Yeonggul Jang

Bio: Yeonggul Jang is an academic researcher from Yonsei University. The author has contributed to research in topics: Coronary arteries & Segmentation. The author has an hindex of 7, co-authored 30 publications receiving 651 citations. Previous affiliations of Yeonggul Jang include Hankuk University of Foreign Studies & University Health System.

Deep Learning Techniques for Automatic MRI Cardiac Multi-Structures Segmentation and Diagnosis: Is the Problem Solved?

Abstract: Delineation of the left ventricular cavity, myocardium, and right ventricle from cardiac magnetic resonance images (multi-slice 2-D cine MRI) is a common clinical task to establish diagnosis. The automation of the corresponding tasks has thus been the subject of intense research over the past decades. In this paper, we introduce the “Automatic Cardiac Diagnosis Challenge” dataset (ACDC), the largest publicly available and fully annotated dataset for the purpose of cardiac MRI (CMR) assessment. The dataset contains data from 150 multi-equipments CMRI recordings with reference measurements and classification from two medical experts. The overarching objective of this paper is to measure how far state-of-the-art deep learning methods can go at assessing CMRI, i.e., segmenting the myocardium and the two ventricles as well as classifying pathologies. In the wake of the 2017 MICCAI-ACDC challenge, we report results from deep learning methods provided by nine research groups for the segmentation task and four groups for the classification task. Results show that the best methods faithfully reproduce the expert analysis, leading to a mean value of 0.97 correlation score for the automatic extraction of clinical indices and an accuracy of 0.96 for automatic diagnosis. These results clearly open the door to highly accurate and fully automatic analysis of cardiac CMRI. We also identify scenarios for which deep learning methods are still failing. Both the dataset and detailed results are publicly available online, while the platform will remain open for new submissions.

Automatic Segmentation of LV and RV in Cardiac MRI

Abstract: Automatic and accurate segmentation of Left Ventricle (LV) and Right Ventricle (RV) in cine-MRI is required to analyze cardiac function and viability. We present a fully convolutional neural network to efficiently segment LV and RV as well as myocardium. The network is trained end-to-end from scratch. Average dice scores from five-fold cross-validation on the ACDC training dataset were 0.94, 0.89, and 0.88 for LV, RV, and myocardium. Experimental results show the robustness of the proposed architecture.

Automatic aortic valve landmark localization in coronary CT angiography using colonial walk.

Abstract: The minimally invasive transcatheter aortic valve implantation (TAVI) is the most prevalent method to treat aortic valve stenosis. For pre-operative surgical planning, contrast-enhanced coronary CT angiography (CCTA) is used as the imaging technique to acquire 3-D measurements of the valve. Accurate localization of the eight aortic valve landmarks in CT images plays a vital role in the TAVI workflow because a small error risks blocking the coronary circulation. In order to examine the valve and mark the landmarks, physicians prefer a view parallel to the hinge plane, instead of using the conventional axial, coronal or sagittal view. However, customizing the view is a difficult and time-consuming task because of unclear aorta pose and different artifacts of CCTA. Therefore, automatic localization of landmarks can serve as a useful guide to the physicians customizing the viewpoint. In this paper, we present an automatic method to localize the aortic valve landmarks using colonial walk, a regression tree-based machine-learning algorithm. For efficient learning from the training set, we propose a two-phase optimized search space learning model in which a representative point inside the valvular area is first learned from the whole CT volume. All eight landmarks are then learned from a smaller area around that point. Experiment with preprocedural CCTA images of TAVI undergoing patients showed that our method is robust under high stenotic variation and notably efficient, as it requires only 12 milliseconds to localize all eight landmarks, as tested on a 3.60 GHz single-core CPU.

