wanglab-broad / mcns-atlas Goto Github PK

Hi,
I'm trying to use your STARMAP+ algorithms for spot detection in 3D and preprocessing. There is no obvious script considered as master where functions are called. Could you please specify if this script exists?

Hi, thanks for sharing this great work!

Why didn't you perform spatial clustering to annotate cell types? Many spatial clustering methods, such as BayesSpace, SpaGCN, claim that they can better capture the spatial transcriptomic patterns by incorporating spatial information into clustering.

Thank you for providing a comprehensive, high-resolution single cell resource that integrates a spatial molecular atlas, cell taxonomy, brain anatomy, and genetic manipulation capabilities of the mammalian central nervous system (CNS)! It's beautiful and useful!

Recently I have been working on an annotation of mouse brains, and I would like to use your data as a reference to automatically annotate our data using the Garnett tool (https://cole-trapnell-lab.github.io/garnett/docs/#1b-train-your-own-classifier). Could you provide me with your markers (26 main cell type's marker and tissue markers, such as from https://github.com/wanglab-broad/mCNS-atlas/blob/main/Tissue_domain/find_tissue_genemarker.ipynb). Many thanks.
If you could provide me with markers from imputed data, that would be even better!