Jonathan Shapey

According to our database, Jonathan Shapey authored at least 32 papers between 2019 and 2025.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of four.

2025

Themed Challenges to Solve Data Scarcity in Africa: A Proposition for Increasing Local Data Collection and Integration.

Mubaraq Yakubu, Udunna Anazodo, Maruf Adewole, Theodore Barfoot, Tiarna Lee, Tom Vercauteren, Jonathan Shapey, Andrew P. King, Alexander Hammers

CoRR, August, 2025

Label tree semantic losses for rich multi-class medical image segmentation.

Junwen Wang, Oscar MacCormac, William Rochford, Aaron Kujawa, Jonathan Shapey, Tom Vercauteren

CoRR, July, 2025

X-RAFT: Cross-Modal Non-Rigid Registration of Blue and White Light Neurosurgical Hyperspectral Images.

Charlie Budd, Silvère Ségaud, Matthew Elliot, Graeme Stasiuk, Yijing Xie, Jonathan Shapey, Tom Vercauteren

CoRR, July, 2025

Tree-based Semantic Losses: Application to Sparsely-supervised Large Multi-class Hyperspectral Segmentation.

Junwen Wang, Oscar MacCormac, William Rochford, Aaron Kujawa, Jonathan Shapey, Tom Vercauteren

CoRR, June, 2025

Systematic Review of Pituitary Gland and Pituitary Adenoma Automatic Segmentation Techniques in Magnetic Resonance Imaging.

Mubaraq Yakubu, Navodini Wijethilake, Jonathan Shapey, Andrew P. King, Alexander Hammers

CoRR, June, 2025

crossMoDA Challenge: Evolution of Cross-Modality Domain Adaptation Techniques for Vestibular Schwannoma and Cochlea Segmentation from 2021 to 2023.

Navodini Wijethilake, Reuben Dorent, Marina Ivory, Aaron Kujawa, Stefan Cornelissen, Patrick Langenhuizen, Mohamed Okasha, Anna Oviedova, Hexin Dong, Bogyeong Kang, Guillaume Sallé, Luyi Han, Ziyuan Zhao, Han Liu, Tao Yang, Shahad Hardan, Hussain Alasmawi, Santosh Sanjeev, Yuzhou Zhuang, Satoshi Kondo, Maria G. Baldeon Calisto, Shaikh Muhammad Uzair Noman, Cancan Chen, Ipek Oguz, Rongguo Zhang, Mina Rezaei, Susana K. Lai-Yuen, Satoshi Kasai, Chih-Cheng Hung, Mohammad Yaqub, Lisheng Wang, Benoit M. Dawant, Cuntai Guan, Ritse Mann, Vincent Jaouen, Ji-Wung Han, Li Zhang, Jonathan Shapey, Tom Vercauteren

CoRR, June, 2025

A generalisable head MRI defacing pipeline: Evaluation on 2,566 meningioma scans.

Lorena Garcia-Foncillas Macias, Aaron Kujawa, Aya Elshalakany, Jonathan Shapey, Tom Vercauteren

CoRR, May, 2025

UltraFlwr - An Efficient Federated Medical and Surgical Object Detection Framework.

Yang Li, Soumya Snigdha Kundu, Maxence Boels, Toktam Mahmoodi, Sébastien Ourselin, Tom Vercauteren, Prokar Dasgupta, Jonathan Shapey, Alejandro Granados

CoRR, March, 2025

2024

Deep learning for automatic segmentation of vestibular schwannoma: a retrospective study from multi-center routine MRI.

Aaron Kujawa, Reuben Dorent, Steve Connor, Suki Thomson, Marina Ivory, Ali Vahedi, Emily Guilhem, Navodini Wijethilake, Robert Bradford, Neil Kitchen, Sotirios Bisdas, Sébastien Ourselin, Tom Vercauteren, Jonathan Shapey

Frontiers Comput. Neurosci., 2024

OOD-SEG: Out-Of-Distribution detection for image SEGmentation with sparse multi-class positive-only annotations.

