Define how omero["name"] should be used #353
Description
During conversion from Tiff to OME-zarr we rename MicroManager positions to match the HCS row/col/fov standard using MicroManagerFOVMapping.hcs_position_labels. This function turns positions named A1-Site_0 into FOVs at A/1/0, for example.
OME-zarr metadata contains an omero["name"] field. We need to define how that field is used. Continuing with the above example, during zarr conversion we write omero["name"] = A1-Site_0, even though the FOV name is now 0, see
/hpc/projects/intracellular_dashboard/viral-sensor/2024_02_13_ZIV_DENV_Timelapse/0-convert/2024_02_13_ZIV_DENV-Timelapse_1.zarr/A/1/0/.zattrs
This omero name is not carried through the different reconstruction steps. For example, after phase reconstruction of that dataset omero["name"] is set to 0 by create_empty_plate.
We should use that field consistently. My vote is to match the HCS FOV name during conversion and set omero["name"] = 0, consistent with downstream reconstruction pipelines. Note that the omero metadata is transitional, and may be removed in the future.