Imperial College London

DrWenjiaBai

Faculty of MedicineDepartment of Brain Sciences

Lecturer in Artificial Intelligence in Medicine
 
 
 
//

Contact

 

+44 (0)20 7594 8291w.bai Website

 
 
//

Location

 

Room 212, Data Science InstituteWilliam Penney LaboratorySouth Kensington Campus

//

Summary

 

Publications

Publication Type
Year
to

134 results found

Wang S, Qin C, Savioli N, Chen C, O'Regan D, Cook S, Guo Y, Rueckert D, Bai Wet al., 2021, Joint motion correction and super resolution for cardiac segmentationvia latent optimisation, International Conference on Medical Image Computing and Computer Assisted Intervention

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.

Conference paper

Chen C, Hammernik K, Ouyang C, Qin C, Bai W, Rueckert Det al., 2021, Cooperative training and latent space data augmentation for robust medical image segmentation, International Conference on Medical Image Computing and Computer Assisted Intervention

Conference paper

Simoes Monteiro de Marvao A, McGurk K, Zheng S, Thanaj M, Bai W, Duan J, Biffi C, Mazzarotto F, Statton B, Dawes T, Savioli N, Halliday B, Xu X, Buchan R, Baksi A, Quinlan M, Tokarczuk P, Tayal U, Francis C, Whiffin N, Theotokis A, Zhang X, Jang M, Berry A, Pantazis A, Barton P, Rueckert D, Prasad S, Walsh R, Ho C, Cook S, Ware J, O'Regan Det al., 2021, Phenotypic expression and outcomes in individuals with rare genetic variants of hypertrophic cardiomyopathy, Journal of the American College of Cardiology, 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.

Journal article

Evangelou E, Suzuki H, Bai W, Pazoki R, Gao H, Matthews P, Elliott Pet al., 2021, Alcohol consumption in the general population is associated with structural changes in multiple organ systems., eLife, Vol: 10, Pages: 1-15, ISSN: 2050-084X

Background:Excessive alcohol consumption is associated with damage to various organs, but its multi-organ effects have not been characterised across the usual range of alcohol drinking in a large general population sample.Methods:We assessed global effect sizes of alcohol consumption on quantitative magnetic resonance imaging phenotypic measures of the brain, heart, aorta, and liver of UK Biobank participants who reported drinking alcohol.Results:We found a monotonic association of higher alcohol consumption with lower normalised brain volume across the range of alcohol intakes (–1.7 × 10−3 ± 0.76 × 10−3 per doubling of alcohol consumption, p=3.0 × 10−14). Alcohol consumption was also associated directly with measures of left ventricular mass index and left ventricular and atrial volume indices. Liver fat increased by a mean of 0.15% per doubling of alcohol consumption.Conclusions:Our results imply that there is not a ‘safe threshold’ below which there are no toxic effects of alcohol. Current public health guidelines concerning alcohol consumption may need to be revisited.

Journal article

Lu P, Bai W, Rueckert D, Noble JAet al., 2021, Dynamic spatio-temporal graph convolutional networks for cardiac motion analysis, Pages: 122-125, ISSN: 1945-7928

We propose a dynamic spatio-temporal graph convolutional network (DST-GCN) approach to learn the left ventricular (LV) motion patterns from cardiac MR cine images. We represent the myocardial geometry using a graph that is constructed from sample nodes on endo-and epicardial contours. The DST-GCN follows an encoder-decoder framework. The encoder accepts a given cardiac motion represented by a sequence of ST-GCN. The decoder employs a graph-based gated recurrent unit (G-GRU) to predict future cardiac motion. We show that the DST-GCN can automatically quantify the spatio-temporal patterns in cardiac MR that characterise cardiac motion. Experiments are performed on the UK Biobank dataset. We compare four methods from two architecture variances. Experiments show that the proposed method inputting node velocities with residual connection in the decoder outperform others, and achieves a mean squared error of 0.135 pixel between the ground truth node locations and our prediction.

Conference paper

Balaban G, Halliday B, Bradley P, Bai W, Nygaard S, Owen R, Hatipoglu S, Ferreira ND, Izgi C, Tayal U, Corden B, Ware J, Pennell D, Rueckert D, Plank G, Rinaldi CA, Prasad SK, Bishop Met al., 2021, Late-gadolinium enhancement interface area and electrophysiological simulations predict arrhythmic events in non-ischemic dilated cardiomyopathy patients, JACC: Clinical Electrophysiology, Vol: 7, Pages: 238-249, ISSN: 2405-5018

