How to use RNA2Seg on cosmx data

[thomas-wright-bioinformatics]

Hi RNA2Seg team.

Your docs show how to use RNA2Seg on spatial data stored as zarr files. I have cosmx data. Any idea how to load cosmx data for RNA2Seg? I can't find any info on this. Thanks

[tdefa]

Hi,Thomas sorry for late answer.

RNA2SEG use spatialdata as input : https://spatialdata.scverse.org/en/stable/

You just have to transform your cosmx data into the spatiadata format. They are different optionS for this. I list below some of them :

https://spatialdata.scverse.org/projects/io/en/stable/generated/spatialdata_io.cosmx.html
https://gustaveroussy.github.io/sopa/api/readers/#sopa.io.cosmx
https://spatialdata.scverse.org/projects/io/en/latest/

Best :)
Thomas