diff --git a/frontend/doc-site/032__Contribute and Publish Data.mdx b/frontend/doc-site/032__Contribute and Publish Data.mdx index af24fb1fcd14..70c8f540504c 100644 --- a/frontend/doc-site/032__Contribute and Publish Data.mdx +++ b/frontend/doc-site/032__Contribute and Publish Data.mdx @@ -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