Medical image registration using unsupervised deep neural network: A scoping literature review
Shiraz University of Medical Sciences（设拉子医科大学）；University of Pittsburgh School of Medicine（匹兹堡大学医学院）；UPMC Hillman Cancer Center（UPMC希尔曼癌症中心）；Shiraz University of Technology（设拉子理工大学）；Mashhad University of Medical Science（马什哈德医科大学）
In medicine, image registration is vital in image-guided interventions and other clinical applications. However, it is a difficult subject to be addressed which by the advent of machine learning, there have been considerable progress in algorithmic performance has recently been achieved for medical image registration in this area. The implementation of deep neural networks provides an opportunity for some medical applications such as conducting image registration in less time with high accuracy, playing a key role in countering tumors during the operation. The current study presents a comprehensive scoping review on the state-of-the-art literature of medical image registration studies based on unsupervised deep neural networks is conducted, encompassing all the related studies published in this field to this date. Here, we have tried to summarize the latest developments and applications of unsupervised deep learning-based registration methods in the medical field. Fundamental and main concepts, techniques, statistical analysis from different viewpoints, novelties, and future directions are elaborately discussed and conveyed in the current comprehensive scoping review. Besides, this review hopes to help those active readers, who are riveted by this field, achieve deep insight into this exciting field.
Image registration is a fundamental building block for various applications in medical image analysis. To better explore the correlation between the fixed and moving images and improve registration performance, we propose a novel deep learning network, Co-Attention guided Registration Network (CAR-Net). CAR-Net employs a co-attention block to learn a new representation of the inputs, which drives the registration of the fixed and moving images. Experiments on UK Biobank cardiac cine-magnetic resonance image data demonstrate that CAR-Net obtains higher registration accuracy and smoother deforma…
University of Cambridge（剑桥大学）；Cancer Research UK Cambridge Centre（英国癌症研究中心剑桥中心）；Medical University Vienna（维也纳医科大学）；Cambridge University Hospitals National Health Service (NHS) Foundation Trust（剑桥大学医院国民保健服务基金会信托）；Eindhoven University of Technology（埃因霍温理工大学）；Leiden University（莱顿大学）；University College London（伦敦大学学院）；Cancer Research UK Cambridge Institute（英国癌症研究中心剑桥研究所）
This study investigates the use of the unsupervised deep learning framework VoxelMorph for deformable registration of longitudinal abdominopelvic CT images acquired in patients with bone metastases from breast cancer. The CT images were refined prior to registration by automatically removing the CT table and all other extra-corporeal components. To improve the learning capabilities of VoxelMorph when only a limited amount of training data is available, a novel incremental training strategy is proposed based on simulated deformations of consecutive CT images. In a 4-fold cross-validation scheme…
Cluster of Excellence – ML for Science（卓越集群——科学机器学习）；University of Tübingen（蒂宾根大学）；Faculty of Health Sciences and Medicine, University of Lucerne（卢塞恩大学健康科学与医学院）；University of Lübeck（吕贝克大学）
Tsinghua University（清华大学）；Shenzhen International Graduate School（深圳国际研究生院）；Harvard Medical School（哈佛医学院）；Brigham and Women’s Hospital（布莱根和妇女医院）
Multimodal image registration (MIR) is a fundamental procedure in many image-guided therapies. Recently, unsupervised learning-based methods have demonstrated promising performance over accuracy and efficiency in deformable image registration. However, the estimated deformation fields of the existing methods fully rely on the to-be-registered image pair. It is difficult for the networks to be aware of the mismatched boundaries, resulting in unsatisfactory organ boundary alignment. In this paper, we propose a novel multimodal registration framework, which leverages the deformation fields estima…
The Hong Kong University of Science and Technology（香港科技大学）
Registration of pre-operative and post-recurrence brain images is often needed to evaluate the effectiveness of brain gliomas treatment. While recent deep learning-based deformable registration methods have achieved remarkable success with healthy brain images, most of them would be unable to accurately align images with pathologies due to the absent correspondences in the reference image. In this paper, we propose a deep learning-based deformable registration method that jointly estimates regions with absent correspondence and bidirectional deformation fields. A forward-backward consistency c…
