Imperial College London

ProfessorDanielRueckert

Faculty of EngineeringDepartment of Computing

Professor of Visual Information Processing
 
 
 
//

Contact

 

+44 (0)20 7594 8333d.rueckert Website

 
 
//

Location

 

568Huxley BuildingSouth Kensington Campus

//

Summary

 

Publications

Publication Type
Year
to

789 results found

Dimitrova R, Arulkumaran S, Carney O, Chew A, Falconer S, Ciarrusta J, Wolfers T, Batalle D, Cordero-Grande L, Price AN, Teixeira RPAG, Hughes E, Egloff A, Hutter J, Makropoulos A, Robinson EC, Schuh A, Vecchiato K, Steinweg JK, Macleod R, Marquand AF, McAlonan G, Rutherford MA, Counsell SJ, Smith SM, Rueckert D, Hajnal JV, O'Muircheartaigh J, Edwards ADet al., 2021, Phenotyping the preterm brain: characterizing individual deviations from normative volumetric development in two large infant cohorts, Cerebral Cortex, ISSN: 1047-3211

The diverse cerebral consequences of preterm birth create significant challenges for understanding pathogenesis or predicting later outcome. Instead of focusing on describing effects common to the group, comparing individual infants against robust normative data offers a powerful alternative to study brain maturation. Here we used Gaussian process regression to create normative curves characterizing brain volumetric development in 274 term-born infants, modeling for age at scan and sex. We then compared 89 preterm infants scanned at term-equivalent age with these normative charts, relating individual deviations from typical volumetric development to perinatal risk factors and later neurocognitive scores. To test generalizability, we used a second independent dataset comprising of 253 preterm infants scanned using different acquisition parameters and scanner. We describe rapid, nonuniform brain growth during the neonatal period. In both preterm cohorts, cerebral atypicalities were widespread, often multiple, and varied highly between individuals. Deviations from normative development were associated with respiratory support, nutrition, birth weight, and later neurocognition, demonstrating their clinical relevance. Group-level understanding of the preterm brain disguises a large degree of individual differences. We provide a method and normative dataset that offer a more precise characterization of the cerebral consequences of preterm birth by profiling the individual neonatal brain.

Journal article

Dou Q, So TY, Jiang M, Liu Q, Vardhanabhuti V, Kaissis G, Li Z, Si W, Lee HHC, Yu K, Feng Z, Dong L, Burian E, Jungmann F, Braren R, Makowski M, Kainz B, Rueckert D, Glocker B, Yu SCH, Heng PAet al., 2021, Federated deep learning for detecting COVID-19 lung abnormalities in CT: a privacy-preserving multinational validation study, NPJ DIGITAL MEDICINE, Vol: 4, ISSN: 2398-6352

Journal article

Eyre M, Fitzgibbon SP, Ciarrusta J, Cordero-Grande L, Price AN, Poppe T, Schuh A, Hughes E, O'Keeffe C, Brandon J, Cromb D, Vecchiato K, Andersson J, Duff EP, Counsell SJ, Smith SM, Rueckert D, Hajnal JV, Arichi T, O'Muircheartaigh J, Batallea D, Edwards ADet al., 2021, The Developing Human Connectome Project: typical and disrupted perinatal functional connectivity, Brain: a journal of neurology, ISSN: 0006-8950

The Developing Human Connectome Project (dHCP) is an Open Science project which provides the first large sample of neonatal functional MRI (fMRI) data with high temporal and spatial resolution. This data enables mapping of intrinsic functional connectivity between spatially distributed brain regions under normal and adverse perinatal circumstances, offering a framework to study the ontogeny of large-scale brain organisation in humans. Here, we characterise in unprecedented detail the maturation and integrity of resting-state networks (RSNs) at term-equivalent age in 337 infants (including 65 born preterm). First, we applied group independent component analysis (ICA) to define 11 RSNs in term-born infants scanned at 43.5-44.5 weeks postmenstrual age (PMA). Adult-like topography was observed in RSNs encompassing primary sensorimotor, visual and auditory cortices. Among six higher-order, association RSNs, analogues of the adult networks for language and ocular control were identified, but a complete default mode network precursor was not. Next, we regressed the subject-level datasets from an independent cohort of infants scanned at 37-43.5 weeks PMA against the group-level RSNs to test for the effects of age, sex and preterm birth. Brain mapping in term-born infants revealed areas of positive association with age across four of six association RSNs, indicating active maturation in functional connectivity from 37 to 43.5 weeks PMA. Female infants showed increased connectivity in inferotemporal regions of the visual association network. Preterm birth was associated with striking impairments of functional connectivity across all RSNs in a dose-dependent manner; conversely, connectivity of the superior parietal lobules within the lateral motor network was abnormally increased in preterm infants, suggesting a possible mechanism for specific difficulties such as developmental coordination disorder which occur frequently in preterm children. Overall, we find a robust, modular

