User

Elodie Puybareau

From LRDE

Contact

Contact information
Email elodie.puybareau@lrde.epita.fr
Tel +33 1 53 14 59 16
Location Salle L7, LRDE

Bio

I obtained a M.Sc degree in biosciences engineering, with a major in medical image processing, from the Institut Superieur des Biosciences de Paris, France, in 2013. I obtained a PhD in medical imaging from the Université Paris-Est Marne-la-Vallée (France) in 2016. I conducted my research under the supervision of Hugues Talbot[1] and Laurent Najman[2]. Since 2017, I conducted my research with EPITA Research & Development Laboratory (LRDE), within the Olena team, as postdoctoral fellow first, and as an Assistant Professor since 2018.

Research

Research interests

I am currently involved in two different research topics:

  1. Machine/Deep learning for medical imagery applications:
    1. MICCAI Challenges: White Matter Hyperintensities 2017, MICCAI Grand Challenge on 6-month Infant Brain MRI Segmentation (iSeg 2017), Multimodal Brain Tumor Segmentation Challenge (BraTS 2018 and 2019), Atrial Segmentation Challenge (AtriaSeg 2018), Liver Cancer Segmentation Challenge (PAIP 2019), Left Ventricle Full Quantification Challenge (LVQUAN 2019), Large Scale Vertebrae Segmentation Challenge (VERSE 2019).
    2. Heart segmentation and evaluation of fibrosis. (thesis of Zhou Zhao, jointly supervised with Thierry Géraud (LRDE))
  1. Mathematical morphology and Machine/Deep learning:
    1. Research on the influence of adding Mathematical morphology tools to Deep Learning for segmentation tasks
    2. Animation of Morphonet, a french group of researchers from several research centers dedicated to the study of mathematical morphology and machine learning.

Other research activities

I also serve as a reviewer for the following journals:

  • Mathematical Morphology Theory & Applications Journal
  • Pattern Recognition Letters
  • Fuzzy Sets and Systems

and conferences:

  • Gretsi
  • International Symposiom on Mathematical Morphology
  • MICCAI Brain Lesion Workshop
  • International Joint Conference on Artificial Intelligence

I am also a PC Member for European Conference on Artificial Intelligence 2020.

In addition, I am a Member of the IEEE and of MICCAI Society].

Publications

For a full list of publications, you can check my Google Scholar webpage.

