KneeBones3Dify: Open-source software for segmentation and 3D reconstruction of knee bones from MRI data

Abstract

KneeBones3Dify is a Python software tool that supports detailed analysis of knee pathologies and preoperative planning for knee replacement surgery based on patient-specific 3D models. It produces printable 3D bones in a stereolithography file format by automatically segmenting the femur, patella, and tibia from high-resolution Magnetic Resonance (MR) images with nearly isotropic voxel dimensions. Our software avoids time-consuming and subjective manual segmentation by specialists, offering an accurate and efficient alternative employing GPU acceleration. We validated the results by computing objective metrics against the ground truth voxel-wise segmentation produced for a 3D MR image by specialists, who also confirmed the reconstruction accuracy qualitatively. KneeBones3Dify and annotated data are publicly available, enabling broader research and clinical practice use.

Keywords

• Knee bone segmentation
• Python
• GPU
• Parallel computing
• 3D bone models for printing