STEPHANE COTIN

Research Director at Inria

Scientific Machine Learning – Medicine – Innovation


Short bio

I am a Research Director at Inria and the leader of the MIMESIS team. My main research interests are in real-time physics-based simulation (of soft tissues, fluids, medical devices, and imaging processes) to improve surgical training, planning, and image-guided therapy. I am the author or co-author of more than 200 scientific articles and involved with several key conferences in our research domain. To disseminate our work and to accelerate research in these fields, I initiated and developed the SOFA project, which is now a reference open-source solution for developing advanced simulations. I am also a co-founder and scientific advisor of 3 companies: InSimo, Twinical, and EVE.

Previously, I was the research lead of the Simulation group at CIMIT in Cambridge (USA) and an instructor at Harvard Medical School in Boston. I also worked as a research scientist at Mitsubishi Electric Research Lab (MERL) in Cambridge after getting my Ph.D. from the University of Nice, in France.

Research

My research, and the main focus of my team, is to develop new technologies at the crossroads between imaging, robotics, medicine, and computer science.  We collaborate closely with clinicians to improve healthcare, and in particular to reduce risks during medical interventions. Over the past years, we have developed numerical methods optimized for real-time computation, with applications in the fields of surgical simulation and computer-aided interventions.

A great example of our success in the field of surgical training is the work we did in collaboration with the HelpMeSee foundation, leading to the creation of our start-up InSimo. We now propose to focus our research on the use of real-time simulation for per-operative guidance. The underlying objectives include patient-specific biophysical modeling, dedicated numerical techniques for real-time computation, data assimilation, and data-driven simulation.

Awards

Innovation Prize – Delivered by Inria and Thales, Dec 2018. More here.
Academy of Sciences Award – Delivered by the French Academy of Sciences, Oct 2018. More here.
Dirk Bartz Medical Prize – Eurographics 2015 – Award for our contribution to medical simulation through the development of SOFA, Zurich, 2015
Best Paper Award – ISMAR 2013 – Image-guided Simulation of Heterogeneous Tissue Deformation For Augmented Reality during Hepatic Surgery
Young Scientist Award – MICCAI 2009 – Toward Real-Time Simulation of Blood-Coil Interaction during Aneurysm Embolization. London, 2009.
Best Paper Award – VRIPHYS 2005 – Interactive physically-based simulation of Catheter and Guidewire, Proc VRIPHYS, Oct 2005.
US Army’s Greatest Inventions Award – Special award for our work on emergency training, Washington DC, 2005
CIMIT Career Award – Personal award and funding for my work on surgical training, Boston, 2004
Edward M. Kennedy Award for Health Care Innovation – 2003 – Award for my contributions to medical training and education

Keynotes

2023: Keynote at the 10th J.FIG conference on Computer Graphics & Animation (Montpellier, France)
2022: Invited talk during the SMIT Conference (Oslo, Norway)

2021: Invited talk at the Technological Innovations for Precision Medicine of Tomorrow workshop (Milano, Italy)

2021: Invited talk at the Next Generation Intelligent Surgical Systems workshop (Verona, Italy) 
2019: invited speaker at the French-African seminar on Computer Science

2019: invited lecture at the Academy of Sciences, “Numerical Simulation in Medicine, from training to per-operative guidance” (Paris, France)
2018: invited lecture on “Virtual and Augmented Reality” (Toulouse, France)
2018: invited lecture on “data-driven simulation” at BEST symposium (Strasbourg, France)
2017: invited talk at the Academy of Surgery (Paris, France)
2017: invited talk at the MEVIS Lab – “Numerical Simulation in Medicine, from Training to Per-Operative Guidance” (Bremen, Germany)
2017: invited talk at the Annual meeting on Image-Guided and Computer-Assisted Liver Surgery – “Augmented Liver Surgery” (Mainz, Germany)
2017: invited talk at the 123rd edition of the French Ophthalmology Association (SFO) – “High-Fidelity Training System for Retina Surgery” (Paris, France)
2016: invited talk at the First European workshop on Nanomedicine, Modeling, Virtual Reality and Robotics applied to surgery (Strasbourg, France)
2016: invited talk at the 14th International Symposium on Computer Methods in Biomechanics and Biomedical Engineering (Tel Aviv, Israel)
2016: invited talk at the Business Engineering and Surgical Technologies symposium (Strasbourg, France)
2016: invited talk at the OpenYourMind seminar (Paris, France)
2015: keynote lecture at the 10th Computational Biomechanics for Medicine (Munich, Germany)

