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docs: add spatial standards to Contribute documentation #7367

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Oct 24, 2024
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docs: add spatial standards to Contribute documentation #7367

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6d25c82
add Visium & Slide-seq standards
jahilton Oct 17, 2024
00d9b15
unbold some text
jahilton Oct 17, 2024
1c68f08
Merge branch 'main' into jason/contribut-doc-addspatial
nayib-jose-gloria Oct 23, 2024
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12 changes: 12 additions & 0 deletions frontend/doc-site/032__Contribute and Publish Data.mdx
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Expand Up @@ -67,6 +67,18 @@ Each dataset needs the following information added to a single h5ad (AnnData 0.1
- **Features in var & raw.var (if present)**:
- index is Ensembl ID
- preference is that gene have not been filtered in order to maximize future data integration efforts
- **Additional standards for single-capture area Visium datasets** (largely aligns with [scanpy’s model](https://scanpy.readthedocs.io/en/stable/generated/scanpy.read_visium.html), [this notebook](https://github.com/Lattice-Data/lattice-tools/blob/main/cellxgene_resources/curation_visium.ipynb) may be helpful to curate from Space Ranger outputs):
- Empty spots must be included (should be 4992 observations)
- obsm['spatial']
- obs['array_row']
- obs['array_col']
- obs['in_tissue']
- uns['spatial'][library_id]['images']['fullres'] fullres image (preferred)
- uns['spatial'][library_id]['images']['hires'] hires image
- uns['spatial'][library_id]['scalefactors']['spot_diameter_fullres']
- uns['spatial'][library_id]['scalefactors']['tissue_hires_scalef']
- **Additional standards for single-puck Slide-seq datasets**:
- obsm['spatial']

## Data Submission Policy

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