Release of Bio-Formats 6.14.0

Today we are releasing Bio-Formats 6.14.0 with a number of format improvements. We have also marked as deprecated a number of older components which rely on external libraries. The full details of these are listed as below, with removal intended for Bio-Formats 7.0.0. 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:

Deprecation warnings:

• Legacy ND2 Reader
  • The LegacyND2Reader and underlying components have been marked as deprecated in preparation for removal in the upcoming 7.0.0 major release of Bio-Formats. This reader depends on an outdated DLL which has not been built in years, is untested and fully superseded by the new NativeND2Reader. From Bio-Formats 7.0.0 onwards the existing NativeND2Reader will be renamed as ND2Reader and act 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 marked as deprecated in preparation for removal in the upcoming 7.0.0 major release of Bio-Formats. These classes depended on the external QuickTime for Java library which is long obsolete. From Bio-Formats 7.0.0 onwards the existing NativeQTReader
    will be renamed as QTReader and support for QuickTime will be limited to non legacy readers and writers.
• LuraWave Codec
  • The LuraWave Codec along with the LuraWaveService and associated components have been marked as deprecated in preparation for removal in the upcoming 7.0.0 major release of Bio-Formats. This codec depends on a third-party proprietary library with a license code. Opera Flex is the format that is most likely to be impacted by this change.
• Woolz
  • The Woolz Reader, Writer and Service have been marked as deprecated in preparation for removal in the upcoming 7.0.0 major release of Bio-Formats. The reader and writer are untested and rely on an underlying library which maintenance status is unclear

File format fixes and improvements:

• CV7000/CV8000
  • updated CV7000 isThisType test to improve performance by skipping extended type checking
  • reader now handles the use case where wells are recorded, but all files were removed
  • fixed channel indexing in scenarios where more channels are defined than acquired
• ICS (Image Cytometry Standard)
  • fixed an Illegal group reference exception when constructing slice label
• KLB (Keller Lab Block)
  • fixed a bug with the reading of image planes in Z stacks
• MicroManager
  • updated handling of truncated files to prevent possible infinite loop and throw an exception

Bio-Formats improvements:

• updated handling of exceptions in Bio-Formats plugins to ensure readers are closed
• updated list of external readers to include new external ZeissQuickStartCZIReader (thanks to Nicolas Chiaruttini)
• updated top-level Git mailmap to normalize commit author variants
• added a new bf-unconfigured tool to the Bio-Formats toolbox. The new tool lists classes which are not configured for testing as part of format reader tests
• replaced use tt tag in java docs with code tag

Documentation improvements:

• fixed a number of broken links
• migrated OME-Model documentation to Read the Docs
• added deprecation warnings to format pages of the affected components

Component updates:

• ome-common was upgraded to 6.0.17