compatibility with 10x visium

[wangjiawen2013]

Hi,
Does NCEM support 10x visium datasets ? This is a widely used platform, if NCEM support 10x visium, I think it will become more active becasue so may labs work with 10x visium. We know that there are some limitations for celltalker and cellphonedb and NCEM will help a lot.

[AnnaChristina]

Hi @wangjiawen2013,

Thanks for your intest in NCEM. We support 10x visium data that was deconvoluted with a method of your choice. Important step is to export cell type abundances and cell-type specific expression values.

We recently added a tutorial how to use this data here: https://github.com/theislab/ncem_tutorials/blob/main/tutorials/type_coupling_visium.ipynb

This tutorial uses cell2location as deconvolution method on a public dataset as described here: https://github.com/theislab/ncem_benchmarks/blob/main/notebooks/data_preparation/deconvolution/cell2location_human_lymphnode.ipynb

Happy to help further.

[boyiguo1]

Hi @AnnaChristina,

Thanks for the great work of NCEM. I have a follow-up question on applying NCEM to Visium data. When inferring the cell-type specific expression using spot deconvolution info, we are not necessarily getting gene expression at the single-cell level. For example, we have two cells that are both cell-type A, and the cell-type specific expression of type A in a spot is the summation of two cells. Is there any implicit assumption made here when interpreting the results as cell-cell communication?

P.S.: I saw this seems to be a relevant answer: #122 (comment)

Thank you very much!

Best,
Boyi

[wangjiawen2013]

Hi @AnnaChristina
Where can I download the dataset used in the tutorial ?

[AnnaChristina]

Hi @wangjiawen2013, the dataset we used for showing the usecase for Visium data can be loaded and deconvolved as described here: https://cell2location.readthedocs.io/en/latest/notebooks/cell2location_tutorial.html