EN FR
EN FR
SERPICO - 2014
SERPICO - 2014
Project-Team Serpico
Members
Overall Objectives
Research Program
Application Domains
New Software and Platforms
New Results
Bilateral Contracts and Grants with Industry
Partnerships and Cooperations
Dissemination
Bibliography
Project-Team Serpico
Members
Overall Objectives
Research Program
Application Domains
New Software and Platforms
New Results
Bilateral Contracts and Grants with Industry
Partnerships and Cooperations
Dissemination
Bibliography


previous Previous | up Home


Bibliography

Major publications by the team in recent years
  • 1J. Boulanger, A. Gidon, C. Kervrann, J. Salamero.

    A Patch-Based Method for Repetitive and Transient Event Detection in Fluorescence Imaging, in: PLoS ONE, Oct 2010, vol. 5, no 10. [ DOI : 10.1371/journal.pone.0013190 ]
  • 2J. Boulanger, C. Kervrann, P. Bouthemy.

    Space-time adaptation for patch based image sequence restoration, in: IEEE Transactions on Pattern Analysis and Machine Intelligence, 2007, vol. 29, no 6, pp. 1096–1102.
  • 3J. Boulanger, C. Kervrann, P. Bouthemy.

    A simulation and estimation framework for intracellular dynamics and trafficking in video-microscopy and fluorescence imagery, in: Medical Image Analysis, 2009, vol. 13, pp. 132–142.
  • 4J. Boulanger, C. Kervrann, P. Bouthemy, P. Elbau, J.-B. Sibarita, J. Salamero.

    Patch-Based Nonlocal Functional for Denoising Fluorescence Microscopy Image Sequences, in: IEEE Transactions on Medical Imaging, Feb 2010, vol. 29, no 2, pp. 442-453. [ DOI : 10.1109/TMI.2009.2033991 ]
  • 5P.M. Carlton, J. Boulanger, C. Kervrann, J.-B. Sibarita, J. Salamero, S. Gordon-Messer, J. Haber, S. Haase, L. Shao, L. Winoto, A. Matsuda, P. Kner, S. Usawa, Y. Strukov, M. Gustafsson, Z. Kam, D. Agard, J.W. Sedat.

    Fast live simultaneous multiwavelength four-dimensional optical microscopy, in: Proc Natl Acad Sci USA, Sep 2010, vol. 107, no 37, pp. 16016-16022. [ DOI : 10.1073/pnas.1004037107 ]
  • 6C. Kervrann, J. Boulanger.

    Optimal spatial adaptation for patch-based image denoising, in: IEEE Transactions on Image Processing, 2006, vol. 15, no 10, pp. 2866–2878.
  • 7C. Kervrann, J. Boulanger.

    Local adaptivity to variable smoothness for exemplar-based image denoising and representation, in: International Journal of Computer Vision, August 2008, vol. 79, no 1, pp. 45–69.
Publications of the year

Doctoral Dissertations and Habilitation Theses

Articles in International Peer-Reviewed Journals

  • 10N. 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.

    An objective comparison of particle tracking methods, in: Nature Methods, 2014, vol. 11, no 3, pp. 281-289.

    https://hal.inria.fr/hal-00932869
  • 11D. Fortun, P. Bouthemy, C. Kervrann.

    Aggregation of local parametric candidates with exemplar-based occlusion handling for optical flow, in: IEEE Transactions on Image Processing, June 2014, 27 p, Revision.

    https://hal.inria.fr/hal-01001758
  • 12D. Fortun, P. Bouthemy, C. Kervrann.

    Optical flow modeling and computation: a survey, in: Computer Vision and Image Understanding, March 2015, 24 p, In revision.

    https://hal.inria.fr/hal-01104081
  • 13T. 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, in: IEEE Transactions on Image Processing, December 2014, 14 p.

    https://hal.inria.fr/hal-01103126

Invited Conferences

  • 14C. Kervrann, J. Salamero.

