Medical Image Registration

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Overview

Medical image registration finds transformations that bring corresponding anatomy into alignment, enabling comparisons across time, modalities, or patients and supporting tasks such as motion correction and surgical guidance. Methods range from intensity- and feature-based optimization to deep networks, implicit deformation models, pretrained image features, and geometric or biomechanical priors; transformations may be rigid, affine, or deformable and diffeomorphic. Researchers evaluate these methods on settings such as brain MRI, lung CT, cardiac imaging, and intraoperative 2D–3D alignment, using landmarks, anatomical overlap, image similarity, and deformation quality. A central challenge is balancing accurate local matches with physically plausible, reliable deformations that generalize across scanners and modalities, since metrics can disagree and better overlap does not always mean better anatomical correspondence.

Latest papers

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96 papers17 papers in the last four weeks, up 55% on the four weeks before. 0.1% of all new papers.

May 16, 2026

Diffeomorphic Cortical Alignment via Direct Warping of Streamline Endpoints

Cortical surface registration is often driven by local geometric descriptors (e.g., sulcal depth and curvature). While this approach achieves geometric correspondence, it neglects the long-range wiring constraints imposed by white-matter anatomy. Diffusion MRI tractography offers these crucial constraints; however, prior connectivity-informed pipelines typically align precomputed connectivity matrices, making the optimization highly sensitive to connectivity estimation and its resolution. In this paper, we introduce a novel connectivity-based surface registration method that aligns cortical surfaces by operating directly on white-matter fiber-tract endpoints. We model tract endpoints as a point cloud on the product manifold Ω×ΩΩ\times Ω, where ΩΩ represents the spherical domain of the inflated cortical hemispheres. Our alignment method iteratively (i) computes a small diffeomorphic warp for ΩΩ by minimizing connectivity mismatch, and (ii) updates the endpoints based on this warp. The method relies on a geometric framework that ensures output warps are diffeomorphisms and has a final goal that optimizes the matching of well-known fiber bundles. Experiments on Human Connectome Project (HCP) data demonstrate improved tract-level correspondence, achieving higher connectivity-level overlap coefficients on major fiber bundles and stronger robustness across grid resolutions for ΩΩ compared to state-of-the-art methods such as ENCORE and MSMAll.

Yang Xiang, Martin Cole, Zhengwu Zhang

Department of Statistics and Operations Research, The University of North Carolina at Chapel Hill · Department of Psychiatry, University of Rochester

Medical Image RegistrationNeuroimagingDeformable Image Registration
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May 13, 2026

VoxCor: Training-Free Volumetric Features for Multimodal Voxel Correspondence

Cross-modal 3D medical image analysis requires voxelwise representations that remain anatomically consistent across imaging contrasts, scanners, and acquisition protocols. Recent work has shown that frozen 2D Vision Transformer (ViT) foundation models can support such representations, but typical pipelines extract features along a single anatomical axis and adapt those features inside a registration solver for one image pair at a time, leaving complementary viewing directions unused and producing representations that do not transfer to new volumes. We introduce VoxCor, a training-free fit--transform method for reusable volumetric feature representations from frozen 2D ViT foundation models. During an offline fitting phase, VoxCor combines triplanar ViT inference with a compact closed-form weighted partial least squares (WPLS) projection that uses fitting-time voxel correspondences to select modality-stable anatomical directions in the triplanar feature space. At transform time, new volumes are mapped by triplanar ViT inference and linear projection alone, without fine-tuning or registration. Voxel correspondences can then be queried directly by nearest-neighbor search. We evaluate VoxCor on intra-subject Abdomen MR--CT and inter-subject HCP T2w--T1w tasks using deformable registration, voxelwise k-nearest-neighbor segmentation, and segmentation-center landmark localization. VoxCor improves the hardest cross-subject, cross-modality transfer settings, reduces encoder sensitivity for dense correspondence transfer, and yields registration performance competitive with handcrafted descriptors and learned 3D features. This positions VoxCor as a reusable feature layer for downstream multimodal analysis beyond pairwise registration. Code, configuration files, and implementation details are publicly available on GitHub at guneytombak/VoxCor.

Guney Tombak, Ertunc Erdil, Ender Konukoglu

Biomedical Image Computing Group, ETH Zurich, Zurich, Switzerland · The LOOP Zurich – Medical Research Center, Zurich, Switzerland

Medical Imaging Foundation ModelsCross-Modal Representation LearningMedical Image RegistrationCross-Modal Feature MatchingCross-Modal Image RegistrationMedical Image Representation Learning
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May 11, 2026

Set-Based Groupwise Registration for Variable-Length, Variable-Contrast Cardiac MRI

Quantitative cardiac magnetic resonance imaging (MRI) enables non-invasive myocardial tissue characterization but relies on robust motion correction within these variable-length, variable-contrast image sequences. Groupwise registration, which simultaneously aligns all images, has shown greater robustness than pairwise registration for motion correction. However, current deep-learning-based groupwise registration methods cannot generalize across MRI sequences: the architecture typically encodes input data as a fixed-length channel stack, which rigidly couples network design to protocol-specific sequence length, input ordering, and contrast dynamics. At inference time, any change in imaging protocols will render the network unusable. In this work, we introduce \AnyTwoReg, a new set-based groupwise registration framework that takes a quantitative MRI sequence as an unordered set. This set formulation fundamentally decouples network design from sequence length and input ordering. By utilizing a shared encoder and correlation-guided feature aggregation, \AnyTwoReg constructs a permutation-invariant canonical reference for registration, and learns a permutation-equivariant mapping from images to deformation fields. Additionally, we extract contrast-insensitive image features from an existing foundation model to handle extreme contrast variations. Trained exclusively on a single public T1T_1 mapping dataset (STONE, sequence length L=11L=11), \AnyTwoReg generalizes to two unseen quantitative MRI datasets (MOLLI, ASL) with variable lengths (L∈[11,60]L \in [11, 60]) and different contrast dynamics. It achieves strong cross-protocol generalization in a zero-shot manner, and consistently improves downstream quantitative mapping quality. Notably, while designed for quantitative MRI sequences, our framework is directly applicable to Cine MRI sequences for inter-cardiac-phase registration.

