Release of 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 reader for the BigDataViewer format developed at MPI-CBG Dresden. 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.

File format fixes and improvements:

• BDV
  • 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 Bio-Formats version history.

The software is available at archived 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.