| --- |
| license: mit |
| language: |
| - en |
| tags: |
| - spatial-transcriptomics |
| - snrna-seq |
| - mus |
| pretty_name: Mouse Brain snRNA-seq Reference (cell2location) |
| size_categories: |
| - 10K<n<100K |
| --- |
| |
| # Mouse Brain snRNA-seq Reference (cell2location) |
| |
| Curated, ready-to-load spatial transcriptomics dataset. |
| |
| ## Source |
| |
| - Paper: [Kleshchevnikov et al., Nat. Biotechnol. 2022 (cell2location)](https://www.nature.com/articles/s41587-021-01139-4) |
| - Canonical download: cell2location.cog.sanger.ac.uk/tutorial/mouse_brain_snrna/all_cells_20200625.h5ad |
|
|
| ## Scale |
| |
| | Property | Value | |
| |---|---| |
| | Technology | snRNA-seq (10x Chromium) | |
| | Species | Mus musculus | |
| | Tissue | Mouse brain | |
| | Sections / slices | 0 | |
| | Total cells / spots | 40,572 | |
| |
| ## Files |
| |
| - `all_cells_20200625.h5ad` |
|
|
| Each `.h5ad` follows the AnnData spec: |
| - `.X` — gene expression matrix (cells × genes), sparse where natural |
| - `.obs` — per-cell annotations (see "Metadata" below) |
| - `.obsm['spatial']` — `(n_cells, 2)` float32 spatial coordinates |
| - (where present) `.layers['count']` — raw integer counts |
| - (where present) `.obsm['spatial3d']` — `(n_cells, 3)` float32 (x, y, z=section) |
| |
| ## Metadata (`obs` columns) |
| |
| `sample`, `barcode` |
| |
| ## Notes |
| |
| Mouse-brain snRNA-seq reference from the cell2location tutorial. 40,572 nuclei × 31,053 genes, raw counts. Useful as an external single-cell atlas for cell-type annotation of MERFISH or Slide-seqV2 spatial data. |
| |
| ## Usage |
| |
| ```python |
| import scanpy as sc |
| from huggingface_hub import snapshot_download |
| d = snapshot_download(repo_id='Shaow/mousebrain_snrnaseq_cell2location', repo_type='dataset') |
| adata_ref = sc.read_h5ad(f'{d}/all_cells_20200625.h5ad') |
| ``` |
| |
|
|
| ## Citation |
| |
| If you use this dataset, please cite the source paper above. |
| |
| ## License |
| |
| MIT for the curation/preparation. Underlying data inherits the license of |
| the upstream publication (typically CC-BY-4.0); please see the source paper. |
| |
