While driving the export of IDR datasets, some wrapper scripts have been written on top of bioformat2raw 0.2.x to handle the bioformats2raw Zarr group layout and only retain the OME-Zarr image and add the OMERO metadata.
Support for HCS data export as OME-Zarr is the last part to be added. The --bf flag now requires bioformat2raw 0.3.0 which brings native support for HCS support and existing code can be re-used to add omero metadata to each well sample.
Probably the main point of review will be to ensure that the layouts are compatible . ome zarr export Plate:xxx uses the plate/well/row/field of view layout as described in https://ngff.openmicroscopy.org/0.1/ while bioformat2raw retains a flat layout where each field of view is 0-based index for compatibility with METADATA.ome.xml and raw2ometiff. My expectation is that both layouts should be equivalent as long as the correct metadata is filled but this will be a good occasion to compare and test via different downstream clients.
See https://github.com/IDR/idr-zarr-tools/pull/1 for the original discussion.
While driving the export of IDR datasets, some wrapper scripts have been written on top of
bioformat2raw 0.2.xto handle the bioformats2raw Zarr group layout and only retain the OME-Zarr image and add the OMERO metadata.In the case of non-HCS data, https://github.com/ome/omero-cli-zarr/pull/75 should have migrated all this logic at the level of this plugin using the command:
Support for HCS data export as OME-Zarr is the last part to be added. The
--bfflag now requiresbioformat2raw 0.3.0which brings native support for HCS support and existing code can be re-used to addomerometadata to each well sample.Probably the main point of review will be to ensure that the layouts are compatible .
ome zarr export Plate:xxxuses the plate/well/row/field of view layout as described in https://ngff.openmicroscopy.org/0.1/ whilebioformat2rawretains a flat layout where each field of view is 0-based index for compatibility withMETADATA.ome.xmlandraw2ometiff. My expectation is that both layouts should be equivalent as long as the correct metadata is filled but this will be a good occasion to compare and test via different downstream clients.