Yi Zhang, Yidong Zhao, Tijmen Toxopeus +3

Department of Imaging Physics, Delft University of Technology, The Netherlands

Medical Image RegistrationMagnetic Resonance ImagingDeformable Image RegistrationCardiac MRI
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Apr 30, 2026

MSR:Hybrid Field Modeling for CT-MRI Rigid-Deformable Registration of the Cervical Spine with an Annotated Dataset

Accurate CT-MRI registration of the cervical spine is essential for preoperative planning because this region is anatomically complex,highly variable,and vulnerable to injury of the vertebral arteries and spinal cord. However,cervical CT-MRI registration remains underexplored,particularly for rigid-deformable hybrid modeling,and the lack of high-quality annotated multimodal data further limits progress. To address these challenges, we construct and release a comprehensively annotated CT-MRI dataset, R-D-Reg, and propose MSR, a rigid-deformable hybrid registration framework for complex joint structures. Specifically, MSR includes a rigid registration module for independent local rigid alignment of individual vertebrae and a deformable registration module with an MSL block that combines Mamba-based global modeling and Swin Transformer-based local modeling through adaptive gating. The rigid and deformable deformation fields are then fused to generate a hybrid field that better preserves local anatomical consistency. The code and dataset are publicly available at https://github.com/ssc1230609-spec/MSR-registration.

Bohai Zhang, Wenjie Chen, Mu Li +8

School of Biomedical Engineering, Southern Medical University, Guangzhou, 510515, China. · Guangdong Provincial Key Laboratory of Medical Image Processing, Guangzhou, 510515, China. · Guangdong Province Engineering Laboratory for Medical Imaging and Diagnostic Technology Guangzhou, 510515, China. +2

Medical ImagingMedical Image RegistrationDeformable Image RegistrationMedical Image Benchmarks
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Apr 27, 2026

Point Cloud Registration for Fusion between SPECT MPI and CTA Images

Clinical fusion of Single Photon Emission Computed Tomography Myocardial Perfusion Imaging (SPECT MPI) and Computed Tomography Angiography (CTA) remains limited by cross-modality misregistration and reliance on manual landmarks, which can hinder accurate ischemia localization and lesion-level functional assessment. To address this issue, we propose a registration and fusion framework for SPECT MPI and CTA that integrates functional and structural information for comprehensive cardiac evaluation. The proposed pipeline performs U-Net-based segmentation on both modalities. On SPECT MPI, only the left ventricle (LV) is extracted, and anatomical landmarks are automatically derived from characteristic LV structures. On CTA, both ventricles are segmented, and their spatial relationship is used to automatically define landmarks at the interventricular septal junction. Scale-space consistency preprocessing and landmark-driven coarse registration are applied to mitigate initial misalignment. Based on this initialization, multiple fine registration methods are evaluated on LV epicardial surface point clouds, including ICP, SICP, CPD, CluReg, FFD, and BCPD-plus-plus. The resulting transformations are then propagated to voxel-level resampling for high-precision SPECT-CTA fusion. In a retrospective cohort of 60 patients, the proposed framework preserved sub-millimeter coronary detail from CTA while accurately overlaying quantitative SPECT perfusion. Among the evaluated methods, BCPD-plus-plus achieved the highest accuracy with a mean point cloud distance of 1.7 mm. By combining robust initialization, comparative fine registration, and voxel-level fusion, the proposed approach provides a practical solution for myocardial ischemia localization and functional evaluation of coronary lesions, while remaining independent of any specific fine registration algorithm.

Ni Yao, Xiangyu Liu, Shaojie Tang +9

School of Computer Science and Artificial Intelligence, Zhengzhou University of Light Industry, Zhengzhou 450001, Henan, China · School of Automation, Xi’an University of Posts and Telecommunications, Xi’an, Shaanxi, 710121, China · Xi'an Key Laboratory of Advanced Control and Intelligent Process, Xi'an, Shaanxi, 710121, China +5

Medical ImagingMedical Image RegistrationPoint Cloud RegistrationMultimodal Fusion
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Apr 24, 2026

CT-Guided Spatially-varying Regularization for Voxel-Wise Deformable Whole-Body PET Registration

Whole-body Positron Emission Tomography (PET) registration is essential for multi-parametric tumor characterization and assessment of metastatic disease progression. In deep learning-based deformable registration, the dense displacement field (DDF) regularizer is crucial for stabilizing optimization and preventing unrealistic deformations in large 3D volumes. A key challenge in whole-body deformable registration is anatomical heterogeneity, rigid structures (e.g., bones) should undergo stronger regularization, whereas soft tissues require more flexible deformation and weaker constraints. In this work, we propose a simple yet effective CT-guided spatially-varying regularization strategy for whole-body cross-tracer deformable PET registration. The key idea is to use the paired CT volume from the PET/CT acquisition to construct a voxel-wise regularization map for the DDF, replacing the conventional single global regularization weight. This yields anatomy-adaptive regularization strength across rigid and soft tissues. The proposed method is evaluated on a real clinical cross-tracer PET/CT dataset of 296 patients involving 18F-PSMA and 18F-FDG, showing that the proposed method achieves statistically significant improvements over weakly-supervised registration baseline in both whole-body registration performance and organ-wise alignment.

Xiangcen Wu, Ruohua Chen, Sichun Li +4

Institute of Medical Technology, Peking University Health Science Center, Beijing, China · Ren Ji Hospital, Shanghai Jiao Tong University, Shanghai, China · University of Oxford, Oxford, United Kingdom

Medical Image RegistrationPET/CT ImagingDeformable Image Registration
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Apr 19, 2026

Deep learning based Non-Rigid Volume-to-Surface Registration for Brain Shift compensation Using Point Cloud

Soft-tissue deformation remains a major limitation in image-guided neurosurgery, where intra-operative anatomy can deviate substantially from pre-operative imaging due to brain shift, compromising navigation accuracy and surgical safety. Existing compensation methods often rely on intra-operative MRI, CT, or ultrasound, which are disruptive and difficult to integrate repeatedly into the surgical workflow. In contrast, partial 3D cortical surfaces can be reconstructed as point clouds from stereoscopic microscopes or laser range scanners (LRS), capturing only a limited portion of the exposed cortex. This makes point cloud registration a practical alternative without interrupting surgery; however, such partial and noisy observations make deformation estimation highly challenging. In this study, we propose a deep learning-based framework for non-rigid volume-to-surface registration, enabling dense displacement field estimation from sparse intra-operative surface observations without explicit point correspondences or volumetric intra-operative imaging. The network leverages multi-scale point-based feature extraction and a hierarchical deformation decoder to capture both global and local deformations. The key contribution lies in integrating partial intra-operative surface information into the full pre-operative point cloud domain, enabling implicit correspondence learning and dense deformation recovery under limited visibility. Quantitative results demonstrate accurate recovery of fine-scale deformations, achieving an Endpoint Error (EPE) of 1.13 +/- 0.75 mm and RMSE of 1.33 +/- 0.81 mm under challenging partial-surface conditions. The proposed approach supports automatic, workflow-compatible brain-shift compensation from sparse surface observations.

