H. Université-de, grosse boule bleue) le long d'un microtubule par l'intermédiaire d'un moteur moléculaire Ce dernier se déplace à la manière d'un piéton, en marchant sur le microtubule. Ces images sont extraites du film d'animation " The inner life of the cell " , développé par l'équipe " BioVisions, Six images successives illustrant le déplacement d'une vésicule, p.25

.. De-la-séquence-d-'images-simulée, Les pixels bleus correspondent à la région du Golgi, les pixels blancs aux bonnes détections, les pixels verts aux faux négatifs

T. Abrahamsson, Estimation of origin-destination matrices using traffic counts -a literature survey, 1998.

S. Awate and R. Whitaker, Unsupervised, information-theoretic, adaptive image filtering for image restoration, IEEE Transactions on Pattern Analysis and Machine Intelligence, vol.28, issue.3, pp.364-376, 2006.
DOI : 10.1109/TPAMI.2006.64

D. Axelrod, Cell-substrate contacts illuminated by total internal reflection fluorescence, The Journal of Cell Biology, vol.89, issue.1, pp.141-145, 1981.
DOI : 10.1083/jcb.89.1.141

K. Bathe and M. Khoshgoftaar, Finite element formulation and solution of nonlinear heat transfer, Nuclear Engineering and Design, vol.51, issue.3, pp.389-401, 1979.
DOI : 10.1016/0029-5493(79)90126-2

R. Baxter, Exactly Solved Models in Statistical Mechanics, 1992.
DOI : 10.1142/9789814415255_0002

M. Bell, The estimation of origin-destination matrices by constrained generalised least squares, Transportation Research Part B: Methodological, vol.25, issue.1, pp.13-22, 1991.
DOI : 10.1016/0191-2615(91)90010-G

D. Benson, J. Bryan, A. Plant, G. Jr, A. Smith et al., Digital imaging fluorescence microscopy: spatial heterogeneity of photobleaching rate constants in individual cells, The Journal of Cell Biology, vol.100, issue.4, pp.1309-1323, 1985.
DOI : 10.1083/jcb.100.4.1309

C. Bergsma, G. Streekstra, A. Smeulders, and E. Manders, Velocity estimation of spots in 3D confocal image sequences of living cells, 2000.

C. Bergsma, G. Streekstra, A. Smeulders, and E. Manders, Velocity estimation of spots in 3D confocal image sequences of living cells, Cytometry, vol.53, issue.4, pp.261-272, 2001.

J. Besag, Spatial interaction and the statistical analysis of lattice systems, Journal Royal Statistical Society, vol.36, pp.192-236, 1974.

E. Betzig, G. Patterson, R. Sougrat, O. Lindwasser, S. Olenych et al., Imaging Intracellular Fluorescent Proteins at Nanometer Resolution, Science, vol.313, issue.5793, pp.1642-1645, 2006.
DOI : 10.1126/science.1127344

S. Bonneau, M. Dahan, and L. Cohen, Tracking single quantum dots in live cells with minimal paths, in 'Computer Vision and Pattern Recognition, pp.141-141, 2005.

J. Boulanger, A. Gidon, C. Kervrann, and J. Salamero, A Patch-Based Method for Repetitive and Transient Event Detection in Fluorescence Imaging, PLoS ONE, vol.5, issue.10, 2010.
DOI : 10.1371/journal.pone.0013190.s006
URL : https://hal.archives-ouvertes.fr/inria-00541072

J. Boulanger, C. Kervrann, and P. Bouthemy, Simulation and estimation of fluorescence in microscopy image sequence, Proc. of the MICCAI Workshop on Microscopic Image Analysis and Application to Biology, 2006.

J. Boulanger, C. Kervrann, and P. Bouthemy, Space-Time Adaptation for Patch-Based Image Sequence Restoration, IEEE Transactions on Pattern Analysis and Machine Intelligence, vol.29, issue.6, pp.1096-1102, 2007.
DOI : 10.1109/TPAMI.2007.1064
URL : https://hal.archives-ouvertes.fr/inria-00071294

J. Boulanger, C. Kervrann, and P. Bouthemy, A simulation and estimation framework for intracellular dynamics and trafficking in video-microscopy and fluorescence imagery, Medical Image Analysis, vol.13, issue.1, pp.132-142, 2009.
DOI : 10.1016/j.media.2008.06.017
URL : https://hal.archives-ouvertes.fr/hal-00794917

J. Boulanger, C. Kervrann, P. Bouthemy, P. Elbau, J. Sibarita et al., Patch-based non-local functional for denoising fluorescence microscopy image sequences, IEEE Transactions on Medical Imaging, vol.28, issue.12, 2009.

J. Boulanger, T. Pécot, P. Bouthemy, J. Salamero, J. Sibarita et al., Microscopic image analysis for life science applications, chapter Simulation and estimation of intracellular dynamics and trafficking, 2008.

