Publications
159 results found
Curran L, de Marvao A, Inglese P, et al., 2023, A phenotypic taxonomy of hypertrophic cardiomyopathy
<jats:title>Abstract</jats:title><jats:sec><jats:title>Background</jats:title><jats:p>Hypertrophic cardiomyopathy (HCM) is an important cause of sudden cardiac death associated with heterogeneous structural phenotypes but there is no systematic framework for classifying morphology or assessing associated risks. In this study we quantitatively survey genotype-phenotype associations in HCM to derive a data-driven taxonomy of disease expression for automated patient stratification.</jats:p></jats:sec><jats:sec><jats:title>Methods</jats:title><jats:p>An observational, single-centre study enrolled 436 HCM patients (median age 60 years; 28.8% women) with clinical, genetic and imaging data. An independent cohort of 60 HCM patients from Singapore (median age 59 years; 11% women) and a normative reference population from UK Biobank (n = 16,691, mean age 55 years; 52.5% women) with equivalent data were also recruited. We used machine learning to analyse the three dimensional structure of the left ventricle from cardiac magnetic resonance imaging and build a tree-based classification of HCM phenotypes. Genotype and mortality risk distributions were projected on the tree.</jats:p></jats:sec><jats:sec><jats:title>Results</jats:title><jats:p>The prevalence of pathogenic or likely pathogenic variants for HCM (P/LP) was 24.6%, while 66% were genotype negative. Carriers of P/LP variants had lower left ventricular mass, but greater basal septal hypertrophy, with reduced lifespan (mean follow-up 9.9 years) compared to genotype negative individuals (hazard ratio: 2.66; 95% confidence interval [CI]: 1.42-4.96;<jats:italic>P</jats:italic>< 0.002). Four main phenotypic branches were identified using unsupervised learning of three dimensional shape: 1) non-sarcomeric hypertrophy with co-existing hypertension; 2) diffuse and basal asymmetric hypertrophy associated w
Qiao M, Wang S, Qiu H, et al., 2023, CHeart: A Conditional Spatio-Temporal Generative Model for Cardiac Anatomy
Two key questions in cardiac image analysis are to assess the anatomy andmotion of the heart from images; and to understand how they are associated withnon-imaging clinical factors such as gender, age and diseases. While the firstquestion can often be addressed by image segmentation and motion trackingalgorithms, our capability to model and to answer the second question is stilllimited. In this work, we propose a novel conditional generative model todescribe the 4D spatio-temporal anatomy of the heart and its interaction withnon-imaging clinical factors. The clinical factors are integrated as theconditions of the generative modelling, which allows us to investigate howthese factors influence the cardiac anatomy. We evaluate the model performancein mainly two tasks, anatomical sequence completion and sequence generation.The model achieves a high performance in anatomical sequence completion,comparable to or outperforming other state-of-the-art generative models. Interms of sequence generation, given clinical conditions, the model can generaterealistic synthetic 4D sequential anatomies that share similar distributionswith the real data.
Qin C, Wang S, Chen C, et al., 2023, Generative myocardial motion tracking via latent space exploration with biomechanics-informed prior, MEDICAL IMAGE ANALYSIS, Vol: 83, ISSN: 1361-8415
Ouyang C, Chen C, Li S, et al., 2022, Causality-inspired single-source domain generalization for medical image segmentation, IEEE Transactions on Medical Imaging, Pages: 1-1, ISSN: 0278-0062
Deep learning models usually suffer from the domain shift issue, where models trained on one source domain do not generalize well to other unseen domains. In this work, we investigate the single-source domain generalization problem: training a deep network that is robust to unseen domains, under the condition that training data are only available from one source domain, which is common in medical imaging applications. We tackle this problem in the context of cross-domain medical image segmentation. In this scenario, domain shifts are mainly caused by different acquisition processes. We propose a simple causality-inspired data augmentation approach to expose a segmentation model to synthesized domain-shifted training examples. Specifically, 1) to make the deep model robust to discrepancies in image intensities and textures, we employ a family of randomly-weighted shallow networks. They augment training images using diverse appearance transformations. 2) Further we show that spurious correlations among objects in an image are detrimental to domain robustness. These correlations might be taken by the network as domain-specific clues for making predictions, and they may break on unseen domains. We remove these spurious correlations via causal intervention. This is achieved by resampling the appearances of potentially correlated objects independently. The proposed approach is validated on three cross-domain segmentation scenarios: cross-modality (CT-MRI) abdominal image segmentation, cross-sequence (bSSFP-LGE) cardiac MRI segmentation, and cross-site prostate MRI segmentation. The proposed approach yields consistent performance gains compared with competitive methods when tested on unseen domains.
