Publications

NEWS / Last publications

  • S. Herbreteau, E. Moebel, C. Kervrann. Normalization-equivariant neural networks with application to image denoising,   Proc. of NeurIPS, New-Orleans, USA, December 2023 (arXiv-2306.05037, doi: 10.48550/arXiv.2306.05037)
  • E. Meunier and P. Bouthemy. Unsupervised space-time network for temporally-consistent segmentation of multiple motions,  Proc. Conference on Computer Vision and Pattern Recognition (CVPR), Vancouver, Canada, June 2023

Thesis and HdR

  • C. Kervrann. Modèles statistiques pour l’analyse d’images, algorithmes et applications en imagerie bio-cellulaire et moléculaire. Habilitation à diriger des recherches, Mention Traitement du Signal et Télécommunications, Université de Rennes 1, June 2010 (see TEL-ARCHIVES-OUVERTES-00541298 / slides and videos)
  • S. Herbreteau.  Machine learning and interpretable convolutional networks for supervised and unsupervised image denoising with application to satellite imagery, , PhD Thesis, Mention AST Signal Image Vision, Université de Rennes, December 2023 (language: english) (see https://theses.hal.science/tel-04403632)
  • E. Meunier. Unsupervised learning for motion segmentation and motion saliency in videos, , PhD Thesis, Mention AST Signal Image Vision, Université de Rennes, December 2023 (language: english) (see https://inria.hal.science/tel-04389253)
  • A. Deschemps. Machine learning and convolutional networks for automated biological dosimetry, PhD Thesis, Mention AST Signal Image Vision, Université de Rennes, December 2023 (language: english)
  • A. Salomon. Statistical modeling for the analysis of molecular diffusion and intracellular trafficking in fluorescence microscopy, PhD Thesis, Mention AST Signal Image Vision, Université de Rennes, December 2023 (language: english)
  • G. Fouché. Immersive and interactive visualization of temporal 3D data, PhD Thesis, INSA Rennes, December 2022 (language: english)
  • A.-G. Caranfil. Signal modeling and Bayesian estimation for cellular mechanism analysis : study of diffusion at the cell membrane and cell division, PhD Thesis, Université de Rennes 1, November 2022 (language: english)
  • Y. Lu. Intracellular dynamics and super-resolution imaging: the bacterial wall probed at the molecular scale, PhD Thesis, Université de Rennes 1, June 2021 (language: english) (see TEL-ARCHIVE-OUVERTES-03268216)
  • L. Maczyta. Dynamic visual saliency in image sequences, PhD Thesis, Mention AST Signal Image Vision, Université de Rennes 1, November 2020 (language: english) (see TEL-ARCHIVE-OUVERTES-03087274)
  • S. Manandhar. 3D motion estimation and assessment in fluorescence microscopy volume sequence, PhD Thesis, Mention AST Signal Image Vision, Université de Rennes 1, November 2019 (language: english) (see TEL-ARCHIVE-OUVERTES-02418551 219)
  • E. Moebel. New strategies for the identification and enumeration of macromolecules in 3D images of cryo electron tomography. PhD Thesis, Mention AST Signal Image Vision, Université de Rennes 1, February 2019 (language: english) (see TEL-ARCHIVE-OUVERTES-02153877)
  • B.M. Toledo Acosta. Multimodal image registration in 2D and 3D correlative microscopy. PhD Thesis, Mention AST Signal Image Vision, Université de Rennes 1, May 2018 (language: english) (see TEL-ARCHIVE-OUVERTES-01868852)
  • V. Briane. Tests statistiques pour l’analyse de trajectoires de particules : application à l’imagerie intracellulaire. PhD Thesis, Mention Traitement du Signal et Télécommunications, Université de Rennes 1, December 2017 (language: english) (see TEL-ARCHIVE-OUVERTES-01727777)
  • H. N. Nguyen. Methods and algorithms of segmentation and deconvolution for quantitative analysis of tissue microarray images. PhD Thesis, Mention Traitement du Signal et Télécommunications, Université de Rennes 1, December 2017 (language: english) (see TEL-ARCHIVE-OUVERTES-01737764)
  • J. M. Perez Rua. Hierarchical motion-based video analysis with applications to video post-production. PhD Thesis, Mention Traitement du Signal et Télécommunications, Université de Rennes 1, December 2017 (see TEL-ARCHIVES-OUVERTES-2017REN1S125) (language: english)
  • A. Basset. Detection and characterization of dynamical events in image sequences based on local statistical approaches: Application to membrane fusion in TIRF microscopy. PhD Thesis, Mention Traitement du Signal et Télécommunications, Université de Rennes 1, December 2015 (see TEL-ARCHIVES-OUVERTES-01304780) (language: english)
  • D. Fortun. Aggregation framework and patch-based image representation for optical flow. PhD Thesis, Mention Traitement du Signal et Télécommunications, Université de Rennes 1, July 2014 (see TEL-ARCHIVES-OUVERTES-0110456) (language: english)
  • P. Roudot. Image processing methods for dynamical intracellular processes analysis in quantitative fluorescence microscopy. PhD Thesis, Mention Traitement du Signal et Télécommunications, Université de Rennes 1, May 2014 (see TEL-ARCHIVES-OUVERTES-01103887) (language: english)
  • T. Pécot. Modélisation et estimation du trafic intracellulaire par tomographie de réseaux et microscopie de fluorescence. PhD Thesis, Mention Traitement du Signal et Télécommunications, Université de Rennes 1, March 2010 (see TEL-ARCHIVES-OUVERTES-00541304)
  • T. Crivelli. Mixed-state Markov models for image motion analysis. PhD Thesis, Mention Traitement du Signal et Télécommunications, Université de Rennes 1, March 2010 (language: english)

