Robust supervised segmentation of neuropathology whole-slide microscopy images. - Michel E. Vandenberghe; Yaël Balbastre; Nicolas Souedet; Anne-Sophie Hérard; Marc Dhenain; Frédérique Frouin; Thierry Delzescaux (EMBC, 2015)

A Quantitative Approach to Characterize MR Contrasts with Histology. - Yaël Balbastre; Michel E. Vandenberghe; Anne-Sophie Hérard; Pauline Gipchtein; Caroline Jan; Anselme L. Perrier; Philippe Hantraye; Romina Aron-Badin; Jean-François Mangin; Thierry Delzescaux (Brainles@MICCAI, 2015)

Automated cell individualization and counting in cerebral microscopic images. - Zhenzhen You; Michel E. Vandenberghe; Yaël Balbastre; Nicolas Souedet; Philippe Hantraye; Caroline Jan; Anne-Sophie Hérard; Thierry Delzescaux (ICIP, 2016)

Développement et validation d'outils pour l'analyse morphologique du cerveau de Macaque. (Morphometry Analysis Tools for the Macaque Brain : Development and Validation). - Yaël Balbastre (2016)

Primatologist: A modular segmentation pipeline for macaque brain morphometry. - Yaël Balbastre; Denis Rivière; Nicolas Souedet; Clara Fischer; Anne-Sophie Hérard; Susannah Williams; Michel E. Vandenberghe; Julien Flament; Romina Aron-Badin; Philippe Hantraye; Jean-François Mangin; Thierry Delzescaux (NeuroImage, 2017)

Diffeomorphic Brain Shape Modelling Using Gauss-Newton Optimisation. - Yaël Balbastre; Mikael Brudfors; Kevin Bronik; John Ashburner (MICCAI (1), 2018)

MRI Super-Resolution Using Multi-channel Total Variation. - Mikael Brudfors; Yaël Balbastre; Parashkev Nachev; John Ashburner (MIUA, 2018)

Nonlinear Markov Random Fields Learned via Backpropagation. - Mikael Brudfors; Yaël Balbastre; John Ashburner (IPMI, 2019)

Empirical Bayesian Mixture Models for Medical Image Translation. - Mikael Brudfors; John Ashburner; Parashkev Nachev; Yaël Balbastre (SASHIMI@MICCAI, 2019)

A Tool for Super-Resolving Multimodal Clinical MRI. - Mikael Brudfors; Yaël Balbastre; Parashkev Nachev; John Ashburner (CoRR, 2019)

An algorithm for learning shape and appearance models without annotations. - John Ashburner; Mikael Brudfors; Kevin Bronik; Yaël Balbastre (Medical Image Anal., 2019)

Joint Total Variation ESTATICS for Robust Multi-parameter Mapping. - Yaël Balbastre; Mikael Brudfors; Michela Azzarito; Christian Lambert; Martina F. Callaghan; John Ashburner (MICCAI (2), 2020)

Flexible Bayesian Modelling for Nonlinear Image Registration. - Mikael Brudfors; Yaël Balbastre; Guillaume Flandin; Parashkev Nachev; John Ashburner (MICCAI (3), 2020)

Groupwise Multimodal Image Registration Using Joint Total Variation. - Mikael Brudfors; Yaël Balbastre; John Ashburner (MIUA, 2020)

Joint super-resolution and synthesis of 1 mm isotropic MP-RAGE volumes from clinical MRI exams with scans of different orientation, resolution and contrast. - Juan Eugenio Iglesias; Benjamin Billot; Yaël Balbastre; Azadeh Tabari; John Conklin; Daniel C. Alexander; Polina Golland; Brian L. Edlow; Bruce Fischl (CoRR, 2020)

An MRF-UNet Product of Experts for Image Segmentation. - Mikael Brudfors; Yaël Balbastre; John Ashburner; Geraint Rees 001; Parashkev Nachev; Sébastien Ourselin; M. Jorge Cardoso (MIDL, 2021)

Correcting inter-scan motion artefacts in quantitative R1 mapping at 7T. - Yaël Balbastre; Ali Aghaeifar; Nadège Corbin; Mikael Brudfors; John Ashburner; Martina F. Callaghan (CoRR, 2021)

Factorisation-based Image Labelling. - Yu Yan; Yaël Balbastre; Mikael Brudfors; John Ashburner (CoRR, 2021)

