Convolutional Neural Networks (CNNs) have achieved high accuracy for cardiac structure segmentation if training cases and testing cases are from the same distribution. However, the performance would be degraded if the testing cases are from a distinct domain (e.g., new MRI scanners, clinical centers). In this paper, we propose a histogram matching (HM) data augmentation method to eliminate the domain gap. Specifically, our method generates new training cases by using HM to transfer the intensity distribution of testing cases to existing training cases. The proposed method is quite simple and can be used in a plug-and-play way in many segmentation tasks. The method is evaluated on MICCAI 2020 M\&Ms challenge, and achieves average Dice scores of 0.9051, 0.8405, and 0.8749, and Hausdorff Distances of 9.996, 12.49, and 12.68 for the left ventricular, myocardium, and right ventricular, respectively. Our results rank the third place in MICCAI 2020 M\&Ms challenge. The code and trained models are publicly available at \url{https://github.com/JunMa11/HM_DataAug}.
King's College London（伦敦国王学院）；Eindhoven University of Technology（埃因霍温理工大学）
Cine cardiac magnetic resonance (CMR) has become the gold standard for the non-invasive evaluation of cardiac function. In particular, it allows the accurate quantification of functional parameters including the chamber volumes and ejection fraction. Deep learning has shown the potential to automate the requisite cardiac structure segmentation. However, the lack of robustness of deep learning models has hindered their widespread clinical adoption. Due to differences in the data characteristics, neural networks trained on data from a specific scanner are not guaranteed to generalise well to dat…
Institute of Computing Technology, Chinese Academy of Sciences（中国科学院计算技术研究所）；University of Chinese Academy of Sciences（中国科学院大学）；University of California, Los Angeles（加州大学洛杉矶分校）；Lenovo Research（联想研究院）；Lenovo Ltd.（联想有限公司）
Accurate segmentation of cardiac structures can assist doctors to diagnose diseases, and to improve treatment planning, which is highly demanded in the clinical practice. However, the shortage of annotation and the variance of the data among different vendors and medical centers restrict the performance of advanced deep learning methods. In this work, we present a fully automatic method to segment cardiac structures including the left (LV) and right ventricle (RV) blood pools, as well as for the left ventricular myocardium (MYO) in MRI volumes. Specifically, we design a semi-supervised learnin…
German Cancer Research Center (DKFZ)（德国癌症研究中心（DKFZ））；Medical Faculty Heidelberg, Heidelberg University（海德堡大学海德堡医学院）
Cardiac magnetic resonance imaging (cMRI) is an integral part of diagnosis in many heart related diseases. Recently, deep neural networks have demonstrated successful automatic segmentation, thus alleviating the burden of time-consuming manual contouring of cardiac structures. Moreover, frameworks such as nnU-Net provide entirely automatic model configuration to unseen datasets enabling out-of-the-box application even by non-experts. However, current studies commonly neglect the clinically realistic scenario, in which a trained network is applied to data from a different domain such as deviati…
LGE CMR is an efficient technology for detecting infarcted myocardium. An efficient and objective ventricle segmentation method in LGE can benefit the location of the infarcted myocardium. In this paper, we proposed an automatic framework for LGE image segmentation. There are just 5 labeled LGE volumes with about 15 slices of each volume. We adopted histogram match, an invariant of rotation registration method, on the other labeled modalities to achieve effective augmentation of the training data. A CNN segmentation model was trained based on the augmented training data by leave-one-out strate…
Austin Health（奥斯汀健康）；The University of Melbourne（墨尔本大学）；Kings College London（伦敦国王学院）；I-MED Radiology（I-MED放射科）；University of Porto（波尔图大学）
Objectives: To develop an image-based automatic deep learning method to classify cardiac MR images by sequence type and imaging plane for improved clinical post-processing efficiency. Methods: Multi-vendor cardiac MRI studies were retrospectively collected from 4 centres and 3 vendors. A two-head convolutional neural network ('CardiSort') was trained to classify 35 sequences by imaging sequence (n=17) and plane (n=10). Single vendor training (SVT) on single centre images (n=234 patients) and multi-vendor training (MVT) with multicentre images (n = 479 patients, 3 centres) was performed. Model …