Eashrat Jahan Muniya, Gernot Kronreif, Ander Biguri +2

Austrian Center for Medical Innovation and Technology, Wiener Neustadt, Austria · Medical University of Vienna, Department of Medical Physics and Biomedical Engineering Vienna, Austria · University of Cambridge, Department of Applied Mathematics and Theoretical Physics (DAMTP) Cambridge, United Kingdom +1

Medical Image RegistrationPoint Cloud RegistrationDeformable Image Registration
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Apr 15, 2026

A Multimodal Clinically Informed Coarse-to-Fine Framework for Longitudinal CT Registration in Proton Therapy

Proton therapy offers superior organ-at-risk sparing but is highly sensitive to anatomical changes, making accurate deformable image registration (DIR) across longitudinal CT scans essential. Conventional DIR methods are often too slow for emerging online adaptive workflows, while existing deep learning-based approaches are primarily designed for generic benchmarks and underutilize clinically relevant information beyond images. To address this gap, we propose a clinically scalable coarse-to-fine deformable registration framework that integrates multimodal information from the proton radiotherapy workflow to accommodate diverse clinical scenarios. The model employs dual CNN-based encoders for hierarchical feature extraction and a transformer-based decoder to progressively refine deformation fields. Beyond CT intensities, clinically critical priors, including target and organ-at-risk contours, dose distributions, and treatment planning text, are incorporated through anatomy- and risk-guided attention, text-conditioned feature modulation, and foreground-aware optimization, enabling anatomically focused and clinically informed deformation estimation. We evaluate the proposed framework on a large-scale proton therapy DIR dataset comprising 1,222 paired planning and repeat CT scans across multiple anatomical regions and disease types. Extensive experiments demonstrate consistent improvements over state-of-the-art methods, enabling fast and robust clinically meaningful registration.

Caiwen Jiang, Yuzhen Ding, Mi Jia +14

Department of Radiation Oncology, Mayo Clinic, Phoenix, Arizona, USA · School of Biomedical Engineering, ShanghaiTech University, Shanghai, China · Shanghai United Imaging Intelligence Co., Ltd., Shanghai 200230, China +2

Medical Image RegistrationDeformable Image RegistrationLongitudinal Medical Image AnalysisComputed Tomography
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Apr 11, 2026

Warm-Started Reinforcement Learning for Iterative 3D/2D Liver Registration

Registration between preoperative CT and intraoperative laparoscopic video plays a crucial role in augmented reality (AR) guidance for minimally invasive surgery. Learning-based methods have recently achieved registration errors comparable to optimization-based approaches while offering faster inference. However, many supervised methods produce coarse alignments that rely on additional optimization-based refinement, thereby increasing inference time. We present a discrete-action reinforcement learning (RL) framework that formulates CT-to-video registration as a sequential decision-making process. A shared feature encoder, warm-started from a supervised pose estimation network to provide stable geometric features and faster convergence, extracts representations from CT renderings and laparoscopic frames, while an RL policy head learns to choose rigid transformations along six degrees of freedom and to decide when to stop the iteration. Experiments on a public laparoscopic dataset demonstrated that our method achieved an average target registration error (TRE) of 15.70 mm, comparable to supervised approaches with optimization, while achieving faster convergence. The proposed RL-based formulation enables automated, efficient iterative registration without manually tuned step sizes or stopping criteria. This discrete framework provides a practical foundation for future continuous-action and deformable registration models in surgical AR applications.

Hanyuan Zhang, Lucas He, Zijie Cheng +5

UCL Hawkes Institute, University College London, London, UK · Medtronic plc., London, UK

Medical Image RegistrationCross-Modal Image RegistrationAR in Surgery
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Apr 11, 2026

Particle Diffusion Matching: Random Walk Correspondence Search for the Alignment of Standard and Ultra-Widefield Fundus Images

We propose a robust alignment technique for Standard Fundus Images (SFIs) and Ultra-Widefield Fundus Images (UWFIs), which are challenging to align due to differences in scale, appearance, and the scarcity of distinctive features. Our method, termed Particle Diffusion Matching (PDM), performs alignment through an iterative Random Walk Correspondence Search (RWCS) guided by a diffusion model. At each iteration, the model estimates displacement vectors for particle points by considering local appearance, the structural distribution of particles, and an estimated global transformation, enabling progressive refinement of correspondences even under difficult conditions. PDM achieves state-of-the-art performance across multiple retinal image alignment benchmarks, showing substantial improvement on a primary dataset of SFI-UWFI pairs and demonstrating its effectiveness in real-world clinical scenarios. By providing accurate and scalable correspondence estimation, PDM overcomes the limitations of existing methods and facilitates the integration of complementary retinal image modalities. This diffusion-guided search strategy offers a new direction for improving downstream supervised learning, disease diagnosis, and multi-modal image analysis in ophthalmology.

