TLRN: Temporal Latent Residual Networks For Large Deformation Image Registration
Department of Electrical and Computer Engineering, University of Virginia, USA（电气与计算机工程系，弗吉尼亚大学）；Department of Computer Science, University of Virginia, USA（计算机科学系，弗吉尼亚大学）
This paper presents a novel approach, termed {\em Temporal Latent Residual Network (TLRN)}, to predict a sequence of deformation fields in time-series image registration. The challenge of registering time-series images often lies in the occurrence of large motions, especially when images differ significantly from a reference (e.g., the start of a cardiac cycle compared to the peak stretching phase). To achieve accurate and robust registration results, we leverage the nature of motion continuity and exploit the temporal smoothness in consecutive image frames. Our proposed TLRN highlights a temporal residual network with residual blocks carefully designed in latent deformation spaces, which are parameterized by time-sequential initial velocity fields. We treat a sequence of residual blocks over time as a dynamic training system, where each block is designed to learn the residual function between desired deformation features and current input accumulated from previous time frames. We validate the effectivenss of TLRN on both synthetic data and real-world cine cardiac magnetic resonance (CMR) image videos. Our experimental results shows that TLRN is able to achieve substantially improved registration accuracy compared to the state-of-the-art. Our code is publicly available at https://github.com/nellie689/TLRN.
Tsinghua University（清华大学）；Brigham and Women’s Hospital（布莱根妇女医院）；Harvard Medical School（哈佛医学院）
Deformable image registration (DIR) is essential for many image-guided therapies. Recently, deep learning approaches have gained substantial popularity and success in DIR. Most deep learning approaches use the so-called mono-stream "high-to-low, low-to-high" network structure, and can achieve satisfactory overall registration results. However, accurate alignments for some severely deformed local regions, which are crucial for pinpointing surgical targets, are often overlooked. Consequently, these approaches are not sensitive to some hard-to-align regions, e.g., intra-patient registration of de…
University of Georgia（佐治亚大学）；Shanghai Jiao Tong University（上海交通大学）
Deep learning based methods provide efficient solutions to medical image registration, including the challenging problem of diffeomorphic image registration. However, most methods register normal image pairs, facing difficulty handling those with missing correspondences, e.g., in the presence of pathology like tumors. We desire an efficient solution to jointly account for spatial deformations and appearance changes in the pathological regions where the correspondences are missing, i.e., finding a solution to metamorphic image registration. Some approaches are proposed to tackle this problem, b…
Reliable feature point matching is a vital yet challenging process in feature-based image registration. In this paper,a robust feature point matching algorithm called Recovery and Filtering Vertex Trichotomy Matching (RFVTM) is proposed to remove outliers and retain sufficient inliers for remote sensing images. A novel affine invariant descriptor called vertex trichotomy descriptor is proposed on the basis of that geometrical relations between any of vertices and lines are preserved after affine transformations, which is constructed by mapping each vertex into trichotomy sets. The outlier remo…
Learning a Model-Driven Variational Network for Deformable Image Registration
University of Birmingham（伯明翰大学）；Alan Turing Institute（阿兰·图灵研究所）；Shenzhen University（深圳大学）；Imperial College London（伦敦帝国学院）；MRC London Institute of Medical Sciences（英国医学研究理事会伦敦医学科学研究所）
Friedrich-Alexander Universität Erlangen-Nürnberg（埃尔朗根-纽伦堡大学）；Bibliotheca Hertziana - Max-Planck-Institut für Kunstgeschichte（赫兹图书馆 - 马克斯·普朗克艺术史研究所）
In this work, we conducted a survey on different registration algorithms and investigated their suitability for hyperspectral historical image registration applications. After the evaluation of different algorithms, we choose an intensity based registration algorithm with a curved transformation model. For the transformation model, we select cubic B-splines since they should be capable to cope with all non-rigid deformations in our hyperspectral images. From a number of similarity measures, we found that residual complexity and localized mutual information are well suited for the task at hand.…
Kuaishou Technology（快手科技）；Cornell University（康奈尔大学）；NVIDIA（英伟达公司）；Tencent（腾讯）；University of California, Irvine（加利福尼亚大学欧文分校）
Registration is a fundamental task in medical robotics and is often a crucial step for many downstream tasks such as motion analysis, intra-operative tracking and image segmentation. Popular registration methods such as ANTs and NiftyReg optimize objective functions for each pair of images from scratch, which are time-consuming for 3D and sequential images with complex deformations. Recently, deep learning-based registration approaches such as VoxelMorph have been emerging and achieve competitive performance. In this work, we construct a test-time training for deep deformable image registratio…
We propose the residual expansion (RE) algorithm: a global (or near-global) optimization method for nonconvex least squares problems. Unlike most existing nonconvex optimization techniques, the RE algorithm is not based on either stochastic or multi-point searches; therefore, it can achieve fast global optimization. Moreover, the RE algorithm is easy to implement and successful in high-dimensional optimization. The RE algorithm exhibits excellent empirical performance in terms of k-means clustering, point-set registration, optimized product quantization, and blind image deblurring.
