publications

A foundation model for brain lesion segmentation with mixture of modality experts

Xinru Zhang, Ni Ou, Berke Doga Basaran, Marco Visentin, Mengyun Qiao, Renyang Gu, Cheng Ouyang, Yaou Liu, Paul M Matthew, Chuyang Ye, Wenjia Bai

International Conference on Medical Image Computing and Computer-Assisted Intervention (MICCAI), 2024. [paper] [code]

G2D: From global to dense radiography representation learning via vision-language pre-training

Che Liu, Cheng Ouyang, Sibo Cheng, Anand Shah, Wenjia Bai, Rossella Arcucci

Advances in Neural Information Processing Systems (NeurIPS), 2024. [paper] [code]

CHeart: A conditional spatio-temporal generative model for cardiac anatomy

Mengyun Qiao, Shuo Wang, Huaqi Qiu, Antonio de Marvao, Declan P O'Regan, Daniel Rueckert, Wenjia Bai

IEEE Transactions on Medical Imaging, 2023. [paper] [code]

M-FLAG: Medical vision-language pre-training with frozen language models and latent space geometry optimization

Che Liu, Sibo Cheng, Chen Chen, Mengyun Qiao, Weitong Zhang, Anand Shah, Wenjia Bai, Rossella Arcucci

Medical Image Computing and Computer-Assisted Intervention (MICCAI), 2023. [paper] [code]

Subject-specific lesion generation and pseudo-healthy synthesis for multiple sclerosis brain images

Berke Doga Basaran, Mengyun Qiao, Paul M Matthews and Wenjia Bai

MICCAI Workshop on Simulation and Synthesis in Medical Imaging (SASHIMI), 2022. [paper] [code]

MaxStyle: Adversarial style composition for robust medical image segmentation

Chen Chen, Zeju Li, Cheng Ouyang, Matt Sinclair, Wenjia Bai and Daniel Rueckert

Medical Image Computing and Computer-Assisted Intervention (MICCAI), 2022. [paper] [code]

Genetic and environmental determinants of diastolic heart function

Marjola Thanaj, Johanna Mielke, Kathryn A McGurk, Wenjia Bai, Nicolò Savioli, Antonio de Marvao, Hannah V Meyer, Lingyao Zeng, Florian Sohler, R Thomas Lumbers, Martin R Wilkins, James S Ware, Christian Bender, Daniel Rueckert, Aidan MacNamara, Daniel F Freitag and Declan P O’Regan

Nature Cardiovascular Research, 2022. [paper]

Joint motion correction and super resolution for cardiac segmentation via latent optimisation

Shuo Wang, Chen Qin, Nicolo Savioli, Chen Chen, Declan O’Regan, Stuart Cook, Yike Guo, Daniel Rueckert and Wenjia Bai

Medical Image Computing and Computer-Assisted Intervention (MICCAI), 2021. [paper] [code]

Cooperative training and latent space data augmentation for robust medical image segmentation

Chen Chen, Kerstin Hammernik, Cheng Ouyang, Chen Qin, Wenjia Bai and Daniel Rueckert

Medical Image Computing and Computer-Assisted Intervention (MICCAI), 2021. [paper] [code]

A population-based phenome-wide association study of cardiac and aortic structure and function

Wenjia Bai, Hideaki Suzuki, Jian Huang, Catherine Francis, Shuo Wang, Giacomo Tarroni, Florian Guitton, Nay Aung, Kenneth Fung, Steffen E. Petersen, Stefan K. Piechnik, Stefan Neubauer, Evangelos Evangelou, Abbas Dehghan, Declan P. O'Regan, Martin R. Wilkins, Yike Guo, Paul M. Matthews and Daniel Rueckert

Nature Medicine, 2020. [paper] [code] [website] [backup]

Genetic and functional insights into the fractal structure of the heart

Hannah V. Meyer, Timothy J. W. Dawes, Marta Serrani, Wenjia Bai, Pawel Tokarczuk, Jiashen Cai, Antonio de Marvao, Albert Henry, R. Thomas Lumbers, Jakob Gierten, Thomas Thumberger, Joachim Wittbrodt, James S. Ware, Daniel Rueckert, Paul M. Matthews, Sanjay K. Prasad, Maria L. Costantino, Stuart A. Cook, Ewan Birney and Declan P. O'Regan

Nature, 2020. [paper]

Suggestive annotation of brain tumour images with gradient-guided sampling

Chengliang Dai, Shuo Wang, Yuanhan Mo, Elsa Angelini, Yike Guo, Wenjia Bai

Medical Image Computing and Computer-Assisted Intervention (MICCAI), 2020. [paper]

