Matrix with the number of cells of each celltype, found in each mouse brain region

I’m interested in getting a matrix, based on the data from this paper: A high-resolution transcriptomic and spatial atlas of cell types in the whole mouse brain | Nature

I understand that the paper determined the cell type of each cell, from the spatial transcriptomic data, and then registered it against brain regions.

I would like the matrix, with X rows and Y columns, where there are X cell types in the dataset, and Y brain regions. Each entry Zij would be the number of cells (from cell type i) detected in brain region j.

Has a matrix like this already been computed? If not, how could I compute it from the publicly available data? Thanks

subclass_per_region.csv (194.5 KB)

Hi Nathan, I have attached a csv file with the requested data. It is at the subclass level which is what we used for the paper. I hope that helps.


That’s amazing, thanks Michael, thats a huge help.

The ontology used, seems to use the same acronyms used by the Allen’s interactive atlas viewer. Is there an ontology API / package I can use to work with this? E.g. to get the acronyms for all regions that are descendents of hypothalamus?