Paul C. Lauterbur Research Center for Biomedical Imaging, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences（中国科学院深圳先进技术研究院保罗·C·劳特伯生物医学成像研究中心）；Pengcheng Laboratory（鹏城实验室）；Pazhou Lab（琶洲实验室）；Guizhou Provincial People’s Hospital（贵州省人民医院）
Multi-contrast magnetic resonance (MR) image registration is useful in the clinic to achieve fast and accurate imaging-based disease diagnosis and treatment planning. Nevertheless, the efficiency and performance of the existing registration algorithms can still be improved. In this paper, we propose a novel unsupervised learning-based framework to achieve accurate and efficient multi-contrast MR image registrations. Specifically, an end-to-end coarse-to-fine network architecture consisting of affine and deformable transformations is designed to improve the robustness and achieve end-to-end reg…
Johns Hopkins Medical Institutes（约翰斯·霍普金斯医学研究所）；Johns Hopkins University（约翰斯·霍普金斯大学）；NVIDIA Corporation（英伟达公司）
In the past, optimization-based registration models have used spatially-varying regularization to account for deformation variations in different image regions. However, deep learning-based registration models have mostly relied on spatially-invariant regularization. Here, we introduce an end-to-end framework that uses neural networks to learn a spatially-varying deformation regularizer directly from data. The hyperparameter of the proposed regularizer is conditioned into the network, enabling easy tuning of the regularization strength. The proposed method is built upon a Transformer-based mod…
Unsupervised Deformable Image Registration with Local-Global Attention and Image Decomposition
Institute of Medical Technology, Peking University Health Science Center（北京大学医学部医学技术研究所）；National Institute of Health Data Science, Peking University（北京大学国家健康数据科学研究院）；Department of Radiology, Peking University Third Hospital（北京大学第三医院放射科）；Department of Pediatrics, Peking University First Hospital（北京大学第一医院儿科）；Pediatric Epilepsy Center, Peking University First Hospital（北京大学第一医院儿童癫痫中心）；School of Biological Science and Medical Engineering, Southeast University（东南大学生物科学与医学工程学院）；Institute for Artificial Intelligence, Peking University（北京大学人工智能研究院）
Johns Hopkins University（约翰斯·霍普金斯大学）；Johns Hopkins Medical Institutes（约翰斯·霍普金斯医学研究所）
In the last decade, convolutional neural networks (ConvNets) have dominated and achieved state-of-the-art performances in a variety of medical imaging applications. However, the performances of ConvNets are still limited by lacking the understanding of long-range spatial relations in an image. The recently proposed Vision Transformer (ViT) for image classification uses a purely self-attention-based model that learns long-range spatial relations to focus on the relevant parts of an image. Nevertheless, ViT emphasizes the low-resolution features because of the consecutive downsamplings, result i…
Multi-modality image registration is one of the most underlined processes in medical image analysis. Recently, convolutional neural networks (CNNs) have shown significant potential in deformable registration. However, the lack of voxel-wise ground truth challenges the training of CNNs for an accurate registration. In this work, we propose a cross-modality similarity metric, based on the KL-divergence of image variables, and implement an efficient estimation method using a CNN. This estimation network, referred to as KLDivNet, can be trained unsupervisedly. We then embed the KLDivNet into a reg…
Korea Advanced Institute of Science and Technology（韩国科学技术院）；University of Ulsan College of Medicine（蔚山大学医学院）；Asan Medical Center（峨山医学中心）
Medical image registration is one of the key processing steps for biomedical image analysis such as cancer diagnosis. Recently, deep learning based supervised and unsupervised image registration methods have been extensively studied due to its excellent performance in spite of ultra-fast computational time compared to the classical approaches. In this paper, we present a novel unsupervised medical image registration method that trains deep neural network for deformable registration of 3D volumes using a cycle-consistency. Thanks to the cycle consistency, the proposed deep neural networks can t…
Korea Advanced Institute of Science and Technology (KAIST)（韩国科学技术院）
