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, p.13190, 2010.
DOI : 10.1371/journal.pone.0013190.s006
URL : https://hal.archives-ouvertes.fr/inria-00541072

A. Gidon, S. Bardin, J. Boulanger, F. Waharte, B. Cinquin et al., A Rab11A/Myosin Vb/Rab11-FIP2 Complex Frames Two Late Recycling Steps of Langerin from the ERC to the Plasma Membrane, Traffic, vol.3, issue.6, pp.815-833, 2012.
DOI : 10.1111/j.1600-0854.2012.01354.x
URL : https://hal.archives-ouvertes.fr/hal-00782005

T. Pécot, P. Bouthemy, J. Boulanger, A. Chessel, S. Bardin et al., Background Fluorescence Estimation and Vesicle Segmentation in Live Cell Imaging With Conditional Random Fields, IEEE Transactions on Image Processing, vol.24, issue.2, pp.667-680, 2015.
DOI : 10.1109/TIP.2014.2380178

T. Pécot, J. Boulanger, C. Kervrann, P. Bouthemy, and J. Salamero, Estimation of the flow of particles within a partition of the image domain in fluorescence video-microscopy, 2014 IEEE 11th International Symposium on Biomedical Imaging (ISBI), pp.453-456, 2014.
DOI : 10.1109/ISBI.2014.6867906

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

J. 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

T. Pécot, C. Kervrann, and P. Bouthemy, Minimal paths and probabilistic models for origin-destination traffic estimation in live cell imaging, 2008 5th IEEE International Symposium on Biomedical Imaging: From Nano to Macro, pp.843-846, 2008.
DOI : 10.1109/ISBI.2008.4541128

S. Mukherjee, N. Ray, and S. T. Acton, Counting cells from microscopy videos without tracking individual cells, 2014 IEEE 11th International Symposium on Biomedical Imaging (ISBI), pp.465-468, 2014.
DOI : 10.1109/ISBI.2014.6867909

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, pp.282-301, 2010.
DOI : 10.1109/TMI.2009.2025127

Y. Kalaidzidis, Intracellular objects tracking, European Journal of Cell Biology, vol.86, issue.9, pp.569-578, 2007.
DOI : 10.1016/j.ejcb.2007.05.005

M. F. Kircher, S. S. Gambhir, and J. Grimm, Noninvasive cell-tracking methods, Nature Reviews Clinical Oncology, vol.6, issue.2, pp.677-688, 2011.
DOI : 10.1038/nrclinonc.2011.141

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

G. Yang, A. Matov, and G. Danuser, Reliable tracking of large scale dense antiparallel particle motion for fluorescence live cell imaging, Proc. Comp. Vision Patt. Recog.-Workshops (CVPR), pp.138-138, 2005.

W. J. Godinez and K. Rohr, Tracking Multiple Particles in Fluorescence Time-Lapse Microscopy Images via Probabilistic Data Association, IEEE Transactions on Medical Imaging, vol.34, issue.2, pp.415-432, 2015.
DOI : 10.1109/TMI.2014.2359541

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

D. Delibaltov, S. Karthikeyan, V. Jagadeesh, and B. Manjunath, Robust biological image sequence analysis using graph based approaches, 2012 Conference Record of the Forty Sixth Asilomar Conference on Signals, Systems and Computers (ASILOMAR), pp.1588-1592
DOI : 10.1109/ACSSC.2012.6489297

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

N. Chenouard, I. Bloch, and J. Olivo-marin, Multiple Hypothesis Tracking for Cluttered Biological Image Sequences, IEEE Transactions on Pattern Analysis and Machine Intelligence, vol.35, issue.11, pp.2736-2750, 2013.
DOI : 10.1109/TPAMI.2013.97

L. Liang, H. Shen, P. D. Camilli, and J. S. Duncan, A Novel Multiple Hypothesis Based Particle Tracking Method for Clathrin Mediated Endocytosis Analysis Using Fluorescence Microscopy, IEEE Transactions on Image Processing, vol.23, issue.4, pp.1844-1857, 2014.
DOI : 10.1109/TIP.2014.2303633

J. Berclaz, F. Fleuret, E. Turetken, and P. Fua, Multiple Object Tracking Using K-Shortest Paths Optimization, IEEE Transactions on Pattern Analysis and Machine Intelligence, vol.33, issue.9, pp.1806-1819, 2011.
DOI : 10.1109/TPAMI.2011.21

L. Ji and G. Danuser, Tracking quasi-stationary flow of weak fluorescent signals by adaptive multi-frame correlation, Journal of Microscopy, vol.9, issue.3, pp.150-167, 2005.
DOI : 10.1109/TPAMI.2003.1251156

K. Rohr, W. J. Godinez, N. Harder, S. Worz, J. Mattes et al., Tracking and Quantitative Analysis of Dynamic Movements of Cells and Particles, Cold Spring Harbor Protocols, vol.2010, issue.6, 2010.
DOI : 10.1101/pdb.top80

D. L. Kolin and P. W. Wiseman, Advances in Image Correlation Spectroscopy: Measuring Number Densities, Aggregation States, and Dynamics of Fluorescently labeled Macromolecules in Cells, Cell Biochemistry and Biophysics, vol.99, issue.Pt 2, pp.141-164, 2007.
DOI : 10.1007/s12013-007-9000-5

B. D. Lucas and T. Kanade, An Iterative Image Registration Technique with an Application to Stereo Vision, Proc. Int. Joint Conf. Artificial Intell, pp.674-679, 1981.

I. H. Kim, Y. C. Chen, D. L. Spector, R. Eils, and K. Rohr, Nonrigid Registration of 2-D and 3-D Dynamic Cell Nuclei Images for Improved Classification of Subcellular Particle Motion, IEEE Transactions on Image Processing, vol.20, issue.4, pp.1011-1022, 2011.
DOI : 10.1109/TIP.2010.2076377

M. Pinot, V. Steiner, B. Dehapiot, B. K. Yoo, F. Chesnel et al., Confinement induces actin flow in a meiotic cytoplasm, Proceedings of the National Academy of Sciences, vol.109, issue.29, pp.11-705, 2012.
DOI : 10.1073/pnas.1121583109
URL : https://hal.archives-ouvertes.fr/inserm-00717415

L. Pizarro, J. Delpiano, P. Aljabar, J. Ruiz-del-solar, and D. Rueckert, Towards dense motion estimation in light and electron microscopy, 2011 IEEE International Symposium on Biomedical Imaging: From Nano to Macro, pp.1939-1942, 2011.
DOI : 10.1109/ISBI.2011.5872789

J. Delpiano, J. Jara, J. Scheer, O. A. Ramírez, J. Ruiz-del-solar et al., Performance of optical flow techniques for motion analysis of fluorescent point signals in confocal microscopy, Machine Vision and Applications, vol.30, issue.12, pp.675-689, 2012.
DOI : 10.1007/s00138-011-0362-8

T. Lecomte, R. Thibeaux, N. Guillen, A. C. Dufour, and J. Olivo-marin, Fluid optical flow for forces and pressure field estimation in cellular biology, 2012 19th IEEE International Conference on Image Processing, pp.69-72
DOI : 10.1109/ICIP.2012.6466797

R. J. Adrian, Particle-Imaging Techniques for Experimental Fluid Mechanics, Annual Review of Fluid Mechanics, vol.23, issue.1, pp.261-304, 1991.
DOI : 10.1146/annurev.fl.23.010191.001401

T. Corpetti, E. Memin, and P. Perez, Dense estimation of fluid flows, IEEE Transactions on Pattern Analysis and Machine Intelligence, vol.24, issue.3, pp.365-380, 2002.
DOI : 10.1109/34.990137
URL : https://hal.archives-ouvertes.fr/hal-00329724

