There's currently one VM configured for the conversion work:

ssh -J idr-pilot.openmicroscopy.org rocky@pilot-idrconv

EBI NFS mounted as usual: /nfs/bioimage and linked to /uod/idr/filesets.

idr-metadata cloned into: /data/idr-metadata.

10Tb data partition for temp ome.zarr storage: /data.

• /data/output - output location
• /data/memo - temporary memo directory for bioformats2raw
• /data/input - input location (if needed, use /nfs/bioimage instead when possible)

bioformats2raw (0.12.0) and bftools (8.5.0) installed too (ie. bioformats2raw, showinf available on commandline)

Run scripts/convert.sh to batch-convert image files to OME-Zarr:

./scripts/convert.sh [--workers N] [--id ID] <input_file>

• <input_file> — path to a tab-separated file (see format below)
• --id ID — output identifier, e.g. idr0026 (prompted if not provided); files are written to /data/output/<ID>/
• --workers N — number of bioformats2raw worker threads (default: 14)

The input file is a two-column, tab-separated file with no header:

Example:

TreatStartDay3_mouse50	/uod/idr/filesets/idr0026-weigelin-immunotherapy/.../Pos00.tif
TreatStartDay3_mouse50	/uod/idr/filesets/idr0026-weigelin-immunotherapy/.../Pos01.tif
TreatStartDay3_mouse55	/uod/idr/filesets/idr0026-weigelin-immunotherapy/.../Pos00.tif

Brief check if all ome.zarr were created: find * -type d -name "*.ome.zarr" | wc -l

Should match: wc -l input.tsv