This OMERO command-line plugin allows you to export images from OMERO as zarr files, according to the spec at https://github.com/ome/omero-ms-zarr/blob/master/spec.md.
It supports export using 2 alternative methods:
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By default the OMERO API is used to load planes as numpy arrays and the zarr file is created from this data. NB: currently, large tiled images are not supported by this method.
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Alternatively, if you can read directly from the OMERO binary repository and have installed https://github.com/glencoesoftware/bioformats2raw then you can use this to create zarr files.
To export images via the OMERO API:
# Image will be saved in current directory as 1.zarr
$ omero zarr Image:1
# Specify an output directory
$ omero zarr Image:1 --output /home/user/zarr_files
# Cache each plane as a numpy file.npy. If connection is lost, and you need
# to export again, we can use these instead of downloading again
# omero zarr Image:1 --cache_numpy
To export images via bioformats2raw we use the --bf flag:
export MANAGED_REPO=/var/omero/data/ManagedRepository
export BF2RAW=/opt/tools/bioformats2raw-0.2.0-SNAPSHOT
$ omero zarr 1 --bf --output /home/user/zarr_files
Image exported to /home/user/zarr_files/2chZT.lsm