Release of Bio-Formats 6.1.0

[David Gault (Staff)]

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Dear all,

Today we are releasing Bio-Formats 6.1.0. This latest release contains the completion of Phase I of OME’s work on improved support for binary vessels. In addition to the KLB format we supported in version 6.0, we have now added a BigDataViewer reader. We hope this work is useful for the light sheet microscopy community.

We’ve also worked to improve the integration of Bio-Formats 6.1 into OMERO 5.5 (to be released Summer 2019). Finally, we’ve also reviewed and updated many of Bio-Formats dependencies to align them with the Fiji ecosystem.  This includes an update of the component netcdf library used by Bio-Formats, which should improve the experience of users working with some of the HDF5-based file formats.

New file formats:

  *   BDV (Big Data Viewer)
     *   added a new reader for Big Data Viewer files

File format fixes and improvements:

  *   Applied Precision CellWorX
     *   improved handling of thumbnail files
  *   DeltaVision
     *   updated handling of rcpnl files to treat each file as a single timepoint
  *   FakeReader
     *   removed header key from original metadata
  *   Hamamatsu VMS
     *   removed header key from original metadata
  *   Hitachi S-4800
     *   removed header key from original metadata
  *   ICS (Image Cytometry Standard)
     *   fixed an issue reading .ics/.ids files written by SVI Huygens (thanks to Jan Eglinger)
  *   Imaris IMS
     *   fixed issues with newer files which had been failing due to older netcdf version
  *   JPEG
     *   improved the reading of EXIF data
  *   Lambert Instruments FLIM
     *   added support for packed UINT12 datatype (thanks to Johan Herz)
  *   LEO
     *   fixed a bug with the parsing of physical sizes
     *   improved support for additional global metadata fields
  *   Olympus OIR
     *   fixed a bug which would show empty pixels when more than 1000 timepoints

Automated test changes:

  *   added additional tests for HCS/SPW datasets to ensure Plate, PlateAcquisition, Well, WellSample, and WellSample position values are configured where present
  *   added a new file-leak-detector test to flag potential memory leaks

Bio-Formats API changes:

  *   ImageConverter as used in bfconvert command line tool is now public
  *   made ImageReader more defensive against exceptions thrown when determining reader type
  *   fixed an issue when performing a non-sequential write for multi-resolution TIFF files

Component changes:

  *   ome-common was upgraded to 6.0.3
  *   perf4j was upgraded to 0.9.16
  *   removed Guava dependency which will be pulled transitively from the upstream ome-common dependency
  *   jhdf5 was upgraded to 14.12.6
  *   metadata-extractor was upgraded to 2.11.0
  *   xercesImpl version 2.8.1 was added as it is no longer a dependency of metadata-extractor
  *   netcdf was upgraded to 4.6.13


Full details can be found at https://docs.openmicroscopy.org/bio-formats/6.1.0/about/whats-new.html

The software is available at:
https://www.openmicroscopy.org/bio-formats/downloads/
and will shortly be available from the Java-8 update site for Fiji users.

Any problems or comments, please use the Image.sc forum<https://forum.image.sc/tags/bio-formats> or mailing lists:

http://www.openmicroscopy.org/support


Regards,

The OME Team

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