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Integrate OME-Zarr and a visualisation for this data #16862

Open bgruening opened 8 months ago

bgruening commented 8 months ago

The spec: https://github.com/ome/ngff A python library: https://github.com/ome/ome-zarr-py A viewer: https://github.com/hms-dbmi/vizarr

beatrizserrano commented 8 months ago

OME-Zarr converter and data transfer were developed within Euro-BioImaging but not available in the ToolShed because of missing dependencies in conda-forge. Let's take this discussion to the BioHackathon :)

bgruening commented 8 months ago

Isn't this what is needed for the converters? https://anaconda.org/bioconda/bftools

bugraoezdemir commented 8 months ago

The converter in the bftools package, unfortunately, cannot convert to OME-Zarr.

Currently, the most commonly-used tool to convert various proprietary image formats to OME-Zarr is bioformats2raw:

https://anaconda.org/ome/bioformats2raw https://github.com/glencoesoftware/bioformats2raw

Bioformats2raw is, however, not registered on conda-forge or bioconda. Previously, we had a discussion on moving it to conda-forge and there was some progress, but then it has been on stall:

https://github.com/ome/conda-bioformats2raw/issues/14

Perhaps we should resume this effort now?

beatrizserrano commented 8 months ago

ping @annefou