A Combined Surface And VOlumetric Registration (SAVOR) Framework to Study Cortical Biomarkers and Volumetric Imaging Data. - Eli Gibson; Ali R. Khan; Mirza Faisal Beg (MICCAI (1), 2009)

Registration of In Vivo Prostate Magnetic Resonance Images to Digital Histopathology Images. - Aaron D. Ward; Cathie Crukley; Charles A. McKenzie; Jacques Montreuil; Eli Gibson; Jose A. Gomez; Madeleine Moussa; Glenn Bauman; Aaron Fenster (Prostate Cancer Imaging, 2010)

Optic Nerve Head Registration Via Hemispherical Surface and Volume Registration. - Eli Gibson; Mei Young; Marinko Sarunic; Mirza Faisal Beg (IEEE Trans. Biomed. Eng., 2010)

Tissue block MRI for slice orientation-independent registration of digital histology images to ex vivo MRI of the prostate. - Eli Gibson; Cathie Crukley; Jose A. Gomez; Madeleine Moussa; Glenn Bauman; Aaron Fenster; Aaron D. Ward (ISBI, 2011)

Validation of Direct Registration of Whole-Mount Prostate Digital Histopathology to ex vivo MR Images. - Eli Gibson; Cathie Crukley; Jose A. Gomez; Madeleine Moussa; Joseph L. Chin; Glenn Bauman; Aaron Fenster; Aaron D. Ward (Prostate Cancer Imaging, 2011)

Registration Accuracy: How Good Is Good Enough? A Statistical Power Calculation Incorporating Image Registration Uncertainty. - Eli Gibson; Aaron Fenster; Aaron D. Ward (MICCAI (2), 2012)

Ultrasound-Based Characterization of Prostate Cancer: An in vivo Clinical Feasibility Study. - Farhad Imani; Purang Abolmaesumi; Eli Gibson; Amir Khojaste; Mena Gaed; Madeleine Moussa; Jose A. Gomez; Cesare Romagnoli; Robert Siemens; Michael Leveridge; Silvia D. Chang; Aaron Fenster; et al. (MICCAI (2), 2013)

3D prostate histology reconstruction: an evaluation of image-based and fiducial-based algorithms. - Eli Gibson; Mena Gaed; José A. Gómez; Madeleine Moussa; Cesare Romagnoli; Joseph L. Chin; Cathie Crukley; Glenn S. Bauman; Aaron Fenster; Aaron D. Ward (Digital Pathology, 2013)

Toward quantitative digital histopathology for prostate cancer: comparison of inter-slide interpolation methods for tumour measurement. - Mehrnoush Salarian; Maysam Shahedi; Eli Gibson; Mena Gaed; José A. Gómez; Madeleine Moussa; Glenn S. Bauman; Aaron D. Ward (Digital Pathology, 2013)

The impact of registration accuracy on imaging validation study design: A novel statistical power calculation. - Eli Gibson; Aaron Fenster; Aaron D. Ward (Medical Image Anal., 2013)

Multiparametric MR imaging of prostate cancer foci: assessing the detectability and localizability of Gleason 7 peripheral zone cancers based on image contrasts. - Eli Gibson; Mena Gaed; W. Thomas Hrinivich; José A. Gómez; Madeleine Moussa; Cesare Romagnoli; Jonathan Mandel; Matthew Bastian-Jordan; Derek W. Cool; Suha Ghoul; Stephen E. Pautler; Joseph L. Chin; et al. (Digital Pathology, 2014)

Accuracy and variability of tumor burden measurement on multi-parametric MRI. - Mehrnoush Salarian; Eli Gibson; Maysam Shahedi; Mena Gaed; José A. Gómez; Madeleine Moussa; Cesare Romagnoli; Derek W. Cool; Matthew Bastian-Jordan; Joseph L. Chin; Stephen E. Pautler; Glenn S. Bauman; et al. (Digital Pathology, 2014)

3D reconstruction of digitized histological sections for vasculature quantification in the mouse hind limb. - Yiwen Xu; J. Geoffrey Pickering; Zengxuan Nong; Eli Gibson; Aaron D. Ward (Digital Pathology, 2014)

