Segmentation of the left atrial chamber and assessing its morphology, are essential for improving our understanding of atrial fibrillation, the most common type of cardiac arrhythmia. Automation of this process in 3D gadolinium enhanced-MRI (GE-MRI) data is desirable, as manual delineation is time-consuming, challenging and observer-dependent. Recently, deep convolutional neural networks (CNNs) have gained tremendous traction and achieved state-of-the-art results in medical image segmentation. However, it is difficult to incorporate local and global information without using contracting (pooling) layers, which in turn reduces segmentation accuracy for smaller structures. In this paper, we propose a 3D CNN for volumetric segmentation of the left atrial chamber in LGE-MRI. Our network is based on the well known U-Net architecture. We employ a 3D fully convolutional network, with dilated convolutions in the lowest level of the network, and residual connections between encoder blocks to incorporate local and global knowledge. The results show that including global context through the use of dilated convolutions, helps in domain adaptation, and the overall segmentation accuracy is improved in comparison to a 3D U-Net.
Royal Brompton Hospital（皇家布朗普顿医院）；National Heart and Lung Institute, Imperial College London（帝国理工学院国家心肺研究所）；Fudan University（复旦大学）；Shanghai Jiao Tong University（上海交通大学）；University of Lincoln（林肯大学）；City University London（伦敦城市大学）
Purpose: Atrial fibrillation (AF) is the most common cardiac arrhythmia and is correlated with increased morbidity and mortality. It is associated with atrial fibrosis, which may be assessed non-invasively using late gadolinium-enhanced (LGE) magnetic resonance imaging (MRI) where scar tissue is visualised as a region of signal enhancement. In this study, we proposed a novel fully automatic pipeline to achieve an accurate and objective atrial scarring segmentation and assessment of LGE MRI scans for the AF patients. Methods: Our fully automatic pipeline uniquely combined: (1) a multi-atlas bas…
Two-Stage Deep Learning Framework for Quality Assessment of Left Atrial Late Gadolinium Enhanced MRI Images
Kahlert School of Computing, University of Utah（犹他大学卡勒特计算学院）；Department of Biomedical Engineering, University of Utah（犹他大学生物医学工程系）；Nora Eccles Harrison Cardiovascular Research and Training Institute, University of Utah（犹他大学诺拉·埃克尔斯·哈里森心血管研究与培训研究所）；Department of Biomedical Engineering, Johns Hopkins（约翰斯·霍普金斯大学生物医学工程系）；Division of Cardiology, University of Utah（犹他大学心脏病学系）；Department of Radiology and Imaging Sciences, University of Utah（犹他大学放射学与影像科学系）；Scientific Computing and Imaging Institute, University of Utah（犹他大学科学计算与成像研究所）
Fudan University（复旦大学）；Shanghai Jiao Tong University（上海交通大学）；Technical University of Munich（慕尼黑工业大学）；Helmholtz Center Munich（慕尼黑亥姆霍兹中心）
Late gadolinium enhancement magnetic resonance imaging (LGE MRI) is commonly used to visualize and quantify left atrial (LA) scars. The position and extent of scars provide important information of the pathophysiology and progression of atrial fibrillation (AF). Hence, LA scar segmentation and quantification from LGE MRI can be useful in computer-assisted diagnosis and treatment stratification of AF patients. Since manual delineation can be time-consuming and subject to intra- and inter-expert variability, automating this computing is highly desired, which nevertheless is still challenging and…
Segmentation of the left atrium (LA) is crucial for assessing its anatomy in both pre-operative atrial fibrillation (AF) ablation planning and post-operative follow-up studies. In this paper, we present a fully automated framework for left atrial segmentation in gadolinium-enhanced magnetic resonance images (GE-MRI) based on deep learning. We propose a fully convolutional neural network and explore the benefits of multi-task learning for performing both atrial segmentation and pre/post ablation classification. Our results show that, by sharing features between related tasks, the network can ga…
Few-Shot Left Atrial Wall Segmentation in 3D LGE MRI via Meta-Learning