    Joint localization, estimation and classification of membrane dynamics in TIRF microscopy image sequences, in: Quantitative BioImaging, Paris, France, January 2015.

    https://hal.inria.fr/hal-01103552

International Conferences with Proceedings

  • 15A. 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, in: ISBI - 2014 IEEE International Symposium on Biomedical Imaging, Beijing, China, April 2014.

    https://hal.inria.fr/hal-00921793
  • 16A. Basset, P. Bouthemy, J. Boulanger, J. Salamero, C. Kervrann.

    Localization and Classification of Membrane Dynamics in TIRF Microscopy Image Sequences, in: ISBI - 2014 IEEE International Symposium on Biomedical Imaging, Beijing, China, April 2014.

    https://hal.inria.fr/hal-00921794
  • 17A. Basset, P. Bouthemy, C. Kervrann.

    Recovery of motion patterns and dominant paths in videos of crowded scenes, in: IEEE International Conference on Image Processing, Paris, France, October 2014.

    https://hal.inria.fr/hal-01097357
  • 18M. Jain, J. Van Gemert, H. Jégou, P. Bouthemy, C. Snoek.

    Action localization with tubelets from motion, in: CVPR - International Conference on Computer Vision and Pattern Recognition, Columbus, United States, June 2014.

    https://hal.inria.fr/hal-00996844
  • 19C. Kervrann, S. Blestel, D. Chrétien.

    Conditional Random Fields for tubulin-microtubule segmentation in cryo-electron tomography, in: IEEE International Conference on Image Processing (top 10%” papers in ICIP 2014), Paris, France, October 2014.

    https://hal.inria.fr/hal-01103330
  • 20C. Kervrann.

    PEWA: Patch-based Exponentially Weighted Aggregation for image denoising, in: NIPS - Neural Information Processing Systems, Montreal, Canada, Neural Information Processing Systems Foundation, December 2014.

    https://hal.inria.fr/hal-01103358
  • 21C. Kervrann, P. Roudot, F. Waharte.

    Approximate Bayesian Computation, stochastic algorithms and non-local means for complex noise models, in: IEEE International Conference on Image Processing, Paris, France, October 2014, 4 p.

    https://hal.inria.fr/hal-01103322
  • 22T. 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, in: ISBI - 11th IEEE International Symposium On Biomedical Imaging : from nano to macro - 2014, Beijing, China, April 2014.

    https://hal.inria.fr/hal-00936063

National Conferences with Proceedings

  • 23A. 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, in: Reconnaissance de Formes et Intelligence Artificielle (RFIA) 2014, France, June 2014.

    https://hal.archives-ouvertes.fr/hal-00988759

Conferences without Proceedings

  • 24A. Basset, J. Boulanger, P. Bouthemy, C. Kervrann, J. Salamero.

    Spot detection in light microscopy images with automatic scale selection and self-adaptive thresholding, in: BioImage Informatics, Leuven, Belgium, October 2014.

    https://hal.inria.fr/hal-01103551
  • 25T. Pecot, J. Boulanger, P. Bouthemy, S. Bardin, J. Salamero, C. Kervrann.

    A quantitative approach for space-time membrane trafficking orientation, in: Quantitative BioImaging, Paris, France, January 2015.

    https://hal.inria.fr/hal-01103553

Other Publications

References in notes
  • 29D. Axelrod.

    Total Internal Reflection Fluorescent Microscopy in cell biology, in: Traffic, 2004, vol. 2, pp. 4658–4668.
  • 30M. Beaumont, W. Zhang, D. Balding.

    Approximate Bayesian computation in population genetics, in: Genetics, 2002, vol. 162, pp. 2025–2035.
  • 31E. Betzig, G. Patterson, R. Sougrat, O. Lindwasser, S. Olenych, J. Bonifacino, M. Davidson, J. Lippincott-Schwartz, H. Hess.

    Imaging intracelluar fluorescent proteins at nanometer resolution, in: Science, 2006, vol. 313, pp. 1642–1645.
  • 32A. Bruhn, J. Weickert, C. Schnörr.

    Lucas/Kanade meets Horn/jaqaSchunck: combining local and global optic flow methods, in: International Journal of Computer Vision, 2005, vol. 61, no 3, pp. 211–231.
  • 33A. Buades, B. Coll, J.-M. Morel.

