官方说明10 个来源MCP 服务8 天前
cafferychen777/ChatSpatial
🐍 🏠 - Spatial transcriptomics analysis: cell annotation, deconvolution, spatial statistics and visualization
在 GitHub 查看 ↗直链 · 无中转页
配置模板（请按你的客户端调整）
claude mcp add chatspatial -- npx -y chatspatial
这是根据仓库名生成的可粘贴骨架，命令行参数与包名请以该项目 README 为准。
- ★ 数取值
- 45 ★ · cafferychen777/ChatSpatial · 取自该仓库的 GitHub 页面 · （2026-10-16 20:00:20 核对）
- 来源明细
- 收录自 punkpeye/awesome-mcp-servers 榜单（我们从中收集的条目之一） · 条目类型：MCP 服务
- 收录与活跃
- 收录于 2026-10-09 · 最近见到 2026-10-16 · 共见到 32 次 · 被 10 个来源列出
- 评分构成
- 综合分 1,003 · 45 ★ · 10 个来源 · mcp
常见问题（答案都来自我们的记录）
怎么安装？
我们【没有】从该仓库取到安装命令（我们的 install 覆盖率只有约 4%）。请看它的 README 或 releases 页。
它适合谁 / 用来做什么？
我们把它归在这些标签下: MCP 服务。标签来自条目自身，不是我们强加的分类。
谁维护它、还在更新吗？
仓库
cafferychen777/ChatSpatial；我们收录于 2026-10-09；最近见到 2026-10-16。这里没有"官方认证"或"质量评级"——我们只记录来源与时间。第三方质量标记
ChatSpatial
以下摘录自该仓库的 README（片段） · 在 GitHub 读完整 README →
**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** — Quick Start
2. **Choose optional method families or a persistent environment** — Installation Guide
3. **Configure another MCP client** — Configuration Guide
4. **Reproduce the manuscript key results without an LLM** — 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** — 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** — Quick Start
2. **Choose optional method families or a persistent environment** — Installation Guide
3. **Configure another MCP client** — Configuration Guide
4. **Reproduce the manuscript key results without an LLM** — 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** — 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 |
- 来源
- awesome · https://github.com/cafferychen777/ChatSpatial
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