| 2025
|
Elife
MorphoNet 2.0: An innovative approach for qualitative assessment and segmentation curation of large-scale 3D time-lapse imaging datasets
Benjamin Gallean, Tao Laurent, Kilian Biasuz, Ange Clement, Noura Faraj, Patrick Lemaire & Emmanuel Faure
|
| 2025
|
Frontiers
End-to-end 3D instance segmentation of synthetic data and embryo microscopy images with a 3D Mask R-CNN
Gabriel David & Emmanuel Faure
|
| 2025
|
Acta Horticulturae
Toward the prediction of flowering date of apple trees from unmanned aerial vehicle (UAV) imagery
Boudon Frédéric, Busnach D., Fernandez Romain, Segura Vincent, Delalande Magalie, Farrera Isabelle, Faure Emmanuel, Andres Fernando, Costes Evelyne.
|
| 2025
|
Elife
Spectral decomposition unlocks ascidian morphogenesis
Joel Dokmegang , Emmanuel Faure , Patrick Lemaire , Ed Munro , Madhav Mani
|
| 2023
|
Frontiers in BioInformatics
Immersive and interactive visualization of 3D spatio-temporal data using a space time hypercube: Application to cell division and morphogenesis analysis
Gwendal Fouché, Ferran Argelaguet , Emmanuel Faure, Charles Kervrann |
| 2022
|
Frontiers in BioInformatics
Challenges of intracellular visualization using virtual and augmented reality
Cesar Augusto Valades-Cruz, Ludovic Leconte, Gwendal Fouché, Thomas Blanc, Nathan van Hille, Kevin Fournier, Tao Laurent, Benjamin Gallean , François Deslandes, Bassam Hajj, Emmanuel Faure, Ferran Argelaguet , Alain Trubuil , Tobias Isenberg , Jean-Baptiste Masson , Jean Salamero, Charles Kervrann |
| 2021
|
Developmental Cell
A multiscale analysis of early flower development in Arabidopsis provides an integrated view of molecular regulation and growth controls
Y.Refahi,A.Zardilis, G. Michelin, R.Wightman, B. Leggio, J. Legrand, E. Faure, L. Vachez, A. Armezzani, AE Risson, F. Zhao, P. Das, N. Prunet, E. M.Meyerowitz, C. Godin, G. Malandain, H. Jönsson, J. Traas.
|
| 2020
|
Science
Contact Area-Dependent Cell Communication and the Morphological Invariance of Ascidian Embryogenesis
L. Guignard, UM. Fiúza, B. Leggio , J. Laussu, E. Faure, G. Michelin, K. Biasuz, L. Hufnagel, G. Malandain, C. Godin, P. Lemaire
|
| 2020
|
bioRxiv
Multiscale mechanical model for cell division orientation in developing biological systems
B. Leggio, J. Laussu, E. Faure, P. Lemaire, C. Godin
|
| 2019
|
Nature Communications
MorphoNet: an interactive online morphological browser to explore complex multi-scale data
B. Leggio, J. laussu, A. Carlier, C. Godin, P. Lemaire, and E. Faure
|
| 2019
|
Nuclei Acid Research
ANISEED 2019: 4D exploration of genetic data for an extended range of tunicates
J. Dardaillon, D. Dauga, P. Simion, E. Faure, T. A Onuma, M. B DeBiasse, A. Louis, K. R Nitta, M. Naville, L. Besnardeau, W. Reeves, K. Wang, M. Fagotto, M. Guéroult-Bellone, S. Fujiwara, R. Dumollard, M. Veeman, JN. Volff, HR. Crollius, E. Douzery, J. F Ryan, B. Davidson, H. Nishida, C. Dantec and P. Lemaire
|
| 2018
|
Developmental Biology
Transcriptional regulation of the Ciona Gsx gene in the neural plate
C. Hudson, R. Esposito, A. Palladino, L. Staiano, D. Ferrier, E. Faure, P. Lemaire, H. Yasuo and A. Spanguolo
|
| 2018
|
Current Opinion in Systems Biology
The “computable egg”: Myth or useful concept?