Preprints and submissions

  • A. Deschemps, E. Grégoire, J.S. Martinez, A. Vaurijoux, P. Fernandez, D. Dugue, L. Bobyk, M. Valente, G. Gruel, E. Moebel, M.A. Benadjaoud, C. Kervrann. Ensembling Unets, sparse representation, and low-dimensional visualization for rare chromosomal aberration detection and identi cation in light microscopy images,  2023
  • S. Papereux, L. Leconte, C.A. Valades-Cruz, T. Liu, J. Dumont, Z. Chen, J. Salamero, C. Kervrann, A. Badoual. DeepCristae, a CNN for the restoration of mitochondria cristae in live microscopy images, bioRxiv-2023.07.05.547594, doi: 10.1101/2023.07.05.547594, 2023
  • S. Herbreteau, C. Kervrann. Unsupervised linear and Iterative combinations of patches for image denoising,   arXiv-2212.00422, HAL-INRIA-03894346, doi: 10.48550/arXiv.2212.00422, 2023
  • S. Herbreteau, C. Kervrann. A unified framework of non-local parametric methods for image denoising, 2023
  • A. Salomon, C. Valades-Cruz, L. Leconte, C. Kervrann. Dense mapping of intracellular diffusion and drift from single particle tracking data analysis, 2022 (in preparation)
  • M. Abdellah, C. A. Valades-Cruz, R. Barth, H. A. Shaban. Genome-wide analysis of the dynamic and biophysical properties of chromatin and nuclear proteins in living cells with Hi-D. bioRxiv 2022.11.17.516893, 2022 (in revision)

