Charles Kervrann

(© Inria / Photo B. Fourrier)
 

Charles Kervrann

Email : charles.kervrann@inria.fr

Google Scholar page: https://scholar.google.fr/citations?user=aOHoWTAAAAAJ&hl=fr&oi=sra

Address : Centre INRIA de l’Université de Rennes
Campus Universitaire de Beaulieu
35042 Rennes cedex – France

Phone : +33 2 99 84 22 21
Fax : +33 2 99 84 71 71
Secretary (Caroline Tanguy) : +33 2 99 84 71 86

 

Brief Vitae

Charles Kervrann was appointed as Inria Research Director in 2010 (DR1 Inria (first class) in 2017), and is currently heading the Sairpico Project-Team (Inria Rennes, U1143 INSERM/UMR 3666 CNRS, Institut Curie, PSL University) jointly located in Rennes and Paris since April 1st, 2023. Previously, he was head of Serpico Project-Team (Inria, UMR 144 CNRS, Institut Curie, PSL University) (2018-2023). He received his PhD and HdR in Signal Processing and Telecommunications from the University of Rennes 1 in 1995 and 2010, respectively. He was appointed INRA CR2 (Applied Mathematics and Informatics, Jouy-en-Josas) in 1997 and moved (on Inria secondment) to Inria Rennes in 2003.

His research interests include mathematical and statistical methods for biological image processing. He focuses on image sequence analysis, motion estimation, object detection, noise modeling for microscopy and traffic, and dynamics modeling in cell biology. He served as member of the program committees of the major conferences in image processing and computer vision. He superivsed 7 post-docs, 19 PhD students and 24 master students. He published have published 60 publications in top ISI-ranked international journals, 80 publications in peer reviewed international conferences with a total of 7432 citations (14 publications with 100+ citations, and 1 with 1000+ citations) yielding a h-index of 36 (google scholar), and an i10 of 59 (2023).

Membership of editorial boards of journals and conferences in recent years
  • Associate editor of IEEE Signal Processing Letters (2015-2019),IEEE Transactions on Image Processing (since 2021), and Biological Imaging (since 2021).
  • Guest Editor of two special issues of the IEEE Selected Topics in Signal Processing Journal (2016) and the IEEE Journal of Selected Topics in Quantum Electronics (2023).
  • Member of scientific committees: IEEE BISP “Biomedical Image and Signal Processing” committee (expert committee for Intl IEEE-ISBI, IEEE-ICASSP and IEEE-ICIP conferences) (2010-2018), “Quantitative BioImaging” technical committee (2019, 2020).
  • Co-General Chair/Head of the organizing committee of the “Quantitative BioImaging” (QBI’2019) conference (350 participants, Rennes, January 2019).
10 years track-record
  • S. Prigent, C. A. Valades-Cruz, L. Leconte, L. Maury, J. Salamero and C. Kervrann. BioImageIT: Open-source framework for integration of image data-management with analysisNature Methods, doi: 10.1038/s41592-022-01642-9, 2022 (citations: 1 | IF: 53.5)

  • S. Herbreteau, C. Kervrann. DCT2net: an interpretable shallow CNN for image denoising, IEEE Trans. on Image Processing, 31: 4292-4305, doi: 10.1109/TIP.2022.318148, 2022 (citations: 9 | IF: 10.7)

  • E. Moebel, A. Martinez-Sanchez, L. Lamm, R.D. Righetto, W. Wietrzynski, S. Albert, D. Larivière, E. Fourmentin, S. Pfeffer, J. Ortiz, W. Baumeister, T. Peng, B.D. Engel, C. KervrannDeep learning improves macromolecule identification in 3D cellular cryo-electron tomograms, Nature Methods, 18: 1386-1394, doi: 10.1038/s41592-021-01275-4, 2021 (citations: 68 | IF: 53.5)

  • T. Pécot, L. Zengzhen, J. Boulanger, F. Waharte, J. Salamero, C. KervrannA quantitative approach for analyzing the spatio-temporal distribution of 3D intracellular events in fluorescence microscopy, eLife 2018;7:e32311, doi:10.7554/eLife.32311, 2018 (citations: 17 | IF: 8.1)

  • V. Briane, C. Kervrann, M. Vimond. Statistical analysis of particle trajectories in living cells, Physical Review E, 97, 062121, doi: 10.1103/PhysRevE.97.062121, 2018 (citations: 50 | IF: 2.37)

