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Download allen brain data #4

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FrancescaDr opened this issue Jun 10, 2024 · 2 comments
Open
2 tasks done

Download allen brain data #4

FrancescaDr opened this issue Jun 10, 2024 · 2 comments

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@FrancescaDr
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FrancescaDr commented Jun 10, 2024 •
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  • script for downloading
  • preprocessing: subset slice section 80
@bmanzato
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https://github.com/AllenInstitute/abc_atlas_access/blob/main/descriptions/Zhuang-ABCA-1.md

@bmanzato
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bmanzato commented Jun 10, 2024 •
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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

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@FrancescaDr @bmanzato