Release of Bio-Formats 6.9.0

Today we are releasing Bio-Formats 6.9.0, which includes several contributions from external partners, including Leica Microsystems. We are grateful for all the contributions. The full list of changes and updates:

New file formats:

• Leica LOF
  • added support for reading Leica LOF files. This functionality was implemented and contributed by Leica Microsystems
• Leica XLEF
  • added support for reading Leica XLEF files. This functionality was implemented and contributed by Leica Microsystems

File format fixes and improvements:

• FEI TIFF
  • fixed parsing of physical pixel sizes for Phenom data
• Imspector OBF
  • improved handling of deflate errors when opening older OBF files (thanks to Nils Gladitz)
• JPEG
  • performance improvements to reduce memory required to read tiles from large JPEGs
• Leica LIF
  • improved parsing of channel metadata (thanks to Zach Marin)

• Nikon NIS-Elements ND2 -improved parsing of metadata tables with invalid characters

• OME-TIFF
  • performance improvements of tile read speeds for some pyramid OME-TIFFs
• PerkinElmer Operetta
  • enabled support for handling sparse planes

Bio-Formats improvements:

• added new API methods to FormatTools for creating well names
• added a swap option to bfconvert to override input dimension order (thanks to Roberto Calabrese)

Documentation improvements:

• new public sample files for Leica XLEF (thanks to Leica Microsystems)
• added documentation for using the swap option with the command line tools
• updated the process for contributing sample files via Zenodo
• updated the link to NDP.view2 software on the Hamamatsu ndpi format page