Junwen Wang, Zhonghao Wang, Oscar MacCormac, Jonathan Shapey, Tom Vercauteren

CoRR, 2024

Scribble-Based Interactive Segmentation of Medical Hyperspectral Images.

Zhonghao Wang, Junwen Wang, Charlie Budd, Oscar MacCormac, Jonathan Shapey, Tom Vercauteren

CoRR, 2024

R-Trans - A Recurrent Transformer Model for Clinical Feedback in Surgical Skill Assessment.

Julien Quarez, Matthew Elliot, Oscar MacCormac, Nawal Khan, Marc Modat, Sébastien Ourselin, Jonathan Shapey, Alejandro Granados

CoRR, 2024

Brain Tumor Segmentation (BraTS) Challenge 2024: Meningioma Radiotherapy Planning Automated Segmentation.

Dominic LaBella, Katherine Schumacher, Michael Mix, Kevin Leu, Shan McBurney-Lin, Pierre Nedelec, Javier E. Villanueva-Meyer, Jonathan Shapey, Tom Vercauteren, Kazumi Chia, Omar Al-Salihi, Justin Leu, Lia Halasz, Yury Velichko, Chunhao Wang, John Kirkpatrick, Scott Floyd, Zachary J. Reitman, Trey Mullikin, Ulas Bagci, Sean Sachdev, Jona A. Hattangadi-Gluth, Tyler M. Seibert, Nikdokht Farid, Connor Puett, Matthew W. Pease, Kevin Shiue, Syed Muhammad Anwar, Shahriar Faghani, Muhammad Ammar Haider, Pranav I. Warman, Jake Albrecht, András Jakab, Mana Moassefi, Verena Chung, Alejandro Aristizabal, Alexandros Karargyris, Hasan Kassem, Sarthak Pati, Micah J. Sheller, Christina Huang, Aaron Coley, Siddharth Ghanta, Alex Schneider, Conrad Sharp, Rachit Saluja, Florian Kofler, Philipp Lohmann, Philipp Vollmuth, Louis Gagnon, Maruf Adewole, Hongwei Bran Li, Anahita Fathi Kazerooni, Nourel Hoda Tahon, Udunna Anazodo, Ahmed W. Moawad, Bjoern H. Menze, Marius George Linguraru, Mariam Aboian, Benedikt Wiestler, Ujjwal Baid, Gian Marco Conte, Andreas M. Rauschecker, Ayman Nada, Aly H. Abayazeed, Raymond Y. Huang, Maria Correia de Verdier, Jeffrey D. Rudie, Spyridon Bakas, Evan Calabrese

CoRR, 2024

MUTUAL: Towards Holistic Sensing and Inference in the Operating Room.

Julien Quarez, Yang Li, Hassna Irzan, Matthew Elliot, Oscar MacCormac, James Knigth, Martin Huber, Toktam Mahmoodi, Prokar Dasgupta, Sébastien Ourselin, Nicholas Raison, Jonathan Shapey, Alejandro Granados

Proceedings of the Medical Image Computing and Computer Assisted Intervention - MICCAI 2024 Workshops, 2024

Blood Harmonisation of Endoscopic Transsphenoidal Surgical Video Frames on Phantom Models.

Mahrukh Saeed, Julien Quarez, Hassna Irzan, Bava Kesavan, Matthew Elliot, Oscar MacCormac, James Knight, Sébastien Ourselin, Jonathan Shapey, Alejandro Granados

Proceedings of the IEEE International Symposium on Biomedical Imaging, 2024

A self-supervised and adversarial approach to hyperspectral demosaicking and RGB reconstruction in surgical imaging.

Peichao Li, Oscar MacCormac, Jonathan Shapey, Tom Vercauteren

Proceedings of the 35th British Machine Vision Conference, 2024

2023

TISS-net: Brain tumor image synthesis and segmentation using cascaded dual-task networks and error-prediction consistency.

Jianghao Wu, Dong Guo, Lu Wang, Shuojue Yang, Yuanjie Zheng, Jonathan Shapey, Tom Vercauteren, Sotirios Bisdas, Robert Bradford, Shakeel R. Saeed, Neil Kitchen, Sébastien Ourselin, Shaoting Zhang, Guotai Wang

Neurocomputing, August, 2023

CrossMoDA 2021 challenge: Benchmark of cross-modality domain adaptation techniques for vestibular schwannoma and cochlea segmentation.