Fully Automatic Segmentation of Coronary Arteries Based on Deep Neural Network in Intravascular Ultrasound Images

Abstract: Accurate segmentation of coronary arteries is important for the diagnosis of cardiovascular diseases. In this paper, we propose a fully convolutional neural network to efficiently delineate the boundaries of the wall and lumen of the coronary arteries using intravascular ultrasound (IVUS) images. Our network addresses multi-label segmentation of the wall and lumen areas at the same time. The primary body of the proposed network is U-shaped which contains the encoding and decoding paths to learn rich hierarchical representations. The multi-scale input layer is adapted to take a multi-scale input. We deploy a multi-label loss function with weighted pixel-wise cross-entropy to alleviate imbalance of the rate of background, wall, and lumen. The proposed method is compared with three existing methods and the segmentation results are measured on four metrics, dice similarity coefficient, Jaccard index, percentage of area difference, and Hausdorff distance on totally 38,478 IVUS images from 35 subjects.

Automatic Coronary Artery Segmentation Using Active Search for Branches and Seemingly Disconnected Vessel Segments from Coronary CT Angiography.

Abstract: We propose a Bayesian tracking and segmentation method of coronary arteries on coronary computed tomographic angiography (CCTA). The geometry of coronary arteries including lumen boundary is estimated in Maximum A Posteriori (MAP) framework. Three consecutive sphere based filtering is combined with a stochastic process that is based on the similarity of the consecutive local neighborhood voxels and the geometric constraint of a vessel. It is also founded on the prior knowledge that an artery can be seen locally disconnected and consist of branches which may be seemingly disconnected due to plaque build up. For such problem, an active search method is proposed to find branches and seemingly disconnected but actually connected vessel segments. Several new measures have been developed for branch detection, disconnection check and planar vesselness measure. Using public domain Rotterdam CT dataset, the accuracy of extracted centerline is demonstrated and automatic reconstruction of coronary artery mesh is shown.

nnU-Net: a self-configuring method for deep learning-based biomedical image segmentation

Abstract: Biomedical imaging is a driver of scientific discovery and a core component of medical care and is being stimulated by the field of deep learning. While semantic segmentation algorithms enable image analysis and quantification in many applications, the design of respective specialized solutions is non-trivial and highly dependent on dataset properties and hardware conditions. We developed nnU-Net, a deep learning-based segmentation method that automatically configures itself, including preprocessing, network architecture, training and post-processing for any new task. The key design choices in this process are modeled as a set of fixed parameters, interdependent rules and empirical decisions. Without manual intervention, nnU-Net surpasses most existing approaches, including highly specialized solutions on 23 public datasets used in international biomedical segmentation competitions. We make nnU-Net publicly available as an out-of-the-box tool, rendering state-of-the-art segmentation accessible to a broad audience by requiring neither expert knowledge nor computing resources beyond standard network training.

Deep Learning Techniques for Automatic MRI Cardiac Multi-Structures Segmentation and Diagnosis: Is the Problem Solved?

Abstract: Delineation of the left ventricular cavity, myocardium, and right ventricle from cardiac magnetic resonance images (multi-slice 2-D cine MRI) is a common clinical task to establish diagnosis. The automation of the corresponding tasks has thus been the subject of intense research over the past decades. In this paper, we introduce the “Automatic Cardiac Diagnosis Challenge” dataset (ACDC), the largest publicly available and fully annotated dataset for the purpose of cardiac MRI (CMR) assessment. The dataset contains data from 150 multi-equipments CMRI recordings with reference measurements and classification from two medical experts. The overarching objective of this paper is to measure how far state-of-the-art deep learning methods can go at assessing CMRI, i.e., segmenting the myocardium and the two ventricles as well as classifying pathologies. In the wake of the 2017 MICCAI-ACDC challenge, we report results from deep learning methods provided by nine research groups for the segmentation task and four groups for the classification task. Results show that the best methods faithfully reproduce the expert analysis, leading to a mean value of 0.97 correlation score for the automatic extraction of clinical indices and an accuracy of 0.96 for automatic diagnosis. These results clearly open the door to highly accurate and fully automatic analysis of cardiac CMRI. We also identify scenarios for which deep learning methods are still failing. Both the dataset and detailed results are publicly available online, while the platform will remain open for new submissions.

