Classification of colorectal polyp regions in optical projection tomography. - Wenqi Li 001; Jianguo Zhang 001; Stephen J. McKenna; Maria Coats; Frank A. Carey (ISBI, 2013)

Learning from Partially Annotated OPT Images by Contextual Relevance Ranking. - Wenqi Li 001; Jianguo Zhang 001; Wei-Shi Zheng 001; Maria Coats; Frank A. Carey; Stephen J. McKenna (MICCAI (3), 2013)

HEp-2 Cell Classification Using Multi-resolution Local Patterns and Ensemble SVMs. - Siyamalan Manivannan; Wenqi Li 001; Shazia Akbar; Ruixuan Wang; Jianguo Zhang 001; Stephen J. McKenna (I3A@ICPR, 2014)

HEp-2 Specimen Classification Using Multi-resolution Local Patterns and SVM. - Siyamalan Manivannan; Wenqi Li 001; Shazia Akbar; Ruixuan Wang; Jianguo Zhang 001; Stephen J. McKenna (I3A@ICPR, 2014)

Multiple Instance Cancer Detection by Boosting Regularised Trees. - Wenqi Li 001; Jianguo Zhang 001; Stephen J. McKenna (MICCAI (1), 2015)

Discriminating dysplasia: Optical tomographic texture analysis of colorectal polyps. - Wenqi Li 001; Maria Coats; Jianguo Zhang 001; Stephen J. McKenna (Medical Image Anal., 2015)

Gland segmentation in colon histology images using hand-crafted features and convolutional neural networks. - Wenqi Li 001; Siyamalan Manivannan; Shazia Akbar; Jianguo Zhang 001; Emanuele Trucco; Stephen J. McKenna (ISBI, 2016)

Local structure prediction for gland segmentation. - Siyamalan Manivannan; Wenqi Li 001; Shazia Akbar; Jianguo Zhang 001; Emanuele Trucco; Stephen J. McKenna (ISBI, 2016)

Real-Time Segmentation of Non-rigid Surgical Tools Based on Deep Learning and Tracking. - Luis C. García-Peraza-Herrera; Wenqi Li 001; Caspar Gruijthuijsen; Alain Devreker; George Attilakos; Jan Deprest; Emmanuel B. Vander Poorten; Danail Stoyanov; Tom Vercauteren; Sébastien Ourselin (CARE@MICCAI, 2016)

An automated pattern recognition system for classifying indirect immunofluorescence images of HEp-2 cells and specimens. - Siyamalan Manivannan; Wenqi Li 001; Shazia Akbar; Ruixuan Wang; Jianguo Zhang 001; Stephen J. McKenna (Pattern Recognit., 2016)

On the Compactness, Efficiency, and Representation of 3D Convolutional Networks: Brain Parcellation as a Pretext Task. - Wenqi Li 001; Guotai Wang; Lucas Fidon; Sébastien Ourselin; M. Jorge Cardoso; Tom Vercauteren (IPMI, 2017)

ToolNet: Holistically-nested real-time segmentation of robotic surgical tools. - Luis C. García-Peraza-Herrera; Wenqi Li 001; Lucas Fidon; Caspar Gruijthuijsen; Alain Devreker; George Attilakos; Jan Deprest; Emmanuel B. Vander Poorten; Danail Stoyanov; Tom Vercauteren; Sébastien Ourselin (IROS, 2017)

Scalable Multimodal Convolutional Networks for Brain Tumour Segmentation. - Lucas Fidon; Wenqi Li 001; Luis C. García-Peraza-Herrera; Jinendra Ekanayake; Neil Kitchen; Sébastien Ourselin; Tom Vercauteren (MICCAI (3), 2017)

Generalised Wasserstein Dice Score for Imbalanced Multi-class Segmentation Using Holistic Convolutional Networks. - Lucas Fidon; Wenqi Li 001; Luis C. García-Peraza-Herrera; Jinendra Ekanayake; Neil Kitchen; Sébastien Ourselin; Tom Vercauteren (BrainLes@MICCAI, 2017)

