How to read nanostring Geomx DSP data

scverse / squidpy

Spatial Single Cell Analysis in Python

https://squidpy.readthedocs.io/en/stable/

BSD 3-Clause "New" or "Revised" License

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How to read nanostring Geomx DSP data #748

Closed jwoods9 closed 2 days ago

jwoods9 commented 10 months ago

It seems that the nanostring tutorial is specific to CosMx data. Is there a way to analyze GeoMx DSP data? I'm having trouble figuring out how to make an AnnData object. Any help would be greatly appreciated. Thanks!

HollyRafique commented 3 months ago

did you make any progress on this? not sure if squidpy is even the right tool for GeoMx but would be interested to hear from anyone who found a way to make it work?

giovp commented 2 days ago

hi, we do not and will not support geomx data, apologies. If you are interested in implementing a reader, I would suggest to do it in spatialdata-io https://spatialdata.scverse.org/projects/io/en/latest/index.html