IMC analysis workflow using python

[Emberwhirl]

Hi, I was wondering if you have a workflow for analyzing IMC data using python (or more specifically, the AnnData-Scanpy-Squidpy ecosystem as mentioned in your preprint 10.1101/2021.11.12.468357). I am having problems importing images in AnnData. Thank you.

[nilseling]

Hi @Emberwhirl,

thanks for reaching out. The steinbock framework allows the output of single-cell data as AnnData files (single acquisitions or aggregated). However, I'm not familiar with loading in the the images into the AnnData object. Maybe @jwindhager or @ndamond can comment on this? Otherwise you might want to reach out to the AnnData developers directly as the import of TIFF files should be relatively straight forward. But for now, we only provide an R based workflow for analysing IMC data.