Generalised Dice Overlap as a Deep Learning Loss Function for Highly Unbalanced Segmentations. - Carole H. Sudre; Wenqi Li 001; Tom Vercauteren; Sébastien Ourselin; M. Jorge Cardoso (DLMIA/ML-CDS@MICCAI, 2017)

Automatic Brain Tumor Segmentation Using Cascaded Anisotropic Convolutional Neural Networks. - Guotai Wang; Wenqi Li 001; Sébastien Ourselin; Tom Vercauteren (BrainLes@MICCAI, 2017)

Multi-scale analysis of the surface morphology of colorectal polyps from optical tomography. - Jingjing Zhang; Jianguo Zhang 001; Maria Coats; Wenqi Li 001; Frank A. Carey; Stephen J. McKenna (Comput. methods Biomech. Biomed. Eng. Imaging Vis., 2017)

NiftyNet: a deep-learning platform for medical imaging. - Eli Gibson; Wenqi Li 001; Carole H. Sudre; Lucas Fidon; Dzhoshkun I. Shakir; Guotai Wang; Zach Eaton-Rosen; Robert J. Gray; Tom Doel; Yipeng Hu; Tom Whyntie; Parashkev Nachev; et al. (CoRR, 2017)

Uncertainty in Multitask Learning: Joint Representations for Probabilistic MR-only Radiotherapy Planning. - Felix J. S. Bragman; Ryutaro Tanno; Zach Eaton-Rosen; Wenqi Li 001; David J. Hawkes; Sébastien Ourselin; Daniel C. Alexander; Jamie R. McClelland; M. Jorge Cardoso (MICCAI (4), 2018)

An Automated Localization, Segmentation and Reconstruction Framework for Fetal Brain MRI. - Michael Ebner; Guotai Wang; Wenqi Li 001; Michael Aertsen; Premal A. Patel; Rosalind Aughwane; Andrew Melbourne; Tom Doel; Anna L. David; Jan Deprest; Sébastien Ourselin; Tom Vercauteren (MICCAI (1), 2018)

Deep Boosted Regression for MR to CT Synthesis. - Kerstin Kläser 002; Pawel Markiewicz; Marta Bianca Maria Ranzini; Wenqi Li 001; Marc Modat; Brian F. Hutton; David Atkinson; Kris Thielemans; M. Jorge Cardoso; Sébastien Ourselin (SASHIMI@MICCAI, 2018)

Automatic Brain Tumor Segmentation Using Convolutional Neural Networks with Test-Time Augmentation. - Guotai Wang; Wenqi Li 001; Sébastien Ourselin; Tom Vercauteren (BrainLes@MICCAI (2), 2018)

NiftyNet: a deep-learning platform for medical imaging. - Eli Gibson; Wenqi Li 001; Carole H. Sudre; Lucas Fidon; Dzhoshkun I. Shakir; Guotai Wang; Zach Eaton-Rosen; Robert J. Gray; Tom Doel; Yipeng Hu; Tom Whyntie; Parashkev Nachev; et al. (Comput. Methods Programs Biomed., 2018)

Interpretable Fully Convolutional Classification of Intrapapillary Capillary Loops for Real-Time Detection of Early Squamous Neoplasia. - Luis C. García-Peraza-Herrera; Martin Everson; Wenqi Li 001; Inmanol Luengo; Lorenz Berger; Omer F. Ahmad; Laurence B. Lovat; Hsiu-Po Wang; Wen-Lun Wang; Rehan J. Haidry; Danail Stoyanov; Tom Vercauteren; et al. (CoRR, 2018)