BACKGROUND: The presence of late-gadolinium enhancement (LGE) predicts life threatening ventricular arrhythmias in non-ischemic dilated cardiomyopathy (NIDCM); however, risk stratification remains imprecise. LGE shape and simulations of electrical activity may be able to provide additional prognostic information.OBJECTIVE: This study sought to investigate whether shape-based LGE metrics and simulations of reentrant electrical activity are associated with arrhythmic events in NIDCM patients.METHODS: CMR-LGE shape metrics were computed for a cohort of 156 NIDCM patients with visible LGE and tested retrospectively for an association with an arrhythmic composite end-point of sudden cardiac death and ventricular tachycardia. Computational models were created from images and used in conjunction with simulated stimulation protocols to assess the potential for reentry induction in each patient’s scar morphology. A mechanistic analysis of the simulations was carried out to explain the associations. RESULTS: During a median follow-up of 1611 [IQR 881-2341] days, 16 patients (10.3%) met the primary endpoint. In an inverse probability weighted Cox regression, the LGE-myocardial interface area (HR:1.75; 95% CI:1.24-2.47; p=0.001), number of simulated reentries (HR: 1.4; 95% CI: 1.23-1.59; p<0.01) and LGE volume (HR:1.44; 95% CI:1.07-1.94; p=0.02) were associated with arrhythmic events. Computational modeling revealed repolarisation heterogeneity and rate-dependent block of electrical wavefronts at the LGE-myocardial interface as putative arrhythmogenic mechanisms directly related to LGE interface area.CONCLUSION: The area of interface between scar and surviving myocardium, as well as simulated reentrant activity, are associated with an elevated risk of major arrhythmic events in NIDCM patients with LGE and represent novel risk predictors.

Journal article

de Marvao A, McGurk KA, Zheng SL, Thanaj M, Bai W, Duan J, Biffi C, Mazzarotto F, Statton B, Dawes TJW, Savioli N, Halliday BP, Xu X, Buchan RJ, Baksi AJ, Quinlan M, Tokarczuk P, Tayal U, Francis C, Whiffin N, Theotokis PI, Zhang X, Jang M, Berry A, Pantazis A, Barton PJR, Rueckert D, Prasad SK, Walsh R, Ho CY, Cook SA, Ware JS, ORegan DPet al., 2021, Outcomes and phenotypic expression of rare variants in hypertrophic cardiomyopathy genes amongst UK Biobank participants, Publisher: Cold Spring Harbor Laboratory

<jats:title>Abstract</jats:title><jats:sec><jats:title>Background</jats:title><jats:p>Hypertrophic 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.</jats:p></jats:sec><jats:sec><jats:title>Methods</jats:title><jats:p>We compared outcomes and cardiovascular phenotypes in UK Biobank participants with whole exome sequencing stratified by sarcomere-encoding variant status.</jats:p></jats:sec><jats:sec><jats:title>Results</jats:title><jats:p>The prevalence of rare variants (allele frequency &lt;0.00004) in HCM-associated sarcomere-encoding genes in 200,584 participants was 2.9% (n=5,727; 1 in 35), of which 0.24% (n=474, 1 in 423) were pathogenic or likely pathogenic variants (SARC-P/LP). SARC-P/LP variants were associated with increased risk of death or major adverse cardiac events compared to controls (HR 1.68, 95% CI 1.37-2.06, p&lt;0.001), mainly due to heart failure (HR 4.40, 95% CI 3.22-6.02, p&lt;0.001) and arrhythmia (HR 1.55, 95% CI 1.18-2.03, p=0.002). In 21,322 participants with cardiac magnetic resonance imaging, SARC-P/LP were associated with increased left ventricular maximum wall thickness (10.9±2.7 vs 9.4±1.6 mm, p&lt;0.001) and concentric remodelling (mass/volume ratio: 0.63±0.12 vs 0.58±0.09 g/mL, p&lt;0.001), but hypertrophy (≥13mm) was only present in 16% (n=7/43, 95% CI 7-31%). Other rare sarcomere-encoding variants had a weak effect on wall thickness (9.5±1.7 vs 9.4±1.6 mm, p=0.002) with no combined excess cardiovascular risk (HR 1.00 95% CI 0.92-1.08, p=0.9).</jats:p></jats:sec><jats:sec><jats:title>Conclusions</jats:title><jats:p>In the general population, SARC-P/LP variants have low aggregate penetrance for overt HCM bu

Working paper

Tadros R, Francis C, Xu X, Vermeer AMC, Harper AR, Huurman R, Bisabu KK, Walsh R, Hoorntje ET, te Rijdt WP, Buchan RJ, van Velzen HG, van Slegtenhorst MA, Vermeulen JM, Offerhaus JA, Bai W, de Marvao A, Lahrouchi N, Beekman L, Karper JC, Veldink JH, Kayvanpour E, Pantazis A, Baksi AJ, Whiffin N, Mazzarotto F, Sloane G, Suzuki H, Schneider-Luftman D, Elliott P, Richard P, Ader F, Villard E, Lichtner P, Meitinger T, Tanck MWT, van Tintelen JP, Thain A, McCarty D, Hegele RA, Roberts JD, Amyot J, Dube M-P, Cadrin-Tourigny J, Giraldeau G, L'Allier PL, Garceau P, Tardif J-C, Boekholdt SM, Lumbers RT, Asselbergs FW, Barton PJR, Cook SA, Prasad SK, O'Regan DP, van der Velden J, Verweij KJH, Talajic M, Lettre G, Pinto YM, Meder B, Charron P, de Boer RA, Christiaans I, Michels M, Wilde AAM, Watkins H, Matthews PM, Ware JS, Bezzina CRet al., 2021, Shared genetic pathways contribute to risk of hypertrophic and dilated cardiomyopathies with opposite directions of effect, NATURE GENETICS, Vol: 53, Pages: 128-+, ISSN: 1061-4036