Kart T, Fischer M, Winzeck S, et al., 2022, Automated imaging-based abdominal organ segmentation and quality control in 20,000 participants of the UK Biobank and German National Cohort Studies, SCIENTIFIC REPORTS, Vol: 12, ISSN: 2045-2322
Chen C, Qin C, Ouyang C, et al., 2022, Enhancing MR image segmentation with realistic adversarial data augmentation, Medical Image Analysis, Vol: 82, Pages: 1-15, ISSN: 1361-8415
The success of neural networks on medical image segmentation tasks typicallyrelies on large labeled datasets for model training. However, acquiring andmanually labeling a large medical image set is resource-intensive, expensive,and sometimes impractical due to data sharing and privacy issues. To addressthis challenge, we propose AdvChain, a generic adversarial data augmentationframework, aiming at improving both the diversity and effectiveness of trainingdata for medical image segmentation tasks. AdvChain augments data with dynamicdata augmentation, generating randomly chained photo-metric and geometrictransformations to resemble realistic yet challenging imaging variations toexpand training data. By jointly optimizing the data augmentation model and asegmentation network during training, challenging examples are generated toenhance network generalizability for the downstream task. The proposedadversarial data augmentation does not rely on generative networks and can beused as a plug-in module in general segmentation networks. It iscomputationally efficient and applicable for both low-shot supervised andsemi-supervised learning. We analyze and evaluate the method on two MR imagesegmentation tasks: cardiac segmentation and prostate segmentation with limitedlabeled data. Results show that the proposed approach can alleviate the needfor labeled data while improving model generalization ability, indicating itspractical value in medical imaging applications.
Basaran B, Matthews PM, Bai W, 2022, New lesion segmentation for multiple sclerosis brain images with imaging and lesion-aware augmentation, Frontiers in Neuroscience, Vol: 16, ISSN: 1662-453X
Multiple sclerosis (MS) is an inflammatory and demyelinating neurological disease of the central nervous system. Image-based biomarkers, such as lesions defined on magnetic resonance imaging (MRI), play an important role in MS diagnosis and patient monitoring. The detection of newly formed lesions provides crucial information for assessing disease progression and treatment outcome. Here, we propose a deep learning-based pipeline for new MS lesion detection and segmentation, which is built upon the nnU-Net framework. In addition to conventional data augmentation, we employ imaging and lesion-aware data augmentation methods, axial subsampling and CarveMix, to generate diverse samples and improve segmentation performance. The proposed pipeline is evaluated on the MICCAI 2021 MS new lesion segmentation challenge (MSSEG-2) dataset. It achieves an average Dice score of 0.510 and F1 score of 0.552 on cases with new lesions, and an average false positive lesion number nFP of 0.036 and false positive lesion volume VFP of 0.192 mm3 on cases with no new lesions. Our method outperforms other participating methods in the challenge and several state-of-the-art network architectures.