Kanggeon Lee, Soochahn Lee, Kyoung Mu Lee

ASRI, Dept. of ECE, Seoul National University, Korea · School of Electrical Engineering, Kookmin University, Korea

Medical Image RegistrationCross-Modal Image RegistrationFundus ImagingCross-Modal Feature Matching
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Apr 11, 2026

Active Diffusion Matching: Score-based Iterative Alignment of Cross-Modal Retinal Images

Objective: The study aims to address the challenge of aligning Standard Fundus Images (SFIs) and Ultra-Widefield Fundus Images (UWFIs), which is difficult due to their substantial differences in viewing range and the amorphous appearance of the retina. Currently, no specialized method exists for this task, and existing image alignment techniques lack accuracy. Methods: We propose Active Diffusion Matching (ADM), a novel cross-modal alignment method. ADM integrates two interdependent score-based diffusion models to jointly estimate global transformations and local deformations via an iterative Langevin Markov chain. This approach facilitates a stochastic, progressive search for optimal alignment. Additionally, custom sampling strategies are introduced to enhance the adaptability of ADM to given input image pairs. Results: Comparative experimental evaluations demonstrate that ADM achieves state-of-the-art alignment accuracy. This was validated on two datasets: a private dataset of SFI-UWFI pairs and a public dataset of SFI-SFI pairs, with mAUC improvements of 5.2 and 0.4 points on the private and public datasets, respectively, compared to existing state-of-the-art methods. Conclusion: ADM effectively bridges the gap in aligning SFIs and UWFIs, providing an innovative solution to a previously unaddressed challenge. The method's ability to jointly optimize global and local alignment makes it highly effective for cross-modal image alignment tasks. Significance: ADM has the potential to transform the integrated analysis of SFIs and UWFIs, enabling better clinical utility and supporting learning-based image enhancements. This advancement could significantly improve diagnostic accuracy and patient outcomes in ophthalmology.

Kanggeon Lee, Su Jeong Song, Soochahn Lee +1

ASRI, Dept. of ECE, Seoul National University, Korea · Dept. of Ophthalmology, Kangbuk Samsung Hospital, Sungkyunkwan University, Korea · School of Electrical Engineering, Kookmin University, Korea

Medical Image RegistrationCross-Modal Image RegistrationDiffusion Model AlignmentDeformable Image RegistrationFundus Imaging
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Apr 10, 2026

Search-MIND: Training-Free Multi-Modal Medical Image Registration

Multi-modal image registration plays a critical role in precision medicine but faces challenges from non-linear intensity relationships and local optima. While deep learning models enable rapid inference, they often suffer from generalization collapse on unseen modalities. To address this, we propose Search-MIND, a training-free, iterative optimization framework for instance-specific registration. Our pipeline utilizes a coarse-to-fine strategy: a hierarchical coarse alignment stage followed by deformable refinement. We introduce two novel loss functions: Variance-Weighted Mutual Information (VWMI), which prioritizes informative tissue regions to shield global alignment from background noise and uniform regions, and Search-MIND (S-MIND), which broadens the convergence basin of structural descriptors by considering larger local search range. Evaluations on CARE Liver 2025 and CHAOS Challenge datasets show that Search-MIND consistently outperforms classical baselines like ANTs and foundation model-based approaches like DINO-reg, offering superior stability across diverse modalities.

Boya Wang, Ruizhe Li, Chao Chen +1

Intelligent Modelling & Analysis Group (IMA), School of Computer Science, University of Nottingham, UK · Lab for Uncertainty in Data and Decision Making (LUCID), Nottingham Biomedical Research Centre (BRC), School of Medicine, University of Nottingham, UK

Medical Image RegistrationCross-Modal Image RegistrationDeformable Image Registration
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Apr 9, 2026

Rotation Equivariant Convolutions in Deformable Registration of Brain MRI

Image registration is a fundamental task that aligns anatomical structures between images. While CNNs perform well, they lack rotation equivariance - a rotated input does not produce a correspondingly rotated output. This hinders performance by failing to exploit the rotational symmetries inherent in anatomical structures, particularly in brain MRI. In this work, we integrate rotation-equivariant convolutions into deformable brain MRI registration networks. We evaluate this approach by replacing standard encoders with equivariant ones in three baseline architectures, testing on multiple public brain MRI datasets. Our experiments demonstrate that equivariant encoders have three key advantages: 1) They achieve higher registration accuracy while reducing network parameters, confirming the benefit of this anatomical inductive bias. 2) They outperform baselines on rotated input pairs, demonstrating robustness to orientation variations common in clinical practice. 3) They show improved performance with less training data, indicating greater sample efficiency. Our results demonstrate that incorporating geometric priors is a critical step toward building more robust, accurate, and efficient registration models.

Arghavan Rezvani, Kun Han, Anthony T. Wu +2

University of California, Irvine

Medical Image RegistrationDeformable Image RegistrationEquivariant Neural NetworksMagnetic Resonance ImagingEquivariant Representation Learning
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Apr 2, 2026

AdamFlow: Adam-based Wasserstein Gradient Flows for Surface Registration in Medical Imaging

Surface registration plays an important role for anatomical shape analysis in medical imaging. Existing surface registration methods often face a trade-off between efficiency and robustness. Local point matching methods are computationally efficient, but vulnerable to noise and initialisation. Methods designed for global point set alignment tend to incur a high computational cost. To address the challenge, here we present a fast surface registration method, which formulates surface meshes as probability measures and surface registration as a distributional optimisation problem. The discrepancy between two meshes is measured using an efficient sliced Wasserstein distance with log-linear computational complexity. We propose a novel optimisation method, AdamFlow, which generalises the well-known Adam optimisation method from the Euclidean space to the probability space for minimising the sliced Wasserstein distance. We theoretically analyse the asymptotic convergence of AdamFlow and empirically demonstrate its superior performance in both affine and non-rigid surface registration across various anatomical structures.

Qiang Ma, Qingjie Meng, Xin Hu +2

Department of Brain Sciences, Imperial College London, London, UK · Department of Computing, Imperial College London, London, UK · School of Computer Science, University of Birmingham, Birmingham, UK +2

Medical Image RegistrationWasserstein Gradient FlowsDeformable Image Registration
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Mar 31, 2026

All-in-One Augmented Reality Guided Head and Neck Tumor Resection

Positive margins are common in head and neck squamous cell carcinoma, yet intraoperative re-resection is often imprecise because margin locations are typically communicated verbally from pathology. We present an all-in-one augmented reality (AR) system that relocalizes positive margins from a resected specimen to the resection bed and visualizes them in situ using HoloLens 2 depth sensing and fully automated markerless surface registration. In a silicone phantom study with six medical trainees, markerless registration achieved target registration errors comparable to a marker-based baseline (median 1.8 mm vs. 1.7 mm; maximum < 4 mm). In a margin relocalization task, AR guidance reduced error from verbal guidance (median 14.2 mm) to a few millimeters (median 3.2 mm), with all AR localizations within 5 mm error. These results support the feasibility of markerless AR margin guidance for more precise intraoperative re-excision.