2015: keynote lecture at Visual Computing in Biology and Medicine (Chester, UK)
2015: invited talk at HCST Medical Robotics (Tel Aviv, Israel)
2015: invited speaker at the International Conference on Augmented and Virtual Reality (Salento, Italy)
2014: lecture at College de France, “Simulation en médecine : présent et futur” (Paris, France)
2014: invited presentation of our work on the HelpMeSee project, Assemblée Nationale (Paris, France)
2013: invited presentation, séminaire intergouvernemental sur le numérique (Paris, France)
2012: keynote at VRIPHYS conference (Darmstadt, Germany)  
2010: invited lecture, INTS conference (Montpellier, France)
2010: invited lecture, Annual National Robotics Meeting  (La Rochelle, France)
2009: invited lecture, Computer Science Colloquium, Korean Institute of Technology (South Korea)
2009: invited lecture, Colloque de la Cité des Géométries (Jeumont, France)

News

    Regional Anesthesia Simulation
    Optimization of percutaneous tumor ablation
    Shape and material optimization for balloon angioplasty and stents

    Projects

    MediTwin

    Digital Twins for precision medicine

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    Premyom

    Biomechanical & optical digital twin of the eye

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    Φ–FEM

    Take support to the next level.

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    Selected publications

    JOURNALS

    Vision-based Force Feedback Estimation for Robot-assisted Surgery using Instrument-constrained Biomechanical 3D Maps Nazim Haouchine, Winnie Kuang, Stéphane Cotin, Michael Yip – IEEE Robotics and Automation Letters, 2018, 

    Calipso: Physics-based Image and Video Editing through CAD Model Proxies Nazim Haouchine, Frédérick Roy, Hadrien Courtecuisse, Matthias Nießner, Stéphane Cotin – The Visual Computer, Springer Verlag, 2018. 

    Biomechanics-based graph matching for augmented CT-CBCT Jaime Garcia Guevara, Igor Peterlik, Marie-Odile Berger, Stephane Cotin. International Journal of Computer Assisted Radiology and Surgery, Springer Verlag, 2018, 13 (6), pp.805-813.

    Blood vessel modeling for interactive simulation of interventional neuroradiology procedures Erwan Kerrien, Ahmed Yureidini, Jeremie Dequidt, Christian Duriez, René Anxionnat, Stéphane Cotin Medical Image Analysis, Elsevier, 2017, 35, pp. 685 – 698. 

    Fast Elastic Registration of Soft Tissues under Large Deformations Igor Peterlik, Hadrien Courtecuisse, Robert Rohling, Purang Abolmaesumi, Christopher Nguan, Stéphane Cotin, Septimiu E Salcudean Medical Image Analysis, Elsevier, Volume 45, April 2018, Pages 24-40.

    Handling Topological Changes during Elastic Registration: Application to Augmented Reality in Laparoscopic Surgery Christoph Joachim Paulus, Nazim Haouchine, Seong-Ho Kong, Renato Vianna Soares, David Cazier, Stéphane Cotin. International Journal of Computer Assisted Radiology and Surgery, Springer Verlag, 2016

    Robust Augmented Reality registration method for Localization of Solid Organs’ Tumors Using CT-derived Virtual Biomechanical Model and Fluorescent Fiducials Seong-Ho Kong, Nazim Haouchine, Renato Soares, Andrey S Klymchenko, Bohdan Andreiuk, Bruno Marques, Galyna Shabat, Thierry Piéchaud, Michele Diana, Stéphane Cotin, Jacques Marescaux. Surgical Endoscopy, Springer 2016,

    Patient-specific Biomechanical Modeling for Guidance during Minimally-invasive Hepatic Surgery Rosalie Plantefève, Igor Peterlik, Nazim Haouchine, Stéphane Cotin Annals of Biomedical Engineering, Springer Verlag, 2015