Wang S, Qin C, Wang C, et al., 2022, The Extreme Cardiac MRI Analysis Challenge under Respiratory Motion (CMRxMotion)
The quality of cardiac magnetic resonance (CMR) imaging is susceptible torespiratory motion artifacts. The model robustness of automated segmentationtechniques in face of real-world respiratory motion artifacts is unclear. Thismanuscript describes the design of extreme cardiac MRI analysis challenge underrespiratory motion (CMRxMotion Challenge). The challenge aims to establish apublic benchmark dataset to assess the effects of respiratory motion on imagequality and examine the robustness of segmentation models. The challengerecruited 40 healthy volunteers to perform different breath-hold behaviorsduring one imaging visit, obtaining paired cine imaging with artifacts.Radiologists assessed the image quality and annotated the level of respiratorymotion artifacts. For those images with diagnostic quality, radiologistsfurther segmented the left ventricle, left ventricle myocardium and rightventricle. The images of training set (20 volunteers) along with theannotations are released to the challenge participants, to develop an automatedimage quality assessment model (Task 1) and an automated segmentation model(Task 2). The images of validation set (5 volunteers) are released to thechallenge participants but the annotations are withheld for online evaluationof submitted predictions. Both the images and annotations of the test set (15volunteers) were withheld and only used for offline evaluation of submittedcontainerized dockers. The image quality assessment task is quantitativelyevaluated by the Cohen's kappa statistics and the segmentation task isevaluated by the Dice scores and Hausdorff distances.
Shah M, Inácio MHDA, Lu C, et al., 2022, Environmental and genetic predictors of human cardiovascular ageing
<jats:title>ABSTRACT</jats:title><jats:p>Cardiovascular ageing is a process that begins early in life and leads to a progressive change in structure and decline in function due to accumulated damage across diverse cell types, tissues and organs contributing to multi-morbidity. Damaging biophysical, metabolic and immunological factors exceed endogenous repair mechanisms resulting in a pro-fibrotic state, cellular senescence and end-organ damage, however the genetic architecture of cardiovascular ageing is not known. Here we used machine learning approaches to quantify cardiovascular age from image-derived traits of vascular function, cardiac motion and myocardial fibrosis, as well as conduction traits from electrocardiograms, in 39,559 participants of UK Biobank. Cardiovascular ageing was found to be significantly associated with common or rare variants in genes regulating sarcomere homeostasis, myocardial immunomodulation, and tissue responses to biophysical stress. Ageing is accelerated by cardiometabolic risk factors and we also identified prescribed medications that were potential modifiers of ageing. Through large-scale modelling of ageing across multiple traits our results reveal insights into the mechanisms driving premature cardiovascular ageing and reveal potential molecular targets to attenuate age-related processes.</jats:p>
Basaran BD, Qiao M, Matthews P, et al., 2022, Subject-specific lesion generation and pseudo-healthy synthesis for multiple sclerosis brain images, SASHIMI: Simulation and Synthesis in Medical Imaging, Publisher: Springer, ISSN: 0302-9743
Understanding the intensity characteristics of brain lesions is key for defining image-based biomarkers in neurological studies and for predicting disease burden and outcome. In this work, we present a novel foreground-based generative method for modelling the local lesion characteristics that can both generate synthetic lesions on healthy images and synthesize subject-specific pseudo-healthy images from pathological images. Furthermore, the proposed method can be used as a data augmentation module to generate synthetic images for training brain image segmentation networks. Experiments on multiple sclerosis (MS) brain images acquired on magnetic resonance imaging (MRI) demonstrate that the proposed method can generate highly realistic pseudo-healthy and pseudo-pathological brain images. Data augmentation using the synthetic images improves the brain image segmentation performance compared to traditional data augmentation methods as well as a recent lesion-aware data augmentation technique, CarveMix. The code will be released at https://github.com/dogabasaran/lesion-synthesis.
Chen C, Li Z, Ouyang C, et al., 2022, MaxStyle: adversarial style composition for robust medical image segmentation, Medical Image Computing and Computer Assisted Interventions (MICCAI) 2022
Convolutional neural networks (CNNs) have achieved remarkable segmentationaccuracy on benchmark datasets where training and test sets are from the samedomain, yet their performance can degrade significantly on unseen domains,which hinders the deployment of CNNs in many clinical scenarios. Most existingworks improve model out-of-domain (OOD) robustness by collecting multi-domaindatasets for training, which is expensive and may not always be feasible due toprivacy and logistical issues. In this work, we focus on improving modelrobustness using a single-domain dataset only. We propose a novel dataaugmentation framework called MaxStyle, which maximizes the effectiveness ofstyle augmentation for model OOD performance. It attaches an auxiliarystyle-augmented image decoder to a segmentation network for robust featurelearning and data augmentation. Importantly, MaxStyle augments data withimproved image style diversity and hardness, by expanding the style space withnoise and searching for the worst-case style composition of latent features viaadversarial training. With extensive experiments on multiple public cardiac andprostate MR datasets, we demonstrate that MaxStyle leads to significantlyimproved out-of-distribution robustness against unseen corruptions as well ascommon distribution shifts across multiple, different, unseen sites and unknownimage sequences under both low- and high-training data settings. The code canbe found at https://github.com/cherise215/MaxStyle.
