From 6d25c82e069c04c427fd42a342de3a838239956b Mon Sep 17 00:00:00 2001 From: jahilton Date: Thu, 17 Oct 2024 16:26:31 -0700 Subject: [PATCH 1/2] add Visium & Slide-seq standards --- .../doc-site/032__Contribute and Publish Data.mdx | 12 ++++++++++++ 1 file changed, 12 insertions(+) diff --git a/frontend/doc-site/032__Contribute and Publish Data.mdx b/frontend/doc-site/032__Contribute and Publish Data.mdx index af24fb1fcd14..86091f98c454 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 From 00d9b15ded21b44604453cabfb84fc7359dc2fd4 Mon Sep 17 00:00:00 2001 From: jahilton Date: Thu, 17 Oct 2024 16:29:36 -0700 Subject: [PATCH 2/2] unbold some text --- frontend/doc-site/032__Contribute and Publish Data.mdx | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/frontend/doc-site/032__Contribute and Publish Data.mdx b/frontend/doc-site/032__Contribute and Publish Data.mdx index 86091f98c454..70c8f540504c 100644 --- a/frontend/doc-site/032__Contribute and Publish Data.mdx +++ b/frontend/doc-site/032__Contribute and Publish Data.mdx @@ -67,7 +67,7 @@ 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)**: +- **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']