Release of Bio-Formats 6.8.0

Today we are releasing Bio-Formats 6.8.0. This new release contains several file format updates including new readers and writers.

New file formats:

• DICOM
  • added support for reading and writing DICOM whole slide images (DICOM WSI format). This functionality was implemented through collaboration with NCI Imaging Data Commons, and has been funded in whole or in part with Federal funds from the National Cancer Institute, National Institutes of Health, under Task Order No. HHSN26110071 under Contract No. HHSN2612015000031 Bio-Formats version history
• Olympus omp2info
  • Added a new reader for the Olympus tile format provided through a partnership with Glencoe Software and OLYMPUS EUROPA SE & Co. KG

File format fixes and improvements:

• Amira Mesh
  • added support for Amira 3.0 keys
• Aperio SVS / Aperio AFI
  • improved handling of macro and label images
• AVI (Audio Video Interleave)
  • set fps from Pixels Time Increment when writing AVI files
• Nikon NIS-Elements ND2
  • updated parsing of newer ND2 files to resolve issues with incorrect dimensions(thanks to Ilya Parmon)
• Olympus OIR
  • fixed a Null Pointer Exception for Laser Data ID
• OME-TIFF
  • fixed handling of partial datasets
  • added a new reader option ometiff.fail_on_missing_tiff to configure behaviour of partial dataset
• PerkinElmer Operetta
  • added support for Phenix v6 data
• TIFF
  • fixed non-sequential offset correction for TIFF files between 2 and 4 GB
• Zeiss CZI
  • added support for zstd compression. This feature will require FIJI users to additionally download the dependency io.airlift.aircompressor 0.18. (funded by a partnership between Glencoe Software and ZEISS)

Bio-Formats improvements:

• updated the ordering of reader.txt
• bfconvert tool updated to use multiple of tile size granularity when writing (thanks to Jeremy Muhlich)
• added a new no-sequential option to enable writing in non sequential order

Component updates:

• jhdf5 was upgraded to 19.04.0
• commons-lang 2.6 was added as a dependency
• aircompressor 0.18 was added as a dependency

Documentation improvements:

• updated page for using Bio-Formats in Python to add links for AICSImageIO and PyImageJ (thanks to Curtis Rueden)