A dimensionless dynamic contrast enhanced MRI parameter for intra-prostatic tumour target volume delineation: initial comparison with histology. - W. Thomas Hrinivich; Eli Gibson; Mena Gaed; Jose A. Gomez; Madeleine Moussa; Charles A. McKenzie; Glenn S. Bauman; Aaron D. Ward; Aaron Fenster; Eugene Wong 002 (Image-Guided Procedures, 2014)

Using Hidden Markov Models to capture temporal aspects of ultrasound data in prostate cancer. - Layan Nahlawi; Farhad Imani; Mena Gaed; Jose A. Gomez; Madeleine Moussa; Eli Gibson; Aaron Fenster; Aaron D. Ward; Purang Abolmaesumi; Parvin Mousavi; Hagit Shatkay (BIBM, 2015)

Statistical Power in Image Segmentation: Relating Sample Size to Reference Standard Quality. - Eli Gibson; Henkjan J. Huisman; Dean C. Barratt (MICCAI (3), 2015)

Population-based prediction of subject-specific prostate deformation for MR-to-ultrasound image registration. - Yipeng Hu; Eli Gibson; Hashim Uddin Ahmed; Caroline M. Moore; Mark Emberton; Dean C. Barratt (Medical Image Anal., 2015)

Ultrasound-Based Characterization of Prostate Cancer Using Joint Independent Component Analysis. - Farhad Imani; Mahdi Ramezani; Saman Nouranian; Eli Gibson; Amir Khojaste; Mena Gaed; Madeleine Moussa; Jose A. Gomez; Cesare Romagnoli; Michael Leveridge; Silvia D. Chang; Aaron Fenster; et al. (IEEE Trans. Biomed. Eng., 2015)

Computer-Aided Prostate Cancer Detection Using Ultrasound RF Time Series: In Vivo Feasibility Study. - Farhad Imani; Purang Abolmaesumi; Eli Gibson; Amir Khojaste; Mena Gaed; Madeleine Moussa; Jose A. Gomez; Cesare Romagnoli; Michael Leveridge; Silvia D. Chang; Robert Siemens; Aaron Fenster; et al. (IEEE Trans. Medical Imaging, 2015)

Fusion of multi-parametric MRI and temporal ultrasound for characterization of prostate cancer: in vivo feasibility study. - Farhad Imani; Sahar Ghavidel; Purang Abolmaesumi; Siavash Khallaghi; Eli Gibson; Amir Khojaste; Mena Gaed; Madeleine Moussa; Jose A. Gomez; Cesare Romagnoli; Derek W. Cool; Matthew Bastian-Jordan; et al. (Computer-Aided Diagnosis, 2016)

2D-3D Registration Accuracy Estimation for Optimised Planning of Image-Guided Pancreatobiliary Interventions. - Yipeng Hu; Ester Bonmati; Eli Gibson; John H. Hipwell; David J. Hawkes; Steven Bandula; Stephen P. Pereira; Dean C. Barratt (MICCAI (1), 2016)

Prostate Cancer: Improved Tissue Characterization by Temporal Modeling of Radio-Frequency Ultrasound Echo Data. - Layan Nahlawi; Farhad Imani; Mena Gaed; Jose A. Gomez; Madeleine Moussa; Eli Gibson; Aaron Fenster; Aaron D. Ward; Purang Abolmaesumi; Hagit Shatkay; Parvin Mousavi (MICCAI (1), 2016)

Classification of prostate cancer grade using temporal ultrasound: in vivo feasibility study. - Sahar Ghavidel; Farhad Imani; Siavash Khallaghi; Eli Gibson; Amir Khojaste; Mena Gaed; Madeleine Moussa; Jose A. Gomez; D. Robert Siemens; Michael Leveridge; Silvia D. Chang; Aaron Fenster; et al. (Image-Guided Procedures, 2016)

Impact of region contouring variability on image-based focal therapy evaluation. - Eli Gibson; Ian A. Donaldson; Taimur T. Shah; Yipeng Hu; Hashim Uddin Ahmed; Dean C. Barratt (Image-Guided Procedures, 2016)

How does prostate biopsy guidance error impact pathologic cancer risk assessment? - Peter R. Martin; Mena Gaed; José A. Gómez; Madeleine Moussa; Eli Gibson; Derek W. Cool; Joseph L. Chin; Stephen E. Pautler; Aaron Fenster; Aaron D. Ward (Image-Guided Procedures, 2016)

