HR-pQCT Geodesic Contour

Standalone geodesic active-contour segmentation for fractured human radius HR-pQCT scans. The package provides a plain NumPy API for use in analysis scripts, notebooks, and 3D Slicer extensions.

Implemented according to:

Ohs N, Collins CJ, Tourolle DC, Atkins PR, Schroeder BJ, Blauth M, Christen P, Mueller R. Automated segmentation of fractured distal radii by 3D geodesic active contouring of in vivo HR-pQCT images. Bone. 2021 Jun;147:115930. doi:10.1016/j.bone.2021.115930. PMID:33753277.

Install

pip install hrpqct-geodesic-contour

For optional HDF5 debug reports:

pip install "hrpqct-geodesic-contour[reports]"

Usage

import numpy as np
from hrpqct_geodesic_contour import contour

density = np.asarray(...)  # 3D density image, typically mg HA/cm^3
mask, auxiliary_masks = contour(density, voxel_size_mm=0.0607)