Department of Systems and Computer Engineering, Carleton University（系统与计算机工程系，卡尔顿大学）；Department of Radiology, Radiation Oncology, and Medical Physics, University of Ottawa（放射科、放射肿瘤学与医学物理系，渥太华大学）；Division of Cardiology, Department of Medicine, University of Ottawa Heart Institute（心内科，医学系，渥太华心脏研究所）
Scientific Computing and Imaging Institute, University of Utah（犹他大学科学计算与成像研究所）；Kahlert School of Computing, University of Utah（犹他大学卡勒特计算学院）；Department of Biomedical Engineering, University of Utah（犹他大学生物医学工程系）；Nora Eccles Harrison Cardiovascular Research and Training Institute, University of Utah（犹他大学诺拉·埃克尔斯·哈里森心血管研究与培训研究所）；Department of Radiology and Imaging Sciences, University of Utah（犹他大学放射学与影像科学系）；Department of Biomedical Engineering, Johns Hopkins（约翰霍普金斯大学生物医学工程系）；Division of Cardiology, University of Utah（犹他大学心脏病学系）
HAMIL-QA: Hierarchical Approach to Multiple Instance Learning for Atrial LGE MRI Quality Assessment
Kahlert School of Computing, University of Utah（犹他大学卡尔特计算机学院）；Department of Biomedical Engineering, University of Utah（犹他大学生物医学工程系）；Nora Eccles Harrison Cardiovascular Research and Training Institute, University of Utah（犹他大学诺拉·埃克尔斯·哈里森心血管研究与培训研究所）；Johns Hopkins（约翰斯·霍普金斯大学）；Division of Cardiology, University of Utah（犹他大学心脏病学系）；Department of Radiology and Imaging Sciences, University of Utah（犹他大学放射学与影像科学系）；Scientific Computing and Imaging Institute, University of Utah（犹他大学科学计算与影像研究所）
Fudan University（复旦大学）；Shanghai Jiao Tong University（上海交通大学）；Imperial College London（帝国理工学院）
We present a fully-automated segmentation and quantification of the left atrial (LA) fibrosis and scars combining two cardiac MRIs, one is the target late gadolinium-enhanced (LGE) image, and the other is an anatomical MRI from the same acquisition session. We formulate the joint distribution of images using a multivariate mixture model (MvMM), and employ the maximum likelihood estimator (MLE) for texture classification of the images simultaneously. The MvMM can also embed transformations assigned to the images to correct the misregistration. The iterated conditional mode algorithm is adopted …
Fudan University（复旦大学）；Shanghai Jiao Tong University（上海交通大学）；King’s College London（伦敦国王学院）
Left atrial (LA) segmentation from late gadolinium enhanced magnetic resonance imaging (LGE MRI) is a crucial step needed for planning the treatment of atrial fibrillation. However, automatic LA segmentation from LGE MRI is still challenging, due to the poor image quality, high variability in LA shapes, and unclear LA boundary. Though deep learning-based methods can provide promising LA segmentation results, they often generalize poorly to unseen domains, such as data from different scanners and/or sites. In this work, we collect 210 LGE MRIs from different centers with different levels of ima…
Integrating Deep Learning in Cardiology: A Comprehensive Review of Atrial Fibrillation, Left Atrial Scar Segmentation, and the Frontiers of State-of-the-Art Techniques
University of Auckland（奥克兰大学）；Auckland Bioengineering Institute（奥克兰生物工程研究所）
Shanghai Jiao Tong University（上海交通大学）；Fudan University（复旦大学）；National Heart and Lung Institute（国家心肺研究所）；Imperial College London（帝国理工学院）
Late Gadolinium Enhancement Magnetic Resonance Imaging (LGE MRI) emerged as a routine scan for patients with atrial fibrillation (AF). However, due to the low image quality automating the quantification and analysis of the atrial scars is challenging. In this study, we pro-posed a fully automated method based on the graph-cuts framework, where the potential of the graph is learned on a surface mesh of the left atrium (LA) using an equidistant projection and a Deep Neural Network (DNN). For validation, we employed 100 datasets with manual delineation. The results showed that the performance of …
Sun Yat-sen University（中山大学）；Royal Brompton Hospital（皇家布朗普顿医院）；Imperial College London（帝国理工学院）
Automated and accurate segmentations of left atrium (LA) and atrial scars from late gadolinium-enhanced cardiac magnetic resonance (LGE CMR) images are in high demand for quantifying atrial scars. The previous quantification of atrial scars relies on a two-phase segmentation for LA and atrial scars due to their large volume difference (unbalanced atrial targets). In this paper, we propose an inter-cascade generative adversarial network, namely JAS-GAN, to segment the unbalanced atrial targets from LGE CMR images automatically and accurately in an end-to-end way. Firstly, JAS-GAN investigates a…