    Monocular 3D Reconstruction and Augmentation of Elastic Surfaces with Self-occlusion Handling Nazim Haouchine, Jeremie Dequidt, Marie-Odile Berger, Stephane Cotin IEEE Transactions on Visualization and Computer Graphics, Institute of Electrical and Electronics Engineers, 2015,

    Virtual Cutting of Deformable Objects based on Efficient Topological Operations Christoph Paulus, Lionel Untereiner, Hadrien Courtecuisse, Stephane Cotin, David Cazier Visual Computer, Springer Verlag, 2015, 31 (6-8), pp.831-841. 〈10.1007/s00371-015-1123-x〉

    Real-time simulation of contact and cutting of heterogeneous soft-tissues Hadrien Courtecuisse, Jeremie Allard, Pierre Kerfriden, Stephane Pierre-Alain Bordas, Stephane Cotin, Christian Duriez Medical Image Analysis, Elsevier, 2014, 18 (2), pp.394-410. 〈10.1016/j.media.2013.11.001〉

    CONFRENCES

    DejaVu: Intra-operative Simulation for Surgical Gesture Rehearsal Nazim Haouchine, Danail Stoyanov, Frederick Roy, Stéphane Cotin Medical Image Computing and Computer Assisted Interventions Conference MICCAI 2017, Oct 2017, Quebec City, Canada

    Silhouette-based Pose Estimation for Deformable Organs Application to Surgical Augmented Reality. Yinoussa Adagolodjo, Raffaella Trivisonne, Nazim Haouchine, Stéphane Cotin, Hadrien Courtecuisse IROS 2017 – IEEE/RSJ International Conference on Intelligent Robots and Systems, Sep 2017, Vancouver, Canada. 2017

    Image-driven Stochastic Identification of Boundary Conditions for Predictive Simulation. Igor Peterlik, Nazim Haouchine, Lukáš Ručka, Stéphane Cotin. 20th International Conference on Medical Image Computing and Computer Assisted Intervention, Sep 2017, Québec, Canada. 2017

    Template-based Monocular 3D Recovery of Elastic Shapes using Lagrangian Multipliers Nazim Haouchine, Stéphane Cotin Computer Vision and Pattern Recognition (CVPR), Jul 2017, Honolulu, Hawai, United States

    Using Contours as Boundary Conditions for Elastic Registration during Minimally Invasive Hepatic Surgery Nazim Haouchine, Frederick Roy, Lionel Untereiner, Stéphane Cotin International Conference on Intelligent Robots and Systems, Oct 2016, Daejeon, South Korea

    Simultaneous Pose Estimation and Augmentation of Elastic Surfaces from a Moving Monocular Camera Nazim Haouchine, Marie-Odile Berger, Stephane Cotin International Symposium on Mixed and Augmented Reality, Sep 2016, Merida, Mexico

    3D Physics-Based Registration of 2D Dynamic MRI Data Raffaella Trivisonne, Igor Peterlik, Stéphane Cotin, Hadrien Courtecuisse MMVR – Medicine Meets Virtual Reality, Apr 2016, Los Angeles, United States. 2016

    Surgical Augmented Reality with Topological Changes Christoph Paulus, Nazim Haouchine, David Cazier, Stéphane Cotin Medical Image Computing and Computer Assisted Interventions, Oct 2015, München, Germany. 〈http://miccai2015.org/〉

    Augmented Reality during Cutting and Tearing of Deformable Objects Christoph Paulus, Nazim Haouchine, David Cazier, Stephane Cotin The 14th IEEE International Symposium on Mixed and Augmented Reality, Sep 2015, Fukuoka, Japan. pp.6

    Surgery Training, Planning and Guidance Using the SOFA Framework Hugo Talbot, Nazim Haouchine, Igor Peterlik, Jeremie Dequidt, Christian Duriez, Hervé Delingette, Stephane Cotin Eurographics, May 2015, Zurich, Switzerland

    Virtual Cutting of Deformable Objects based on Efficient Topological Operations Christoph Paulus, Lionel Untereiner, Hadrien Courtecuisse, Stéphane Cotin, David Cazier Computer Graphics International, 2015, Strasbourg, France. 2015

