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Team Serpico


Contracts and Grants with Industry
Bibliography


Team Serpico


Contracts and Grants with Industry
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.