| --- |
| license: mit |
| language: |
| - en |
| tags: |
| - spatial-transcriptomics |
| - 10x |
| - homo |
| pretty_name: Human DLPFC Visium · 4 adjacent slices |
| size_categories: |
| - 10K<n<100K |
| --- |
| |
| # Human DLPFC Visium · 4 adjacent slices |
| |
| Curated, ready-to-load spatial transcriptomics dataset. |
| |
| ## Source |
| |
| - Paper: [Maynard et al., Nat. Neurosci. 2021](https://www.nature.com/articles/s41593-020-00787-0) |
| - Canonical download: spatialLIBD R package · slices 151673–151676 |
|
|
| ## Scale |
| |
| | Property | Value | |
| |---|---| |
| | Technology | 10x Genomics Visium | |
| | Species | Homo sapiens | |
| | Tissue | Human dorsolateral prefrontal cortex | |
| | Sections / slices | 4 | |
| | Total cells / spots | 14,243 | |
| |
| ## Files |
| |
| - `h5ad/adata_1.h5ad` |
| - `h5ad/adata_2.h5ad` |
| - `h5ad/adata_3.h5ad` |
| - `h5ad/adata_4.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) |
| |
| `layer`, `in_tissue`, `array_row`, `array_col` |
| |
| ## Notes |
| |
| 4 of the 12-slice Maynard atlas (slices 151673–151676), preprocessed as ready-to-load AnnData. `obs['layer']` carries the manual L1–L6 + WM annotation. |
| |
| ## Usage |
| |
| ```python |
| import scanpy as sc |
| from huggingface_hub import snapshot_download |
| d = snapshot_download(repo_id='Shaow/dlpfc_visium_4slice', repo_type='dataset') |
| adata_st_list = [sc.read_h5ad(f'{d}/h5ad/adata_{i}.h5ad') for i in range(1, 5)] |
| ``` |
| |
|
|
| ## 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. |
| |
