This page is for your first successful analysis after installation.
- Install first: Installation
- Configure your client first: Configuration Guide
- If something fails: Troubleshooting
Open your MCP client and type:
Load /absolute/path/to/spatial_data.h5ad and show me the tissue structure
Then continue with:
Normalize and cluster the data
Identify spatial domains with SpaGCN
| Task | Say This |
|---|---|
| Load data | Load my Visium data from /absolute/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 |
| Find spatial genes | Find spatially variable genes |
| Visualize | Show expression of CD3D on the tissue |
Try these public test files:
- card_spatial.h5ad — pancreatic spatial data
- card_reference_filtered.h5ad — reference dataset
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 or client UI.
Check these three things first:
- Use an absolute data path, not
~/...or./... - 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.
- Concepts — choose the right analysis strategy
- Examples — complete workflow recipes
- Methods Reference — exact tool parameters and defaults