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, n^o 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, n^o 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, n^o 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, n^o 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, n^o 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, n^o 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, n^o 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, n^o 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, n^o 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, n^o 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, n^o 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, n^o 2, 14 p. [ DOI : 10.1109/TIP.2014.2380178 ]
  
  https://hal.inria.fr/hal-01103126

Publications of the year

Articles in International Peer-Reviewed Journals

• 15A. 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, n^o 1, 352 p. [ DOI : 10.1186/s12859-017-1765-y ]
  
  https://hal.inria.fr/hal-01561310
• 16J.-F. Coeurjolly, F. Lavancier.
  
  Parametric estimation of pairwise Gibbs point processes with infinite range interaction, in: Bernoulli, February 2017, vol. 23, n^o 2, pp. 1299-1334, https://arxiv.org/abs/1412.2557. [ DOI : 10.3150/15-BEJ779 ]
  
  https://hal.archives-ouvertes.fr/hal-01092225
• 17M. Jain, J. Van Gemert, H. Jégou, P. Bouthemy, C. Snoek.
  
  Tubelets: Unsupervised action proposals from spatiotemporal super-voxels, in: International Journal of Computer Vision, June 2017, pp. 1–25, https://arxiv.org/abs/1607.02003. [ DOI : 10.1007/s11263-017-1023-9 ]
  
  https://hal.archives-ouvertes.fr/hal-01561056
• 18Q. Jin, I. Grama, C. Kervrann, Q. Liu.
  
  Non-local means and optimal weights for noise removal, in: SIAM Journal on Imaging Sciences, December 2017.
  
  https://hal.inria.fr/hal-01575918
• 19J.-M. Pérez-Rúa, A. Basset, P. Bouthemy.
  
  Detection and Localization of Anomalous Motion in Video Sequences from Local Histograms of Labeled Affine Flows , in: Frontiers in information and communication technologies, May 2017. [ DOI : 10.3389/fict.2017.00010 ]
  
  https://hal.archives-ouvertes.fr/hal-01561069
• 20P. Roudot, L. Ding, K. Jaqaman, C. Kervrann, G. Danuser.
  
  Piecewise-stationary motion modeling and iterative smoothing to track heterogeneous particle motions in dense environments, in: IEEE Transactions on Image Processing, June 2017, vol. 26, n^o 11, pp. 5395 - 5410. [ DOI : 10.1109/TIP.2017.2707803 ]
  
  https://hal.inria.fr/hal-01575754

Invited Conferences

• 21P. Bouthemy.
  
  An automatic image-based registration method for correlative light-electron microscopy, in: 15ème colloque de la Société Française des Microscopies, Bordeaux, France, July 2017.
  
  https://hal.inria.fr/hal-01561172

International Conferences with Proceedings

• 22D. Fortun, N. Debroux, C. Kervrann.
  
  Spatially-variant kernel for optical flow under low signal-to-noise ratios: application to microscopy, in: ICCV Workshop - BioImage Computing (BIC), Venice, Italy, IEEE, October 2017, 9 p.
  
  https://hal.inria.fr/hal-01575720
• 23O. Miksik, J.-M. Pérez-Rúa, P. H. S. Torr, P. Perez.
  
  ROAM: a Rich Object Appearance Model with Application to Rotoscoping, in: 2017 IEEE Conference on Computer Vision and Pattern Recognition (CVPR), Honolulu, United States, July 2017.
  
  https://hal.archives-ouvertes.fr/hal-01576017
• 24B. M. Toledo Acosta, A. Basset, P. Bouthemy, C. Kervrann.
  
  Multi-scale spot segmentation with selection of image scales, in: ICASSP 2017 - The 42nd IEEE International Conference on Acoustics, Speech and Signal Processing, New Orleans, United States, March 2017, 5 p. [ DOI : 10.1109/ICASSP.2017.7952489 ]
  
  https://hal.inria.fr/hal-01561164

Conferences without Proceedings

• 25V. Briane, M. Vimond, C. Kervrann.
  
