Label-map overlap for isotropic medical images

This Python example overlays a medical-image slice with a transparent label map derived from tissue probability maps in NIfTI files. The example assumes isotropic voxel spacing and extracts slices from the ICBM 152 2009a Nonlinear Symmetric template.

Scope of the example

This repository demonstrates how to:

• load 3D medical images in NIfTI format
• extract and orient corresponding 2D subarrays
• convert tissue probabilities into a discrete label map
• explicitly define an RGBA color overlay
• save a PNG image overlaid with a transparent label map

The goal is to export square images as an intermediate data representation for more complex example figures.

Quick start

Install dependencies:

pip install matplotlib nibabel numpy

Run the example:

python recipe.py

This downloads the template and generates a square image overlaid with gray- and white-matter labels (overlay.png).