Seurat Xenium QC

Question

[yura.grabovska]

I'm working with some Xenium data. I've gone through the Seurat vignette and am pretty happy with some of the basic tools for visualising and analysing cell types.

I'm more wondering what QC are people typically doing for Xenium and/or Visium assays? I've not been able to find much discussion about this. Should I just be filtering out low feature cells?

The Seurat objects contain assays: BlankCodeword, ControlCodeword, ControlProbe - what do I do with these?

[Bastien Hervé]

You can check some papers using these technologies to see what QC they apply and would help you make your own for your dataset. The Seurat vignette for spatial is somehow limited, squidpy is a bit more informative.

The codeword is part of the concept of Xenium : https://www.10xgenomics.com/support/software/xenium-panel-designer/latest/tutorials/xenium-panel-design-concepts-terms