Release of Bio-Formats 6.1.0

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:

and will shortly be available from the Java-8 update site for Fiji users.

Any problems or comments, please use the #bio-formats tag on this forum: Image.sc forum

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