Deep generative model-based quality control for cardiac MRI segmentation

Shuo Wang, Giacomo Tarroni, Chen Qin, Yuanhan Mo, Chengliang Dai, Chen Chen, Ben Glocker, Yike Guo, Daniel Rueckert, Wenjia Bai

Medical Image Computing and Computer-Assisted Intervention (MICCAI), 2020. [paper]

Realistic adversarial data augmentation for MR image segmentation

Chen Chen, Chen Qin, Huaqi Qiu, Cheng Ouyang, Shuo Wang, Liang Chen, Giacomo Tarroni, Wenjia Bai, Daniel Rueckert

Medical Image Computing and Computer-Assisted Intervention (MICCAI), 2020. [paper]

Biomechanics-informed neural networks for myocardial motion tracking in MRI

Chen Qin, Shuo Wang, Chen Chen, Huaqi Qiu, Wenjia Bai, Daniel Rueckert

Medical Image Computing and Computer-Assisted Intervention (MICCAI), 2020. [paper] [code]

Deep learning for cardiac image segmentation: A review

Chen Chen, Chen Qin, Huaqi Qiu, Giacomo Tarroni, Jinming Duan, Wenjia Bai, Daniel Rueckert

Frontiers in Cardiovascular Medicine, 2020. [paper]

Large-scale quality control of cardiac imaging in population studies: Application to UK Biobank

Giacomo Tarroni, Wenjia Bai, Ozan Oktay, Andreas Schuh, Hideaki Suzuki, Ben Glocker, Paul M Matthews, Daniel Rueckert

Scientific Reports, 2020. [paper]

Clinical quantitative cardiac imaging for the assessment of myocardial ischaemia

Marc Dewey, Maria Siebes, Marc Kachelrieß, Klaus F Kofoed, Pál Maurovich-Horvat, Konstantin Nikolaou, Wenjia Bai, Andreas Kofler, Robert Manka, Sebastian Kozerke, Amedeo Chiribiri, Tobias Schaeffter, Florian Michallek, Frank Bengel, Stephan Nekolla, Paul Knaapen, Mark Lubberink, Roxy Senior, Meng-Xing Tang, Jan J Piek, Tim van de Hoef, Johannes Martens, Laura Schreiber

Nature Reviews Cardiology, 2020. [paper]

Self-supervised learning for cardiac MR image segmentation by anatomical position prediction

Wenjia Bai, Chen Chen, Giacomo Tarroni, Jinming Duan, Florian Guitton, Steffen E. Petersen, Yike Guo, Paul M. Matthews, Daniel Rueckert

Medical Image Computing and Computer-Assisted Intervention (MICCAI), 2019. [paper]

Learning shape priors for robust cardiac MR segmentation from multi-view images

Chen Chen, Carlo Biffi, Giacomo Tarroni, Steffen Petersen, Wenjia Bai, Daniel Rueckert

Medical Image Computing and Computer-Assisted Intervention (MICCAI), 2019. [paper]

Unsupervised multi-modal style transfer for cardiac MR segmentation

Chen Chen, Cheng Ouyang, Giacomo Tarroni, Jo Schlemper, Huaqi Qiu, Wenjia Bai, Daniel Rueckert

MICCAI Workshop on Statistical Atlases and Computational Modelling of the Heart, 2019. (Best workshop paper award) [paper]

Automatic brain tumour segmentation and biophysics-guided survival prediction

Shuo Wang, Chengliang Dai, Yuanhan Mo, Elsa Angelini, Yike Guo, Wenjia Bai

MICCAI Brain Lesion (BrainLes) Workshop, 2019. (2nd place in survival prediction challenge) [paper]

Transfer learning from partial annotations for whole brain segmentation

Chengliang Dai, Yuanhan Mo, Elsa Angelini, Yike Guo, Wenjia Bai

MICCAI Workshop on Medical Image Learning with Less Labels and Imperfect Data, 2019. [paper]

Automated cardiovascular magnetic resonance image analysis with fully convolutional networks

Wenjia Bai, Matthew Sinclair, Giacomo Tarroni, Ozan Oktay, Martin Rajchl, Ghislain Vaillant, Aaron M Lee, Nay Aung, Elena Lukaschuk, Mihir M Sanghvi, Filip Zemrak, Kenneth Fung, Jose Miguel Paiva, Valentina Carapella, Young Jin Kim, Hideaki Suzuki, Bernhard Kainz, Paul M Matthews, Steffen E Petersen, Stefan K Piechnik, Stefan Neubauer, Ben Glocker, Daniel Rueckert

Journal of Cardiovascular Magnetic Resonance, 2018. (Best JCMR Paper Award 2018) [paper] [code]

Recurrent neural networks for aortic image sequence segmentation with sparse annotations

Wenjia Bai, Hideaki Suzuki, Chen Qin, Giacomo Tarroni, Ozan Oktay, Paul M Matthews, Daniel Rueckert