Fuzhou University（福州大学）；College of Physics and Information Engineering, Fuzhou University（福州大学物理与信息工程学院）
Automatic segmentation of left atrial (LA) scars from late gadolinium enhanced CMR images is a crucial step for atrial fibrillation (AF) recurrence analysis. However, delineating LA scars is tedious and error-prone due to the variation of scar shapes. In this work, we propose a boundary-aware LA scar segmentation network, which is composed of two branches to segment LA and LA scars, respectively. We explore the inherent spatial relationship between LA and LA scars. By introducing a Sobel fusion module between the two segmentation branches, the spatial information of LA boundaries can be propag…
Anhui University（安徽大学）；Royal Brompton Hospital（皇家布朗普顿医院）；National Heart & Lung Institute, Imperial College London（帝国理工学院国家心肺研究所）；Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences（中国科学院深圳先进技术研究院）；University College London（伦敦大学学院）；Alan Turing Institute（艾伦·图灵研究所）；Imperial College London（帝国理工学院）
Late Gadolinium Enhanced Cardiac MRI (LGE-CMRI) for detecting atrial scars in atrial fibrillation (AF) patients has recently emerged as a promising technique to stratify patients, guide ablation therapy and predict treatment success. Visualisation and quantification of scar tissues require a segmentation of both the left atrium (LA) and the high intensity scar regions from LGE-CMRI images. These two segmentation tasks are challenging due to the cancelling of healthy tissue signal, low signal-to-noise ratio and often limited image quality in these patients. Most approaches require manual superv…
Fudan University（复旦大学）；Shanghai Jiao Tong University（上海交通大学）；King’s College London（伦敦国王学院）；Technical University Munich（慕尼黑工业大学）；Helmholtz Center Munich（慕尼黑亥姆霍兹中心）
Left atrial (LA) and atrial scar segmentation from late gadolinium enhanced magnetic resonance imaging (LGE MRI) is an important task in clinical practice. %, to guide ablation therapy and predict treatment results for atrial fibrillation (AF) patients. The automatic segmentation is however still challenging, due to the poor image quality, the various LA shapes, the thin wall, and the surrounding enhanced regions. Previous methods normally solved the two tasks independently and ignored the intrinsic spatial relationship between LA and scars. In this work, we develop a new framework, namely Atr…
Accurate cardiac computing, analysis and modeling from multi-modality images are important for the diagnosis and treatment of cardiac disease. Late gadolinium enhancement magnetic resonance imaging (LGE MRI) is a promising technique to visualize and quantify myocardial infarction (MI) and atrial scars. Automating quantification of MI and atrial scars can be challenging due to the low image quality and complex enhancement patterns of LGE MRI. Moreover, compared with the other sequences LGE MRIs with gold standard labels are particularly limited, which represents another obstacle for developing …
LA-CaRe-CNN: Cascading Refinement CNN for Left Atrial Scar Segmentation
Gottfried Schatz Research Center: Medical Physics and Biophysics（戈特弗里德·施蔡茨研究所以及生物物理学）；Medical University of Graz（格拉茨医科大学）；Institute of Computer Graphics and Vision（计算机图形学与视觉研究所）；Graz University of Technology（格拉茨理工大学）；AVL List GmbH；Institute for Medical Informatics, Statistics and Documentation（医学信息学、统计学与文档研究所）
Tencent YouTu Lab（腾讯优图实验室）；The Chinese University of Hong Kong（香港中文大学）；Beth Israel Deaconess Medical Center（贝斯以色列女执事医疗中心）；Harvard Medical School（哈佛医学院）
Accurately segmenting left atrium in MR volume can benefit the ablation procedure of atrial fibrillation. Traditional automated solutions often fail in relieving experts from the labor-intensive manual labeling. In this paper, we propose a deep neural network based solution for automated left atrium segmentation in gadolinium-enhanced MR volumes with promising performance. We firstly argue that, for this volumetric segmentation task, networks in 2D fashion can present great superiorities in time efficiency and segmentation accuracy than networks with 3D fashion. Considering the highly varying …
