Release of Bio-Formats 5.6.0



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 … s-new.html

The software is available at:

and is now 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

Blank windows when opening czi files
Error message when updating imageJ and opening large "-dimensional image with imageJ