E. Meijering, I. Smal, and G. Danuser, Tracking in molecular bioimaging, IEEE Signal Processing Magazine, vol.23, issue.3, pp.46-53, 2006.
DOI : 10.1109/MSP.2006.1628877

URL : http://www.imagescience.org/meijering/publications/download/spm2006.pdf

N. Chenouard, A. Dufour, and J. C. Olivo-marin, Tracking algorithms chase down pathogens, Biotechnology Journal, vol.211, issue.6, pp.838-845, 2009.
DOI : 10.1046/j.1365-2818.2003.01223.x

URL : https://hal.archives-ouvertes.fr/hal-00494028

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

J. Shorte, K. Willemse, G. P. Celler, H. W. Van-wezel, Y. S. Dan et al., Objective comparison of particle tracking methods, Nat. Methods, vol.11, issue.3, pp.281-289, 2014.
URL : https://hal.archives-ouvertes.fr/hal-00932869

J. I. Murray, Z. Bao, T. J. Boyle, and R. H. Waterston, The lineaging of fluorescently-labeled Caenorhabditis elegans embryos with StarryNite and AceTree, Nature Protocols, vol.122, issue.3, pp.1468-1476, 2006.
DOI : 10.1038/nprot.2006.222

D. Sage, F. R. Neumann, F. Hediger, S. M. 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

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

URL : http://europepmc.org/articles/pmc2747604?pdf=render

F. De-chaumont, S. Dallongeville, N. Chenouard, N. Herve, S. Pop et al., Icy: an open bioimage informatics platform for extended reproducible research, Nature Methods, vol.9, issue.7, pp.690-696, 2012.
DOI : 10.1038/nmeth.1924

N. Chenouard, I. Bloch, and J. C. 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

J. C. Crocker and D. G. Grier, Methods of Digital Video Microscopy for Colloidal Studies, Journal of Colloid and Interface Science, vol.179, issue.1, pp.298-310, 1996.
DOI : 10.1006/jcis.1996.0217

A. Serge, N. Bertaux, H. Rigneault, and D. Marguet, Dynamic multiple-target tracing to probe spatiotemporal cartography of cell membranes, Nature Methods, vol.84, issue.8, pp.687-694, 2008.
DOI : 10.1038/nmeth.1176

URL : https://hal.archives-ouvertes.fr/hal-00295014

I. F. 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

F. P. Cordelières, V. Petit, M. Kumasaka, O. Debeir, V. Letort et al., Automated Cell Tracking and Analysis in Phase-Contrast Videos (iTrack4U): Development of Java Software Based on Combined Mean-Shift Processes, PLoS ONE, vol.74, issue.11, p.81266, 2013.
DOI : 10.1371/journal.pone.0081266.s004

J. Schindelin, I. Arganda-carreras, E. Frise, V. Kaynig, M. Longair et al., Fiji: an open-source platform for biological-image analysis, Nature Methods, vol.27, issue.7, pp.676-682, 2012.
DOI : 10.1093/bioinformatics/btr390

URL : http://europepmc.org/articles/pmc3855844?pdf=render

A. E. Carpenter, L. Kamentsky, and K. W. Eliceiri, A call for bioimaging software usability, Nature Methods, vol.9, issue.7, pp.666-670, 2012.
DOI : 10.1038/nmeth.2083

URL : http://europepmc.org/articles/pmc3641581?pdf=render

B. Schmid, J. Schindelin, A. Cardona, M. Longair, and M. Heisenberg, A high-level 3D visualization API for Java and ImageJ, BMC Bioinformatics, vol.11, issue.1, p.11, 2010.
DOI : 10.1186/1471-2105-11-274

URL : https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/1471-2105-11-274?site=bmcbioinformatics.biomedcentral.com

R. E. Kalman, A New Approach to Linear Filtering and Prediction Problems, Journal of Basic Engineering, vol.82, issue.1, pp.35-45, 1960.
DOI : 10.1115/1.3662552

URL : http://fluidsengineering.asmedigitalcollection.asme.org/data/journals/jfega4/27220/35_1.pdf

J. Schindelin, C. T. Rueden, M. C. Hiner, and K. W. Eliceiri, The ImageJ ecosystem: An open platform for biomedical image analysis, Molecular Reproduction and Development, vol.15, issue.7-8, pp.7-8
DOI : 10.1038/nmeth.2089

URL : http://onlinelibrary.wiley.com/doi/10.1002/mrd.22489/pdf

J. Y. Tinevez, J. Dragavon, L. Baba-aissa, P. Roux, E. Perret et al., A Quantitative Method for Measuring Phototoxicity of a Live Cell Imaging Microscope, Methods Enzymol, vol.506, pp.291-309, 2012.
DOI : 10.1016/B978-0-12-391856-7.00039-1

