:

  • Aperio AFI
  • Inveon
  • 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