Single sample within group

[RunyuXia]

Description of feature

Hi! I have two Visium HD samples, one belongs to the disease phenotype and the other one wild type. I was wondering if it’s possible to use CellCharter to compare the spatial niches between these two samples? Thank you for your help!

[marcovarrone]

Hi @RunyuXia, absolutely!

If you managed to load the Visium HD dataset in anndata format, you can follow the same steps shown in the CosMx tutorial. The procedure should be the same.

In that tutorial, I compute niches for multiple samples, as it is in your case.

Let me know if you have any trouble in running CellCharter on your samples :)

[drosop]

Is it possible to run cellcharter for multiple samples together? clustering all samples coming from different TMAs together? Thank you,