Official description10 sourcesMCP servers8d ago
cafferychen777/ChatSpatial
๐ ๐ - Spatial transcriptomics analysis: cell annotation, deconvolution, spatial statistics and visualization
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Config template (adjust for your client)
claude mcp add chatspatial -- npx -y chatspatial
A pasteable skeleton generated from the repository name. Check the project README for the exact package and arguments.
- Star count
- 45 โ ยท cafferychen777/ChatSpatial ยท read from the repository page ยท (checked 2026-10-16 20:00:20)
- Source
- collected from the punkpeye/awesome-mcp-servers list ยท type: MCP server
- Harvest history
- first seen 2026-10-09 ยท last seen 2026-10-16 ยท seen 32ร ยท listed by 10 sources
- Score
- score 1,003 ยท 45 โ ยท 10 sources ยท mcp
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cafferychen777/ChatSpatial๏ผfirst catalogued 2026-10-09๏ผlast seen 2026-10-16ใThere is no official certification or quality rating here โ we record sources and dates only.Third-party quality signals
ChatSpatial
ไปฅไธๆๅฝ่ช่ฏฅไปๅบ็ README๏ผ็ๆฎต๏ผ ยท ๅจ GitHub ่ฏปๅฎๆด README โ
**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 **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:**
**Claude Code:**
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:
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:
1. **Run your first analysis** โ Quick Start
2. **Choose optional method families or a persistent environment** โ Installation Guide
3. **Configure another MCP client** โ Configuration Guide
4. **Reproduce the manuscript key results without an LLM** โ Reproduction image
**Docker quick start:**
**Minimal example prompt:**
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** โ Claude Code, Claude Desktop, Codex, OpenCode, and other MCP-capable tools.
---
Capabilities
Current coverage includes 65 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 |
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 **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:**
**Claude Code:**
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:
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:
1. **Run your first analysis** โ Quick Start
2. **Choose optional method families or a persistent environment** โ Installation Guide
3. **Configure another MCP client** โ Configuration Guide
4. **Reproduce the manuscript key results without an LLM** โ Reproduction image
**Docker quick start:**
**Minimal example prompt:**
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** โ Claude Code, Claude Desktop, Codex, OpenCode, and other MCP-capable tools.
---
Capabilities
Current coverage includes 65 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 |
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- awesome ยท https://github.com/cafferychen777/ChatSpatial
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