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SERPICO - 2019
SERPICO - 2019
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, 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 ]
  • 5V. Briane, C. Kervrann, M. Vimond.

    Statistical analysis of particle trajectories in living cells, in: Physical Review E , June 2018, vol. 97, no 6, pp. 1-20. [ DOI : 10.1103/PhysRevE.97.062121 ]

    https://hal.inria.fr/hal-01961971
  • 6P.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 ]
  • 7T. 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
  • 8C. 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
  • 9T. 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
  • 10T. 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
Publications of the year

Doctoral Dissertations and Habilitation Theses

Articles in International Peer-Reviewed Journals

  • 13P. Bouthemy, B. M. Toledo Acosta, B. Delyon.

    Robust model selection in 2D parametric motion estimation, in: Journal of Mathematical Imaging and Vision, September 2019, vol. 61, no 7, pp. 1022-1036. [ DOI : 10.1007/s10851-019-00883-2 ]

    https://hal.archives-ouvertes.fr/hal-02315977
  • 14V. Briane, A. Salomon, M. Vimond, C. Kervrann.

    A computational approach for detecting microdomains and confinement domains in cells: a simulation study, in: Physical Biology, December 2019, pp. 1-26, forthcoming. [ DOI : 10.1088/1478-3975/ab5e1d ]

    https://hal.inria.fr/hal-02424860
  • 15V. Briane, M. Vimond, C. Kervrann.

    An overview of diffusion models for intracellular dynamics analysis, in: Briefings in Bioinformatics, June 2019, pp. 1-15. [ DOI : 10.1093/bib/bbz052 ]

    https://hal.inria.fr/hal-02424761
  • 16V. Briane, M. Vimond, C. A. Valadés-Cruz, A. Salomon, C. Wunder, C. Kervrann.

    A sequential algorithm to detect diffusion switching along intracellular particle trajectories, in: Bioinformatics, June 2019, pp. 1-13. [ DOI : 10.1093/bioinformatics/btz489 ]

    https://hal.inria.fr/hal-02424777
  • 17B. Combès, S. Prima.

    An efficient EM-ICP algorithm for non-linear registration of large 3D point sets, in: Computer Vision and Image Understanding, November 2019, pp. 1-14. [ DOI : 10.1016/j.cviu.2019.102854 ]

    https://hal.inria.fr/hal-02414127
  • 18F. Lavancier, A. Poinas, R. Waagepetersen.

    Adaptive estimating function inference for non-stationary determinantal point processes, in: Scandinavian Journal of Statistics, 2019, pp. 1-35, forthcoming.

    https://hal.archives-ouvertes.fr/hal-01816528
  • 19F. Lavancier, T. Pécot, L. Zengzhen, C. Kervrann.

    Testing independence between two random sets for the analysis of colocalization in bioimaging, in: Biometrics, August 2019. [ DOI : 10.1111/biom.13115 ]

    https://hal.archives-ouvertes.fr/hal-02369555
  • 20L. Maczyta, P. Bouthemy, O. Le Meur.

    CNN-based temporal detection of motion saliency in videos, in: Pattern Recognition Letters, December 2019, vol. 128, pp. 298-305. [ DOI : 10.1016/j.patrec.2019.09.016 ]

    https://hal.inria.fr/hal-02345209
  • 21S. Manandhar, P. Bouthemy, E. Welf, G. Danuser, P. Roudot, C. Kervrann.

    3D Flow Field Estimation and Assessment for Live Cell Fluorescence Microscopy, in: Bioinformatics, October 2019, pp. 1-19, forthcoming. [ DOI : 10.1093/bioinformatics/btz780 ]

    https://hal.archives-ouvertes.fr/hal-02308001
  • 22E. Moebel, C. Kervrann.

    A Monte Carlo framework for missing wedge restoration and noise removal in cryo-electron tomography, in: Journal of Structural Biology: X, October 2019, pp. 1-18, Free Open Access. [ DOI : 10.1016/j.yjsbx.2019.100013 ]

    https://hal.inria.fr/hal-02424804
  • 23A. Poinas, B. Delyon, F. Lavancier.