A Graph-Based Multi-kernel Feature Weight Learning Framework for Detection and Grading of Prostate Lesions Using Multi-parametric MR Images. - Weifu Chen; Bernard Chiu; Eli Gibson; Matthew Bastian-Jordan; Derek Cool; Zahra Kassam; Huageng Liang; Aaron D. Ward; Qi Shen; Guocan Feng (ACPR, 2017)

Prostate lesion detection and localization based on locality alignment discriminant analysis. - Mingquan Lin; Weifu Chen; Mingbo Zhao; Eli Gibson; Matthew Bastian-Jordan; Derek W. Cool; Zahra Kassam; Tommy W. S. Chow; Aaron D. Ward; Bernard Chiu (Computer-Aided Diagnosis, 2017)

Towards Image-Guided Pancreas and Biliary Endoscopy: Automatic Multi-organ Segmentation on Abdominal CT with Dense Dilated Networks. - Eli Gibson; Francesco Giganti; Yipeng Hu; Ester Bonmati; Steve Bandula; Kurinchi Gurusamy; Brian R. Davidson; Stephen P. Pereira; Matthew J. Clarkson; Dean C. Barratt (MICCAI (1), 2017)

Freehand Ultrasound Image Simulation with Spatially-Conditioned Generative Adversarial Networks. - Yipeng Hu; Eli Gibson; Li-Lin Lee; Weidi Xie; Dean C. Barratt; Tom Vercauteren; J. Alison Noble (CMMI/RAMBO/SWITCH@MICCAI, 2017)

Intraoperative Organ Motion Models with an Ensemble of Conditional Generative Adversarial Networks. - Yipeng Hu; Eli Gibson; Tom Vercauteren; Hashim Uddin Ahmed; Mark Emberton; Caroline M. Moore; J. Alison Noble; Dean C. Barratt (MICCAI (2), 2017)

Deep residual networks for automatic segmentation of laparoscopic videos of the liver. - Eli Gibson; Maria R. Robu; Stephen A. Thompson; Eddie Edwards; Crispin Schneider; Kurinchi Gurusamy; Brian R. Davidson; David J. Hawkes; Dean C. Barratt; Matthew J. Clarkson (Image-Guided Procedures, 2017)

Models of temporal enhanced ultrasound data for prostate cancer diagnosis: the impact of time-series order. - Layan Nahlawi; Caroline Goncalves; Farhad Imani; Mena Gaed; Jose A. Gomez; Madeleine Moussa; Eli Gibson; Aaron Fenster; Aaron D. Ward; Purang Abolmaesumi; Parvin Mousavi; Hagit Shatkay (Image-Guided Procedures, 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)

Label-driven weakly-supervised learning for multimodal deformable image registration. - Yipeng Hu; Marc Modat; Eli Gibson; Nooshin Ghavami; Ester Bonmati; Caroline M. Moore; Mark Emberton; J. Alison Noble; Dean C. Barratt; Tom Vercauteren (CoRR, 2017)

Designing image segmentation studies: Statistical power, sample size and reference standard quality. - Eli Gibson; Yipeng Hu; Henkjan J. Huisman; Dean C. Barratt (Medical Image Anal., 2017)

Label-driven weakly-supervised learning for multimodal deformarle image registration. - Yipeng Hu; Marc Modat; Eli Gibson; Nooshin Ghavami; Ester Bonmati; Caroline M. Moore; Mark Emberton; J. Alison Noble; Dean C. Barratt; Tom Vercauteren (ISBI, 2018)

Development of a computer aided diagnosis model for prostate cancer classification on multi-parametric MRI. - Ryan Alfano; D. Soetemans; Glenn S. Bauman; Eli Gibson; Mena Gaed; Madeleine Moussa; Jose A. Gomez; Joseph L. Chin; Stephen E. Pautler; Aaron D. Ward (Computer-Aided Diagnosis, 2018)

Inter-site Variability in Prostate Segmentation Accuracy Using Deep Learning. - Eli Gibson; Yipeng Hu; Nooshin Ghavami; Hashim Uddin Ahmed; Caroline M. Moore; Mark Emberton; Henkjan J. Huisman; Dean C. Barratt (MICCAI (4), 2018)

