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ome / omero-cli-zarr

https://pypi.org/project/omero-cli-zarr/
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bioformats2raw 0.5.0 upgrade and specification compatibility #113

Open sbesson opened 2 years ago

sbesson commented 2 years ago

omero zarr export can write OME-NGFF from OMERO images using either bioformats2raw or ome-zarr-py depending on whether the --bf flag is passed.

As of the 0.3.0 release, omero-cli-zarr will write OME-NGFF according to the 0.4 specification when using ome-zarr-py and according to the 0.2 specification when using the current stable release of bioformats2raw 0.4.0.

From the bioformats2raw front, the upcoming 0.5.0 release should add support for writing OME-NGFF 0.4 specification - see https://github.com/orgs/glencoesoftware/projects/11. As soon as a release candidate/full release is available, a first action should be to test this workflow and confirm the data is written as expected.

A related question is whether we should enforce a dependency on the version of bioformats2raw so that the tool writes the datasets using the same version of the OME-NGFF specification independently of the passed flag. This is not something that can be defined at the Python packaging metadata level as bioformats2raw needs to be installed separately and is rather installed separately as a Java runtime dependency.

One simple approach would be to check for the return value of bioformatsraw --version. Alternatively, we might want to look into an API and possible a command-line option allowing to return the version of the OME-NGFF specification written by bioformats2raw ?

/cc @melissalinkert

melissalinkert commented 2 years ago

https://github.com/glencoesoftware/bioformats2raw/pull/155 might help with this?