Deformable image registration is one of the fundamental tasks in medical imaging. Classical registration algorithms usually require a high computational cost for iterative optimizations. Although deep-learning-based methods have been developed for fast image registration, it is still challenging to obtain realistic continuous deformations from a moving image to a fixed image with less topological folding problem. To address this, here we present a novel diffusion-model-based image registration method, called DiffuseMorph. DiffuseMorph not only generates synthetic deformed images through revers…
Institute of Medical Informatics, Universität zu Lübeck（吕贝克大学医学信息学研究所）
Multimodal image registration is a very challenging problem for deep learning approaches. Most current work focuses on either supervised learning that requires labelled training scans and may yield models that bias towards annotated structures or unsupervised approaches that are based on hand-crafted similarity metrics and may therefore not outperform their classical non-trained counterparts. We believe that unsupervised domain adaptation can be beneficial in overcoming the current limitations for multimodal registration, where good metrics are hard to define. Domain adaptation has so far been…
Southeast University（东南大学）；Tencent Healthcare Co.（腾讯医疗健康有限公司）；The Chinese University of Hong Kong（香港中文大学）
Recently, deep-learning-based approaches have been widely studied for deformable image registration task. However, most efforts directly map the composite image representation to spatial transformation through the convolutional neural network, ignoring its limited ability to capture spatial correspondence. On the other hand, Transformer can better characterize the spatial relationship with attention mechanism, its long-range dependency may be harmful to the registration task, where voxels with too large distances are unlikely to be corresponding pairs. In this study, we propose a novel Deforme…
Image Sciences Institute, University Medical Center Utrecht and Utrecht University（乌得勒支大学医学中心与乌得勒支大学影像科学研究所）；Division of Image Processing of the Leiden University Medical Center（莱顿大学医学中心图像处理部）
Image registration, the process of aligning two or more images, is the core technique of many (semi-)automatic medical image analysis tasks. Recent studies have shown that deep learning methods, notably convolutional neural networks (ConvNets), can be used for image registration. Thus far training of ConvNets for registration was supervised using predefined example registrations. However, obtaining example registrations is not trivial. To circumvent the need for predefined examples, and thereby to increase convenience of training ConvNets for image registration, we propose the Deep Learning Im…
UDCR: Unsupervised Aortic DSA/CTA Rigid Registration Using Deep Reinforcement Learning and Overlap Degree Calculation
School of Artificial Intelligence, Beijing University of Posts and Telecommunications（北京邮电大学人工智能学院）；Shanghai Changhai Hospital, Naval Medical University（海军军医大学上海长海医院）；Dalian University of Technology（大连理工大学）；School of Computer Science and Information Security, Guilin University of Electronic Technology（桂林电子科技大学计算机科学与信息安全学院）；The Fourth Hospital of Hebei Medical University and Hebei Tumor Hospital（河北医科大学第四医院暨河北省肿瘤医院）；Erasmus MC, University Medical Center Rotterdam（鹿特丹伊拉斯姆斯大学医学中心）
Australian Institute for Machine Learning（澳大利亚机器学习研究所）；University of Adelaide（阿德莱德大学）；South Australian Health and Medical Research Institute（南澳大利亚健康与医学研究所）
Many applications in image-guided surgery and therapy require fast and reliable non-linear, multi-modal image registration. Recently proposed unsupervised deep learning-based registration methods have demonstrated superior performance compared to iterative methods in just a fraction of the time. Most of the learning-based methods have focused on mono-modal image registration. The extension to multi-modal registration depends on the use of an appropriate similarity function, such as the mutual information (MI). We propose guiding the training of a deep learning-based registration method with MI…
Image Sciences Institute, University Medical Center Utrecht（乌得勒支大学医学中心图像科学研究所）；Division of Image Processing, Leiden University Medical Center（莱顿大学医学中心图像处理部）
In this work we propose a deep learning network for deformable image registration (DIRNet). The DIRNet consists of a convolutional neural network (ConvNet) regressor, a spatial transformer, and a resampler. The ConvNet analyzes a pair of fixed and moving images and outputs parameters for the spatial transformer, which generates the displacement vector field that enables the resampler to warp the moving image to the fixed image. The DIRNet is trained end-to-end by unsupervised optimization of a similarity metric between input image pairs. A trained DIRNet can be applied to perform registration …
