The bioformats2raw.layout could be generated from a Fileset or from a list of Image IDs.
In the case of a Fileset, we can get Image IDs with fileset.copyImages().
With a list of Image IDs, we can export each individual OME-NGFF under paths 0/, 1/ etc and manually generate
OME-XML according to https://docs.openmicroscopy.org/ome-model/6.2.2/specifications/minimum.html (with <MetadataOnly/>) for each Image.
I don't see a way to get export this OME-XML automatically from OMERO for a Fileset. But also, it would be handy to generate bioformats2raw.layout collection of Images that are NOT a Fileset, which should be possible with this approach.
See https://github.com/ome/ngff/pull/112#issuecomment-1174890546
The bioformats2raw.layout could be generated from a Fileset or from a list of Image IDs.
In the case of a Fileset, we can get Image IDs with
fileset.copyImages().With a list of Image IDs, we can export each individual OME-NGFF under paths
0/,1/etc and manually generate OME-XML according to https://docs.openmicroscopy.org/ome-model/6.2.2/specifications/minimum.html (with<MetadataOnly/>) for each Image. I don't see a way to get export this OME-XML automatically from OMERO for a Fileset. But also, it would be handy to generate bioformats2raw.layout collection of Images that are NOT a Fileset, which should be possible with this approach.I imagine the cli could look like:
Going to start looking into this... cc @sbesson @joshmoore