Yue Yang, Matthieu Chabanas, Carrie Reale +5

Vanderbilt Institute for Surgery and Engineering, Nashville, TN 37235, USA · Vanderbilt University Medical Center, Nashville, TN 37232, USA

AR in SurgeryMedical Image LocalizationOncologyMedical Image Registration
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Mar 24, 2026

CoRe: Joint Optimization with Contrastive Learning for Medical Image Registration

Medical image registration is a fundamental task in medical image analysis, enabling the alignment of images from different modalities or time points. However, intensity inconsistencies and nonlinear tissue deformations pose significant challenges to the robustness of registration methods. Recent approaches leveraging self-supervised representation learning show promise by pre-training feature extractors to generate robust anatomical embeddings, that farther used for the registration. In this work, we propose a novel framework that integrates equivariant contrastive learning directly into the registration model. Our approach leverages the power of contrastive learning to learn robust feature representations that are invariant to tissue deformations. By jointly optimizing the contrastive and registration objectives, we ensure that the learned representations are not only informative but also suitable for the registration task. We evaluate our method on abdominal and thoracic image registration tasks, including both intra-patient and inter-patient scenarios. Experimental results demonstrate that the integration of contrastive learning directly into the registration framework significantly improves performance, surpassing strong baseline methods.

Eytan Kats, Christoph Grossbroehmer, Ziad Al-Haj Hemidi +3

Insitute of Medical Informatics, University of Luebeck, Luebeck, Germany

Medical Image RegistrationDeformable Image RegistrationMedical Image Representation LearningContrastive Learning
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Mar 23, 2026

Cycle Inverse-Consistent TransMorph: A Balanced Deep Learning Framework for Brain MRI Registration

Deformable image registration plays a fundamental role in medical image analysis by enabling spatial alignment of anatomical structures across subjects. While recent deep learning-based approaches have significantly improved computational efficiency, many existing methods remain limited in capturing long-range anatomical correspondence and maintaining deformation consistency. In this work, we present a cycle inverse-consistent transformer-based framework for deformable brain MRI registration. The model integrates a Swin-UNet architecture with bidirectional consistency constraints, enabling the joint estimation of forward and backward deformation fields. This design allows the framework to capture both local anatomical details and global spatial relationships while improving deformation stability. We conduct a comprehensive evaluation of the proposed framework on a large multi-center dataset consisting of 2851 T1-weighted brain MRI scans aggregated from 13 public datasets. Experimental results demonstrate that the proposed framework achieves strong and balanced performance across multiple quantitative evaluation metrics while maintaining stable and physically plausible deformation fields. Detailed quantitative comparisons with baseline methods, including ANTs, ICNet, and VoxelMorph, are provided in the appendix. Experimental results demonstrate that CICTM achieves consistently strong performance across multiple evaluation criteria while maintaining stable and physically plausible deformation fields. These properties make the proposed framework suitable for large-scale neuroimaging datasets where both accuracy and deformation stability are critical.

Jiaqi Shang, Haojin Wu, Yinyi Lai +3

Medical Image RegistrationDeformable Image RegistrationBrain MRI
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Mar 19, 2026

Factored Levenberg-Marquardt for Diffeomorphic Image Registration: An efficient optimizer for FireANTs

FireANTs introduced a novel Eulerian descent method for plug-and-play behavior with arbitrary optimizers adapted for diffeomorphic image registration as a test-time optimization problem, with a GPU-accelerated implementation. FireANTs uses Adam as its default optimizer for fast and more robust optimization. However, Adam requires storing state variables (i.e. momentum and squared-momentum estimates), each of which can consume significant memory, prohibiting its use for significantly large images. In this work, we propose a modified Levenberg-Marquardt (LM) optimizer that requires only a single scalar damping parameter as optimizer state, that is adaptively tuned using a trust region approach. The resulting optimizer reduces memory by up to 24.6% for large volumes, and retaining performance across all four datasets. A single hyperparameter configuration tuned on brain MRI transfers without modification to lung CT and cross-modal abdominal registration, matching or outperforming Adam on three of four benchmarks. We also perform ablations on the effectiveness of using Metropolis-Hastings style rejection step to prevent updates that worsen the loss function.

Rohit Jena, Pratik Chaudhari, James C. Gee

Department of Computer and Information Science, University of Pennsylvania, Philadelphia, PA 19104, USA · Department of Electrical and Systems Engineering, University of Pennsylvania, Philadelphia, PA 19104, USA · Department of Radiology & Penn Image Computing and Science Laboratory (PICSL), Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA

Medical Image RegistrationDeformable Image RegistrationSecond-Order OptimizationTrust-Region Optimization
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Mar 18, 2026

Structured SIR: Efficient and Expressive Importance-Weighted Inference for High-Dimensional Image Registration

Image registration is an ill-posed dense vision task, where multiple solutions achieve similar loss values, motivating probabilistic inference. Variational inference has previously been employed to capture these distributions, however restrictive assumptions about the posterior form can lead to poor characterisation, overconfidence and low-quality samples. More flexible posteriors are typically bottlenecked by the complexity of high-dimensional covariance matrices required for dense 3D image registration. In this work, we present a memory and computationally efficient inference method, Structured SIR, that enables expressive, multi-modal, characterisation of uncertainty with high quality samples. We propose the use of a Sampled Importance Resampling (SIR) algorithm with a novel memory-efficient high-dimensional covariance parameterisation as the sum of a low-rank covariance and a sparse, spatially structured Cholesky precision factor. This structure enables capturing complex spatial correlations while remaining computationally tractable. We evaluate the efficacy of this approach in 3D dense image registration of brain MRI data, which is a very high-dimensional problem. We demonstrate that our proposed method produces uncertainty estimates that are significantly better calibrated than those produced by variational methods, achieving equivalent or better accuracy. Crucially, we show that the model yields highly structured multi-modal posterior distributions, enable effective and efficient uncertainty quantification.

