快速开始

This page is for your first successful analysis after installation.

你的第一次分析

Open your MCP client and type:

Load /absolute/path/to/spatial_data.h5ad and show me the tissue structure

If you configured ChatSpatial through Docker, use the container path from your mount instead:

Load /data/spatial_data.h5ad and show me the tissue structure

For example, -v /Users/alice/spatial-data:/data:ro makes host files under /Users/alice/spatial-data visible as /data inside ChatSpatial.

Then continue with:

Normalize and cluster the data

Identify spatial domains with SpaGCN

Common First Prompts

任务

这样说

加载数据

Load my Visium data from /absolute/path/to/data

预处理

Normalize and cluster the data

识别空间区域

Identify spatial domains with SpaGCN

细胞注释

Annotate cell types using the reference

去卷积

Estimate cell type proportions

Find spatial genes

Find spatially variable genes

可视化

Show expression of CD3D on the tissue

示例数据

Try these public test files:

成功示例

加载完成后：

Dataset loaded successfully
- ID: spatial_data_abc123
- 3000 spots, 18000 genes
- Platform: Visium

预处理完成后：

Preprocessing complete
- Filtered to 2800 spots, 2000 HVGs
- Computed 30 PCs, UMAP
- Found 8 clusters (Leiden)

Visualizations appear directly in the chat or client UI.

Before You Troubleshoot

Check these three things first:

  • Use an absolute data path, not ~/... or ./...

  • If using Docker, use the container path from your mount, such as /data/sample.h5ad

  • Restart your client after MCP configuration changes

  • Run preprocessing before most downstream analyses

If that does not fix the problem, go to the Troubleshooting Guide.

下一步