Submitted by: Fakhruddin Ahmad Course: Special Topics in Bioinformatics Deadline: 26th April 2026
A complete spatial transcriptomics analysis project following the 10x Genomics pipeline tutorials covering Scanpy basics, Visium fluorescence, Visium H&E, and Xenium single-cell resolution analysis.
Spatial transcriptomics answers a fundamental question in biology: not just which genes are expressed, but where they are expressed inside a tissue. Traditional scRNA-seq destroys spatial information during dissociation. Spatial transcriptomics preserves the physical location of each measurement, allowing us to map gene expression onto tissue architecture.
spatial-transcriptomics-10x/ ├── notebooks/ │ ├── 01_scanpy_basics.ipynb │ ├── 02_visium_fluorescence.ipynb │ ├── 03_visium_hne.ipynb │ └── 04_xenium_analysis.ipynb ├── figures/ │ ├── 01_scanpy/ │ ├── 02_visium_fluorescence/ │ ├── 03_visium_hne/ │ └── 04_xenium/ ├── data/ │ └── README.md ├── docs/ │ └── methodology.md ├── requirements.txt └── README.md
| Notebook | Dataset | Key Analysis |
|---|---|---|
| 01 — Scanpy Basics | Human Lymph Node (Visium) | QC, clustering, UMAP, spatial plots |
| 02 — Visium Fluorescence | Mouse Brain (fluorescence) | Image segmentation, DAPI/NEUN/GFAP features |
| 03 — Visium H&E | Mouse Brain (H&E) | Spatial graphs, ligand-receptor, Moran's I |
| 04 — Xenium Analysis | Synthetic Lung Cancer | Single-cell resolution, Delaunay graph |
- Visium spot-level analysis
- Image feature extraction
- Spatial graph construction
- Neighborhood enrichment
- Co-occurrence analysis
- Ligand-receptor interactions
- Moran's I spatial autocorrelation
- Delaunay triangulation
- Centrality scores
pip install -r requirements.txt| Package | Purpose |
|---|---|
| scanpy | Core single-cell analysis |
| squidpy | Spatial transcriptomics |
| anndata | Data format |
| pandas | Data manipulation |
| numpy | Numerical computing |
| matplotlib | Plotting |
| Dataset | Source |
|---|---|
| Human Lymph Node | 10x Genomics |
| Mouse Brain Fluorescence | Squidpy built-in |
| Mouse Brain H&E | Squidpy built-in |
| Xenium Lung Cancer | Synthetic |