Deep models often suffer from severe performance drop due to the appearance shift in the real clinical setting. Most of the existing learning-based methods rely on images from multiple sites/vendors or even corresponding labels. However, collecting enough unknown data to robustly model segmentation cannot always hold since the complex appearance shift caused by imaging factors in daily application. In this paper, we propose a novel style-invariant method for cardiac image segmentation. Based on the zero-shot style transfer to remove appearance shift and test-time augmentation to explore divers…
Automatic segmentation of the heart cavity is an essential task for the diagnosis of cardiac diseases. In this paper, we propose a semi-supervised segmentation setup for leveraging unlabeled data to segment Left-ventricle, Right-ventricle, and Myocardium. We utilize an enhanced version of residual U-Net architecture on a large-scale cardiac MRI dataset. Handling the class imbalanced data issue using dice loss, the enhanced supervised model is able to achieve better dice scores in comparison with a vanilla U-Net model. We applied several augmentation techniques including histogram matching to i…
Technical University of Munich（慕尼黑工业大学）；Southern University of Science and Technology（南方科技大学）
Tackling domain shifts in multi-centre and multi-vendor data sets remains challenging for cardiac image segmentation. In this paper, we propose a generalisable segmentation framework for cardiac image segmentation in which multi-centre, multi-vendor, multi-disease datasets are involved. A generative adversarial networks with an attention loss was proposed to translate the images from existing source domains to a target domain, thus to generate good-quality synthetic cardiac structure and enlarge the training set. A stack of data augmentation techniques was further used to simulate real-world t…
SNR-Adaptive Unified Diffusion for Multi-Task Medical Image Segmentation
School of Telecommunications Engineering, Xidian University（西安电子科技大学通信工程学院）；School of Computer Science and Technology, Xidian University（西安电子科技大学计算机科学与技术学院）
Manipal Institute of Technology, Manipal Academy of Higher Education（马尼帕尔高等教育学院马尼帕尔理工学院）
Segmentation of the left ventricle in cardiac magnetic resonance imaging MRI scans enables cardiologists to calculate the volume of the left ventricle and subsequently its ejection fraction. The ejection fraction is a measurement that expresses the percentage of blood leaving the heart with each contraction. Cardiologists often use ejection fraction to determine one's cardiac function. We propose multiscale template matching technique for detection and an elliptical active disc for automated segmentation of the left ventricle in MR images. The elliptical active disc optimizes the local energy …
Fudan University（复旦大学）；Ruijin Hospital, Shanghai Jiaotong University（上海交通大学医学院附属瑞金医院）；Tongji Hospital, Huazhong University of Science and Technology（华中科技大学同济医学院附属同济医院）；Leiden University Medical Center（莱顿大学医学中心）
Convolutional neural network (CNN), in particular the Unet, is a powerful method for medical image segmentation. To date Unet has demonstrated state-of-art performance in many complex medical image segmentation tasks, especially under the condition when the training and testing data share the same distribution (i.e. come from the same source domain). However, in clinical practice, medical images are acquired from different vendors and centers. The performance of a U-Net trained from a particular source domain, when transferred to a different target domain (e.g. different vendor, acquisition pa…
Rutgers University（罗格斯大学）；SenseBrain（感知大脑公司）；Shanghai AI Laboratory（上海人工智能实验室）；Centre for Perceptual and Interactive Intelligence（感知与交互智能中心）
Transformer architecture has emerged to be successful in a number of natural language processing tasks. However, its applications to medical vision remain largely unexplored. In this study, we present UTNet, a simple yet powerful hybrid Transformer architecture that integrates self-attention into a convolutional neural network for enhancing medical image segmentation. UTNet applies self-attention modules in both encoder and decoder for capturing long-range dependency at different scales with minimal overhead. To this end, we propose an efficient self-attention mechanism along with relative pos…
Learning from Acquisition: Metadata-driven Multimodal Pre-training for Cardiac MRI
Department of Surgery & Cancer（外科与癌症系）；Bioengineering Department and Imperial-X（生物工程系和Imperial-X）；National Heart and Lung Institute（国家心脏和肺研究所）；Cardiovascular Research Centre（心血管研究中心）；School of Biomedical Engineering & Imaging Sciences（生物医学工程与成像科学学院）
Department of Electrical Engineering, Syed Babar Ali School of Science and Engineering, LUMS（拉合尔管理科学大学，赛义德·巴巴尔·阿里科学与工程学院，电气工程系）