Ivor J. A. Simpson, Neill D. F. Campbell

Department of Informatics University of Sussex, UK · Department of Computer Science University College London, UK · Department of Computer Science University of Bath, UK

Uncertainty QuantificationImportance SamplingMedical Image RegistrationDeformable Image Registration
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Mar 17, 2026

Volumetrically Consistent Implicit Atlas Learning via Neural Diffeomorphic Flow for Placenta MRI

Establishing dense volumetric correspondences across anatomical shapes is essential for group-level analysis but remains challenging for implicit neural representations. Most existing implicit registration methods rely on supervision near the zero-level set and thus capture only surface correspondences, leaving interior deformations under-constrained. We introduce a volumetrically consistent implicit model that couples reconstruction of signed distance functions (SDFs) with neural diffeomorphic flow to learn a shared canonical template of the placenta. Volumetric regularization, including Jacobian-determinant and biharmonic penalties, suppresses local folding and promotes globally coherent deformations. In the motivating application to placenta MRI, our formulation jointly reconstructs individual placentas, aligns them to a population-derived implicit template, and enables voxel-wise intensity mapping in a unified canonical space. Experiments on in-vivo placenta MRI scans demonstrate improved geometric fidelity and volumetric alignment over surface-based implicit baseline methods, yielding anatomically interpretable and topologically consistent flattening suitable for group analysis.

Athena Taymourtash, S. Mazdak Abulnaga, Esra Abaci Turk +2

MIT Computer Science and Artificial Intelligence Laboratory · Massachusetts General Hospital, Harvard Medical School · Boston Children’s Hospital, Harvard Medical School

Medical Image AnalysisMedical Image RegistrationDeformable Image RegistrationImplicit Neural Representations
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Mar 15, 2026

On the Degrees of Freedom of Gridded Control Points in Learning-Based Medical Image Registration

Many registration problems are ill-posed in homogeneous or noisy regions, and dense voxel-wise decoders can be unnecessarily high-dimensional. A sparse control-point parameterisation provides a compact, smooth deformation representation while reducing memory and improving stability. This work investigates the required control points for learning-based registration network development. We present GridReg, a learning-based registration framework that replaces dense voxel-wise decoding with displacement predictions at a sparse grid of control points. This design substantially cuts the parameter count and memory while retaining registration accuracy. Multiscale 3D encoder feature maps are flattened into a 1D token sequence with positional encoding to retain spatial context. The model then predicts a sparse gridded deformation field using a cross-attention module. We further introduce grid-adaptive training, enabling an adaptive model to operate at multiple grid sizes at inference without retraining. This work quantitatively demonstrates the benefits of using sparse grids. Using three data sets for registering prostate gland, pelvic organs and neurological structures, the results suggested a significant improvement with the usage of grid-controled displacement field. Alternatively, the superior registration performance was obtained using the proposed approach, with a similar or less computational cost, compared with existing algorithms that predict DDFs or displacements sampled on scattered key points.

Wen Yan, Qianye Yang, Yipei Wang +5

UCL Hawkes Institute; Department of Medical Physics and Biomedical Engineering, University College London, Gower St, London WC1E 6BT, London, U.K. · Centre for Medical Imaging, Division of Medicine, University College London, Gower St, London WC1E 6BT, London, U.K. · Division of Surgery and Interventional Science, University College London, 10 Pond St, London NW3 2PS, U.K. +2

Medical Image RegistrationDeformable Image Registration
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Mar 14, 2026

Effective Feature Learning for 3D Medical Registration via Domain-Specialized DINO Pretraining

Medical image registration is a critical component of clinical imaging workflows, enabling accurate longitudinal assessment, multi-modal data fusion, and image-guided interventions. Intensity-based approaches often struggle with interscanner variability and complex anatomical deformations, whereas feature-based methods offer improved robustness by leveraging semantically informed representations. In this work, we investigate DINO-style self-supervised pretraining directly on 3D medical imaging data, aiming to learn dense volumetric features well suited for deformable registration. We assess the resulting representations on challenging interpatient abdominal registration task across both MRI and CT modalities. Our domain-specialized pretraining outperforms the DINOv2 model trained on a large-scale collection of natural images, while requiring substantially lower computational resources at inference time. Moreover, it surpasses established registration models under out-of-domain evaluation, demonstrating the value of task-agnostic yet medical imaging-focused pretraining for robust and efficient 3D image registration.

Eytan Kats, Mattias P. Heinrich

Institute of Medical Informatics, University of Lübeck, Germany

Medical Image RegistrationDeformable Image RegistrationMedical Image Representation LearningSelf-Supervised LearningCross-Modal Image Registration
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Mar 6, 2026

Match4Annotate: Cross-Video Annotation Transfer in Ultrasound via Implicit Feature Flow-Guided Matching

Acquiring per-frame annotations for ultrasound videos is costly and requires clinical expertise, limiting learning-based analysis. We study cross-video annotation transfer: propagating user-specified annotations from a labeled ultrasound video to an independently acquired target video with no target-side labels or manual initialization. Video trackers and segmentation propagators rely on temporal continuity and require a prompt in every new sequence, whereas cross-image feature matching and one-shot segmentation estimate correspondences independently, without enforcing coherent deformations or supporting both point and mask annotations. We present Match4Annotate, a test-time framework with three stages. A spatiotemporal implicit feature representation lifts frozen vision foundation-model features into a continuous field over space and time, enabling queries beyond the backbone resolution. A continuous implicit feature flow then aligns the source and target fields under a smooth-deformation prior, estimating correspondence in feature space rather than relying on intensity consistency, which is often violated in ultrasound by speckle and acquisition-dependent appearance. Finally, flow-guided annotation transfer uses the estimated flow as a spatial prior over feature similarity. This formulation unifies sparse point and dense mask transfer and includes unconstrained feature matching and direct flow warping as limiting cases. On four clinical ultrasound datasets spanning echocardiography and musculoskeletal imaging, Match4Annotate achieves state-of-the-art annotation transfer, outperforming dense feature-matching baselines across PCK thresholds and one-shot segmentation methods in Dice score. It also demonstrates bidirectional transfer of left-ventricular annotations across datasets. It requires no task-specific training and adapts to each video in minutes on a single consumer GPU.

