| --- |
| license: mit |
| language: |
| - en |
| tags: |
| - spatial-transcriptomics |
| - slide-seqv2 |
| - mus |
| pretty_name: Mouse Hippocampus Slide-seqV2 · Puck_200115_08 |
| size_categories: |
| - 10K<n<100K |
| --- |
| |
| # Mouse Hippocampus Slide-seqV2 · Puck_200115_08 |
| |
| Curated, ready-to-load spatial transcriptomics dataset. |
| |
| ## Source |
| |
| - Paper: [Stickels et al., Nat. Biotechnol. 2021](https://www.nature.com/articles/s41587-020-0739-1) |
| - Canonical download: figshare 21829905 (file id 38736651) — derived from Single Cell Portal SCP815 |
|
|
| ## Scale |
| |
| | Property | Value | |
| |---|---| |
| | Technology | Slide-seqV2 (10 µm beads) | |
| | Species | Mus musculus | |
| | Tissue | Mouse hippocampus | |
| | Sections / slices | 1 | |
| | Total cells / spots | 35,349 | |
| |
| ## Files |
| |
| - `AdataMH1.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) |
| |
| `leiden`, `n_genes_by_counts`, `total_counts` |
| |
| ## Notes |
| |
| Puck_200115_08 mouse-hippocampus Slide-seqV2 puck (35,349 beads × 20,527 genes), QC-filtered and normalized. `obsm['spatial']` is set from `obs[xcoord, ycoord]`. Raw counts in `.X` (sparse float32, max ≈ 1900). |
| |
| ## Usage |
| |
| ```python |
| import scanpy as sc |
| from huggingface_hub import snapshot_download |
| d = snapshot_download(repo_id='Shaow/mousehippocampus_slideseqv2', repo_type='dataset') |
| adata = sc.read_h5ad(f'{d}/AdataMH1.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. |
| |
