Deep-Learning-Based 3D Medical Image Segmentation and Registration

Abstract

Understanding the importance of image segmentation and registration in clinical diagnosis and treatment is critical for advancing precision medicine. Medical image analysis involves complex data processing tasks, particularly in scenarios with limited annotated data and multi-modality feature inconsistencies. Recent deep learning-based methods have provided breakthroughs in image segmentation and registration, especially in modalities like MRI and CT. However, challenges such as one-shot learning, incremental learning, and efficient deformable registration still persist. This thesis introduces a series of innovative deep learning frameworks, focusing on three one-shot segmentation settings and three Segment Anything Model (SAM) -assisted registration methods, to address the issues of annotation scarcity and feature misalignment in medical imaging. For segmentation, we develop three methods for one-shot, class-incremental, and novel-class tract segmentation. These incorporate uncertainty estimation, knowledge distillation, and voxel-level contrastive learning to enhance performance and generalization in one-shot settings. For registration, we propose three SAM-guided frameworks that leverage segmentation masks and anatomical prompts, as well as attention mechanisms, prototype learning, and contour-aware losses. These approaches achieve state-of-the-art accuracy in unsupervised deformable registration. Overall, our methods yield substantial improvements in segmentation and registration accuracy across diverse datasets and demonstrate strong potential for clinical application.