Release of Bio-Formats 6.4.0

[David Gault (Staff)]

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Dear all,

Today we are releasing Bio-Formats 6.4.0 which includes the following changes:

File format fixes and improvements:

* Applied Precision CellWorX
   - added support for multiple Z sections

* DeltaVision
   - added and updated objective metadata based on values from softWoRx 7.2.0 (thanks to David Pinto)

* Hamamatsu NDPI
   - added support for JPEG-XR compression
   - added full support for files larger than 4 GB
   - improved support for a number of additional metadata tags
   - the Hamamatsu NDPI reader improvements are provided via work from Glencoe Software

* InCell
   - inverted Y coordinate in plane/field positions to correct stitching of tiles

* PerkinElmer Vectra QPTIFF
   - plane position values will now be populated on OME-XML

* TIFF
   - values for XPosition and YPosition in original metadata will now be more accurately stored as doubles
   - implemented a fix to prevent integer overflow when reading from a large tile greater than 2 GB

* Ventana BIF
   - improved handling of physical sizes for pre-stitched TIFFs

* Zeiss CZI
   - added a fix for uncompressed pixels incorrectly flagged as JPEG-XR
   - fixed a bug so that line-scans are now read correctly (thanks to Stephan Wagner-Conrad)
   - improved parsing of detector metadata

Bio-Formats tools improvements:

* added a new nobigtiff option to bfconvert to disable automatic switching to BigTiff based upon the number of pixel bytes (TIFF files larger than 4GB). This may be useful when converting using a compression codec so that the output file size is less than 4GB
* fixed a bug in xmlvalid tool to properly handle lowercasing of file names
* added new bfGetPlaneAtZCT function to MATLAB toolbox to retrieve a particular plane at a ZCT coordinate (thanks to Mark Kittisopikul)
* added a new bfTestInRange helper function to MATLAB toolbox with improved performance and error handling (thanks to Mark Kittisopikul)
* fixed a bug when using bfconvert on multi-series files with only a single timepoint, channel or Z slice selected

Bio-Formats API updates:

* version of jxrlib has been updated to 0.2.2
* version of ome-codecs has been updated to 0.3.0 which includes performance upgrades for LZW compression (thanks to Alexander Popiel)
* moved JPEG-XR codec and service from formats-gpl to formats-bsd component
* TiffParser and TiffSaver have now been updated to implement Closeable
* added a documentation note to use one IFD instance per plane with saveBytes in TiffWriter
* FormatWriter will now create output file's parent directory if needed
* FakeReader now allows for DeltaT to be set in INI file
* FakeReader now handles INI files in plates created by mkfake
* fixed a number of deprecation warnings in various readers

Full details can be found at https://docs.openmicroscopy.org/bio-formats/6.4.0/about/whats-new.html

The software is available at:
https://www.openmicroscopy.org/bio-formats/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<https://forum.image.sc/tag/bio-formats>


Regards,

The OME Team

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