Francis C, Futschik M, Huang J, et al., 2022, Genome-wide associations of aortic distensibility suggest causality for aortic aneurysms and brain white matter hyperintensities, Nature Communications, Vol: 13, ISSN: 2041-1723
Aortic dimensions and distensibility are key risk factors for aortic aneurysms and dissections, as well as for other cardiovascular and cerebrovascular diseases. We present genome-wide associations of ascending and descending aortic distensibility and area derived from cardiac magnetic resonance imaging (MRI) data of up to 32,590 Caucasian individuals in UK Biobank. We identify 102 loci (including 27 novel associations) tagging genes related to cardiovascular development, extracellular matrix production, smooth muscle cell contraction and heritable aortic diseases. Functional analyses highlight four signalling pathways associated with aortic distensibility (TGF-, IGF, VEGF and PDGF). We identify distinct sex-specific associations with aortic traits. We develop co-expression networks associated with aortic traits and apply phenome-wide Mendelian randomization (MR-PheWAS), generating evidence for a causal role for aortic distensibility in development of aortic aneurysms. Multivariable MR suggests a causal relationship between aortic distensibility and cerebral white matter hyperintensities, mechanistically linking aortic traits and brain small vessel disease.
Meng Q, Bai W, Liu T, et al., 2022, MulViMotion: shape-aware 3D myocardial motion tracking from multi-view cardiac MRI, IEEE Transactions on Medical Imaging, Vol: 41, Pages: 1961-1974, ISSN: 0278-0062
Recovering the 3D motion of the heart from cine cardiac magnetic resonance (CMR) imaging enables the assessment of regional myocardial function and is important for understanding and analyzing cardiovascular disease. However, 3D cardiac motion estimation is challenging because the acquired cine CMR images are usually 2D slices which limit the accurate estimation of through-plane motion. To address this problem, we propose a novel multi-view motion estimation network (MulViMotion), which integrates 2D cine CMR images acquired in short-axis and long-axis planes to learn a consistent 3D motion field of the heart. In the proposed method, a hybrid 2D/3D network is built to generate dense 3D motion fields by learning fused representations from multi-view images. To ensure that the motion estimation is consistent in 3D, a shape regularization module is introduced during training, where shape information from multi-view images is exploited to provide weak supervision to 3D motion estimation. We extensively evaluate the proposed method on 2D cine CMR images from 580 subjects of the UK Biobank study for 3D motion tracking of the left ventricular myocardium. Experimental results show that the proposed method quantitatively and qualitatively outperforms competing methods.
Wang Y, Blackie L, Miguel-Aliaga I, et al., 2022, Memory-efficient segmentation of high-resolution volumetric MicroCTimages, Publisher: ArXiv
In recent years, 3D convolutional neural networks have become the dominantapproach for volumetric medical image segmentation. However, compared to their2D counterparts, 3D networks introduce substantially more training parametersand higher requirement for the GPU memory. This has become a major limitingfactor for designing and training 3D networks for high-resolution volumetricimages. In this work, we propose a novel memory-efficient network architecturefor 3D high-resolution image segmentation. The network incorporates both globaland local features via a two-stage U-net-based cascaded framework and at thefirst stage, a memory-efficient U-net (meU-net) is developed. The featureslearnt at the two stages are connected via post-concatenation, which furtherimproves the information flow. The proposed segmentation method is evaluated onan ultra high-resolution microCT dataset with typically 250 million voxels pervolume. Experiments show that it outperforms state-of-the-art 3D segmentationmethods in terms of both segmentation accuracy and memory efficiency.
