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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.
http://www.openmicroscopy.org/site/products/bio-formats
GNU General Public License v2.0
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OME-TIFF: memory usage and file handles improvements #27

Closed sbesson closed 2 years ago

sbesson commented 2 years ago

Ports https://github.com/ome/bioformats/pull/3418 and https://github.com/ome/bioformats/pull/3766 to the IDR fork of Bio-Formats

To be tested in the context of submissions with HCS OME-TIFF spanning several thousands of files

sbesson commented 2 years ago

Tested in the context of idr0120. An OME-TIFF plate composed of 5581 files previously failed to load systematically with Too many open files errors but with these fixes included, the plate is correctly imported, all thumbnails generated and the individual image access works as expected.