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SERPICO - 2013
SERPICO - 2013
Project-Team Serpico
Members
Overall Objectives
Research Program
Application Domains
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
Software and Platforms
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. [ 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, 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 ]

    http://hal.inria.fr/inria-00541082/en
  • 5P. 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. 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 ]

    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, 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

Articles in International Peer-Reviewed Journals

  • 8N. Chenouard, I. Smal, F. De Chaumont, M. Maska, I. Sbalzarini, Y. Gon, J. Cardinale, C. Carthel, S. Coraluppi, M. Winter, R. Cohen Andrew, J. Godinez William, 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, 2013, (Accepted).

    http://hal.inria.fr/hal-00932869
  • 9T. Crivelli, B. Cernuschi-Frias, P. Bouthemy, J.-F. Yao.

    Motion Textures: Modeling, Classification, and Segmentation Using Mixed-State, in: SIAM Journal on Imaging Sciences, December 2013, vol. 6, no 4, pp. 2484-2520. [ DOI : 10.1137/120872048 ]

    http://hal.inria.fr/hal-00931667
  • 10A. 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, February 2013, vol. 181, no 2, pp. 169-78. [ DOI : 10.1016/j.jsb.2012.11.004 ]

    http://hal.inria.fr/inserm-00831759
  • 11C. Wang, T. Pécot, D. L. Zynger, R. Machiraju, C. L. Shapiro, K. Huang.

    Research and applications: Identifying survival associated morphological features of triple negative breast cancer using multiple datasets, in: Journal of the American Medical Informatics Association, April 2013.

    http://hal.inria.fr/hal-00921660

International Conferences with Proceedings

  • 12A. 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, 2014.

    http://hal.inria.fr/hal-00921793
  • 13A. 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, 2014.

    http://hal.inria.fr/hal-00921794
  • 14A. Basset, P. Bouthemy, C. Kervrann.

    Frame-by-frame crowd motion classification from affine motion models, in: AVSS - 10th IEEE International Conference on Advanced Video and Signal Based Surveillance - 2013, Krakòw, Poland, 2013, pp. 282-287. [ DOI : 10.1109/AVSS.2013.6636653 ]

    http://hal.inria.fr/hal-00921786
  • 15A. Chessel, F. Waharte, J. Salamero, C. Kervrann.

    A maximum likelihood method for lifetime estimation in photon counting-based fluorescence lifetime imaging microscopy, in: EUSIPCO - European Signal Processing Conference, Marrakech, Morocco, M. Ghogho, A. Zoubir (editors), September 2013, pp. 1-5.

    http://hal.inria.fr/hal-00931631
  • 16D. Fortun, P. Bouthemy, P. Paul-Gilloteaux, C. Kervrann.

    Aggregation of patch-based estimations for illumination-invariant optical flow in live cell imaging, in: ISBI - IEEE International Symposium on Biomedical Imaging, San-Francisco, United States, B. Parvin (editor), April 2013, pp. 660-663, Finalist for Best Student Paper Award. [ DOI : 10.1109/ISBI.2013.6556561 ]

    http://hal.inria.fr/hal-00931377
  • 17D. Fortun, C. Chen, P. Paul-Gilloteaux, F. Waharte, J. Salamero, C. Kervrann.

    Correlation and variational approaches for motion and diffusion estimation in fluorescence imaging, in: EUSIPCO 2013 - European Signal Processing Conference, Marrakech, Morocco, Eurasip, September 2013, pp. 1-5.

    http://hal.inria.fr/hal-00931408
  • 18M. Jain, H. Jégou, P. Bouthemy.

    Better exploiting motion for better action recognition, in: CVPR - International Conference on Computer Vision and Pattern Recognition, Portland, United States, April 2013.

    http://hal.inria.fr/hal-00813014
  • 19S. 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: ISBI - IEEE International Symposium on Biomedical Imaging, San-Francisco, United States, B. Parvin (editor), April 2013, pp. 468-471. [ DOI : 10.1109/ISBI.2013.6556513 ]

    http://hal.inria.fr/hal-00931371
  • 20T. 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.

    http://hal.inria.fr/hal-00936063
  • 21P. Roudot, C. Kervrann, J. Boulanger, F. Waharte.

    Noise modeling for intensified camera in fluorescence imaging: application to image denoising, in: ISBI - IEEE International Symposium on Biomedical Imaging, San-Francisco, United States, B. Parvin (editor), April 2013, pp. 600-603. [ DOI : 10.1109/ISBI.2013.6556546 ]

    http://hal.inria.fr/hal-00931360
  • 22D. Young Park, D. Jones, N. I. Moldovan, R. Machiraju, T. Pécot.

    Robust Detection and Visualization of Cytoskeletal Structures in Fibrillar Scaffolds from 3-Dimensional Confocal Image, in: BioVis - IEEE Symposium on Biological Data Visualization - 2013, Atlanta, United States, October 2013.

    http://hal.inria.fr/hal-00921551

National Conferences with Proceedings

  • 23A. Basset, P. Bouthemy, C. Kervrann.

    Classification instantanée de mouvements de foules dans des vidéos, in: Gretsi - XXIVe Colloque Gretsi - Traitement du Signal et des Images - 2013, Brest, France, 2013.

    http://hal.inria.fr/hal-00921787
  • 24J. Boulanger, T. Pécot, C. Kervrann, P. Bouthemy, J. Salamero.

    Estimation de flux d'objets fluorescents dans les séquences de vidéo-microscopie, in: Gretsi - XXIVe Colloque Gretsi - Traitement du Signal et des Images - 2013, Brest, France, September 2013, pp. 1-4.

    http://hal.inria.fr/hal-00931577
  • 25D. Fortun, P. Bouthemy, C. Kervrann.

