Quick Start¶

First time? Complete Installation first, then come back here.

Your First Analysis¶

Open your MCP client (Claude, OpenCode, Codex, etc.) and type:

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

ChatSpatial handles the rest.

Task	Say This
Load data	“Load my Visium data from /path/to/data”
Preprocess	“Normalize and cluster the data”
Find domains	“Identify spatial domains with SpaGCN”
Annotate cells	“Annotate cell types using the reference”
Deconvolve	“Estimate cell type proportions”
Analyze patterns	“Find spatially variable genes”
Visualize	“Show expression of CD3D on the tissue”

Test with our datasets:

After loading:

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

After preprocessing:

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

Visualizations appear directly in the chat.

Issue	Fix
Tools not showing	Restart your MCP client
“Dataset not found”	Use absolute path: `/Users/you/data.h5ad`
Analysis fails	Run preprocessing first