Download allen brain data

saeyslab / spatial_ccc_experiments

MIT License

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Download allen brain data #4

Open FrancescaDr opened 3 weeks ago

FrancescaDr commented 3 weeks ago

[x] script for downloading
[x] preprocessing: subset slice section 80

bmanzato commented 3 weeks ago

https://github.com/AllenInstitute/abc_atlas_access/blob/main/descriptions/Zhuang-ABCA-1.md

bmanzato commented 3 weeks ago

cell_metadata_sub = cell_metadata[cell_metadata['brain_section_label'] == 'Zhuang-ABCA-1.080'] cell_metadata_extended_sub = cell_metadata_extended[cell_metadata_extended['brain_section_label'] == 'Zhuang-ABCA-1.080']

adata_section80 = adata[adata.obs.index.isin(list(cell_metadata_sub.index))]

check if the indexes are in the same order first

then: adata_section80.obs = cell_metadata_extended_sub