Journal article

Meng Q, Matthew J, Zimmer VA, Gomez A, Lloyd DFA, Rueckert D, Kainz Bet al., 2021, Mutual information-based disentangled neural networks for classifying unseen categories in different domains: application to fetal ultrasound imaging, IEEE Transactions on Medical Imaging, Vol: 40, Pages: 722-734, ISSN: 0278-0062

Deep neural networks exhibit limited generalizability across images with different entangled domain features and categorical features. Learning generalizable features that can form universal categorical decision boundaries across domains is an interesting and difficult challenge. This problem occurs frequently in medical imaging applications when attempts are made to deploy and improve deep learning models across different image acquisition devices, across acquisition parameters or if some classes are unavailable in new training databases. To ad-dress this problem, we propose Mutual Information-based Disentangled Neural Networks (MIDNet), which extract generalizable categorical features to transfer knowledge to unseen categories in a target domain. The proposed MID-Net adopts a semi-supervised learning paradigm to alleviate the dependency on labeled data. This is important for real-world applications where data annotation is time-consuming, costly and requires training and expertise. We extensively evaluate the proposed method on fetal ultra-sound datasets for two different image classification tasks where domain features are respectively defined by shadow artifacts and image acquisition devices. Experimental results show that the proposed method outperforms the state-of-the-art on the classification of unseen categories in a target domain with sparsely labeled training data.

Journal article

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

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

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

Zhou SK, Greenspan H, Davatzikos C, Duncan JS, van Ginneken B, Madabhushi A, Prince JL, Rueckert D, Summers RMet al., 2021, A Review of Deep Learning in Medical Imaging: Imaging Traits, Technology Trends, Case Studies With Progress Highlights, and Future Promises, Proceedings of the IEEE, ISSN: 0018-9219

Since its renaissance, deep learning (DL) has been widely used in various medical imaging tasks and has achieved remarkable success in many medical imaging applications, thereby propelling us into the so-called artificial intelligence (AI) era. It is known that the success of AI is mostly attributed to the availability of big data with annotations for a single task and the advances in high-performance computing. However, medical imaging presents unique challenges that confront DL approaches. In this survey article, we first present traits of medical imaging, highlight both clinical needs and technical challenges in medical imaging, and describe how emerging trends in DL are addressing these issues. We cover the topics of network architecture, sparse and noisy labels, federating learning, interpretability, uncertainty quantification, and so on. Then, we present several case studies that are commonly found in clinical practice, including digital pathology and chest, brain, cardiovascular, and abdominal imaging. Rather than presenting an exhaustive literature survey, we instead describe some prominent research highlights related to these case study applications. We conclude with a discussion and presentation of promising future directions.

Journal article

Kustner T, Pan J, Gilliam C, Qi H, Cruz G, Hammernik K, Yang B, Blu T, Rueckert D, Botnar R, Prieto C, Gatidis Set al., 2020, Deep-learning based motion-corrected image reconstruction in 4D magnetic resonance imaging of the body trunk, Pages: 976-985

