Research | People | Publications | Software | Data | Vacancies

Space-timE RePresentation, Imaging

and cellular dynamics of

molecular COmplexes




Charles Kervrann

(Team Leader, Inria Research Director)

Contact

Email : charles.kervrann@inria.fr
Adress : INRIA Rennes - Bretagne Atlantique
Campus Universitaire de Beaulieu
35042 Rennes cedex - France
Phone : +33 2 99 84 22 21
Fax : +33 2 99 84 71 71
Secretary (Huguette Béchu) : +33 2 99 84 72 28

Brief Vitae

He received the PhD degree in signal processing and telecommunications from University of Rennes 1 in 1995. From 1995 to 1997, he was an INRIA (French National Institute for Research in Computer Science and Control) expert-engineer in the TEMIS research group (IRISA/INRIA Rennes, France). In 1997, he was appointed at INRA (French National Institute for Research in Agronomy) in the MIA - Applied Mathematics and Computer Science Department as a full-time research scientist in Jouy-en-Josas, France. From September 2003 to September 2010, he was on INRIA secondment (INRIA Rennes - Bretagne Atlantique, France). Since 01/10/2010, he is INRIA Research Director (DR) and head of the SERPICO Team (Space-TimE RePresentation, Imaging and cellular dynamics of molecular COmplexes) Team created on 01/10/2010 at (INRIA Rennes - Bretagne Atlantique, in collaboration with Institut Curie (UMR 144 Cnrs, Paris), France.

Research Topics

Image denoising

  • Q. Jin, I. Grama, C. Kervrann, Q. Liu. Non-local means and optimal weights for noise removal , SIAM Journal on Imaging Sciences, 2017 (to appear), (HAL-INRIA-01575918)
  • C. Kervrann. PEWA: Patch-based Exponentially Weighted Aggregation for image denoising. Proc. Neural Information Processing Systems (NIPS'14), Montreal, Canada, Décembre 2014 (see NIPS 2014 page) (see HAL-INRIA-01103358) (see Poster )
  • C. Kervrann, P. Roudot, F. Waharte. Approximate Bayesian Computation, stochastic algorithms and non-local means for complex noise models. Proc. IEEE Int. Conf. on Image Processing (ICIP'14), Paris, October 2014 (see HAL-INRIA-01103322)
  • P.M. Carlton, J. Boulanger, Ch. Kervrann, J.-B. Sibarita, J. Salamero, S. Gordon-Messer, J.E. Haber, S. Haase, L. Shao, L. Winoto, A. Matsuda,, P. Kner, S. Usawa, Y. Strukov, M. Gustafsson, Z. Kam, D. Agard, J. Sedat. Fast live simultaneous multi-wavelength 4-dimensional optical microscopy. Proc Natl Acad Sci USA, 107(37):16016-16022, 2010 (see HAL-INRIA-00540978) pdf
  • A. Matsuda, L.Shao, J. Boulanger, Ch. Kervrann, P.M. Carlton, P. Kner, E. Brandlund, D. Agard, J.W. Sedat. Condensed mitotic chromosome structure at nanometer resolution using PALM and EGFP-histones. PloS One, (9):e12768, 2010 (see HAL-INRIA-00541020)
  • 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)
  • P. Coupé, P. Hellier, Ch. Kervrann, Ch. Barillot. NonLocal Means-based speckle filtering for ultrasound images. IEEE Trans. on Image Processing, 18(10): 2221-2229, 2009
  • P. Coupé, P. Yger, S. Prima, P. Hellier, Ch. Kervrann, Ch. Barillot. An optimized blockwise Non-Local means denoising filter for 3D Magnetic Resonance Images. IEEE Trans on Medical Imaging, 27(4):325-441, 2008.
  • Ch. Kervrann, J. Boulanger. Local adaptivity to variable smoothness for exemplar-based image denoising and representation. Int J Computer Vision, 79(1):45-69, August 2008.
  • J. Boulanger, Ch. Kervrann, P. Bouthemy. Space-time adaptation for patch based image sequence restoration. IEEE Trans on Pattern Analysis and Machine Intelligence, 29(6): 1096-1102, 2007
  • Ch. Kervrann, J. Boulanger. Optimal spatial adaptation for patch-based image denoising. IEEE Trans on Image Processing, 15(10): 2866-2878, 2006