K. Biasuz, B. Leggio, E. Faure and P. Lemaire
|
| 2017
|
bioRxiv
Contact-dependent cell-cell communications drive morphological invariance during ascidian embryogenesis
L. Guignard*, U.M. Fiuza*, B. Leggio, E. Faure, J. Laussu, L. Hufnagel, G. Malandain, C. Godin and P. Lemaire(*equally contributing)
|
| 2017
|
Nuclei Acid Research
ANISEED 2017: extending the integrated ascidian database to the exploration and evolutionary comparison of genome-scale datasets
M. Brozovic,C. Dantec,J. Dardaillon,D. Dauga,E. Faure,M. Gineste,A. Louis,M. Naville,KR. Nitta,J. Piette,W. Reeves,C. Scornavacca,P. Simion,R. Vincentelli,M. Bellec,SB. Aicha,M. Fagotto,M. Guéroult-Bellone,M. Haeussler,E. Jacox,EK. Lowe,M. Mendez,A. Roberge,A. Stolfi,R. Yokomori, CT. Brown,C. Cambillau,L. Christiaen,F. Delsuc,E. Douzery,R. Dumollard,T. Kusakabe,K. Nakai,H. Nishida,Y. Satou,B. Swalla,M. Veeman,JN. Volff andP. Lemaire |
| 2016
|
Nature Communication
A workflow to process 3D+time microscopy images of developing organisms and reconstruct their cell lineage
E. Faure*, T. Savy*, B. Rizzi*, C. Melani*, O. Strasova*, D. Fabrèges*, R. Spir, M. Hammons, R. Cunderlík, G. Recher, B. Lombardot, L. Duloquin, I. Colin, J. Kollár, S. Desnoulez, P. Affaticati, B. Maury, A. Boyreau, J.Y. Nief, P. Calvat,P. Vernier, M. Frain, G. Lutfalla, Y. Kergosien, P. Suret,M. Remesíková,R. Doursat, A. Sarti, K. Mikula, N. Peyriéras and P. Bourgine (*equally contributing) |
| 2014
|
Applied Numerical Mathematics.
Nonlinear PDE based numerical methods for cell tracking in zebrafish embryogenesis
K. Mikula, R. Spir, M. Smisek, E. Faure and N. Peyriéras |
| 2013
|
Journal of Computational Biology
A New Software Package for Predictive GRN Modeling and Redesign
E. Faure*, I.S. Peter* and E.H. Davidson (*equally contributing) |
| 2012
|
Proceedings of the National Academy of Sciences identified by the Editorial Board as reporting findings of exceptional significance
Predictive computation of genomic logic processing functions in embryonic development
E. Faure*, I.S. Peter* and E.H. Davidson (*equally contributing)
|
| 2012
|
Transactions on Image Processing - IEEE
3D+t Morphological Processing: Applications to Embryogenesis Image Analysis
M.A. Luengo-Oroz, D. Pastor, C. Castro, E. Faure, T. Savy, B. Lombardot, J.L. Rubio-Guivernau, L. Duloquin, M.J. Ledesma-Carbayo, P. Bourgine, N. Peyriéras and A. Santos
|
| 2011
|
Transactions on Image Processing - IEEE
Methodology for reconstructing early zebrafish development from in vivo multiphoton microscopy
M.A. Luengo-Oroz, J.L. Rubio-Guivernau, E. Faure, T. Savy, L. Duloquin, N. Olivier, D. Pastor, M.J. Ledesma-Carbayo, D. Debarre, P. Bourgine, E. Beaurepaire, N. Peyriéras and A. Santos
|
| 2010
|
Science
Cell Lineage Reconstruction of Early Zebrafish Embryos Using Label-Free Nonlinear Microscopy
