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SERPICO - 2018
SERPICO - 2018
Project-Team Serpico
Team, Visitors, External Collaborators
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
Team, Visitors, External Collaborators
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
  • 1A. 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
  • 2A. Basset, P. Bouthemy, J. Boulanger, F. Waharte, J. Salamero, C. Kervrann.

    An extended model of vesicle fusion at the plasma membrane to estimate protein lateral diffusion from TIRF microscopy images, in: BMC Bioinformatics, 2017, vol. 18, no 1, 352 p. [ DOI : 10.1186/s12859-017-1765-y ]

    https://hal.inria.fr/hal-01561310
  • 3J. 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 ]
  • 4J. 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.
  • 5J. 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.
  • 6J. 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 ]
  • 7P.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 ]
  • 8N. Chenouard, I. Smal, F. De Chaumont, M. Maska, I. F. Sbalzarini, Y. Gon, J. Cardinale, C. Carthel, S. Coraluppi, M. Winter, A. R. Cohen, W. J. Godinez, K. Rohr, Y. Kalaidzidis, L. Liang, J. Duncan, H. Shen, Y. Xu, K. Magnusson, J. Jalden, H. M. Blau, P. Paul-Gilloteaux, P. Roudot, C. Kervrann, F. Waharte, J.-Y. Tinevez, S. L. Shorte, J. Willemse, K. Celler, G. P. Van Wezel, H.-W. Dan, Y.-S. Tsai, C. Ortiz De Solorzano, J.-C. Olivo-Marin, E. Meijering.

    Objective comparison of particle tracking methods, in: Nature Methods, 2014, vol. 11, no 3, pp. 281–289. [ DOI : 10.1038/nmeth.2808 ]

    https://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 ]

    https://hal.inria.fr/hal-00931667
  • 10A. 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
  • 11C. 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.
  • 12C. 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.
  • 13C. 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
  • 14T. 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
Publications of the year

Doctoral Dissertations and Habilitation Theses

Articles in International Peer-Reviewed Journals

  • 16V. Briane, C. Kervrann, M. Vimond.

    Statistical analysis of particle trajectories in living cells, in: Physical Review E , June 2018.

    https://hal.inria.fr/hal-01961971
  • 17H.-N. Nguyen, V. Paveau, C. Cauchois, C. Kervrann.

    A variational method for dejittering large fluorescence line scanner images, in: IEEE Transactions on Computational Imaging, June 2018, vol. 4, no 2, 16 p.

    https://hal.inria.fr/hal-01577139
  • 18H.-N. Nguyen, V. Paveau, C. Cauchois, C. Kervrann.

    ATMAD : robust image analysis for Automatic Tissue MicroArray De-arraying, in: BMC Bioinformatics, April 2018, vol. 19, no 148, 23 p.

    https://hal.inria.fr/hal-01577238
  • 19T. Pécot, L. Zengzhen, J. Boulanger, J. Salamero, C. Kervrann.

    A quantitative approach for analyzing the spatio-temporal distribution of 3D intracellular events in fluorescence microscopy, in: eLife, August 2018.

    https://hal.inria.fr/hal-01966817
  • 20J.-M. Pérez-Rúa, O. Miksik, T. Crivelli, P. Bouthemy, P. H. S. Torr, P. Pérez.

    ROAM: a Rich Object Appearance Model with Application to Rotoscoping, in: IEEE Transactions on Pattern Analysis and Machine Intelligence, November 2018.

    https://hal.inria.fr/hal-01923059

Invited Conferences

  • 21C. Kervrann.

    Computational methods for fluorescence microscopy and intracellular dynamics analysis, in: Workshop on "Reverse Mathematical Methods for Reconstructing Molecular Dynamics in Single Cell", Pisa, Italy, October 2018.

    https://hal.inria.fr/hal-01962608
  • 22C. Kervrann.

    Computational methods for fluorescence microscopy and quantitative bioimaging, in: NEUBIAS - Network of European Bioimage Analysts, Szeged, Hungary, January 2018.

    https://hal.inria.fr/hal-01962562
  • 23C. Kervrann.

    GcoPS: a fast automatic colocalization method for 3D live cell imaging and super-resolution microscopy, in: SIAM Conference on Imaging Science, Bologna, Italy, June 2018.

    https://hal.inria.fr/hal-01962601

International Conferences with Proceedings

  • 24A. Caranfil, Y. Le Cunff, C. Kervrann, J. Pecreaux.

