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README.md

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+---
+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.