Multi-Phase Automated Segmentation of Dental Structures in CBCT Using a Lightweight Auto3DSeg and SegResNet Implementation

Abstract: Cone-beam computed tomography (CBCT) has become an invaluable imaging modality in dentistry, enabling 3D visualization of teeth and surrounding structures for diagnosis and treatment planning. Automated segmentation of dental structures in CBCT can efficiently assist in identifying pathology (e.g., pulpal or periapical lesions) and facilitate radiation therapy planning in head and neck cancer patients. We describe the DLaBella29 team's approach for the MICCAI 2025 ToothFairy3 Challenge, which involves a deep learning pipeline for multi-class tooth segmentation. We utilized the MONAI Auto3DSeg framework with a 3D SegResNet architecture, trained on a subset of the ToothFairy3 dataset (63 CBCT scans) with 5-fold cross-validation. Key preprocessing steps included image resampling to 0.6 mm isotropic resolution and intensity clipping. We applied an ensemble fusion using Multi-Label STAPLE on the 5-fold predictions to infer a Phase 1 segmentation and then conducted tight cropping around the easily segmented Phase 1 mandible to perform Phase 2 segmentation on the smaller nerve structures. Our method achieved an average Dice of 0.87 on the ToothFairy3 challenge out-of-sample validation set. This paper details the clinical context, data preparation, model development, results of our approach, and discusses the relevance of automated dental segmentation for improving patient care in radiation oncology.