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# ChatSpatial
**MCP server for spatial transcriptomics analysis via natural language**
[](https://github.com/cafferychen777/ChatSpatial/actions/workflows/ci.yml)
[](https://pypi.org/project/chatspatial/)
[](https://www.python.org/downloads/)
[](https://opensource.org/licenses/MIT)
[](https://cafferychen777.github.io/ChatSpatial/)
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---
<table>
<tr>
<td width="50%">
### Before
```python
import scanpy as sc
import squidpy as sq
adata = sc.read_h5ad("data.h5ad")
sc.pp.filter_cells(adata, min_genes=200)
sc.pp.normalize_total(adata)
sc.pp.log1p(adata)
sc.pp.highly_variable_genes(adata)
sc.tl.pca(adata)
sc.pp.neighbors(adata)
# ... 40 more lines
```
</td>
<td width="50%">
### After
```text
"Load my Visium data and identify
spatial domains"
```
```
Loaded 3,456 spots, 18,078 genes
Identified 7 spatial domains
Generated visualization
```
</td>
</tr>
</table>
---
## Quick Start
**Using Claude Code / Codex / OpenCode?** Just paste this:
```
Install ChatSpatial following https://github.com/cafferychen777/ChatSpatial/blob/main/INSTALLATION.md
```
<details>
<summary>Manual installation</summary>
```bash
# Install uv (recommended - handles complex dependencies)
curl -LsSf https://astral.sh/uv/install.sh | sh
# Create environment and install
python3 -m venv venv && source venv/bin/activate
uv pip install chatspatial
# Configure (use your venv Python path)
claude mcp add chatspatial /path/to/venv/bin/python -- -m chatspatial server
```
</details>
> **Works with any MCP-compatible client** — not just Claude. Use with [OpenCode](https://opencode.ai/), Codex, or any client supporting [Model Context Protocol](https://modelcontextprotocol.io/). Configure your preferred LLM (Qwen, DeepSeek, Doubao, etc.) as the backend.
See [Installation Guide](INSTALLATION.md) for detailed setup including virtual environments and all MCP clients.
---
## Use
```text
Load /path/to/spatial_data.h5ad and show me the tissue structure
```
```text
Identify spatial domains using SpaGCN
```
```text
Find spatially variable genes and create a heatmap
```
---
## Capabilities
| Category | Methods |
|----------|---------|
| **Spatial Domains** | SpaGCN, STAGATE, GraphST, Leiden, Louvain |
| **Deconvolution** | FlashDeconv, Cell2location, RCTD, DestVI, Stereoscope, SPOTlight, Tangram, CARD |
| **Cell Communication** | LIANA+, CellPhoneDB, CellChat, FastCCC |
| **Cell Type Annotation** | Tangram, scANVI, CellAssign, mLLMCelltype, scType, SingleR |
| **Trajectory & Velocity** | CellRank, Palantir, DPT, scVelo, VeloVI |
| **Spatial Statistics** | Moran's I, Local Moran, Geary's C, Getis-Ord Gi*, Ripley's K, Neighborhood Enrichment |
| **Enrichment** | GSEA, ORA, Enrichr, ssGSEA, Spatial EnrichMap |
| **Spatial Genes** | SpatialDE, SPARK-X |
| **Integration** | Harmony, BBKNN, Scanorama, scVI |
| **Other** | CNV Analysis, Spatial Registration |
**60+ methods** across 15 categories. **Supports** 10x Visium, Xenium, Slide-seq v2, MERFISH, seqFISH.
---
## Documentation
| Guide | Description |
|-------|-------------|
| [Installation](INSTALLATION.md) | Virtual environment setup, all platforms |
| [Quick Start](docs/quickstart.md) | 5-minute first analysis |
| [Examples](docs/examples.md) | Step-by-step workflows |
| [Methods Reference](docs/advanced/methods-reference.md) | All 20 tools with parameters |
| [Full Docs](https://cafferychen777.github.io/ChatSpatial/) | Complete reference |
---
## Citation
```bibtex
@software{chatspatial2025,
title={ChatSpatial: Agentic Workflow for Spatial Transcriptomics},
author={Chen Yang and Xianyang Zhang and Jun Chen},
year={2025},
url={https://github.com/cafferychen777/ChatSpatial}
}
```
<div align="center">
**MIT License** · [GitHub](https://github.com/cafferychen777/ChatSpatial) · [Issues](https://github.com/cafferychen777/ChatSpatial/issues)
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<!-- mcp-name: io.github.cafferychen777/chatspatial -->