Adversarial Deformation Regularization for Training Image Registration Neural Networks. - Yipeng Hu; Eli Gibson; Nooshin Ghavami; Ester Bonmati; Caroline M. Moore; Mark Emberton; Tom Vercauteren; J. Alison Noble; Dean C. Barratt (MICCAI (1), 2018)

Automatic slice segmentation of intraoperative transrectal ultrasound images using convolutional neural networks. - Nooshin Ghavami; Yipeng Hu; Ester Bonmati; Rachael Rodell; Eli Gibson; Caroline M. Moore; Dean C. Barratt (Image-Guided Procedures, 2018)

Determination of optimal ultrasound planes for the initialisation of image registration during endoscopic ultrasound-guided procedures. - Ester Bonmati; Yipeng Hu; Eli Gibson; Laura Uribarri; Geri Keane; Kurinchi Gurusamy; Brian R. Davidson; Stephen P. Pereira; Matthew J. Clarkson; Dean C. Barratt (Int. J. Comput. Assist. Radiol. Surg., 2018)

A self-tuned graph-based framework for localization and grading prostate cancer lesions: An initial evaluation based on multiparametric magnetic resonance imaging. - Weifu Chen; Mingquan Lin; Eli Gibson; Matthew Bastian-Jordan; Derek W. Cool; Zahra Kassam; Huageng Liang; Guocan Feng; Aaron D. Ward; Bernard Chiu (Comput. Biol. Medicine, 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)

Decompose to manipulate: Manipulable Object Synthesis in 3D Medical Images with Structured Image Decomposition. - Siqi Liu 001; Eli Gibson; Sasa Grbic; Zhoubing Xu; Arnaud Arindra Adiyoso Setio; Jie Yang 041; Bogdan Georgescu; Dorin Comaniciu (CoRR, 2018)

The semiotics of medical image Segmentation. - John S. H. Baxter; Eli Gibson; Roy Eagleson; Terry M. Peters (Medical Image Anal., 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)

Stochastic Modeling of Temporal Enhanced Ultrasound: Impact of Temporal Properties on Prostate Cancer Characterization. - Layan Nahlawi; Caroline Goncalves; Farhad Imani; Mena Gaed; Jose A. Gomez; Madeleine Moussa; Eli Gibson; Aaron Fenster; Aaron D. Ward; Purang Abolmaesumi; Hagit Shatkay; Parvin Mousavi (IEEE Trans. Biomed. Eng., 2018)

Automatic Multi-Organ Segmentation on Abdominal CT With Dense V-Networks. - Eli Gibson; Francesco Giganti; Yipeng Hu; Ester Bonmati; Steve Bandula; Kurinchi Gurusamy; Brian R. Davidson; Stephen P. Pereira; Matthew J. Clarkson; Dean C. Barratt (IEEE Trans. Medical Imaging, 2018)

Class-Aware Adversarial Lung Nodule Synthesis In CT Images. - Jie Yang 041; Siqi Liu 001; Sasa Grbic; Arnaud Arindra Adiyoso Setio; Zhoubing Xu; Eli Gibson; Guillaume Chabin; Bogdan Georgescu; Andrew F. Laine; Dorin Comaniciu (ISBI, 2019)

Quantifying and Leveraging Classification Uncertainty for Chest Radiograph Assessment. - Florin C. Ghesu; Bogdan Georgescu; Eli Gibson; Sebastian Gündel; Mannudeep K. Kalra; Ramandeep Singh; Subba R. Digumarthy; Sasa Grbic; Dorin Comaniciu (MICCAI (6), 2019)

Conditional Segmentation in Lieu of Image Registration. - Yipeng Hu; Eli Gibson; Dean C. Barratt; Mark Emberton; J. Alison Noble; Tom Vercauteren (MICCAI (2), 2019)

Multi-task Learning for Chest X-ray Abnormality Classification on Noisy Labels. - Sebastian Gündel; Florin C. Ghesu; Sasa Grbic; Eli Gibson; Bogdan Georgescu; Andreas K. Maier; Dorin Comaniciu (CoRR, 2019)

Automatic segmentation of prostate MRI using convolutional neural networks: Investigating the impact of network architecture on the accuracy of volume measurement and MRI-ultrasound registration. - Nooshin Ghavami; Yipeng Hu; Eli Gibson; Ester Bonmati; Mark Emberton; Caroline M. Moore; Dean C. Barratt (Medical Image Anal., 2019)

