| --- |
| license: mit |
| language: |
| - en |
| tags: |
| - spatial-transcriptomics |
| - 10x |
| - mus |
| pretty_name: Mouse Brain Visium · 3 complementary sections |
| size_categories: |
| - 10K<n<100K |
| --- |
| |
| # Mouse Brain Visium · 3 complementary sections |
| |
| Curated, ready-to-load spatial transcriptomics dataset. |
| |
| ## Source |
| |
| - Paper: [10x Genomics public datasets](https://www.10xgenomics.com/datasets) |
| - Canonical download: cf.10xgenomics.com/samples/spatial-exp/1.1.0/V1_* |
| |
| ## Scale |
| |
| | Property | Value | |
| |---|---| |
| | Technology | 10x Genomics Visium | |
| | Species | Mus musculus | |
| | Tissue | Mouse brain (sagittal anterior, sagittal posterior, coronal) | |
| | Sections / slices | 3 | |
| | Total cells / spots | 8,816 | |
| |
| ## Files |
| |
| - `Visium_sagittal-anterior2/V1_Mouse_Brain_Sagittal_Anterior_Section_2_filtered_feature_bc_matrix.h5` |
| - `Visium_sagittal-posterior2/V1_Mouse_Brain_Sagittal_Posterior_Section_2_filtered_feature_bc_matrix.h5` |
| - `Visium_coronal/V1_Adult_Mouse_Brain_filtered_feature_bc_matrix.h5` |
|
|
| 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) |
| |
| `in_tissue`, `array_row`, `array_col` |
| |
| ## Notes |
| |
| Three 10x Visium mouse-brain serial sections offering complementary tissue views. Original 10x outputs (filtered h5 + spatial/) kept in conventional subfolders so `sc.read_visium(folder)` works directly. After filtering to in_tissue==1: 2825 / 3289 / 2702 spots respectively. |
| |
| ## Usage |
| |
| ```python |
| import scanpy as sc |
| from huggingface_hub import snapshot_download |
| d = snapshot_download(repo_id='Shaow/mousebrain_visium_3section', repo_type='dataset') |
| adata_st_list = [] |
| for sub, h5 in [ |
| ('Visium_sagittal-anterior2', 'V1_Mouse_Brain_Sagittal_Anterior_Section_2_filtered_feature_bc_matrix.h5'), |
| ('Visium_sagittal-posterior2', 'V1_Mouse_Brain_Sagittal_Posterior_Section_2_filtered_feature_bc_matrix.h5'), |
| ('Visium_coronal', 'V1_Adult_Mouse_Brain_filtered_feature_bc_matrix.h5'), |
| ]: |
| a = sc.read_visium(f'{d}/{sub}', count_file=h5) |
| a.var_names_make_unique() |
| adata_st_list.append(a[a.obs['in_tissue'] == 1].copy()) |
| ``` |
| |
|
|
| ## 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. |
| |
