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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 the file "all_cells_20200625.h5ad" and "snRNA_annotation_astro_subtypes_refined59_20200823.csv"? #3

Closed cristalliao closed 1 year ago

cristalliao commented 1 year ago

Dear Professor, I want to know where I can find this file when I try this great STitch3D. adata_ref = ad.read_h5ad("./data/MouseBrain/all_cells_20200625.h5ad") and labels = pd.read_csv("./data/MouseBrain/snRNA_annotation_astro_subtypes_refined59_20200823.csv", index_col=0) in this part "Run STitch3D on the adult mouse brain dataset". Thanks in advance!

jiazhao97 commented 1 year ago

Hi there,

Thank you for your interest in our STitch3D method!

We obtained the mouse brain snRNA-seq reference from cell2location paper. The two files you mentioned can be accessed through these two links: https://cell2location.cog.sanger.ac.uk/tutorial/mouse_brain_snrna/all_cells_20200625.h5ad, https://cell2location.cog.sanger.ac.uk/tutorial/mouse_brain_snrna/snRNA_annotation_astro_subtypes_refined59_20200823.csv. See this website for more details.

Best, Jia

cristalliao commented 1 year ago

Dear Jia,

Thanks a lot! This problem has been solved. However, I still cannot find the dataset "slicestable.tsv" when I run the code. Could you tell me where can I find it? Thanks in advance!

Best regards, Cristal

gefeiwang commented 1 year ago

This issue is discussed in https://github.com/YangLabHKUST/STitch3D/issues/5#issuecomment-1515931760.

Dear Jia,

Thanks a lot! This problem has been solved. However, I still cannot find the dataset "slicestable.tsv" when I run the code. Could you tell me where can I find it? Thanks in advance!

Best regards, Cristal