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SERPICO - 2011
SERPICO - 2011


Team Serpico


Members
Overall Objectives
Scientific Foundations
Application Domains
Software
New Results
Contracts and Grants with Industry
Partnerships and Cooperations
Dissemination
Bibliography


Team Serpico


Members
Overall Objectives
Scientific Foundations
Application Domains
Software
New Results
Contracts and Grants with Industry
Partnerships and Cooperations
Dissemination
Bibliography




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, e13190 p. [ DOI : 10.1371/journal.pone.0013190 ]

    http://hal.inria.fr/inria-00541072/en
  • 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, p. 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, p. 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, p. 442-453. [ DOI : 10.1109/TMI.2009.2033991 ]

    http://hal.inria.fr/inria-00541082/en
  • 5P. M. Carlton, J. Boulanger, C. Kervrann, J.-B. Sibarita, J. Salamero, S. Gordon-Messer, J. Haber, S. Haase, L. Shao, A. Winoto, 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, p. 16016-16022. [ DOI : 10.1073/pnas.1004037107 ]

    http://hal.inria.fr/inria-00540978/en/
  • 6C. Kervrann, J. Boulanger.

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

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

Articles in International Peer-Reviewed Journal

  • 8B. Cinquin, A. Gidon, A. Chessel, T. Pécot, J. Boulanger, C. Gueudry, C. Kervrann, J. Salamero.

    Advanced microcopy to study tracking and spatiotemporal organization of intracellular membranes, in: Bio-medical materials and engineering, 2011.

    http://hal.inria.fr/inria-00541284/en
  • 9F. Coquelle, S. Blestel, C. Heichette, I. Arnal, C. Kervrann, D. Chrétien.

    Cryo-Electron Tomography of microtubules assembled in vitro from purified components., in: Methods in Molecular Biology -Clifton then Totowa-, July 2011, vol. 777, p. 193-208.

    http://hal.inria.fr/hal-00651384/en/
  • 10T. 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, September 2011, vol. 94, no 3, p. 295–316. [ DOI : 10.1007/s11263-011-0429-z ]

    http://hal.inria.fr/hal-00651558/en/
  • 11A. 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, in: Traffic, 2011, to appear.
  • 12C. Kervrann, J. Boulanger, T. Pécot, P. Pérez, J. Salamero.

    Multiscale neighborhood-wise decision fusion for redundancy detection in image pairs, in: SIAM Journal Multiscale Modeling & Simulation (accepted), 2011, to appear.

    http://hal.inria.fr/inria-00487051/en

Conferences without Proceedings

  • 13F. Coquelle, A. Guesdon, M. Angevin, T. Chenuel, M. Chrétien, C. Heichette, S. Blestel, C. Kervrann, I. Arnal, D. Chrétien.

    Interaction of +TIPs with microtubule ends, in: 12th Congres of the French Society for Microscopy, Strasbourg, France, Société Française des Microscopies, June 2011.

    http://hal.inria.fr/hal-00651851/en/
  • 14A. Guesdon, S. Blestel, C. Kervrann, D. Chrétien.

    How does GTP-hydrolysis destabilize the microtubule lattice ?, in: 12th Congres of the French Society for Microscopy, Strasbourg, France, Société Française des Microscopies, June 2011.

    http://hal.inria.fr/hal-00651848/en/
  • 15A. Guesdon, F. Coquelle, S. Blestel, E. Pollet, B. Vitre, M. Angevin, C. Heichette, I. Arnal, C. Kervrann, D. Chrétien.

    Cryo-electron tomography of macromolecular assemblies: from quantum dots to 3D crystals of proteins, in: 12th Congres of the French Society for Microscopy, Strasbourg, France, Société Française des Microscopies, June 2011.

    http://hal.inria.fr/hal-00651880/en/
  • 16C. Kervrann, J. Boulanger, A. Chessel, B. Cinquin, J. Salamero.

    Change detection methods in fluorescence live cell imaging for sub-cellular trafficking analysis, in: BioImage Informatics II, Ashburn VA, États-Unis, Janelia Farm - Howard Hugues Medical Institute, September 2011, invited talk.

    http://hal.inria.fr/hal-00651919/en/
  • 17E. Pollet, C. Fisch, A. Guesdon, C. Heichette, P. Dupuis-Williams, C. Kervrann, A. Leforestier, D. Chrétien.

    Structure of Paramecium trichocysts, in: 12th Congres of the French Society for Microscopy, Strasbourg, France, Société Française des Microscopies, June 2011.

    http://hal.inria.fr/hal-00651898/en/

Scientific Books (or Scientific Book chapters)

  • 18T. Crivelli, B. Cernuschi-Frias, P. Bouthemy, J.-F. Yao.