N. Olivier*, M.A. Luengo-Oroz*, L. Duloquin*, E. Faure, T. Savy, I. Veilleux, X. Solina, D. Débarre, P. Bourgine, A. Santos, N. Peyriéras and E. Beaurepaire (*equally contributing)
|
| 2010
|
Development
Dual mechanism controls asymmetric spindle position in ascidian germ cell precursors
F. Prodon, J. Chenevert, C. Hébras, R. Dumollard, E. Faure, J. Gonzalz-Garcia, H. Nishida, C. Sarder and A. McDougall
|
| 2010
|
Image and Vision Computing Invited Paper : 8/97 for NICE-I challenge [nice1.di.ubi.pt]
Robust iris segmentation on uncalibrated noisy images using mathematical morphology
M.A Luengo-Oroz, E. Faure and J. Angulo
|
| 07-2024 link |
12th ITM Meeting (Santa Cruz-USA)
MorphoNet for Ascidian Embryos
Emmanuel Faure
|
| 05-2024 link |
ISBI 2024 (Athens-Greece)
Light My CElls: Bright field to fluorescence imaging FBI Challenge
Dorian Kauffmann, Guillaume Gay, Edouard Bertrand, Thomas Walter, Christophe Zimmer & Emmanuel Faure
|
| 2022 link
|
ACM Symposium on Virtual Reality Software and Technology
Timeline Design Space for Immersive Exploration of Time-Varying Spatial 3D Data
Gwendal Fouché, Ferran Argelaguet , Emmanuel Faure, Charles Kervrann |
| 2022 link |
11th International Tunicate Meeting - Japan
MorphoNet fully connected with Anissed
B. Gallean, T. Laurent, K. Biasuz, P. Lemaire, and E. Faure |
| 2019 link |
BioImaging - Prague - Czech Republic
Deep Analysis of CNN Settings for New Cancer whole-slide Histological Images Segmentation: the Case of Small Training Sets
S. Mejbri, C. Franchet, R. Ismat-Ara, J. Mothe, P. Brousset, and E. Faure |
| 2019 link |
ASPAI - Barcelona - Spain
Training Set Class Distribution Analysis for Deep Learning Model – Application to Cancer Detection
R. Ismat-Ara, M. Gaspard, C. Franchet, P. Brousset, E. Faure, S. Mejbri and J. Mothe |
| 2017 Abstract |
ACM Multimedia, Mountain View - USA
Outlining Objects for Interactive Segmentation on Touch Devices
M. Pizenberg, A. Carlier, E. Faure, V. Charvillat |
| 2017 Paper |
Machine Learning for Health (ML4H 2017), Long Beach - USA
Cost-Effective Active Learning for Melanoma Segmentation
M. Gorriz Blanch, A. Carlier, E. Faure, X. Giro I Nieto |
| 2017 |
9th International Tunicate Meeting- New York - USA
The 4D Cloud Embryos
B. Leggio, J. Laussu, C. Godin, P. Lemaire and E.Faure
|
| 2012 Abstract |
Developmental Biology of the Sea Urchin XXI - Woods Hole - USA
A quantitative framework to define normal embryonic development and its range of variation
P. Villoutreix, L. Duloquin, B. Rizzi, E. Faure, T Savy and N. Peyriéras |
| 2012 Abstract |
Developmental Biology of the Sea Urchin XXI - Woods Hole - USA
Reconstruction of a Digital Sea Urchin Embryo during Early Development
B. Rizzi, L. Duloquin, T Savy, P. Villoutreix, E. Faure and N. Peyriéras |
| 2011 Abstract |
Annual International Conference on Intelligent Systems for Molecular Biology and European Conference on Computational Biology - Chicago - USA}
