常见问题（FAQ）

This page gives short answers and pointers to the canonical docs.

General

什么是 ChatSpatial？

ChatSpatial is an MCP server for spatial transcriptomics analysis through natural language. See the project overview on the documentation home.

什么是 MCP？

MCP (Model Context Protocol) is the interface layer that lets AI clients call external tools safely. ChatSpatial uses MCP so clients can run spatial analysis tools through structured commands.

ChatSpatial 支持哪些数据格式？

Common formats include H5AD, 10X Visium folders, 10X H5, MTX, Slide-seq, and MERFISH-style spatial data. For a first successful run, see Quick Start.

需要编程经验吗？

No. ChatSpatial is designed for natural-language use, though basic spatial transcriptomics knowledge still helps.

Setup

需要什么版本的 Python？

Python 3.11-3.13 is supported, with 3.12 recommended. See Installation.

应该使用虚拟环境吗？

Yes. Use a dedicated environment to avoid dependency conflicts. See Installation.

How do I configure ChatSpatial in my client?

Use the Configuration Guide for exact client syntax.

不用 Claude 也能用 ChatSpatial 吗？

Yes. ChatSpatial works with any MCP-compatible client.

Analysis

如何选择合适的方法？

Use:

为什么分析会这么慢？

Large datasets and heavier methods can be slow. Try:

  • smaller datasets for testing

  • faster baseline methods first

  • GPU where supported

  • checking memory and CPU limits

If performance is failing rather than merely slow, see Troubleshooting.

需要多少内存？

A rough rule:

  • small datasets: 8GB RAM

  • medium datasets: 16GB RAM

  • large datasets: 32GB+ RAM

See Troubleshooting for failure-mode guidance.

Advanced

Can I use ChatSpatial in publications?

Yes. It is MIT licensed. See citation details in the documentation home.

如何参与贡献？

See Contributing.

可以添加自己的分析方法吗？

Yes. The project is modular, but contributor-facing implementation guidance belongs in the codebase and contributor docs rather than the FAQ.

支持 GPU 加速吗？

Yes, for many methods. See Methods Reference for exact support.

数据与隐私

我的数据会发送到外部服务器吗？

No. ChatSpatial runs locally; your analysis data stays on your machine.

可以离线使用 ChatSpatial 吗？

The analysis stack can run locally, but you still need an LLM client for natural-language interaction.

数据如何存储？

Saved data locations can be controlled through CHATSPATIAL_DATA_DIR. See Configuration Guide.

还有问题？