headCTools
Open-source Python toolkit for cranial reconstruction from CT scans. Published at MICCAI 2020.
Python toolkit for preprocessing, brain segmentation, and skull reconstruction on craniectomy CT images. Built during my PhD, used in 3 published papers.
What it does
- Preprocessing: Registration to MNI atlas, resampling, skull extraction via thresholding
- Virtual craniectomy: Generates synthetic training data by simulating surgical defects on healthy skulls
- Reconstruction: 3D U-Net and autoencoder models for predicting complete skull from defective input
- Shape priors: PCA-based anatomical constraints for implant design
Publications
- Self-supervised skull reconstruction (IEEE TMI 2021)
- Cranial implant design via virtual craniectomy (MICCAI 2020 Best Paper)
- AutoImplant 2020 challenge (Medical Image Analysis 2023)
Technologies
- Core: Python, PyTorch, SimpleITK, NiBabel
- 3D Processing: VTK, Open3D, scikit-image (marching cubes)
- Experiment tracking: MLflow