| --- |
| license: mit |
| language: |
| - en |
| tags: |
| - spatial-transcriptomics |
| - 10x |
| - homo |
| pretty_name: Human Breast Cancer Xenium · Sample 1 Rep1+Rep2 |
| size_categories: |
| - 100K<n<1M |
| --- |
| |
| # Human Breast Cancer Xenium · Sample 1 Rep1+Rep2 |
| |
| Curated, ready-to-load spatial transcriptomics dataset. |
| |
| ## Source |
| |
| - Paper: [Janesick et al., Nat. Commun. 2023](https://www.nature.com/articles/s41467-023-43458-x) |
| - Canonical download: cf.10xgenomics.com/samples/xenium/1.0.1/Xenium_FFPE_Human_Breast_Cancer_Rep{1,2} |
| |
| ## Scale |
| |
| | Property | Value | |
| |---|---| |
| | Technology | 10x Genomics Xenium (313-gene panel) | |
| | Species | Homo sapiens | |
| | Tissue | Human breast cancer (FFPE, sample 1, 2 technical replicates) | |
| | Sections / slices | 2 | |
| | Total cells / spots | 286,532 | |
| |
| ## Files |
| |
| - `h5ad/adata_xenium_rep1.h5ad` |
| - `h5ad/adata_xenium_rep2.h5ad` |
| - `Sample1_replicate1/cell_feature_matrix.h5` |
| - `Sample1_replicate1/cells.csv.gz` |
| - `Sample1_replicate2/cell_feature_matrix.h5` |
| - `Sample1_replicate2/cells.csv.gz` |
|
|
| 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) |
| |
| `rep` |
| |
| ## Notes |
| |
| Xenium FFPE Human Breast Cancer dataset, 2 technical replicates of Sample 1. Rep1: 167,780 cells × 313 genes; Rep2: 118,752 cells × 313 genes. We ship both the convenient h5ad versions and the original raw outputs (`cell_feature_matrix.h5` + `cells.csv.gz`). |
| |
| ## Usage |
| |
| ```python |
| import scanpy as sc |
| from huggingface_hub import snapshot_download |
| d = snapshot_download(repo_id='Shaow/humanbreast_xenium_janesick', repo_type='dataset', |
| allow_patterns='h5ad/*.h5ad') |
| adata_rep1 = sc.read_h5ad(f'{d}/h5ad/adata_xenium_rep1.h5ad') |
| adata_rep2 = sc.read_h5ad(f'{d}/h5ad/adata_xenium_rep2.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. |
| |
