Research | People | Publications | Software | Data | Vacancies

Space-timE RePresentation, Imaging

and cellular dynamics of

molecular COmplexes




Patrick Bouthemy

(Inria Research Director)

Contact

Email : patrick.bouthemy”-at-“inria.fr
Adress : INRIA Rennes - Bretagne Atlantique
Campus Universitaire de Beaulieu
35042 Rennes cedex - France
Phone : +33 2 99 84 72 74
Fax : +33 2 99 84 71 71
Secretary (Huguette Béchu) : +33 2 99 84 72 28

Brief Vitae

Patrick Bouthemy graduated from Ecole Nationale Supérieure des Télécommunications, Paris, in 1980, and received the Ph.D degree in Computer Science from the University of Rennes, France, in 1982. From December 1982 until February 1984, he was employed by INRS-Telecommunications, Montreal, Canada, in the Department of Visual Communications. Since April 1984 he has been with INRIA, in Rennes. He is currently “Directeur de Recherche” Inria.

In 1997, he launched the Vista Inria research group, which he headed until 2007. In 1998-2002, he was Deputy Scientific Director of the Inria Research Centre in Rennes. From July 2007 to September 2011, he was Head of the Inria Research Centre in Rennes. Since 2007, he has been member of the board of the Images-and-Networks competitiveness cluster gathering large companies, SMEs and academic labs of the West part of France, and since 2012, deputy member of the board of the ICT Technical Research Institute b<>com. In 2012-2014, he was head of the AFRIF national scientific association in pattern recognition and computer vision. Since April 2014, he has been head of the laboratory of excellence CominLabs.

He is presently co-editor in chief of the open access journal Frontiers in ICT, specialty Computer Image Analysis launched in 2014. He was associate editor of the IEEE Transactions on Image Processing from 1999 to 2003, and co-general chair of ICCV'2007. Recently, he was area chair for IEEE ICIP 2014 and 2016, member of the scientific committee of ELMI (European Light Microscopy Initiative) conference in 2013, associate editor for IEEE ISBI 2016 and 2017. He organized and chaired a mini-symposium on “Image analysis advances in dynamic microscopy and live cell imaging” at the SIAM Conference on Imaging Sciences in Albuquerque, May 2016. He was the main organizer of the ECCV satellite workshop BioImage Computing 2016.

Research Topics

My main research interests are concerned with image sequence analysis based on statistical approaches. More specifically, they involve all aspects of motion computation, that is, motion detection, motion segmentation, optical flow estimation, tracking, dynamic texture analysis. They also encompass modelling, learning, and classification of dynamic contents in video, including action recognition and action localization, and crowd motion analysis. In recent years, I have been dealing with microscopy imaging, including image denoising, spot detection, diffusion estimation, and CLEM registration.

Recent Thesis Supervision

  • L. Maczyta. on Dynamic saliency in videos. On going work (started in October 2017).
  • S. Manandhar. on 3D optical flow in 3D microscopy image sequences. On going work (started in October 2016).
  • B.M. Toledo Acosta. Multimodal image registration in 2D and 3D correlative microscopy. University of Rennes 1, defended in May 2018.
  • J.M. Perez Rua. Hierarchical motion-based video analysis with applications to video post-production. University of Rennes 1, defended in December 2017, in collaboration with Technicolor (P. Pérez and T. Crivelli).
  • A. Basset. Detection and characterization of dynamical events in image sequences based on local statistical approaches: Application to membrane fusion in TIRF microscopy. University of Rennes 1, defended in December 2015. More information and demos available on membrane dynamics, spot detection and crowd motion analysis. Antoine is now with CNES.
  • D. Fortun. Aggregation framework and patch-based image representation for optical flow. University of Rennes 1, defended in July 2014 (see TEL-ARCHIVES-OUVERTES-0110456). Denis is now with BIG at EPFL.
  • T. Pécot. Modélisation et estimation du trafic intracellulaire par tomographie de réseaux et microscopie de fluorescence. University of Rennes 1, defended in March 2010 (see TEL-ARCHIVES-OUVERTES-00541304).
  • T. Crivelli. Mixed-state Markov models for image motion analysis. University of Rennes 1, defended in March 2010, in collaboration with University of Buenos-Aires (Prof. B. Cernuschi-Frias). Tomas is now with Technicolor.

Recent Papers

See also my previous publication page for publications before 2010 with pdf files, and my Google scholar page.

