Dataset Viewer
The dataset viewer is not available because its heuristics could not detect any supported data files. You can try uploading some data files, or configuring the data files location manually.
# 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.
- Downloads last month
- -