Processing pipeline for the digitalizing the lineage tree of early zebrafish embryogenesis from multiharmonic imaging
M.A. Luengo-Oroz, J.L. Rubio-Guivernau, E. Faure, T Savy, L. Duloquin, N. Olivier, M.J. Ledesma-Carbayo,
D. Debarre, P. Bourgine, E. Beaurepaire, N. Peyriéras and A. Santos |
| 2010 Poster |
Morphogenesis in Living Systems - Paris - France
Relevance of the SPIM/DSLM for in toto, in vivo imaging
V.V. Gurchenkov, J.L. Rubio, L. Duloquin, E. Faure, J.F. Gille, M. Frain, N. Peyriéras. |
| 2010 Article |
Advanced Information Networking and Applications - IEEE - Perth - Australie
Global Strategy of Active Machine Learning for Complex Systems : Embryogenesis Application on Cell Division Detection
E. Faure, C. Taramasco, J. Demongeot, L. Duloquin, B. Lombardot, N. Peyriéras and P. Bourgine |
| 2010 Poster |
ITMO Neurosciences, 10th Neurobiology Conferences Ladislav Tauc - Gif sur Yvette - France
BioEmergences Platform
L. Duloquin*, T. Savy*, E. Faure*, C. Melani*,P. Bourgine and N. Peyriéras (* equally contributing) |
| 2009 Poster |
Morphogenesis in Living Systems - Paris - France Best Poster Price for 4 Images
Multi-Scale Reconstruction
E. Faure, N.Peyriéras and P. Bourgine |
| 2008 Article |
Microscopic image analysis with application in biology - MIAAB08 workshop of IEEE - New-York - USA
Evaluation of four 3D non rigid registration methods applied to early zebrafish development sequences
B.Lombardot, M.A.Luengo-Oroz, C.Melani, E. Faure, A.Santos, N.Peyriéras, M.Ledesma-Carbayo and P. Bourgine |
| 2008 Article |
ISBI - Biomedical Imaging : From Nano to Macro - Paris
Can voronoi diagram model cell geometries in early sea-urchin embryogenesis ?
M.A. Luengo-Oroz, L. Duloquin, C. Castro, T. Savy, E. Faure, B. Lombardot, P. Bourgine, N. Peyriéras and A. Santos |
| 2007 Article |
European Conference on Complex Systems - Dresden - Germany
Active Learning For Embryogenesis
E. Faure, B. Lombardot, M.A. Luengo-Oroz, M. Campana, N. Peyriéras, R. Doursat and P. Bourgine |
| 2007 Article |
IEEE International Conference on Image Processing - San Antonio, Texas - USA
Twister segment morphological filtering. A new method for live Zebrafish embryos confocal images processing
M.A. Luengo-Oroz, E. Faure, B. Lombardot, R. Sance, P. Bourgine, N. Peyriéras and A. Santos |
| 2007 Article |
International Conference on Weblogs and Social Media - Boulder - USA
Intertemporal topic correlations in online media
J.P. Cointet, E. Faure and C. Roth |
| 2007 Poster |
System Complex National Network - Paris - France
Embryomics
E. Faure, B. Lombardot, and M.A. Luengo-Oroz |
| 04-2025 QLife 2025 |
Workshop
MorphoNet 2.0
|
| 11-2024 FBI Annual Meeting |
Mission officer
FBI.DATA & FBI.Challenges
|
| 11-2023 MifoBio 2023 |
Table Ronde
AI and Microscopy
|
| 11-2023 MifoBio 2023 |
Atelier MorphoNet
MorphoNet : How to segment a 3D dataset in just a few clicks?
