Is Chatspatial MCP Server safe to use?

Chatspatial MCP Server has no known CVEs as of the latest MCPpedia security scan. It does not require authentication, so any local process can connect — keep this in mind in shared environments.

How do I install Chatspatial MCP Server?

Chatspatial MCP Server can be installed by cloning its GitHub repository and following the setup instructions in the README.

What AI clients work with Chatspatial MCP Server?

Chatspatial MCP Server is compatible with claude-desktop, cursor, claude-code. It uses sse transport.

Is Chatspatial MCP Server actively maintained?

Chatspatial MCP Server is actively maintained — last commit was 0 days ago. It has 38 GitHub stars.

Chatspatial MCP Server

Natural language-driven spatial transcriptomics analysis with 60+ methods via MCP

38 0 tools GitHub

No known CVEs

No license

Actively maintained

Last commit 0d ago

Works with most clients

Transport: sse

0 tools

Grade F

Edit this pageView history

Health Data

Step 1

Install in your client

Config is the same across clients — only the file and path differ.

Supported in Claude Desktopsse · Node 18+

Paste into ~/Library/Application Support/Claude/claude_desktop_config.json

{
  "mcpServers": {
    "chatspatial-mcp-server": {
      "command": "<see-readme>",
      "args": []
    }
  }
}

Are you the author?

Add this badge to your README to show your security score and help users find safe servers.

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[![MCPpedia Score](https://mcppedia.org/api/badge/io-github-cafferychen777-chatspatial)](https://mcppedia.org/s/io-github-cafferychen777-chatspatial)

Read me

What Chatspatial MCP Server does

MCP server for spatial transcriptomics analysis via natural language

Test This Server

No automated test available for this server. Check the GitHub README for setup instructions.

Loading README…

Scored, not listed

Why this score

Five weighted categories — click any category to see the underlying evidence.

Score breakdown

37/100across 5 weighted dimensions

How we score →

0255075100

−63

Security

Maintenance

Efficiency

Documentation

Compatibility

Categoriesclick a row to see evidence

Security

OSV.dev

No known CVEs.

No package registry to scan.

Community

Reviews

Be the first to review

Have you used this server?

Share your experience — it helps other developers decide.

How easy was setup?Did it work reliably?How was the documentation?

Frequently Asked Questions

Is Chatspatial MCP Server safe to use?: Chatspatial MCP Server has no known CVEs as of the latest MCPpedia security scan. It does not require authentication, so any local process can connect — keep this in mind in shared environments.
How do I install Chatspatial MCP Server?: Chatspatial MCP Server can be installed by cloning its GitHub repository and following the setup instructions in the README.
What AI clients work with Chatspatial MCP Server?: Chatspatial MCP Server is compatible with claude-desktop, cursor, claude-code. It uses sse transport.
Is Chatspatial MCP Server actively maintained?: Chatspatial MCP Server is actively maintained — last commit was 0 days ago. It has 38 GitHub stars.

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Community

Discussion

Start a conversation

Ask a question, share a tip, or report an issue.

Has anyone used this with Cursor?How do you handle auth?Any alternatives?

Edit this pageView history

Health Data

Step 1

Install in your client

Config is the same across clients — only the file and path differ.

Supported in Claude Desktopsse · Node 18+

Paste into ~/Library/Application Support/Claude/claude_desktop_config.json

{
  "mcpServers": {
    "chatspatial-mcp-server": {
      "command": "<see-readme>",
      "args": []
    }
  }
}

Are you the author?

Add this badge to your README to show your security score and help users find safe servers.

Embed in your READMEAbout badges →

[![MCPpedia Score](https://mcppedia.org/api/badge/io-github-cafferychen777-chatspatial)](https://mcppedia.org/s/io-github-cafferychen777-chatspatial)

Read me

What Chatspatial MCP Server does

MCP server for spatial transcriptomics analysis via natural language

Test This Server

No automated test available for this server. Check the GitHub README for setup instructions.

README

ChatSpatial

MCP server for spatial transcriptomics analysis via natural language

ChatSpatial replaces ad-hoc LLM code generation with schema-enforced orchestration. Instead of generating arbitrary scripts, the LLM selects tools and parameters from a curated registry, making spatial transcriptomics workflows more reproducible across sessions and clients.

ChatSpatial exposes 20 schema-validated MCP tools that orchestrate 65 spatial transcriptomics methods across 15 analytical categories. The tools are the stable natural-language interface; the methods are the analysis backends selected through tool parameters.

Start Here

Install ChatSpatial — Installation Guide for Python/uv setup, or Docker Guide for the GHCR image
Configure your MCP client — Configuration Guide
Run your first analysis — Quick Start

Docker quick start:

docker pull ghcr.io/cafferychen777/chatspatial:v1.2.9

Minimal example prompt:

Load /absolute/path/to/spatial_data.h5ad and show me the tissue structure

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 65 methods across 15 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, Leiden, Louvain
Deconvolution	FlashDeconv, Cell2location, RCTD, DestVI, Stereoscope, SPOTlight, Tangram, CARD
Cell-Cell Communication	LIANA+, CellPhoneDB, CellChat (`cellchat_r`), FastCCC
Cell Type Annotation	Tangram, scANVI, CellAssign, mLLMCelltype, scType, SingleR
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	Spat

... View full README on GitHub

Loading README…

Scored, not listed

Why this score

Five weighted categories — click any category to see the underlying evidence.

Score breakdown

37/100across 5 weighted dimensions

How we score →

0255075100

−63

Security

Maintenance

Efficiency

Documentation

Compatibility

Categoriesclick a row to see evidence

Security

OSV.dev

No known CVEs.

No package registry to scan.

Community

Reviews

Be the first to review

Have you used this server?

Share your experience — it helps other developers decide.

How easy was setup?Did it work reliably?How was the documentation?

Frequently Asked Questions

Is Chatspatial MCP Server safe to use?: Chatspatial MCP Server has no known CVEs as of the latest MCPpedia security scan. It does not require authentication, so any local process can connect — keep this in mind in shared environments.
How do I install Chatspatial MCP Server?: Chatspatial MCP Server can be installed by cloning its GitHub repository and following the setup instructions in the README.
What AI clients work with Chatspatial MCP Server?: Chatspatial MCP Server is compatible with claude-desktop, cursor, claude-code. It uses sse transport.
Is Chatspatial MCP Server actively maintained?: Chatspatial MCP Server is actively maintained — last commit was 0 days ago. It has 38 GitHub stars.