2017

  • M. Jain, J. van Gemert, H. Jégou, P. Bouthemy, C.G.M Snoek. Tubelets: Unsupervised action proposals from spatiotemporal super-voxels, International Journal of Computer Vision, 124(3):287-311, September 2017
  • A. Basset, P. Bouthemy, J. Boulanger, F. Waharte, J. Salamero, C. Kervrann. An extended model of vesicle fusion at the plasma membrane to estimate protein lateral diffusion from TIRF microscopy images, BMC Bioinformatics, 18:352, July 2017
  • P. Bouthemy. An automatic image-based registration method for correlative light-electron microscopy.. 15ème colloque de la Société Française des Microscopies (invited conference), Bordeaux, July 2017
  • J.M. Perez Rua, A. Basset, P. Bouthemy. Detection and localization of anomalous motion in video sequences from local histograms of labeled affine flows, Frontiers in ICT: Computer Image Analysis, May 2017 (paper on-line)
  • B.M. Toledo Acosta, A. Basset, P. Bouthemy, C. Kervrann. Multi-scale spot segmentation with selection of image scales. Proc. IEEE Int. Conference on Acoustics, Speech and Signal Processing (ICASSP'17), New Orleans, March 2017

2016

  • D. Fortun, P. Bouthemy, C. Kervrann. A variational aggregation framework for patch-based optical flow estimation, Journal of Mathematical Imaging and Vision, 56(2):280–299, October 2016
  • D. Fortun, P. Bouthemy, C. Kervrann. Aggregation of local parametric candidates with exemplar-based occlusion handling for optical flow, Computer Vision and Image Understanding, 145: 1-182, April 2016
  • M. Jain, H. Jégou, P. Bouthemy. Improved motion description for action classification, Frontiers in ICT: Computer Image Analysis, January 2016 (paper on-line)
  • P. Bouthemy, B.M. Toledo Acosta, B. Delyon. Robust selection of parametric motion models in image sequences. Proc. IEEE Int. Conference on Image Processing (ICIP'16), Phoenix, September 2016
  • J.M. Perez Rua, T. Crivelli, P. Perez, P. Bouthemy. Hierarchical motion decomposition for dynamic scene parsing. Proc. IEEE Int. Conference on Image Processing (ICIP'16), Phoenix, September 2016
  • J.M. Perez Rua, T. Crivelli, P. Perez, P. Bouthemy. Discovering motion hierarchies via tree-structured coding of trajectories. Proc. 27th British Machine Vision Conference (BMVC'2016), York, September 2016
  • J.M. Perez Rua, T. Crivelli, P. Bouthemy, P. Perez. Determining occlusions from space and time image reconstructions. Proc. Conference on Computer Vision and Pattern Recognition (CVPR'16), Las Vegas, June 2016
  • B.M. Toledo Acosta, P. Bouthemy, C. Kervrann. A common image representation and a patch-based search for correlative light-electron-microscopy (CLEM) registration. Proc. IEEE Int. Symp. on Biomedical Imaging (ISBI'16), Prague, April 2016

2015

  • A. Basset, J. Boulanger, J. Salamero, P. Bouthemy, C. Kervrann. Adaptive spot detection with optimal scale selection in fluorescence microscopy images, IEEE Transactions on Image Processing, 24(11):4512-4527, Nov. 2015
  • D. Fortun, P. Bouthemy, C. Kervrann. Optic flow modeling and computation: a survey, Computer Vision and Image Understanding, 134:1-21, May 2015
  • T. Pécot, P. Bouthemy, J. Boulanger, A. Chessel, S. Bardin, J. Salamero, C. Kervrann. Background fluorescence estimation and vesicle segmentation in live cell imaging with conditional random fields, IEEE Transactions on Image Processing, 24(2):667-680, 2015
  • D. Fortun, P. Bouthemy, C. Kervrann. Sparse aggregation framework for optical flow estimation. Fifth Int. Conf. on Scale Space and Variational Methods in Computer Vision (SSVM'15), Liège Cap Ferret, June 2015
  • A. Basset, P. Bouthemy, J. Boulanger, F. Waharte, C. Kervrann, J. Salamero. Detection and estimation of membrane diffusion during exocytosis in TIRFM image sequences . Proc. IEEE Int. Symp. on Biomedical Imaging (ISBI'15), New-York City, April 2015
  • A. Basset, J. Boulanger, P. Bouthemy, C. Kervrann, J. Salamero. Détection de spots avec sélection d’échelle automatique et seuillage adaptatif en microscopie de fluorescence, Traitement du Signal, 32(2-3):287-310, 2015