|
| 02-2021 Qlife winter schools in Quantitative Biology |
Numerical Workshop
Cell Dynamics in Developmental Systems
|
| 07-2019 CAp 2019 |
Organizer Member
La Conférence sur l'Apprentissage automatique
|
| 10-2018 TSDL 2018 |
Main Symposium Organizer -- 2 days, 10 Speakers, 300 attendes
Toulouse Symposium on Deep Learning
|
| 03-2018 Spring School |
Data Instructor
-- Workshop organized by Patrick Lemaire and Christophe Godin
A multidisciplinary approach to animal and plant morphogenesis
|
| 03-2018 Workshop |
Workshop co-organizer with Sylvain Cussat Blanc
Modélisation et Simulation pour les sciences du vivant
|
| 02-2018 Workshop |
Workshop co-organizer with Josianne Mothe
Rencontres : Information médicale, Recherche d’information et Sciences des données
|
| 2016 Workshop |
Workshop organizer
Rencontre des équipes VORTEX de l'IRIT et ICAR au LIRMM
|
| 2010 GridDay |
Conference co-organizer
Multi-scale data mass and grid processing
Organizers: Arnaud Banos, Emmanuel Faure, Jean-Louis Giavitto, Romain Reuillon |
| 2010 Contest |
Dataset Organizer
Active Learning Challenge
Organizers : Isabelle Guyon - Berkeley - USA |
| 2006-2009 Embryomics |
Technical Coordinator
Embryomics European Project Reconstructing in space and time the cell lineage tree
Manager : Nadine Peyriéras |
| 2008-2009 AFIA |
Lecture Group Coordinator at the ISCPIF
Machine Learning Lecture Group
French Association for Artificial Intelligence |
| 2007 |
Research internship
Department of Electrical, Electronic and Information Engineering, Bologna University - Italy
Advisor : Alexandro Sarti
Research topic: Cells tracking with high level features |
| 04-2025 QLife 2025 |
Invited Speaker
MorphoNet 2.0
|
| 09-2024 Workshop Biothérapie et IA |
Invited Speaker
Virtual Reality for 3D + t Biological Images
|
| 2022 |
Light Sheet Fluorescence Microscopy: Principles and Systems Overview - Inserm Workshop
MorphoNet is dedicated for Light Sheet Fluorescence Microscopy ! |
| 2021 |
Digital 113
MorphoNet : a morphodynamic browser to interactively visualize complex 4D image datasets |
| 2021 |
France Bio Imaging 6th Annual Meeting
MorphoNet : a morphodynamic browser to interactively visualize complex 4D image datasets coupled with genetic data |
| 2021 |
Quantitative Biology Winter School 2021 Cell Dynamics in Developmental Systems
From quantitative microscopy to function analysis of gene function
|
| 2020 |
Workshop Modeling Shape and Size in Biological Development
MorphoNet |
| 2020 |
Numev 9th Annual Meeting
Apprentissage profond pour la reconstruction d’images biologiques 4D |
| 2017 |
Bioinformatics Institute - A*STAR Singapore
Towards integrated modeling of animal morphogenesis by data-assimilation
|
| 2017 |
Institut de Biologie Computationnelle Annual Scientific Meeting - Montpellier - France
Méthodes de reconstructions de l’embryogenèse précoce : de l’acquisition à la visualisation de données 4D
|
| 2016 ppt |
Modélisation biostatistique et biomathématique des données d'imagerie en cancérologie - Bordeaux - France
A workflow to process 3D+time microscopy images of developing organisms and reconstruct their cell lineage |
| 2010 ppt |
GridDay - Multi-scale data mass and grid processing - Paris - France
Automatic Multi-Scale Reconstruction of the spatio-temporal lineage tree of the embryo |
| 2010 ppt |
BioImage Analysis Workshop organized by Uwe Straehle - Karlsruhe Institute of Technology - Germany
Automatic Reconstruction of the spatio-temporal lineage tree |
| 2009 |
Epigenesis Workshop - Paris
Multi-agent modeling for embryogenesis: Heterogeneous collective motion or moving pattern formation ? |
| 2008 ppt |
AFIA - Machine Learning and Causality Teleconference Seminars organized by Nicolas Brodu, Dominik Janzing, Isabelle Guyon and Michele Sebag - Paris - France
Active Learning For Embryogenesis |
2008 ppt
| Universidad de los Andes - Bogota - Colombia
Embryomics - BioEmergences European Project |
|
(+33) 6 52 97 24 06
emmanuel.faure[at]lirmm.fr
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