  • 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 Trans on Image Processing, 26(11):5395-5410, hal-01575754, doi: 10.1109/TIP.2017.2707803, 2017 (citations: 35 | IF: 10.7)
  • A. Basset, J. Boulanger, J. Salamero, P. Bouthemy, C. Kervrann. Adaptive spot detection with optimal scale selection in fluorescence microscopy images, IEEE Trans on Image Processing, 24(11):4512-4527, 2015 (citations: 65 | IF: 10.7)
  • 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 J Selected Topics in Signal Processing, 10(1):6-30, hal-01246375, doi: 10.1109.JSTSP.2015.2505402, , 2016 (citations: 66 | IF: 6.9)
  • D. Fortun, P. Bouthemy, C. Kervrann. Optic flow modeling and computation: a survey, Computer Vision and Image Understanding, 134:1-21, 2015. (citations: 448 | IF: 3.9)
  • C. Kervrann. PEWA: Patch-based Exponentially Weighted Aggregation for image denoising. Proc. Neural Information Processing Systems (NIPS’14), Montreal, Canada, 2014 (citations: 28 | H5-index: 169)
  • 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 (citations: 57 | IF: 11.2)
  • A. Matsuda, L. Shao, J. Boulanger, C. 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 (citations: 96 | IF: 3.2)
  • J. Boulanger, C. Kervrann, P. Bouthemy, P. Elbau, J.-B. Sibarita, J. Salamero, Patch-based nonlocal functional for denoising fluorescence microscopy image sequences, IEEE Trans Medical imaging 29(2): 442-454, 2010. (citations: 253 | IF: 9.71)
  • P.M. Carlton, J. Boulanger, C. 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, doi: 10.1073/pnas.1004037107, 2010. (citations: 201 | IF: 11.2)
Recent invited international talks in conferences, workshops, and seminars (2018 – )
  • Natl IABM conference (Paris, 2023)
  • Intl “Quantitative BioImaging” conference (QBI’2020) (Oxford, UK, 2020)
  • Intl “Bioimage Processing” workshop (Cambridge, 2019)
  • Int “Random Walks and Intracellular Transport” workhop (Manchester, UK, 2019)
  • Intl “Statistical modeling for Shapes and Imaging” workshop (Paris, 2019)
  • Intl “Reverse Problems in Reconstructing Single Cell Molecular Dynamics” workshop (Pisa, Italy)
  • Intl SIAM Conference on Imaging Sciences (Bologna, Italy, 2018).
  • Intl NEUBIAS (European Network of BioImage Analysts, EU framework COST) conference (Szeged, Hungary, 2018).
  • Seminars at Institut Curie (2019-2022, Paris), Institut Pasteur (20202, 2018, Paris), European Molecular Biology Laboratory – EMBL (2018, Heidelberg, Germany).
Publications

See below (Research Topics) and visit the Serpico publication web page (publications since 2010) and and http:www.irisa.fr/vista/Publis/Auteur/Charles.Kervrann.english.html  (publications before 2010).

Main academic collaborators since 2021
  • Ludger Johannes (U1143 Institut Curie, Paris)
  • Giulia Bertolin (IGDR, Rennes)
  • Rut Carballido-Lopez (INRAe, MICALIS Unit, Jouy-en-Josas)
  • Renaud Fraisse (AIRBUS Defense and Space SAS, Toulouse)
  • Mohamedamine Benadjaoud (IRSN, Fontenay-aux-Roses)
  • Mikhail Eltsov (IGBMC, Strasbourg)
  • Kristin Schauer (Institut Gustave Roussy, Villejuif)
  • Benjamin D. Engel (Helmholtz Pioneer Campus, Helmholtz Zentrum München, Neuherberg, Germany)
  • Leila Muresan (University of Cambridge, UK)
  • Qiyin Fang (MacMaster University, Canada)
Sofware development

The most recent sofware can be found here.

Teaching

I teach courses for a total number of about 50 hours per year on “Statistical Models and Image Analysis” at ENSAI (Engineering school) (since 2000), “Geometric Modeling for Shapes and Images” at Master level at the University of Rennes 1 (2005-2020), “From Bioimage Processing to BioImage Informatics” at Master level at University of Strasbourg (since 2014, coordinator of the 25-hours module) and MINES ParisTech (2017-2019). I gave lectures for PhD students in 5 Summer/Winter schools (25 hours) in France since 2010.  

Research Topics

My research interests are in the field of signal-image processing, and mathematical and statistical methods for biological imaging and multidimensional microscopy. I focus on inverse problems, image representation and noise modeling, image sequence analysis, molecule detection and tracking in cell imaging, motion estimation and dynamics analysis in bioimaging. The most recent scientific projects are the following ones:

