Shaow/mouseembryo_stereoseq_temporal

# Mouse Embryo Stereo-seq · 8 developmental stages (E9.5 → E16.5)

Curated, ready-to-load spatial transcriptomics dataset.

## Source

• —Paper: Chen et al., Cell 2022 (MOSTA)00399-3)
• —Canonical download: https://db.cngb.org/stomics/mosta · STDS0000058

## Scale

## Files

• —h5ad/E9.5_E1S1.MOSTA.h5ad
• —h5ad/E10.5_E2S1.MOSTA.h5ad
• —h5ad/E11.5_E1S1.MOSTA.h5ad
• —h5ad/E12.5_E1S1.MOSTA.h5ad
• —h5ad/E13.5_E1S3.MOSTA.h5ad
• —h5ad/E14.5_E1S1.MOSTA.h5ad
• —h5ad/E15.5_E1S2.MOSTA.h5ad
• —h5ad/E16.5_E1S1.MOSTA.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)

annotation

## Notes

8 MOSTA Stereo-seq slices, one per developmental stage from E9.5 to E16.5. Total 514,804 cells across the 8 stages. .X holds log-normalized values; .layers['count'] holds raw int64 counts (use adata.X = adata.layers['count'] for tools that expect raw counts). Per-stage cell counts: E9.5=5,913, E10.5=8,494, E11.5=30,124, E12.5=51,365, E13.5=84,811, E14.5=102,519, E15.5=109,811, E16.5=121,767.

## Usage

import scanpy as sc
from huggingface_hub import snapshot_download
d = snapshot_download(repo_id='Shaow/mouseembryo_stereoseq_temporal', repo_type='dataset')
slices = ['E9.5_E1S1', 'E10.5_E2S1', 'E11.5_E1S1', 'E12.5_E1S1',
          'E13.5_E1S3', 'E14.5_E1S1', 'E15.5_E1S2', 'E16.5_E1S1']
adata_st_list = []
for s in slices:
    a = sc.read_h5ad(f'{d}/h5ad/{s}.MOSTA.h5ad')
    a.X = a.layers['count']
    adata_st_list.append(a)

## 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.