ChatSpatial

MCP server for spatial transcriptomics analysis through natural language interfaces.

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1{2  "mcpServers": {3    "cafferychen777-chatspatial": {4      "command": "uvx",5      "args": [6        "chatspatial==1.6.0"7      ]8    }9  }10}

.cursor/mcp.jsonMCP server

Transport: stdio
Status: Local

Power your agent

Add this server

The publisher's own command. Not a PlugMCP endpoint.

Add to Cursor Add to VS Code Run on PlugMCP

Host a copy with our keys and logs.

Local command

uvx chatspatial==1.6.0

Claude Code has no install link for a local command. Copy the command below and run it in a terminal.

shClaude Code

1claude mcp add cafferychen777-chatspatial -- uvx chatspatial==1.6.0

Run in a terminal.

jsonClaude Desktop

1{2  "mcpServers": {3    "cafferychen777-chatspatial": {4      "command": "uvx",5      "args": [6        "chatspatial==1.6.0"7      ]8    }9  }10}

claude_desktop_config.json

Local · pypiPublisher installStep-by-step: add this in Claude

Remote URL or a command on your machine? How the two installs differ

Run on PlugMCP

Host a copy with our keys and logs.

A new server you create. It is not this listing's official endpoint. Use the publisher install when you want their URL and their credentials.

Launch

Server facts

Local

Transport: stdio
License: MIT
Last checked: 2026-10-27

Stars: 45
Tools: —
Uptime: —

Tools

No tool list yet. Remote servers get one after the first health check.

FAQ

Questions

How do I install ChatSpatial?

Copy the stdio config for Cursor, Claude Desktop, Claude Code, or VS Code on this page. It uses the publisher's install, not a PlugMCP proxy.

Does ChatSpatial need an API key?

No required environment variable is listed on this record.

What transport does ChatSpatial use?

ChatSpatial runs locally over stdio.

When was ChatSpatial last checked?

Last checked 2026-10-27. MCP server for spatial transcriptomics analysis through natural language interfaces.

From the publisher

Documentation

ChatSpatial

MCP server for spatial transcriptomics analysis via natural language

ChatSpatial exposes 20 schema-validated MCP tools that orchestrate 67 spatial transcriptomics methods across 13 analytical categories. The tools are the stable natural-language interface; the methods are the analysis backends selected through tool parameters.

The server implements MCP 2026-07-28 through the official Python SDK v2 and continues to serve 2025-11-25 clients through SDK-managed protocol negotiation. STDIO remains the secure local default; Streamable HTTP is available for explicitly configured HTTP deployments.

Start Here

Install uv once, then register ChatSpatial without creating or managing a Python environment:

Codex:

codex mcp add chatspatial -- uvx --from chatspatial chatspatial server

Claude Code:

claude mcp add --scope user chatspatial -- \
  uvx --from chatspatial chatspatial server

uvx creates an isolated environment on first launch and reuses its cache on later launches. Restart the MCP client after adding the server.

The command above installs the standard runtime. To make all 15 composable Python method families available in the same isolated MCP environment, use:

uvx --from 'chatspatial[full]' chatspatial server

full includes CellRank, FastCCC, the maintained spatial-domain and registration backends, annotation, enrichment, and the other portable Python families. R bridges, AESTETIK, and rctd-py remain separate because they have system, platform, or large-runtime requirements. See the installation guide before enabling those families.

Then:

Run your first analysis — Quick Start
Choose optional method families or a persistent environment — Installation Guide
Configure another MCP client — Configuration Guide
Reproduce the manuscript key results without an LLM — Reproduction image

Docker quick start:

docker pull cafferyyang777/chatspatial:latest

Minimal example prompt:

Load /absolute/path/to/spatial_data.h5ad and plot gene expression at the spatial coordinates

The Quick Start provides a downloadable sample and a Leiden workflow that runs with the standard installation. Its sample has spatial coordinates but no H&E image. SpaGCN requires the optional spatial-domains extra.

If you use Docker, mount host data to /data and prompt with the container path, for example /data/spatial_data.h5ad.

ChatSpatial works with any MCP-compatible client — Claude Code, Claude Desktop, Codex, OpenCode, and other MCP-capable tools.

Capabilities

Current coverage includes 67 methods across 13 analytical categories, exposed through 20 MCP tools. Supports 10x Visium, Xenium, Slide-seq v2, MERFISH, seqFISH.

