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SERPICO - 2015
SERPICO - 2015
Project-Team Serpico
Members
Overall Objectives
Research Program
Application Domains
Highlights of the Year
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
Highlights of the Year
New 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 ]
  • 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 ]
  • 6T. 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 ]

    https://hal.inria.fr/hal-00931667
  • 7A. Gidon, S. Bardin, B. Cinquin, J. Boulanger, F. Waharte, L. Héliot, H. De La Salle, D. Hanau, C. Kervrann, B. Goud, J. Salamero.

    A Rab11A/myosin Vb/Rab11-FIP2 complex frames two late recycling steps of langerin from the ERC to the plasma membrane, in: Traffic, April 2012, vol. 13, no 6, pp. 815-833. [ DOI : 10.1111/j.1600-0854.2012.01354.x ]

    https://hal.inria.fr/hal-00782005
  • 8C. 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.
  • 9C. 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.
  • 10C. 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
Publications of the year

Doctoral Dissertations and Habilitation Theses

  • 11A. Basset.

    Detection and characterization with local statistical approaches of dynamical events in image sequences: Application to membrane fusion in TIRF microscopy, Université Rennes 1, December 2015.

    https://hal.inria.fr/tel-01259185

Articles in International Peer-Reviewed Journals

  • 12A. Basset, J. Boulanger, J. Salamero, P. Bouthemy, C. Kervrann.

    Adaptive spot detection with optimal scale selection in fluorescence microscopy images, in: IEEE Transactions on Image Processing, November 2015, vol. 24, no 11, 16 p. [ DOI : 10.1109/TIP.2015.2450996 ]

    https://hal.inria.fr/hal-01248290
  • 13C. A. N. Biscio, F. Lavancier.

    Quantifying repulsiveness of determinantal point processes, in: Bernoulli, 2016.

    https://hal.archives-ouvertes.fr/hal-01003155
  • 14E. Caserta, O. Egriboz, H. Wang, C. Martin, C. Koivisto, T. Pécot, R. Kladney, C. Shen, K.-S. Shim, T. Pham, M. K. Karikomi, M. J. Mauntel, S. Majumder, M. C. Cuitiño, X. Tang, A. Srivastava, L. Yu, J. Wallace, X. Mo, M. Park, S. A. Fernandez, R. Pilarski, K. M. La Perle, T. J. Rosol, V. Coppola, D. H. Castrillon, C. Timmers, D. E. Cohn, D. M. O'Malley, F. Backes, A. A. Suarez, P. Goodfellow, H. M. Chamberlin, E. R. Macrae, C. L. Shapiro, M. C. Ostrowski, G. Leone.

    Noncatalytic PTEN missense mutation predisposes to organ-selective cancer development in vivo, in: Genes and Development, August 2015. [ DOI : 10.1101/gad.262568.115 ]

    https://hal.inria.fr/hal-01244933
  • 15J.-F. Coeurjolly, F. Lavancier.

    Parametric estimation of pairwise Gibbs point processes with infinite range interaction, in: Bernoulli, January 2016.

    https://hal.archives-ouvertes.fr/hal-01092225
  • 16D. Fortun, P. Bouthemy, C. Kervrann.

    Optical flow modeling and computation: a survey, in: Computer Vision and Image Understanding, May 2015, vol. 134, 21 p.

    https://hal.inria.fr/hal-01104081
  • 17D. Fortun, P. Bouthemy, C. Kervrann.

    Aggregation of local parametric candidates with exemplar-based occlusion handling for optical flow, in: Computer Vision and Image Understanding, January 2016, 17 p. [ DOI : 10.1016/j.cviu.2015.11.020 ]

    https://hal.inria.fr/hal-01001758
  • 18M. Jain, H. Jégou, P. Bouthemy.

    Improved motion description for action classification, in: Frontiers in ICT, December 2015. [ DOI : 10.3389/fict.2015.00028 ]

    https://hal.inria.fr/hal-01247605
  • 19D. Jones, D.-Y. Park, M. Anghelina, T. Pécot, R. Machiraju, R. Xue, J. J. Lannuti, J. Thomas, S. L. Cole, L. Moldovan, N. I. Moldovan.

    Actin grips: circular actin-rich cytoskeletal structures that mediate the wrapping of polymeric microfibers by endothelial cells, in: Biomaterials, June 2015, vol. 52, 12 p. [ DOI : 10.1016/j.biomaterials.2015.02.034 ]

    https://hal.inria.fr/hal-01244825
  • 20C. Kervrann, S. T. Acton, J.-C. Olivo-Marin, C. O. S. Sorzano, M. Unser.

    Introduction to the issue on Advanced Signal Processing in Microscopy and Cell Imaging, in: IEEE Journal of Selected Topics in Signal Processing, February 2016, vol. 10, no 1, 2 p.

    https://hal.archives-ouvertes.fr/hal-01251394
  • 21C. Kervrann, C. O. S. Sorzano, S. T. Acton, J.-C. Olivo-Marin, M. Unser.

    A guided tour of selected image processing and analysis methods for fluorescence and electron microscopy, in: IEEE Selected Topics in Signal Processing, December 2015, 26 p.

    https://hal.inria.fr/hal-01246375
  • 22F. Lavancier, J. Møller.

    Modelling aggregation on the large scale and regularity on the small scale in spatial point pattern datasets, in: Scandinavian Journal of Statistics, December 2015.

    https://hal.archives-ouvertes.fr/hal-01155646
  • 23F. Lavancier, J. Møller, E. Rubak.

    Determinantal point process models and statistical inference, in: Journal of the Royal Statistical Society: Series B, 2015, vol. 77, no 4, pp. 853–877. [ DOI : 10.1111/rssb.12096 ]

    https://hal.archives-ouvertes.fr/hal-01241077
  • 24F. Lavancier, P. Rochet.