    A review of image denoising algorithms, with a new one, in: SIAM J. Multiscale Modeling and Simulation, 2005, vol. 4, no 2, pp. 490–530.
  • 34A. Chessel, B. Cinquin, S. Bardin, J. Boulanger, J. Salamero, C. Kervrann.

    A detection-based framework for the analysis of recycling in TIRF microscopy, in: IEEE International Symposium on Biomedical Imaging: From Nano to Macro (ISBI 2010), Pays-Bas Rotterdam, IEEE Signal Processing Society, Apr 2010, pp. 1281-1284. [ DOI : 10.1109/ISBI.2010.5490230 ]
  • 35A. Chessel, B. Cinquin, S. Bardin, J. Salamero, C. Kervrann.

    Computational geometry-based scale-space and modal image decomposition: application to light video-microscopy imaging, in: Conf. on Scale Space and Variational Methods (SSVM'09), Voss, Norway, June 2009, pp. 770–781.
  • 36T. Corpetti, E. Mémin, P. Pérez.

    Dense estimation fluid flows, in: IEEE Trans. Pattern Analysis and Machine Intelligence, 2002, vol. 24, no 3, pp. 365–380.
  • 37T. Crivelli, P. Bouthemy, B. Cernuschi-Frias, J.-F. Yao.

    Simultaneous motion detection and background reconstruction with a conditional mixed-state Markov random field, in: International Journal of Computer Vision, 2011, vol. 94, no 3, pp. 295–316.
  • 38K. Dabov, A. Foi, V. Katkovnik, K. Egiazarian.

    Image denoising by sparse 3-d transform-domain collaborative filtering, in: IEEE Trans. Image Processing, 2007, vol. 16, no 8, pp. 2080–2095.
  • 39A. Genovesio, T. Liedl, V. Emiliani, W. Parak, M. Coppey-Moisan, J.-C. Olivo-Marin.

    Multiple particle tracking in 3D+t microscopy: method and application to the tracking of endocytosed quantum dots, in: IEEE Trans. Image Processing, 2006, vol. 15, no 5, pp. 1062–1070.
  • 40M. Gustafsson, L. Shao, P.M. Carlton, R. Wang, I. Golubovskaya, W. Cande, D. Agard, J.W. Sedat.

    3D resolution doubling in wide-filed fluorescence microscopy by structured illumination, in: Biophysical J., 2008, vol. 94, pp. 4957–4970.
  • 41H. Haussecker, D. Fleet.

    Computing optical flow with physical models of brightness variation, in: IEEE Trans. Pattern Analysis and Machine Intelligence, 2001, vol. 23, no 6, pp. 661–673.
  • 42K. Jaqaman, D. Loerke, M. Mettlen, H. Kuwata, S. Grinstein, S. Schmid, G. Danuser.

    Robust single-particle tracking in live-cell time-lapse sequences, in: Nature methods, 2008, vol. 5, no 8, pp. 695–702.
  • 43T. Klar, S. Jakobs, M. Dyba, A. Egner, S. Hell.

    Fluorescence microscopy with diffraction resolution barrier broken by stimulated emission, in: Proc. Natl. Acad. Sci. USA, 2000, vol. 97, pp. 8206–8210.
  • 44C. Lavelle, H. Berry, G. Beslon, F. Ginelli, J. Giavitto, Z. Kapoula, A. Le Bivic, N. Peyrieras, O. Radulescu, A. Six, V. Thomas-Vaslin, P. Bourgine.

    From molecules to organisms: towards multiscale integrated model of biological systems, in: Theoretical Biology Insights, 2008, vol. 1, pp. 13–22.
  • 45T. Lindeberg.

    Scale-space for discrete signals, in: IEEE Transactions on Pattern Analysis and Machine Intelligence, 1990, vol. 12, no 3, pp. 234–254.
  • 46P. Marjoram, P. Molitor, V. Plagnol, S. Tavare.