News : https://www.lrde.epita.fr/wiki/challenges_codes


    Conference papers

    Title Authors Published in Date
    bloch.21.dgmm On Some Associations Between Mathematical Morphology and Artificial Intelligence Isabelle Bloch, Samy Blusseau, Ramón Pino Pérez, Élodie Puybareau, Guillaume Tochon Proceedings of the IAPR International Conference on Discrete Geometry and Mathematical Morphology (DGMM) 16 February 2021
    kirszenberg.21.dgmm Going beyond p-convolutions to learn grayscale morphological operators Alexandre Kirszenberg, Guillaume Tochon, Élodie Puybareau, Jesus Angulo Proceedings of the IAPR International Conference on Discrete Geometry and Mathematical Morphology (DGMM) 16 February 2021
    zhao.20.icpr.1 FOANet: A Focus of Attention Network with Application to Myocardium Segmentation Zhou Zhao, Nicolas Boutry, Élodie Puybareau, Thierry Géraud Proceedings of the 25th International Conference on Pattern Recognition (ICPR) 2 November 2020
    zhao.20.icpr.2 Do not Treat Boundaries and Regions Differently: An Example on Heart Left Atrial Segmentation Zhou Zhao, Nicolas Boutry, Élodie Puybareau, Thierry Géraud Proceedings of the 25th International Conference on Pattern Recognition (ICPR) 2 November 2020
    buatois.19.brainles Two Stages CNN-Based Segmentation of GliomasUncertainty Quantification and Prediction of Overall Patient Survival Thibault Buatois, Élodie Puybareau, Joseph Chazalon, Guillaume Tochon International MICCAI Brainlesion Workshop 3 September 2020
    boutry.20.brainles Using Separated Inputs for Multimodal Brain Tumor Segmentation with 3D U-Net-like Architectures Nicolas Boutry, Joseph Chazalon, Élodie Puybareau, Guillaume Tochon, Hugues Talbot, Thierry Géraud Proceedings of the 4th International Workshop, BrainLes 2019, Held in Conjunction with MICCAI 2019 1 June 2020
    zhao.19.stacom A Two-Stage Temporal-Like Fully Convolutional Network Framework for Left Ventricle Segmentation and Quantification on MR Images Zhou Zhao, Nicolas Boutry, Élodie Puybareau, Thierry Géraud Statistical Atlases and Computational Models of the Heart. Multi-Sequence CMR Segmentation, CRT-EPiggy and LV Full Quantification Challenges—10th International WorkshopSTACOM 2019, Held in Conjunction with MICCAI 2019Shenzhen, China, October 13, 2019, Revised Selected Papers 7 February 2020
    zhao.19.myops Stacked and parallel U-nets with multi-output for myocardial pathology segmentation Zhou Zhao, Nicolas Boutry, Elodie Puybareau Myocardial Pathology Segmentation Combining Multi-Sequence CMR Challenge 1 January 2020
    puybareau.19.ismm Spherical fluorescent particle segmentation and tracking in 3D confocal microscopy Élodie Puybareau, Edwin Carlinet, Alessandro Benfenati, Hugues Talbot Mathematical Morphology and Its Application to Signal and Image Processing – Proceedings of the 14th International Symposium on Mathematical Morphology (ISMM) 13 March 2019
    puybareau.18.brainles Segmentation of Gliomas and Prediction of Patient Overall Survival: A Simple and Fast Procedure Élodie Puybareau, Guillaume Tochon, Joseph Chazalon, Jonathan Fabrizio Proceedings of the Workshop on Brain Lesions (BrainLes)in conjunction with MICCAI 5 November 2018
    puybareau.18.stacom Left Atrial Segmentation In a Few Seconds Using Fully Convolutional Network and Transfer Learning Élodie Puybareau, Zhou Zhao, Younes Khoudli, Yongchao Xu, Thierry Géraud, Edwin Carlinet, Jérôme Lacotte Proceedings of the Workshop on Statistical Atlases and Computational Modelling of the Heart (STACOM 2018), in conjunction with MICCAI 25 October 2018
    puybareau.18.icip Real-Time Document Detection in Smartphone Videos Élodie Puybareau, Thierry Géraud Proceedings of the 24th IEEE International Conference on Image Processing (ICIP) 10 May 2018
    puybareau.18.rfiap Segmentation des hyperintensités de la matière blanche en quelques secondes à l'aide d'un réseau de neurones convolutif et de transfert d'apprentissage Élodie Puybareau, Yongchao Xu, Joseph Chazalon, Isabelle Bloch, Thierry Géraud Actes du congrès Reconnaissance des Formes, ImageApprentissage et Perception (RFIAP), session spéciale “Deep Learning, deep in France” 4 May 2018
    xu.18.brainles White Matter Hyperintensities Segmentation In a Few Seconds Using Fully Convolutional Network and Transfer Learning Yongchao Xu, Thierry Géraud, Élodie Puybareau, Isabelle Bloch, Joseph Chazalon Brainlesion: Glioma, Multiple Sclerosis, Stroke and Traumatic Brain Injuries— 3rd International WorkshopBrainLes 2017, Held in Conjunction with MICCAI 2017, Quebec City, QC, Canada, September 14 2017, Revised Selected Papers 6 February 2018
    dangla.18.das A first step toward a fair comparison of evaluation protocols for text detection algorithms Aliona Dangla, Élodie Puybareau, Guillaume Tochon, Jonathan Fabrizio Proceedings of the IAPR International Workshop on Document Analysis Systems (DAS) 2 February 2018
    puybareau.17.gretsi Caractérisation des zones de mouvement périodiques pour applications bio-médicales Élodie Puybareau, Hugues Talbot, Laurent Najman Actes du 26e Colloque GRETSI 28 June 2017
    puybareau.17.ismm Morphological Analysis of Brownian Motion for Physical Measurements Élodie Puybareau, Hugues Talbot, Noha Gaber, Tarik Bourouina Mathematical Morphology and Its Application to Signal and Image Processing – Proceedings of the 13th International Symposium on Mathematical Morphology (ISMM) 23 February 2017
    puybareau.17.isbi Periodic Area-of-Motion characterization for Bio-Medical applications Élodie Puybareau, Hugues Talbot, Laurent Najman Proceedings of the IEEE International Symposium on Bio-Medical Imaging (ISBI) 20 February 2017

