SAMv2: A Unified Framework for Learning Appearance, Semantic and Cross-Modality Anatomical Embeddings

Identifying anatomical structures (e.g., lesions or landmarks) in medical images plays a fundamental role in medical image analysis. As an exemplar-based landmark detection method, Self-supervised Anatomical eMbedding (SAM) learns a discriminative embedding for each voxel in the image and has shown promising results on various tasks. However, SAM still faces challenges in: (1) differentiating voxels with similar appearance but different semantic meanings (\textit{e.g.}, two adjacent structures without clear borders); (2) matching voxels with similar semantics but markedly different appearance (e.g., the same vessel before and after contrast injection); and (3) cross-modality matching (e.g., CT-MRI registration). To overcome these challenges, we propose SAMv2, which is a unified framework designed to learn appearance, semantic, and cross-modality anatomical embeddings. Specifically, SAMv2 incorporates three key innovations: (1) semantic embedding learning with prototypical contrastive loss; (2) a fixed-point-based matching strategy; and (3) an iterative approach for cross-modality embedding learning. We thoroughly evaluated SAMv2 across three tasks, including one-shot landmark detection, lesion tracking on longitudinal CT scans, and CT-MRI affine/rigid registration with varying field of view. Our results suggest that SAMv2 outperforms SAM and other state-of-the-art methods, offering a robust and versatile approach for landmark based medical image analysis tasks. Code and trained models are available at: https://github.com/alibaba-damo-academy/self-supervised-anatomical-embedding-v2