Medical Image Computing and Computer-Assisted Intervention (MICCAI), 2018. [paper]

Joint learning of motion estimation and segmentation for cardiac MR image sequences

Chen Qin, Wenjia Bai, Jo Schlemper, Steffen E Petersen, Stefan K Piechnik, Stefan Neubauer, Daniel Rueckert

Medical Image Computing and Computer-Assisted Intervention (MICCAI), 2018. [paper]

Learning interpretable anatomical features through deep generative models: Application to cardiac remodeling

Carlo Biffi, Ozan Oktay, Giacomo Tarroni, Wenjia Bai, Antonio De Marvao, Georgia Doumou, Martin Rajchl, Reem Bedair, Sanjay Prasad, Stuart Cook, Declan O’Regan, Daniel Rueckert

Medical Image Computing and Computer-Assisted Intervention (MICCAI), 2018. [paper]

Semi-supervised learning for network-based cardiac MR image segmentation

Wenjia Bai, Ozan Oktay, Matthew Sinclair, Hideaki Suzuki, Martin Rajchl, Giacomo Tarroni, Ben Glocker, Andrew King, Paul M Matthews, Daniel Rueckert

Medical Image Computing and Computer-Assisted Intervention (MICCAI), 2017. [paper]

Fully automated segmentation-based respiratory motion correction of multiplanar cardiac magnetic resonance images for large-scale datasets

Matthew Sinclair, Wenjia Bai, Esther Puyol-Antón, Ozan Oktay, Daniel Rueckert, Andrew P King

Medical Image Computing and Computer-Assisted Intervention (MICCAI), 2017. [paper]

Multi-atlas segmentation using partially annotated data: Methods and annotation strategies

Lisa M Koch, Martin Rajchl, Wenjia Bai, Christian F Baumgartner, Tong Tong, Jonathan Passerat-Palmbach, Paul Aljabar, Daniel Rueckert

IEEE Transactions on Pattern Analysis and Machine Intelligence (PAMI), 2017. [paper]

Ensembles of multiple models and architectures for robust brain tumour segmentation

Konstantinos Kamnitsas, Wenjia Bai, Enzo Ferrante, Steven McDonagh, Matthew Sinclair, Nick Pawlowski, Martin Rajchl, Matthew Lee, Bernhard Kainz, Daniel Rueckert, Ben Glocker

MICCAI Brain Lesion (BrainLes) Workshop, 2017. (1st place in brain tumour segmentation challenge) [paper]

Multi-input cardiac image super-resolution using convolutional neural networks

Ozan Oktay, Wenjia Bai, Matthew Lee, Ricardo Guerrero, Konstantinos Kamnitsas, Jose Caballero, Antonio de Marvao, Stuart Cook, Declan O’Regan, Daniel Rueckert

Medical Image Computing and Computer-Assisted Intervention (MICCAI), 2016. [paper]

A bi-ventricular cardiac atlas built from 1000+ high resolution MR images of healthy subjects and an analysis of shape and motion

Wenjia Bai, Wenzhe Shi, Antonio de Marvao, Timothy JW Dawes, Declan P O’Regan, Stuart A Cook, Daniel Rueckert

Medical Image Analysis, 2015. [paper]

Multi-atlas segmentation with augmented features for cardiac MR images

Wenjia Bai, Wenzhe Shi, Christian Ledig, Daniel Rueckert

Medical Image Analysis, 2014. [paper]

A probabilistic patch-based label fusion model for multi-atlas segmentation with registration refinement: Application to cardiac MR images

Wenjia Bai, Wenzhe Shi, Declan P O'Regan, Tong Tong, Haiyan Wang, Shahnaz Jamil-Copley, Nicholas S Peters, Daniel Rueckert

IEEE Transactions on Medical Imaging, 2013. [paper]

Multi-atlas based segmentation with local label fusion for right ventricle MR images

Wenjia Bai, Wenzhe Shi, Haiyan Wang, Nicholas S Peters, Daniel Rueckert

MICCAI 2012 RV Segmentation Challenge in Cardiac MRI, 2012. (Best semi-automated method for the challenge) [paper]

Motion correction and attenuation correction for respiratory gated PET images

Wenjia Bai, Michael Brady

IEEE Transactions on Medical Imaging, 2011. [paper]

Regularized B-spline deformable registration for respiratory motion correction in PET images

Wenjia Bai, Michael Brady

Physics in Medicine & Biology, 2009. [paper]

Automatic dendritic spine analysis in two‐photon laser scanning microscopy images

Wenjia Bai, Xiaobo Zhou, Liang Ji, Jie Cheng, Stephen TC Wong

Cytometry A, 2007. [paper]