Weakly-supervised convolutional neural networks for multimodal image registration. - Yipeng Hu; Marc Modat; Eli Gibson; Wenqi Li 001; Nooshin Ghavami; Ester Bonmati; Guotai Wang; Steven Bandula; Caroline M. Moore; Mark Emberton; Sébastien Ourselin; J. Alison Noble; et al. (Medical Image Anal., 2018)

Structure Prediction for Gland Segmentation With Hand-Crafted and Deep Convolutional Features. - Siyamalan Manivannan; Wenqi Li 001; Jianguo Zhang 001; Emanuele Trucco; Stephen J. McKenna (IEEE Trans. Medical Imaging, 2018)

Interactive Medical Image Segmentation Using Deep Learning With Image-Specific Fine Tuning. - Guotai Wang; Wenqi Li 001; Maria A. Zuluaga; Rosalind Pratt; Premal A. Patel; Michael Aertsen; Tom Doel; Anna L. David; Jan Deprest; Sébastien Ourselin; Tom Vercauteren (IEEE Trans. Medical Imaging, 2018)

Privacy-Preserving Federated Brain Tumour Segmentation. - Wenqi Li 001; Fausto Milletarì; Daguang Xu; Nicola Rieke; Jonny Hancox; Wentao Zhu 001; Maximilian Baust; Yan Cheng; Sébastien Ourselin; M. Jorge Cardoso; Andrew Feng (MLMI@MICCAI, 2019)

Automatic Segmentation of Vestibular Schwannoma from T2-Weighted MRI by Deep Spatial Attention with Hardness-Weighted Loss. - Guotai Wang; Jonathan Shapey; Wenqi Li 001; Reuben Dorent; Alex Demitriadis; Sotirios Bisdas; Ian Paddick; Robert Bradford; Shaoting Zhang 001; Sébastien Ourselin; Tom Vercauteren (MICCAI (2), 2019)

Learning joint lesion and tissue segmentation from task-specific hetero-modal datasets. - Reuben Dorent; Wenqi Li 001; Jinendra Ekanayake; Sébastien Ourselin; Tom Vercauteren (MIDL, 2019)

2017 Robotic Instrument Segmentation Challenge. - Max Allan; Alexey Shvets; Thomas Kurmann; Zichen Zhang 001; Rahul Duggal; Yun-Hsuan Su; Nicola Rieke; Iro Laina; Niveditha Kalavakonda; Sebastian Bodenstedt; Luis C. García-Peraza; Wenqi Li 001; et al. (CoRR, 2019)

Automatic Segmentation of Vestibular Schwannoma from T2-Weighted MRI by Deep Spatial Attention with Hardness-Weighted Loss. - Guotai Wang; Jonathan Shapey; Wenqi Li 001; Reuben Dorent; Alex Demitriadis; Sotirios Bisdas; Ian Paddick; Robert Bradford; Sébastien Ourselin; Tom Vercauteren (CoRR, 2019)

Automatic Brain Tumor Segmentation Based on Cascaded Convolutional Neural Networks With Uncertainty Estimation. - Guotai Wang; Wenqi Li 001; Sébastien Ourselin; Tom Vercauteren (Frontiers Comput. Neurosci., 2019)

Aleatoric uncertainty estimation with test-time augmentation for medical image segmentation with convolutional neural networks. - Guotai Wang; Wenqi Li 001; Michael Aertsen; Jan Deprest; Sébastien Ourselin; Tom Vercauteren (Neurocomputing, 2019)

DeepIGeoS: A Deep Interactive Geodesic Framework for Medical Image Segmentation. - Guotai Wang; Maria A. Zuluaga; Wenqi Li 001; Rosalind Pratt; Premal A. Patel; Michael Aertsen; Tom Doel; Anna L. David; Jan Deprest; Sébastien Ourselin; Tom Vercauteren (IEEE Trans. Pattern Anal. Mach. Intell., 2019)

Deep Class-Specific Affinity-Guided Convolutional Network for Multimodal Unpaired Image Segmentation. - Jingkun Chen; Wenqi Li 001; Hongwei Li 004; Jianguo Zhang 001 (MICCAI (4), 2020)