J. Boulanger, J. Sibarita, C. Kervrann, and P. Bouthemy, Non-parametric regression for patchbased fluorescence microscopy image sequence denoising, Proceedings of the IEEE International Symposium on Biomedical Images, pp.748-751, 2008.
URL : https://hal.archives-ouvertes.fr/inria-00322321

J. E. Boyd, J. Meloche, and Y. Vardi, Statistical tracking in video traffic surveillance, Proceedings of the Seventh IEEE International Conference on Computer Vision, pp.163-168, 1999.
DOI : 10.1109/ICCV.1999.791213

Y. Boykov and M. Joly, Interactive graph cuts for optimal boundary & region segmentation of objects in N-D images, Proceedings Eighth IEEE International Conference on Computer Vision. ICCV 2001, pp.105-112, 2001.
DOI : 10.1109/ICCV.2001.937505

Y. Boykov and V. Kolmogorov, An experimental comparison of min-cut/max- flow algorithms for energy minimization in vision, IEEE Transactions on Pattern Analysis and Machine Intelligence, vol.26, issue.9, pp.1124-1137, 2004.
DOI : 10.1109/TPAMI.2004.60

L. Bregman, The method of successive projection for finding a common point of convex sets, pp.688-692, 1965.

A. Brown, L. Wang, and P. Jung, Stochastic Simulation of Neurofilament Transport in Axons: The "Stop-and-Go" Hypothesis, Molecular Biology of the Cell, vol.16, issue.9, pp.4243-4255, 2005.
DOI : 10.1091/mbc.E05-02-0141

A. Bruckstein, On shape from shading, Computer Vision, Graphics, and Image Processing, pp.139-154, 1988.

T. Bu, N. Duffield, F. Lo-presti, and D. Towsley, Network tomography on general topologies, ACM SIGMETRICS Performance Evaluation Review, vol.30, issue.1, pp.21-30, 2002.
DOI : 10.1145/511399.511338

A. Buades, B. Coll, and J. Morel, A review of image denoising algorithms, with a new one', Multiscale Modeling and Simulation : A, SIAM Interdisciplinary Journal, vol.4, issue.2, pp.490-530, 2005.

J. Cao, D. Davis, S. Vander-wiel, and B. Yu, Time-Varying Network Tomography: Router Link Data, Journal of the American Statistical Association, vol.91, issue.442, 2000.
DOI : 10.1080/01621459.2000.10474303

J. Cao, V. Scott, S. Wiel, B. Yu, and Z. Zhu, A scalable method for estimating network traffic matrices from link counts, 2000.

B. Carter, G. Shubeita, and S. Gross, Tracking single particles: a user-friendly quantitative evaluation, Physical Biology, vol.2, issue.1, pp.60-72, 2005.
DOI : 10.1088/1478-3967/2/1/008

E. Cascetta, Estimation of trip matrices from traffic counts and survey data: A generalized least squares estimator, Transportation Research Part B: Methodological, vol.18, issue.4-5, pp.4-5, 1984.
DOI : 10.1016/0191-2615(84)90012-2

E. Cascetta and S. Nguyen, A unified framework for estimating or updating origin/destination matrices from traffic counts, Transportation Research Part B: Methodological, vol.22, issue.6, pp.437-455, 1988.
DOI : 10.1016/0191-2615(88)90024-0

G. Casella and C. Robert, Rao-Blackwellisation of sampling schemes, Biometrika, vol.83, issue.1, pp.81-94, 1996.
DOI : 10.1093/biomet/83.1.81

R. Castro, M. Coates, G. Liang, R. Nowak, and B. Yu, Network Tomography: Recent Developments, Statistical Science, vol.19, issue.3, pp.499-517, 2004.
DOI : 10.1214/088342304000000422

M. Chalfie, Y. Tu, G. Euskirchen, W. Ward, and D. Prasher, Green fluorescent protein as a marker for gene expression, Science, vol.263, issue.5148, pp.802-805, 1994.
DOI : 10.1126/science.8303295

B. Chalmond, PSF estimation for image deblurring, CVGIP : Graphical Models and Image Processing, pp.364-372, 1991.
DOI : 10.1016/1049-9652(91)90039-M

B. Chalmond, Éléments de modélisation pour l'analyse d'images, Mathématiques et Applications edn, 2000.

Y. Chang, S. Kadaba, P. Doerschuk, and S. Gelfand, Image restoration using recursive Markov random field models driven by Cauchy distributed noise, IEEE Signal Processing Letters, vol.8, issue.3, pp.65-66, 2001.
DOI : 10.1109/97.905941

P. Chavrier and B. Goud, The role of ARF and Rab GTPases in membrane transport, Current Opinion in Cell Biology, vol.11, issue.4, pp.466-475, 1999.
DOI : 10.1016/S0955-0674(99)80067-2

M. Cheezum, W. Walker, and W. Guilford, Quantitative Comparison of Algorithms for Tracking Single Fluorescent Particles, Biophysical Journal, vol.81, issue.4, pp.2378-2388, 2001.
DOI : 10.1016/S0006-3495(01)75884-5

A. Chen, J. Cao, and T. Bu, Network tomography : Identifiability and Fourier domain estimation, Proceedings of the 26th IEEE International Conference on Computer, pp.1875-1883, 2007.

N. Chenouard, I. Bloch, and J. Olivo-marin, Multiple hypothesis tracking in microscopy images, 2009 IEEE International Symposium on Biomedical Imaging: From Nano to Macro, pp.1346-1349, 2009.
DOI : 10.1109/ISBI.2009.5193314

A. Chessel, B. Cinquin, S. Bardin, C. J. Kervrann, and S. , Computational geometry-based scalespace and modal image decomposition : Application to light video-microscopy imaging, in 'Conference on Scale Space and Variational Methods, pp.770-781, 2009.

L. Cohen, Minimal Paths and Fast Marching Methods for Image Analysis, Mathematical Models in Computer Vision : the Handbook, 2005.
DOI : 10.1007/0-387-28831-7_6

L. D. Cohen, Multiple contour finding and perceptual grouping using minimal paths, Proceedings IEEE Workshop on Variational and Level Set Methods in Computer Vision, pp.225-236, 2001.
DOI : 10.1109/VLSM.2001.938886

L. Cohen and R. Kimmel, Global minimum for active contour models: a minimal path approach, Proceedings CVPR IEEE Computer Society Conference on Computer Vision and Pattern Recognition, pp.57-78, 1997.
DOI : 10.1109/CVPR.1996.517144

A. Criminisi, G. Cross, A. Blake, and K. Kolmogorov, Bilayer segmentation of live video, in 'Computer Vision and Pattern Recognition, pp.53-60, 2006.

T. Crivelli, G. Piriou, B. Cernuschi-frias, P. Bouthemy, and J. Yao, Simultaneous motion detection and background reconstruction with mixed-state conditional Markov random field, Proc. Eur. Conf. Computer Vision', pp.113-126, 2008.
URL : https://hal.archives-ouvertes.fr/hal-00651558

G. Dantzig, A. Orden, and P. Wolfe, The generalized simplex method for minimizing a linear form under linear inequality restraints, Pacific Journal of Mathematics, vol.5, issue.2, pp.183-195, 1955.
DOI : 10.2140/pjm.1955.5.183

D. Moral and P. , Nonlinear filtering : Interacting particle resolution', Comptes rendus de l, Académie des sciences, vol.325, issue.6, pp.653-658, 2002.

A. Dempster, N. Laird, and D. Rubin, Maximum likelihood from incomplete data via the EM algorithm, Journal of the Royal statistical society, Series B, vol.39, issue.1, pp.1-38, 1977.

R. Deriche and O. Faugeras, Tracking line segments, Proceedings of the European Conference on Computer Vision, pp.259-268, 1990.
DOI : 10.1016/0262-8856(90)80002-B

N. Dey, L. Blanc-féraud, C. Zimmer, Z. Kam, P. Roux et al., Richardson???Lucy algorithm with total variation regularization for 3D confocal microscope deconvolution, Microscopy Research Technique, pp.260-266, 2006.
DOI : 10.1002/jemt.20294

E. Dijkstra, A note on two problems in connexion with graphs, Numerische Mathematik, vol.4, issue.1, pp.269-271, 1959.
DOI : 10.1007/BF01386390

A. Dinh, C. Pangarkar, T. Theofanus, and S. Mitragotri, Understanding Intracellular Transport Processes Pertinent to Synthetic Gene Delivery via Stochastic Simulations and Sensitivity Analyses, Biophysical Journal, vol.92, issue.3, pp.831-846, 2007.
DOI : 10.1529/biophysj.106.095521

A. Dinh, T. Theofanus, and S. Mitragotri, A Model for Intracellular Trafficking of Adenoviral Vectors, Biophysical Journal, vol.89, issue.3, pp.1574-1588, 2005.
DOI : 10.1529/biophysj.105.059477

E. Dinic, Algorithm for solution of a problem of maximum flow in a network with power estimation, Doklady Akademii Nauk SSSR, vol.194, issue.4, pp.1270-1280, 1970.

A. Doucet, S. Godsill, and C. Andrieu, On sequential Monte Carlo sampling methods for Bayesian filtering, Statistics and Computing, vol.10, issue.3, pp.197-208, 2000.
DOI : 10.1023/A:1008935410038

R. Duda and P. Hart, Pattern Classification and Scene Analysis, 1973.

N. El-zehiry and A. Elmaghraby, Brain MRI tissue classification using graph cut optimization of the Mumford-Shah functional, Proc. of Image and Vision Computing, pp.321-326, 2007.

S. Erlander, S. Nguyen, and N. Stewart, On the calibration of the combined distribution-assignment model, Transportation Research Part B: Methodological, vol.13, issue.3, pp.259-267, 1979.
DOI : 10.1016/0191-2615(79)90017-1

C. Fisk, On combining maximum entropy trip matrix estimation with user optimal assignment, Transportation Research Part B: Methodological, vol.22, issue.1, pp.69-73, 1988.
DOI : 10.1016/0191-2615(88)90035-5

C. Fisk and D. E. Boyce, A note on trip matrix estimation from link traffic count data, Transportation Research Part B: Methodological, vol.17, issue.3, pp.331-336, 1983.
DOI : 10.1016/0191-2615(83)90018-8

E. Fontaine, A. Barr, and J. Burdick, Tracking multiple worms and fish for biological studies, Proceedings of ICCV Workshop on Dynamical Vision, 2007.

M. Garcia-parajo, G. Segers-nolten, J. Veerman, J. Greve, and N. Van-hulst, Real-time light-driven dynamics of the fluorescence emission in single green fluorescent protein molecules, Proceedings of the National Academy of Sciences of the United States of America, pp.7237-7242, 2000.
DOI : 10.1073/pnas.97.13.7237

S. Geman and D. Geman, Stochastic relaxation, Gibbs distributions, and the Bayesian restoration of images, PAMI, vol.6, issue.6, pp.721-741, 1984.

A. Genovesio, T. Liedl, V. Emiliani, W. Parak, M. Coppey-moisan et al., Multiple particle tracking in 3-D+t microscopy: method and application to the tracking of endocytosed quantum dots, IEEE Transactions on Image Processing, vol.15, issue.5, pp.1062-1070, 2006.
DOI : 10.1109/TIP.2006.872323

R. Ghozi and B. Levy, Critical Markov random fields and fractional Brownian motion in texture synthesis, in 'Internation Conference on Image Processing, pp.426-430, 1994.

F. Gibbons, J. Chauwin, M. Despósito, and J. José, A Dynamical Model of Kinesin-Microtubule Motility Assays, Biophysical Journal, vol.80, issue.6, pp.2515-2526, 2001.
DOI : 10.1016/S0006-3495(01)76223-6

A. Girod, B. Storrie, J. Simpson, L. Johannes, B. Goud et al., Evidence for a COP-I-independent transport route from the Golgi complex to the endoplasmic reticulum, Nature Cell Biology, vol.1, pp.423-430, 1999.

A. Goldberg and R. Tarjan, A new approach to the maximum-flow problem, Journal of the ACM, vol.35, issue.4, pp.921-940, 1988.
DOI : 10.1145/48014.61051

A. Goldenshuger, On pointwise adaptive nonparametric deconvolution, pp.907-925, 1999.

N. Gordon, D. Salmond, and A. Smith, Novel approach to nonlinear/non-Gaussian Bayesian state estimation, Proceedings of the IEEE F, pp.107-113, 1993.
DOI : 10.1049/ip-f-2.1993.0015

D. Greig, B. Porteous, and A. Seheult, Exact maximum a posteriori estimation for binary images, Journal Royal Statistical Society, vol.51, issue.2, pp.271-279, 1989.

A. Gunnar, M. Johansson, and T. Telkamp, Traffic matrix estimation on a large IP backbone, Proceedings of the 4th ACM SIGCOMM conference on Internet measurement , IMC '04, pp.149-160, 2004.
DOI : 10.1145/1028788.1028807

M. Gustafsson, L. Shao, P. Carlton, C. Wang, I. Golubovskaya et al., Threedimensional resolution doubling in wide-field fluorescence microscopy by structured illumination, Biophysical Journal, issue.12, pp.94-4957, 2008.

D. Gustavo, D. Veciana, G. Evans, and B. , Network tomography based on flow level measurements, Proceedings of the IEEE International Conference on Acoustics, Speech, and Signal Processing, 2004.

G. Hager, M. Dewan, and C. Stewart, Multiple kernel tracking with SSD, in 'Computer Vision and Pattern Recognition, pp.790-797, 2004.

F. Heitz and P. Bouthemy, Multimodal estimation of discontinuous optical flow using Markov random fields, IEEE Transactions on Pattern Analysis and Machine Intelligence, vol.15, issue.12, pp.1217-1232, 1993.
DOI : 10.1109/34.250841
URL : https://hal.archives-ouvertes.fr/inria-00075193

N. Hirokawa, Kinesin and Dynein Superfamily Proteins and the Mechanism of Organelle Transport, Science, vol.279, issue.5350, pp.519-526, 1998.
DOI : 10.1126/science.279.5350.519

M. Holschneider, R. Kronland-martinet, J. Morlet, and P. Tchamitchian, A real-time algorithm for signal analysis with the help of the wavelet transform, 1989.

J. Hoogenboom, E. Van-dijk, J. Hernando, N. Van-hulst, and M. Garcia-parajo, Power-Law-Distributed Dark States are the Main Pathway for Photobleaching of Single Organic Molecules, Physical Review Letters, vol.95, issue.9, pp.97401-97402, 2005.
DOI : 10.1103/PhysRevLett.95.097401

B. Horn and B. Schunk, Determining optical flow, Artificial Intelligence, vol.17, issue.1-3, pp.185-203, 1981.
DOI : 10.1016/0004-3702(81)90024-2
URL : http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.185.1651

C. Hue, Méthodes séquentielles de Monte Carlo pour le filtrage non linéaire multi-objets dans un environnement bruité. Applications au pistage multi-cibles et à la trajectographie d'entités dans des séquences d'images 2D, 2003.

C. Hue, J. Le-cadre, and P. Pérez, Sequential Monte Carlo methods for multiple target tracking and data fusion, IEEE Transactions on Signal Processing, vol.50, issue.2, pp.309-325, 2002.
DOI : 10.1109/78.978386

M. Isard and A. Blake, Condensation -conditional density propagation for visual tracking, International Journal of Computer Vision, vol.1, pp.343-356, 1998.

K. Jaqaman, D. Loerke, M. Mettlen, H. Kuwata, S. Grinstein et al., Robust single-particle tracking in live-cell time-lapse sequences, Nature Methods, vol.4, issue.8, pp.695-702, 2008.
DOI : 10.1046/j.1365-2818.2002.01066.x

S. Jiang, X. Zhou, T. Kirchhausen, and S. Wong, Detection of molecular particles in live cells via machine learning, Cytometry Part A, vol.11, issue.8, pp.563-575, 2007.
DOI : 10.1002/cyto.a.20404

N. Kachouie, P. Fieguth, J. Ramunas, and E. Jervis, Probabilistic Model-Based Cell Tracking, International Journal of Biomedical Imaging, vol.6, issue.3, pp.1-10, 2006.
DOI : 10.1002/glia.20127

J. Kapur, P. Sahoo, and A. Wong, A new method for gray-level picture thresholding using the entropy of the histogram, Computer Vision, Graphics, and Image Processing, vol.29, issue.3, pp.273-285, 1985.
DOI : 10.1016/0734-189X(85)90125-2

Z. Kato and T. Pong, A Markov random field image segmentation model for color textured images, Image and Vision Computing, vol.24, issue.10, pp.1103-1114, 2006.
DOI : 10.1016/j.imavis.2006.03.005

C. Kervrann and J. Boulanger, Optimal Spatial Adaptation for Patch-Based Image Denoising, IEEE Transactions on Image Processing, vol.15, issue.10, pp.2866-2878, 2006.
DOI : 10.1109/TIP.2006.877529

G. Kitagawa, Monte Carlo filter and smoother for non-Gaussian nonlinear state space models, Journal of Computational and Graphical Statistics, vol.5, pp.1-25, 1996.
DOI : 10.1080/10618600.1996.10474692

V. Kolmogorov and M. Wainwright, On the optimality of tree-reweighted max-product messagepassing, Conference on Uncertainity in Artificial Intelligence, 2005.

A. Kong, J. Liu, and W. Wong, Sequential Imputations and Bayesian Missing Data Problems, Journal of the American Statistical Association, vol.52, issue.425, pp.278-298, 1994.
DOI : 10.1080/01621459.1987.10478458

S. Kumar and M. Hebert, Discriminative Random Fields, International Journal of Computer Vision, vol.21, issue.1, pp.179-201, 2006.
DOI : 10.1007/s11263-006-7007-9

V. Kwatra, A. Schödl, I. Essa, G. Turk, and A. Bobick, Graphcut textures, ACM Transactions on Graphics, vol.22, issue.3, pp.277-286, 2003.
DOI : 10.1145/882262.882264

J. Lafferty, A. Mccallum, and F. Pereira, Conditional random fields : Probabilistic models for segmenting and labeling sequence data, Proceedings of International Conference on Machine Learning, pp.282-289, 2001.

T. Lagache and D. Holcman, Quantifying intermittent transport in cell cytoplasm, Physical Review E, vol.77, issue.3, pp.1-30901, 2008.
DOI : 10.1103/PhysRevE.77.030901

C. Lawson and R. Hanson, Solving least squares problem, 1974.
DOI : 10.1137/1.9781611971217

L. Leblanc and K. Farhangian, Selection of a trip table which reproduces observed link flows, Transportation Research Part B: Methodological, vol.16, issue.2, pp.83-88, 1982.
DOI : 10.1016/0191-2615(82)90029-7

K. Li, E. Miller, L. Weiss, P. Campbell, and T. Kanade, Online tracking of migrating and proliferating cells images with phase-contrast microscopy, Proceedings of the Conference on Computer Vision and Pattern Recognition, pp.65-72, 2006.

B. T. Lucas and K. , An iterative image registration technique with an application to stereo vision, Proc. DARPA Image Understanding Workshop, 1981.

W. Lukosz, Optical Systems with Resolving Powers Exceeding the Classical Limit*, Journal of the Optical Society of America, vol.56, issue.11, pp.1463-1471, 1961.
DOI : 10.1364/JOSA.56.001463

M. Maher, Inferences on trip matrices from observations on link volumes: A Bayesian statistical approach, Transportation Research Part B: Methodological, vol.17, issue.6, pp.435-447, 1983.
DOI : 10.1016/0191-2615(83)90030-9

N. Metropolis and S. Ulam, The Monte Carlo Method, Journal of the American Statistical Association, vol.44, issue.247, pp.335-341, 1949.
DOI : 10.1080/01621459.1949.10483310

F. Meyer, Quantitative analysis of microstructures in material sciences, biology and medicine, Riederer-Verlag, chapter Contrast feature extraction, 1977.

C. Morefield, Application of 0-1 integer programming to multitarget tracking problems, IEEE Transactions on Automatic Control, vol.22, issue.3, pp.856-864, 1977.
DOI : 10.1109/TAC.1977.1101500

J. Morin and J. Hastings, Energy transfer in a bioluminescent system, Journal of Cellular Physiology, vol.28, issue.3, pp.313-318, 1971.
DOI : 10.1002/jcp.1040770305

K. Morton and D. Mayers, Numerical Solution of Partial Differential Equations, an Introduction, 2005.

V. Murino, Acoustic image reconstruction by Markov random fields, Electronics Letters, vol.32, issue.7, pp.32-607, 1996.
DOI : 10.1049/el:19960406

S. Nguyen, Estimation of an OD matrix from network data : A network equilibrium approach, 1977.

R. Nishii and S. Eguchi, Image classification based on Markov random field models with Jeffreys divergence, Journal of Multivariate Analysis, vol.97, issue.9, 1997.
DOI : 10.1016/j.jmva.2006.01.009

F. Nédélec, Computer simulations reveal motor properties generating stable antiparallel microtubule interactions, The Journal of Cell Biology, vol.6, issue.24, pp.1005-1015, 2001.
DOI : 10.1038/35050669

F. Nédélec and T. Surrey, De l'action collective des moteurs à l'ordre cellulaire, pp.739-744, 2000.

J. Odobez and P. Bouthemy, Separation of moving region from background in an image sequence acquired with a mobile camera, pp.295-311, 1997.

J. Olivo-marin, Extraction of spots in biological images using multiscale products, Pattern Recognition, vol.35, issue.9, pp.1989-1996, 2002.
DOI : 10.1016/S0031-3203(01)00127-3

B. Olshausen and D. Field, Sparse coding with an overcomplete basis set: A strategy employed by V1?, Vision Research, vol.37, issue.23, pp.3311-3325, 1997.
DOI : 10.1016/S0042-6989(97)00169-7

F. Opdam, A. Echard, H. Croes, J. Van-den-hurk, R. Van-de-vorstenbosch et al., The small GTPase Rab6B, a novel Rab6 subfamily member, is cell-type specifically expressed and localised to the Golgi apparatus, Journal of Cell Science, vol.113, pp.2725-2735, 2000.

G. Palade, Intracellular aspects of the process of protein synthesis, Science, vol.189, issue.4200, pp.347-358, 1975.
DOI : 10.1126/science.1096303

P. Pankajashkan, B. Zhang, L. Blanc-féraud, Z. Kam, J. Olivo-marin et al., Blind deconvolution for thin layered confocal imaging, Applied Optics, issue.48, pp.22-4437, 2009.

P. Pérez, Document d'habilitation, Modèles et algorithmes pour l'analyse probabiliste des images, 2003.

P. Pérez, J. Vermaak, and A. Blake, Data fusion for visual tracking with particles, in 'Issue on State Estimation, pp.495-513, 2004.

R. Pinho, J. Tavares, and M. Correia, Efficient Approximation of the Mahalanobis Distance for Tracking with the Kalman Filter, International Journal of Simulation Modelling, vol.6, issue.2, pp.84-92, 2007.
DOI : 10.2507/IJSIMM06(2)S.03

D. Prasher, V. Eckenrode, W. Ward, F. Prendergast, and M. Cormier, Primary structure of the Aequorea victoria green-fluorescent protein, Gene, vol.111, issue.2, pp.229-233, 1992.
DOI : 10.1016/0378-1119(92)90691-H

V. Racine, M. Saschse, J. Salamero, V. Fraisier, A. Trubuil et al., Visualization and quantification of vesicle trafficking on a 3D cytoskeleton network in living cells, Journal of Microscopy, pp.214-228, 2007.

D. Reid, An algorithm for tracking multiple targets, IEEE Transactions on Automatic Control, vol.24, issue.6, pp.843-854, 1979.
DOI : 10.1109/TAC.1979.1102177

M. Reyes, X. Zhao, D. Neuhoff, and T. Pappas, Lossy compression of bilevel images based on markov random fields, in 'Internation Conference on Image Processing, pp.373-376, 2007.

S. Roth and M. J. Black, Fields of Experts, International Journal of Computer Vision, vol.27, issue.2, pp.860-867, 2005.
DOI : 10.1007/s11263-008-0197-6

C. Rother, V. Kolmogorov, and A. Blake, "GrabCut", ACM Transactions on Graphics, vol.23, issue.3, pp.309-314, 2004.
DOI : 10.1145/1015706.1015720

J. Rust, M. Bates, and X. Zhuang, Sub-diffraction-limit imaging by stochastic optical reconstruction microscopy (STORM), Nature Methods, vol.127, issue.10, pp.793-795, 2006.
DOI : 10.1038/nmeth929

D. Sage, F. Neumann, H. Hediger, S. Gasser, and M. Unser, Automatic tracking of individual fluorescence particles: application to the study of chromosome dynamics, IEEE Transactions on Image Processing, vol.14, issue.9, pp.1372-1383, 2005.
DOI : 10.1109/TIP.2005.852787

P. Sahoo, D. Slaaf, and T. Albert, Threshold selection using a minimal histogram entropy difference' , Society of Photo-Optical Instrumentation Engineers 36, 1997.

J. Salamero, La "révolution verte" est en marche, pp.987-988, 2008.

I. Sbalzarini and P. Koumoutsakos, Feature point tracking and trajectory analysis for video imaging in cell biology, Journal of Structural Biology, vol.151, issue.2, pp.182-195, 2005.
DOI : 10.1016/j.jsb.2005.06.002

M. Seabra, E. Mules, and A. Hume, Rab GTPases, intracellular traffic and disease, Trends in Molecular Medicine, vol.8, issue.1, pp.23-30, 2002.
DOI : 10.1016/S1471-4914(01)02227-4

J. Serra, Buts et réalisation de l'analyseur de textures, R.I.M, vol.49, pp.1-14, 1967.

H. Shen, G. Nelson, S. Kennedy, D. Nelson, J. Johnson et al., Automatic tracking of biological cells and compartments using particle filters and active contours, Chemometrics and Intelligent Laboratory Systems, vol.82, issue.1-2, pp.276-282, 2006.
DOI : 10.1016/j.chemolab.2005.07.007

J. Shi and C. Tomasi, Good features to track, Proceedings of IEEE Conference on Computer Vision and Pattern Recognition, 1994.

O. Shimomura, F. Johnson, and Y. Saiga, Extraction, Purification and Properties of Aequorin, a Bioluminescent Protein from the Luminous Hydromedusan,Aequorea, Journal of Cellular and Comparative Physiology, vol.5, issue.3, pp.223-239, 1962.
DOI : 10.1002/jcp.1030590302

J. Sibarita, H. Magnin, and J. De-mey, Ultra-fast 4D microscopy and high throughput distributed deconvolution, Proceedings IEEE International Symposium on Biomedical Imaging, pp.769-772, 2002.
DOI : 10.1109/ISBI.2002.1029371

I. Smal, K. Draegestein, N. Galjart, W. Niessen, and E. Meijering, Particle Filtering for Multiple Object Tracking in Dynamic Fluorescence Microscopy Images: Application to Microtubule Growth Analysis, IEEE Transactions on Medical Imaging, vol.27, issue.6, pp.789-804, 2008.
DOI : 10.1109/TMI.2008.916964

I. Smal, M. Loog, W. Niessen, and E. Meijering, Quantitative Comparison of Spot Detection Methods in Fluorescence Microscopy, IEEE Transactions on Medical Imaging, vol.29, issue.2, 2009.
DOI : 10.1109/TMI.2009.2025127

I. Smal, E. Meijering, K. Draegestein, N. Galjart, I. Grigoriev et al., Multiple object tracking in molecular bioimaging by Rao-Blackwellized marginal particle filtering, Medical Image Analysis, vol.12, issue.6, pp.764-777, 2008.
DOI : 10.1016/j.media.2008.03.004

M. Smith, The existence, uniqueness and stability of traffic equilibria, Transportation Research Part B: Methodological, vol.13, issue.4, pp.295-304, 1979.
DOI : 10.1016/0191-2615(79)90022-5

P. Smith and . Buechler, A branching algorithm for discriminating and tracking multiple objects, IEEE Transactions on Automatic Control, vol.20, issue.1, pp.101-104, 1975.
DOI : 10.1109/TAC.1975.1100851

F. Snickars and J. Weibull, A minimum information principle, Regional Science and Urban Economics, vol.7, issue.1-2, pp.137-168, 1977.
DOI : 10.1016/0166-0462(77)90021-7

A. Soule, A. Nucci, R. Cruz, E. Leonardi, and N. Taft, How to identify and estimate the largest traffic matrix elements in a dynamic environment, ACM SIGMETRICS Performance Evaluation Review, vol.32, issue.1, pp.73-84, 2004.
DOI : 10.1145/1012888.1005698

H. Spiess, A maximum likelihood model for estimating origin-destination matrices, Transportation Research Part B: Methodological, vol.21, issue.5, pp.395-412, 1987.
DOI : 10.1016/0191-2615(87)90037-3

J. Starck, J. Fadili, and F. Murtagh, The Undecimated Wavelet Decomposition and its Reconstruction, IEEE Transactions on Image Processing, vol.16, issue.2, pp.297-309, 2007.
DOI : 10.1109/TIP.2006.887733
URL : https://hal.archives-ouvertes.fr/hal-00080092

C. Steger, An unbiased detector of curvilinear structures, IEEE Transactions on Pattern Analysis and Machine Intelligence, vol.20, issue.2, 1996.
DOI : 10.1109/34.659930

S. Sternberg, Biomedical Image Processing, Computer, vol.16, issue.1, pp.22-34, 1983.
DOI : 10.1109/MC.1983.1654163

C. Tebaldi and M. West, Bayesian inference on network traffic using link count data, Journal of the American Statistical Association, vol.93, issue.442, 1998.

M. Thery, V. Racine, A. Pepin, A. Dimitrov, Y. Chen et al., Anisotropy of cell adhesive microenvironment governs cell internal organization and orientation of polarity, in 'Proceeding of National Academy of Science USA, pp.19771-19776, 2006.

M. Thery, V. Racine, A. Pepin, M. Piel, Y. Chen et al., The extracellular matrix guides the orientation of the cell division axis, Nature Cell Biology, vol.124, issue.10, pp.947-953, 2005.
DOI : 10.1007/s00249-003-0282-2

D. Thomann, J. Dorn, P. Sorger, and G. Danuser, Automatic fluorescent tag localization II: improvement in super-resolution by relative tracking, Journal of Microscopy, vol.208, issue.3, pp.230-248, 2003.
DOI : 10.1046/j.1365-2818.2003.01223.x

D. Thomann, D. Rines, P. Sorger, and G. Danuser, Automatic fluorescent tag detection in 3D with super-resolution: application to the analysis of chromosome movement, Journal of Microscopy, vol.208, issue.1, 2002.
DOI : 10.1046/j.1365-2818.2002.01066.x

A. Tsai, W. Wells, S. Warfield, and A. Willsky, An EM algorithm for shape classification based on level sets, Medical Image Analysis, vol.9, issue.5, pp.491-502, 2005.
DOI : 10.1016/j.media.2005.05.001

R. Tsien, THE GREEN FLUORESCENT PROTEIN, Annual Review of Biochemistry, vol.67, issue.1, pp.509-544, 1998.
DOI : 10.1146/annurev.biochem.67.1.509

H. Van-zuylen and L. Willumsen, The most likely trip matrix estimated from traffic counts', Transportation research 14, pp.281-293, 1980.

Y. Vardi, Network tomography I : Estimating source-destination traffic intensities from link datas -fixed routing, 1994.

Y. Vardi, Network Tomography: Estimating Source-Destination Traffic Intensities from Link Data, Journal of the American Statistical Association, vol.55, issue.8, pp.365-377, 1996.
DOI : 10.1080/01621459.1985.10477119

S. Vaton, J. Bedo, and A. Gravey, Performance Evaluation and Planning Methods for the Next Generation Internet, Springer, chapter Advanced Methods for the Estimation of the Origin Destination traffic matrix, 2005.

L. Vincent, Morphological grayscale reconstruction in image analysis: applications and efficient algorithms, IEEE Transactions on Image Processing, vol.2, issue.2, pp.176-201, 1993.
DOI : 10.1109/83.217222

P. Viola and M. Jones, Rapid object detection using a boosted cascade of simple features, Proceedings of the 2001 IEEE Computer Society Conference on Computer Vision and Pattern Recognition. CVPR 2001, pp.511-518, 2001.
DOI : 10.1109/CVPR.2001.990517

Y. Wang and S. Zhu, A Generative Method for Textured Motion: Analysis and Synthesis, Proceding of European Conference on Computer Vision, 2002.
DOI : 10.1007/3-540-47969-4_39

Y. Wang and S. Zhu, Modeling textured motion : Particle, wave and sketch, in 'Internationa Conference on Computer Vision, 2003.

J. Wardrop, Some theoretical aspects of road traffic research, in 'Proceedings Institute of Civil Engineers, pp.325-378, 1952.

Q. Wen, J. Gao, A. Kosaka, H. Iwaki, K. Luby-phelps et al., A particle filter framework using optimal importance function for protein molecules tracking, IEEE International Conference on Image Processing 2005, pp.1161-1164, 2005.
DOI : 10.1109/ICIP.2005.1529962

J. White, L. Johannes, F. Mallar, A. Girod, G. Stephan et al., Rab6 Coordinates a Novel Golgi to ER Retrograde Transport Pathway in Live Cells, The Journal of Cell Biology, vol.112, issue.4, pp.743-760, 1999.
DOI : 10.1083/jcb.143.6.1505

J. White and E. Stelzer, Photobleaching GFP reveals protein dynamics inside live cells, Trends in Cell Biology, vol.9, issue.2, pp.61-65, 1999.
DOI : 10.1016/S0962-8924(98)01433-0

S. Wilson, Statistical notes on the evaluation of calibrated gravity models, Transportation Research, vol.10, issue.5, pp.343-345, 1976.
DOI : 10.1016/0041-1647(76)90114-3

J. Wolf, W. Burgard, and H. Burkhardt, Robust vision-based localization by combining an image-retrieval system with Monte Carlo localization, IEEE Transactions on Robotics, vol.21, issue.2, pp.208-216, 2005.
DOI : 10.1109/TRO.2004.835453

S. S. Work and D. M. Warshaw, Computer-assisted tracking of actin filament motility, Analytical Biochemistry, vol.202, issue.2, pp.275-285, 1992.
DOI : 10.1016/0003-2697(92)90106-H

W. Wright, A Markov random field approach to data fusion and colour segmentation, Image and Vision Computing, vol.7, issue.2, pp.144-150, 1989.
DOI : 10.1016/0262-8856(89)90009-7

Y. Wu, J. Lin, and T. Huang, Analysing and capturing articulated hand motion in image sequences, IEEE Transactions on Pattern Analysis and Machine Intelligence, vol.27, issue.12, pp.1910-1922, 2005.

H. Yang, T. Sasaki, Y. Iida, and Y. Asakura, Estimation of origin-destination matrices from link traffic counts on congested networks, Transportation Research Part B: Methodological, vol.26, issue.6, pp.417-434, 1992.
DOI : 10.1016/0191-2615(92)90008-K

J. Yao and J. Odobez, Fast human detection from videos using covariance features, European Conference on Computer Vision Visual Surveillance workshop, 2008.
URL : https://hal.archives-ouvertes.fr/inria-00325628

J. Yen, Shortest Loopless Paths in a Network, Management Science, vol.17, issue.11, pp.712-716, 1971.
DOI : 10.1287/mnsc.17.11.712

L. Younes, Calibrating Parameters of Cost Functionals, European Conference on Computer Vision, pp.212-223, 2000.
DOI : 10.1007/3-540-45053-X_14

M. Zerial and H. Mcbride, Rab proteins as membrane organizers', Nature Rev, Molecular Cell Biology, vol.2, issue.2, pp.107-117, 2001.

Y. Zhang, M. Roughan, C. Lund, and D. Donoho, An information-theoric approach to traffic matrix estimation, 'ACM SIGCOMM'03, pp.301-312, 2003.

S. Zhu, Y. Wu, and D. Mumford, Frame : Filters, Random fields, and Minimax Entropy ? towards a unified theory for texture modeling, International Journal of Computer Vision, vol.27, issue.2, pp.1-20, 1998.