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SERPICO - 2012
SERPICO - 2012




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




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


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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 of Computer Vision, August 2008, vol. 79, no 1, p. 45–69.
Publications of the year

Articles in International Peer-Reviewed Journals

  • 8A. 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, 2012, vol. 13, no 6, p. 815–833.
  • 9A. Guesdon, S. Blestel, C. Kervrann, D. Chrétien.

    Single versus dual-axis cryo-electron tomography of microtubules assembled in vitro: Limits and perspectives, in: Journal of Structural Biology, December 2012.

    http://hal.inria.fr/hal-00763814
  • 10M. 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, p. 11705–11710. [ DOI : 10.1073/pnas.1121583109 ]

    http://hal.inria.fr/inserm-00717415

International Conferences with Proceedings

  • 11D. Fortun, C. Kervrann.

    Semi-local variational optical flow estimation, in: IEEE International Conference on Image Processing, ICIP 2012, Orlando, FL, États-Unis, October 2012.

    http://hal.inria.fr/hal-00763806
  • 12P. Roudot, C. Kervrann, F. Waharte, J. Boulanger.

    Lifetime MAP reconstruction in frequency-domain fluorescence lifetime imaging microscopy, in: IEEE International Conference on Image Processing, ICIP 2012, Orlando, FL, États-Unis, October 2012.

    http://hal.inria.fr/hal-00763803
  • 13P. Roudot, C. Kervrann, F. Waharte.

    Lifetime estimation of moving vesicles in frequency-domain fluorescence lifetime imaging microscopy, in: IEEE International Symposium on Biomedical Imaging: From Nano to Macro, ISBI 2012, Barcelona, Espagne, May 2012, p. 668-671. [ DOI : 10.1109/ISBI.2012.6235636 ]

    http://hal.inria.fr/hal-00763790
  • 14H.-F. Yang, X. Descombes, C. Kervrann, C. Medioni, F. Besse.

    Tracking Growing Axons by Particle Filtering in 3D+t Fluorescent Two-Photon Microscopy Images, in: Asian Conference on Computer Vision, Daejeon, Korea, Republic Of, November 2012.

    http://hal.inria.fr/hal-00740966

Conferences without Proceedings

  • 15L. Guyon, C. Mignon, F. Senger, L. Blanchoin, J. Xie, C. Kervrann, D. Bourgeois.

    Lateral drift correction without fiduciary markers in PALM experiments, in: Swiss Single Molecule Localization Microscopy, Lausanne, Suisse, August 2012.

    http://hal.inria.fr/hal-00763829
  • 16C. Kervrann, D. Fortun, P. Bouthemy.

    Aggregation methods for optical flow computation, in: SIAM Conference on Imaging Science, Philadelphia, États-Unis, May 2012.

    http://hal.inria.fr/hal-00763845
  • 17C. Kervrann.

    Patch-based methods and algorithms for breaking the signal-to-noise ratio in fluorescence microscopy and cryo-electron microscopy, in: BioImage Informatics, Dresde, Allemagne, September 2012.

    http://hal.inria.fr/hal-00763905
  • 18P. Roudot, C. Kervrann, F. Waharte.

    Semi-parametric robust Gaussian fitting, in: IEEE ISBI 2012 Workshop: Particle Tracking Challenge, Barcelona, Espagne, May 2012.

    http://hal.inria.fr/hal-00763820
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.
  • 21G. Boncompain, S. Divoux, N. Gareil, H. de Forges, A. Lescure, L. Latreche, V. Mercanti, F. Jollivet, G. Raposo, F. Perez.

    Synchronization of secretory protein traffic in populations of cells, in: Nature Methods, 2012, vol. 9, no 5, p. 493–498.
  • 22T. Brox, J. Malik.

    Large displacement optical flow: descriptor matching in variational motion estimation, in: IEEE Trans. Pattern Analysis and Machine Intelligence, 2011, vol. 33, no 3, p. 500–513.
  • 23A. 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, p. 490–530.
  • 24A. 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, p. 1281-1284. [ DOI : 10.1109/ISBI.2010.5490230 ]

    http://hal.inria.fr/inria-00541102/en
  • 25A. 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.
  • 26T. 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.
  • 27K. 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, p. 2080–2095.
  • 28A. Desolneux, L. Moisan, J.-M. Morel.

    Maximal meaningful events and applications to image analysis, in: Annals of Statistics, 2003, vol. 31, no 6, p. 1822-1851.
  • 29A. 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.
  • 30M. 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.
  • 31H. 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.
  • 32T. 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.
  • 33C. 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.
  • 34F. Nédélec, D. Foethke.

    Collective Langevin dynamics of flexible cytoskeletal fibers, in: New Journal of Physics, 2007, vol. 9, no 11 (427).
  • 35F. 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.
  • 36J.-M. Odobez, P. Bouthemy.

    Robust multiresolution estimation of parametric motion models, in: J. Visual Communication and Image Representation, 1995, vol. 6, no 4, p. 348–365.
  • 37P. Pérez, J. Vermaak, A. Blake.

    Data fusion for visual tracking with particles, in: Proc. IEEE, 2004, vol. 92, no 3, p. 495–513.
  • 38I. 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.
  • 39I. 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.
  • 40I. 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.
  • 41B. Spring, R. Clegg.

    Image analysis for denoising full- field frequency-domain fluorescence lifetime images, in: J. Microscopy, 2009, vol. 235, no 2, p. 221–237.
  • 42D. Sun, S. Roth, M. Black.

    Secrets of optical flow estimation and their principles, in: IEEE Conference on Computer Vision and Pattern Recognition (CVPR'10), San Francis, CA, 2010, p. 2432–2439.
  • 43D. 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.
  • 44Y. Vardi.

    Network tomography: estimating source-destination traffic intensities from link data, in: J. American Statistical Association, 1996, vol. 91, p. 365–377.
  • 45T. 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.
  • 46R. G. von Gioi, J. Jakubowicz, J.-M. Morel, G. Randall.

    On Straight Line Segment Detection, in: J. Mathematical Imaging and Vision, 2008, vol. 32, no 3, p. 313–347.


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