Elodie Puybareau



Contact information
Tel +33 1 53 14 59 16
Location Salle L7, LRDE


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 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].


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

News :

    Conference papers

    Title Authors Published in Date
    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
    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
    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 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