    Agrégation d'estimations semi-locales pour le flot optique, in: Gretsi - XXIVe Colloque Gretsi - Traitement du Signal et des Images - 2013, Brest, France, September 2013, pp. 1-4.

    http://hal.inria.fr/hal-00931568

Conferences without Proceedings

  • 26D. Fortun, C. Chen, P. Paul-Gilloteaux, F. Waharte, J. Salamero, C. Kervrann.

    Correlation and variational approaches for motion and diffusion estimation in fluorescence imaging, in: European Light Microscopy Initiative (ELMI'13), Arcachon, France, May 2013.

    http://hal.inria.fr/hal-00931593
References in notes
  • 27R. Achanta, A. Shaji, K. Smith, A. Lucchi, P. Fua, S. Süsstrunk.

    SLIC Superpixels Compared to State-of-the-art Superpixel Methods, in: IEEE Transactions on Pattern Analysis and Machine Intelligence, 2012, vol. 34, no 11, pp. 2274-2282.
  • 28P. Allain, N. Courty, T. Corpetti.

    Agoraset: a dataset for crowd video analysis, in: 1st Int. Work. Pattern Recog. and Crowd Analysis, Tsukuba, ICPR'12, Nov 2012.
  • 29D. Axelrod.

    Total Internal Reflection Fluorescent Microscopy in cell biology, in: Traffic, 2004, vol. 2, pp. 4658–4668.
  • 30E. 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.
  • 31A. 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 ]

    http://hal.inria.fr/inria-00541102/en
  • 32A. 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.
  • 33P. Combettes, J.-C. Pescquet.

    Fixed-Point Algorithms for Inverse Problems in Science and Engineering, in: Proximal splitting methods in signal processing, Tsukuba, Japan, Springer, New York, 2011, vol. 10, pp. 185-212.
  • 34T. 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.
  • 35T. 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.
  • 36A. Genovesio, T. Liedl, V. Emiliani, W. Parak, M. Coppey-Moisan, J.-C. Olivo-Marin.

    Multiple particle tracking in 3-D+ t microscopy: method and application to the tracking of endocytosed quantum dots, in: Image Processing, IEEE Transactions on, 2006, vol. 15, no 5, pp. 1062–1070.
  • 37A. 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.
  • 38M. 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.
  • 39H. 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.
  • 40K. 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.
  • 41T. 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.
  • 42D. Kolin, P. Wiseman.

    Advances in image correlation spectroscopy: measuring number densities, aggregation states, and dynamics of fluorescently labeled macromolecules in cells, in: Cell biochemistry and biophysics, 2007, vol. 49, no 3, pp. 141–164.
  • 43C. 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.
  • 44C. Lawson, R. Hanson.

    Solving Least Squares Problems, in: Society for Industrial and Applied Mathematics, 1974.
  • 45F. Nédélec, D. Foethke.

    Collective Langevin dynamics of flexible cytoskeletal fibers, in: New Journal of Physics, 2007, vol. 9, no 11 (427).
  • 46F. 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.
  • 47J.-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.
  • 48M. 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
  • 49K. Prydz, H. Tveit, A. Vedeler, J. Saraste.

    Arrivals and departures at the plasma membrane: direct and indirect transport routes, in: Cell and Tissue Research, 2013, vol. 352, no 1, pp. 5-20.
  • 50T. 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.
  • 51P. Pérez, J. Vermaak, A. Blake.

    Data fusion for visual tracking with particles, in: Proc. IEEE, 2004, vol. 92, no 3, pp. 495–513.
  • 52S. H. Rezatofighi, R. Hartley, W. E. Hughes.

    A new approach for spot detection in total internal reflection fluorescence microscopy, in: IEEE Int. Symp. Biomedical Imaging, Barcelona, ISBI'12, May 2012.
  • 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.
  • 54K. Schauer, T. Duong, K. Bleakley, S. Bardin, M. Bornens, B. Goud.

    Probabilistic density maps to study global endomembrane organization, in: Nature Methods, 2010, vol. 7, pp. 560–566.
  • 55M. Schick, R. Stiefelhagen.

    Measuring and Evaluating the Compactness of Superpixels, in: International Conference on Pattern Recognition (ICPR'2012), Tsukuba, Japan, 2012, pp. 930-934.
  • 56I. 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.
  • 57I. 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.
  • 58B. Solmaz, B. E. Moore, M. Shah.

    Identifying behaviors in crowded scenes using stability analysis for dynamical systems, in: IEEE Trans. Pattern Analysis and Machine Intel., 2012, vol. 34, no 10, pp. 1–8.
  • 59M. 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.
  • 60D. 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.
  • 61Y. Vardi.

    Network tomography: estimating source-destination traffic intensities from link data, in: J. American Statistical Association, 1996, vol. 91, pp. 365–377.
  • 62T. 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.
  • 63P. Weinzaepfel, J. Revaud, Z. Harchaoui, C. Schmid.

    DeepFlow: Large displacement optical flow with deep matching, in: Intenational Conference on Computer Vision (ICCV), 2013.
  • 64L. Xu, J. Jia, Y. Matsushita.

    Motion detail preserving optical flow estimation, in: Trans. Pattern Analysis and Machine Intelligence, 2012, vol. 34, no 9, pp. 1744–1757.
  • 65B. Zhan, D. N. Monekosso, P. Remagnino, S. A. Velastin, L.-Q. Xu.

    Crowd analysis: a survey, in: Machine Vis. and Applic., 2008, vol. 19, no 5–6, pp. 345–357.


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