    Mixed-state Markov models in image motion analysis, in: Machine Learning for Vision-Based Motion Analysis, Springer (editor), Theory and Techniques Series: Advances in Pattern Recognition / Wang, L.; Zhao, G.; Cheng, L.; Pietikäinen, M. (Eds.), SpringerLink, 2011, vol. 1st Edition., 2011, XIV, 372 pages, p. Part 2, 77-115. [ DOI : 10.1007/978-0-85729-057-1_4 ]

    http://hal.inria.fr/inria-00541253/en
References in notes
  • 19D. Axelrod.

    Total Internal Reflection Fluorescent Microscopy in cell biology, in: Traffic, 2004, vol. 2, p. 4658–4668.
  • 20E. 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, p. 1642–1645.
  • 21J. 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, e13190 p. [ DOI : 10.1371/journal.pone.0013190 ]

    http://hal.inria.fr/inria-00541072/en
  • 22T. Brox, A. Bruhn, N. Papenberg, J. Weickert.

    High Accuracy Optical Flow Estimation Based on a Theory for Warping, in: European Conference on Computer Vision (ECCV'04), Prague, Czech Republic, 2004, vol. 4, p. 25-36.
  • 23A. 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 (editor), IEEE Signal Processing Society, Apr 2010, p. 1281-1284. [ DOI : 10.1109/ISBI.2010.5490230 ]

    http://hal.inria.fr/inria-00541102/en
  • 24A. 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, p. 770–781.
  • 25T. Corpetti, E. Mémin, P. Pérez.

    Dense estimation fluid flows, in: IEEE Trans. Pattern Analysis and Machine Intelligence, 2002, vol. 24, no 3, p. 365–380.
  • 26A. Genovesio, T. Liedl, V. Emiliani, W. Parak, M. Coppey-Moisan, J. 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, p. 1062–1070.
  • 27M. Gustafsson, L. Shao, Peter M. Carlton, R. Wang, I. Golubovskaya, W. Cande, D. Agard, John W. Sedat.

    3D resolution doubling in wide-filed fluorescence microscopy by structured illumination, in: Biophysical J., 2008, vol. 94, p. 4957–4970.
  • 28H. 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, p. 661–673.
  • 29T. 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, p. 8206–8210.
  • 30C. 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, p. 13–22.
  • 31E. Mémin, P. Pérez.

    Hierarchical estimation and segmentation of dense motion fields, in: Int. Journal of Computer Vision, February 2002, vol. 46, no 2, p. 129–155.
  • 32F. Nédélec.

    Computer simulations reveal motor properties generating stable antiparallel microtubule interactions, in: The Journal of Cell Biology, 2002, vol. 158, no 6, p. 1005–1015.
  • 33P. Pérez, J. Vermaak, A. Blake.

    Data fusion for visual tracking with particles, in: Proc. IEEE, 2004, vol. 92, no 3, p. 495–513.
  • 34A. Sartori, R. Gatz, F. Beck, A. Rigort, W. Baumeister, J. Plitzko.

    Correlative microscopy: bridging the gap between fluorescence light microscopy and cryo-electron tomography, in: J. Structural Biology, 2007, vol. 160, no 2, p. 135–145.
  • 35I. Sbalzarini, P. Koumoutsakos.

    Feature point tracking and trajectory analysis for video Imaging in cell biology, in: J. Structural Biology, 2005, vol. 151, p. 182–195.
  • 36J. Shi, C. Tomasi.

    Good features to track, in: IEEE Conference on Computer Vision and Pattern Recognition (CVPR'94), Seattle, Washington, 1994, p. 593–600.
  • 37I. 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, p. 282–301.
  • 38I. 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, p. 764–777.
  • 39D. 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, p. 49–64.
  • 40C. Tomasi, T. Kanade.

    Detection and Tracking of Point Features, Carnegie Mellon University, 1991, no CMU-CS-91-132.
  • 41Y. Vardi.

    Network tomography: estimating source-destination traffic intensities from link data, in: J American Statistical Association, 1996, vol. 91, p. 365–377.
  • 42G. Vicidomini, M. Gagliani, M. Canfora, K. Cortese, F. Frosi, C. Santangelo, P. Di Fiore, P. Boccacci, A. Diaspro, C. Tacchetti.

    High data output and automated 3D correlative light-electron microscopy method, in: Traffic, 2008, vol. 9, p. 1828–1838.
  • 43T. 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), p. S26–41.
  • 44W. Wells, P. Viola, H. Atsumi, S. Nakajima, R. Kikinis.

    Multi-modal registration by maximization of mutual information, in: Medical Image Analysis, 1996, vol. 1, no 1, p. 35–51.