Reuben Dorent, Aaron Kujawa, Marina Ivory, Spyridon Bakas, Nicola Rieke, Samuel Joutard, Ben Glocker, M. Jorge Cardoso, Marc Modat, Kayhan Batmanghelich, Arseniy Belkov, Maria G. Baldeon Calisto, Jae Won Choi, Benoit M. Dawant, Hexin Dong, Sergio Escalera, Yubo Fan, Lasse Hansen, Mattias P. Heinrich, Smriti Joshi, Victoriya Kashtanova, Hyeongyu Kim, Satoshi Kondo, Christian N. Kruse, Susana K. Lai-Yuen, Hao Li, Han Liu, Buntheng Ly, Ipek Oguz, Hyungseob Shin, Boris Shirokikh, Zixian Su, Guotai Wang, Jianghao Wu, Yanwu Xu, Kai Yao, Li Zhang, Sébastien Ourselin, Jonathan Shapey, Tom Vercauteren

Medical Image Anal., 2023

A Clinical Guideline Driven Automated Linear Feature Extraction for Vestibular Schwannoma.

Navodini Wijethilake, Steve Connor, Anna Oviedova, Rebecca Burger, Tom Vercauteren, Jonathan Shapey

CoRR, 2023

MedShapeNet - A Large-Scale Dataset of 3D Medical Shapes for Computer Vision.

Jianning Li, Antonio Pepe, Christina Gsaxner, Gijs Luijten, Yuan Jin, Narmada Ambigapathy, Enrico Nasca, Naida Solak, Gian Marco Melito, Afaque R. Memon, Xiaojun Chen, Jan Stefan Kirschke, Ezequiel de la Rosa, Patrick Ferdinand Christ, Hongwei Bran Li, David G. Ellis, Michele R. Aizenberg, Sergios Gatidis, Thomas Küstner, Nadya Shusharina, Nicholas Heller, Vincent Andrearczyk, Adrien Depeursinge, Mathieu Hatt, Anjany Sekuboyina, Maximilian Löffler, Hans Liebl, Reuben Dorent, Tom Vercauteren, Jonathan Shapey, Aaron Kujawa, Stefan Cornelissen, Patrick Langenhuizen, Achraf Ben-Hamadou, Ahmed Rekik, Sergi Pujades, Edmond Boyer, Federico Bolelli, Costantino Grana, Luca Lumetti, Hamidreza Salehi, Jun Ma, Yao Zhang, Ramtin Gharleghi, Susann Beier, Arcot Sowmya, Eduardo A. Garza-Villarreal, Thania Balducci, et al.

CoRR, 2023

Spatial gradient consistency for unsupervised learning of hyperspectral demosaicking: application to surgical imaging.

Peichao Li, Muhammad Asad, Conor C. Horgan, Oscar MacCormac, Jonathan Shapey, Tom Vercauteren

Int. J. Comput. Assist. Radiol. Surg., 2023

Deep Reinforcement Learning Based System for Intraoperative Hyperspectral Video Autofocusing.

Charlie Budd, Jianrong Qiu, Oscar MacCormac, Martin Huber, Christopher E. Mower, Mirek Janatka, Théo Trotouin, Jonathan Shapey, Mads S. Bergholt, Tom Vercauteren

Proceedings of the Medical Image Computing and Computer Assisted Intervention - MICCAI 2023, 2023

2022

CrossMoDA 2021 challenge: Benchmark of Cross-Modality Domain Adaptation techniques for Vestibular Schwnannoma and Cochlea Segmentation.