Image denoising and restoration
  • S. Herbreteau, E. Moebel, C. Kervrann.  Normalization-equivariant neural netowrks with application to image denoising, 2023,  arXiv-2212.00422
  • S. Herbreteau, C. Kervrann. Unsupervised linear and Iterative combinations of patches for image denoising, 2022,  arXiv-2212.00422HAL-INRIA-03894346, doi: 10.48550/arXiv.2212.00422
  • S. Prigent, H.-N. Nguyen, L. Leconte, C. A. Valades-Cruz, B. Hajj, J. Salamero and C. Kervrann. SPITFIRe: a supermaneuverable algorithm for fast denoising and deconvolution of 3D fluorescence microscopy images and videos,  Nat. Scientific Reports, doi: 10.1038/s41598-022-26178-y, 13(1): 1489, 2023, bioRxiv-2022.01.04.474883,  HAL-INRIA-03518618
  • S. Prigent, S. Dutertre, A. Bidaud-Meynard, G. Bertolin, G. Michaux, C. Kervrann. Sparse denoising and adaptive estimation enhances the resolution and contrast of fluorescence emission difference microscopy based on array detector, Optics Letters, 48(4): 847–919, doi: 10.1364/OL.474883, 2023, bioRxiv-2021.08.02.454749, HAL-INRIA-03931575 
  • S. Herbreteau, C. Kervrann. DCT2net: an interpretable shallow CNN for image denoising, IEEE Trans. on Image Processing, 31: 4292-4305, doi: 10.1109/TIP.2022.318148, 2022, arXiv-2107.14803, HAL-INRIA-03511641
  • E. Moebel, C. Kervrann.  A Monte Carlo framework for missing wedge restoration and noise removal in cryo-electron tomography, Journal of Structural Biology: X, 100013, pp. 1-18, doi:10.1016/j.yjsbx.2019.100013, 2019, HAL-INRIA-02424804
  • H.-N. Nguyen, V. Paveau, C. Cauchois, C. Kervrann. A variational method for dejittering large fluorescence line scanner images, IEEE Transactions on Computational Imaging, 4(2) :241-256, 2018 (HAL-INRIA-01577139)
  • H.-N. Nguyen, V. Paveau, C. Cauchois, C. Kervrann. Generalized sparse variation regularization for large fluorescence image deconvolution, preprint 2017 (HAL-INRIA-01609810)
  • Q. Jin, I. Grama, C. Kervrann, Q. Liu. Non-local means and optimal weights for noise removal, SIAM Journal on Imaging Sciences, 10(4):1878-1920, 2017, (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, C. 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, C. 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, C. 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, C. 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, C. 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.
  • C. Kervrann, J. Boulanger, P. Coupé. Bayesian non-local means filter, image redundancy and adaptive dictionaries for noise removal. In Proc. Conf. Scale-Space and Variational Methods (SSVM’ 07), Pages 520-532, Ischia, Italy, 2007.
  • C. 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, C. 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
  • C. 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
  • S. Manandhar, P. Bouthemy, E. Welf, G. Danuser, P. Roudot, C. Kervrann. 3D flow field estimation and assessment for live cell fluorescence microscopy. Bioinformatics, pp. 1-19,  btz780, HAL-INRIA-02308001, 2019
  • D. Fortun, N. Debroux, C. Kervrann. Spatially-variant kernel for optical flow under low signal-to-noise ratios: application to microscopy, Proc. of ICCV Workshop – BioImage Computing (BIC), Venice, Italy, October 2017 (HAL-INRIA-01561164)
  • 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, 145:81-94, 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
  • C. 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
  • B. DurelC. Kervrann, G. Bertolin. Quantitative dSTORM super-resolution microscopy localizes Aurora kinase A/AURKA in the mitochondrial matrix, HAL-03086955, bio-arXiv, Biology of the Cell, 113(11): 458-473, 2021 (open access)
  • F. Lavancier, T. Pécot, L. Zengzhen, C. Kervrann. Testing independence between two random sets for the analysis of colocalization in bio-imaging,  Biometrics, doi:10.1111/BIOM.13115,  arXiv, HAL-INRIA-02369555, 2019
  • F. Lavancier, T. Pécot, L. Zengzhen, C. Kervrann. A fast automatic colocalization method for 3D live cell and super-resolution microscopy, preprint, 2017 (HAL-INRIA-01577118)
  • 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) http://windhampharmacy.com
  • 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
Biophysics and analyis of intracellular trajectories
  • Y. Lu, P. Hodara, C. Kervrann, A. Trubuil. Probabilistic reconstruction of truncated particle trajectories on a closed surface, SIAM J. Multiscale Modeling & Simulation, HAL-INRIA-02323939,19(1): 87-112, 2021
