ChatSpatial

Name: ChatSpatial
Author: cafferychen777

MCP server for spatial transcriptomics analysis via natural language

PyPI Python 3.10+ License: MIT Docs

❌ 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

Note: This is a demo version. If you encounter any issues or have feedback, please open an issue or contact us anytime. Your feedback helps us improve!

Install

pip install chatspatial

Configure

Claude Desktop — add to ~/Library/Application Support/Claude/claude_desktop_config.json:

{ "mcpServers": { "chatspatial": { "command": "python", "args": ["-m", "chatspatial", "server"] } } }

Claude Code:

claude mcp add chatspatial python -- -m chatspatial server

Restart Claude after configuration.

Use

Open Claude and chat:

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 (inferCNVpy, Numbat), Spatial Registration (PASTE, STalign)

60+ methods across 15 categories. Supports 10x Visium, Xenium, Slide-seq v2, MERFISH, seqFISH.

Docs

Installation Guide — detailed setup for all platforms
Examples — step-by-step workflows
Full Documentation — complete reference

Citation

@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} }

MIT License · GitHub · Issues