Version history
===============
5.3.0-m2 (2016 November 23)
---------------------------
Updated build system:
* dropped embedded JARs and now use the Maven Ant Tasks plugin to unify the
dependencies using the pom.xml
* improved Ant JAR and bundle target
* dropped deprecated osgi targets, OME Tools bundle and ome-jxr component
* removed PDF generation from the docs-sphinx target
* added version number to Javadoc zip bundle name
* migrated unit tests out of test-suite into formats-bsd
* fixed test-suite targets, paths and symlink handling
* fixed test-metadata and migrated it into test-suite
* fixed mismatch between ``ND2HandlerTest`` package and location
* cleaned up test-build to remove obsolete and decoupled components
and folders
* simplified Travis build
* POM repositories clean up to reduce complexity and use Maven Central as the
first location to look for dependencies
* now storing all versions in the top-level pom.xml
* updated build versioning from Maven by unified versioning strategy,
reviewing meta information stored in the manifests of each JAR and
introspecting this information in the ``FormatTools`` API to retrieve
version and revision numbers
* updated developer documentation on updated build system
Component architecture changes/decoupling:
* removed formats-common component - now decoupled to the new
`ome/ome-common-java GitHub repository <https://github.com/ome/ome-common-java>`_
and consumed as 'org.openmicroscopy:ome-common' artifact from Maven
Central
* removed ome-poi component - now decoupled to the new
`ome/ome-poi GitHub repository <https://github.com/ome/ome-poi>`_
and consumed as 'org.openmicroscopy:ome-poi' artifact from Maven Central
* removed specification, xsd-fu and ome-xml components - now decoupled to the
new `ome/ome-model Github repository <https://github.com/ome/ome-model>`_
and consumed as 'org.openmicroscopy:{specification,ome-xml}'
artifacts from Maven Central
* removed mdbtools component - now decoupled to the new
`ome/ome-mdbtools GitHub repository <https://github.com/ome/ome-mdbtools>`_
and consumed as 'org.openmicroscopy:ome-mdbtools' artifact from Maven
Central
* removed stubs components - now decoupled to the new
`ome/ome-stubs GitHub repository <https://github.com/ome/ome-stubs>`_ and
consumed as 'org.openmicroscopy:{lwf-stubs,mipav-stubs}' artifacts from
Maven Central
* removed metakit component - now decoupled to the new
`ome/ome-metakit GitHub repository <https://github.com/ome/ome-metakit>`_
and consumed as 'org.openmicroscopy:metakit' artifacts from
Maven Central
* updated developer documentation for the decoupled components
New features/API:
* added support for JPEG-XR compressed CZI data (funded by a
`partnership between Glencoe Software and ZEISS <http://glencoesoftware.com/2016-08-30-glencoe-software-zeiss-partner-open-source-file-reader-whole-slide.html>`_), adding 'ome:jxrlib' as a new dependency
of Bio-Formats
5.2.4 (2016 October 18)
-----------------------
Java bug fixes:
* OME-TIFF
- fixed regression when populating plane metadata
* CZI
- populated series metadata with the scene/position information
5.2.3 (2016 October 5)
----------------------
Java bug fixes:
* CZI
- fixed imageCount for RGB images
* ICS writing
- fixed ordering of image dimensions
* DeltaVision
- fixed reading of large time dimensions
Command-line tools improvements:
* :file:`bftools.zip` now includes the version history as :file:`NEWS.rst`
(thanks to Gerhard Burger)
Code clean-up/improvements:
* switched to `String.indexOf(int)` in GPL-licensed reader code so that a
simpler library method can be used
* strings now extended with characters where possible
* completed deprecation of `DataTools.sanitizeDouble()`
* deprecated unused OSGi and ome-tools bundle build targets
OME-XML changes/improvements:
* bumped schema version number to 2 (schema namespace left unchanged)
* added acquisition modes `BrightField`, `SweptFieldConfocal` and `SPIM`
* added parsing for Laser Scan Confocal and Swept Field Confocal
Documentation improvements:
* documented versioning policy
* clarified supported versions for Micro-Manager and Olympus ScanR files
5.2.2 (2016 September 13)
-------------------------
Java bug fixes and improvements:
* fixed a regression in which the DataTools number parsing API would not be
thread-safe anymore
* InCell
- improved handling of Analyzer 2000 datasets to find TIFF files
* FV1000
- fixed preview names ordering
* OME-TIFF
- enabled all BigTIFF extensions
* various code cleanup across the Java code
* added test coverage for all example codes in the developer documentations
* added tests covering the semantics of the INI parser
ImageJ bug fixes and improvements:
* fixed a bug in ImageJ when swapping dimensions of an image with multiple
series of different dimensions
* added an option to the exporter to pad filename indexes with zeros
Command-line tools improvements:
* allowed the binaries to be symlinked (thanks to Gerhard Burger)
* added an option to bfconvert to pad filename indexes with zeros
5.2.1 (2016 August 25)
----------------------
Java bug fixes:
* Zeiss CZI
- fixed NumberFormatException when the position object is not null but the
values of child are null
* SimplePCI
- made IniParser less stringent to allow reading of imperfectly formatted
TIFF description headers
* fixed stitching of file patterns in ImageJ to remove duplication of
directory names in the file path
* added an option to bfconvert to allow creation of OME-TIFF without lookup
tables
* addition of MetadataOnly elements containing no BinData or TiffData now
handled via MetadataTools API in ImageInfo
* example code in developer docs is now tested via a new Maven module
5.2.0 (2016 August 18)
----------------------
Java format support improvements are listed below.
