Does squidpy support the analysis of CODEX data? I see various ST data types in the Palla et al. paper and in the example/tutorial section, but I can’t find a mention of compatibility with CODEX. Thanks!
hey @gvestal, what’s the format of (post processed) codex data? This tutorial could help Import spatial data in AnnData and Squidpy — Squidpy main documentation
I have the same question!
Hi @gvestal @wangjiawen2013
Squidpy currently has no reader for Flow Cytometry Standard (fcs) files, which is the output format of CODEX (now PhenoCycler). This functionality will soon be added to Squidpy see the issue on github here.
Will mention it here as well, once the functionality has been added.
Hi @gvestal, @wangjiawen2013, this issue has been solved
CODEX formatted files can now also be used with Squidpy, by using spatialdata-io, which is now used for readers of spatial-omics technologies.
first install latest development version of spatialdata-io:
pip install git+https://github.com/scverse/spatialdata-io.git@main
then import spatialdata_io and load the data:
import spatialdata_io
sdata = spatialdata_io.codex(path="path/to/directory/")
adata = sdata.table
Note: if you don’t use .fcs files but .csv files, set fcs=False in codex().