Zhuorui Zhang, Roger Pallarès-López, Praneeth Namburi +1

Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, USA · Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, USA · MIT.nano Immersion Lab, Massachusetts Institute of Technology, Cambridge, USA

Image MatchingMedical Image RegistrationUltrasound ImagingTransfer Learning
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Mar 2, 2026

Preoperative-to-intraoperative Liver Registration for Laparoscopic Surgery via Latent-Grounded Correspondence Constraints

In laparoscopic liver surgery, augmented reality technology enhances intraoperative anatomical guidance by overlaying 3D liver models from preoperative CT/MRI onto laparoscopic 2D views. However, existing registration methods lack explicit modeling of reliable 2D-3D geometric correspondences supported by latent evidence, leading to limited interpretability and potentially unstable alignment in clinical scenarios. In this work, we introduce Land-Reg, a correspondence-driven deformable registration framework that explicitly learns latent-grounded 2D-3D landmark correspondences as an interpretable intermediate representation to bridge cross-modal alignment. For rigid registration, Land-Reg embraces a Cross-modal Latent Alignment module to map multi-modal features into a unified latent space. Further, an Uncertainty-enhanced Overlap Landmark Detector with similarity matching is proposed to robustly estimate explicit 2D-3D landmark correspondences. For non-rigid registration, we design a novel shape-constrained supervision strategy that anchors shape deformation to matched landmarks through reprojection consistency and incorporates local-isometric regularization to alleviate inherent 2D-3D depth ambiguity, while a rendered-mask alignment enforces global shape consistency. Experimental results on the P2ILF dataset demonstrate the superiority of our method on both rigid pose estimation and non-rigid deformation. Our code will be available at https://github.com/cuiruize/Land-Reg.

Ruize Cui, Jialun Pei, Haiqiao Wang +4

The Hong Kong Polytechnic University, Hong Kong, China · The Chinese University of Hong Kong, Hong Kong, China

2D-3D Image RegistrationLaparoscopic SurgeryMedical Image RegistrationCross-Modal Image RegistrationDeformable Image Registration
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Mar 1, 2026

Flow Matching-enabled Test-Time Refinement for Unsupervised Cardiac MR Registration

Diffusion-based unsupervised image registration has been explored for cardiac cine MR, but expensive multi-step inference limits practical use. We propose FlowReg, a flow-matching framework in displacement field space that achieves strong registration in as few as two steps and supports further refinement with more steps. FlowReg uses warmup-reflow training: a single-step network first acts as a teacher, then a student learns to refine from arbitrary intermediate states, removing the need for a pre-trained model as in existing methods. An Initial Guess strategy feeds back the model prediction as the next starting point, improving refinement from step two onward. On ACDC and MM2 across six tasks (including cross-dataset generalization), FlowReg outperforms the state of the art on five tasks (+0.6% mean Dice score on average), with the largest gain in the left ventricle (+1.09%), and reduces LVEF estimation error on all six tasks (-2.58 percentage points), using only 0.7% extra parameters and no segmentation labels. Code is available at https://github.com/mathpluscode/FlowReg.

Yunguan Fu, Wenjia Bai, Wen Yan +3

University College London · InstaDeep · Imperial College London

Medical Image RegistrationDeformable Image RegistrationCardiac MRIFlow Matching
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Feb 27, 2026

GLIDE-Reg: Global-to-Local Deformable Registration Using Co-Optimized Foundation and Handcrafted Features

Deformable registration is crucial in medical imaging. Several existing applications include lesion tracking, probabilistic atlas generation, and treatment response evaluation. However, current methods often lack robustness and generalizability across two key factors: spatial resolution and differences in anatomical coverage. We jointly optimize a registration field and a learnable dimensionality reduction module so that compressed VFM embeddings remain registration-relevant, and fuse these global semantic cues with MIND local descriptors. GLIDE-Reg achieves average dice similarity coefficients (DSC) across 6 anatomical structures of 0.859, 0.862, and 0.901 in two public cohorts (Lung250M and NLST) and one institution cohort (UCLA5DCT), and outperforms the state-of-the-art DEEDS (0.834, 0.858, 0.900) with relative improvements of 3.0%, 0.5%, and 0.1%. For target registration errors, GLIDE-Reg achieves 1.58 mm on Lung250M landmarks (compared to 1.25 mm on corrField and 1.91 mm on DEEDS) and 1.11 mm on NLST nodule centers (compared to 1.11 mm on DEEDS). The substantiated performance on the nodule centers also demonstrates its robustness across challenging downstream tasks, such as nodule tracking, which is an essential prior step for early-stage lung cancer diagnosis.

Yunzheng Zhu, Aichi Chien, Kimaya kulkarni +5

Medical & Imaging Informatics, Department of Radiological Sciences, David Geffen School of Medicine at UCLA, USA · Magnetic Resonance Research Labs, Department of Radiological Sciences, David Geffen School of Medicine at UCLA, USA · Department of Radiation Oncology, David Geffen School of Medicine at UCLA, Los Angeles, USA

Medical Image RegistrationDeformable Image RegistrationMedical Image Representation Learning
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Feb 19, 2026

Depth Augmented and FE Free 3D/2D Liver Registration for Laparoscopic Liver AR

Augmented reality (AR) guidance in laparoscopic liver surgery requires accurate registration of preoperative 3D models to intraoperative 2D video, but remains challenging due to partial visibility, specularities, and tissue deformation. Existing methods often rely on contour-based rigid initialization and finite-element (FE) models for deformable registration, increasing modeling and engineering complexity. We present a depth-augmented, FE-free 3D--2D registration pipeline that combines robust rigid initialization with patient-specific non-rigid refinement. For rigid alignment, we adapt the RefineNet module of FoundationPose to laparoscopic liver scenes by using multi-class contour maps and monocular depth for relative pose refinement. For deformable alignment, we construct a patient-specific statistical deformation model from non-rigid ICP (NICP) correspondences and optimize pose and shape parameters using a coarse-to-fine L-BFGS-B strategy. On a public clinical laparoscopic liver dataset, the proposed method achieves a mean target registration error (TRE) of 14.73,mm under a controlled manual-contour setting designed to isolate registration performance. Ablation studies show that monocular depth improves rigid initialization over contour-only inputs, while tumor-mapping analysis indicates that good surface alignment does not necessarily translate into lower target localization error. On an external dataset without ground truth, the method produces visually plausible overlays for qualitative assessment. These results suggest that depth-augmented pose refinement and FE-free statistical deformation modeling provide a promising alternative to FE-based pipelines for controlled 3D--2D liver registration in surgical AR.

