Error reading Xenium data: morphology file missing

[enric-bazz]

While trying to read Xenium data with spatialdata_io.xenium(), I get the following error:

The file "path/to/xenium/data/morphology_mip.ome.tif" does not exist.

Inspecting the folder shows that the file is actually named:

morphology.ome.tif

The dataset and software versions are the same as in issue #361:

• spatialdata_io version: 0.6.0
• Xenium platform: Xenium Onboard Analysis 4.0.0

[LucaMarconato]

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.

[enric-bazz]

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.