Brain image registration transforms a pair of images into one system with the matched imaging contents, which is of essential importance for brain image analysis. This paper presents a novel framework for unsupervised 3D brain image registration by capturing the feature-level transformation relationships between the unaligned image and reference image. To achieve this, we develop a feature-level probabilistic model to provide the direct regularization to the hidden layers of two deep convolutional neural networks, which are constructed from two input images. This model design is developed into…
Unsupervised training of keypoint-agnostic descriptors for flexible retinal image registration
Grupo VARPA, Instituto de Investigacion Biomédica de A Coruña (INIBIC), Universidade da Coruña（VARPA组，阿维拉生物医学研究所（INIBIC），科鲁纳大学）；Departamento de Ciencias de la Computación y Tecnologías de la Información, Universidade da Coruña（计算机科学与信息技术部门，科鲁纳大学）
Ryerson University（瑞尔森大学）；University of Toronto（多伦多大学）；Institute for Biomedical Engineering, Science and Technology (iBEST)（生物医学工程、科学与技术研究所（iBEST））
We propose FlowReg, a deep learning-based framework for unsupervised image registration for neuroimaging applications. The system is composed of two architectures that are trained sequentially: FlowReg-A which affinely corrects for gross differences between moving and fixed volumes in 3D followed by FlowReg-O which performs pixel-wise deformations on a slice-by-slice basis for fine tuning in 2D. The affine network regresses the 3D affine matrix based on a correlation loss function that enforces global similarity. The deformable network operates on 2D image slices based on the optical flow netw…
Technical University of Munich (TUM)（慕尼黑工业大学）；Klinikum Rechts der Isar（伊萨尔河右岸医院）；Imperial College London（伦敦帝国理工学院）
Diffeomorphic deformable multi-modal image registration is a challenging task which aims to bring images acquired by different modalities to the same coordinate space and at the same time to preserve the topology and the invertibility of the transformation. Recent research has focused on leveraging deep learning approaches for this task as these have been shown to achieve competitive registration accuracy while being computationally more efficient than traditional iterative registration methods. In this work, we propose a simple yet effective unsupervised deep learning-based {\em multi-modal} …
Korea Advanced Institute of Science and Technology（韩国科学技术院）；The Catholic University of Korea（韩国加图立大学）；University of Ulsan College of Medicine（蔚山大学医学院）；Asan Medical Center（峨山医疗中心）；Korea Automotive Technology Institute（韩国汽车技术研究院）
Image registration is a fundamental task in medical image analysis. Recently, deep learning based image registration methods have been extensively investigated due to their excellent performance despite the ultra-fast computational time. However, the existing deep learning methods still have limitation in the preservation of original topology during the deformation with registration vector fields. To address this issues, here we present a cycle-consistent deformable image registration. The cycle consistency enhances image registration performance by providing an implicit regularization to pres…
Technion – Israel Institute of Technology（以色列理工学院）
Unsupervised deep-learning (DL) models were recently proposed for deformable image registration tasks. In such models, a neural-network is trained to predict the best deformation field by minimizing some dissimilarity function between the moving and the target images. After training on a dataset without reference deformation fields available, such a model can be used to rapidly predict the deformation field between newly seen moving and target images. Currently, the training process effectively provides a point-estimate of the network weights rather than characterizing their entire posterior d…
Image registration is a crucial task in signal processing, but it often encounters issues with stability and efficiency. Non-learning registration approaches rely on optimizing similarity metrics between fixed and moving images, which can be expensive in terms of time and space complexity. This problem can be exacerbated when the images are large or there are significant deformations between them. Recently, deep learning, specifically convolutional neural network (CNN)-based methods, have been explored as an effective solution to the weaknesses of non-learning approaches. To further advance le…