2014

  • A. Basset, P. Bouthemy, C. Kervrann. Recovery of motion patterns and dominant paths in videos of crowded scenes. Proc. IEEE Int. Conf. on Image Processing (ICIP'14), Paris, October 2014
  • M. Jain, J. Van Gemert, H. Jegou, P. Bouthemy, C. Snoek. Action localization by tubelets from motion. Proc. Conference on Computer Vision and Pattern Recognition (CVPR'14), Columbus, Ohio, June 2014
  • A. Basset, J. Boulanger, P. Bouthemy, C. Kervrann, J. Salamero. SLT-LoG: A vesicle segmentation method with automatic scale selection and local thresholding applied to TIRF microscopy. Proc. IEEE Int. Symp. on Biomedical Imaging (ISBI'14), Beijing, April 2014.
  • A. Basset, P. Bouthemy, J. Boulanger, J. Salamero, C. Kervrann. Localization and classification of membrane dynamics in TIRF microscopy image sequences. Proc. IEEE Int. Symp. on Biomedical Imaging (ISBI'14), Beijing, April 2014
  • T. Pécot, J. Boulanger, C. Kervrann, P. Bouthemy, J. Salamero. Estimation of the flow of particles within a partition of the image domain in fluorescence video-microscopy. Proc. IEEE Int. Symp. on Biomedical Imaging (ISBI'14), Beijing, April 2014

2013 - 2010

  • T. Crivelli, B. Cernuschi-Frias, P. Bouthemy and J.-F. Yao. Motion textures: modeling, classification and segmentation using mixed-state Markov random fields. SIAM Journal on Imaging Sciences, 6(4):2484-2520, 2013
  • A. Basset, P. Bouthemy, C. Kervrann. Frame-by-frame crowd motion classification from affine motion models. Proc. IEEE Int. Conf. on Advanced Video and Signal-Based Surveillance (AVSS'13), Krakow, August 2013
  • M. Jain, H. Jegou, P. Bouthemy. Better exploiting motion for better action recognition. Proc. Conference on Computer Vision and Pattern Recognition (CVPR'13), Portland, Oregon, June 2013
  • D. Fortun, P. Bouthemy, P. Paul-Gilloteaux, C. Kervrann. Aggregation of patch-based estimations for illumination-invariant optical flow in live cell imaging. Finalist for Best Student Paper Award, Proc. IEEE Int. Symp. on Biomedical Imaging (ISBI'13), San-Francisco, CA, April 2013
  • S. Ozeré, P. Bouthemy, F. Spindler, P. Paul-Gilloteaux, C. Kervrann. Robust parametric stabilization of moving cells with intensity correction in light microscopy image sequences. Proc. IEEE Int. Symp. on Biomedical Imaging (ISBI'13), San-Francisco, CA, April 2013
  • T. Crivelli, P. Bouthemy, B. Cernuschi-Frias and J.-F. Yao. Simultaneous motion detection and background reconstruction with a conditional mixed-state Markov random field. International Journal of Computer Vision, 94(3):295-316, 2011
  • J. Boulanger, Ch. Kervrann, P. Bouthemy, P. Elbau, J.-B. Sibarita, J. Salamero. Patch-based non-local functional for denoising fluorescence microscopy image sequences. IEEE Trans on Medical Imaging, 29(2):442-454, 2010 pdf (see HAL-INRIA-00541082)
  • T. Crivelli, B. Cernuschi-Frias, P. Bouthemy, J.-F. Yao. Mixed-state causal modeling for statistical KL-based motion texture tracking. Pattern Recognition Letters, 31(14):2286-2294, 2010 (see HAL-INRIA-00541270)
  • T. Crivelli, P. Bouthemy, B. Cernuschi-Frias, J.-F. Yao. Mixed-state Markov models in image motion analysis. In Machine Learning for Vision-based Motion Analysis, L. Wang, G. Zhao, L. Cheng, M. Pietikäinen (eds), Springer, Part 2, pages 77-115, 2010 (see HAL-INRIA-00541253)
  • A. Hervieu, P. Bouthemy, J.-P. Le Cadre. Understanding sports video using players trajectories. In Intelligent Video Event Analysis and Understanding, J. Zhang, L. Shao, L. Zhang, G.A. Jones (eds), Springer, 2010