Journal article

Lu P, Bai W, Rueckert D, Noble JAet al., 2021, Modelling Cardiac Motion via Spatio-Temporal Graph Convolutional Networks to Boost the Diagnosis of Heart Conditions, Pages: 56-65, ISSN: 0302-9743

We present a novel spatio-temporal graph convolutional networks (ST-GCN) approach to learn spatio-temporal patterns of left ventricular (LV) motion in cardiac MR cine images for improving the characterization of heart conditions. Specifically, a novel GCN architecture is used, where the sample nodes of endocardial and epicardial contours are connected as a graph to represent the myocardial geometry. We show that the ST-GCN can automatically quantify the spatio-temporal patterns in cine MR that characterise cardiac motion. Experiments are performed on healthy volunteers from the UK Biobank dataset. We compare different strategies for constructing cardiac structure graphs. Experiments show that the proposed methods perform well in estimating endocardial radii and characterising cardiac motion features for regional LV analysis.

Conference paper

Lu P, Bai W, Rueckert D, Noble JAet al., 2021, Multiscale Graph Convolutional Networks for Cardiac Motion Analysis, Pages: 264-272, ISBN: 9783030787097

We propose a multiscale spatio-temporal graph convolutional network (MST-GCN) approach to learn the left ventricular (LV) motion patterns from cardiac MR image sequences. The MST-GCN follows an encoder-decoder framework. The encoder uses a sequence of multiscale graph computation units (MGCUs). The myocardial geometry is represented as a graph. The network models the internal relations of the graph nodes via feature extraction at different scales and fuses the feature across scales to form a global representation of the input cardiac motion. Based on this, the decoder employs a graph-based gated recurrent unit (G-GRU) to predict future cardiac motion. We show that the MST-GCN can automatically quantify the spatio-temporal patterns in cardiac MR that characterise cardiac motion. Experiments are performed on mid-ventricular short-axis view cardiac MR image sequence from the UK Biobank dataset. We compare the performance of cardiac motion prediction of the proposed method with ten different architectures and parameter settings. Experiments show that the proposed method inputting node positions and node velocities with multiscale graphs achieves the best performance with a mean squared error of 0.25 pixel between the ground truth node locations and our prediction. We also show that the proposed method can estimate a number of motion-related metrics, including endocardial radii, thickness and strain which are useful for regional LV function assessment.

Book chapter

Dai C, Wang S, Raynaud H, Mo Y, Angelini E, Guo Y, Bai Wet al., 2021, Self-training for Brain Tumour Segmentation with Uncertainty Estimation and Biophysics-Guided Survival Prediction, Pages: 514-523, ISSN: 0302-9743

Gliomas are among the most common types of malignant brain tumours in adults. Given the intrinsic heterogeneity of gliomas, the multi-parametric magnetic resonance imaging (mpMRI) is the most effective technique for characterising gliomas and their sub-regions. Accurate segmentation of the tumour sub-regions on mpMRI is of clinical significance, which provides valuable information for treatment planning and survival prediction. Thanks to the recent developments on deep learning, the accuracy of automated medical image segmentation has improved significantly. In this paper, we leverage the widely used attention and self-training techniques to conduct reliable brain tumour segmentation and uncertainty estimation. Based on the segmentation result, we present a biophysics-guided prognostic model for the prediction of overall survival. Our method of uncertainty estimation has won the second place of the MICCAI 2020 BraTS Challenge.

Conference paper

Xiong Z, Xia Q, Hu Z, Huang N, Bian C, Zheng Y, Vesal S, Ravikumar N, Maier A, Yang X, Heng P-A, Ni D, Li C, Tong Q, Si W, Puybareau E, Khoudli Y, Geraud T, Chen C, Bai W, Rueckert D, Xu L, Zhuang X, Luo X, Jia S, Sermesant M, Liu Y, Wang K, Borra D, Masci A, Corsi C, de Vente C, Veta M, Karim R, Preetha CJ, Engelhardt S, Qiao M, Wang Y, Tao Q, Nunez-Garcia M, Camara O, Savioli N, Lamata P, Zhao Jet al., 2021, A global benchmark of algorithms for segmenting the left atrium from late gadolinium-enhanced cardiac magnetic resonance imaging, Medical Image Analysis, Vol: 67, Pages: 1-14, ISSN: 1361-8415