    Journal papers

    Title Authors Published in Date
    hermary.22.jmiv Learning Grayscale Mathematical Morphology with Smooth Morphological Layers Romain Hermary, Guillaume Tochon, Élodie Puybareau, Alexandre Kirszenberg, Jesús Angulo Journal of Mathematical Imaging and Vision 4 April 2022
    mehta.22.melba QU-BraTS: MICCAI BraTS 2020 Challenge on Quantifying Uncertainty in Brain Tumor Segmentation — Analysis of Ranking Scores and Benchmarking Results Raghav Mehta, Angelos Filos, Ujjwal Baid, Chiharu Sako, Richard McKinley, Michael Rebsamen, Katrin Dätwyler, Raphael Meier, Piotr Radojewski, Gowtham Krishnan Murugesan, Sahil Nalawade, Chandan Ganesh, Ben Wagner, YuFang F., Baowei Fei, Ananth J Madhuranthakam, Joseph A Maldjian, Laura Daza, GómezCatalina, Pablo Arbeláez, Chengliang Dai, Shuo Wang, Hadrien Reynaud, Yuanhan Mo, Elsa Angelini, Yike Guo, Wenjia Bai, BanerjeeSubhashis, Linmin Pei, Murat AK, Sarahi Rosas-González, Ilyess Zemmoura, Clovis Tauber, Minh Hoang Vu, Tufve Nyholm, Tommy Löfstedt, Laura Mora Ballestar, Veronica Vilaplana, Hugh McHugh, Gonzalo Maso Talou, Alan Wang, Jay Patel, Ken Chang, Katharina Hoebel, Mishka Gidwani, Nishanth Arun, Sharut Gupta, Mehak Aggarwal, Praveer Singh, Elizabeth R Gerstner, Jayashree Kalpathy-Cramer, Nicolas Boutry, Alexis Huard, VidyaratneLasitha, Md Monibor Rahman, Khan M Iftekharuddin, Joseph Chazalon, Elodie Puybareau, TochonGuillaume, Jun Ma, Mariano Cabezas, LladoXavier, Arnau Oliver, Liliana Valencia, Sergi Valverde, Mehdi Amian, SoltaninejadMohammadreza, Andriy Myronenko, Ali Hatamizadeh, Xue Feng, Quan Dou, Nicholas Tustison, MeyerCraig, Nisarg A Shah, Sanjay Talbar, WeberMarc-André, Abhishek Mahajan, Andras Jakab, Roland Wiest, Hassan M Fathallah-Shaykh, Arash Nazeri, Mikhail Milchenko, Daniel Marcus, Aikaterini Kotrotsou, Rivka Colen, John Freymann, Justin Kirby, Christos Davatzikos, MenzeBjoern, Spyridon Bakas, Yarin Gal, Tal Arbel Journal of Machine Learning for Biomedical Imaging (MELBA) 9 January 2022
    sekuboyina.21.media VerSe: A Vertebrae Labelling and Segmentation Benchmark for Multi-detector CT Images Anjany Sekuboyina, Malek E Husseini, Amirhossein Bayat, Maximilian Löffler, Hans Liebl, Hongwei Li, Giles Tetteh, Jan Kukačka, Christian Payer, Darko Stern, Martin Urschler, Maodong Chen, Dalong Cheng, Nikolas Lessmann, Yujin Hu, Tianfu Wang, Dong Yang, Daguang Xu, and Felix Ambellan, Tamaz Amiranashvili, Moritz Ehlke, Hans Lamecker, Sebastian Lehnert, Marilia Lirio, Nicolás Pérez de Olaguer, Heiko Ramm, Manish Sahu, Alexander Tack, Stefan Zachow, Tao Jiang, Xinjun Ma, Christoph Angerman, Xin Wang, Kevin Brown, Matthias Wolf, Alexandre Kirszenberg, Élodie Puybareau, Di Chen, Yiwei Bai, Brandon H Rapazzo, Timyoas Yeah, Amber Zhang, Shangliang Xu, Feng Houa, Zhiqiang He, Chan Zeng, Zheng Xiangshang, Xu Liming, Tucker J Netherton, Raymond P Mumme, Laurence E Court, Zixun Huang, Chenhang He, Li-Wen Wang, Sai Ho Ling, Lê Duy Huỳnh, Nicolas Boutry, Roman Jakubicek, Jiri Chmelik, Supriti Mulay, Mohanasankar Sivaprakasam, Johannes C Paetzold, Suprosanna Shit, Ivan Ezhov, Benedikt Wiestler, Ben Glocker, Alexander Valentinitsch, Markus Rempfler, Björn H Menze, Jan S Kirschke Medical Image Analysis 22 July 2021
