[ome-devel] Release of Bio-Formats 5.2.0

[Helen Flynn (Staff)]

Dear All,

Today we are releasing Bio-Formats 5.2.0. This release updates the Data Model to the June 2016 schema[1] introducing Folders and simplifying both the graphical aspects of the model and code generation, adds support for two new formats; Becker & Hickl FIFO .spc and Princeton Instruments .spe, improves performance, and features many bug fixes. With this release Java 1.7 is now the minimum supported version.

Support is improved for the following formats:

  *   CellSens VSI†
     *   fixes for correctly reading dimensions
  *   FlowSight
     *   fixes to infer channel count from channel names (thanks to Lee Kamentsky)
  *   Hamamatsu VMS†
     *   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
  *   SVS
     *   fixed NumberFormatException
  *   Tiff
     *   fixed integer overflow to read resolutions correctly
     *   fixed handling of tiled images with tile width less than 64[/list]
  *   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 ZVI†
     *   reworked image ordering calculation to allow for tiles

† 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.

In addition, Slidebook6Reader is now completely external and fully maintained by 3i (see http://www.openmicroscopy.org/info/slidebook).

Other improvements include:

  *   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

Documentation improvements include:

  *   new Micro-Manager user documentation
  *   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

Developer updates include:

  *   dependency bumps for native-lib-loader and xalan
  *   DataTools, Logging, FormatTools, Formats and ClassList API updates
  *   added many automated tests and improved FakeReader testing framework
  *   licensing updates for XSL transforms, specification code and xsd-fu Python code (to Simplified 2-clause BSD)
  *   Jace C++ implementation has been decoupled and marked as legacy[2]
  *   Bio-Formats C++ native implementation has been decoupled and is now being released as OME Files C++[3]

Full details of all of these changes are available on the Bio-Formats version history page -
http://www.openmicroscopy.org/site/support/bio-formats5.2/about/whats-new.html

Bio-Formats 5.2.0 is available to download from

http://downloads.openmicroscopy.org/bio-formats/5.2.0/

and will shortly be available for recent Fiji versions via the Java-8 update site. If you are using an older version of Fiji (pre-2016), you will need to upgrade to Java 8 and install a newer version, see
http://imagej.net/2016-05-10_-_ImageJ_HOWTO_-_Java_8,_Java_6,_Java_3D for advice.

Any problems or comments, please use the OME Forums or mailing lists:

http://www.openmicroscopy.org/site/community

Regards,

The OME Team

[1] http://www.openmicroscopy.org/site/support/ome-model/schemas/june-2016.html
[2] https://github.com/ome/bio-formats-jace
[3] http://downloads.openmicroscopy.org/ome-files-cpp/


Dr Helen Flynn
OME Technical Writer
Centre for Gene Regulation & Expression
Open Microscopy Environment
University of Dundee
http://openmicroscopy.org


The University of Dundee is a registered Scottish Charity, No: SC015096
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