Bio-Formats 6 upgrade - Githubissues

IDR / bioformats

Bio-Formats is a Java library for reading and writing data in life sciences image file formats. It is developed by the Open Microscopy Environment (particularly UW-Madison LOCI and Glencoe Software). Bio-Formats is released under the GNU General Public License (GPL); commercial licenses are available from Glencoe Software.

GNU General Public License v2.0

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This merges https://github.com/openmicroscopy/bioformats/releases/tag/v6.2.0 into the master branch of the IDR fork of Bio-Formats

Most changes merged cleanly apart from a couple of merge conflicts merged manually in c58972243a5f35ead1d46cf8412469d82abfbc8e

all pom.xml were fixed to keep to 0.6.0-SNAPSHOT versions
FlexReader required changes to combine the file leak fixes with the plate acquisition support
FilePatternReader was kept identical to the 0.5.3 version. Several attempts were made to merge the WrappedReader refactoring introduced in Bio-Formats 6.0.0 but none was successful to fix a workflow combining setId and openBytes while keeping the memoization performance improvements.

Tests were performed using a copy of the current IDR production instance with the software was upgraded to use OMERO 5.5 including this version of the Bio-Formats library. The memo files were regenerated for the first dataset/plate of each project/screen and file access was tested using the OMERO viewer for each study.

Overall, most of the testing was successful with the imaging data matching the expectation from production IDR. The new readers introduced in Bio-Formats 6 (BDV, pyramidal OME-TIFF) also imported meaning submissions using these formats will be loadable into the upgraded IDR. The only two issues reported were:

initial issues and slowness when opening FilePatternReader-based datasets e.g. https://idr.openmicroscopy.org/search/?query=Name:idr0045-reichmann-zygotespindle/experimentA. This is a known issue probably since IDR 0.5.0 as the memoization of sub-files happens when reading the images
https://idr.openmicroscopy.org/search/?query=Name:idr0011-ledesmafernandez-dad4/screenD is broken after the upgrade. This is related to an improvement of the ZeissCZIReader made in Bio-Formats 6.1.1 which fails to read the variant of the file format. https://github.com/openmicroscopy/bioformats/pull/3412 was opened to correct this issue.

Merging this and releasing as 0.6.0 and the second issue above will be fixed in the mainline and merged as a patch release of this fork.

IDR / bioformats

Bio-Formats 6 upgrade #12