APCReg: Anatomical-Prior-Guided Coarse-to-Fine CBCT--IOS Registration via Multi-View Projection and Reliability-Controlled Residual Correction
Hangzhou Dianzi University（杭州电子科技大学）；Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine（上海交通大学医学院附属第九人民医院）；Sir Run Run Shaw Hospital, Zhejiang University School of Medicine（浙江大学医学院附属邵逸夫医院）；Shanghai Stomatological Hospital & School of Stomatology, Fudan University（复旦大学附属口腔医院·口腔医学院）
Télécom Paris, Institut Polytechnique de Paris（巴黎理工学院巴黎电信学院）；CNRS（法国国家科学研究中心）
In medical imaging, most of the image registration methods implicitly assume a one-to-one correspondence between the source and target images (i.e., diffeomorphism). However, this is not necessarily the case when dealing with pathological medical images (e.g., presence of a tumor, lesion, etc.). To cope with this issue, the Metamorphosis model has been proposed. It modifies both the shape and the appearance of an image to deal with the geometrical and topological differences. However, the high computational time and load have hampered its applications so far. Here, we propose a deep residual l…
Southern Medical University（南方医科大学）；Shenzhen University（深圳大学）
Deformation field estimation is an important and challenging issue in many medical image registration applications. In recent years, deep learning technique has become a promising approach for simplifying registration problems, and has been gradually applied to medical image registration. However, most existing deep learning registrations do not consider the problem that when the receptive field cannot cover the corresponding features in the moving image and the fixed image, it cannot output accurate displacement values. In fact, due to the limitation of the receptive field, the 3 x 3 kernel h…
Duke University（杜克大学）；Duke University School of Medicine（杜克大学医学院）
Purpose: Often, the inverse deformation vector field (DVF) is needed together with the corresponding forward DVF in 4D reconstruction and dose calculation, adaptive radiation therapy, and simultaneous deformable registration. This study aims at improving both accuracy and efficiency of iterative algorithms for DVF inversion, and advancing our understanding of divergence and latency conditions. Method: We introduce a framework of fixed-point iteration algorithms with active feedback control for DVF inversion. Based on rigorous convergence analysis, we design control mechanisms for modulating th…
The Kennedy Institute of Rheumatology, University of Oxford（牛津大学肯尼迪风湿病研究所）；Big Data Institute, University of Oxford（牛津大学大数据研究所）；Department of Computer Science, University of Oxford（牛津大学计算机科学系）；Department of Surgery and Cancer, Imperial College London（帝国理工学院外科与癌症系）；Nuffield Department of Population Health, University of Oxford（牛津大学纳菲尔德人口健康系）
iPEAR: Iterative Pyramid Estimation with Attention and Residuals for Deformable Medical Image Registration
College of Software, Jilin University（吉林大学软件学院）；Joint NTU-UBC Research Centre of Excellence in Active Living for the Elderly, Nanyang Technological University（老年活跃生活卓越研究中⼼（NTU-UBC）, 新加坡国立大学）；College of Computer Science（计算机科学学院）；Technology, Zhejiang University（技术, 浙江大学）；Key Laboratory of Symbolic Computation（符号计算重点实验室）；Knowledge Engineering of Ministry of Education, College of Computer Science（教育部知识工程重点实验室, 计算机科学学院）；Technology, Jilin University（技术, 吉林大学）；School of Artificial Intelligence, Beijing Normal University（北京师范大学人工智能学院）
Fusing live fluoroscopy images with a 3D rotational reconstruction of the vasculature allows to navigate endovascular devices in minimally invasive neuro-vascular treatment, while reducing the usage of harmful iodine contrast medium. The alignment of the fluoroscopy images and the 3D reconstruction is initialized using the sensor information of the X-ray C-arm geometry. Patient motion is then corrected by an image-based registration algorithm, based on a gradient difference similarity measure using digital reconstructed radiographs of the 3D reconstruction. This algorithm does not require the …
Institute of Parallel and Distributed Systems, University of Stuttgart（斯图加特大学并行与分布式系统研究所）
