stile 0.0.1

Python Boilerplate contains all the boilerplate you need to create a Python package.

TMA de-arraying for spatial transcriptomics

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.
• stile prepare_data: Convert Vizgen/Xenium/CosMx output directories into an .h5ad plus cell_id, x_centroid, y_centroid CSV for further processing.

Quickstart

# Build AnnData and centroid CSV from a platform run directory
stile prepare_data xenium path/to/xenium/output path/to/save
stile run