URL : https://hal.archives-ouvertes.fr/hal-01543608

N. Tarantino, J. Y. Tinevez, E. F. Crowell, B. Boisson, R. Henriques et al., TNF and IL-1 exhibit distinct ubiquitin requirements for inducing NEMO???IKK supramolecular structures, The Journal of Cell Biology, vol.19, issue.2, pp.231-245, 2014.
DOI : 10.1016/S1074-7613(00)80183-1

URL : https://hal.archives-ouvertes.fr/pasteur-01539965

C. A. Konopka, S. K. Backues, and S. Y. Bednarek, Dynamics of Arabidopsis Dynamin-Related Protein 1C and a Clathrin Light Chain at the Plasma Membrane, THE PLANT CELL ONLINE, vol.20, issue.5, pp.1363-1380, 2008.
DOI : 10.1105/tpc.108.059428

URL : http://www.plantcell.org/content/plantcell/20/5/1363.full.pdf

C. A. Konopka and S. Y. Bednarek, Variable-angle epifluorescence microscopy: a new way to look at protein dynamics in the plant cell cortex, The Plant Journal, vol.218, issue.1, pp.186-196, 2008.
DOI : 10.1111/j.1365-313X.2007.03306.x

URL : http://onlinelibrary.wiley.com/doi/10.1111/j.1365-313X.2007.03306.x/pdf

Z. Bao, Z. Zhao, T. J. Boyle, J. I. Murray, and R. H. Waterston, Control of cell cycle timing during C. elegans embryogenesis, Developmental Biology, vol.318, issue.1, pp.65-72, 2008.
DOI : 10.1016/j.ydbio.2008.02.054

URL : https://doi.org/10.1016/j.ydbio.2008.02.054

V. Praitis, E. Casey, D. Collar, and J. Austin, Creation of low-copy integrated transgenic lines in Caenorhabditis elegans, Genetics, vol.157, issue.3, pp.1217-1226, 2001.

Z. Bao, J. I. Murray, T. Boyle, S. L. Ooi, M. J. Sandel et al., Automated cell lineage tracing in Caenorhabditis elegans, Proceedings of the National Academy of Sciences, vol.22, issue.12, pp.2707-2712, 2006.
DOI : 10.1038/nbt1037

URL : http://www.pnas.org/content/103/8/2707.full.pdf

S. G. Megason, In Toto Imaging of Embryogenesis with Confocal Time-Lapse Microscopy, Methods Mol. Biol, vol.546, pp.317-332, 2009.
DOI : 10.1007/978-1-60327-977-2_19

URL : http://europepmc.org/articles/pmc2826616?pdf=render

R. Schnabel, H. Hutter, D. Moerman, and H. Schnabel, Assessing Normal Embryogenesis inCaenorhabditis elegansUsing a 4D Microscope: Variability of Development and Regional Specification, Developmental Biology, vol.184, issue.2, pp.234-265, 1997.
DOI : 10.1006/dbio.1997.8509

URL : https://doi.org/10.1006/dbio.1997.8509

J. E. Sulston and H. R. Horvitz, Post-embryonic cell lineages of the nematode, Caenorhabditis elegans, Developmental Biology, vol.56, issue.1, pp.110-156, 1977.
DOI : 10.1016/0012-1606(77)90158-0

J. Caron, C. Fallet, J. Y. Tinevez, L. Moisan, L. P. Braitbart et al., Conical diffraction illumination opens the way for low phototoxicity super-resolution imaging, Cell Adhesion & Migration, vol.112, issue.5, pp.430-439, 2014.
DOI : 10.1038/nmeth.2019

URL : https://hal.archives-ouvertes.fr/hal-01386722

E. T. Kipreos and C. , C. elegans cell cycles: invariance and stem cell divisions, Nature Reviews Molecular Cell Biology, vol.268, issue.10, pp.766-776, 2005.
DOI : 10.1016/j.ydbio.2003.12.023

M. S. Hayden and S. Ghosh, NF-??B, the first quarter-century: remarkable progress and outstanding questions, Genes & Development, vol.26, issue.3, pp.203-234, 2012.
DOI : 10.1101/gad.183434.111

URL : http://genesdev.cshlp.org/content/26/3/203.full.pdf

H. Qian, M. P. Sheetz, and E. L. Elson, Single particle tracking. Analysis of diffusion and flow in two-dimensional systems, Biophysical Journal, vol.60, issue.4, pp.910-921, 1991.
DOI : 10.1016/S0006-3495(91)82125-7

X. Chen, N. G. Irani, and J. , Clathrin-mediated endocytosis: the gateway into plant cells, Current Opinion in Plant Biology, vol.14, issue.6, pp.674-682, 2011.
DOI : 10.1016/j.pbi.2011.08.006