Respiratory and cardiac motion can cause artifacts in magnetic resonance imaging of the body trunk if patients cannot hold their breath or triggered acquisitions are not practical. Retrospective correction strategies usually cope with motion by fast imaging sequences with integrated motion tracking under free-movement conditions. These acquisitions perform sub-Nyquist sampling and retrospectively bin the data into the respective motion states, yielding subsampled and motionresolved k-space data. The motion-resolved k-spaces are linked to each other by non-rigid deformation fields. The accurate estimation of such motion is thus an important task in the successful correction of respiratory and cardiac motion. Usually this problem is formulated in image space via diffusion, parametric-spline or optical flow methods. Image-based registration can be however impaired by aliasing artifacts or by estimation from low-resolution images. Subsequently, any motion-corrected reconstruction can be biased by errors in the deformation fields. In this work, we propose a novel deep-learning based motion-corrected 4D (3D spatial + time) image reconstruction which combines a non-rigid registration network and a(3+1)D reconstruction network. Non-rigid motion is estimated directly in k-space based on an optical flow idea and incorporated into the reconstruction network. The proposed method is evaluated on in-vivo 4D motionresolved magnetic resonance images of patients with suspected liver or lung metastases and healthy subjects.

Conference paper

Cullen H, Dimitrakopoulou K, Batalle D, Gale-Grant O, Patel H, Curtis C, Chung R, Schuh A, Cordero-Grande L, Hughes E, Price A, Rueckert D, Hajnal J, Smith S, Edwards Aet al., 2020, Can genetic determinants of brain structure be detected soon after birth?, Publisher: SPRINGERNATURE, Pages: 984-985, ISSN: 1018-4813

Conference paper

Fitzgibbon SP, Harrison SJ, Jenkinson M, Baxter L, Robinson EC, Bastiani M, Bozek J, Karolis V, Grande LC, Price AN, Hughes E, Makropoulos A, Passerat-Palmbach J, Schuh A, Gao J, Farahibozorg S-R, O'Muircheartaigh J, Ciarrusta J, O'Keeffe C, Brandon J, Arichi T, Rueckert D, Hajnal J, Edwards AD, Smith SM, Duff E, Andersson Jet al., 2020, The developing Human Connectome Project (dHCP) automated resting-state functional processing framework for newborn infants, NEUROIMAGE, Vol: 223, ISSN: 1053-8119

Journal article

Weatheritt J, Joules R, Wolz R, Rueckert Det al., 2020, Fully Automatic AI Segmentation of Subcortical Regions, Publisher: SPRINGER, Pages: 21-21, ISSN: 1933-7213

Conference paper

Haralampieva V, Rueckert D, Passerat-Palmbach J, 2020, A systematic comparison of encrypted machine learning solutions for image classification, CCS '20: 2020 ACM SIGSAC Conference on Computer and Communications Security, Publisher: ACM, Pages: 55-59

This work provides a comprehensive review of existing frameworks based on secure computing techniques in the context of private image classification. The in-depth analysis of these approaches is followed by careful examination of their performance costs, in particular runtime and communication overhead.To further illustrate the practical considerations when using different privacy-preserving technologies, experiments were conducted using four state-of-the-art libraries implementing secure computing at the heart of the data science stack: PySyft and CrypTen supporting private inference via Secure Multi-Party Computation, TF-Trusted utilising Trusted Execution Environments and HE-Transformer relying on Homomorphic encryption.Our work aims to evaluate the suitability of these frameworks from a usability, runtime requirements and accuracy point of view. In order to better understand the gap between state-of-the-art protocols and what is currently available in practice for a data scientist, we designed three neural network architecture to obtain secure predictions via each of the four aforementioned frameworks. Two networks were evaluated on the MNIST dataset and one on the Malaria Cell image dataset. We observed satisfying performances for TF-Trusted and CrypTen and noted that all frameworks perfectly preserved the accuracy of the corresponding plaintext model.