Optical flow, motion analysis and change detection

  • D. Fortun, P. Bouthemy, C. Kervrann. Aggregation of local parametric candidates with exemplar-based occlusion handling for optical flow, Computer Vision and Image Understanding, 2016 (preprint (HAL-INRIA-01001758)
  • D. Fortun, P. Bouthemy, C. Kervrann. Optic flow modeling and computation: a survey, Computer Vision and Image Understanding, 134:1-21, May 2015 (paper on-line)
  • 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, 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
  • D. Fortun, C. Chen, P. Paul-Gilloteaux, F. Waharte, J. Salamero, C. Kervrann. Correlation and variational approaches for motion and diffusion estimation in fluorescence imaging. Proc. IEEE European Signal Processing Conference (EUSIPCO'13), Marrakech, September 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
  • 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
  • Ch. Kervrann, J. Boulanger, T. Pécot, P. Pérez, J. Salamero. Multiscale neighborhood-wise decision fusion for redundancy detection in image pairs. SIAM J. Multiscale Modeling & Simulation, 9(4):1829–1865, 2011 pdf (see HAL-INRIA-00487051)
  • D. Fortun, C. Kervrann. Semi-local variational optical flow estimation. Proc. IEEE Int. Symp. on Image Processing (ICIP'12), Orlando, Florida, September 2012 (see HAL-INRIA-00763806)

Spatial statistics

  • F. Lavancier, C. Kervrann . A two-color interacting random balls model for co-localization analysis of proteins. Second Int. Conf. in Geometric Science of Information (GSI'2015), Palaiseau, France, October 28-30, 2015 (Springer, 9389, Lecture notes in computer science (LNCS)
  • A. Chessel, F. Waharte, J. Salamero, C. Kervrann. A maximum likelihood method for lifetime estimation in photon counting-based fluorescence lifetime imaging microscopy. Proc. IEEE European Signal Processing Conference (EUSIPCO'13), Marrakech, September 2013