G. A. Baisa, J. R. Mayers, and S. Y. Bednarek, Budding and braking news about clathrin-mediated endocytosis, Current Opinion in Plant Biology, vol.16, issue.6, pp.718-725, 2013.
DOI : 10.1016/j.pbi.2013.09.005

Y. Zhang, S. Persson, J. Hirst, M. S. Robinson, D. Van-damme et al., Change your Tplate, change your fate: plant CME and beyond, Trends in Plant Science, vol.20, issue.1, pp.41-48, 2015.
DOI : 10.1016/j.tplants.2014.09.002

T. Kirchhausen, Imaging endocytic clathrin structures in living cells, Trends in Cell Biology, vol.19, issue.11, pp.596-605, 2009.
DOI : 10.1016/j.tcb.2009.09.002

URL : http://europepmc.org/articles/pmc2796618?pdf=render

G. Vizcay-barrena, S. E. Webb, M. L. Martin-fernandez, and Z. A. Wilson, Subcellular and single-molecule imaging of plant fluorescent proteins using total internal reflection fluorescence microscopy (TIRFM), Journal of Experimental Botany, vol.22, issue.15, pp.62-5419, 2011.
DOI : 10.1105/tpc.110.076257

URL : https://academic.oup.com/jxb/article-pdf/62/15/5419/16928968/err212.pdf

L. Bashline, S. Li, C. T. Anderson, L. Lei, and Y. Gu, The Endocytosis of Cellulose Synthase in Arabidopsis Is Dependent on ??2, a Clathrin-Mediated Endocytosis Adaptin, PLANT PHYSIOLOGY, vol.163, issue.1, pp.150-160, 2013.
DOI : 10.1104/pp.113.221234

A. Gadeyne, C. Sánchez-rodríguez, S. Vanneste, S. Di-rubbo, H. Zauber et al., The TPLATE Adaptor Complex Drives Clathrin-Mediated Endocytosis in Plants, Cell, vol.156, issue.4, pp.691-704, 2014.
DOI : 10.1016/j.cell.2014.01.039

URL : https://doi.org/10.1016/j.cell.2014.01.039

M. E. Tanenbaum, L. A. Gilbert, L. S. Qi, J. S. Weissman, and R. D. Vale, A Protein-Tagging System for Signal Amplification in Gene Expression and Fluorescence Imaging, Cell, vol.159, issue.3, pp.635-646, 2014.
DOI : 10.1016/j.cell.2014.09.039

URL : https://doi.org/10.1016/j.cell.2014.09.039

M. F. Mossuto, S. Sannino, D. Mazza, C. Fagioli, M. Vitale et al., A Dynamic Study of Protein Secretion and Aggregation in the Secretory Pathway, PLoS ONE, vol.9, issue.10, p.108496, 2014.
DOI : 10.1371/journal.pone.0108496.s001

A. Reversat, M. I. Yuseff, D. Lankar, O. Malbec, D. Obino et al., Polarity protein Par3 controls B-cell receptor dynamics and antigen extraction at the immune synapse, Molecular Biology of the Cell, vol.35, issue.7, pp.1273-1285, 2015.
DOI : 10.1016/j.immuni.2011.07.008

URL : http://www.molbiolcell.org/content/26/7/1273.full.pdf

S. Gluska, M. Chein, N. Rotem, A. Ionescu, and E. Perlson, Tracking Quantum-Dot labeled neurotropic factors transport along primary neuronal axons in compartmental microfluidic chambers, Methods Cell Biol, vol.131, pp.365-387, 2016.
DOI : 10.1016/bs.mcb.2015.06.016

P. Denninger, A. Bleckmann, A. Lausser, F. Vogler, T. Ott et al., Male???female communication triggers calcium signatures during fertilization in Arabidopsis, Nature Communications, vol.11, issue.1, p.4645, 2014.
DOI : 10.1111/j.1399-3054.1962.tb08052.x

URL : http://www.nature.com/articles/ncomms5645.pdf

B. Sporsheim, A. Øverby, and A. M. Bones, Allyl Isothiocyanate Inhibits Actin-Dependent Intracellular Transport in Arabidopsis thaliana, International Journal of Molecular Sciences, vol.109, issue.12, pp.29134-29147, 2015.
DOI : 10.1038/nmeth.2019

M. S. Minns, G. Teicher, C. B. Rich, and V. Trinkaus-randall, Purinoreceptor P2X7 Regulation of Ca2+ Mobilization and Cytoskeletal Rearrangement Is Required for Corneal Reepithelialization after Injury, The American Journal of Pathology, vol.186, issue.2, pp.285-296, 2016.
DOI : 10.1016/j.ajpath.2015.10.006