    Markov chain Monte Carlo without likelihoods, in: Proceedings of the National Academy of Sciences, 2003, vol. 100, no 26, pp. 15324–15328.
  • 47F. Nédélec.

    Computer simulations reveal motor properties generating stable antiparallel microtubule interactions, in: The Journal of Cell Biology, 2002, vol. 158, no 6, pp. 1005–1015.
  • 48J.-M. Odobez, P. Bouthemy.

    Robust multiresolution estimation of parametric motion models, in: J. Visual Communication and Image Representation, 1995, vol. 6, no 4, pp. 348–365.
  • 49S. Ozere, P. Bouthemy, F. Spindler, P. Paul-Gilloteaux, C. Kervrann.

    Robust parametric stabilization of moving cells with intensity correction in light microscopy image sequences, in: 10th International Symposium on Biomedical Imaging (ISBI), IEEE, 2013, pp. 468–471.
  • 50M. Pinot, V. Steiner, B. Dehapiot, B.-K. Yoo, F. Chesnel, L. Blanchoin, C. Kervrann, Z. Gueroui.

    Confinement induces actin flow in a meiotic cytoplasm, in: Proceedings National Academy of Sciences USA, July 2012, vol. 109, no 29, pp. 11705–11710. [ DOI : 10.1073/pnas.1121583109 ]

    http://hal.inria.fr/inserm-00717415
  • 51T. Pécot, C. Kervrann, S. Bardin, B. Goud, J. Salamero.

    Patch-based Markov models for event detection in fluorescence bioimaging, in: Int. Conf. on Medical Image Computing and Computer Assisted Intervention (MICCAI'08), New York City, USA, September 2008, vol. 2, pp. 95–103.
  • 52P. Pérez, J. Vermaak, A. Blake.

    Data fusion for visual tracking with particles, in: Proc. IEEE, 2004, vol. 92, no 3, pp. 495–513.
  • 53I. Sbalzarini, P. Koumoutsakos.

    Feature point tracking and trajectory analysis for video Imaging in cell biology, in: J. Structural Biology, 2005, vol. 151, pp. 182–195.
  • 54I. Smal, M. Loog, W. Niessen, E. Meijering.

    Quantitative comparison of spot detection methods in fluorescence microscopy, in: IEEE Trans. Medical Imaging, 2010, vol. 29, no 2, pp. 282–301.
  • 55I. Smal, E. Meijering, K. Draegestein, N. Galjart, I. Grigoriev, A. Akhmanova, M. van Royen, A. Houtsmuller, W. Niessen.

    Multiple object tracking in molecular bioimaging by Rao-Blackwellized marginal particle filtering,, in: Medical Image Analysis, 2008, vol. 12, no 6, pp. 764–777.
  • 56M. Thery, V. Racine, A. Pepin, M. Piel, Y. Chen, J.-B. Sibarita, M. Bornens.

    The extracellular matrix guides the orientation of the cell division axis, in: Nature Cell Bioliogy, 2005, vol. 7, pp. 947-953.
  • 57D. Thomann, D. Rines, P. Sorger, G. Danuser.

    Automatic fluorescent tag detection in 3D with super-resolution: application to the analysis of chromosome movement, in: J. Microscopy, 2002, vol. 298, no Part 1, pp. 49–64.
  • 58Y. Vardi.

    Network tomography: estimating source-destination traffic intensities from link data, in: J. American Statistical Association, 1996, vol. 91, pp. 365–377.
  • 59T. Walter, D. Shattuck, R. Baldock, M. Bastin, A. Carpenter, S. Duce, J. Ellenberg, A. Fraser, N. Hamilton, S. Pieper, M. Ragan, J. Schneider, P. Tomancak, J. Heriche.

    Visualization of image data from cells to organisms, in: Nature Methods, 2010, vol. 7, no 3 (Suppl), pp. S26–41.
  • 60B. Zhang, J. Fadili, J. Starck, J.-C. Olivo-Marin.

    Multiscale variance-stabilizing transform for mixed-Poisson-Gaussian processes and its applications in bioimaging, in: IEEE International Conference on Image Processing, San-Antonio, '07, 2007.


previous Previous | up Home