Segmentation of medical images, particularly late gadolinium-enhanced magnetic resonance imaging (LGE-MRI) used for visualizing diseased atrial structures, is a crucial first step for ablation treatment of atrial fibrillation. However, direct segmentation of LGE-MRIs is challenging due to the varying intensities caused by contrast agents. Since most clinical studies have relied on manual, labor-intensive approaches, automatic methods are of high interest, particularly optimized machine learning approaches. To address this, we organized the 2018 Left Atrium Segmentation Challenge using 154 3D LGE-MRIs, currently the world's largest atrial LGE-MRI dataset, and associated labels of the left atrium segmented by three medical experts, ultimately attracting the participation of 27 international teams. In this paper, extensive analysis of the submitted algorithms using technical and biological metrics was performed by undergoing subgroup analysis and conducting hyper-parameter analysis, offering an overall picture of the major design choices of convolutional neural networks (CNNs) and practical considerations for achieving state-of-the-art left atrium segmentation. Results show that the top method achieved a Dice score of 93.2% and a mean surface to surface distance of 0.7 mm, significantly outperforming prior state-of-the-art. Particularly, our analysis demonstrated that double sequentially used CNNs, in which a first CNN is used for automatic region-of-interest localization and a subsequent CNN is used for refined regional segmentation, achieved superior results than traditional methods and machine learning approaches containing single CNNs. This large-scale benchmarking study makes a significant step towards much-improved segmentation methods for atrial LGE-MRIs, and will serve as an important benchmark for evaluating and comparing the future works in the field. Furthermore, the findings from this study can potentially be extended to other imaging datasets and modalitie

Journal article

Bai W, Suzuki H, Huang J, Francis C, Wang S, Tarroni G, Guitton F, Aung N, Fung K, Petersen SE, Piechnik SK, Neubauer S, Evangelou E, Dehghan A, O'Regan DP, Wilkins MR, Guo Y, Matthews PM, Rueckert Det al., 2020, A population-based phenome-wide association study of cardiac and aortic structure and function, Nature Medicine, Vol: 26, Pages: 1654-1662, ISSN: 1078-8956

Differences in cardiac and aortic structure and function are associated with cardiovascular diseases and a wide range of other types of disease. Here we analyzed cardiovascular magnetic resonance images from a population-based study, the UK Biobank, using an automated machine-learning-based analysis pipeline. We report a comprehensive range of structural and functional phenotypes for the heart and aorta across 26,893 participants, and explore how these phenotypes vary according to sex, age and major cardiovascular risk factors. We extended this analysis with a phenome-wide association study, in which we tested for correlations of a wide range of non-imaging phenotypes of the participants with imaging phenotypes. We further explored the associations of imaging phenotypes with early-life factors, mental health and cognitive function using both observational analysis and Mendelian randomization. Our study illustrates how population-based cardiac and aortic imaging phenotypes can be used to better define cardiovascular disease risks as well as heart–brain health interactions, highlighting new opportunities for studying disease mechanisms and developing image-based biomarkers.

Journal article

Qin C, Wang S, Chen C, Qiu H, Bai W, Rueckert Det al., 2020, Biomechanics-informed neural networks for myocardial motion tracking in MRI, International Conference on Medical Image Computing and Computer-Assisted Intervention (MICCAI), Publisher: Springer International Publishing, Pages: 296-306, ISSN: 0302-9743

Image registration is an ill-posed inverse problem which often requires regularisation on the solution space. In contrast to most of the current approaches which impose explicit regularisation terms such as smoothness, in this paper we propose a novel method that can implicitly learn biomechanics-informed regularisation. Such an approach can incorporate application-specific prior knowledge into deep learning based registration. Particularly, the proposed biomechanics-informed regularisation leverages a variational autoencoder (VAE) to learn a manifold for biomechanically plausible deformations and to implicitly capture their underlying properties via reconstructing biomechanical simulations. The learnt VAE regulariser then can be coupled with any deep learning based registration network to regularise the solution space to be biomechanically plausible. The proposed method is validated in the context of myocardial motion tracking on 2D stacks of cardiac MRI data from two different datasets. The results show that it can achieve better performance against other competing methods in terms of motion tracking accuracy and has the ability to learn biomechanical properties such as incompressibility and strains. The method has also been shown to have better generalisability to unseen domains compared with commonly used L2 regularisation schemes.

Conference paper

Dai C, Wang S, Mo Y, Zhou K, Angelini E, Guo Y, Bai Wet al., 2020, Suggestive annotation of brain tumour images with gradient-guided sampling, International Conference on Medical Image Computing and Computer-Assisted Intervention (MICCAI), Publisher: Springer International Publishing, Pages: 156-165, ISSN: 0302-9743

Machine learning has been widely adopted for medical image analysis in recent years given its promising performance in image segmentation and classification tasks. As a data-driven science, the success of machine learning, in particular supervised learning, largely 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 tumour images that is able to suggest informative sample images for human experts to annotate. Our experiments show that training a segmentation model with only 19% suggestively annotated patient scans from BraTS 2019 dataset can achieve a comparable performance to training a model on the full dataset for whole tumour segmentation task. It demonstrates a promising way to save manual annotation cost and improve data efficiency in medical imaging applications.