Thanaj M, Mielke J, McGurk K, et al., 2022, Genetic and environmental determinants of diastolic heart function, Nature Cardiovascular Research, Vol: 1, Pages: 361-371, ISSN: 2731-0590
Diastole is the sequence of physiological events that occur in the heart during ventricular filling and principally depends onmyocardial relaxation and chamber stiffness. Abnormal diastolic function is related to many cardiovascular disease processesand is predictive of health outcomes, but its genetic architecture is largely unknown. Here, we use machine learning cardiacmotion analysis to measure diastolic functional traits in 39,559 participants of the UK Biobank and perform a genome-wideassociation study. We identified 9 significant, independent loci near genes that are associated with maintaining sarcomericfunction under biomechanical stress and genes implicated in the development of cardiomyopathy. Age, sex and diabetes wereindependent predictors of diastolic function and we found a causal relationship between genetically-determined ventricularstiffness and incident heart failure. Our results provide insights into the genetic and environmental factors influencing diastolicfunction that are relevant for identifying causal relationships and potential tractable targets.
Zhang D, Barbot A, Seichepine F, et al., 2022, Micro-object pose estimation with sim-to-real transfer learning using small dataset, Communications Physics, Vol: 5, ISSN: 2399-3650
Davies RH, Augusto JB, Bhuva A, et al., 2022, Precision measurement of cardiac structure and function in cardiovascular magnetic resonance using machine learning, Journal of Cardiovascular Magnetic Resonance, Vol: 24, ISSN: 1097-6647
BackgroundMeasurement of cardiac structure and function from images (e.g. volumes, mass and derived parameters such as left ventricular (LV) ejection fraction [LVEF]) guides care for millions. This is best assessed using cardiovascular magnetic resonance (CMR), but image analysis is currently performed by individual clinicians, which introduces error. We sought to develop a machine learning algorithm for volumetric analysis of CMR images with demonstrably better precision than human analysis.MethodsA fully automated machine learning algorithm was trained on 1923 scans (10 scanner models, 13 institutions, 9 clinical conditions, 60,000 contours) and used to segment the LV blood volume and myocardium. Performance was quantified by measuring precision on an independent multi-site validation dataset with multiple pathologies with n = 109 patients, scanned twice. This dataset was augmented with a further 1277 patients scanned as part of routine clinical care to allow qualitative assessment of generalization ability by identifying mis-segmentations. Machine learning algorithm (‘machine’) performance was compared to three clinicians (‘human’) and a commercial tool (cvi42, Circle Cardiovascular Imaging).FindingsMachine analysis was quicker (20 s per patient) than human (13 min). Overall machine mis-segmentation rate was 1 in 479 images for the combined dataset, occurring mostly in rare pathologies not encountered in training. Without correcting these mis-segmentations, machine analysis had superior precision to three clinicians (e.g. scan-rescan coefficients of variation of human vs machine: LVEF 6.0% vs 4.2%, LV mass 4.8% vs. 3.6%; both P < 0.05), translating to a 46% reduction in required trial sample size using an LVEF endpoint.ConclusionWe present a fully automated algorithm for measuring LV structure and global systolic function that betters human performance for speed and precision.
Meng Q, Bai W, Liu T, et al., 2022, Multiview Motion Estimation for 3D cardiac motion tracking
Code for paper ''MulViMotion: Shape-aware 3D Myocardial Motion Tracking from Multi-View Cardiac MRI''
Dai C, Wang S, Mo Y, et al., 2022, Suggestive annotation of brain MR images with gradient-guided sampling, Medical Image Analysis, Vol: 77, Pages: 1-12, ISSN: 1361-8415
Machine learning has been widely adopted for medical image analysis in recent years given its promising performance in image segmentation and classification tasks. The success of machine learning, in particular supervised learning, depends on the availability of manually annotated datasets. For medical imaging applications, such annotated datasets are not easy to acquire, it takes a substantial amount of time and resource to curate an annotated medical image set. In this paper, we propose an efficient annotation framework for brain MR images that can suggest informative sample images for human experts to annotate. We evaluate the framework on two different brain image analysis tasks, namely brain tumour segmentation and whole brain segmentation. Experiments show that for brain tumour segmentation task on the BraTS 2019 dataset, training a segmentation model with only 7% suggestively annotated image samples can achieve a performance comparable to that of training on the full dataset. For whole brain segmentation on the MALC dataset, training with 42% suggestively annotated image samples can achieve a comparable performance to training on the full dataset. The proposed framework demonstrates a promising way to save manual annotation cost and improve data efficiency in medical imaging applications.