Category	Example methods
Data Loading & Preprocessing	Scanpy I/O, QC, Normalization, HVG, PCA, Neighbors
Visualization	Spatial plots, Embedding plots, Gene expression overlays
Spatial Domain Identification	SpaGCN, STAGATE, GraphST, BANKSY, AESTETIK, Leiden, Louvain
Deconvolution	FlashDeconv, Cell2location, RCTD (spacexr or rctd-py), DestVI, Stereoscope, SPOTlight, Tangram, CARD
Cell-Cell Communication	LIANA+, CellPhoneDB, CellChat (`cellchat_r`), FastCCC
Cell Type Annotation	Tangram, scANVI, CellAssign, mLLMCelltype, scType, SingleR, marker-score and threshold rules
Differential Expression	Wilcoxon, t-test, Logistic Regression, pyDESeq2
Trajectory Inference	CellRank, Palantir, DPT
RNA Velocity	scVelo, VeloVI
Spatial Statistics	Moran's I, Local Moran, Geary's C, Getis-Ord Gi*, Ripley's K, Co-occurrence, Neighborhood Enrichment, Centrality Scores, Local Join Count, Network Properties
Enrichment Analysis	GSEA, ORA, Enrichr, ssGSEA, Spatial EnrichMap
Spatially Variable Genes	SpatialDE, SPARK-X, FlashS
Multi-sample Integration	Harmony, BBKNN, Scanorama, scVI
CNV Analysis	InferCNVPy, Numbat
Spatial Registration	PASTE, STalign

Documentation

Guide	Use this when...
Installation	You need optional methods or a persistent Python environment
Docker	You want a reproducible container runtime or local dependency resolution fails
Configuration	You need exact MCP client syntax or the runtime path model
Quick Start	ChatSpatial is installed and you want the first successful analysis
Concepts	You need to choose an analysis strategy from a biological question
Examples	You want copy-pasteable natural-language workflow prompts
Methods Reference	You need canonical tool names, method names, parameters, and defaults
Troubleshooting	Setup, data loading, or analysis behavior is not working
Full Docs	You want the complete documentation site

Reproducibility

Each release publishes a reproduction image under the -repro tag. It re-executes the DLPFC spatial-domain and OSCC CARD deconvolution tool calls recorded during the manuscript experiments, without calling any LLM, and compares the results with the reported values:

docker run --rm -v "$PWD/out:/outputs" \
  cafferyyang777/chatspatial@sha256:ac3ba1ed8235c3d53ca72005d8ad2556cac007f5ddb932ae3e1d1241fa2cf9d8 \
  chatspatial-reproduce

reproducibility/ contains the image definition and describes what it checks. The experiment and analysis scripts for the manuscript are in ChatSpatial-Reproducibility.

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}
}

ChatSpatial orchestrates many excellent third-party methods. Please also cite the original tools your analysis used.

Contributing

Documentation improvements, bug reports, and new analysis methods are all welcome. See CONTRIBUTING.md.

MIT License · GitHub · Issues

ChatSpatial

cafferychen77745starsClaim this server

MCP server for spatial transcriptomics analysis through natural language interfaces.

Data Science Ml

Add to Cursor Add to VS Code Run on PlugMCPClaim this server

GitHub Website

Add to Cursor Add to VS Code Run on PlugMCP

1{2  "mcpServers": {3    "cafferychen777-chatspatial": {4      "command": "uvx",5      "args": [6        "chatspatial==1.6.0"7      ]8    }9  }10}

.cursor/mcp.jsonMCP server

Transport: stdio
Status: Local

Power your agent

Add this server

The publisher's own command. Not a PlugMCP endpoint.

Add to Cursor Add to VS Code Run on PlugMCP

Host a copy with our keys and logs.

Local command

uvx chatspatial==1.6.0

Claude Code has no install link for a local command. Copy the command below and run it in a terminal.

shClaude Code

1claude mcp add cafferychen777-chatspatial -- uvx chatspatial==1.6.0

Run in a terminal.

jsonClaude Desktop

1{2  "mcpServers": {3    "cafferychen777-chatspatial": {4      "command": "uvx",5      "args": [6        "chatspatial==1.6.0"7      ]8    }9  }10}

claude_desktop_config.json

Local · pypiPublisher installStep-by-step: add this in Claude

Remote URL or a command on your machine? How the two installs differ

Run on PlugMCP

Host a copy with our keys and logs.

A new server you create. It is not this listing's official endpoint. Use the publisher install when you want their URL and their credentials.

Launch

Server facts

Local

Transport: stdio
License: MIT
Last checked: 2026-10-27

Stars: 45
Tools: —
Uptime: —

Tools

No tool list yet. Remote servers get one after the first health check.

FAQ

Questions

How do I install ChatSpatial?

Copy the stdio config for Cursor, Claude Desktop, Claude Code, or VS Code on this page. It uses the publisher's install, not a PlugMCP proxy.