    Interactive Training System for Interventional Electrocardiology Procedures H Talbot, F Spadoni, Christian Duriez, M Sermesant, Stéphane Cotin, Hervé Delingette 6th International Symposium on Biomedical Simulation – ISBMS 2014, Oct 2014, Strabsourg, France. pp.11 – 19, 2014, 〈10.1007/978-3-319-12057-7_2〉

    Testbed for assessing the accuracy of interventional radiology simulations Mario Sanz-Lopez, Jérémie Dequidt, Erwan Kerrien, Christian Duriez, Marie-Odile Berger, Stéphane Cotin ISBMS – 6th International Symposium on Biomedical Simulation, Oct 2014, Strasbourg, France. Springer, 2014, LNCS

    Intra-operative Registration for Deep Brain Stimulation Procedures based on a Full Physics Head Model Alexandre Bilger, Eric Bardinet, Sara Fernández-Vidal, Christian Duriez, Pierre Jannin, Stéphane Cotin MICCAI 2014 Workshop on Deep Brain Stimulation Methodological Challenges – 2nd edition, Sep 2014, Boston, United States. 2014

    Single View Augmentation of 3D Elastic Objects Nazim Haouchine, Jérémie Dequidt, Marie-Odile Berger, Stéphane Cotin International Symposium on Mixed and Augmented Reality – ISMAR, Sep 2014, Munich, Germany. 2014

    Atlas-based Transfer of Boundary Conditions for Biomechanical Simulation Rosalie Plantefeve, Igor Peterlik, Hadrien Courtecuisse, Raffaella Trivisonne, Jean-Pierre Radoux, Stéphane Cotin MICCAI – 17th International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI), Sep 2014, Boston, United States. 2014

    Réalité augmentée pour la chirurgie minimalement invasive du foie utilisant un modèle biomécanique guidé par l’image Nazim Haouchine, Stéphane Cotin, Jérémie Dequidt, Erwan Kerrien, Marie-Odile Berger Reconnaissance de Formes et Intelligence Artificielle (RFIA) 2014, Jun 2014, France. 2014

    Model-Based Identification of Anatomical Boundary Conditions in Living Tissues Igor Peterlik, Hadrien Courtecuisse, Christian Duriez, Stéphane Cotin Information Processing in Computer Assisted Interventions, Jun 2014, Fukuoka, Japan. 2014, 〈10.1007/978-3-319-07521-1_21〉

    Haptic Rendering on Deformable Anatomical Tissues with Strong Heterogeneities Guillaume Kazmitcheff, Hadrien Courtecuisse, Yann Nguyen, Mathieu Miroir, Alexis Bozorg-Grayeli, Stéphane Cotin, Olivier Sterkers, Christian Duriez Eurohaptics 2014, Jun 2014, Versailles, France. Springer, 2014

    Towards an Accurate Tracking of Liver Tumors for Augmented Reality in Robotic Assisted Surgery Nazim Haouchine, Jérémie Dequidt, Igor Peterlik, Erwan Kerrien, Marie-Odile Berger, Stéphane Cotin International Conference on Robotics and Automation (ICRA), Jun 2014, Hong Kong, China. 2014

    Virtual Simulation of Stapedotomy Surgery Guillaume Kazmitcheff, Yann Nguyen, Mathieu Miroir, Evelyne Ferrary, Stéphane Cotin, Christian Duriez, Olivier Sterkers ARO 2014, Feb 2014, San Diego, CA, United States. 2014

    Constraint-Based Simulation for Non-Rigid Real-Time Registration Hadrien Courtecuisse, Igor Peterlik, Raffaella Trivisonne, Christian Duriez, Stéphane Cotin Medicine Meets Virtual Reality, Feb 2014, Manhattan Beach, California., United States. 2014

    Interactive Planning of Cryotherapy Using Physically-Based Simulation Hugo Talbot, Myriam Lekkal, Rémi Béssard-Duparc, Stéphane Cotin. MMVR 21 – Medicine Meets Virtual Reality – 2014, Feb 2014, Manhattan Beach, California, United States. 2014

    Computation and Visualization of Risk Assessment in Deep Brain Stimulation Alexandre Bilger, Christian Duriez, Stéphane Cotin MMVR 21 – Medicine Meets Virtual Reality, Feb 2014, Manhattan Beach, California, United States. IOS Press, 2014