    Mixing properties and central limit theorem for associated point processes, in: Bernoulli, 2019, vol. 25, no 3, pp. 1724-1754. [ DOI : 10.3150/18-BEJ1033 ]

    https://hal.archives-ouvertes.fr/hal-01519096
  • 24G. Potier, R. Capoulade, J. Mérot, F. Lavancier, X. Heiligenstein, J. Salamero, P. Paul-Gilloteaux.

    Automatic Registration of Correlative Microscopies with Error Assessment and Applications for the Optimization of Multimodal Acquisitions, in: Microscopy and Microanalysis, August 2019, vol. 25, no S2, pp. 1020-1021. [ DOI : 10.1017/S143192761900583X ]

    https://hal.archives-ouvertes.fr/hal-02267554
  • 25S. Raman, S. Singh, T. Pécot, E. Caserta, K. Huang, J. Rittscher, G. Leone, R. Machiraju.

    Capturing variations in nuclear phenotypes, in: Journal of computational science, September 2019, vol. 36, pp. 1-12. [ DOI : 10.1016/j.jocs.2019.07.001 ]

    https://hal.inria.fr/hal-02424723

Invited Conferences

  • 26P. Bouthemy.

    Intensity-based methods for fully automated registration in 2D and 3D CLEM, in: CMI 2019 - Correlated Multimodal Imaging Conference, Vienne, Austria, November 2019.

    https://hal.inria.fr/hal-02419522
  • 27C. Kervrann.

    A fast statistical colocalization method for 3D live cell imaging and super-resolutionmicroscopy, in: "Statistical modeling for Shapes and Imaging” workshop, Paris, France, March 2019.

    https://hal.inria.fr/hal-02424596
  • 28C. Kervrann.

    Computational methods for intracellular dynamics in live cell imaging, in: “Random Walks and Intracellular Transport” workshop, Manchester, United Kingdom, April 2019.

    https://hal.inria.fr/hal-02424594
  • 29C. Kervrann.

    Statistical methods for intracellular dynamics classification in live cell imaging, in: “Bioimage Processing” workshop, Cambridge, United Kingdom, June 2019.

    https://hal.inria.fr/hal-02424593

International Conferences with Proceedings

  • 30I. Gubins, G. Van Der Schot, R. Veltkamp, F. Forster, X. Du, X. Zeng, Z. Zhu, L. Chang, M. Xu, E. Moebel, A. Martinez-Sanchez, C. Kervrann, T. M. Lai, X. Han, G. Terashi, D. Kihara, B. A. Himes, J. Zhang, S. Gao, Y. Hao, Z. Lv, X. Wan, Z. Yang, Z. Ding, X. Cui, F. Zhang.

    Classification in cryo-electron tomograms, in: Eurographics Workshop on 3D Object Retrieval, Genova, Italy, May 2019. [ DOI : 10.2312/3dor.20191061 ]

    https://hal.inria.fr/hal-02424712
  • 31L. Maczyta, P. Bouthemy, O. Le Meur.

    Unsupervised motion saliency map estimation based on optical flow inpainting, in: ICIP 2019 - IEEE International Conference on Image Processing, Taipei, Taiwan, IEEE, September 2019, pp. 4469-4473. [ DOI : 10.1109/ICIP.2019.8803542 ]

    https://hal.inria.fr/hal-02065112

Conferences without Proceedings

  • 32H. Bouvrais, D. Fairbrass, L. Chesneau, N. Soler, Y. Le Cunff, T. Pécot, C. Kervrann, J. Pécréaux.

    Two dynamic behaviours of the microtubules at the cell cortex reveal the pulling and pushing forces that position the mitotic spondle in C. elegans embryos, in: QBI 2019 - Quantitative BioImaging Conference, Rennes, France, January 2019.

    https://hal.inria.fr/hal-02424688
  • 33A. Caranfil, C. Kervrann, Y. Le Cunff, J. Pecreaux.