Zaydullin R, Bharath AA, Grisan E, et al., 2022, Motion Correction Using Deep Learning Neural Networks - Effects of Data Representation, IEEE International Ultrasonics Symposium (IUS), Publisher: IEEE, ISSN: 1948-5719
Ouyang C, Wang S, Chen C, et al., 2022, Improved Post-hoc Probability Calibration for Out-of-Domain MRI Segmentation, 4th International Workshop on Uncertainty for Safe Utilization of Machine Learning in Medical Imaging (UNSURE), Publisher: SPRINGER INTERNATIONAL PUBLISHING AG, Pages: 59-69, ISSN: 0302-9743
Qiao M, Basaran BD, Qiu H, et al., 2022, Generative Modelling of the Ageing Heart with Cross-Sectional Imaging and Clinical Data, Pages: 3-12, ISSN: 0302-9743
Cardiovascular disease, the leading cause of death globally, is an age-related disease. Understanding the morphological and functional changes of the heart during ageing is a key scientific question, the answer to which will help us define important risk factors of cardiovascular disease and monitor disease progression. In this work, we propose a novel conditional generative model to describe the changes of 3D anatomy of the heart during ageing. The proposed model is flexible and allows integration of multiple clinical factors (e.g. age, gender) into the generating process. We train the model on a large-scale cross-sectional dataset of cardiac anatomies and evaluate on both cross-sectional and longitudinal datasets. The model demonstrates excellent performance in predicting the longitudinal evolution of the ageing heart and modelling its data distribution. The codes are available at https://github.com/MengyunQ/AgeHeart.
Meng Q, Bai W, Liu T, et al., 2022, Mesh-Based 3D Motion Tracking in Cardiac MRI Using Deep Learning, 25th International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI), Publisher: SPRINGER INTERNATIONAL PUBLISHING AG, Pages: 248-258, ISSN: 0302-9743
Venkataraman AV, Bai W, Whittington A, et al., 2021, Boosting the diagnostic power of amyloid-β PET using a data-driven spatially informed classifier for decision support, Alzheimer's Research and Therapy, Vol: 13, Pages: 1-12, ISSN: 1758-9193
BackgroundAmyloid-β (Aβ) PET has emerged as clinically useful for more accurate diagnosis of patients with cognitive decline. Aβ deposition is a necessary cause or response to the cellular pathology of Alzheimer’s disease (AD). Usual clinical and research interpretation of amyloid PET does not fully utilise all information regarding the spatial distribution of signal. We present a data-driven, spatially informed classifier to boost the diagnostic power of amyloid PET in AD.MethodsVoxel-wise k-means clustering of amyloid-positive voxels was performed; clusters were mapped to brain anatomy and tested for their associations by diagnostic category and disease severity with 758 amyloid PET scans from volunteers in the AD continuum from the Alzheimer’s Disease Neuroimaging Initiative (ADNI). A machine learning approach based on this spatially constrained model using an optimised quadratic support vector machine was developed for automatic classification of scans for AD vs non-AD pathology.ResultsThis classifier boosted the accuracy of classification of AD scans to 81% using the amyloid PET alone with an area under the curve (AUC) of 0.91 compared to other spatial methods. This increased sensitivity to detect AD by 15% and the AUC by 9% compared to the use of a composite region of interest SUVr.ConclusionsThe diagnostic classification accuracy of amyloid PET was improved using an automated data-driven spatial classifier. Our classifier highlights the importance of considering the spatial variation in Aβ PET signal for optimal interpretation of scans. The algorithm now is available to be evaluated prospectively as a tool for automated clinical decision support in research settings.
