Sébastien Besson

Hi, chiming in late but I would to cross-reference this issue with the one reported [upstream](https://github.com/openmicroscopy/bioformats/issues/2132). Shortly, there is a known limitation/bug during the initialization of very large JPEG files....

Following-up on https://github.com/zarr-developers/community/issues/15#issuecomment-610345738, the process used by OME for releasing some of its Java components to Sonatype is documented [here](https://docs.openmicroscopy.org/contributing/java-development.html#release-process) with the relevant links to OSSRH in case it's useful....

Pretty sure that `BF_MAX_MEM` is specific to the Bio-Formats command-line utilities and will not be recognized by `bioformats2raw`. Have you tried `JAVA_OPTS="-XmxG"` ?

50G definitely feels excessive. I recall some improvements were targeting at handling similar issues for large Micro-Manager metadata files in the past. One thing possibly worth testing independently is whether...

The error rings a bell as I recall there were historical issues with some data from this historical submission. Does this happen for all plates? If not, do you have...

It looks like this observation on the duplication of plate P132 was [already made](https://trello.com/c/n0C3Ehuz/483-idr0004-thorpe-rad52-issues#comment-5ae303df37fe47422b846ba9) but not actioned > They both appear to have the same Wells, but in different positions!...

Have you unlinked the map annotations linked to the images of these plates first, especially the multi-linked annotations (organism, genes...) before running the deletion?

Note that this study will have the same caveats as of https://github.com/IDR/idr-metadata/issues/640#issuecomment-1552697868 in terms of channel order. So similar decisions will need to be done in terms of the conversion...

The logs give more clues about ``` Aug 31 17:01:05 pilot-idr0125-omeroreadwrite systemd: Removed slice User Slice of root. Aug 31 17:03:44 pilot-idr0125-omeroreadwrite kernel: gunicorn invoked oom-killer: gfp_mask=0x201da, order=0, oom_score_adj=0 Aug...

In general ``` sudo /opt/goofys --endpoint https://uk1s3.embassy.ebi.ac.uk/ -o allow_other ``` is the way to mount the bucket