Spec Driven Development
MCP Server that facilitates spec-driven development workflows, not just Vibe Coding.
在你的电脑上运行
ChatSpatial
概览
作者提供的说明（英文原文）
Schema-enforced spatial transcriptomics analysis with 20 tools and 67 methods via MCP
PopNx MCP 的三大支柱
这三项永远不会合并成一个分数：意见、测量和人气是不同的东西。
- 用户评价i暂无评价评价功能将在后续阶段与账户功能一起开放
- 我们的基础检查i1 项中通过 1 项依据公开信息检查；尚未扫描代码
- 使用情况i非常新↓ 232/周 · ★ –
它能帮你做什么
我们还没有为它写通俗的介绍。下面是我们从注册中心读取到的事实。
- 连接方式: 在你的电脑上运行
- 传输方式: stdio
- 分类: 其他
安装
选择你使用的 AI 应用，然后复制设置。
安装之前
- 基础检查：1 项中通过 1 项
- 在你的电脑上运行，拥有你的用户账户的权限（文件、网络、应用）。
- 注册中心没有列出需要填写的密钥。
你需要
- PyPI已安装 Python 的 uv（用于 uvx 命令）
你用的是哪个应用？
在上方选择你的应用。我们会记住它，下次按钮会显示“安装到 …”。
打开 Claude Desktop → Settings → Developer → Edit Config，把下面的内容粘贴到 claude_desktop_config.json
{
"mcpServers": {
"chatspatial": {
"command": "uvx",
"args": [
"chatspatial",
"server"
]
}
}
}在终端中运行这条命令
claude mcp add chatspatial -- uvx chatspatial server或者自己复制设置
粘贴到项目中的 .cursor/mcp.json，或 ~/.cursor/mcp.json
{
"mcpServers": {
"chatspatial": {
"command": "uvx",
"args": [
"chatspatial",
"server"
]
}
}
}浏览器会先询问是否打开应用，然后应用会显示设置并请你确认。密钥的值会留空，由你自己填写。
或者自己复制设置
粘贴到项目中的 .vscode/mcp.json
{
"servers": {
"chatspatial": {
"type": "stdio",
"command": "uvx",
"args": [
"chatspatial",
"server"
]
}
}
}浏览器会先询问是否打开应用，然后应用会显示设置并请你确认。密钥的值会留空，由你自己填写。
这个服务器在你的电脑上运行，而 ChatGPT 只能连接互联网上的服务器。请选择其他应用。
你的选择通过 Cookie 保存在这台设备上，无需账户。
这些设置是根据作者在注册中心的条目生成的。如果 README 的写法不同，请以 README 为准。
它能做什么
它在你的电脑上运行；安装后，工具列表会显示在你的 AI 应用中。
基础检查i
我们检查的是任何人都能看到的信息；我们没有阅读代码。不适用的检查项不计入总数。 · 检查于 2026年11月10日
- ✓ 通过
作者与仓库一致
注册名称已通过 GitHub 账户 cafferychen777 验证，该账户拥有此仓库
- … 尚未检查
仍在维护
我们还没有从 GitHub 读取这个仓库
- … 尚未检查
有许可证
我们还没有从 GitHub 读取这个仓库
- – 不适用
端点有响应
它在你的电脑上运行，没有互联网端点
- – 不适用
使用 OAuth 登录
在你的电脑上运行，改用本地设置
- … 尚未检查
工具描述中没有隐藏指令
它在你的电脑上运行；我们只能读取互联网端点的工具列表
与“其他”中的其他服务器比较i
- 星标数多于此分类中其他 19023 个服务器的 0%
- 发布到注册中心的时间比此分类中其他 19023 个服务器的 67% 更新
- 基础检查结果等于或优于此分类中其他 19023 个服务器的 100%
与注册中心里这个分类中所有活跃的服务器比较。只有当发布者拥有该仓库时，星标数才计入。
常见问题
ChatSpatial 安全吗？
它在 1 项适用的基础检查中通过了 1 项。我们没有阅读代码。在添加密钥或令牌之前，请先看看这个服务器要求哪些权限，并使用只具备所需权限的密钥。
它需要哪些密钥或代码？
注册中心没有列出必需的密钥，不过有些服务器会在首次使用时要求你登录。
它在我的电脑上运行还是在云端？
它在你的电脑上运行。你的 AI 应用会在需要时启动它，数据不会经过作者的服务器（除非它自己调用在线服务）。
它还在维护吗？
GitHub 仓库最后更新于–，最新版本（1.6.0）于20天前进入注册中心。
哪些应用可以使用它？
支持 MCP 的应用，例如 Claude Desktop、Claude Code、Cursor 和 VS Code。你的电脑上还需要有 Python (uv)。
有什么可以替代它？
同一分类中有：Spec Driven Development, Remote Desktop Commander, KEVAREMESH Agent Discovery MCP
替代选择
同一分类中其他作者的服务器，按星标数排序。
如何看卡片：↓ 每周下载量i★ GitHub 星标i三大支柱：评价 · 检查 · 使用情况i更新 = 最新版本发布到注册中心的时间i
Remote Desktop Commander
Remote Desktop Commander: use files, terminal and processes on your own computers from any AI app.
在云端运行✓ desktopcommander.app
KEVAREMESH Agent Discovery MCP
Discover 25 owned APIs and 11 rights-scoped external operations via 15 MCP tools and x402.
在云端运行
作者的 README
打开 README
按原文从作者的仓库复制。PopNx MCP 没有审查或背书其内容。HTML、图片和脚本已被移除。链接会离开本站。
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 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 serverClaude 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 serverfull 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:latestMinimal example prompt:
Load /absolute/path/to/spatial_data.h5ad and plot gene expression at the spatial coordinatesThe 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.