Automated cardiovascular magnetic resonance image analysis with fully convolutional networks

Abstract: Cardiovascular resonance (CMR) imaging is a standard imaging modality for assessing cardiovascular diseases (CVDs), the leading cause of death globally. CMR enables accurate quantification of the cardiac chamber volume, ejection fraction and myocardial mass, providing information for diagnosis and monitoring of CVDs. However, for years, clinicians have been relying on manual approaches for CMR image analysis, which is time consuming and prone to subjective errors. It is a major clinical challenge to automatically derive quantitative and clinically relevant information from CMR images. Deep neural networks have shown a great potential in image pattern recognition and segmentation for a variety of tasks. Here we demonstrate an automated analysis method for CMR images, which is based on a fully convolutional network (FCN). The network is trained and evaluated on a large-scale dataset from the UK Biobank, consisting of 4,875 subjects with 93,500 pixelwise annotated images. The performance of the method has been evaluated using a number of technical metrics, including the Dice metric, mean contour distance and Hausdorff distance, as well as clinically relevant measures, including left ventricle (LV) end-diastolic volume (LVEDV) and end-systolic volume (LVESV), LV mass (LVM); right ventricle (RV) end-diastolic volume (RVEDV) and end-systolic volume (RVESV). By combining FCN with a large-scale annotated dataset, the proposed automated method achieves a high performance in segmenting the LV and RV on short-axis CMR images and the left atrium (LA) and right atrium (RA) on long-axis CMR images. On a short-axis image test set of 600 subjects, it achieves an average Dice metric of 0.94 for the LV cavity, 0.88 for the LV myocardium and 0.90 for the RV cavity. The mean absolute difference between automated measurement and manual measurement is 6.1 mL for LVEDV, 5.3 mL for LVESV, 6.9 gram for LVM, 8.5 mL for RVEDV and 7.2 mL for RVESV. On long-axis image test sets, the average Dice metric is 0.93 for the LA cavity (2-chamber view), 0.95 for the LA cavity (4-chamber view) and 0.96 for the RA cavity (4-chamber view). The performance is comparable to human inter-observer variability. We show that an automated method achieves a performance on par with human experts in analysing CMR images and deriving clinically relevant measures.

Automated Design of Deep Learning Methods for Biomedical Image Segmentation

Abstract: Biomedical imaging is a driver of scientific discovery and core component of medical care, currently stimulated by the field of deep learning. While semantic segmentation algorithms enable 3D image analysis and quantification in many applications, the design of respective specialised solutions is non-trivial and highly dependent on dataset properties and hardware conditions. We propose nnU-Net, a deep learning framework that condenses the current domain knowledge and autonomously takes the key decisions required to transfer a basic architecture to different datasets and segmentation tasks. Without manual tuning, nnU-Net surpasses most specialised deep learning pipelines in 19 public international competitions and sets a new state of the art in the majority of the 49 tasks. The results demonstrate a vast hidden potential in the systematic adaptation of deep learning methods to different datasets. We make nnU-Net publicly available as an open-source tool that can effectively be used out-of-the-box, rendering state of the art segmentation accessible to non-experts and catalyzing scientific progress as a framework for automated method design.

Deep learning for cardiac image segmentation: A review

Abstract: Deep learning has become the most widely used approach for cardiac image segmentation in recent years. In this paper, we provide a review of over 100 cardiac image segmentation papers using deep learning, which covers common imaging modalities including magnetic resonance imaging (MRI), computed tomography (CT), and ultrasound (US) and major anatomical structures of interest (ventricles, atria and vessels). In addition, a summary of publicly available cardiac image datasets and code repositories are included to provide a base for encouraging reproducible research. Finally, we discuss the challenges and limitations with current deep learning-based approaches (scarcity of labels, model generalizability across different domains, interpretability) and suggest potential directions for future research.