Conference paper

Chen L, Cuervas-Mons CG, Ramji S, Dumba M, Hallett C, Cohen D, Fernandes C, Lobotesis K, Rueckert D, Bentley Pet al., 2020, AUTOMATED AGE ESTIMATION OF ISCHAEMIC LESIONS FROM UNENHANCED CT, Publisher: SAGE PUBLICATIONS LTD, Pages: 296-296, ISSN: 1747-4930

Conference paper

Ball G, Seidlitz J, O'Muircheartaigh J, Dimitrova R, Fenchel D, Makropoulos A, Christiaens D, Schuh A, Passerat-Palmbach J, Hutter J, Cordero-Grande L, Hughes E, Price A, Hajnal J, Rueckert D, Robinson EC, Edwards ADet al., 2020, Cortical morphology at birth reflects spatiotemporal patterns of gene expression in the fetal human brain, PLOS BIOLOGY, Vol: 18, ISSN: 1544-9173

Journal article

Fenchel D, Dimitrova R, Seidlitz J, Robinson EC, Batalle D, Hutter J, Christiaens D, Pietsch M, Brandon J, Hughes EJ, Allsop J, O'Keeffe C, Price AN, Cordero-Grande L, Schuh A, Makropoulos A, Passerat-Palmbach J, Bozek J, Rueckert D, Hajnal JV, Raznahan A, McAlonan G, Edwards AD, O'Muircheartaigh Jet al., 2020, Development of microstructural and morphological cortical profiles in the neonatal brain, Cerebral Cortex, Vol: 30, Pages: 5767-5779, ISSN: 1047-3211

Interruptions to neurodevelopment during the perinatal period may have long-lasting consequences. However, to be able to investigate deviations in the foundation of proper connectivity and functional circuits, we need a measure of how this architecture evolves in the typically developing brain. To this end, in a cohort of 241 term-born infants, we used magnetic resonance imaging to estimate cortical profiles based on morphometry and microstructure over the perinatal period (37-44 weeks postmenstrual age, PMA). Using the covariance of these profiles as a measure of inter-areal network similarity (morphometric similarity networks; MSN), we clustered these networks into distinct modules. The resulting modules were consistent and symmetric, and corresponded to known functional distinctions, including sensory-motor, limbic, and association regions, and were spatially mapped onto known cytoarchitectonic tissue classes. Posterior regions became more morphometrically similar with increasing age, while peri-cingulate and medial temporal regions became more dissimilar. Network strength was associated with age: Within-network similarity increased over age suggesting emerging network distinction. These changes in cortical network architecture over an 8-week period are consistent with, and likely underpin, the highly dynamic processes occurring during this critical period. The resulting cortical profiles might provide normative reference to investigate atypical early brain development.

Journal article

Howard JP, Zaman S, Ragavan A, Hall K, Leonard G, Sutanto S, Ramadoss V, Razvi Y, Linton NF, Bharath A, Shun-Shin M, Rueckert D, Francis D, Cole Get al., 2020, Automated analysis and detection of abnormalities in transaxial anatomical cardiovascular magnetic resonance images: a proof of concept study with potential to optimize image acquisition, International Journal of Cardiovascular Imaging, Vol: 37, Pages: 1033-1042, ISSN: 1569-5794

The large number of available MRI sequences means patients cannot realistically undergo them all, so the range of sequences to be acquired during a scan are protocolled based on clinical details. Adapting this to unexpected findings identified early on in the scan requires experience and vigilance. We investigated whether deep learning of the images acquired in the first few minutes of a scan could provide an automated early alert of abnormal features. Anatomy sequences from 375 CMR scans were used as a training set. From these, we annotated 1500 individual slices and used these to train a convolutional neural network to perform automatic segmentation of the cardiac chambers, great vessels and any pleural effusions. 200 scans were used as a testing set. The system then assembled a 3D model of the thorax from which it made clinical measurements to identify important abnormalities. The system was successful in segmenting the anatomy slices (Dice 0.910) and identified multiple features which may guide further image acquisition. Diagnostic accuracy was 90.5% and 85.5% for left and right ventricular dilatation, 85% for left ventricular hypertrophy and 94.4% for ascending aorta dilatation. The area under ROC curve for diagnosing pleural effusions was 0.91. We present proof-of-concept that a neural network can segment and derive accurate clinical measurements from a 3D model of the thorax made from transaxial anatomy images acquired in the first few minutes of a scan. This early information could lead to dynamic adaptive scanning protocols, and by focusing scanner time appropriately and prioritizing cases for supervision and early reporting, improve patient experience and efficiency.