Academic Journals

2023
  • L. Balsollier, F. Lavancier, J. Salamero, C. Kervrann. A generative model to synthetize spatio-temporal dynamics of biomolecules in cells, Biological Imaging Biological Imaging, 3:e22, doi:10.1017/S2633903X2300020X (arXiv-2303.06951, DOI: 10.48550/arXiv.2303.06951), 2023
  • 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, DOI: 10.3389/fbinf.2023.998991, 2023
  • A. Caranfil, Y. Le Cunff, C. Kervrann. BayesTICS: Local temporal image correlation spectroscopy and Bayesian simulation technique for sparse estimation of diffusion in fluorescence imaging, HAL-INRIA-03540375, Biological Imaging, 3(E5), DOI: 0.1017/S2633903X23000041, 2023
  • E. Meunier, A. Badoual and P. Bouthemy. EM-driven unsupervised learning for efficient motion segmentation,  IEEE Transactions on Pattern Analysis and Machine Intelligence, HAL-INRIA-03516617, 45(4):4462-4473, April 2023
  • 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, bioRxiv-2022.01.04.474883,  HAL-INRIA-03518618, Nat. Scientific Reports, doi: 10.1038/s41598-022-26178-y, 13(1): 1489, 2023
  • 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, bioRxiv-2021.08.02.454749, HAL-INRIA-03931575, Optics Letters, 48(4): 847–919, doi: 10.1364/OL.474883, 2023
  • C. Lemaigre, A. Ceuppens, C. A. Valades-Cruz, B. Ledoux, B. Vanbeneden, M. Hassan, F. R. Zetterberg, U. J. Nilsson, L. Johannes, C. Wunder, H-F. Renard, P. Morsomme. N-BAR and F-BAR proteins – Endophilin-A3 and PSTPIP1 – control clathrin-independent endocytosis of L1CAM, Traffic, doi:10.1111/tra.12883, 2023
2022
  • 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 analysis,  Nature Methods, doi: 10.1038/s41592-022-01642-9, bioRxiv-2021.12.09.471919, HAL-INRIA-03474512,  2022 (view-only link)
  • 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 reality, Frontiers in Bioinformatics, section Computational BioImaging,  HAL-INRIA-03790274, doi: 10.3389/fbinf.2022.997082, 2022
  • A. Covelo, A. Badoual and A. Denizot. Advocating for interdisciplinary collaborations to unravel the astrocyte “Calcium Code”, Journal of Molecular Neuroscience, HAL-INRIA-03520863, doi: 10.1007/s12031-022-02006-w, 2022
  • 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)”,  bioRxiv-2022.03.10.483789, doi: 10.1016/j.cmpb.2022.107017, 2022
  • S. Herbreteau, C. Kervrann. DCT2net: an interpretable shallow CNN for image denoising, IEEE Transactions on Image Processing, 31: 4292-4305, arXiv-2107.14803, HAL-INRIA-03511641, doi: 10.1109/TIP.2022.318148, 2022
  • 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, HAL-03688217, 2022
  • L. Maczyta, P. Bouthemy, O. Le Meur. Trajectory saliency detection using consistency-oriented latent codes from a recurrent auto-encoder, IEEE Transactions on Circuits and Systems for Video Technology, HAL-INRIA-03079998, 32(4):1724 – 1738, April 2022
  • J. Jiménez de la Morena, P. Conesa, Y.C. Fonseca, F.P. de Isidro-Gómez,  D. Herreros,  E. Fernández-Giménez, D. Strelak, E. Moebel, T.O. Buchholz, F. Jug,  A. Martinez-Sanchez, M. Harastani, S. Jonic, J.J. Conesa, A. Cuervo, P. Losana, I. Sánchez, M. Iceta, L. Del Cano, L. M. Gragera, R. Melero, G. Sharov, D. Castaño-Díez, A. Koster, J.G. Piccirillo, J.L. Vilas, J. Otón, R. Marabini, C.O.S. Sorzano, J.M. Carazo. ScipionTomo: Towards cryo-electron tomography software integration, reproducibility, Journal of Structural Biology, 214(3): 107872, doi: 10.1016/j.jsb.2022.107872, 2022
  • C. V. Rimoli, C. A. Valades Cruz, V. Curcio, M. Mavrakis and S. Brasselet, 4polar-STORM polarized super-resolution imaging of actin filament organization in cells, Nature Communications, 13(1) , doi: 10.1101/2021.03.17.435879, HAL-archives-ouvertes, 2022
  • K. Kivinen, H. GAMvan Luenen,M. Alcalay, C. Bock, J. Dodzian, K.Hoskova,D.Hoyle,O.Hradil, S. K. Christensen, B. Korn, T. Kosteas, M.Morales, K. Skowronek, V. Theodorou, G. vanMinnebruggen, J. Salamero and L. Premvardhan, Acknowledging and citing core facilities, EMBO Reports 23(9): 1–3. doi: 10.15252/embr.202255734,  HAL-03796258.
2021
  • 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, 10, C. Kervrann. Deep learning improves macromolecule identification in 3D cellular cryo-electron tomograms, bioRxiv, Nature Methods, 18: 1386-1394, HAL-INRIA-03509223,  doi: 10.1038/s41592-021-01275-4, 2021
  • B. Durel, C. Kervrann, G. Bertolin. Quantitative dSTORM super-resolution microscopy localizes Aurora kinase A/AURKA in the mitochondrial matrix, HAL-03086955, bio-arXiv, HAL-archives-ouvertes-03367309, Biology of the Cell, 113(11): 458-473, 2021 (open access)
  • A. Badoual, L. Romani, M. Unser. Active subdivision surfaces for the semiautomatic segmentation of biomedical, IEEE Transactions on Image Processing, 30: 5739-5753, HAL-INRIA-032867905, 2021
  • 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-03088288, 19(1): 87-112, 2021
  • H. Bouvrais, L. Chesneau, Y. Le Cunff, D. Fairbrass, N. Soler, S. Pastezeur, T. 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 cortex, bio-arXiv,HAL-INRIA-02424717, EMBO Reports, e50770, 2021
  • F. Lavancier, A. Poinas and R. Waagepetersen, Adaptive estimating function inference for nonstationary determinantal point processes, Scandinavian Journal of Statistics, 48(1): 87–107,  HAL-archives-ouvertes-01816528, (DOI: 10.1111/sjos.12440) . URL: https://hal.archives-ouvertes.fr/hal-01816528, 2021
  • V. Colson, V. H. B. Ferreira, A. C. Luchiari, C. Valotaire, F. Borel, J. Bugeon, S. Prigent, L. Dickel, L. Calandreau and V. Guesdon, Loss of light colour preference after chronic embryonic stress in rainbow trout fry: a novel and potential indicator of fish welfare ?  Applied Animal Behaviour Science 239: 105335, (DOI: 10.1016/j.applanim.2021.105335), HAL-INRAE-03207748, 2021
  • L. Johannes and C. A. Valades-Cruz, The final twist in endocytic membrane scission,  Nature Cell Biology, 23(8): 812–813, (DOI: 10.1038/s41556-021-00711-z), HAL-archives-ouvertes-03517154, 2021