    Modelling oscillatory behavior in asymmetric division of C.elegans embryo, in: Mathematical Biology Days, Besancon, France, June 2018.

    https://hal.inria.fr/hal-01970360
  • 25C. Kervrann.

    GcoPS: a Geo-coPositionning System for live cell imaging and superresolution microscopy, in: Quantitative BioImaging (QBI), Gottingen, Germany, January 2018.

    https://hal.inria.fr/hal-01962578
  • 26S. Manandhar, P. Bouthemy, E. Welf, P. Roudot, C. Kervrann.

    A sparse-to-dense method for 3D optical flow estimation in 3D light microscopy image sequences, in: IEEE International Symposium on Biomedical Imaging (ISBI), Washington DC, United States, April 2018.

    https://hal.inria.fr/hal-01960109
  • 27E. Moebel, C. Kervrann.

    A Monte Carlo framework for denoising and missing wedge reconstruction in cryo-electron tomography, in: 4th International Workshop on Patch-based Techniques in Medical Imaging, Grenade, Spain, September 2018.

    https://hal.inria.fr/hal-01961938
  • 28B. M. Toledo Acosta, X. Heiligenstein, G. Malandain, P. Bouthemy.

    Intensity-based matching and registration for 3D correlative microscopy with large discrepancies, in: ISBI 2018 - IEEE 15th International Symposium on Biomedical Imaging, Washington, United States, IEEE, April 2018, pp. 493-496. [ DOI : 10.1109/ISBI.2018.8363623 ]

    https://hal.inria.fr/hal-01930740

National Conferences with Proceedings

  • 29L. Maczyta, P. Bouthemy, O. Le Meur.

    Détection temporelle de saillance dynamique dans des vidéos par apprentissage profond, in: RFIAP 2018 - Reconnaissance des Formes, Image, Apprentissage et Perception, Marne-la-Vallée, France, June 2018, pp. 1-8.

    https://hal.inria.fr/hal-01926351

Other Publications

  • 30V. Briane, M. Vimond, C. Kervrann.

    An overview of diffusion models for intracellular dynamics analysis, December 2018, working paper or preprint.

    https://hal.inria.fr/hal-01966825
  • 31V. Briane, M. Vimond, C. A. Valades Cruz, A. Salomon, C. Wunder, C. Kervrann.

    A sequential algorithm to detect diffusion switching along intracellular particle trajectories, December 2018, working paper or preprint.

    https://hal.inria.fr/hal-01966831
  • 32F. Lavancier, A. Poinas, R. Waagepetersen.

    Adaptive estimating function inference for non-stationary determinantal point processes, 2018, working paper or preprint.

    https://hal.archives-ouvertes.fr/hal-01816528
  • 33E. Moebel, C. Kervrann.

    A Monte Carlo framework for noise removal and missing wedge restoration in cryo-electron tomography, December 2018, working paper or preprint.

    https://hal.inria.fr/hal-01966821
  • 34E. Moebel, A. Martinez, D. Larivière, J. Ortiz, W. Baumeister, C. Kervrann.

    3D ConvNet improves macromolecule localization in 3D cellular cryo-electron tomograms, December 2018, working paper or preprint.

    https://hal.inria.fr/hal-01966819
  • 35J.-M. Pérez-Rúa, T. Crivelli, P. Bouthemy, P. Pérez.

    Learning how to be robust: Deep polynomial regression, November 2018, working paper or preprint.

    https://hal.inria.fr/hal-01923068
References in notes
  • 36D. Axelrod.

    Total Internal Reflection Fluorescent Microscopy in cell biology, in: Traffic, 2004, vol. 2, pp. 4658–4668.
  • 37E. 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.
  • 38A. 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.
  • 39T. 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.
  • 40M. 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.
  • 41N. Hoze, D. Nair, E. Hosy, C. Sieben, S. Manley, A. Herrmann, J.-B. Sibarita, D. Choquet, D. Holcman.

    Heterogeneity of AMPA receptor trafficking and molecular interactions revealed by superresolution analysis of live cell imaging, in: Proc. Natl. Academy Sciences, 2012, vol. 10, no 42, pp. 17052-17057.
  • 42J. Li, F. Luisier, T. Blu.

    PURE-LET image deconvolution, in: IEEE Trans. Image Processing, 2018, vol. 27, no 1, pp. 92–105.
  • 43S. 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.
  • 44M. 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


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