    Studying oscillatory behavior in asymmetric division of Caenorhabditis elegans embryo with fluorescence microscopy, in: QBI 2019 - Quantitative BioImaging Conference, Rennes, France, January 2019.

    https://hal.inria.fr/hal-02424686
  • 34A. Caranfil, Y. Le Le Cunff, C. Kervrann, J. Pécréaux.

    Modelling oscillatory behavior in asymmetric division of C. elegans embryo, in: BioHazard – Stochastic Models for Biology – Conference, Rennes, France, August 2019.

    https://hal.inria.fr/hal-02424703
  • 35Y. Lu, C. Billaudeau, R. Carballlido-Lopez, C. Kervrann, A. Trubuil.

    3D stochastic process simulation for better interpretation of molecular dynamics related to cell wall biogenesis observed with TIRF microscopy, in: QBI 2019 - Quantitative BioImaging Conference, Rennes, France, January 2019.

    https://hal.inria.fr/hal-02424699
  • 36Y. Lu, P. Hodara, C. Kervrann, A. Trubuil.

    Probabilistic overall reconstruction of membrane-associated molecular dynamics from partial observations in rod-shaped bacteria, in: "Seeing is Believing" Conference, Heidelberg, Germany, October 2019.

    https://hal.inria.fr/hal-02424598
  • 37S. Manandhar, P. Bouthemy, P. Roudot, C. Kervrann.

    3D motion estimation in 3D light microscopy image sequences: application to cell migration, in: QBI 2019 - Quantitative BioImaging Conference, Rennes, France, January 2019.

    https://hal.inria.fr/hal-02424694
  • 38E. Moebel, C. Kervrann.

    3D ConvNets improve macromolecule localization in 3D cellular cryo-electron tomograms, in: Quantitative BioImaging (QBI) Conference, Rennes, France, January 2019, vol. 2.

    https://hal.inria.fr/hal-02424696
  • 39A. Salomon, V. Briane, M. Vimond, C. A. Valadés-Cruz, C. Kervrann.

    Analysing and quantifying intracellular particles movements in 3D LLSM data, in: QBI 2019 - Quantitative BioImaging Conference, Rennes, France, January 2019.

    https://hal.inria.fr/hal-02424609
  • 40C. A. Valadés-Cruz, A. Forrester, C. Wunder, C. Kervrann, J. Salamero, L. Johannes.

    3D tracking of endocytic events using lattice light sheet microscopy, in: QBI 2019 - Quantitative BioImaging Conference, Rennes, France, January 2019.

    https://hal.inria.fr/hal-02424697

Other Publications

  • 41H. Bouvrais, L. Chesneau, D. Fairbrass, Y. Le Cunff, N. Soler, T. Pécot, C. Kervrann, J. Pecreaux.

    Two dynamical behaviours of the microtubules at cell cortex reveal pulling and pushing forces that position the spindle in C. elegans embryo, May 2019, working paper or preprint.

    https://hal.inria.fr/hal-02424717
  • 42X. Le Goff, J. Comelles, C. Kervrann, D. Riveline.

    Ends and middle: global force balance determines septum location in fission yeast, December 2019, working paper or preprint. [ DOI : 10.1101/520007 ]

    https://hal.archives-ouvertes.fr/hal-02398985
  • 43Y. Lu, P. Hodara, C. Kervrann, A. Trubuil.

    An inverse problem approach to the probabilistic reconstruction of particle tracks on a censored and closed surface, October 2019, working paper or preprint.

    https://hal.inria.fr/hal-02323939
References in notes
  • 44F. Amat, E. Myers, P. Keller.

    Fast and robust optical flow for time-lapse microscopy using super-voxel, in: Bioinformatics, 2012, vol. 29, no 3, pp. 373–380.
  • 45D. Axelrod.

    Total Internal Reflection Fluorescent Microscopy in cell biology, in: Traffic, 2004, vol. 2, pp. 4658–4668.
  • 46E. 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.
  • 47B. Chen et al.

    Lattice light-sheet microscopy: Imaging molecules to embryos at high spatiotemporal resolution, in: Science, 2014, vol. 346, no 6208, 1257998 p.
  • 48A. 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.
  • 49T. 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.
  • 50N. 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.
  • 51S. 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.
  • 52M. 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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