Conference paper

Wang S, Tarroni G, Qin C, Mo Y, Dai C, Chen C, Glocker B, Guo Y, Rueckert D, Bai Wet al., 2020, Deep generative model-based quality control for cardiac MRI segmentation, International Conference on Medical Image Computing and Computer-Assisted Intervention (MICCAI), Publisher: Springer Verlag, Pages: 88-97, ISSN: 0302-9743

In recent years, convolutional neural networks have demonstrated promising performance in a variety of medical image segmentation tasks. However, when a trained segmentation model is deployed into the real clinical world, the model may not perform optimally. A major challenge is the potential poor-quality segmentations generated due to degraded image quality or domain shift issues. There is a timely need to develop an automated quality control method that can detect poor segmentations and feedback to clinicians. Here we propose a novel deep generative model-based framework for quality control of cardiac MRI segmentation. It first learns a manifold of good-quality image-segmentation pairs using a generative model. The quality of a given test segmentation is then assessed by evaluating the difference from its projection onto the good-quality manifold. In particular, the projection is refined through iterative search in the latent space. The proposed method achieves high prediction accuracy on two publicly available cardiac MRI datasets. Moreover, it shows better generalisation ability than traditional regression-based methods. Our approach provides a real-time and model-agnostic quality control for cardiac MRI segmentation, which has the potential to be integrated into clinical image analysis workflows.

Conference paper

Zhang D, Lo FP-W, Zheng J-Q, Bai W, Yang G-Z, Lo Bet al., 2020, Data-driven microscopic pose and depth estimation for optical microrobot manipulation, ACS Photonics, Vol: 7, Pages: 3003-3014, ISSN: 2330-4022

Optical microrobots have a wide range of applications in biomedical research for both in vitro and in vivo studies. In most microrobotic systems, the video captured by a monocular camera is the only way for visualizing the movements of microrobots, and only planar motion, in general, can be captured by a monocular camera system. Accurate depth estimation is essential for 3D reconstruction or autofocusing of microplatforms, while the pose and depth estimation are necessary to enhance the 3D perception of the microrobotic systems to enable dexterous micromanipulation and other tasks. In this paper, we propose a data-driven method for pose and depth estimation in an optically manipulated microrobotic system. Focus measurement is used to obtain features for Gaussian Process Regression (GPR), which enables precise depth estimation. For mobile microrobots with varying poses, a novel method is developed based on a deep residual neural network with the incorporation of prior domain knowledge about the optical microrobots encoded via GPR. The method can simultaneously track microrobots with complex shapes and estimate the pose and depth values of the optical microrobots. Cross-validation has been conducted to demonstrate the submicron accuracy of the proposed method and precise pose and depth perception for microrobots. We further demonstrate the generalizability of the method by adapting it to microrobots of different shapes using transfer learning with few-shot calibration. Intuitive visualization is provided to facilitate effective human-robot interaction during micromanipulation based on pose and depth estimation results.

Journal article

Meyer H, Dawes T, Serrani M, Bai W, Tokarczuk P, Cai J, Simoes Monteiro de Marvao A, Henry A, Lumbers T, Gierten J, Thumberger T, Wittbrodt J, Ware J, Rueckert D, Matthews P, Prasad S, Costantino M, Cook S, Birney E, O'Regan Det al., 2020, Genetic and functional insights into the fractal structure of the heart, Nature, Vol: 584, Pages: 589-594, ISSN: 0028-0836

The inner surfaces of the human heart are covered by a complex network of muscular strands that is thought to be a vestigeof embryonic development.1,2 The function of these trabeculae in adults and their genetic architecture are unknown. Toinvestigate this we performed a genome-wide association study using fractal analysis of trabecular morphology as animage-derived phenotype in 18,096 UK Biobank participants. We identified 16 significant loci containing genes associatedwith haemodynamic phenotypes and regulation of cytoskeletal arborisation.3,4 Using biomechanical simulations and humanobservational data, we demonstrate that trabecular morphology is an important determinant of cardiac performance. Throughgenetic association studies with cardiac disease phenotypes and Mendelian randomisation, we find a causal relationshipbetween trabecular morphology and cardiovascular disease risk. These findings suggest an unexpected role for myocardialtrabeculae in the function of the adult heart, identify conserved pathways that regulate structural complexity, and reveal theirinfluence on susceptibility to disease

Journal article

Chen C, Qin C, Qiu H, Ouyang C, Wang S, Chen L, Tarroni G, Bai W, Rueckert Det al., 2020, Realistic adversarial data augmentation for MR image segmentation, International Conference on Medical Image Computing and Computer-Assisted Intervention (MICCAI)

Neural network-based approaches can achieve high accuracy in various medicalimage segmentation tasks. However, they generally require large labelleddatasets for supervised learning. Acquiring and manually labelling a largemedical dataset is expensive and sometimes impractical due to data sharing andprivacy issues. In this work, we propose an adversarial data augmentationmethod for training neural networks for medical image segmentation. Instead ofgenerating pixel-wise adversarial attacks, our model generates plausible andrealistic signal corruptions, which models the intensity inhomogeneities causedby a common type of artefacts in MR imaging: bias field. The proposed methoddoes not rely on generative networks, and can be used as a plug-in module forgeneral segmentation networks in both supervised and semi-supervised learning.Using cardiac MR imaging we show that such an approach can improve thegeneralization ability and robustness of models as well as provide significantimprovements in low-data scenarios.