Motion analysis and tracking in fluorescence microscopy

  • 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 (paper on-line)
  • P. Roudot, L. Ding, K. Jaqaman, C. Kervrann, G. Danuser. Piecewise-stationary motion modeling and iterative smoothing to track heterogeneous motion in dense intracellular environments , IEEE T. Image Processing, 26(11):5395-5410, 2017 (HAL-INRIA-01575754)
  • C.Kervrann, C.O. Sorzano, S.T. Acton, J.-C. Olivo-Marin, M. Unser. A guided tour of selected image processing and analysis methods for fluorescence and electron microscopy, IEEE Journal of Selected Topics in Signal Processing, Special issue on Advanced Signal Processing in Microscopy and Cell Imaging, 2016 (HAL-INRIA-01246375) pdf
  • T. Pécot, C. Kervrann, J. Salamero, J. Boulanger. Counting-based particle flux estimation for traffic analysis in live cell imaging, IEEE Journal of Selected Topics in Signal Processing, Special issue on Advanced Signal Processing in Microscopy and Cell Imaging, 2016
  • P. Roudot, C. Kervrann, C. Blouin, C., F. Waharte. Lifetime estimation on moving sub-cellular objects in frequency domain FLIM imaging, J. Optic. Soc. Am., 32(10), 1821-1835, 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
  • 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
  • N. Chenouard, I. Smal, F. De Chaumont, M. Maska, I.F. Sbalzarini, Y.Gon, J. Cardinale, C. Carthel, S. Coraluppi, M. Winter, A.R. Cohen, W.J. Godinez, K. Rohr, Y. Kalaidzidis, L. Liang, J. Duncan, H. Shen, K. Magnusson, J. Jalden, P. Paul-Gilloteaux, P. Roudot, C. Kervrann, F. Waharte, J.-Y. Tinevez, J. Willemse, K. Celler, H.-W. Dan, Y.-S Tsai, C. Ortiz De Solorzano, J.-C. Olivo-Marin, E. Meijering. Objective comparison of particle tracking methods: Results and lessons from the first particle tracking challenge, Nature Methods, 11(3):281–289, 2014 (paper.pdf)
  • 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, Feb. 2015
  • P. Allain, C. Kervrann. Physical modeling of microtubules network. Proc. Int. Workshop on New Computational Methods for Inverse Problems (NMCIP'14), Paris, May 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
  • P. Roudot, C. Kervrann, J. Boulanger, F. Waharte. Noise modeling for intensified camera in fluorescence imaging: application to image denoising. Proc. IEEE Int. Symp. on Biomedical Imaging (ISBI'13), San-Francisco, CA, April 2013
  • M. Pinot, V. Steiner, B. Dehapiot, B.-K. Yoo, F. Chesnel, L. Blanchoin, C. Kervrann, Z. Gueroui. Confinement induces actin flow in a meiotic cytoplasm. Proc Natl Acad Sci USA. 109(29):11705-11710, 2012 (see HAL-INSERM-0717415)
  • A. Gidon, S. Bardin, J. Boulanger, F. Waharte, B. Cinquin, L. Heliot, H. de la salle, D. Hanau, Ch. Kervrann, B. Goud, J. Salamero. Rab11A/MyosinVb/Rab11-FIP2 complex frames two late recycling steps of langerin from ERC to plasma membrane. Traffic, 13(6):815-833, 2012
  • H.-F. Yang, X. Descombes, C. Kervrann, C. Medioni, F. Besse.. Tracking growing axons by particle filtering in 3D+t fluorescent two-photon microscopy images. Proc. Asian Conference on Computer Vision (ACCV'12), Daejeon, Korea, Republic Of, November 2012 (see HAL-INRIA-00740966)
  • P. Roudot, C. Kervrann, J. Boulanger, F. Waharte. Lifetime map reconstruction in frequency-domain fluorescence lifetime imaging microscopy. Proc. IEEE Int. Conf. on Image Processing (ICIP'12), Orlando, Florida, September 2012 (see HAL-INRIA-00763803)
  • P. Roudot, C. Kervrann, F. Waharte. Lifetime estimation of moving vesicles in frequency-domain fluorescence lifetime imaging microscopy. Proc. IEEE Int. Symp. on Biomedical Imaging (ISBI'12), pp. 668-671, Barcelona, Spain, May 2012 (see HAL-INRIA-00763790)
  • J. Boulanger, A. Gidon, Ch. Kervrann, J. Salamero. A patch-based method for repetitive and transient event detection in fluorescence Imaging. PLoS One, 5(10): e13190, 2010 (see HAL-INRIA-00541072)
  • J. Boulanger, Ch. Kervrann, P. Bouthemy. A simulation and estimation framework for intracellular dynamics and trafficking in video-microscopy and fluorescence imagery. Medical Image Analysis, 13(1): 132-142, 2009

Cryo-electron tomography

  • C. Kervrann, S. Blestel, D. Chrétien. Conditional Random Fields for tubulin-microtubule segmentation in cryo-electron tomography . Proc. IEEE Int. Conf. on Image Processing (ICIP'14), Paris, October 2014 (see HAL-INRIA-01103330)
  • A. Guesdon, S. Blestel, C. Kervrann, D. Chrétien. Single versus dual-axis cryo-electron tomography of microtubules assembled in vitro: Limits and perspectives. Journal of Structural Biology, 181(2):169–178, Feb. 2013 (see HAL-INRIA-00763814 and doi.j.jsb.2012.11.004)
  • F. Coquelle, S. Blestel, C. Heichette, I. Arnal, C. Kervrann, D. Chrétien D. Cryo-electron tomography of microtubules assembled in vitro from purified components. Methods Molecular Biology, 777:193-208, 2011

Other publications