De Marvao A, McGurk K, Zheng S, et al., 2021, Outcomes and phenotypic expression of rare variants in hypertrophic cardiomyopathy genes in over 200,000 adults, ESC Congress 2021, Publisher: European Society of Cardiology, Pages: 1731-1731, ISSN: 0195-668X
BackgroundHypertrophic cardiomyopathy (HCM) is caused by rare variants in sarcomere-encoding genes, but little is known about the clinical significance of these variants in the general population.PurposeTo determine the population prevalence of HCM-associated sarcomeric variants, characterise their phenotypic manifestations, estimate penetrance, and identify associations between sarcomeric variants and clinical outcomes, we performed an observational study of 218,813 adults in the UK Biobank (UKBB), of whom 200,584 have whole exome sequencing (WES).MethodsWe carried out an integrated analysis of WES and cardiac magnetic resonance (CMR) imaging in UK Biobank participants stratified by sarcomere-encoding variant status. Computer vision techniques were used to automatically segment the four chambers of the heart (Figure 1). Cardiac motion analysis was used to derive strain and strain rates. Regional analysis of left ventricular wall thickness was performed using three-dimensional modelling of these segmentations.ResultsMedian age at recruitment was 58 (IQR 50–63 years), and participants were followed up for a median of 10.8 years (IQR 9.9–11.6 years) with a total of 19,507 primary clinical events reported.The prevalence of rare variants (allele frequency <0.ehab724.17314) in HCM-associated sarcomere-encoding genes in 200,584 participants was 2.9% (n=5,727; 1 in 35), and the prevalence of pathogenic or likely pathogenic variants (SARC-P/LP) was 0.24% (n=474, 1 in 423).SARC-P/LP variants were associated with increased risk of death or major adverse cardiac events (MACE) compared to controls (HR 1.68, 95% CI 1.37–2.06, p<0.001), mainly due to heart failure endpoints (Figure 2: cumulative hazard curves with zoomed plots for lifetime risk of A) death and MACE or B) heart failure, stratified by genotype; genotype negative (SARC-NEG), carriers of indeterminate sarcomeric variants (SARC-IND) or SARC-P/LP; C) Forest plot of comparative lifetime risk of c
Chen C, Hammernik K, Ouyang C, et al., 2021, Cooperative training and latent space data augmentation for robust medical image segmentation, International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI)
Wang S, Qin C, Savioli N, et al., 2021, Joint motion correction and super resolution for cardiac segmentationvia latent optimisation, International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI), Publisher: Springer, Pages: 14-24
In cardiac magnetic resonance (CMR) imaging, a 3D high-resolution segmentation of the heart is essential for detailed description of its anatomical structures. However, due to the limit of acquisition duration andrespiratory/cardiac motion, stacks of multi-slice 2D images are acquired inclinical routine. The segmentation of these images provides a low-resolution representation of cardiac anatomy, which may contain artefacts caused by motion. Here we propose a novel latent optimisation framework that jointly performs motion correction and super resolution for cardiac image segmentations. Given a low-resolution segmentation as input, the framework accounts for inter-slice motion in cardiac MR imaging and super-resolves the input into a high-resolution segmentation consistent with input. A multi-view loss is incorporated to leverage information from both short-axis view and long-axis view of cardiac imaging. To solve the inverse problem, iterative optimisation is performed in a latent space, which ensures the anatomical plausibility. This alleviates the need of paired low-resolution and high-resolution images for supervised learning. Experiments on two cardiac MR datasets show that the proposed framework achieves high performance, comparable to state-of-the-art super-resolution approaches and with better cross-domain generalisability and anatomical plausibility.
