The lack of spatial information in ST data

[tqwang743]

Hi,

Thank you very much for providing a rich dataset for research! I am trying to use the data you provide to do the cell type deconvolution task but I meet some difficulties.

In the simulationDataUpload.zip, you offer Spatial.h5ad and scRNA.h5ad for cell type deconvolution, but there are no spatial information in Spatial.h5ad. Also, In all methods mentioned in your paper, there are some methods that require spatial information in ST data to perform cell type deconvolution task, such as DestVI. So, how do you deal with it?

I would appreciate it if you could give me some suggestions to the difficulties I meet. Thank you very much!

best,
tqwang