Medical image registration is a fundamental and critical task in medical image analysis. With the rapid development of deep learning, convolutional neural networks (CNN) have dominated the medical image registration field. Due to the disadvantage of the local receptive field of CNN, some recent registration methods have focused on using transformers for non-local registration. However, the standard Transformer has a vast number of parameters and high computational complexity, which causes Transformer can only be applied at the bottom of the registration models. As a result, only coarse informa…
This study proposes an end-to-end unsupervised diffeomorphic deformable registration framework based on moving mesh parameterization. Using this parameterization, a deformation field can be modeled with its transformation Jacobian determinant and curl of end velocity field. The new model of the deformation field has three important advantages; firstly, it relaxes the need for an explicit regularization term and the corresponding weight in the cost function. The smoothness is implicitly embedded in the solution which results in a physically plausible deformation field. Secondly, it guarantees d…
University of Edinburgh（爱丁堡大学）；Imperial College London（帝国理工学院）；University of Essex（埃塞克斯大学）
Magnetic Resonance Imaging (MRI) typically recruits multiple sequences (defined here as "modalities"). As each modality is designed to offer different anatomical and functional clinical information, there are evident disparities in the imaging content across modalities. Inter- and intra-modality affine and non-rigid image registration is an essential medical image analysis process in clinical imaging, as for example before imaging biomarkers need to be derived and clinically evaluated across different MRI modalities, time phases and slices. Although commonly needed in real clinical scenarios, …
Deformable image registration is a fundamental task in medical image analysis, aiming to establish a dense and non-linear correspondence between a pair of images. Previous deep-learning studies usually employ supervised neural networks to directly learn the spatial transformation from one image to another, requiring task-specific ground-truth registration for model training. Due to the difficulty in collecting precise ground-truth registration, implementation of these supervised methods is practically challenging. Although several unsupervised networks have been recently developed, these metho…
New York University（纽约大学）；Hyperfine Research（Hyperfine研究公司）；Yale University（耶鲁大学）
Establishing voxelwise semantic correspondence across distinct imaging modalities is a foundational yet formidable computer vision task. Current multi-modality registration techniques maximize hand-crafted inter-domain similarity functions, are limited in modeling nonlinear intensity-relationships and deformations, and may require significant re-engineering or underperform on new tasks, datasets, and domain pairs. This work presents ContraReg, an unsupervised contrastive representation learning approach to multi-modality deformable registration. By projecting learned multi-scale local patch fe…
Johns Hopkins Medical Institutes（约翰霍普金斯医学研究所）；Johns Hopkins University（约翰霍普金斯大学）
Objectives: Computerized phantoms play an essential role in various applications of medical imaging research. Although the existing computerized phantoms can model anatomical variations through organ and phantom scaling, this does not provide a way to fully reproduce anatomical variations seen in humans. However, having a population of phantoms that models the variations in patient anatomy and, in nuclear medicine, uptake realization is essential for comprehensive validation and training. In this work, we present a novel image registration method for creating highly anatomically detailed anthr…
Unsupervised Deformable Image Registration with Structural Nonparametric Smoothing
Cornell University（康奈尔大学）；Hunan University（湖南大学）；University of Pennsylvania（宾夕法尼亚大学）；Johns Hopkins University（约翰霍普金斯大学）；Shanghai Jiao Tong University（上海交通大学）；University of Birmingham（伯明翰大学）；University of Manchester（曼彻斯特大学）
Chengdu University of Information Technology（成都信息工程大学）；Keya Medical（科亚医疗）；University at Buffalo, SUNY（纽约州立大学布法罗分校）