University of Utah（犹他大学）；Scientific Computing and Imaging Institute（科学计算与成像研究所）；Comprehensive Arrhythmia Research and Management Center（综合心律失常研究与管理中心）
Difficult image segmentation problems, for instance left atrium MRI, can be addressed by incorporating shape priors to find solutions that are consistent with known objects. Nonetheless, a single multivariate Gaussian is not an adequate model in cases with significant nonlinear shape variation or where the prior distribution is multimodal. Nonparametric density estimation is more general, but has a ravenous appetite for training samples and poses serious challenges in optimization, especially in high dimensional spaces. Here, we propose a maximum-a-posteriori formulation that relies on a gener…
The Chinese University of Hong Kong（香港中文大学）；Shenzhen University（深圳大学）；Beth Israel Deaconess Medical Center（贝斯以色列女执事医疗中心）；Harvard Medical School（哈佛医学院）
Segmenting left atrium in MR volume holds great potentials in promoting the treatment of atrial fibrillation. However, the varying anatomies, artifacts and low contrasts among tissues hinder the advance of both manual and automated solutions. In this paper, we propose a fully-automated framework to segment left atrium in gadolinium-enhanced MR volumes. The region of left atrium is firstly automatically localized by a detection module. Our framework then originates with a customized 3D deep neural network to fully explore the spatial dependency in the region for segmentation. To alleviate the r…
Cardiovascular Research Centre, Royal Brompton Hospital（皇家布朗普顿医院心血管研究中心）；National Heart and Lung Institute, Imperial College London（帝国理工学院国家心肺研究所）；Anhui University（安徽大学）；Western University（西安大略大学）；University College London（伦敦大学学院）；Alan Turing Institute（阿兰·图灵研究所）；NIHR Imperial Biomedical Research Centre（NIHR帝国生物医学研究中心）；Beijing Anzhen Hospital, Capital Medical University（首都医科大学附属北京安贞医院）；School of Biomedical Engineering, Sun Yat-Sen University（中山大学医学院生物医学工程学院）
Three-dimensional late gadolinium enhanced (LGE) cardiac MR (CMR) of left atrial scar in patients with atrial fibrillation (AF) has recently emerged as a promising technique to stratify patients, to guide ablation therapy and to predict treatment success. This requires a segmentation of the high intensity scar tissue and also a segmentation of the left atrium (LA) anatomy, the latter usually being derived from a separate bright-blood acquisition. Performing both segmentations automatically from a single 3D LGE CMR acquisition would eliminate the need for an additional acquisition and avoid sub…
Medical image segmentation has significantly benefitted thanks to deep learning architectures. Furthermore, semi-supervised learning (SSL) has recently been a growing trend for improving a model's overall performance by leveraging abundant unlabeled data. Moreover, learning multiple tasks within the same model further improves model generalizability. To generate smoother and accurate segmentation masks from 3D cardiac MR images, we present a Multi-task Cross-task learning consistency approach to enforce the correlation between the pixel-level (segmentation) and the geometric-level (distance ma…
University of Dundee（邓迪大学）；Technical University of Munich（慕尼黑工业大学）；Shenzhen Institute of Artificial Intelligence and Robotics for Society（深圳人工智能与机器人研究院）；Southern University of Science and Technology（南方科技大学）
Analysis and modeling of the ventricles and myocardium are important in the diagnostic and treatment of heart diseases. Manual delineation of those tissues in cardiac MR (CMR) scans is laborious and time-consuming. The ambiguity of the boundaries makes the segmentation task rather challenging. Furthermore, the annotations on some modalities such as Late Gadolinium Enhancement (LGE) MRI, are often not available. We propose an end-to-end segmentation framework based on convolutional neural network (CNN) and adversarial learning. A dilated residual U-shape network is used as a segmentor to genera…
