A community effort to collect a curated set of analysis pipelines built using Nextflow.

nf-core

MCCELLPOSE fails on coreograph outputs as it receives flat tiff outputs but requires ome-tiffs with pixel size. Old issue <https://github.com/nf-core/mcmicro/issues/143|here>, but bumping into it as I use v2.

I think the fix should be in coreograph to output OME-TIFF, or we could drop the input read conditions to mccellpose but that feels less clean

Alternatively we follow the same pattern of mesmer and cellpose (which do work with coreograph) and feed them pixel size via ext.args.

<@U044B2ABJUT> <@U0919399YT1> what do you think is best?

Coreograph should output proper metadata in the tiffs but I’m not against passing the pixel size explicitly anyway 

Yes, I think Coreograph tiffs have metadata.... but mccellopse requires OME-XML metadata.

```ome = ome_types.from_xml(tiff.ome_metadata)   # cli.py:245
...
raise TypeError(f"Unsupported source type {type(source)!r}")
TypeError: Unsupported source type &lt;class 'NoneType'&gt;```

that's what I meant by "proper metadata" :slightly_smiling_face:

also by "should" I meant it as an aspiration :sweat_smile: