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
• 2J. 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 ]
• 3J. 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.
• 4J. 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.
• 5J. 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 ]
• 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, n^o 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, n^o 4, pp. 2484-2520. [ DOI : 10.1137/120872048 ]
  
  https://hal.inria.fr/hal-00931667
• 8A. 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
• 9C. 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.
• 10C. 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.
• 11C. 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
• 12T. 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

• 13C. A. N. Biscio, F. Lavancier.
  
  Brillinger mixing of determinantal point processes and statistical applications, in: Electronic journal of statistics , March 2016, vol. 10, n^o 1, pp. 582-607.
  
  https://hal.archives-ouvertes.fr/hal-01179831
• 14C. A. N. Biscio, F. Lavancier.
  
  Contrast estimation for parametric stationary determinantal point processes, in: Scandinavian Journal of Statistics, 2016.
  
  https://hal.archives-ouvertes.fr/hal-01215582
• 15C. A. N. Biscio, F. Lavancier.
  
  Quantifying repulsiveness of determinantal point processes, in: Bernoulli, May 2016, vol. 22, n^o 4, pp. 2001-2028.
  
  https://hal.archives-ouvertes.fr/hal-01003155
• 16J.-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
• 17D. Dereudre, F. Lavancier.
  
  Consistency of likelihood estimation for Gibbs point processes, in: The Annals of Statistics, 2016.
  
  https://hal.archives-ouvertes.fr/hal-01144877
• 18D. Fortun, P. Bouthemy, C. Kervrann.
  
  A Variational Aggregation Framework for Patch-Based Optical Flow Estimation, in: Journal of Mathematical Imaging and Vision, 2016, vol. 56, pp. 280 - 299. [ DOI : 10.1007/s10851-016-0664-6 ]
  
  https://hal.archives-ouvertes.fr/hal-01408771
• 19D. 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
• 20M. Jain, H. Jégou, P. Bouthemy.
  
  Improved Motion Description for Action Classification , in: Frontiers in information and communication technologies, January 2016. [ DOI : 10.3389/fict.2015.00028 ]
  
  https://hal.inria.fr/hal-01401833
• 21C. 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, 2016, vol. 10, n^o 1, pp. 3-5. [ DOI : 10.1109/JSTSP.2015.2511299 ]
  
  https://hal.archives-ouvertes.fr/hal-01251394
• 22C. 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, February 2016, vol. 10, n^o 2, pp. 6-30.
  
  https://hal.inria.fr/hal-01246375
• 23F. 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, 2016, vol. 43, n^o 2, pp. 587-609.
  
  https://hal.archives-ouvertes.fr/hal-01155646
• 24F. Lavancier, P. Rochet.
  
  A general procedure to combine estimators, in: Computational Statistics and Data Analysis, 2016, vol. 94, pp. 175-192.
  
  https://hal.archives-ouvertes.fr/hal-00936024
• 25T. 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, February 2016, vol. 10, n^o 1, pp. 203-216.
  
  https://hal.inria.fr/hal-01417147

Invited Conferences

• 26V. Briane, M. Vimond, C. Kervrann.
  
  An adaptive statistical test to detect non Brownian diffusion from particle trajectories, in: Workshop SSIAB - Spatial Statistics and Image Analysis in Biology, Rennes, France, May 2016.
  
  https://hal.inria.fr/hal-01416812
• 27C. Kervrann.
  
  PEWA: Patch-Based Exponentially Weighted Aggregation for Image Denoising, in: SIAM Imaging Science, Albuquerque, United States, SIAM, May 2016.
  
  https://hal.inria.fr/hal-01416847
• 28T. Pécot, F. Lavancier, C. Kervrann.
  
  A non-parametric procedure for co-localization studies in fluorescence microscopy, in: Workshop SSIAB - Spatial Statistics and Image Analysis in Biology, Rennes, France, May 2016.
  
  https://hal.inria.fr/hal-01416844
• 29B. M. Toledo Acosta, P. Bouthemy, C. Kervrann.
  
  A scale-adaptive method for retracing and registering in correlative light-electron microscopy, in: SIAM Imaging Science, Albuquerque, United States, SIAM, May 2016.
  
  https://hal.inria.fr/hal-01416850

International Conferences with Proceedings

• 30P. Bouthemy, B. M. Toledo Acosta, B. Delyon.
  
  Robust selection of parametric motion models in image sequences, in: 2016 IEEE International Conference on Image Processing (ICIP), Phoenix, United States, October 2016, pp. 3743 - 3747. [ DOI : 10.1109/ICIP.2016.7533059 ]
  
  https://hal.inria.fr/hal-01400895
• 31V. Briane, M. Vimond, C. Kervrann.
  
  An adaptive statistical test to detect non Brownian diffusion from particle trajectories, in: ISBI 2016 - IEEE Symposium on Biomedical Imaging, Prague, Czech Republic, IEEE, April 2016, pp. 1-4.
  
  https://hal.inria.fr/hal-01416855
• 32J.-M. Pérez-Rúa, T. Crivelli, P. Bouthemy, P. Pérez.
  
  Determining occlusions from space and time image reconstructions, in: 2016 IEEE Conference on Computer Vision and Pattern Recognition (CVPR), Las Vegas, United States, June 2016, Peer-reviewed paper accepted for presentation at the IEEE Conference on Computer Vision and Pattern Recognition 2016, in Las Vegas, USA.
  
  https://hal.archives-ouvertes.fr/hal-01307703
• 33J.-M. Pérez-Rúa, T. Crivelli, P. Pérez, P. Bouthemy.
  
  Discovering motion hierarchies via tree-structured coding of trajectories, in: Proceedings of the British Machine Vision Conference 2016, York, United Kingdom, BMVA, September 2016.
  
  https://hal.archives-ouvertes.fr/hal-01358454
• 34J.-M. Pérez-Rúa, T. Crivelli, P. Pérez, P. Bouthemy.
  
  Hierarchical Motion Decomposition for Dynamic Scene Parsing , in: 2016 IEEE International Conference on Image Processing (ICIP), Phoenix, United States, IEEE, September 2016, Peer-reviewed paper accepted for presentation at the IEEE International Conference on Image Processing 2016.
  
  https://hal.archives-ouvertes.fr/hal-01314095
• 35B. M. Toledo Acosta, P. Bouthemy, C. Kervrann.
  
  A Common Image Representation And A Patch-Based Search For Correlative Light-Electron-Microscopy (Clem) Registration, in: 2016 IEEE 13th International Symposium on Biomedical Imaging (ISBI), Prague, Czech Republic, April 2016, pp. 257- 260. [ DOI : 10.1109/ISBI.2016.7493258 ]
  
  https://hal.inria.fr/hal-01400854

National Conferences with Proceedings

• 36A. Basset, P. Bouthemy, J. Boulanger, F. Waharte, J. Salamero, C. Kervrann.
  
  Modélisation et estimation de la diffusion de protéines à l’exocytose dans des séquences d’images de microscopie TIRF, in: Reconnaissance des Formes et l'Intelligence Artificielle (RFIA'16), Clermont-Ferrand, France, Association Française de Reconnaissance et d'Interprétation des Formes (AFRIF), Association Française d'Intelligence Artificielle (AFIA), June 2016, pp. 1-8.
  
  https://hal.inria.fr/hal-01416868
• 37V. Briane, C. Kervrann, M. Vimond.
  
  Test statistique pour détecter les diffusions non browniennes, in: 48e Journées de Statistique, Montpellier, France, SFdS, May 2016, pp. 1-6.
  
  https://hal.inria.fr/hal-01416862

Conferences without Proceedings

• 38E. Moebel, C. Kervrann.
  
  Denoising and compensation of the missing wedge in cryo electron tomography, in: 16th European Microscopy Congress, Lyon, France, European Microscopy Society, August 2016.
  
  https://hal.inria.fr/hal-01416801

Other Publications

• 39F. Lavancier, P. Rochet.
  
  A tutorial on estimator averaging in Spatial Statistics models, July 2016, working paper or preprint.
  
  https://hal.archives-ouvertes.fr/hal-01341125

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. Bruhn, J. Weickert, C. Schnörr.
  
  Lucas/Kanade meets Horn/jaqaSchunck: combining local and global optic flow methods, in: International Journal of Computer Vision, 2005, vol. 61, n^o 3, pp. 211–231.
• 43A. 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.
• 44A. 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 ]
• 45A. 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.
• 46T. Corpetti, E. Mémin, P. Pérez.
  
  Dense estimation fluid flows, in: IEEE Trans. Pattern Analysis and Machine Intelligence, 2002, vol. 24, n^o 3, pp. 365–380.
• 47T. 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.
• 48A. 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, n^o 5, pp. 1062–1070.
• 49M. 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.
• 50H. Haussecker, D. Fleet.
  
  Computing optical flow with physical models of brightness variation, in: IEEE Trans. Pattern Analysis and Machine Intelligence, 2001, vol. 23, n^o 6, pp. 661–673.
• 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, n^o 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, n^o 29, pp. 11705–11710. [ DOI : 10.1073/pnas.1121583109 ]
  
  http://hal.inria.fr/inserm-00717415
• 56T. 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.
• 57P. Pérez, J. Vermaak, A. Blake.
  
  Data fusion for visual tracking with particles, in: Proc. IEEE, 2004, vol. 92, n^o 3, pp. 495–513.
• 58I. 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.
• 59I. Smal, M. Loog, W. Niessen, E. Meijering.
  
  Quantitative comparison of spot detection methods in fluorescence microscopy, in: IEEE Trans. Medical Imaging, 2010, vol. 29, n^o 2, pp. 282–301.
• 60I. 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, n^o 6, pp. 764–777.
• 61D. 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, n^o Part 1, pp. 49–64.
• 62Y. Vardi.
  
  Network tomography: estimating source-destination traffic intensities from link data, in: J. American Statistical Association, 1996, vol. 91, pp. 365–377.
• 63T. 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, n^o 3 (Suppl), pp. S26–41.