One thing to be aware of is that OME-Zarr doesn't have a fully standardized way to store OME-XML metadata yet! There is a "transitional" section in the specification (just adopting what the

bioformats2raw

tool implemented for its own internal use) but the official replacement doesn't seem to be anywhere in sight. https://ngff.openmicroscopy.org/latest/index.html#bf2raw

right, that is an issue, but I hope once the OME-XML is standardised, the OME team simply updates the bf2raw lib in a way we can easily update our containers and modules, and continue to use it. In any case, OME-TIFF should be the safe bet for formatting the final output

Transitional means that these elements will change in the future (largely perhaps because their naming is not ideal, like the “omero” block). There are a series of efforts currently that will eventually give the OME-XML a final place: the additional top-level namespace from RFC-2, the work on collections that’s currently investigating RO-Crate, and outside of the NGFF spec, work on defining a JSON representation of OME to not require the jump to XML.

Josh I had no idea you were on here or I would have summoned you myself 😅

Heh. 😉