2020
  • F. Lavancier, T. Pécot, L. Zengzhen, C. Kervrann, Testing independence between two random sets for the analysis of colocalization in bio-imaging, Biometrics, 76(1): 36–46, doi:10.1111/BIOM.13115,  arXiv, HAL-02369555, 2020
  • E. Moebel, C. Kervrann. A Monte Carlo framework for missing wedge restoration and noise removal in cryo-electron tomography, Journal of Structural Biology: X, 4:100013, pp. 1-18, doi:10.1016/j.yjsbx.2019.100013, HAL-INRIA-02424804, 2020
  • 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
  • I. Gubins, M.L. Chaillet, G. van der Schot, R.C. Veltkamp, F. Förster, Y. Hao, X. Wan, X. Cui, F. Zhang, E. Moebel, X. Wang, D. Kihara, X. Zeng, M. Xu, N.P. Nguyen, T. White, F. Bunyak. SHREC 2020: Classification in cryo-electron tomograms, Computers & Graphics, 91: 279-289, https://doi.org/10.1016/j.cag.2020.07.010, 2020
  • V. Briane, M. Vimond, C. Kervrann. An overview of diffusion models for intracellular dynamics analysis, bbz052, Briefings in Bioinformatics, 21(4): 1136–1150, HAL-INRIA-0196682, 2020
  • G. Volohonsky, P. Paul-Gilloteaux, J. Štáfková, J. Soichot, J. Salamero, E.A. Levashina. Kinetics of Plasmodium midgut invasion in Anopheles mosquitoes. PLoS Pathogens, 16(9), DOI: 10.1371/journal.ppat.1008739, HAL-02509933, 2020
  • 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-x,  bioRxiv, HAL-02862900, 2020
  • J.-M. Perez Rua, O. Miksik, T. Crivelli, P. Bouthemy, P. Torr, P. Pérez. ROAM: A rich object appearance model with application to rotoscoping, IEEE Transactions on Pattern Analysis and Machine Intelligence, 42(8): 1996 – 2010, doi:10.1109/tpami.2019.2904963, HAL- hal-015760172020, 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 (Institute of Physics: Hybrid Open Access), 17(2), 025002, pp. 1-15, HAL-INRIA-02424860, DOI: 10.1088/1478-3975/ab5e1d , 2020
  • S. Manandhar, P. Bouthemy, E. Welf, G. Danuser, P. Roudot, C. Kervrann. 3D flow field estimation and assessment for live cell fluorescence microscopy, Bioinformatics Oxford, 36(5):1317–1325, 10.1093/bioinformatics/btz780, HAL-INRIA-02308001, 2020
  • H.-F. Renard, F. Tyckaert, C. Lo Giudice, T. Hirsch, C. A. Valades-Cruz, C. Lemaigre, M. Shafaq-Zadah, C. Wunder, R. Wattiez, L. Johannes, P. van der Bruggen, D. Alsteens, P. Morsomme. Endophilin-A3 and Galectin-8 control the clathrin-independent endocytosis of CD166. Nature Communications, 11, 1457, doi: 10.1038/s41467-020-15303-y , HAL-02619135, 2020
2019
  • B. Combès, S. Prima. An efficient EM-ICP algorithm for non-linear registration of large3D point sets,  Computer Vision and Image Understanding”,  102854,  doi:10.1016/J.CVIU.2019.102854, HAL-INRIA-02414127, 2019
  • F. Lavancier, A. Poinas, R. Waagepetersen. Adaptive estimating function inference for non-stationarydeterminantal point processes, Scandinavian Journal of Statistics, pp. 1-35, HAL-INRIA-01816528, 2019
  • 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,  HAL-INRIA-01966831, 2019
  • L. Maczyta, P. Bouthemy, O. Le Meur. CNN-based temporal detection of motion saliency in videos, Pattern Recognition Letters, 128:298-305, doi:10.1016/J.PATREC.2019.09.016, HAL-INRIA-02345209, 2019
  • P. Bouthemy, B.M. Toledo Acosta, B. Delyon. Robust model selection in 2D parametric motion estimation, Journal of Mathematical Imaging and Vision, 61(7): 1022–1036, doi:10.1007/S10851-019-00883-2, HAL-INRIA-02315977,  2019
  • S. Raman, S. Singh, T. Pécot, E. Caserta, K. Huang, J. Rittscher, G. Leone, R. Machiraju. Capturing variations in nuclear phenotypes, Journal of Computer Science, 36, 1011014, HAL-INRIA-02424723, 2019
  • H. Folz, C.A. Niño, S. Taranum, S. Caesar, L. Latta, F. Waharte, J. Salamero, G. Schlenstedt, C. Dargemont. SUMOylation of the nuclear pore complex basket is involved in sensing cellular stresses, Journal of Cell Science, 132:jcs224279,  doi:10.1242/jcs.224279, 2019
  • F. Kang, M. Zhou, X. Huang, J. Fan, L. Wei, J. Boulanger, Z. Liu, J. Salamero, Y. Liu, L. Chen. E-syt1 Re-arranges STIM1 clusters to stabilize ring-shaped ER-PM contact sites and accelerate Ca2+ store replenishment, Scientific Reports, 9:3975 (https://www.nature.com/articles/s41598-019-40331-0), 2019
  • A. Poinas, B. Delyon, F. Lavancier. Mixing properties and central limit theorem for associated point processes, Bernoulli,  25(3): 1724-1754, doi:10.3150/18-BEJ1033, HAL-INRIA-01519096, 2019
  • G. Potier, R. Capoulade, J. Mérot, F. Lavancier, X. Heiligenstein, J. Salamero, P. Paul-Gilloteaux. Automatic registration of correlative microscopies with error assessment and applications for the optimization of multimodal acquisitions, Microscopy and Microanalysis, 25:S2, 1020-1021 , https://doi.org/10.1017/S143192761900583X, HAL-INRIA-02267554, 2019
2018
  • J.-C. Röper, D. Mitrossilis, G. Stirnemann, F. Waharte, I. Brito, M.-E. Fernandez-Sanchez, M. Baaden, J. Salamero, E. Farge. The major beta-catenin/E-cadherin junctional binding site is a primary molecular mechano-transductor of differentiation in vivo, Elife, 7:e33381 (doi:10.7554/eLife.33381), 2018
  • A. Poinas, B. Delyon, F. Lavancier. Mixing properties and central limit theorem for associated point processes, Bernoulli, 2018 (arXiv)
  • 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)
  • 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. ATMAD : robust image analysis for Automatic Tissue MicroArray De-arraying, BMC Bioinformatics, 19:148, 2018 (HAL-INRIA-01577238)
2017
  • F. Lavancier, P. Rochet. A tutorial on estimator averaging in spatial point process models, Journal de la SFDS, 158(3) :106-123, 2017 (arXiv)
  • 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 (open access)
  • 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)
  • 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, 4:1-19 2017 (paper on-line)
