Sébastien Besson

> Do I need to clone all of https://github.com/IDR/idr-metadata here? For the sake of testing, you might just want to copy the single `.pattern` file you want to test directly....

`conda deactivate`

@will-moore I think I found the source of the issue. Can you try one more test with your last configuration, running `sudo /opt/bioformats2raw/bioformats2raw-0.6.0-24/bin/bioformats2raw -p /uod/idr/metadata/idr0026-weigelin-immunotherapy/patterns/3.49.6-3.140922_11-33-57.01.pattern 3.49.6-3.140922_11-33-57.01.ome.zarr` (note the `sudo` at...

So the difference is really whether the directory containing the pattern file is writeable or not, meaning that a memo file can be saved or not. I suspect something incorrect...

From my side, the immediate candidates are: - an issue with https://github.com/IDR/bioformats custom additions to FilePatternReader to support channel names - an issue with https://github.com/IDR/bioformats being behind the ome/bioformats mainline...

Retested with a simpler version of the pattern file with 2 timepoints compatible with upstream Bio-Formats ``` cat 3.49.6-3.140922_11-33-57.00.pattern /uod/idr/filesets/idr0026-weigelin-immunotherapy/20170222-symlinks/PNAS_2015/treatment start day 3/mouse 49/day 6-3/time lapse/140922_11-33-57/11-33-57_PMT - PMT [] [00]_Time...

Specifically on https://github.com/IDR/idr-metadata/issues/641#issuecomment-1680177849. A few comments: - the plate loaded on IDR is stuck in an `Import in progress` state - trying to reimport the `5-12` plate in a testing...

As discussed earlier today, converted a sample plate from this study using `bioformats2raw` for comparison. All the TIFFs from the `20585-` folders were symlinked under the same directory and a...

Thanks, echoing what I mentioned post-conversion ``` importantly note that the order of the channels (Hoechst, ERSysto, ERSystoBleed, PhGolgi, Mito) is different from the images in IDR (ERSysto, ERSystoBleed, Hoechst,...

A few additional notes on the channel order: - the decisions made here will also affect idr0016 which orginally included the plates now published as idr0036 - the NGFF representation...