Conference paper

Biffi C, Cerrolaza Martinez JJ, Tarroni G, Bai W, Simoes Monteiro de Marvao A, Oktay O, Ledig C, Le Folgoc L, Kamnitsas K, Doumou G, Duan J, Prasad S, Cook S, O'Regan D, Rueckert Det al., 2020, Explainable anatomical shape analysis through deep hierarchical generative models, IEEE Transactions on Medical Imaging, Vol: 39, Pages: 2088-2099, ISSN: 0278-0062

Quantification of anatomical shape changes currently relies on scalar global indexes which are largely insensitive to regional or asymmetric modifications. Accurate assessment of pathology-driven anatomical remodeling is a crucial step for the diagnosis and treatment of many conditions. Deep learning approaches have recently achieved wide success in the analysis of medical images, but they lack interpretability in the feature extraction and decision processes. In this work, we propose a new interpretable deep learning model for shape analysis. In particular, we exploit deep generative networks to model a population of anatomical segmentations through a hierarchy of conditional latent variables. At the highest level of this hierarchy, a two-dimensional latent space is simultaneously optimised to discriminate distinct clinical conditions, enabling the direct visualisation of the classification space. Moreover, the anatomical variability encoded by this discriminative latent space can be visualised in the segmentation space thanks to the generative properties of the model, making the classification task transparent. This approach yielded high accuracy in the categorisation of healthy and remodelled left ventricles when tested on unseen segmentations from our own multi-centre dataset as well as in an external validation set, and on hippocampi from healthy controls and patients with Alzheimer’s disease when tested on ADNI data. More importantly, it enabled the visualisation in three-dimensions of both global and regional anatomical features which better discriminate between the conditions under exam. The proposed approach scales effectively to large populations, facilitating highthroughput analysis of normal anatomy and pathology in largescale studies of volumetric imaging.

Journal article

Chen C, Bai W, Davies R, Bhuva A, Manisty C, Moon J, Aung N, Lee A, Sanghvi M, Fung K, Paiva J, Petersen S, Lukaschuk E, Piechnik S, Neubauer S, Rueckert Det al., 2020, Improving the generalizability of convolutional neural network-based segmentation on CMR images, Frontiers in Cardiovascular Medicine, ISSN: 2297-055X

Journal article

Bhuva AN, Treibel TA, De Marvao A, Biffi C, Dawes TJW, Doumou G, Bai W, Patel K, Boubertakh R, Rueckert D, O'Regan DP, Hughes AD, Moon JC, Manisty CHet al., 2020, Sex and regional differences inmyocardial plasticity in aortic stenosis are revealed by 3D modelmachine learning, EUROPEAN HEART JOURNAL-CARDIOVASCULAR IMAGING, Vol: 21, Pages: 417-427, ISSN: 2047-2404

Journal article

Chen C, Qin C, Qiu H, Tarroni G, Duan J, Bai W, Rueckert Det al., 2020, Deep learning for cardiac image segmentation: A review, Frontiers in Cardiovascular Medicine, Vol: 7, Pages: 1-33, ISSN: 2297-055X

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

Journal article

Ruijsink B, Puyol-Antón E, Oksuz I, Sinclair M, Bai W, Schnabel JA, Razavi R, King APet al., 2020, Fully automated, quality-controlled cardiac analysis from CMR: Validation and large-scale application to characterize cardiac function, JACC: Cardiovascular Imaging, Vol: 13, Pages: 684-695, ISSN: 1876-7591

OBJECTIVES: This study sought to develop a fully automated framework for cardiac function analysis from cardiac magnetic resonance (CMR), including comprehensive quality control (QC) algorithms to detect erroneous output. BACKGROUND: Analysis of cine CMR imaging using deep learning (DL) algorithms could automate ventricular function assessment. However, variable image quality, variability in phenotypes of disease, and unavoidable weaknesses in training of DL algorithms currently prevent their use in clinical practice. METHODS: The framework consists of a pre-analysis DL image QC, followed by a DL algorithm for biventricular segmentation in long-axis and short-axis views, myocardial feature-tracking (FT), and a post-analysis QC to detect erroneous results. The study validated the framework in healthy subjects and cardiac patients by comparison against manual analysis (n = 100) and evaluation of the QC steps' ability to detect erroneous results (n = 700). Next, this method was used to obtain reference values for cardiac function metrics from the UK Biobank. RESULTS: Automated analysis correlated highly with manual analysis for left and right ventricular volumes (all r > 0.95), strain (circumferential r = 0.89, longitudinal r > 0.89), and filling and ejection rates (all r ≥ 0.93). There was no significant bias for cardiac volumes and filling and ejection rates, except for right ventricular end-systolic volume (bias +1.80 ml; p = 0.01). The bias for FT strain was <1.3%. The sensitivity of detection of erroneous output was 95% for volume-derived parameters and 93% for FT strain. Finally, reference values were automatically derived from 2,029 CMR exams in healthy subjects. CONCLUSIONS: The study demonstrates a DL-based framework for automated, quality-controlled characterization of cardiac function from cine CMR, without the need for direct clinician oversight.