Journal article

Jaubert O, Cruz G, Bustin A, Hajhosseiny R, Nazir S, Schneider T, Koken P, Doneva M, Rueckert D, Masci P-G, Botnar RM, Prieto Cet al., 2020, T1, T2, and Fat Fraction Cardiac MR Fingerprinting: Preliminary Clinical Evaluation, JOURNAL OF MAGNETIC RESONANCE IMAGING, Vol: 53, Pages: 1253-1265, ISSN: 1053-1807

Journal article

Hou B, Vlontzos A, Alansary A, Rueckert D, Kainz Bet al., 2020, Flexible conditional image generation of missing data with learned mental maps, Machine Learning for Medical Image Reconstruction: Second International Workshop, Publisher: Springer International Publishing, Pages: 139-150, ISSN: 0302-9743

Real-world settings often do not allow acquisition of high-resolution volumetric images for accurate morphological assessment and diagnostic. In clinical practice it is frequently common to acquire only sparse data (e.g. individual slices) for initial diagnostic decision making. Thereby, physicians rely on their prior knowledge (or mental maps) of the human anatomy to extrapolate the underlying 3D information. Accurate mental maps require years of anatomy training, which in the first instance relies on normative learning, i.e. excluding pathology. In this paper, we leverage Bayesian Deep Learning and environment mapping to generate full volumetric anatomy representations from none to a small, sparse set of slices. We evaluate proof of concept implementations based on Generative Query Networks (GQN) and Conditional BRUNO using abdominal CT and brain MRI as well as in a clinical application involving sparse, motion-corrupted MR acquisition for fetal imaging. Our approach allows to reconstruct 3D volumes from 1 to 4 tomographic slices, with a SSIM of 0.7+ and cross-correlation of 0.8+ compared to the 3D ground truth.

Conference paper

van Wijk RPJ, van Dijck JTJM, Timmers M, van Veen E, Citerio G, Lingsma HF, Maas AIR, Menon DK, Peul WC, Stocchetti N, Kompanje EJO, Akerlund C, Amrein K, Andelic N, Andreassen L, Anke A, Antoni A, Audibert G, Azouvi P, Azzolini ML, Bartels R, Barzo P, Beauvais R, Beer R, Bellander B-M, Belli A, Benali H, Berardino M, Beretta L, Blaabjerg M, Bragge P, Brazinova A, Brinck V, Brooker J, Brorsson C, Buki A, Bullinger M, Cabeleira M, Caccioppola A, Calappi E, Calvi MR, Cameron P, Lozano GC, Carbonara M, Cavallo S, Chevallard G, Chieregato A, Ceyisakar I, Coburn M, Coles J, Cooper JD, Correia M, Covic A, Curry N, Czeiter E, Czosnyka M, Dahyot-Fizelier C, Dark P, Dawes H, De Keyser V, Degos V, Della Corte F, den Boogert H, Depreitere B, Dilvesi D, Dixit A, Donoghue E, Dreier J, Duliere G-L, Ercole A, Esser P, Ezer E, Fabricius M, Feigin VL, Foks K, Frisvold S, Furmanov A, Gagliardo P, Galanaud D, Gantner D, Gao G, George P, Ghuysen A, Giga L, Glocker B, Golubovic J, Gomez PA, Gratz J, Gravesteijn B, Grossi F, Gruen RL, Gupta D, Haagsma JA, Haitsma I, Helbok R, Helseth E, Horton L, Huijben J, Hutchinson PJ, Jacobs B, Jankowski S, Jarrett M, Jiang J-Y, Johnson F, Jones K, Karan M, Kolias AG, Kompanje E, Kondziella D, Koraropoulos E, Koskinen L-O, Kovacs N, Kowark A, Lagares A, Lanyon L, Laureys S, Lecky F, Ledoux D, Lefering R, Legrand V, Lejeune A, Levi L, Lightfoot R, Lingsma H, Castano-Leon AM, Maegele M, Majdan M, Manara A, Manley G, Martino C, Marechal H, Mattern J, McMahon C, Melegh B, Menon D, Menovsky T, Misset B, Mulazzi D, Muraleedharan V, Murray L, Negru A, Nelson D, Newcombe V, Nieboer D, Nyiradi J, Olubukola O, Oresic M, Ortolano F, Palotie A, Parizel PM, Payen J-F, Perera N, Perlbarg V, Persona P, Peul W, Piippo-Karjalainen A, Pirinen M, Ples H, Polinder S, Pomposo I, Posti JP, Puybasset L, Radoi A, Ragauskas A, Raj R, Rambadagalla M, Rhodes J, Richardson S, Richter S, Ripatti S, Rocka S, Roe C, Roise O, Rosand J, Rosenfeld J, Rosenlund C, Rosenthal G, Rossainet al., 2020, Informed consent procedures in patients with an acute inability to provide informed consent: Policy and practice in the CENTER-TBI study, JOURNAL OF CRITICAL CARE, Vol: 59, Pages: 6-15, ISSN: 0883-9441