Federated Learning for Breast Density Classification: A Real-World Implementation. - Holger R. Roth; Ken Chang; Praveer Singh; Nir Neumark; Wenqi Li 001; Vikash Gupta; Sharut Gupta; Liangqiong Qu; Alvin Ihsani; Bernardo C. Bizzo; Yuhong Wen; Varun Buch; et al. (DART/DCL@MICCAI, 2020)

LAMP: Large Deep Nets with Automated Model Parallelism for Image Segmentation. - Wentao Zhu 001; Can Zhao 001; Wenqi Li 001; Holger Roth; Ziyue Xu 001; Daguang Xu (MICCAI (4), 2020)

NeurReg: Neural Registration and Its Application to Image Segmentation. - Wentao Zhu 001; Andriy Myronenko; Ziyue Xu 001; Wenqi Li 001; Holger Roth; Yufang Huang; Fausto Milletari; Daguang Xu (WACV, 2020)

An automated framework for localization, segmentation and super-resolution reconstruction of fetal brain MRI. - Michael Ebner; Guotai Wang; Wenqi Li 001; Michael Aertsen; Premal A. Patel; Rosalind Aughwane; Andrew Melbourne; Tom Doel; Steven Dymarkowski; Paolo De Coppi; Anna L. David; Jan Deprest; et al. (NeuroImage, 2020)

The future of digital health with federated learning. - Nicola Rieke; Jonny Hancox; Wenqi Li 001; Fausto Milletarì; Holger R. Roth; Shadi Albarqouni; Spyridon Bakas; Mathieu N. Galtier; Bennett A. Landman; Klaus H. Maier-Hein; Sébastien Ourselin; Micah J. Sheller; et al. (npj Digit. Medicine, 2020)

Federated Whole Prostate Segmentation in MRI with Personalized Neural Architectures. - Holger R. Roth; Dong Yang 005; Wenqi Li 001; Andriy Myronenko; Wentao Zhu 001; Ziyue Xu 001; Xiaosong Wang 001; Daguang Xu (MICCAI (3), 2021)

Auto-FedAvg: Learnable Federated Averaging for Multi-Institutional Medical Image Segmentation. - Yingda Xia; Dong Yang 005; Wenqi Li 001; Andriy Myronenko; Daguang Xu; Hirofumi Obinata; Hitoshi Mori; Peng An; Stephanie A. Harmon; Evrim Turkbey; Baris Turkbey; Bradford J. Wood; et al. (CoRR, 2021)

Federated semi-supervised learning for COVID region segmentation in chest CT using multi-national data from China, Italy, Japan. - Dong Yang 005; Ziyue Xu 001; Wenqi Li 001; Andriy Myronenko; Holger R. Roth; Stephanie A. Harmon; Sheng Xu 001; Baris Turkbey; Evrim Turkbey; Xiaosong Wang 001; Wentao Zhu 001; Gianpaolo Carrafiello; et al. (Medical Image Anal., 2021)

Learning joint segmentation of tissues and brain lesions from task-specific hetero-modal domain-shifted datasets. - Reuben Dorent; Thomas C. Booth; Wenqi Li 001; Carole H. Sudre; Sina Kafiabadi; Manuel Jorge Cardoso; Sébastien Ourselin; Tom Vercauteren (Medical Image Anal., 2021)

GradViT: Gradient Inversion of Vision Transformers. - Ali Hatamizadeh; Hongxu Yin; Holger Roth; Wenqi Li 001; Jan Kautz; Daguang Xu; Pavlo Molchanov 001 (CVPR, 2022)

Self-Supervised Pre-Training of Swin Transformers for 3D Medical Image Analysis. - Yucheng Tang; Dong Yang 005; Wenqi Li 001; Holger R. Roth; Bennett A. Landman; Daguang Xu; Vishwesh Nath; Ali Hatamizadeh (CVPR, 2022)

