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Support making bioformats2raw collection from /0 /1 etc#27

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BioNGFF:mainfrom
will-moore:zarr_ome_xml_tweaks
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Support making bioformats2raw collection from /0 /1 etc#27
will-moore wants to merge 1 commit into
BioNGFF:mainfrom
will-moore:zarr_ome_xml_tweaks

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@will-moore

@will-moore will-moore commented Sep 15, 2025

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I modified the zarr_ome_xml.py script a bit to generate a bioformats2raw.layout and /OME/METADATA.ome.xml for a collection of images...

  • Create a dir, e.g. idr0079_images.zarr
  • Create some image.zarrs. E.g. used omero-cli-zarr to export from OMERO
  • I manually updated .zattrs of each to set multiscales[0]["name"] field to preserve the name.
  • Renamed and moved each dir, e.g. 1234.ome.zarr -> idr0079_images.zarr/0 and idr0079_images.zarr/1 etc
  • Then ran:
python /path/to/omero-import-utils/metadata/zarr_ome_xml.py idr0079_images.zarr/

That goes through /0, /1, /2 etc and collects these images into /OME/METADATA.ome.xml.
It also creates idr0079_images.zarr/.zgroup and idr0079_images.zarr/.zattrs with {"bioformats2raw.layout": 3} so that this is recognised as such.

The output of this is uploaded at:

https://ome.github.io/ome-ngff-validator/?source=https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.4/idr0079A/idr0079_images.zarr

and also imported into merge-ci OK.

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