How can I find cell type for Example 2 dataset?

YangLabHKUST / STitch3D

Construction of a 3D whole organism spatial atlas by joint modeling of multiple slices

https://stitch3d-tutorial.readthedocs.io/en/latest/index.html#

MIT License

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How can I find cell type for Example 2 dataset? #17

Open cristalliao opened 1 year ago

cristalliao commented 1 year ago

Hi Professor, I have a question about the cell type, I want to know how can I find the cell type for the Example 2 dataset. For example, we have different slices such as 17x26-slice0, I want to know which cell type this slice is. How can I find this information? Could you provide some guidelines? Now I want to do is to find the "ground truth" of each slice. Thanks a lot!

Best regards, Cristal

gefeiwang commented 1 year ago

Hi Cristal,

Cell-type information produced by STitch3D is saved in the output of model.eval() function. For the human heart example, after running result = model.eval(adata_st_list_raw, save=True, output_path=save_path), you will get a list of anndata objects and cell-type proportions are saved in the .obs view of anndata objects.

Best, Gefei