Closing the Generalization Gap of Cross-silo Federated Medical Image Segmentation. - An Xu; Wenqi Li 001; Pengfei Guo; Dong Yang 005; Holger Roth; Ali Hatamizadeh; Can Zhao 001; Daguang Xu; Heng Huang; Ziyue Xu 001 (CVPR, 2022)

Auto-FedRL: Federated Hyperparameter Optimization for Multi-institutional Medical Image Segmentation. - Pengfei Guo; Dong Yang 005; Ali Hatamizadeh; An Xu; Ziyue Xu 001; Wenqi Li 001; Can Zhao 001; Daguang Xu; Stephanie A. Harmon; Evrim Turkbey; Baris Turkbey; Bradford J. Wood; et al. (ECCV (21), 2022)

Split-U-Net: Preventing Data Leakage in Split Learning for Collaborative Multi-modal Brain Tumor Segmentation. - Holger R. Roth; Ali Hatamizadeh; Ziyue Xu 001; Can Zhao 001; Wenqi Li 001; Andriy Myronenko; Daguang Xu (DeCaF/FAIR@MICCAI, 2022)

MONAI Label: A framework for AI-assisted Interactive Labeling of 3D Medical Images. - Andres Diaz-Pinto; Sachidanand Alle; Alvin Ihsani; Muhammad Asad 001; Vishwesh Nath; Fernando Pérez-García; Pritesh Mehta; Wenqi Li 001; Holger R. Roth; Tom Vercauteren; Daguang Xu; Prerna Dogra; et al. (CoRR, 2022)

UNetFormer: A Unified Vision Transformer Model and Pre-Training Framework for 3D Medical Image Segmentation. - Ali Hatamizadeh; Ziyue Xu 001; Dong Yang 005; Wenqi Li 001; Holger Roth; Daguang Xu (CoRR, 2022)

MONAI: An open-source framework for deep learning in healthcare. - M. Jorge Cardoso; Wenqi Li 001; Richard Brown 004; Nic Ma; Eric Kerfoot; Yiheng Wang; Benjamin Murray; Andriy Myronenko; Can Zhao 001; Dong Yang 005; Vishwesh Nath; Yufan He; et al. (CoRR, 2022)

Rapid artificial intelligence solutions in a pandemic - The COVID-19-20 Lung CT Lesion Segmentation Challenge. - Holger R. Roth; Ziyue Xu 001; Carlos Tor-Díez; Ramon Sánchez-Jacob; Jonathan Zember; Jose Molto; Wenqi Li 001; Sheng Xu 001; Baris Turkbey; Evrim Turkbey; Dong Yang 005; Ahmed Harouni; et al. (Medical Image Anal., 2022)

Fair Federated Medical Image Segmentation via Client Contribution Estimation. - Meirui Jiang; Holger R. Roth; Wenqi Li 001; Dong Yang 005; Can Zhao 001; Vishwesh Nath; Daguang Xu; Qi Dou 001; Ziyue Xu 001 (CVPR, 2023)

Communication-Efficient Vertical Federated Learning with Limited Overlapping Samples. - Jingwei Sun 002; Ziyue Xu 001; Dong Yang 005; Vishwesh Nath; Wenqi Li 001; Can Zhao 001; Daguang Xu; Yiran Chen 001; Holger R. Roth (ICCV, 2023)

DAST: Differentiable Architecture Search with Transformer for 3D Medical Image Segmentation. - Dong Yang 005; Ziyue Xu 001; Yufan He; Vishwesh Nath; Wenqi Li 001; Andriy Myronenko; Ali Hatamizadeh; Can Zhao 001; Holger R. Roth; Daguang Xu (MICCAI (3), 2023)