  • C.A.N. Biscio, F. Lavancier. Contrast estimation for parametric stationary determinantal point processes, Scandinavian Journal of Statistics 44(1):204–229, 2017 (HAL-INRIA-01215582)
  • J.-F. Coeurjolly, F. Lavancier. Parametric estimation of pairwise Gibbs point processes with infinite range interaction, Bernoulli 23(2):1299-1334, 2017 (HAL-INRIA-01092225)
  • D. Dereudre, F. Lavancier. Consistency of likelihood estimation for Gibbs point processes, The Annals of Statistics 45(2):744–770, 2017 (HAL-INRIA-01144877)
  • 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)
  • 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, 2017 (HAL-INRIA-01575754)
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
  • C. A. N. Biscio, F. Lavancier. Quantifying repulsiveness of determinantal point processes, to appear, Bernouilli, 22(4):2001-2028, 2016 (HAL-INRIA-01003155)
  • C. A. N. Biscio, F. Lavancier. Brillinger mixing of determinantal point processes and statistical applications, Electronic Journal of Statistics 10(1):582–607, 2016 (HAL-INRIA-01179831 )
  • J.-F. Coeurjolly, F. Lavancier. Parametric estimation of pairwise Gibbs point processes with infinite range interaction, Bernoulli, 2016 (HAL-INRIA-01092225)
  • F. Lavancier, J. Moeller. Modelling aggregation on the large scale and regularity on the small scale in spatial point pattern datasets, Scandinavian Journal of Statistics 43(2):587–609, 2016 (HAL-INRIA-01155646) [hal:hal-01155646].
  • X. Tang, H. Liu, A. Srivastatva, T. Pécot, Z. Chen, Q. Wang, K. Huang, M. Sàenzrobles, P. Cantalupo, J. Pipas, G. Leone. Transcriptome regulation and chromatin occupancy by E2F3 and MYC in mice, Scientific Data 3:160008, February 2016, (HAL-INRIA-01416818)
  • 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, April 2016
  • F. Lavancier, P. Rochet. A general procedure to combine estimators, Computational Statistics and Data Analysis, 94:175–192, February 2016 (HAL-INRIA-00936024)
  • 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, 10(1):6-30, February 2016 (HAL-INRIA-01246375) pdf
  • C. Kervrann, C.O. Sorzano, S.T. Acton, J.-C. Olivo-Marin, M. Unser. Introduction to the Issue on Advanced Signal Processing in Microscopy and Cell Imaging, IEEE Journal of Selected Topics in Signal Processing, Special issue on Advanced Signal Processing in Microscopy and Cell Imaging, 10(1):3-5, February 2016
  • 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, 10(1): 203-216, February 2016
  • M. Jain, H. Jégou, P. Bouthemy. Improved motion description for action classification, Frontiers in ICT: Computer Image Analysis, 1-17, January 2016 (paper on-line)
2015
  • P. Trikha, N. Sharma, C. Pena, A. Reyes, T. Pécot, et al. E2f3 in tumor macrophages promotes lung metastasis, Oncogene, Nov. 2015 (HAL-INRIA-01244951)
  • H. Liu, X. Tang, A. Srivastava, T. Pécot, P. Daniel, et al. Redeployment of Myc and E2f1-3 drives Rb-deficient cell cycles, Nature Cell Biology, 17(8):1036-1048, 2015 (HAL-INRIA-01244839)
  • D. Jones, D.-Y. Park, M. Anghelina, T. Pécot, R. Machiraju, et al. Actin grips: circular actin-rich cytoskeletal structures that mediate the wrapping of polymeric microfibers by endothelial cells, Biomaterials, 52:395-406, 2015 (HAL-INRIA-01244825)
  • E. Caserta, O. Egriboz, H. Wang, C. Martin, C. Koivisto, T. Pécot et al. Noncatalytic PTEN missense mutation predisposes to organ-selective cancer development in vivo, Genes and Development, 29(16):1707-1720, 2015 (HAL-INRIA-01244933)
  • F. Lavancier , J. Moller, R. Ege. Determinantal point process models and statistical inference, Journal of the Royal Statistical Society: Series B, 77(4):853–877, 2015 (HAL-01241077)
  • F. Lavancier, J. Moller. Modelling aggregation on the large scale and regularity on the small scale in spatial point pattern datasets, Scandinavian Journal of Statistics, December 2015 (HAL-01155646)
  • P. Roudot, C. Kervrann, C. Blouin, C., F. Waharte. Lifetime estimation on moving sub-cellular objects in frequency domain FLIM imaging, Journal of the Optical Society of America A, 32(10):1821-1835, 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
  • 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, 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 Trans. on Image Processing, 24(2):667-680, 2015
2014
  • 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 (see HAL-INRIA-00932869)
2013
  • 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 (doi:10.1137/120872048)
  • 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)
2012
  • 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
2011
  • 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
  • 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
  • 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)
  • F. Palhano, G. Andrade Barroso, P. Coupé, P. Hellier. Real time ultrasound image denoising, Journal of Real-Time Image Processing, 6(1):15-22, March 2011 (see HAL-INRIA-00476122)
2010
  • 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
  • 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)
  • 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)
  • B. Cinquin, A. Chessel, A. Gidon, S. Bardin, T. Pécot, J. Boulanger, Ch. Kervrann, J. Salamero. Advanced microcopy to study tracking and spatiotemporal organization of intracellular membranes, Bio-Medical Materials and Engineering, 2010 (see HAL-INRIA-00541284)
  • C. Nauczyciel, P. Hellier, X. Morandi, S. Blestel, D. Drapier, J.C. Ferre, C. Barillot, B. Millet. Assessment of standard coil positioning in transcranial magnetic stimulation in depression, Psychiatry Research, 2010 (see HAL-INRIA-00535787)
  • P. Hellier, P. Coupé, X. Morandi, D. L. Collins. An automatic geometrical and statistical method to detect acoustic shadows in intraoperative ultrasound brain images, Medical Image Analysis, 14(2):195-204, 2010 (see HAL-INRIA-00432724)
  • 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)

