# TMA Dearraying for Spatial Transcriptomics

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STile helps segment tissue microarray (TMA) cores from single-cell spatial transcriptomics data and prepare platform-specific outputs for downstream analysis.

## What it does

- Detects tissue cores by clustering cell centroids with HDBSCAN and refining core labels for Vizgen, Xenium, and CosMx outputs.

## Main entry points

- `stile identify_tissue_cores`: Load a `.h5ad`, cluster cells, assign cores, and save core plots.
## Quickstart

```bash
# Build AnnData and centroid CSV from a platform run directory
stile run
```