  • X. Le Goff, J. Comelles, C. Kervrann, D. Riveline. Ends and middle: global force balance and septum location in fission yeast, The European Physical Journal E, DOI: 10.1140/epje/i2020-11955-xbioRxiv, HAL-02862900, 2020
  • V. Briane, A. Salomon, M. Vimond, C. Kervrann. A computational approach for detecting micro-domains and confinement domains in cells: a simulation study, Physical Biology, 17(2), 025002, HAL-INRIA-02424860, 2020
  • V. Briane, M. Vimond, C. Valades Cruz, A. Salomon, C. Wunder, C. Kervrann. A sequential algorithm to detect diffusion switching along intracellular particle trajectories, Bioinformatics, btz489, 36(1): 317-329, HAL-INRIA-01966831, 2020
  • V. Briane, M. Vimond, C. Kervrann. An overview of diffusion models for intracellular dynamics analysis, Briefings in Bioinformatics, bbz052, 21(4): 1136–115,  HAL-INRIA-0196682, 2020
  • H. Bouvrais, L. Chesneau, Y. Le Cunff, D. Fairbrass, N. Soler, S. PastezeurT. Pécot, C. Kervrann, J. Pécréaux. The coordination of spindle-positioning forces during the asymmetric division of the C. elegans zygote is revealed by distinct microtubule dynamics at the cortexbio-arXiv,HAL-INRIA-02424717, EMBO Reports, 2021 (in Press)
  • T. Pécot, L. Zengzhen, J. Boulanger, F. Waharte, J. Salamero, C. Kervrann. A quantitative approach for analyzing the spatio-temporal distribution of 3D intracellular events in fluorescence microscopy, eLife 2018;7:e32311 (doi:10.7554/eLife.32311), 2018 (HAL-INRIA-01966817)
  • V. Briane, C. Kervrann, M. Vimond. Statistical analysis of particle trajectories in living cells, Phys. Rev. E 97, 062121 (doi:10.1103/PhysRevE.97.062121), 2018 (arXiv) (HAL-INRIA-01557705
Motion analysis and tracking in fluorescence microscopy
  • A. Caranfil, Y. Le Cunff, C. Kervrann. Local temporal image correlation spectroscopy and Bayesian simulation technique for sparse estimation of diffusion in fluorescence imaging, Biological Imaging, 2023 (in press),  HAL-INRIA-03540375
  • S. Prigent, C. A. Valades-Cruz, L. Leconte, J. Salamero and C. Kervrann. STracking: a free and open-source Python library for particle tracking and analysis, Bioinformatics, btac365, 2022, HAL-03688217
  • 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, C. 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, C. 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, C. 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
  • E. Moebel, C. Kervrann. Towards unsupervised classification of macromolecular complexes in cryo electron tomography: challenges and opportunities, Computer Methods and Programs in Medicine, Special issue on “Computational Methods for Three-Dimensional Electron Microscopy (3DEM)”, 2022, bioRxiv-2022.03.10.483789doi: 10.1016/j.cmpb.2022.107017
  • E. Moebel, A. Martinez-Sanchez, L. Lamm, R.D. Righetto, W. Wietrzynski, S. AlbertD. Larivière, E. Fourmentin, S. Pfeffer, J. Ortiz, W. Baumeister, T. PengB.D. Engel, 10, C. Kervrann. Deep learning improves macromolecule identification in 3D cellular cryo-electron tomograms, bioRxiv, Nature Methods, 18: 1386-1394, 2021 (doi: 10.1038/s41592-021-01275-4)
  • S. Ku, C. Messaoudi, C. Guyomar, C. Kervrann, D. Chrétien. Determination of microtubule lattice parameters from cryo-electro microscope images using TubuleJ. Bio-protocol 10(21): e3814,  DOI: 10.21769/BioProtoc.3814, HAL-03040292v1, 2020
  • 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
Visualization and virtual reality
  • G. Fouché, F. Argelaguet, E. Faure, C. Kervrann. Immersive and interactive visualization of 3D spatio-temporal data using a space time hypercube: application to cell division and morphogenesis analysis, Frontiers in Bioinformatics, 2023 (accepted)
  • C.A. Valades-Cruz, L. Leconte, G. Fouché, T. Blanc, N. Van Hille, K. Fournier, L. Tao, B. Gallean, F. Deslandes, B. Hajj, E, Faure, F. Argelaguet, A. Trubuil, T. Isenberg, J.-B. Masson, J. Salamero, C. Kervrann. Challenges of intracellular visualization using virtual and augmented realityFrontiers in Bioinformatics, section Computational BioImaging, doi: 10.3389/fbinf.2022.997082, 2022, HAL-INRIA-03790274
  • G. Fouché, F. Argelaguet, E. Faure, C. Kervrann. Timeline design space for immersive exploration of time-varying spatial 3D data10.48550/arXiv.2206.09910, Proc. ACM Symp. on Virtual Reality Software and Technology (VRST’22), Tsukuba, Japan, 2022
Non-conventional imaging systems
  • H.-N. Nguyen, V. Paveau, C. Cauchois, C. Kervrann. ATMAD : robust image analysis for Automatic Tissue MicroArray De-arraying, BMC Bioinformatics, 19:148, 2018 (HAL-INRIA-01577238)

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