Book Chapters

  • C. Kervrann. Biomolecule trafficking and network tomography-based simulations, HAL-INRIA-03518596, In Biomedical Image Synthesis and Simulations, Ninon Burgos, David Svoboda (eds), Academic Press, pages 543-569, 2022, doi: 10.1016/B978-0-12-824349-7.00031-1
  • 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

International Conferences with Proceedings

2023
  • S. Herbreteau, E. Moebel, C. Kervrann. Normalization-equivariant neural networks with application to image denoising,   Proc. of NeurIPS, New-Orleans, USA, December 2023 (arXiv-2306.05037, doi: 10.48550/arXiv.2306.05037)
  • E. Meunier and P. Bouthemy. Unsupervised space-time network for temporally-consistent segmentation of multiple motions,  Proc. Conference on Computer Vision and Pattern Recognition (CVPR), Vancouver, Canada, June 2023
2022
  • G. Fouché, F. Argelaguet, E. Faure, C. Kervrann. Timeline design space for immersive exploration of time-varying spatial 3D data, 10.48550/arXiv.2206.09910, Proc. ACM Symp. on Virtual Reality Software and Technology (VRST’22), Tsukuba, Japan, 2022
  • S. Herbreteau, C. Kervrann. Towards a unified view of unsupervised non-local methods for image denoising: the NL-Ridge approach, Proc. IEEE Int. Conf. Image Processing (ICIP), arXiv-2203.00570, Bordeaux, France, 2022
2021
  • E. Meunier and P. Bouthemy. Unsupervised computation of salient motion maps from the interpretation of a frame-based classification network,  Proc. 32th British Machine Vision Conference (online BMVC’2021), HAL-INRIA-03469574, UK, November 2021
  • A. Badoual, M. Arizono, A. Denizot, M. Ducros, H. Berry, V. Nägerl, C. Kervrann. Simulation of astrocytic calcium dynamics in Lattice Light Sheet Microscopy images. Proc IEEE Int. Symp. Biomedical Imaging (ISBI’21), HAL-INRIA-03106797, Nice, France, April  2021
  • I. Gubins et al. Classification in cryo-electron tomograms. In Proc. Eurographics Workshop on 3D Object Retrieval – SHREC – 3D Shape Retrieval Contest (2021), Vienna, Austria, May 2021
2020
  • S. Prigent, S. Dutertre, C. Kervrann. Empirical SURE-guided microscopy super-resolution image reconstruction from confocal multi-array detectors. Proc IEEE Int. Conf.  Acoustics, Speech and Signal Processing (ICASSP’20), Barcelona, Spain, May, 2020
  • A. Salomon, C. Valades-Cruz, L. Leconte, C. Kervrann. Dense mapping of intracellular diffusion and drift from single particle tracking data analysis, Proc IEEE Int. Conf.  Acoustics, Speech and Signal Processing (ICASSP’20), Barcelona, Spain, May, 2020
  • S. Manandhar, P. Bouthemy, E. Welf, P. Roudot, C. Kervrann. 3D optical flow estimation combining 3D Census signature and total  variation regularization,  Proc IEEE Int. Symp.  Biomedical Imaging (ISBI’20), Iowa City, USA, April, 2020
2019
  • L. Maczyta, P. Bouthemy, O. Le Meur. Unsupervised motion saliency map estimation based on optical flow inpainting. Proc. IEEE Int. Conference on Image Processing (ICIP’19), Taipei, Taiwan, September 2019
  • I. Gubins et al. Classification in cryo-electron tomograms. In Proc. Eurographics Workshop on 3D Object Retrieval – SHREC – 3D Shape Retrieval Contest (2019), Genova, Italy, May 2019
2018
  • E. Moebel, C. Kervrann. A Monte Carlo framework for denoising and missing wedge reconstruction in cryo-electron tomography. Proc. MICCAI- Workshop on Patch-based Techniques in Medical Imaging, Grenade, Spain, September 2018
  • B.M. Toledo Acosta, X. Heiligenstein, G. Malandain, P. Bouthemy. Intensity-based matching and registration for 3D correlative microscopy with large discrepancies. Proc. IEEE Int. Symp. on Biomedical Imaging (ISBI’18), Washington, April 2018
  • S. Manandhar, P. Bouthemy, E. Welf, P. Roudot, C. Kervrann. A sparse-to-dense method for 3D optical flow estimation in 3D light-microscopy image sequences. Proc. IEEE Int. Symp. on Biomedical Imaging (ISBI’18), Washington, April 2018
2017
  • 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 (HAL-INRIA-01575720)
  • 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)
  • O. Miksik, J.-M. Pérez-Rùa, P.H.S. Torr, P. Pérez. ROAM: a Rich Object Appearance Model with application to rotoscoping. Proc. of Conference on Computer Vision and Pattern Recognition (CVPR), Honolulu, United States, July 2017, (HAL-INRIA-01576017)
2016
  • 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
  • V. Briane, M. Vimond, C. Kervrann. An adaptive statistical test to detect non Brownian diffusion from particle trajectories. Proc. IEEE Int. Symp. on Biomedical Imaging (ISBI’16), Prague, April 2016
2015
  • 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)
  • 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
  • H.-N. Nguyen, C. Kervrann, C. Cauchois, V. Paveau . Automatic core segmentation and registration for fast tissue microarray de-arraying. Proc. IEEE Int. Symp. on Biomedical Imaging (ISBI’15), New-York City, April 2015
2014
  • 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)
  • 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. 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 (see HAL-INRIA-00996844)
  • 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
2013
  • 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
  • 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
  • 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
  • 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
  • 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
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)
  • 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)
  • 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. Semi-parametric robust Gaussian fitting. IEEE ISBI 2012 Workshop: Particle Tracking Challenge, Barcelona, Spain, May 2012
  • 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)
2010
  • A. Chessel, B. Cinquin, S. Bardin, J. Salamero, J. Boulanger, C. Kervrann. A detection-based framework for the analysis of recycling in TIRF microsocopy. In Proc. IEEE Int. Symp. on Biomedical Imaging: from nano to macro (ISBI’10), pp. 1281-1284, Rotterdam, The Netherlands, April 2010 pdf (see HAL-INRIA-00541102)

