Error reading Xenium data: morphology file missing #362

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1. LucaMarconato

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   xenium

   on Feb 1, 2026
2. LucaMarconato commented on Feb 1, 2026

   

   LucaMarconato

   on Feb 1, 2026

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   Thanks for reporting, I suggest to make a symlink for the expected file name. A fix in xenium() would be to look also for the alternative file name.
3. enric-bazz commented on Feb 2, 2026

   

   enric-bazz

   on Feb 2, 2026

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   Thanks for the reply, following up with some observations.
   Looking at the Xenium reader source code, for Xenium versions > 2.0.0, morphology_mip.ome.tif is no longer consumed. Only images under morphology_focus/ are parsed into the SpatialData object, and the full Z-stack morphology.ome.tif is not used. Is this the intended behavior?

   For the dataset I'm using, the "analysis_sw_version": "R&D" specification in the experiment.xenium file is not recognized by the parser. This triggers the < 2.0.0 code path, causing the reader to look for the morphology_mip.ome.tif file that does not exist. The root cause appears to be the same as issue #361.

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