†Denotes a major breaking change to the reader (typically modification of core
metadata). Code changes or re-import may be necessary in ImageJ/FIJI and
OMERO.
* added support (and public sample files) for
:doc:`Becker & Hickl .spc FIFO </formats/becker-hickl-fifo>` data
* added support for :doc:`Princeton Instruments .spe </formats/princeton-instruments-spe>` data
* bug fixes for many formats including:
- CellSens VSIâ€
- fixes for correctly reading dimensions
- FlowSight
- fixes to infer channel count from channel names (thanks to Lee
Kamentsky)
- Hamamatsu VMSâ€
- fixed dimensions of full-resolution images
- ICS writing
- fixed dimension population for split files
- Kodak BIP
- fixed handling of CCD temperature stored in hexadecimal
- Leica LIF
- fixed incorrect plane offsets for large multi-tile files
- LiFlim
- fixed ``ExposureTime`` check and units usage
- Micro-Manager
- fixed handling of large datasets saved as image stacks and split
over multiple files
- added user documentation for file saving options
- MRC and Spider
- fixed format type checking
- Nifti
- fixed ``planeSize`` to prevent crashes when loading large files
(thanks to Christian Niedworok)
- added support for gzipped compressed .nii.gz files (thanks to Eric
Barnhill)
- added public samples and updated documented supported file extensions
- OME-TIFF
- fixed ``Plane`` population errors
- fixed ``NullPointerException`` when closing reader for partial
multi-file filesets
- reduced buffer size for ``RandomAccessInputStreams`` to improve
performance
- deprecated ``getMetadataStoreForConversion`` and
``getMetadataStoreForDisplay`` methods
- OME-XML
- fixed metadata store
- PicoQuant
- updated reader to always buffer data
- PNG writing
- SDT
- performance improvements for loading of large files
- Slidebook
- Slidebook6Reader is now completely external and fully maintained by
3i (see http://www.openmicroscopy.org/info/slidebook) and is
specified as such in the :file:`readers.txt` configuration file
- SVS
- fixed ``NumberFormatException``
- Tiff
- fixed integer overflow to read resolutions correctly
- fixed handling of tiled images with tile width less than 64
- Zeiss CZI
- fixed timestamp indexing when multiple separate channels are present
- improved slide support - slides are now detected as a complete
full-resolution image (instead of each tile being a separate series)
and pyramid sub-resolutions and label/overview images are also
detected
- Zeiss LSM
- fixed ``Plane`` population errors
- Zeiss ZVIâ€
- reworked image ordering calculation to allow for tiles
Top-level Bio-Formats API changes:
* Java 1.7 is now the minimum supported version
* the native-lib-loader dependency has been bumped to version 2.1.4
* the xalan dependency has been bumped to version 2.7.2
* all the ome.jxr classes have been deprecated to make clear that there is no
JPEG-XR support implemented in Bio-Formats as yet
* the DataTools API has been extended to add a number of utility functions to:
- account for decimal separators in different locales
- parse a ``String`` into ``Double``, ``Float``, ``Integer`` etc
- handle ``NumberFormatException`` thrown when parsing Unit tests
* the Logging API has been updated to respect logging frameworks
(log4j/logback) initialized via a binding-specific configuration file and
to prevent ``DebugTools.enableLogging(String)`` from overriding initialized
logger levels (see :doc:`/developers/logging` for more information)
* helper methods have been added to FormatTools allowing a stage position to
be formatted from an input ``Double`` and an input unit
* the Formats API has also been updated to add a new validate property to
``MetadataOptions`` and support for ``MetadataOptions`` has been moved to
FormatHandler level to allow it to be used by both Readers and Writers
* initial work on `Reader discoverability <https://github.com/openmicroscopy/design/issues/42>`_
extended the ClassList API to allow the :file:`readers.txt` configuration
file to be annotated using key/value pairs to mark optional Readers and
specify additional per-Reader options
Other general improvements include:
* improved performance of ``getUsedFiles``
* fixes for ``FilePatternBlock``, ``AxisGuesser``, ``FilePattern``
* fixes for the detection of CSV pattern blocks by ``FilePatternBlock``
* :file:`bioformats_package.jar` now includes bio-formats-tools as a
dependency so ``ImageConverter``, ``ImageFaker`` and ``ImageInfo`` classes
are included in the bundle
* the JACE C++ implementation has been decoupled as it does not function with
Java 1.8 (see `legacy repo <https://github.com/ome/bio-formats-jace>`_)
* ImageJ fixes
- to allow reader delegation when a legacy reader is enabled
but not working
- to allow ROIs to be imported to the ImageJ ROI manager or added to a new
overlay
* MATLAB fixes
- improved integration with Octave (thanks to Carnë Draug)
- added logging initialization
* Command-line tools fixes
- upgrade check no longer run when passing -version
- common methods refactoring
- showinf improvements to preload format
- tiffcomment now warns that it requires an ImageDescription tag to be
present in the TIFF file
* added many automated tests and improved FakeReader testing framework
* documentation improvements include:
- clarifying status of legacy Quicktime and ND2 readers
- noting that the Gatan reader does not currently support stacks
- more Java examples added to the developer documentation
- new units page for developers
The Data Model version 2016-06 has been released to introduce
`Folders <http://blog.openmicroscopy.org/data-model/future-plans/2016/05/23/folders-upcoming/>`_,
and to simplify both the graphical aspects of the model and code generation.
Full details are available in the
:model_doc:`OME Model and Formats Documentation <schemas/june-2016.html>`.
OME-XML changes include:
* `Map` is now a complexType rather than an element and `MapPairs` has been
dropped
* extended enum metadata has been introduced to better support units
* `Shape` and `LightSource` are now complexTypes rather than elements
* BinData has been added to code generation to handle raw binary data
* various code generation improvements to:
- simplify and standardize the generation process
- remove a number of hard-coded exceptional cases allowing for easier
maintenance and growth
- allow for genuine abstract model types and enable C++ model
implementation
* updated OME-XML and OME-TIFF public sample files
The Bio-Formats C++ native implementation has been decoupled from
the Java codebase and will be released as
`OME-Files C++ <http://downloads.openmicroscopy.org/ome-files-cpp/>`_ from now
on, with the exception of OME-XML which is still within Bio-Formats at present
(there is a plan to decouple both the Java and the C++ versions of OME-XML in
future).
The following components have had their licensing updated to Simplified
(2-clause) BSD:
* XSL transforms
* specification code
* xsd-fu Python code
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 <https://www.intelligent-imaging.com>`_)
* 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 <http://www.openmicroscopy.org/site/support/bio-formats5.1/developers/cpp/overview.html>`__
* Improved support for opening and saving ROI data with ImageJ
* Added support for :doc:`CellH5 </formats/cellh5>` data (thanks to Christoph Sommer)
* Added support for :doc:`Perkin Elmer Nuance </formats/perkinelmer-nuance>` data (thanks to Lee Kamentsky)
* Added support for :doc:`Amnis FlowSight </formats/amnis-flowsight>` data (thanks to Lee Kamentsky and Sebastien Simard)
* Added support for :doc:`Veeco AFM </formats/veeco-afm>` data
* Added support for :doc:`Zeiss .lms </formats/zeiss-axio-csm>` data (not to be confused with .lsm)
* Added support for :doc:`I2I </formats/i2i>` data
* Added support for writing Vaa3D data (thanks to Brian Long)
* Updated to :model_doc:`OME schema 2015-01 </schemas/january-2015.html>`
* 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 </users/comlinetools/index>`
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 </formats/bio-rad-scn>`
- :doc:`Yokogawa CellVoyager </formats/cellvoyager>` (thanks to
Jean-Yves Tinevez)
- :doc:`LaVision Imspector </formats/lavision-imspector>`
- :doc:`PCORAW </formats/pcoraw>`
- :doc:`Woolz </formats/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 </users/matlab/index>` and
:doc:`developers </developers/matlab-dev>` 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 </formats/aperio-afi>`
- :doc:`Inveon </formats/inveon>`
- :doc:`MPI-BPC Imspector </formats/imspector-obf>`
* 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