J. M. Fitzpatrick, The existence of geometrical density-image transformations corresponding to object motion, Computer Vision, Graphics, and Image Processing, vol.44, issue.2, pp.155-174, 1988.
DOI : 10.1016/S0734-189X(88)80003-3

S. Ozeré, P. Bouthemy, F. Spindler, P. Paul-gilloteaux, and C. Kervrann, Robust parametric stabilization of moving cells with intensity correction in light microscopy image sequences, 2013 IEEE 10th International Symposium on Biomedical Imaging, pp.468-471, 2013.
DOI : 10.1109/ISBI.2013.6556513

R. Tibshirani, Regression Shrinkage and Selection via the Lasso, J. Royal Stat. Soc, vol.58, issue.1, pp.267-288, 1996.

D. Gabay and B. Mercier, A dual algorithm for the solution of nonlinear variational problems via finite element approximation, Computers & Mathematics with Applications, vol.2, issue.1, pp.17-40, 1976.
DOI : 10.1016/0898-1221(76)90003-1

S. Boyd, N. Parikh, E. Chu, B. Peleato, and J. Eckstein, Distributed Optimization and Statistical Learning via the Alternating Direction Method of Multipliers, Foundations and Trends?? in Machine Learning, vol.3, issue.1, pp.1-122, 2011.
DOI : 10.1561/2200000016

P. L. Combettes and J. Pesquet, Fixed-Point Algorithms for Inverse Problems in Science and Engineering Proximal splitting methods in signal processing, pp.185-212

J. Douglas and H. H. Rachford, On the numerical solution of heat conduction problems in two and three space variables, Transactions of the American Mathematical Society, vol.82, issue.2, pp.421-439, 1956.
DOI : 10.1090/S0002-9947-1956-0084194-4

A. Beck and M. Teboulle, A Fast Iterative Shrinkage-Thresholding Algorithm for Linear Inverse Problems, SIAM Journal on Imaging Sciences, vol.2, issue.1, pp.183-202, 2009.
DOI : 10.1137/080716542

N. Chenouard, Objective comparison of particle tracking methods, Nature Methods, vol.6362, issue.3, pp.281-289, 2014.
DOI : 10.1038/nmeth.2019
URL : https://hal.archives-ouvertes.fr/hal-00932869

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

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

K. Schauer, T. Duong, K. Bleakley, S. Bardin, M. Bornens et al., Probabilistic density maps to study global endomembrane organization, Nature Methods, vol.17, issue.7, pp.560-566, 2010.
DOI : 10.1038/nmeth.1462

J. Boulanger, C. Kervrann, P. Bouthemy, P. Elbau, J. Sibarita et al., Patch-Based Nonlocal Functional for Denoising Fluorescence Microscopy Image Sequences, IEEE Transactions on Medical Imaging, vol.29, issue.2, pp.442-454, 2010.
DOI : 10.1109/TMI.2009.2033991
URL : https://hal.archives-ouvertes.fr/inria-00541082

K. Schauer, T. Duong, C. Gomes-santos, and B. Goud, Studying Intracellular Trafficking Pathways with Probabilistic Density Maps, Meth. Cell Biol, vol.118, pp.325-343, 2013.
DOI : 10.1016/B978-0-12-417164-0.00020-3

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, J. Microsc, pp.214-228, 2007.

B. K. Horn and B. G. Schunck, Determining optical flow, Artificial Intelligence, vol.17, issue.1-3, pp.185-203, 1981.
DOI : 10.1016/0004-3702(81)90024-2

R. Achanta, K. Shaji, A. Smith, P. Lucchi, S. Fua et al., SLIC Superpixels Compared to State-of-the-Art Superpixel Methods, IEEE Transactions on Pattern Analysis and Machine Intelligence, vol.34, issue.11, pp.2274-2282, 2012.
DOI : 10.1109/TPAMI.2012.120