Large deformations of organs, caused by diverse shapes and nonlinear shape changes, pose a significant challenge for medical image registration. Traditional registration methods need to iteratively optimize an objective function via a specific deformation model along with meticulous parameter tuning, but which have limited capabilities in registering images with large deformations. While deep learning-based methods can learn the complex mapping from input images to their respective deformation field, it is regression-based and is prone to be stuck at local minima, particularly when large defor…
Large Scale Unsupervised Brain MRI Image Registration Solution for Learn2Reg 2024
College of Electrical and Information Engineering, Hunan University（湖南大学电气与信息工程学院）；National Engineering Research Center of Robot Visual Perception and Control Technology, Hunan University（湖南大学机器人视觉感知与控制技术国家工程研究中心）
Queensland University of Technology（昆士兰科技大学）；CSIRO（联邦科学与工业研究组织）
The recent application of deep learning technologies in medical image registration has exponentially decreased the registration time and gradually increased registration accuracy when compared to their traditional counterparts. Most of the learning-based registration approaches considers this task as a one directional problem. As a result, only correspondence from the moving image to the target image is considered. However, in some medical procedures bidirectional registration is required to be performed. Unlike other learning-based registration, we propose a registration framework with invers…
Fast Diffeomorphic Image Registration using Patch based Fully Convolutional Networks
School of Computer and Electrical Engineering, Hunan University of Arts and Science（湖南文理学院计算机与电气工程学院）；Furong College, Hunan University of Arts and Science（湖南文理学院芙蓉学院）；The University of Hong Kong（香港大学）
University of Oxford（牛津大学）；Institute of Biomedical Engineering（生物医学工程研究所）
Recent successes in deep learning based deformable image registration (DIR) methods have demonstrated that complex deformation can be learnt directly from data while reducing computation time when compared to traditional methods. However, the reliance on fully linear convolutional layers imposes a uniform sampling of pixel/voxel locations which ultimately limits their performance. To address this problem, we propose a novel approach of learning a continuous warp of the source image. Here, the required deformation vector fields are obtained from a concatenated linear and non-linear convolution …
Unsupervised learning of spatially varying regularization for diffeomorphic image registration
Department of Radiology and Radiological Science, Johns Hopkins School of Medicine, MD, USA（放射科与放射科学系，约翰霍普金斯医学院，马里兰州，美国）；Image Analysis and Communications Laboratory, Department of Electrical and Computer Engineering, Johns Hopkins University, MD, USA（图像分析与通信实验室，电气与计算机工程系，约翰霍普金斯大学，马里兰州，美国）；Department of Electrical and Computer Engineering, Vanderbilt University, TN, USA（电气与计算机工程系，范德比尔特大学，田纳西州，美国）；NVIDIA Corporation, Santa Clara, CA, USA（英伟达公司，圣克拉拉，加利福尼亚州，美国）
Bayesian Unsupervised Disentanglement of Anatomy and Geometry for Deep Groupwise Image Registration
School of Data Science, Fudan University（复旦大学数据科学学院）；Department of Electrical and Electronic Engineering and I-X, Imperial College London（帝国理工学院电子与电气工程系）；Department of Electrical and Computer Engineering, University of Washington（华盛顿大学电气与计算机工程系）；Paul G. Allen School of Computer Science and Engineering, University of Washington（华盛顿大学保罗·G·艾伦计算机科学与工程学院）；Department of Radiology and Imaging Sciences, University of Utah（犹他大学放射科与成像科学系）；Department of Radiology, University of Washington（华盛顿大学放射科）；Institute of Science and Technology for Brain-Inspired Intellengence, Fudan University（复旦大学脑启发智能科学技术研究院）
Unsupervised MR-US Multimodal Image Registration with Multilevel Correlation Pyramidal Optimization
School of Artificial Intelligence and Robotics, Hunan University, Changsha, Hunan, China（人工智能与机器人学院，湖南大学，长沙，湖南，中国）；National Engineering Research Center of Robot Visual Perception and Control Technology, Hunan University, Changsha, Hunan, China（机器人视觉感知与控制技术国家工程研究中心，湖南大学，长沙，湖南，中国）；National University of Singapore（新加坡国立大学）；Cornell University（康奈尔大学）
University of North Carolina, Chapel Hill（北卡罗来纳大学教堂山分校）
Deep convolutional neural networks (CNNs) are state-of-the-art for semantic image segmentation, but typically require many labeled training samples. Obtaining 3D segmentations of medical images for supervised training is difficult and labor intensive. Motivated by classical approaches for joint segmentation and registration we therefore propose a deep learning framework that jointly learns networks for image registration and image segmentation. In contrast to previous work on deep unsupervised image registration, which showed the benefit of weak supervision via image segmentations, our approac…
