与空间转录组对话
cafferychen777/ChatSpatial
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更新于 2026-08-23
ChatSpatial 是一个通过自然语言进行空间转录组分析的MCP服务器。它简化了空间数据的分析过程，支持超过60种方法和12个类别以及多种空间转录组平台。
MCP 服务配置
复制以下 JSON 到 OPClaw 或其他 MCP 客户端的配置文件中即可使用
{
"mcpServers": {
"chatspatial": {
"args": [
"-m",
"chatspatial",
"server"
],
"command": "python"
}
}
}服务介绍
ChatSpatial
MCP server for spatial transcriptomics analysis via natural language
❌ 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
✅ After
"Load my Visium data and identify
spatial domains"
✓ Loaded 3,456 spots, 18,078 genes
✓ Identified 7 spatial domains
✓ Generated visualization
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.
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
Capabilities
| Category | Methods |
|---|---|
| Spatial Domains | SpaGCN, STAGATE, Leiden |
| Deconvolution | Cell2location, RCTD, Tangram, SPOTlight |
| Cell Communication | LIANA+, CellPhoneDB |
| Cell Type Annotation | Tangram, scANVI, CellAssign, mLLMCelltype |
| Trajectory | CellRank, Palantir, scVelo |
| Spatial Statistics | Moran's I, Getis-Ord Gi*, Ripley's K |
| Gene Set Enrichment | GSEA, ORA, Enrichr |
60+ methods across 12 categories. Supports 10x Visium, Xenium, Slide-seq v2, MERFISH, seqFISH.
Docs
- Installation Guide — detailed setup for all platforms
- Examples — step-by-step workflows
- Full Documentation — complete reference
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}
}