Journal article

Dewey M, Siebes M, Kachelrieß M, Kofoed KF, Maurovich-Horvat P, Nikolaou K, Bai W, Kofler A, Manka R, Kozerke S, Chiribiri A, Schaeffter T, Michallek F, Bengel F, Nekolla S, Knaapen P, Lubberink M, Senior R, Tang M-X, Piek JJ, van de Hoef T, Martens J, Schreiber L, Quantitative Cardiac Imaging Study Groupet al., 2020, Clinical quantitative cardiac imaging for the assessment of myocardial ischaemia, Nature Reviews Cardiology, Vol: 17, Pages: 427-450, ISSN: 1759-5002

Cardiac imaging has a pivotal role in the prevention, diagnosis and treatment of ischaemic heart disease. SPECT is most commonly used for clinical myocardial perfusion imaging, whereas PET is the clinical reference standard for the quantification of myocardial perfusion. MRI does not involve exposure to ionizing radiation, similar to echocardiography, which can be performed at the bedside. CT perfusion imaging is not frequently used but CT offers coronary angiography data, and invasive catheter-based methods can measure coronary flow and pressure. Technical improvements to the quantification of pathophysiological parameters of myocardial ischaemia can be achieved. Clinical consensus recommendations on the appropriateness of each technique were derived following a European quantitative cardiac imaging meeting and using a real-time Delphi process. SPECT using new detectors allows the quantification of myocardial blood flow and is now also suited to patients with a high BMI. PET is well suited to patients with multivessel disease to confirm or exclude balanced ischaemia. MRI allows the evaluation of patients with complex disease who would benefit from imaging of function and fibrosis in addition to perfusion. Echocardiography remains the preferred technique for assessing ischaemia in bedside situations, whereas CT has the greatest value for combined quantification of stenosis and characterization of atherosclerosis in relation to myocardial ischaemia. In patients with a high probability of needing invasive treatment, invasive coronary flow and pressure measurement is well suited to guide treatment decisions. In this Consensus Statement, we summarize the strengths and weaknesses as well as the future technological potential of each imaging modality.

Journal article

Tarroni G, Bai W, Oktay O, Schuh A, Suzuki H, Glocker B, Matthews P, Rueckert Det al., 2020, Large-scale quality control of cardiac imaging in population studies: application to UK Biobank, Scientific Reports, Vol: 10, ISSN: 2045-2322

In large population studies such as the UK Biobank (UKBB), quality control of the acquired images by visual assessment isunfeasible. In this paper, we apply a recently developed fully-automated quality control pipeline for cardiac MR (CMR) imagesto the first 19,265 short-axis (SA) cine stacks from the UKBB. We present the results for the three estimated quality metrics(heart coverage, inter-slice motion and image contrast in the cardiac region) as well as their potential associations with factorsincluding acquisition details and subject-related phenotypes. Up to 14.2% of the analysed SA stacks had sub-optimal coverage(i.e. missing basal and/or apical slices), however most of them were limited to the first year of acquisition. Up to 16% of thestacks were affected by noticeable inter-slice motion (i.e. average inter-slice misalignment greater than 3.4 mm). Inter-slicemotion was positively correlated with weight and body surface area. Only 2.1% of the stacks had an average end-diastoliccardiac image contrast below 30% of the dynamic range. These findings will be highly valuable for both the scientists involvedin UKBB CMR acquisition and for the ones who use the dataset for research purposes.

Journal article

Chen C, Ouyang C, Tarroni G, Schlemper J, Qiu H, Bai W, Rueckert Det al., 2020, Unsupervised multi-modal style transfer for cardiac MR segmentation, MICCAI STACOM Workshop, Publisher: Springer International Publishing, Pages: 209-219, ISSN: 0302-9743

In this work, we present a fully automatic method to segment cardiac structures from late-gadolinium enhanced (LGE) images without using labelled LGE data for training, but instead by transferring the anatomical knowledge and features learned on annotated balanced steady-state free precession (bSSFP) images, which are easier to acquire. Our framework mainly consists of two neural networks: a multi-modal image translation network for style transfer and a cascaded segmentation network for image segmentation. The multi-modal image translation network generates realistic and diverse synthetic LGE images conditioned on a single annotated bSSFP image, forming a synthetic LGE training set. This set is then utilized to fine-tune the segmentation network pre-trained on labelled bSSFP images, achieving the goal of unsupervised LGE image segmentation. In particular, the proposed cascaded segmentation network is able to produce accurate segmentation by taking both shape prior and image appearance into account, achieving an average Dice score of 0.92 for the left ventricle, 0.83 for the myocardium, and 0.88 for the right ventricle on the test set.