Graph Attention Network based Pruning for Reconstructing 3D Liver Vessel Morphology from Contrasted CT Images. - Donghao Zhang; Siqi Liu 001; Shikha Chaganti; Eli Gibson; Zhoubing Xu; Sasa Grbic; Weidong Cai 001; Dorin Comaniciu (CoRR, 2020)

Brain midline shift detection and quantification by a cascaded deep network pipeline on non-contrast computed tomography scans. - Nguyen P. Nguyen; Youngjin Yoo; Andrei Chekkoury; Eva Eibenberger; Thomas J. Re; Jyotipriya Das; Abishek Balachandran; Yvonne W. Lui; Pina C. Sanelli; Thomas J. Schroeppel; Uttam Bodanapally; Savvas Nicolaou; et al. (ICCVW, 2021)

Quantifying and leveraging predictive uncertainty for medical image assessment. - Florin C. Ghesu; Bogdan Georgescu; Awais Mansoor; Youngjin Yoo; Eli Gibson; R. S. Vishwanath; Abishek Balachandran; James M. Balter; Yue Cao; Ramandeep Singh; Subba R. Digumarthy; Mannudeep K. Kalra; et al. (Medical Image Anal., 2021)

No Surprises: Training Robust Lung Nodule Detection for Low-Dose CT Scans by Augmenting With Adversarial Attacks. - Siqi Liu 001; Arnaud Arindra Adiyoso Setio; Florin C. Ghesu; Eli Gibson; Sasa Grbic; Bogdan Georgescu; Dorin Comaniciu (IEEE Trans. Medical Imaging, 2021)

The importance of data domain on self-supervised learning for brain metastasis detection and segmentation. - Youngjin Yoo; Gengyan Zhao; Andreea Sandu; Thomas J. Re; Jyotipriya Das; Hesheng Wang 003; Michelle Kim; Colette Shen; Yueh Lee; Douglas Kondziolka; Mohannad Ibrahim; Jun Lian; et al. (Computer-Aided Diagnosis, 2023)

3D-2D GAN based brain metastasis synthesis with configurable parameters for fully 3D data augmentation. - Gengyan Zhao; Youngjin Yoo; Thomas J. Re; Jyotipriya Das; Hesheng Wang 003; Michelle Kim; Colette Shen; Yueh Lee; Douglas Kondziolka; Mohannad Ibrahim; Jun Lian; Rajan Jain; et al. (Image Processing, 2023)

Self Pre-Training with Adaptive Mask Autoencoders for Variable-Contrast 3D Medical Imaging. - Badhan Kumar Das; Gengyan Zhao; Han Liu; Thomas J. Re; Dorin Comaniciu; Eli Gibson; Andreas K. Maier (ISBI, 2025)

A Non-contrast Head CT Foundation Model for Comprehensive Neuro-Trauma Triage. - Youngjin Yoo; Bogdan Georgescu; Yanbo Zhang; Sasa Grbic; Han Liu; Gabriela D. Aldea; Thomas J. Re; Jyotipriya Das; Poikavila Ullaskrishnan; Eva Eibenberger; Andrei Chekkoury; Uttam Bodanapally; et al. (CoRR, 2025)

AdaViT: Adaptive Vision Transformer for Flexible Pretrain and Finetune with Variable 3D Medical Image Modalities. - Badhan Kumar Das; Gengyan Zhao; Han Liu; Thomas J. Re; Dorin Comaniciu; Eli Gibson; Andreas K. Maier (CoRR, 2025)

Multi-Plane Vision Transformer for Hemorrhage Classification Using Axial and Sagittal MRI Data. - Badhan Kumar Das; Gengyan Zhao; Boris Mailhé; Thomas J. Re; Dorin Comaniciu; Eli Gibson; Andreas K. Maier (CoRR, 2025)

VIViT: Variable-Input Vision Transformer Framework for 3D MR Image Segmentation. - Badhan Kumar Das; Ajay Singh; Gengyan Zhao; Han Liu; Thomas J. Re; Dorin Comaniciu; Eli Gibson; Andreas K. Maier (CoRR, 2025)