International Conferences, Workshops, Invited Talks

2022
  • S. Herbreteau,  C. Kervrann, DCT2net: a DCT-based interpretable shallow CNN method for efficient and fast image denoising,  SIAM Conference on Imaging Science (IS22),  Berlin, Germany, 2022
  • S. Herbreteau,  C. Kervrann , NL-Ridge: a novel statistical partch-based apporach for image denoising, International Conference on Curves and Surfaces, Arcachon, France, 2022
2021
  • L. Leconte, S. Prigent, L. Maury, C. A. Valades Cruz, J. Salamero and C. Kervrann, BioImageIT: Integration of image data-management with analysis,  BioImage Informatics conference, Paris, France, November 2021 (poster)
  • 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 and C. Kervrann, Deep learning improves macromolecule identification in 3D cellular cryo-electron tomograms,  BioImage Informatics conference, Paris, France, November 2021 (selected talk)
  • S. Prigent, C. A. Valades-Cruz, L. Leconte, J. Salamero and C. Kervrann, SPITFIR(e): a supermaneuverable image restoration algorithm for 2D, 3D and 3D+Time microscopy images,  BioImage Informatics conference, Paris, France, November 2021 (poster)In: BioImage Informatics 2021 (poster).
  • A. Badoual, Active subdivision surfaces for the segmentation of biomedical volumes,  online Seminars on Numerical Approximation and Applications (OSNA2), April 28, 2021 (invited talk)
  • A. Badoual, Generation of synthetic datasets of astrocytic calcium activity to support the development of learning based analysis tools”,Workshop proposal for the Virtual Conference of the European Society for Neurochemistry, May 25-26, 2021 (invited talk)
  • A. Badoual, Simulation of astrocytic calcium signals in microscopy images based on kinetic models,  online Symposiumon “Spatiotemporal Encoding and Decoding in Cell Signaling” organized by the Multi-Organization Thematic, Cell Biology, Development and Evolution (ITMO – BCDE), March 18, 2021. (selected talk)
2020
  • G. Fouché, F. Argelaguet, E. Faure, C. Kervrann, MorphoNet VR: Visualization of 3D Temporal Light-Sheet Microscopy Imagery in VR, NEUBIAS Network of EUropean BioImage Analysts Conference, Bordeaux, France, February 2020
  • C. Kervrann, Statistical and computational methods for intracellular trajectory analyis in fluorescence imaging, Quantitative BioImaging (QBI), Oxford, UK, January 2020 (Invited Talk)
  • C.A. Valades-Cruz , L. Leconte, C. Wunder, C. Kervrann, L. Johannes, J. Salamero, 3D tracking of endocytic and exocytic events using lattice light sheet microscopy, Quantitative BioImaging (QBI), Oxford, UK, January 2020
  • T. Pécot, Z. Liu, J. Boulanger, J. Salamero, C. Kervrann, QuantEv: A quantitative approach for analyzing the spatio-temporal distribution of 3D events in fluorescence microscopy, Quantitative BioImaging (QBI), Oxford, UK, January 2020
  • A. Salomon, C. Kervrann, Precise mapping of intracellular diffusion and drift from SPT data analysis, Quantitative BioImaging (QBI), Oxford, UK, January 2020
  • Y. Lu, C. Kervrann, A. Trubuil, P. Hodara, Probabilistic overall reconstruction of membrane-associated molecular dynamics from partial observations in rod-shaped bacteria, Quantitative BioImaging (QBI), Oxford, UK, January 2020
  • S. Prigent, C. Kervrann, J. Salamero, BioImage-IT, Quantitative BioImaging (QBI), Oxford, UK, January 2020
  • S. Prigent, C. Kervrann, J. Salamero, BioImage-IT: Design data analysis workflows using tools from different languages and keep track of the metadata, Network of BioImage Analysts (NEUBIAS), Bordeaux February 2020
2019
  • Y. Lu, P. Hodara, C. Kervrann, A. Trubuil, Probabilistic reconstruction of particle tracks on a censored and closed surface, “Seeing is Believing” conference, Heidelberg (EMBL), Germany, October 2019
  • A. Caranfil, Y. Le Cunff, C. Kervrann, J. Pécréaux. Modelling oscillatory behavior in asymmetric division of C. elegans embryo. BioHazard – Stochastic Models for Biology – Conference,  Rennes, France, August 2019
  • C. Kervrann, Statistical methods for intracellular dynamics classification in live cell imaging, “Bioimage Processing” workshop, Cambridge, June 2019 (Invited Talk)
  • C. Kervrann, Computational methods for intracellular dynamics in live cell imaging, “Random Walks and Intracellular Transport” workshop, Manchester, UK, April 2019 (Invited Talk)
  • C. Kervrann, A fast statistical colocalization method for 3D live cell imaging and super-resolution microscopy, “Statistical modeling for Shapes and Imaging” workshop, Paris, March 2019 (Invited Talk)
  • A. Salomon, V. Briane, M. Vimond, C.A. Vlades-Cruz, C. Kervrann, Analysing and quantifying intracellular particles movements in 3D LLSM data, Quantitative BioImaging (QBI), Rennes, France, January 2019
  • C.A. Valades-Cruz, A. Forrester, C. Wunder, C. Kervrann, J. Salamero, L. Johannes, 3D tracking of endocytic events using lattice light sheet microscopy, Quantitative BioImaging (QBI), Rennes, France, January 2019
  • Y. Lu, C. Billaudeau, R. Carballido-Lopez, C. Kervrannn, A. Trubuil, 3D stochastic process simulation for better interpretation of molecular dynamics related to cell wall biogenesis observed with TIRF microscopy, Quantitative BioImaging (QBI), Rennes, France, January 2019
  • E. Moebel, C. Kervrann, 3D ConvNets improve macromolecule localization in 3D cellular cryo-electron tomograms, Quantitative BioImaging (QBI), Rennes, France, January 2019
  • S. Manandhar, P. Bouthemy, P. Roudot, C. Kervrann, 3D motion estimation in 3D light microscopy image sequences: application to cell migration, Quantitative BioImaging (QBI), Rennes, France, January 2019
  • H. Bouvrais, D. Fairbrass, L. Chesneau, N. Soler, Y. Le Cunff, T. Pécot, C. Kervrann, Y. Lu, J. Pécréaux,  Two dynamic behaviours of the microtubules at the cell conterx reveal the pulling and pushing forces that position the mitotic spindle in C.Elegans embryos, Quantitative BioImaging (QBI), Rennes, France, January 2019
  • A. Caranfil, C. Kervrann, Y. Le Cunff, J. Pécréaux, Studying oscillatory behavior in asymmetric division of Caenorhabditis elegans embryo with fluorescence miscroscopy, Quantitative BioImaging (QBI), Rennes, France, January 2019
2018
  • C. Kervrann, Computational methods for fluorescence microscopy and intracellular dynamics analysis, Workshop on “Reverse Mathematical Methods for Reconstructing Molecular Dynamics in Single Cell”, Pisa, Italy, October 2018 (Invited Talk)
  • C. Kervrann, GcoPS: a fast automatic colocalization method for 3D live cell imaging and super-resolution microscopy, SIAM Conference on Imaging Science, Bologna, Italy, June 2018 (Invited Talk)
  • C. Kervrann, Computational methods for fluorescence microscopy and quantitative bioimaging, NEUBIAS – Network of European Bioimage Analysts, Szeged, Hungary, January 2018 (Invited Talk)
  • C. Kervrann, GcoPS: a Geo-coPositionning System for live cell imaging and superresolution microscopy, Quantitative BioImaging (QBI), Gottingen, Germany, January 2018
2017
  • V. Briane, M. Vimond, C. Kervrann, Classification of diffusion dynamics from particle trajectories, Quantitative BioImaging (QBI), College-Station, United States, January 2017