Learn2Reg: comprehensive multi-task medical image registration challenge, dataset and evaluation in the era of deep learning. - Alessa Hering; Lasse Hansen; Tony C. W. Mok; Albert C. S. Chung; Hanna Siebert; Stephanie Häger; Annkristin Lange; Sven Kuckertz; Stefan Heldmann; Wei Shao 008; Sulaiman Vesal; Mirabela Rusu; et al. (CoRR, 2021)

Model-based multi-parameter mapping. - Yaël Balbastre; Mikael Brudfors; Michela Azzarito; Christian Lambert; Martina F. Callaghan; John Ashburner (Medical Image Anal., 2021)

Joint super-resolution and synthesis of 1 mm isotropic MP-RAGE volumes from clinical MRI exams with scans of different orientation, resolution and contrast. - Juan Eugenio Iglesias; Benjamin Billot; Yaël Balbastre; Azadeh Tabari; John Conklin; R. Gilberto González; Daniel C. Alexander; Polina Golland; Brian L. Edlow; Bruce Fischl (NeuroImage, 2021)

Fitting Segmentation Networks on Varying Image Resolutions Using Splatting. - Mikael Brudfors; Yaël Balbastre; John Ashburner; Geraint Rees 001; Parashkev Nachev; Sébastien Ourselin; M. Jorge Cardoso (MIUA, 2022)

SuperWarp: Supervised Learning and Warping on U-Net for Invariant Subvoxel-Precise Registration. - Sean I. Young; Yaël Balbastre; Adrian V. Dalca; William M. Wells III; Juan Eugenio Iglesias; Bruce Fischl (WBIR, 2022)

Volumetric Characterization of Microvasculature in Ex Vivo Human Brain Samples By Serial Sectioning Optical Coherence Tomography. - Jiarui Yang; Shuaibin Chang; Ichun Anderson Chen; Sreekanth Kura; Grace A. Rosen; Nicole A. Saltiel; Bertrand R. Huber; Divya Varadarajan; Yaël Balbastre; Caroline Magnain; Shih-Chi Chen; Bruce Fischl; et al. (IEEE Trans. Biomed. Eng., 2022)

Diffeomorphic Multi-Resolution Deep Learning Registration for Applications in Breast MRI. - Matthew G. French; Gonzalo D. Maso Talou; Thiranja P. Babarenda Gamage; Martyn P. Nash; Poul M. F. Nielsen; Anthony J. Doyle; Juan Eugenio Iglesias; Yaël Balbastre; Sean I. Young (CoRR, 2023)

Learn2Reg: Comprehensive Multi-Task Medical Image Registration Challenge, Dataset and Evaluation in the Era of Deep Learning. - Alessa Hering; Lasse Hansen; Tony C. W. Mok; Albert C. S. Chung; Hanna Siebert; Stephanie Häger; Annkristin Lange; Sven Kuckertz; Stefan Heldmann; Wei Shao 008; Sulaiman Vesal; Mirabela Rusu; et al. (IEEE Trans. Medical Imaging, 2023)

Fully Convolutional Slice-to-Volume Reconstruction for Single-Stack MRI. - Sean I. Young; Yaël Balbastre; Bruce Fischl; Polina Golland; Juan Eugenio Iglesias (CVPR, 2024)

A label-free and data-free training strategy for vasculature segmentation in serial sectioning OCT data. - Etienne Chollet; Yaël Balbastre; Caroline Magnain; Bruce Fischl; Hui Wang 060 (CoRR, 2024)

Neurovascular Segmentation in sOCT with Deep Learning and Synthetic Training Data. - Etienne Chollet; Yaël Balbastre; Chiara Mauri; Caroline Magnain; Bruce Fischl; Hui Wang 060 (CoRR, 2024)

Learn2Synth: Learning Optimal Data Synthesis Using Hypergradients. - Xiaoling Hu 002; Oula Puonti; Juan Eugenio Iglesias; Bruce Fischl; Yaël Balbastre (CoRR, 2024)

SPM 25: open source neuroimaging analysis software. - Tim M. Tierney; Nicholas Alexander; John Ashburner; Nicole Labra Avila; Yaël Balbastre; Gareth R. Barnes; Yulia Bezsudnova; Mikael Brudfors; Korbinian Eckstein; Guillaume Flandin; Karl J. Friston; Amirhossein Jafarian; et al. (J. Open Source Softw., 2025)