Deformable image registration is a fundamental task in medical imaging. Due to the large computational complexity of deformable registration of volumetric images, conventional iterative methods usually face the tradeoff between the registration accuracy and the computation time in practice. In order to boost the registration performance in both accuracy and runtime, we propose a fast convolutional neural network. Specially, to efficiently utilize the memory resources and enlarge the model capacity, we adopt additive forwarding instead of channel concatenation and deepen the network in each enc…
Newton-Wellesley Hospital and Harvard Medical School（牛顿-韦尔斯利医院与哈佛医学院）；Massachusetts General Hospital and Harvard Medical School（麻省总医院与哈佛医学院）
Registration of 3D anatomic structures to their 2D dual fluoroscopic X-ray images is a widely used motion tracking technique. However, deep learning implementation is often impeded by a paucity of medical images and ground truths. In this study, we proposed a transfer learning strategy for 3D-to-2D registration using deep neural networks trained from an artificial dataset. Digitally reconstructed radiographs (DRRs) and radiographic skull landmarks were automatically created from craniocervical CT data of a female subject. They were used to train a residual network (ResNet) for landmark detecti…
Institute for Parallel and Distributed Systems, University of Stuttgart（斯图加特大学并行与分布式系统研究所）
Image registration is a fundamental task for medical imaging. Resampling of the intensity values is required during registration and better spatial resolution with finer and sharper structures can improve the resampling performance and hence the registration accuracy. Super-resolution (SR) is an algorithmic technique targeting at spatial resolution enhancement which can achieve an image resolution beyond the hardware limitation. In this work, we consider SR as a preprocessing technique and present a CNN-based resolution enhancement module (REM) which can be easily plugged into the registration…
University of California, San Francisco（加州大学旧金山分校）；Weill Institute for Neurosciences（威尔神经科学研究所）；Iran Science and Technology University（伊朗科技大学）；Sharif University of Technology（谢里夫理工大学）
Spatially-varying intensity noise is a common source of distortion in medical images. Bias field noise is one example of such a distortion that is often present in the magnetic resonance (MR) images or other modalities such as retina images. In this paper, we first show that the bias field noise can be considerably reduced using Empirical Mode Decomposition (EMD) technique. EMD is a multi-resolution tool that decomposes a signal into several principle patterns and residual components. We show that the spatially-varying noise is highly expressed in the residual component of the EMD and could be…
Center for Computational Mathematics（计算数学中心）；University of Colorado at Denver and Health Sciences Center（科罗拉多大学丹佛健康科学中心）；National Center for Atmospheric Research（美国国家大气研究中心）
A new type of ensemble filter is proposed, which combines an ensemble Kalman filter (EnKF) with the ideas of morphing and registration from image processing. This results in filters suitable for nonlinear problems whose solutions exhibit moving coherent features, such as thin interfaces in wildfire modeling. The ensemble members are represented as the composition of one common state with a spatial transformation, called registration mapping, plus a residual. A fully automatic registration method is used that requires only gridded data, so the features in the model state do not need to be ident…
Deep Biomechanically-Guided Interpolation for Keypoint-Based Brain Shift Registration
LASIGE, Faculdade de Ciências da Universidade de Lisboa（里斯本大学科学学院LASIGE中心）；CRUK Cambridge Centre, University of Cambridge（剑桥大学CRUK剑桥中心）；Department of Oncology, University of Cambridge（剑桥大学肿瘤学系）；Intelligent System for Medicine Laboratory (ISML), School of Mechanical Engineering, The University of Western Australia（西澳大学机械工程学院医学智能系统实验室）；MIND Team, Inria Saclay, Université Paris-Saclay, Palaiseau, France（法国巴黎萨克利大学MIND团队）；Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, CNRS, Inria, Inserm, AP-HP, Hôpital de la Pitié Salpêtrière（索邦大学巴黎脑研究所-ICM）
