Release of Bio-Formats 6.1.1

Today we are releasing Bio-Formats 6.1.1 which included the following changes:

File format fixes and improvements:

• DeltaVision
  • added new lens definitions associated with rcpnl files
• Gatan Digital Micrograph (DM3/DM4)
  • now parsing the Montage tag to determine if tiles are present
• Leica LAS AF LIF (Leica Image File Format)
  • added fix to correctly read scale from polygon regions of interest (thanks to Sean Warren)
• PerkinElmer Columbus
  • improved handling of truncated TIFF files to return blank planes
• PerkinElmer Opera Flex
  • plate barcodes are now used to improve grouping and handling of truncated files
• TIFF (Tagged Image File Format)
  • improved parsing times for images stored as uncompressed contiguous strips
• Zeiss CZI
  • improved plane position metadata for many CZI datasets

Automated test changes:

• format reader tests have been updated to handle PerkinElmer Columbus datasets with flex files

Documentation improvements:

• added help for missing options in bfconvert command line tool

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.

The following are issues which are being considered for the next minor release 6.2.0:

• inclusion of a new reader for Mikroscan TIFF
• inclusion of a new reader for Ventana .bif files
• fix for NDPI files with empty marker tag. This was originally aimed for a patch release with the fix https://github.com/openmicroscopy/bioformats/pull/3248 but after further investigation it will require a larger fix to our JPEG Turbo Service which will mean it is suitable for a minor release.

Any problems or comments, please use the image.sc forum.