Release of Bio-Formats 7.0.0

Today we are releasing Bio-Formats 7.0.0 which includes support for writing dual-personality DICOM files. We have also removed a number of previously deprecated components which rely on external libraries, most of which are not well-supported. The full details of these are listed as below. For users who wish to retain support for files using these readers or codecs, we recommend converting these file-sets to an actively maintained open format such as OME-TIFF. This can be achieved using the Bio-Formats bfconvert command line tool as outlined in the command line tools documentation.

The full list of changes included in this release are as follows:

Removal of deprecated components:

• Legacy ND2 Reader
  • The LegacyND2Reader and underlying components have been removed. This reader depended on an outdated DLL which had not been built in years, was untested and fully superseded by the new NativeND2Reader. The existing NativeND2Reader has been renamed as ND2Reader and now acts as the sole reader for the format. Support for the ND2 format will be unaffected and continue via this newly renamed reader.
• Legacy QuickTime
  • The LegacyQT Reader, Writer and Tools have been removed. These classes depended on the external QuickTime for Java library which is long obsolete. The existing NativeQTReader has been renamed as QTReader and support for QuickTime is now limited to non legacy readers and writers.
• LuraWave Codec
  • The LuraWave Codec along with the LuraWaveService and associated components have been removed and are no longer supported. This codec was dependent on a third-party proprietary library with a license code. This may impact LuraWave compressed files for the Opera Flex format.
• Woolz
  • The Woolz Reader, Writer and Service have been removed and are no longer supported. The reader and writer are untested and rely on an underlying library which has an unclear maintenance status.

File format fixes and improvements:

• DICOM
  • Support has been added for the writing dual-personality DICOM/TIFF. The DICOM writer will now, by default, include TIFF metadata as described in Clunie DA. Dual-Personality DICOM-TIFF for Whole Slide Images: A Migration Technique for Legacy Software. J Pathol Inform. 2019 Apr 3;10:12. doi: 10.4103/jpi.jpi_93_18. PMID: 31057981; PMCID: PMC6489422. These new dual-personality files can be read either by the DICOM reader or can also be recognised as TIFF. A new option named dicom.dual_personality has been added to the DicomWriter. Setting this new option to false will revert writing of DICOM files back to the original plain DICOM files. 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.
• PerkinElmer Opera Flex
  • reader will now ignore files in which the compression cannot be identified
• PerkinElmer Operetta
  • fixed an exception when reading null planes (thanks to Nicolas Chiaruttini)

Component updates:

• ome-common was upgraded to 6.0.19
• ome-stubs was upgraded to 6.0.1
• ome-codecs was upgraded to 1.0.0
• native-lib-loader was upgraded to 2.4.0 (thanks to Can Gokhan Dogan)

Documentation improvements:

• fixed a number of broken links