Does ChatSpatial need an API key?

No required environment variable is listed on this record.

What transport does ChatSpatial use?

ChatSpatial runs locally over stdio.

When was ChatSpatial last checked?

Last checked 2026-10-27. MCP server for spatial transcriptomics analysis through natural language interfaces.

From the publisher

Documentation

ChatSpatial

MCP server for spatial transcriptomics analysis via natural language

Start Here

Install uv once, then register ChatSpatial without creating or managing a Python environment:

Codex:

codex mcp add chatspatial -- uvx --from chatspatial chatspatial server

Claude Code:

claude mcp add --scope user chatspatial -- \
  uvx --from chatspatial chatspatial server

uvx creates an isolated environment on first launch and reuses its cache on later launches. Restart the MCP client after adding the server.

The command above installs the standard runtime. To make all 15 composable Python method families available in the same isolated MCP environment, use:

uvx --from 'chatspatial[full]' chatspatial server

Then:

Run your first analysis — Quick Start
Choose optional method families or a persistent environment — Installation Guide
Configure another MCP client — Configuration Guide
Reproduce the manuscript key results without an LLM — Reproduction image

Docker quick start:

docker pull cafferyyang777/chatspatial:latest

Minimal example prompt:

Load /absolute/path/to/spatial_data.h5ad and plot gene expression at the spatial coordinates

If you use Docker, mount host data to /data and prompt with the container path, for example /data/spatial_data.h5ad.

ChatSpatial works with any MCP-compatible client — Claude Code, Claude Desktop, Codex, OpenCode, and other MCP-capable tools.

Capabilities

Current coverage includes 67 methods across 13 analytical categories, exposed through 20 MCP tools. Supports 10x Visium, Xenium, Slide-seq v2, MERFISH, seqFISH.

Category	Example methods
Data Loading & Preprocessing	Scanpy I/O, QC, Normalization, HVG, PCA, Neighbors
Visualization	Spatial plots, Embedding plots, Gene expression overlays
Spatial Domain Identification	SpaGCN, STAGATE, GraphST, BANKSY, AESTETIK, Leiden, Louvain
Deconvolution	FlashDeconv, Cell2location, RCTD (spacexr or rctd-py), DestVI, Stereoscope, SPOTlight, Tangram, CARD
Cell-Cell Communication	LIANA+, CellPhoneDB, CellChat (`cellchat_r`), FastCCC
Cell Type Annotation	Tangram, scANVI, CellAssign, mLLMCelltype, scType, SingleR, marker-score and threshold rules
Differential Expression	Wilcoxon, t-test, Logistic Regression, pyDESeq2
Trajectory Inference	CellRank, Palantir, DPT
RNA Velocity	scVelo, VeloVI
Spatial Statistics	Moran's I, Local Moran, Geary's C, Getis-Ord Gi*, Ripley's K, Co-occurrence, Neighborhood Enrichment, Centrality Scores, Local Join Count, Network Properties
Enrichment Analysis	GSEA, ORA, Enrichr, ssGSEA, Spatial EnrichMap
Spatially Variable Genes	SpatialDE, SPARK-X, FlashS
Multi-sample Integration	Harmony, BBKNN, Scanorama, scVI
CNV Analysis	InferCNVPy, Numbat
Spatial Registration	PASTE, STalign

Documentation

Guide	Use this when...
Installation	You need optional methods or a persistent Python environment
Docker	You want a reproducible container runtime or local dependency resolution fails
Configuration	You need exact MCP client syntax or the runtime path model
Quick Start	ChatSpatial is installed and you want the first successful analysis
Concepts	You need to choose an analysis strategy from a biological question
Examples	You want copy-pasteable natural-language workflow prompts
Methods Reference	You need canonical tool names, method names, parameters, and defaults
Troubleshooting	Setup, data loading, or analysis behavior is not working
Full Docs	You want the complete documentation site

Reproducibility

docker run --rm -v "$PWD/out:/outputs" \
  cafferyyang777/chatspatial@sha256:ac3ba1ed8235c3d53ca72005d8ad2556cac007f5ddb932ae3e1d1241fa2cf9d8 \
  chatspatial-reproduce

reproducibility/ contains the image definition and describes what it checks. The experiment and analysis scripts for the manuscript are in ChatSpatial-Reproducibility.

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}
}

ChatSpatial orchestrates many excellent third-party methods. Please also cite the original tools your analysis used.

Contributing

Documentation improvements, bug reports, and new analysis methods are all welcome. See CONTRIBUTING.md.

MIT License · GitHub · Issues