    A general procedure to combine estimators, in: Computational Statistics and Data Analysis, 2016.

    https://hal.archives-ouvertes.fr/hal-00936024
  • 25H. Liu, X. Tang, A. Srivastava, T. Pécot, P. Daniel, B. Hemmelgarn, S. Reyes, N. Fackler, A. Bajwa, R. Kladney, C. Koivisto, Z. Chen, Q. Wang, K. Huang, R. Machiraju, M. T. Saenz-Robles, P. Cantalupo, J. M. Pipas, G. Leone.

    Redeployment of Myc and E2f1-3 drives Rb-deficient cell cycles, in: Nature Cell Biology, July 2015, vol. 17, pp. 1036–1048. [ DOI : 10.1038/ncb3210 ]

    https://hal.inria.fr/hal-01244839
  • 26T. 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, February 2015, vol. 24, no 2, 14 p. [ DOI : 10.1109/TIP.2014.2380178 ]

    https://hal.inria.fr/hal-01103126
  • 27T. Pécot, C. Kervrann, J. Salamero, J. Boulanger.

    Counting-based particle flux estimation for traffic analysis in live cell imaging, in: IEEE Journal of Selected Topics in Signal Processing, September 2015. [ DOI : 10.1109/JSTSP.2015.2482460 ]

    https://hal.inria.fr/hal-01244946
  • 28P. Roudot, C. Kervrann, C. Blouin, F. Waharte.

    Lifetime estimation on moving sub-cellular objects in frequency domain FLIM imaging, in: Journal of the Optical Society of America A, May 2015, vol. 32, no 10, 15 p. [ DOI : 10.1364/JOSAA.32.001821 ]

    https://hal.inria.fr/hal-01246392
  • 29P. Trikha, N. Sharma, C. Pena, A. Reyes, T. Pécot, S. Khurshid, M. Rawahneh, J. Moffat, J. Stephens, S. A. Fernandez, M. C. Ostrowski, G. Leone.

    E2f3 in tumor macrophages promotes lung metastasis, in: Oncogene, November 2015. [ DOI : 10.1038/onc.2015.429 ]

    https://hal.inria.fr/hal-01244951

Articles in National Peer-Reviewed Journals

  • 30A. Basset, J. Boulanger, P. Bouthemy, C. Kervrann, J. Salamero.

    Détection de spots avec sélection d’échelle automatique et seuillage adaptatif en microscopie de fluorescence, in: TS. Traitement du Signal, September 2015, vol. 32, no 2-3, 24 p. [ DOI : 10.3166/ts.32.287-310 ]

    https://hal.inria.fr/hal-01246429

Invited Conferences

  • 31C. 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

  • 32A. Basset, P. Bouthemy, J. Boulanger, F. Waharte, C. Kervrann, J. Salamero.

    Detection and estimation of membrane diffusion during exocytosis in TIRFM image sequences, in: IEEE International Symposium on Biomedical Imaging, New-York, United States, IEEE, April 2015, 4 p. [ DOI : 10.1109/ISBI.2015.7163968 ]

    https://hal.inria.fr/hal-01246448
  • 33D. Fortun, P. Bouthemy, C. Kervrann.

    Sparse Aggregation Framework for Optical Flow Estimation, in: Scale Space and Variational Methods in Computer Vision, Lège Cap Ferret, France, May 2015.

    https://hal.inria.fr/hal-01138012
  • 34H.-N. Nguyen, C. Kervrann, C. Cauchois, V. Paveau.

    Automatic core segmentation and registration for fast tissue microarray de-arraying, in: IEEE International Symposium on Biomedical Imaging, New-York, United States, April 2015, 4 p.

    https://hal.inria.fr/hal-01246466

Conferences without Proceedings

  • 35T. Pécot, 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

Scientific Books (or Scientific Book chapters)

  • 36C. Kervrann, F. Lavancier.

    A two-color interacting random balls model for co-localization analysis of proteins, in: Geometric Science of Information, F. Nielsen, F. Barbaresco (editors), Lecture Notes in Computer Science, Springer, 2015, vol. 9389.

    https://hal.archives-ouvertes.fr/hal-01241727

Other Publications

References in notes
  • 40D. Axelrod.

    Total Internal Reflection Fluorescent Microscopy in cell biology, in: Traffic, 2004, vol. 2, pp. 4658–4668.
  • 41E. 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.
  • 42A. 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 ]
  • 43A. 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.
  • 44T. 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.
  • 45T. 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.
  • 46A. 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.
  • 47D. Guet.

    Combining Spinach-tagged RNA and gene localization to image gene expression in live yeast, in: Nature Communications, 2015, vol. 6. [ DOI : 10.1038/ncomms9882 ]
  • 48M. 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.
  • 49H. 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.
  • 50K. 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.
  • 51T. 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.
  • 52C. 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.
  • 53F. 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.
  • 54S. 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.
  • 55M. 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
  • 56M. Primet, L. Moisan.

    Point tracking: an a-contrario approach, 2011, Preprint MAP5.
  • 57T. 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.
  • 58P. Pérez, J. Vermaak, A. Blake.

    Data fusion for visual tracking with particles, in: Proc. IEEE, 2004, vol. 92, no 3, pp. 495–513.
  • 59I. 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.
  • 60I. 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.
  • 61I. 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.
  • 62D. 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.
  • 63Y. Vardi.

    Network tomography: estimating source-destination traffic intensities from link data, in: J. American Statistical Association, 1996, vol. 91, pp. 365–377.
  • 64T. 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.


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