We proposed a multi-view SA-LA model for simultaneous segmentation of RV on the short-axis (SA) and long-axis (LA) cardiac MR images. The multi-view SA-LA model is a multi-encoder, multi-decoder U-Net architecture based on the U-Net model. One encoder-decoder pair segments the RV on SA images and the other pair on LA images. Multi-view SA-LA model assembles an extremely rich set of synergistic features, at the root of the encoder branch, by combining feature maps learned from matched SA and LA cardiac MR images. Segmentation performance is further enhanced by: (1) incorporating spatial context…
Deep learning (DL)-based models have demonstrated good performance in medical image segmentation. However, the models trained on a known dataset often fail when performed on an unseen dataset collected from different centers, vendors and disease populations. In this work, we present a random style transfer network to tackle the domain generalization problem for multi-vendor and center cardiac image segmentation. Style transfer is used to generate training data with a wider distribution/ heterogeneity, namely domain augmentation. As the target domain could be unknown, we randomly generate a mod…
Eindhoven University of Technology（埃因霍温理工大学）；Philips Research Laboratories（飞利浦研究院）；Philips Healthcare（飞利浦医疗）
We propose a hybrid controllable image generation method to synthesize anatomically meaningful 3D+t labeled Cardiac Magnetic Resonance (CMR) images. Our hybrid method takes the mechanistic 4D eXtended CArdiac Torso (XCAT) heart model as the anatomical ground truth and synthesizes CMR images via a data-driven Generative Adversarial Network (GAN). We employ the state-of-the-art SPatially Adaptive De-normalization (SPADE) technique for conditional image synthesis to preserve the semantic spatial information of ground truth anatomy. Using the parameterized motion model of the XCAT heart, we genera…
University of Amsterdam（阿姆斯特丹大学）；University Medical Center Utrecht（乌得勒支大学医学中心）
Deep learning-based whole-heart segmentation in coronary CT angiography (CCTA) allows the extraction of quantitative imaging measures for cardiovascular risk prediction. Automatic extraction of these measures in patients undergoing only non-contrast-enhanced CT (NCCT) scanning would be valuable. In this work, we leverage information provided by a dual-layer detector CT scanner to obtain a reference standard in virtual non-contrast (VNC) CT images mimicking NCCT images, and train a 3D convolutional neural network (CNN) for the segmentation of VNC as well as NCCT images. Contrast-enhanced acquis…
Universitat de Barcelona（巴塞罗那大学）；Hospital de la Santa Creu i Sant Pau（圣十字圣保罗医院）；Universitat Autònoma de Barcelona（巴塞罗那自治大学）；Hospital Universitari Vall d’Hebron（瓦尔德希伯伦大学医院）
The domain generalization problem has been widely investigated in deep learning for non-contrast imaging over the last years, but it received limited attention for contrast-enhanced imaging. However, there are marked differences in contrast imaging protocols across clinical centers, in particular in the time between contrast injection and image acquisition, while access to multi-center contrast-enhanced image data is limited compared to available datasets for non-contrast imaging. This calls for new tools for generalizing single-domain, single-center deep learning models across new unseen doma…
Right ventricular (RV) segmentation from magnetic resonance imaging (MRI) is a crucial step for cardiac morphology and function analysis. However, automatic RV segmentation from MRI is still challenging, mainly due to the heterogeneous intensity, the complex variable shapes, and the unclear RV boundary. Moreover, current methods for the RV segmentation tend to suffer from performance degradation at the basal and apical slices of MRI. In this work, we propose an automatic RV segmentation framework, where the information from long-axis (LA) views is utilized to assist the segmentation of short-a…
The MYOSAIQ Challenge: Myocardial Segmentation with Automated Infarct Quantification
INSA-Lyon, Universite Claude Bernard Lyon 1, UJM-Saint Etienne, CNRS, Inserm, CREATIS UMR 5220, U1294（里昂国立应用科学学院、里昂第一大学克洛德·贝尔纳大学、圣艾蒂安大学、法国国家科学研究中心、法国国家健康与医学研究院、CREATIS联合研究机构）；Institut Universitaire de France (IUF)（法兰西大学研究院）；University of Sherbrooke（谢布鲁克大学）；Huazhong University of Science and Technology（华中科技大学）；Sunnybrook Research Institute, University of Toronto（多伦多大学桑尼布鲁克研究所）；Imperial College London（伦敦帝国理工学院）；University College London（伦敦大学学院）；Fudan University（复旦大学）；Medical University of Graz（格拉茨医科大学）；Graz University of Technology（格拉茨技术大学）；Universidad de Zaragoza（萨拉戈萨大学）；Instituto de Investigación Sanitaria de Aragón (IIS Aragón)（阿拉贡卫生研究所）；Centre Hospitalier Annecy Genevois（阿讷西日内瓦中心医院）；Hôpital Universitaire Cardiologique Louis Pradel（路易·普拉德尔大学心脏病医院）