  Classification of diffusion dynamics from particle trajectories, in: QBI - Quantitative BioImaging, College-Station, United States, January 2017.
  
  https://hal.inria.fr/hal-01575467
• 26V. Briane, M. Vimond, C. Kervrann.
  
  Robust classification of particle tracks for characterization of diffusion and dynamics in fluorescence microscopy, in: FOM - Focus on Microscopy, Bordeaux, France, April 2017.
  
  https://hal.inria.fr/hal-01575465

Other Publications

• 27R. Bardenet, F. Lavancier, X. MARY, A. Vasseur.
  
  On a few statistical applications of determinantal point processes, 2017, To appear in ESAIM: proceedings and surveys.
  
  https://hal.archives-ouvertes.fr/hal-01580353
• 28V. Briane, C. Kervrann, M. Vimond.
  
  A Statistical Analysis of Particle Trajectories in Living Cells, June 2017, working paper or preprint.
  
  https://hal.inria.fr/hal-01557705
• 29F. Lavancier, J.-F. Coeurjolly.
  
  Approximation intensity for pairwise interaction Gibbs point processes using determinantal point processes, December 2017, working paper or preprint.
  
  https://hal.archives-ouvertes.fr/hal-01659150
• 30F. Lavancier, T. Pécot, L. Zengzhen, C. Kervrann.
  
  A Fast Automatic Colocalization Method for 3D Live Cell and Super-Resolution Microscopy, August 2017, working paper or preprint.
  
  https://hal.inria.fr/hal-01577118
• 31F. Lavancier, P. Rochet.
  
  A tutorial on estimator averaging in spatial point process models, March 2017, https://arxiv.org/abs/1607.00864 - working paper or preprint.
  
  https://hal.archives-ouvertes.fr/hal-01341125
• 32H.-N. Nguyen, V. Paveau, C. Cauchois, C. Kervrann.
  
  A variational method for dejittering large fluorescence line scanner images , August 2017, working paper or preprint.
  
  https://hal.inria.fr/hal-01577139
• 33H.-N. Nguyen, V. Paveau, C. Cauchois, C. Kervrann.
  
  ATMAD : robust image analysis for Automatic Tissue MicroArray De-arraying, August 2017, working paper or preprint.
  
  https://hal.inria.fr/hal-01577238
• 34H.-N. Nguyen, V. Paveau, C. Cauchois, C. Kervrann.
  
  Generalized Sparse Variation Regularization for Large Fluorescence Image Deconvolution, October 2017, working paper or preprint.
  
  https://hal.inria.fr/hal-01609810
• 35A. POINAS, B. Delyon, F. Lavancier.
  
  Mixing properties and central limit theorem for associated point processes, May 2017, working paper or preprint.
  
  https://hal.archives-ouvertes.fr/hal-01519096
• 36T. Pécot, L. Zengzhen, J. Boulanger, J. Salamero, C. Kervrann.
  
  QuantEv: quantifying the spatial distribution of intracellular events, August 2017, working paper or preprint.
  
  https://hal.inria.fr/hal-01575913

References in notes

• 37D. Axelrod.
  
  Total Internal Reflection Fluorescent Microscopy in cell biology, in: Traffic, 2004, vol. 2, pp. 4658–4668.
• 38E. 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.
• 39A. Buades, B. Coll, J.-M. Morel.
  
  A review of image denoising algorithms, with a new one, in: SIAM J. Multiscale Modeling & Simulation, 2005, vol. 4, n^o 2, pp. 490–530.
• 40A. 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.
• 41T. 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, n^o 3, pp. 295–316.
• 42M. 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.
• 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, n^o 29, pp. 11705–11710. [ DOI : 10.1073/pnas.1121583109 ]
  
  http://hal.inria.fr/inserm-00717415