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ChatSpatial

MCP server for spatial transcriptomics analysis via natural language

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❌ 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

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✅ After

"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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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!

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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.

Codex (CLI or IDE extension) — MCP config is shared in ~/.codex/config.toml.

Option A: add via CLI

codex mcp add chatspatial -- python -m chatspatial server

Option B: edit ~/.codex/config.toml

[mcp_servers.chatspatial]
command = "python"
args = ["-m", "chatspatial", "server"]

Virtual environment note: Codex runs whatever command you configure. To pin a venv, point command to that environment’s Python, e.g. command = "/path/to/venv/bin/python", or use the full path in the CLI:

codex mcp add chatspatial -- /path/to/venv/bin/python -m chatspatial server

In the Codex TUI, run /mcp to verify the server is active.

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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

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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.

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Docs

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

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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}
}

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MIT License · GitHub · Issues

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<!-- mcp-name: io.github.cafferychen777/chatspatial -->