Reuben Dorent, Aaron Kujawa, Marina Ivory, Spyridon Bakas, Nicola Rieke, Samuel Joutard, Ben Glocker, Jorge Cardoso, Marc Modat, Kayhan Batmanghelich, Arseniy Belkov, Maria G. Baldeon Calisto, Jae Won Choi, Benoit M. Dawant, Hexin Dong, Sergio Escalera, Yubo Fan, Lasse Hansen, Mattias P. Heinrich, Smriti Joshi, Victoriya Kashtanova, Hyeongyu Kim, Satoshi Kondo, Christian N. Kruse, Susana K. Lai-Yuen, Hao Li, Han Liu, Buntheng Ly, Ipek Oguz, Hyungseob Shin, Boris Shirokikh, Zixian Su, Guotai Wang, Jianghao Wu, Yanwu Xu, Kai Yao, Li Zhang, Sébastien Ourselin, Jonathan Shapey, Tom Vercauteren

CoRR, 2022

Deep learning approach for hyperspectral image demosaicking, spectral correction and high-resolution RGB reconstruction.

Peichao Li, Michael Ebner, Philip J. Noonan, Conor C. Horgan, Anisha Bahl, Sébastien Ourselin, Jonathan Shapey, Tom Vercauteren

Comput. methods Biomech. Biomed. Eng. Imaging Vis., 2022

Boundary Distance Loss for Intra-/Extra-meatal Segmentation of Vestibular Schwannoma.

Navodini Wijethilake, Aaron Kujawa, Reuben Dorent, Muhammad Asad, Anna Oviedova, Tom Vercauteren, Jonathan Shapey

Proceedings of the Machine Learning in Clinical Neuroimaging - 5th International Workshop, 2022

2021

Inter Extreme Points Geodesics for Weakly Supervised Segmentation.

Reuben Dorent, Samuel Joutard, Jonathan Shapey, Aaron Kujawa, Marc Modat, Sébastien Ourselin, Tom Vercauteren

CoRR, 2021

Integrated multi-modality image-guided navigation for neurosurgery: open-source software platform using state-of-the-art clinical hardware.

Jonathan Shapey, Thomas Dowrick, Rémi Delaunay, Eleanor C. Mackle, Stephen A. Thompson, Mirek Janatka, Roland Guichard, Anastasis Georgoulas, David Pérez-Suárez, Robert Bradford, Shakeel R. Saeed, Sébastien Ourselin, Matthew J. Clarkson, Tom Vercauteren

Int. J. Comput. Assist. Radiol. Surg., 2021

Inter Extreme Points Geodesics for End-to-End Weakly Supervised Image Segmentation.

Reuben Dorent, Samuel Joutard, Jonathan Shapey, Aaron Kujawa, Marc Modat, Sébastien Ourselin, Tom Vercauteren

Proceedings of the Medical Image Computing and Computer Assisted Intervention - MICCAI 2021 - 24th International Conference, Strasbourg, France, September 27, 2021

2020

Manual segmentation versus semi-automated segmentation for quantifying vestibular schwannoma volume on MRI.

Hari McGrath, Peichao Li, Reuben Dorent, Robert Bradford, Shakeel R. Saeed, Sotirios Bisdas, Sébastien Ourselin, Jonathan Shapey, Tom Vercauteren

Int. J. Comput. Assist. Radiol. Surg., 2020

Scribble-Based Domain Adaptation via Co-segmentation.

Reuben Dorent, Samuel Joutard, Jonathan Shapey, Sotirios Bisdas, Neil Kitchen, Robert Bradford, Shakeel R. Saeed, Marc Modat, Sébastien Ourselin, Tom Vercauteren

Proceedings of the Medical Image Computing and Computer Assisted Intervention - MICCAI 2020, 2020

2019

Automatic Segmentation of Vestibular Schwannoma from T2-Weighted MRI by Deep Spatial Attention with Hardness-Weighted Loss.

Guotai Wang, Jonathan Shapey, Wenqi Li, Reuben Dorent, Alex Demitriadis, Sotirios Bisdas, Ian Paddick, Robert Bradford, Sébastien Ourselin, Tom Vercauteren

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, Reuben Dorent, Alex Demitriadis, Sotirios Bisdas, Ian Paddick, Robert Bradford, Shaoting Zhang, Sébastien Ourselin, Tom Vercauteren

Proceedings of the Medical Image Computing and Computer Assisted Intervention - MICCAI 2019, 2019