NVIDIA FLARE: Federated Learning from Simulation to Real-World. - Holger R. Roth; Yan Cheng; Yuhong Wen; Isaac Yang; Ziyue Xu 001; Yuan-Ting Hsieh; Kristopher Kersten; Ahmed Harouni; Can Zhao 001; Kevin Lu; Zhihong Zhang 001; Wenqi Li 001; et al. (IEEE Data Eng. Bull., 2023)

Do Gradient Inversion Attacks Make Federated Learning Unsafe? - Ali Hatamizadeh; Hongxu Yin; Pavlo Molchanov 001; Andriy Myronenko; Wenqi Li 001; Prerna Dogra; Andrew Feng; Mona G. Flores; Jan Kautz; Daguang Xu; Holger R. Roth (IEEE Trans. Medical Imaging, 2023)

Disruptive Autoencoders: Leveraging Low-level features for 3D Medical Image Pre-training. - Jeya Maria Jose Valanarasu; Yucheng Tang; Dong Yang 005; Ziyue Xu 001; Can Zhao 001; Wenqi Li 001; Vishal M. Patel; Bennett Allan Landman; Daguang Xu; Yufan He; Vishwesh Nath (MIDL, 2024)

IR-FRestormer: Iterative Refinement with Fourier-Based Restormer for Accelerated MRI Reconstruction. - Mohammad Zalbagi Darestani; Vishwesh Nath; Wenqi Li 001; Yufan He; Holger R. Roth; Ziyue Xu 001; Daguang Xu; Reinhard Heckel; Can Zhao 001 (WACV, 2024)

VISTA3D: Versatile Imaging SegmenTation and Annotation model for 3D Computed Tomography. - Yufan He; Pengfei Guo; Yucheng Tang; Andriy Myronenko; Vishwesh Nath; Ziyue Xu 001; Dong Yang 005; Can Zhao 001; Benjamin Simon; Mason Belue; Stephanie A. Harmon; Baris Turkbey; et al. (CoRR, 2024)

A Short Review and Evaluation of SAM2's Performance in 3D CT Image Segmentation. - Yufan He; Pengfei Guo; Yucheng Tang; Andriy Myronenko; Vishwesh Nath; Ziyue Xu 001; Dong Yang 005; Can Zhao 001; Daguang Xu; Wenqi Li 001 (CoRR, 2024)

VILA-M3: Enhancing Vision-Language Models with Medical Expert Knowledge. - Vishwesh Nath; Wenqi Li 001; Dong Yang 005; Andriy Myronenko; Mingxin Zheng; Yao Lu 006; Zhijian Liu; Hongxu Yin; Yee Man Law; Yucheng Tang; Pengfei Guo; Can Zhao 001; et al. (CoRR, 2024)

MONAI Label: A framework for AI-assisted interactive labeling of 3D medical images. - Andres Diaz-Pinto; Sachidanand Alle; Vishwesh Nath; Yucheng Tang; Alvin Ihsani; Muhammad Asad 001; Fernando Pérez-García; Pritesh Mehta; Wenqi Li 001; Mona Flores; Holger R. Roth; Tom Vercauteren; et al. (Medical Image Anal., 2024)

VISTA3D: A Unified Segmentation Foundation Model For 3D Medical Imaging. - Yufan He; Pengfei Guo; Yucheng Tang; Andriy Myronenko; Vishwesh Nath; Ziyue Xu 001; Dong Yang 005; Can Zhao 001; Benjamin Simon; Mason Belue; Stephanie A. Harmon; Baris Turkbey; et al. (CVPR, 2025)

VILA-M3: Enhancing Vision-Language Models with Medical Expert Knowledge. - Vishwesh Nath; Wenqi Li 001; Dong Yang 005; Andriy Myronenko; Mingxin Zheng; Yao Lu 006; Zhijian Liu; Hongxu Yin; Yee Man Law; Yucheng Tang; Pengfei Guo; Can Zhao 001; et al. (CVPR, 2025)