This paper describes a new spatial correspondence representation based on paired regions-of-interest (ROIs), for medical image registration. The distinct properties of the proposed ROI-based correspondence are discussed, in the context of potential benefits in clinical applications following image registration, compared with alternative correspondence-representing approaches, such as those based on sampled displacements and spatial transformation functions. These benefits include a clear connection between learning-based image registration and segmentation, which in turn motivates two cases of image registration approaches using (pre-)trained segmentation networks. Based on the segment anything model (SAM), a vision foundation model for segmentation, we develop a new registration algorithm SAMReg, which does not require any training (or training data), gradient-based fine-tuning or prompt engineering. The proposed SAMReg models are evaluated across five real-world applications, including intra-subject registration tasks with cardiac MR and lung CT, challenging inter-subject registration scenarios with prostate MR and retinal imaging, and an additional evaluation with a non-clinical example with aerial image registration. The proposed methods outperform both intensity-based iterative algorithms and DDF-predicting learning-based networks across tested metrics including Dice and target registration errors on anatomical structures, and further demonstrates competitive performance compared to weakly-supervised registration approaches that rely on fully-segmented training data. Open source code and examples are available at: https://github.com/sqhuang0103/SAMReg.git.
Learning-based medical image registration has matched the accuracy of conventional methods while offering superior computational efficiency. However, existing approaches suffer from poor generalization across diverse clinical scenarios, requiring the laborious development of multiple isolated networks for specific registration tasks, \emph{e.g.}, inter-/intra-subject registration or anatomical region-specific alignment, leading to cumbersome development pipelines. To overcome this limitation, we propose \textbf{UniReg}, the first conditional unified model for multi-scenario medical image registration, which combines the precision advantages of task-specific learning methods with the generalization of traditional optimization methods. Our key innovation is a unified registration framework that adaptively estimates deformation fields conditioned on: (1) anatomical structure priors, (2) registration type constraints (inter/intra-subject), and (3) instance-specific features, enabling effective alignment across heterogeneous CT and MR registration scenarios within a single model. Through comprehensive experiments on multiple CT/MR registration datasets, UniReg achieves superior average registration accuracy compared with current state-of-the-art learning-based methods while exhibiting strong cross-scenario generalization. Moreover, by replacing multiple isolated task-specific models with a compact unified model, UniReg substantially reduces the overall training burden in terms of total training cost and model redundancy.
Reliable correspondence estimation is a fundamental problem in image processing, underpinning applications such as Structure from Motion, visual localization, and image registration. Existing learning-based methods have significantly improved local feature representations, yet most still operate at the pixel or patch level and lack explicit modeling of regions that are jointly visible across views. We propose SAMatcher, a feature matching framework that formulates correspondence estimation through co-visibility modeling. Instead of directly matching local features, SAMatcher first predicts co-visible region masks and bounding boxes as structured priors for correspondence estimation. Built upon the Segment Anything Model (SAM), it introduces a symmetric cross-view interaction mechanism that enables bidirectional feature exchange and cross-view semantic alignment. We further develop a unified supervision scheme that jointly optimizes mask prediction and box localization through mask learning, box regression, and mask-box consistency constraints. Extensive experiments on challenging benchmarks demonstrate substantial improvements over existing matching pipelines, particularly under large viewpoint and scale variations. Our results show that foundation models originally designed for monocular segmentation can be effectively extended to multi-view correspondence reasoning through explicit co-visibility modeling, offering a new perspective on structured representation learning for image matching. Code and project page: https://xupan.top/Projects/samatcher
Foundation models such as Segment Anything Model 2 (SAM2) have transformed natural-image and video segmentation, and recent work has begun adapting them to medical imaging. These adaptations, however, are largely general-purpose models that treat MRI as one modality among many; large-scale, MRI-specific modelling and benchmarking remain limited, even though MRI's low soft-tissue contrast leaves many boundaries effectively invisible on individual slices. We present SAMRI-3D, a benchmark and method for 3D MRI segmentation with SAM2. The SAMRI-3D benchmark is the largest MRI-only evaluation to date - 10,392 volumes from 34 datasets (27 public, 7 in-house) spanning 12 anatomical domains and 10+ sequences, with explicit seen/unseen splits. Freezing the image encoder and fine-tuning only the lightweight decoder and memory modules raises mean Dice from 0.58 (zero-shot SAM2) to 0.76, surpassing recent SAM-based medical models (SAMed-2 0.69, Medical-SAM2 0.49, SAM-Med3D 0.37) with strong statistical significance. To target invisible boundaries, we introduce Global Volume Tokens (GVT): persistent memory tokens trained with a Truncated Signed Distance Field (TSDF) reconstruction objective that is discarded at inference (zero added cost). This full model, SAMRI-3D, attains the best accuracy (0.78) and lowest variance across all 34 datasets and, uniquely, shows no drop on 8 held-out datasets (0.79 unseen vs. 0.78 seen); per-sequence analysis confirms the TSDF objective helps most where per-slice contrast is weakest. We will release the benchmark, code, and models in this paper.