Release of Bio-Formats 5.6.0

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Release of Bio-Formats 5.6.0

David Gault (Staff)
Dear all,

Today we are releasing Bio-Formats 5.6.0 which includes the following changes:

File format fixes and improvements:

  *   Zeiss CZI
     *   added support for images from Elyra PALM system
     *   prevented a potential infinite loop when a scene with a pyramid is missing
  *   cellSens VSI
     *   a new option has been added to throw an exception rather than logging a  warning if .ets file is missing. The option, 'cellsens.fail_on_missing_ets', can be used via the MetadataOptions API, as a parameter in the command line tools or via the Bio-Formats configuration dialog in ImageJ
  *   MetaMorph Stack (STK)
     *   fixed an error with HCS style datasets always returning the first plane regardless of the requested index
     *   updated to use stage labels starting with 'Scan' to detect when a whole plate is saved in a single .stk file
     *   fixed a bug for ArrayIndexOutOfBoundsException when an image contains a single Z plane
  *   Gatan Digital Micrograph
     *   added support for Z stacks and ROIs
     *   fixed several bugs in tag parsing
  *   PerkinElmer Operetta
     *   ensure TIFF files exist before reading
  *   JPEG
     *   support added for images with more than Integer.MAX_VALUE pixels

Bug fixes and improvements:

  *   JPEGTileDecoder
     *   class now implements AutoCloseable to prevent resource leaks
  *   Bio-Formats Plugin
     *   improved performance when using options to concatenate multiple series together
  *   TiffSaver
     *   made performance improvements to prevent the writing of a new IFD for each tile, resulting in significant file size reductions for images with a large quantity of tiles

Documentation improvements:

  *   updated website and URL links for new<> website
  *   added missing Andor SIF<> to supported formats page
  *   added a new page Working with whole slide images<> outlining the API support for pyramids/resolutions
  *   fixed broken documentation links for external resources which are no longer available
  *   updated the style of Sphinx documentation

Component architecture changes/decoupling:

  *   decoupled image encoding and decoding routines to the new ome/ome-codecs<> GitHub repository and consumed as 'org.openmicroscopy:ome-codecs' artifact from Maven Central
  *   removed components/forks/jai - decoupled to the new ome/ome-jai<> GitHub repository and consumed as part of 'org.openmicroscopy:ome-jai' artifact from Maven Central
  *   replaced components/formats-api/codecs classes with wrappers around 'org.openmicroscopy:ome-codecs'
  *   replaced components/formats-bsd/codecs classes with wrappers around 'org.openmicroscopy:ome-codecs'

Updated build system:

  *   ant now removes the build files of the bundles during 'clean' to prevent a mix of dependencies

Full details can be found at

The software is available at:
and will shortly be available from the Java-8 update site for Fiji users.

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


The OME Team

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

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