Release of Bio-Formats 6.2.0

Today we are releasing Bio-Formats 6.2.0 which included the following changes:

New file formats:

• Mikroscan TIFF
  • a new reader for Mikroscan TIFF files has been contributed with thanks to Jim Crowe, Mikroscan Technologies, Inc.
• Ventana BIF
  • added a new reader for Ventana BIF files which has been commissioned via Glencoe Software

These new formats have added in accordance with the guidelines in our blog post which stated that the open source team would not be developing the addition of new readers outside of our funded priorities. New formats can however be supported via the following means:

• external contributions directly to the Bio-Formats library
• companies managing their own closed source readers which live outside Bio-Formats
• commissioning the work via Glencoe Software

File format fixes and improvements:

• Cellomics
  • fixed indexing for plates with a single well or missing fields
• DeltaVision
  • added support for the reading of the new panel count field (provided through a collaboration between GE Healthcare and Glencoe Software Inc.)
• PerkinElmer Operetta
  • images with smaller XY dimensions than all other TIFF files in dataset will now be padded
• TIFF
  • updated functionality for overwriting IFD values to ensure that previous value is completely overwritten and no orphaned tags are left
• Zeiss CZI
  • expanded support for auto-stitching of tiles

Bug fixes and improvements:

• added -cache, -cache-dir and -no-sas options to bfconvert tool
• deprecated broken TRUNK and DAILY builds from upgrade checker
• disabled Oracle JDK from Travis CI checks

Documentation improvements:

• fixed broken link for discontinued Dcraw software
• updated links for Zeiss formats

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.