Conference paper

Biffi C, Doumou G, Duan J, Prasad SK, Cook SA, O Regan DP, Rueckert D, Cerrolaza JJ, Tarroni G, Bai W, De Marvao A, Oktay O, Ledig C, Le Folgoc L, Kamnitsas Ket al., 2020, Explainable anatomical shape analysis through deep hierarchical generative models., Publisher: arXiv

Quantification of anatomical shape changes currently relies on scalar global indexes which are largely insensitive to regional or asymmetric modifications. Accurate assessment of pathology-driven anatomical remodeling is a crucial step for the diagnosis and treatment of many conditions. Deep learning approaches have recently achieved wide success in the analysis of medical images, but they lack interpretability in the feature extraction and decision processes. In this work, we propose a new interpretable deep learning model for shape analysis. In particular, we exploit deep generative networks to model a population of anatomical segmentations through a hierarchy of conditional latent variables. At the highest level of this hierarchy, a two-dimensional latent space is simultaneously optimised to discriminate distinct clinical conditions, enabling the direct visualisation of the classification space. Moreover, the anatomical variability encoded by this discriminative latent space can be visualised in the segmentation space thanks to the generative properties of the model, making the classification task transparent. This approach yielded high accuracy in the categorisation of healthy and remodelled left ventricles when tested on unseen segmentations from our own multi-centre dataset as well as in an external validation set, and on hippocampi from healthy controls and patients with Alzheimer's disease when tested on ADNI data. More importantly, it enabled the visualisation in three-dimensions of both global and regional anatomical features which better discriminate between the conditions under exam. The proposed approach scales effectively to large populations, facilitating highthroughput analysis of normal anatomy and pathology in largescale studies of volumetric imaging.

Working paper

Lu P, Qiu H, Qin C, Bai W, Rueckert D, Noble JAet al., 2020, Going Deeper into Cardiac Motion Analysis to Model Fine Spatio-Temporal Features, Pages: 294-306, ISSN: 1865-0929

This paper shows that deep modelling of subtle changes of cardiac motion can help in automated diagnosis of early onset of cardiac disease. In this paper, we model left ventricular (LV) cardiac motion in MRI sequences, based on a hybrid spatio-temporal network. Temporal data over long time periods is used as inputs to the model and delivers a dense displacement field (DDF) for regional analysis of LV function. A segmentation mask of the end-diastole (ED) frame is deformed by the predicted DDF from which regional analysis of LV function endocardial radius, thickness, circumferential strain (Ecc) and radial strain (Err) are estimated. Cardiac motion is estimated over MR cine loops. We compare the proposed technique to two other deep learning-based approaches and show that the proposed approach achieves promising predicted DDFs. Predicted DDFs are estimated on imaging data from healthy volunteers and patients with primary pulmonary hypertension from the UK Biobank. Experiments demonstrate that the proposed methods perform well in obtaining estimates of endocardial radii as cardiac motion-characteristic features for regional LV analysis.

Conference paper

Ruijsink B, Puyol-Antón E, Li Y, Bai W, Kerfoot E, Razavi R, King APet al., 2020, Quality-aware semi-supervised learning for CMR segmentation., Pages: 97-107

One of the challenges in developing deep learning algorithms for medical image segmentation is the scarcity of annotated training data. To overcome this limitation, data augmentation and semi-supervised learning (SSL) methods have been developed. However, these methods have limited effectiveness as they either exploit the existing data set only (data augmentation) or risk negative impact by adding poor training examples (SSL). Segmentations are rarely the final product of medical image analysis -they are typically used in downstream tasks to infer higher-order patterns to evaluate diseases. Clinicians take into account a wealth of prior knowledge on biophysics and physiology when evaluating image analysis results. We have used these clinical assessments in previous works to create robust quality-control (QC) classifiers for automated cardiac magnetic resonance (CMR) analysis. In this paper, we propose a novel scheme that uses QC of the downstream task to identify high quality outputs of CMR segmentation networks, that are subsequently utilised for further network training. In essence, this provides quality-aware augmentation of training data in a variant of SSL for segmentation networks (semiQCSeg). We evaluate our approach in two CMR segmentation tasks (aortic and short axis cardiac volume segmentation) using UK Biobank data and two commonly used network architectures (U-net and a Fully Convolutional Network) and compare against supervised and SSL strategies. We show that semiQCSeg improves training of the segmentation networks. It decreases the need for labelled data, while outperforming the other methods in terms of Dice and clinical metrics. SemiQCSeg can be an efficient approach for training segmentation networks for medical image data when labelled datasets are scarce.

Conference paper

This data is extracted from the Web of Science and reproduced under a licence from Thomson Reuters. You may not copy or re-distribute this data in whole or in part without the written consent of the Science business of Thomson Reuters.

Request URL: http://wlsprd.imperial.ac.uk:80/respub/WEB-INF/jsp/search-html.jsp Request URI: /respub/WEB-INF/jsp/search-html.jsp Query String: respub-action=search.html&id=00484405&limit=30&person=true