Simoes Monteiro de Marvao A, McGurk K, Zheng S, et al., 2021, Phenotypic expression and outcomes in individuals with rare genetic variants of hypertrophic cardiomyopathy, Journal of the American College of Cardiology, Vol: 78, Pages: 1097-1110, ISSN: 0735-1097
Background: Hypertrophic cardiomyopathy (HCM) is caused by rare variants in sarcomereencoding genes, but little is known about the clinical significance of these variants in thegeneral population.Objectives: To compare lifetime outcomes and cardiovascular phenotypes according to thepresence of rare variants in sarcomere-encoding genes amongst middle-aged adults.Methods: We analysed whole exome sequencing and cardiac magnetic resonance (CMR)imaging in UK Biobank participants stratified by sarcomere-encoding variant status.Results: The prevalence of rare variants (allele frequency <0.00004) in HCM-associatedsarcomere-encoding genes in 200,584 participants was 2.9% (n=5,712; 1 in 35), and theprevalence of variants pathogenic or likely pathogenic for HCM (SARC-HCM-P/LP) was0.25% (n=493, 1 in 407). SARC-HCM-P/LP variants were associated with increased risk ofdeath or major adverse cardiac events compared to controls (HR 1.69, 95% CI 1.38 to 2.07,p<0.001), mainly due to heart failure endpoints (HR 4.23, 95% CI 3.07 to 5.83, p<0.001). In21,322 participants with CMR, SARC-HCM-P/LP were associated with asymmetric increasein left ventricular maximum wall thickness (10.9±2.7 vs 9.4±1.6 mm, p<0.001) buthypertrophy (≥13mm) was only present in 18.4% (n=9/49, 95% CI 9 to 32%). SARC-HCMP/LP were still associated with heart failure after adjustment for wall thickness (HR 6.74,95% CI 2.43 to 18.7, p<0.001).Conclusions: In this population of middle-aged adults, SARC-HCM-P/LP variants have lowaggregate penetrance for overt HCM but are associated with increased risk of adversecardiovascular outcomes and an attenuated cardiomyopathic phenotype. Although absoluteevent rates are low, identification of these variants may enhance risk stratification beyondfamilial disease.
Savioli N, Marvao AD, Bai W, et al., 2021, Joint Semi-supervised 3D Super-Resolution and Segmentation with Mixed Adversarial Gaussian Domain Adaptation
Optimising the analysis of cardiac structure and function requires accurate3D representations of shape and motion. However, techniques such as cardiacmagnetic resonance imaging are conventionally limited to acquiring contiguouscross-sectional slices with low through-plane resolution and potentialinter-slice spatial misalignment. Super-resolution in medical imaging aims toincrease the resolution of images but is conventionally trained on featuresfrom low resolution datasets and does not super-resolve correspondingsegmentations. Here we propose a semi-supervised multi-task generativeadversarial network (Gemini-GAN) that performs joint super-resolution of theimages and their labels using a ground truth of high resolution 3D cines andsegmentations, while an unsupervised variational adversarial mixtureautoencoder (V-AMA) is used for continuous domain adaptation. Our proposedapproach is extensively evaluated on two transnational multi-ethnic populationsof 1,331 and 205 adults respectively, delivering an improvement on state of theart methods in terms of Dice index, peak signal to noise ratio, and structuralsimilarity index measure. This framework also exceeds the performance of stateof the art generative domain adaptation models on external validation (Diceindex 0.81 vs 0.74 for the left ventricle). This demonstrates how jointsuper-resolution and segmentation, trained on 3D ground-truth data withcross-domain generalization, enables robust precision phenotyping in diversepopulations.
Thanaj M, Mielke J, McGurk KA, et al., 2021, Genetic and environmental determinants of diastolic heart function, Publisher: Cold Spring Harbor Laboratory
<jats:title>ABSTRACT</jats:title><jats:p>Diastole is the sequence of physiological events that occur in the heart during ventricular filling and principally depends on myocardial relaxation and chamber stiffness. Abnormal diastolic function is related to many cardiovascular disease processes and is predictive of health outcomes, but its genetic architecture is largely unknown. Here, we use machine learning cardiac motion analysis to measure diastolic functional traits in 39,559 participants of UK Biobank and perform a genome-wide association study. We identified 9 significant, independent loci near genes that are associated with maintaining sarcomeric function under biomechanical stress and genes implicated in the development of cardiomyopathy. Age, sex and diabetes were independent predictors of diastolic function and we found a causal relationship between ventricular stiffness and heart failure. Our results provide novel insights into the genetic and environmental factors influencing diastolic function that are relevant for identifying causal relationships and tractable targets in heart failure.</jats:p>
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