In case ppl are interested in using OME-Zarr, here is resource that might be relevant: https://github.com/BioImageTools/ome-zarr-image-analysis-nextflow

There has recently also been the following snakemake pipeline using spatialdata internally: https://github.com/gustaveroussy/sopa

nice!

Thanks for posting 🙂 I am also writing a subworkflow to apply flatfield correction to both WSI and HCS

ome-zarr

data (still polishing and writing docs), in case any one is interested.