ChatSpatial
MCP server for spatial transcriptomics analysis with 60+ integrated methods
ChatSpatial
MCP server for spatial transcriptomics analysis via natural language
Before
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
After
"Load my Visium data and identify
spatial domains"
Loaded 3,456 spots, 18,078 genes
Identified 7 spatial domains
Generated visualization
Quick Start
Using Claude Code / Codex / OpenCode? Just paste this:
Install ChatSpatial following https://github.com/cafferychen777/ChatSpatial/blob/main/INSTALLATION.md
# 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
Works with any MCP-compatible client — not just Claude. Use with OpenCode, Codex, or any client supporting Model Context Protocol. Configure your preferred LLM (Qwen, DeepSeek, Doubao, etc.) as the backend.
See Installation Guide for detailed setup including virtual environments and all MCP clients.
Use
Load /path/to/spatial_data.h5ad and show me the tissue structure
Identify spatial domains using SpaGCN
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 | Virtual environment setup, all platforms |
| Quick Start | 5-minute first analysis |
| Examples | Step-by-step workflows |
| Methods Reference | All 20 tools with parameters |
| Full Docs | Complete reference |
Citation
If you use ChatSpatial in your research, please cite:
@article{Yang2026.02.26.708361,
author = {Yang, Chen and Zhang, Xianyang and Chen, Jun},
title = {ChatSpatial: Schema-Enforced Agentic Orchestration for Reproducible and Cross-Platform Spatial Transcriptomics},
elocation-id = {2026.02.26.708361},
year = {2026},
doi = {10.64898/2026.02.26.708361},
publisher = {Cold Spring Harbor Laboratory},
URL = {https://www.biorxiv.org/content/early/2026/03/01/2026.02.26.708361},
journal = {bioRxiv}
}
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