URL : http://europepmc.org/articles/pmc4729273?pdf=render

S. C. Chew, S. A. Rice, S. Kjelleberg, and L. Yang, <em>In Situ</em> Mapping of the Mechanical Properties of Biofilms by Particle-tracking Microrheology, Journal of Visualized Experiments, vol.106, issue.106, p.53093, 2015.
DOI : 10.3791/53093

K. A. Mosiewicz, L. Kolb, A. J. Van-der-vlies, and M. P. Lutolf, Microscale patterning of hydrogel stiffness through light-triggered uncaging of thiols, Biomater. Sci., vol.99, issue.Pt 2, pp.1640-1651, 2014.
DOI : 10.1016/j.bpj.2009.06.021

A. Pauli, M. L. Norris, E. Valen, G. L. Chew, J. A. Gagnon et al., Toddler: An Embryonic Signal That Promotes Cell Movement via Apelin Receptors, Science, vol.5, issue.8, pp.6172-2014
DOI : 10.1038/nmeth.1237

URL : http://europepmc.org/articles/pmc4107353?pdf=render

K. Campbell and J. Casanova, A role for E-cadherin in ensuring cohesive migration of a heterogeneous population of non-epithelial cells, Nature Communications, vol.122, issue.1, p.7998, 2015.
DOI : 10.1038/pr.2013.201

B. Spiesschaert, B. Goldenbogen, S. Taferner, M. Schade, M. Mahmoud et al., ABSTRACT, Journal of Virology, vol.89, issue.23, pp.89-11899, 2015.
DOI : 10.1128/JVI.01809-15

P. Schattling, B. Thingholm, and B. Städler, Enhanced Diffusion of Glucose-Fueled Janus Particles, Chemistry of Materials, vol.27, issue.21, pp.7412-7418, 2015.
DOI : 10.1021/acs.chemmater.5b03303

A. H. Chen, A. Robinson-mosher, D. F. Savage, P. A. Silver, and J. K. Polka, The Bacterial Carbon-Fixing Organelle Is Formed by Shell Envelopment of Preassembled Cargo, PLoS ONE, vol.9, issue.9, p.76127, 2013.
DOI : 10.1371/journal.pone.0076127.s008

URL : https://doi.org/10.1371/journal.pone.0076127

R. Müller, O. Stranik, F. Schlenk, S. Werner, D. Malsch et al., Optical detection of nanoparticle agglomeration in a living system under the influence of a magnetic field, Journal of Magnetism and Magnetic Materials, vol.380, pp.380-61, 2015.
DOI : 10.1016/j.jmmm.2014.10.043

K. G. Bondoc, J. Heuschele, J. Gillard, W. Vyverman, and G. Pohnert, Selective silicate-directed motility in diatoms, Nature Communications, vol.92, p.10540, 2016.
DOI : 10.1016/j.ejop.2003.09.001

URL : http://www.nature.com/articles/ncomms10540.pdf

C. Noble, N. Smulders, N. H. Green, R. Lewis, M. J. Carré et al., Creating a model of diseased artery damage and failure from healthy porcine aorta, Journal of the Mechanical Behavior of Biomedical Materials, vol.60, pp.60-378, 2016.
DOI : 10.1016/j.jmbbm.2016.02.018

URL : http://eprints.whiterose.ac.uk/96999/7/Creating%20a%20model%20of%20diseased%20artery%20damage%20and%20failure%20from%20healthy%20porcine%20aorta.pdf

M. Linkert, C. T. Rueden, C. Allan, J. M. Burel, W. Moore et al., Metadata matters: access to image data in the real world, The Journal of Cell Biology, vol.189, issue.5, pp.777-782, 2010.
DOI : 10.1083/jcb.201004104.dv

URL : http://europepmc.org/articles/pmc2878938?pdf=render

T. Pietzsch, S. Preibisch, P. Tomancak, and S. Saalfeld, ImgLib2???generic image processing in Java, ImgLib2 ? generic image processing in Java, pp.3009-3011, 2012.
DOI : 10.1038/nmeth.2019

URL : https://academic.oup.com/bioinformatics/article-pdf/29/2/298/530471/bts685.pdf

C. Dietz and M. R. Berthold, KNIME for Open-Source Bioimage Analysis: A Tutorial, Adv. Anat. Embryol. Cell Biol, vol.8, issue.6, pp.179-197, 2016.
DOI : 10.1109/TSMC.1978.4309999

N. Scherf and J. Huisken, The smart and gentle microscope, Nature Biotechnology, vol.4, issue.8, pp.815-818, 2015.
DOI : 10.1038/nmeth.1175