Journal article

Tan J, Au A, Meng Q, FinesilverSmith S, Simpson J, Rueckert D, Razavi R, Day T, Lloyd D, Kainz Bet al., 2020, Automated Detection of Congenital Heart Disease in Fetal Ultrasound Screening, ASMUS 2020, PIPPI 2020: Medical Ultrasound, and Preterm, Perinatal and Paediatric Image Analysis, Publisher: Springer International Publishing, Pages: 243-252, ISSN: 0302-9743

Conference paper

Liu T, Meng Q, Vlontzos A, Tan J, Rueckert D, Kainz Bet al., 2020, Ultrasound video summarization using deep reinforcement learning, 23rd INTERNATIONAL CONFERENCE ON MEDICAL IMAGE COMPUTING & COMPUTER ASSISTED INTERVENTION, Publisher: Springer International Publishing, Pages: 483-492, ISSN: 0302-9743

Video is an essential imaging modality for diagnostics, e.g. in ultrasound imaging, for endoscopy, or movement assessment. However, video hasn’t received a lot of attention in the medical image analysis community. In the clinical practice, it is challenging to utilise raw diagnostic video data efficiently as video data takes a long time to process, annotate or audit. In this paper we introduce a novel, fully automatic video summarization method that is tailored to the needs of medical video data. Our approach is framed as reinforcement learning problem and produces agents focusing on the preservation of important diagnostic information. We evaluate our method on videos from fetal ultrasound screening, where commonly only a small amount of the recorded data is used diagnostically. We show that our method is superior to alternative video summarization methods and that it preserves essential information required by clinical diagnostic standards.

Conference paper

Meng Q, Rueckert D, Kainz B, 2020, Unsupervised cross-domain image classification by distance metric guided feature alignment, ASMUS 2020, PIPPI 2020: Medical Ultrasound, and Preterm, Perinatal and Paediatric Image Analysis, Publisher: Springer International Publishing, Pages: 146-157, ISSN: 0302-9743

Learning deep neural networks that are generalizable across different domains remains a challenge due to the problem of domain shift. Unsupervised domain adaptation is a promising avenue which transfers knowledge from a source domain to a target domain without using any labels in the target domain. Contemporary techniques focus on extracting domain-invariant features using domain adversarial training. However, these techniques neglect to learn discriminative class boundaries in the latent representation space on a target domain and yield limited adaptation performance. To address this problem, we propose distance metric guided feature alignment (MetFA) to extract discriminative as well as domain-invariant features on both source and target domains. The proposed MetFA method explicitly and directly learns the latent representation without using domain adversarial training. Our model integrates class distribution alignment to transfer semantic knowledge from a source domain to a target domain. We evaluate the proposed method on fetal ultrasound datasets for cross-device image classification. Experimental results demonstrate that the proposed method outperforms the state-of-the-art and enables model generalization.