Precise determination of target is an essential procedure in prostate interventions, such as the prostate biopsy, lesion detection and targeted therapy. However, the prostate delineation may be tough in some cases due to tissue ambiguity or lack of partial anatomical boundary. To address this problem, we proposed a weakly supervised registration-based framework for the precise prostate segmentation, by combining convolutional neural network (CNN) with statistical shape model (SSM). To obtain the prostate region, an inception-based neural network (SSM-Net) was firstly exploited to predict the m…
Inception Institute of Artificial Intelligence（起源人工智能研究院）；Université de Lille（里尔大学）；Terminus Group（特斯联集团）
In deformable registration, the geometric framework - large deformation diffeomorphic metric mapping or LDDMM, in short - has inspired numerous techniques for comparing, deforming, averaging and analyzing shapes or images. Grounded in flows, which are akin to the equations of motion used in fluid dynamics, LDDMM algorithms solve the flow equation in the space of plausible deformations, i.e. diffeomorphisms. In this work, we make use of deep residual neural networks to solve the non-stationary ODE (flow equation) based on a Euler's discretization scheme. The central idea is to represent time-de…
Universidad de Alcalá（阿尔卡拉大学）；Universidad Rey Juan Carlos（胡安卡洛斯国王大学）；Institut de Recherche contre les Cancers de l’Appareil Digestif（消化道癌症研究所）；Université Clermont-Auvergne（克莱蒙奥弗涅大学）
We present Deep Shape-from-Template (DeepSfT), a novel Deep Neural Network (DNN) method for solving real-time automatic registration and 3D reconstruction of a deformable object viewed in a single monocular image.DeepSfT advances the state-of-the-art in various aspects. Compared to existing DNN SfT methods, it is the first fully convolutional real-time approach that handles an arbitrary object geometry, topology and surface representation. It also does not require ground truth registration with real data and scales well to very complex object models with large numbers of elements. Compared to …
Children’s Hospital of Philadelphia（费城儿童医院）；RWTH Aachen University（亚琛工业大学）；Cardiff University（卡迪夫大学）
Diffusion imaging is an important method in the field of neuroscience, as it is sensitive to changes within the tissue microstructure of the human brain. However, a major challenge when using MRI to derive quantitative measures is that the use of different scanners, as used in multi-site group studies, introduces measurement variability. This can lead to an increased variance in quantitative metrics, even if the same brain is scanned. Contrary to the assumption that these characteristics are comparable and similar, small changes in these values are observed in many clinical studies, hence harm…
Technische Universität München（慕尼黑工业大学）；Johns Hopkins University（约翰斯·霍普金斯大学）
Although the segmentation of brain structures in ultrasound helps initialize image based registration, assist brain shift compensation, and provides interventional decision support, the task of segmenting grey and white matter in cranial ultrasound is very challenging and has not been addressed yet. We train a multi-scale fully convolutional neural network simultaneously for two classes in order to segment real clinical 3D ultrasound data. Parallel pathways working at different levels of resolution account for high frequency speckle noise and global 3D image features. To ensure reproducibility…
Centre for Medical Image Computing, University College London（伦敦大学学院医学图像计算中心）；Institute of Biomedical Engineering, University of Oxford（牛津大学生物医学工程研究所）；Department of Diagnostic Imaging, Royal Free London NHS Foundation Trust（伦敦皇家自由NHS基金会信托诊断影像科）
Sonography synthesis has a wide range of applications, including medical procedure simulation, clinical training and multimodality image registration. In this paper, we propose a machine learning approach to simulate ultrasound images at given 3D spatial locations (relative to the patient anatomy), based on conditional generative adversarial networks (GANs). In particular, we introduce a novel neural network architecture that can sample anatomically accurate images conditionally on spatial position of the (real or mock) freehand ultrasound probe. To ensure an effective and efficient spatial in…
