The Open Microscopy Environment

Today we are releasing Bio-Formats 6.5.0 which includes the following changes:

File format fixes and improvements:

Big Data Viewer
- improved performance of tiled reading
DeltaVision
- implemented additional sanity check to header to ensure correct panel count
DICOM
- improved performance of initialization of multi-file datasets. Files spread across multiple directories are now handled by a DICOMDIR file that groups the dataset
Imspector OBF
- added support for OBF Version 6 stacks (thanks to Nils Gladitz)
- added support for OBF Version 4 stack flush points (thanks to Nils Gladitz)
MetaMorph
- ensured dimension metadata read from tags and/or .nd file rather than allowing the underlying TIFF reader to treat each IFD as a series
MetaXpress
- added support for single site HCS variant
Zeiss CZI
- fixed the position count when only one position is present and the starting index is greater than 0
Various Readers
- reviewed and updated readers to prevent potential cases of integer overflow

OME-Model updates:

version of OME-Model has been updated to 6.1.0
added support for Python 3.8 and made code-generation Python 3 only (thanks to Roger Leigh)
added getters and setters for OME@Creator attribute for ome.xml metadata interfaces and implementations (thanks to Nils Gladitz)
removed unmaintained C++ OME-XML implementation (thanks to Roger Leigh)
updated code-generation for building on Python 3.6, 3.7 (thanks to Roger Leigh)
uncapped the Sphinx version for OME-Model documentation

Documentation improvements:

Release of Bio-Formats 6.5.0