    kim.20.media PAIP 2019: Liver Cancer Segmentation Challenge Yoo Jung Kim, Hyungjoon Jang, Kyoungbun Lee, Seongkeun Park, Sung-Gyu Min, Choyeon Hong, Jeong Hwan Park, Kanggeun Lee, Jisoo Kim, Wonjae Hong, Hyun Jung, Yanling Liu, Haran Rajkumar, Mahendra Khened, Ganapathy Krishnamurthi, Sen Yang, Xiyue Wang, Chang Hee Han, Jin Tae Kwak, Jianqiang Ma, Zhe Tang, Bahram Marami, Jack Zeineh, Zixu Zhao, Pheng-Ann Heng, Rudiger Schmitz, Frederic Madesta, Thomas Rosch, Rene Werner, Jie Tian, Matteo Bovio, Xiufeng Zhang, Yifeng Zhu, Se Young Chun, Won-Ki Jeong, Peom Park, Jinwook Choi, Élodie Puybareau Medical Image Analysis 10 November 2020
    xiong.20.media A Global Benchmark of Algorithms for Segmenting the Left Atrium from Late Gadolinium-Enhanced Cardiac Magnetic Resonance Imaging Zhaohan Xiong, Qing Xia, Zhiqiang Hu, Ning Huang, Cheng Bian, Yefeng Zheng, Sulaiman Vesal, Nishant Ravikumar, Andreas Maier, Xin Yang, Pheng-Ann Heng, Dong Ni, Caizi Li, Qianqian Tong, Weixin Si, Younes Khoudli, Thierry Géraud, Chen Chen, Wenjia Bai, Daniel Rueckert, Lingchao Xu, Xiahai Zhuang, Xinzhe Luo, Shuman Jia, Maxime Sermesant, Yashu Liu, Kuanquan Wang, Davide Borra, Alessandro Masci, Cristiana Corsi, Coen de Vente, Mitko Veta, Rashed Karim, Chandrakanth Jayachandran Preetha, Sandy Engelhardt, Menyun Qiao, Yuanyuan Wang, Qian Tao, Marta Nunez-Garcia, Oscar Camara, Nicolo Savioli, Pablo Lamata, Jichao Zhao, Élodie Puybareau Medical Image Analysis 10 November 2020
    wang.19.tmi Benchmark on Automatic 6-month-old Infant Brain Segmentation Algorithms: The iSeg-2017 Challenge Li Wang, Dong Nie, Guannan Li, Élodie Puybareau, Jose Dolz, Qian Zhang, Fan Wang, Jing Xia, Zhengwang Wu, Jiawei Chen, Kim-Han Thung, Toan Duc Bui, Jitae Shin, Guodong Zeng, Guoyan Zheng, Vladimir S Fonov, Andrew Doyle, Yongchao Xu, Pim Moeskops, Josien P W Pluim, Christian Desrosiers, Ismail Ben Ayed, Gerard Sanroma, Oualid M Benkarim, Adrià Casamitjana, Verónica Vilaplana, Weili Lin, Gang Li, Dinggang Shen IEEE Transactions on Medical Imaging 11 April 2019
    kuijf.19.tmi Standardized Assessment of Automatic Segmentation of White Matter Hyperintensities: Results of the WMH Segmentation Challenge H J Kuijf, J M Biesbroek, J de Bresser, R Heinen, S Andermatt, M Bento, M Berseth, M Belyaev, M J Cardoso, A Casamitjana, D L Collins, M Dadar, A Georgiou, M Ghafoorian, D Jin, A Khademi, J Knight, H Li, X Lladó, M Luna, Q Mahmood, R McKinley, A Mehrtash, S Ourselin, B Park, H Park, S H Park, S Pezold, L Rittner, C H Sudre, S Valverde, V Vilaplana, R Wiest, Z Xu, G Zeng, J Zhang, G Zheng, C Chen, W van der Flier, F Barkhof, M A Viergever, G J Biessels, Élodie Puybareau, Yongchao Xu IEEE Transactions on Medical Imaging 10 April 2019
    puybareau.19.cbm High Throughput Automated Detection of Axial Malformations in Medaka Embryo Diane Genest, Élodie Puybareau, Marc Léonard, Jean Cousty, Noémie De Crozé, Hugues Talbot Computers in Biology and Medicine 22 January 2019
    xu.18.media The Challenge of Cerebral Magnetic Resonance Imaging in Neonates: A New Method using Mathematical Morphology for the Segmentation of Structures Including Diffuse Excessive High Signal Intensities Yongchao Xu, Baptiste Morel, Sonia Dahdouh, Élodie Puybareau, Alessio Virzì, Hélène Urien, Catherine Adamsbaum, Isabelle Bloch, Thierry Géraud Medical Image Analysis 22 March 2018
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