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# ChatSpatial
**MCP server for spatial transcriptomics analysis via natural language**
[](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
```
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</table>
---
> **Note**: This is a **demo version**. If you encounter any issues or have feedback, please [open an issue](https://github.com/cafferychen777/ChatSpatial/issues) or contact us anytime. Your feedback helps us improve!
---
## Install
```bash
pip install chatspatial
```
## Configure
**Claude Desktop** — add to `~/Library/Application Support/Claude/claude_desktop_config.json`:
```json
{
"mcpServers": {
"chatspatial": {
"command": "python",
"args": ["-m", "chatspatial", "server"]
}
}
}
```
**Claude Code**:
```bash
claude mcp add chatspatial python -- -m chatspatial server
```
> Restart Claude after configuration.
---
## Use
Open Claude and chat:
```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 (inferCNVpy, Numbat), Spatial Registration (PASTE, STalign) |
**60+ methods** across 15 categories. **Supports** 10x Visium, Xenium, Slide-seq v2, MERFISH, seqFISH.
---
## Docs
- [Installation Guide](INSTALLATION.md) — detailed setup for all platforms
- [Examples](docs/examples/) — step-by-step workflows
- [Full Documentation](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}
}
```
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**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 -->