  • V. Briane, M. Vimond, C. Kervrann, Robust classification of particle tracks for characterization of diffusion and dynamics in fluorescence microscopy, Focus on Microscopy (FOM), Bordeaux, France, April 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, France, July 2017
2016
  • E. Moebel, C. Kervrann, Denoising and missing wedge reconstruction in cryo electron tomography, Eur. Microscopy Congress (ECM), Lyon, France, September 2016
  • V. Briane, M. Vimond, C. Kervrann, An adaptive statistical test to detect non Brownian diffusion from particle trajectories, French-Danish Workshop Spatial Statistics and Image Analysis in Biology (SSIAB 2016), Rennes, France, May 2016
  • T. Pécot, F. Lavancier, C. Kervrann, A non-parametric procedure for co-localization studies in fluorescence microscopy, French-Danish Workshop Spatial Statistics and Image Analysis in Biology (SSIAB 2016), Rennes, France, May 2016
  • C. Kervrann, PEWA: Patch-based Exponentially Weighted Aggregation for image denoising, SIAM Conf. Imaging Science 2016 (IS16), Albuquerque, USA, May 2016
  • P. Roudot, L. Ding, K. Jaqaman, C. Kervrann, G. Danuser, Tracking heterogeneous particle motions in dense intra-cellular environments, SIAM Conf. Imaging Science 2016 (IS16), Albuquerque, USA, May 2016
  • B.M. Toledo Acosta, P. Bouthemy, C. Kervrann, A scale-adaptive method for retracing and registering in correlative light-electron microscopy, SIAM Conference on Imaging Sciences 2016, Albuquerque, May 2016
2015
  • C. Kervrann, J. Salamero. Joint localization, estimation and classification of membrane dynamics in TIRF microscopy image sequences, Quantitative BioImaging (invited conference), Paris, France, January 2015
  • T. Pécot, J. Boulanger, P. Bouthemy, S. Bardin, J. Salamero, C. Kervrann, A quantitative approach for space-time membrane trafficking orientation, Quantitative BioImaging, Paris, France, January 2015
2014
  • A. Basset, J. Boulanger, P. Bouthemy, C. Kervrann, J. Salamero, Spot detection in light microscopy images with automatic scale selection and self-adaptive thresholding, BioImage Informatics, Leuven, October 2014
2013
  • P. Roudot, L. Ding, K. Jaqaman, C. Burckhardt, C. Kervrann, G. Danuser, Tracking heterogeneous motions in dense condition, Symposium “Seing is Believing – Imaging the Processes of Life”, Heidelberg, Germany, October 2013
  • 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, European Light Microscopy initiative (ELMI’13), Arcachon, France, May 2013
2012
  • L. Guyon, C. Mignon, F. Senger, L. Blanchoin, J. Xie, C. Kervrann, D. Bourgeois, Lateral drift correction without fiduciary markers in PALM experiments, Swiss Single Molecule Localization Microscopy, Lausanne, Switzerland, August 2012
  • C. Kervrann, D. Fortun, P. Bouthemy, Aggregation methods for optical flow computation, SIAM Conference on Imaging Science 2012, Philadelphia, USA, May 2012
  • C. Kervrann. Patch-based methods and algorithms for breaking the signal-to-noise ratio in fluorescence microscopy and cryo-electron microscopy, BioImage Informatics, Dresde, Allemagne, September 2012
2010
  • I. Arnal, F. Coquelle, S. Blestel, B. Vitre, C. Heichette, C. Kervrann, D. Chrétien, Structural basis of the interaction between microtubules and +TIPs, EMBO Conference Series Microtubules – Structure, Regulation and Functions, Heidelberg, Germany, June 2010
  • S. Blestel, C.and Heichette, C. Fish, P. Dupuys-Williams, D. Chrétien, C. Kervrann, Electron cryo-tomography of microtubule assemblies: automatic segmentation of tomograms with CryoSeg, In EMBO Conference Series Microtubules – Structure, Regulation and Functions , Heidelberg, Germany, June 2010
  • F. Coquelle, S. Blestel, K. Kinoshita, B. Vitre, C. Heichette, C. Kervrann, I. Arnal, D. Chrétien, Effects of XMAP215 on Microtubule Dynamics and Structure and its Visualization by Electron Cryo-Tomography, In EMBO Conference Series Microtubules – Structure, Regulation and Functions, Heidelberg, Germany, June 2010
  • A. Guesdon, S. Blestel, C. Heichette, C. Kervrann, D. Chrétien, Three dimensional reconstruction of 14 protofilaments GMPCPP-microtubules using TubuleJ, In EMBO Conference Series Microtubules – Structure, Regulation and Functions, Heidelberg, Germany, June 2010
  • C. Kervrann, Non-local means filter and novel bayesian approximations for non-local image regularization, In SIAM Conf. on Imaging Science, Chicago, Illinois, April 2010
  • A. Chessel, B. Cinquin, F. Waharte, Ch. Kervrann, J. Salamero, A detection based framework for systematic analysis of dual color TIRF microscopy, In Focus on Microscopy (FOM’10), Shanghai, China, March 2010
National Conferences
  • E. Meunier and P. Bouthemy. Apprentissage profond non supervisé fondé sur l’algorithme EM pour la segmentation du mouvement. Reconnaissance des Formes, Image, Apprentissage et Perception (RFIAP), Vannes, France, juillet 2022
  • E. Meunier and P. Bouthemy. Localisation de mouvements saillants dans des cartes de flot optique par l’interprétation d’un réseau de classification. Journées des jeunes chercheurs en vision par ordinateur (ORASIS’2021), HAL-INRIA-03339650, Saint Ferréol, France, septembre 2021
  • L. Maczyta, P. Bouthemy, O. Le Meur. Détection temporelle de saillance dynamique dans des vidéos par apprentissage profond. Congrès Reconnaissance des Formes, Image, Apprentissage et Perception (RFIAP’18), Marne-la-Vallée, juin 2018
  • A. Basset, P. Bouthemy, F. Waharte, J. Salamero, C. Kervrann. Modélisation et estimation de la diffusion de protéines à l’exocytose dans des séquences d’images de microscopie TIRF. 20ème Congrès de Reconnaissance des Formes et d’Intelligence Artificielle (RFIA’16), Clermont-Ferrand, juin 2016
  • V. Briane, M. Vimond, C. Kervrann. Test statistique pour détecter les diffusions non browniennes. Journées de Statistique, Montpellier, 2016
  • A. Basset, J. Boulanger, P. Bouthemy, C. Kervrann, J. Salamero. Sélection d’échelle automatique précise et seuillage localement adapté pour la segmentation de vésicules en microscopie TIRF. 19ème Congrès de Reconnaissance des Formes et d’Intelligence Artificielle (RFIA’14), Rouen, juillet 2014
  • D. Fortun, P. Bouthemy, C. Kervrann. Agrégation d’estimations semi-locales pour le flot optique. 24ème colloque GRETSI Traitement du Signal et des Images, Brest, septembre 2013
  • J. Boulanger, T. Pécot, C. Kervrann, P. Bouthemy, J. Salamero. Estimation de flux d’objets fluorescents dans les séquences de vidéo-microscopie. 24ème colloque GRETSI Traitement du Signal et des Images, Brest, septembre 2013
  • A. Basset, P. Bouthemy, C. Kervrann. Classification instantanée de mouvements de foules dans des vidéos. 24ème colloque GRETSI Traitement du Signal et des Images, Brest, septembre 2013

Misc.

  • F. Lavancier, T. Pécot, L. Zengzhen, C. Kervrann. A fast automatic colocalization method for 3D live cell and super-resolution microscopy, preprint, HAL-INRIA-01577118, 2017
  • H.-N. Nguyen, V. Paveau, C. Cauchois, C. Kervrann. Generalized sparse variation regularization for large fluorescence image deconvolution, preprint, HAL-INRIA-01609810, 2017

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