Conference paper

Vlontzos A, Budd S, Hou B, Rueckert D, Kainz Bet al., 2020, 3D Probabilistic Segmentation and Volumetry from 2D Projection Images, Thoracic Image Analysis, Publisher: Springer International Publishing, Pages: 48-57, ISSN: 0302-9743

Conference paper

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

Gravesteijn BY, Sewalt CA, Nieboer D, Menon DK, Maas A, Lecky F, Klimek M, Lingsma HF, CENTER-TBI collaboratorset al., 2020, Tracheal intubation in traumatic brain injury: a multicentre prospective observational study., Br J Anaesth, Vol: 125, Pages: 505-517

BACKGROUND: We aimed to study the associations between pre- and in-hospital tracheal intubation and outcomes in traumatic brain injury (TBI), and whether the association varied according to injury severity. METHODS: Data from the international prospective pan-European cohort study, Collaborative European NeuroTrauma Effectiveness Research for TBI (CENTER-TBI), were used (n=4509). For prehospital intubation, we excluded self-presenters. For in-hospital intubation, patients whose tracheas were intubated on-scene were excluded. The association between intubation and outcome was analysed with ordinal regression with adjustment for the International Mission for Prognosis and Analysis of Clinical Trials in TBI variables and extracranial injury. We assessed whether the effect of intubation varied by injury severity by testing the added value of an interaction term with likelihood ratio tests. RESULTS: In the prehospital analysis, 890/3736 (24%) patients had their tracheas intubated at scene. In the in-hospital analysis, 460/2930 (16%) patients had their tracheas intubated in the emergency department. There was no adjusted overall effect on functional outcome of prehospital intubation (odds ratio=1.01; 95% confidence interval, 0.79-1.28; P=0.96), and the adjusted overall effect of in-hospital intubation was not significant (odds ratio=0.86; 95% confidence interval, 0.65-1.13; P=0.28). However, prehospital intubation was associated with better functional outcome in patients with higher thorax and abdominal Abbreviated Injury Scale scores (P=0.009 and P=0.02, respectively), whereas in-hospital intubation was associated with better outcome in patients with lower Glasgow Coma Scale scores (P=0.01): in-hospital intubation was associated with better functional outcome in patients with Glasgow Coma Scale scores of 10 or lower. CONCLUSION: The benefits and harms of tracheal intubation should be carefully evaluated in patients with TBI to optimise benefit. This study suggests that e

Journal article

Robinson R, Dou Q, Castro DC, Kamnitsas K, Groot MD, Summers RM, Rueckert D, Glocker Bet al., 2020, Image-level harmonization of multi-site data using image-and-spatial transformer networks, 23rd International Conference on Medical Image Computing and Computer Assisted Intervention

We investigate the use of image-and-spatial transformer networks (ISTNs) totackle domain shift in multi-site medical imaging data. Commonly, domainadaptation (DA) is performed with little regard for explainability of theinter-domain transformation and is often conducted at the feature-level in thelatent space. We employ ISTNs for DA at the image-level which constrainstransformations to explainable appearance and shape changes. Asproof-of-concept we demonstrate that ISTNs can be trained adversarially on aclassification problem with simulated 2D data. For real-data validation, weconstruct two 3D brain MRI datasets from the Cam-CAN and UK Biobank studies toinvestigate domain shift due to acquisition and population differences. We showthat age regression and sex classification models trained on ISTN outputimprove generalization when training on data from one and testing on the othersite.

Conference paper

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

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)

In recent years, convolutional neural networks have demonstrated promisingperformance in a variety of medical image segmentation tasks. However, when atrained segmentation model is deployed into the real clinical world, the modelmay not perform optimally. A major challenge is the potential poor-qualitysegmentations generated due to degraded image quality or domain shift issues.There is a timely need to develop an automated quality control method that candetect poor segmentations and feedback to clinicians. Here we propose a noveldeep generative model-based framework for quality control of cardiac MRIsegmentation. It first learns a manifold of good-quality image-segmentationpairs using a generative model. The quality of a given test segmentation isthen assessed by evaluating the difference from its projection onto thegood-quality manifold. In particular, the projection is refined throughiterative search in the latent space. The proposed method achieves highprediction accuracy on two publicly available cardiac MRI datasets. Moreover,it shows better generalisation ability than traditional regression-basedmethods. Our approach provides a real-time and model-agnostic quality controlfor cardiac MRI segmentation, which has the potential to be integrated intoclinical image analysis workflows.

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=00172041&limit=30&person=true