Hanyuan Zhang, Lucas He, Runlong He +6

UCL Hawkes Institute, University College London, London WC1E 6BT, UK · Unit for Lifelong Health and Ageing at UCL, University College London, London WC1E 7HB, UK · Medtronic plc., London, UK +1

2D-3D Image RegistrationAR in SurgeryMedical Image RegistrationDeformable Image RegistrationLaparoscopic Surgery
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Feb 19, 2026

Polaffini: A feature-based approach for robust affine and polyaffine image registration

In this work we present Polaffini, a robust and versatile framework for anatomically grounded registration. Medical image registration is dominated by intensity-based registration methods that rely on surrogate measures of alignment quality. In contrast, feature-based approaches that operate by identifying explicit anatomical correspondences, while more desirable in theory, have largely fallen out of favor due to the challenges of reliably extracting features. However, such challenges are now significantly overcome thanks to recent advances in deep learning, which provide pre-trained segmentation models capable of instantly delivering reliable, fine-grained anatomical delineations. We aim to demonstrate that these advances can be leveraged to create new anatomically-grounded image registration algorithms. To this end, we propose Polaffini, which obtains, from these segmented regions, anatomically grounded feature points with 1-to-1 correspondence in a particularly simple way: extracting their centroids. These enable efficient global and local affine matching via closed-form solutions. Those are used to produce an overall transformation ranging from affine to polyaffine with tunable smoothness. Polyaffine transformations can have many more degrees of freedom than affine ones allowing for finer alignment, and their embedding in the log-Euclidean framework ensures diffeomorphic properties. Polaffini has applications both for standalone registration and as pre-alignment for subsequent non-linear registration, and we evaluate it against popular intensity-based registration techniques. Results demonstrate that Polaffini outperforms competing methods in terms of structural alignment and provides improved initialisation for downstream non-linear registration. Polaffini is fast, robust, and accurate, making it particularly well-suited for integration into medical image processing pipelines.

Antoine Legouhy, Cosimo Campo, Ross Callaghan +2

Hawkes Institute & Department of Computer Science, University College London, London, UK · Institut Pasteur, Universit´e Paris Cit´e, Unit´e de Neuroanatomie Appliqu´ee et Th´eorique, France · AINOSTICS ltd., Manchester, UK

Medical Image RegistrationDeformable Image Registration
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Nov 18, 2025

NeuralBoneReg: An Instance-Specific Label-Free Point Cloud-Based Method for Multi-Modal Bone Surface Registration

In computer- and robot-assisted orthopedic surgery (CAOS), patient-specific surgical plans derived from preoperative imaging define target locations and implant trajectories. During surgery, these plans must be accurately transferred, relying on precise cross-registration between preoperative and intraoperative data. However, substantial modality heterogeneity across imaging modalities makes this registration challenging and error-prone. Robust, automatic, and modality-agnostic bone surface registration is therefore clinically important. We propose NeuralBoneReg, a self-supervised, surface-based framework that registers bone surfaces using 3D point clouds as a modality-agnostic representation. NeuralBoneReg includes two modules: an implicit neural unsigned distance field (UDF) that learns the preoperative bone model, and an MLP-based registration module that performs global initialization and local refinement by generating transformation hypotheses to align the intraoperative point cloud with the neural UDF. Unlike SOTA supervised methods, NeuralBoneReg operates in a self-supervised manner, without requiring inter-subject training data. We evaluated NeuralBoneReg against baseline methods on two publicly available multi-modal datasets: a CT-ultrasound dataset of the fibula and tibia (UltraBones100k) and a CT-RGB-D dataset of spinal vertebrae (SpineDepth). The evaluation also includes a newly introduced CT-ultrasound dataset of cadaveric subjects containing femur and pelvis (UltraBones-Hip), which will be made publicly available. NeuralBoneReg matches or surpasses existing methods across all datasets, achieving mean RRE/RTE of 1.83°/2.02 mm on UltraBones100k, 1.90°/1.56 mm on UltraBones-Hip, and 3.78°/2.80 mm on SpineDepth. These results demonstrate strong generalizability across anatomies and modalities, providing robust and accurate cross-modal alignment for CAOS.

Luohong Wu, Matthias Seibold, Nicola A. Cavalcanti +5

Research in Orthopedic Computer Science, Balgrist University Hospital, University of Zurich, Lengghalde 5, Zurich, 8008, Zurich, Switzerland · AI Center, ETH Zurich, Ramistrasse 101, Zurich, 8092, Zurich, Switzerland

Medical Image RegistrationPoint Cloud RegistrationCross-Modal Image RegistrationSurgical Robotics
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Nov 11, 2025

The Impact of Longitudinal Mammogram Alignment on Breast Cancer Risk Assessment

Regular mammography screening is crucial for early breast cancer detection. By leveraging deep learning-based risk models, screening intervals can be personalized, especially for high-risk individuals. While recent methods increasingly incorporate longitudinal information from prior mammograms, accurate spatial alignment across time points remains a key challenge. Misalignment can obscure meaningful tissue changes and degrade model performance. In this study, we provide insights into various alignment strategies, image-based registration, feature-level (representation space) alignment with and without regularization, and implicit alignment methods, for their effectiveness in longitudinal deep learning-based risk modeling. Using two large-scale mammography datasets, we assess each method across key metrics, including predictive accuracy, precision, recall, and deformation field quality. Our results show that image-based registration consistently outperforms the more recently favored feature-based and implicit approaches across all metrics, enabling more accurate, temporally consistent predictions and generating smooth, anatomically plausible deformation fields. Although regularizing the deformation field improves deformation quality, it reduces the risk prediction performance of feature-level alignment. Applying image-based deformation fields within the feature space yields the best risk prediction performance. These findings underscore the importance of image-based deformation fields for spatial alignment in longitudinal risk modeling, offering improved prediction accuracy and robustness. This approach has strong potential to enhance personalized screening and enable earlier interventions for high-risk individuals. The code is available at https://github.com/sot176/Mammogram_Alignment_Study_Risk_Prediction.git, allowing full reproducibility of the results.

Solveig Thrun, Stine Hansen, Zijun Sun +8

Department of Physics and Technology, UiT The Arctic University of Norway, Tromsø, 9037, Norway · SPKI The Norwegian Centre for Clinical Artificial Intelligence, University Hospital of North Norway, Tromsø, 9019, Norway · Department of Computer Science and Engineering, University of Bologna, 40126, Bologna, Italy +4

Longitudinal Medical Image AnalysisMammographyBreast CancerMedical Image RegistrationDeformable Image RegistrationLatent Space Alignment
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