A simulation and estimation framework for intracellular dynamics and trafficking in video-microscopy and fluorescence imagery

Allende, 2006, M-estimator with asymmetric influence function: the Ga0 distribution case, Journal of Statistical Computation and Simulation, 76, 941, 10.1080/10629360600569154 Anderson, 1992, Tracking of cell surface receptors by fluorescence digital imaging microscopy using a charged-coupled device camera. Low-density lipoprotein and influenza virus receptor mobility at 4°C, Journal of Cell Science, 101, 415, 10.1242/jcs.101.2.415 Barron, 1994, Performance of optical flow techniques, International Journal of Computer Vision, 12, 43, 10.1007/BF01420984 Birgé, 2001, Gaussian model selection, Journal of European Mathematical Society, 3, 203, 10.1007/s100970100031 Black, 1998, Robust anisotropic diffusion, IEEE Transactions on Image Processing, 7, 421, 10.1109/83.661192 Bonneau, S., Dahan, M., Cohen, L.D., 2005. Tracking single quantum dots in live cells with minimal paths. In: Proceedings of the IEEE Conference on Computer Vision and Pattern Recognition, CVPR’2005, vol. 3, San Diego, CA, pp. 141–149. Boulanger, 2007, Space–time adaptation for patch-based image sequence restoration, IEEE Transactions on Pattern Analysis and Machine Intelligence, 29, 1096, 10.1109/TPAMI.2007.1064 Boulanger, J., Sibarita, J., Kervrann, C., Bouthemy, P., 2008. On-parametric regression for patch-based fluoresence microscopy image sequence denoising. In: Proceedings of the IEEE International Symposium on Biomedical Imaging: From Nano to Macro (ISBI’08), Paris, France. Dijkstra, 1959, A note on two problems in connexion with graphs, Numerische Mathematik, 1, 269, 10.1007/BF01386390 Ercole, C., Foi, A., Katkovnik, V., Egiazarian, K., 2005. Spatio-temporal pointwise adaptive denoising in video: 3D non parametric approach. In: Proceedings of the 1st International Workshop on Video Processing and Quality Metrics for Consumer Electronics, VPQM’2005, Scottsdale. Gasser, 1986, Residual variance and residual pattern in nonlinear regression, Biometrika, 73, 625, 10.1093/biomet/73.3.625 Genovesio, 2006, Multiple particle tracking in 3D+t microscopy: method and application to the tracking of endocytosed quantum dots, IEEE Transactions on Image Processing, 15, 1062, 10.1109/TIP.2006.872323 Gibbons, 2001, A dynamical model of kinesin-microtubule motility assays, Biophysical Journal, 80, 2515, 10.1016/S0006-3495(01)76223-6 Hadjidemetriou, S., Toomre, D., Duncan, J.S., 2006. Tracking the motion of the outer tips of microtubules. In: Proceedings of the IEEE International Symposium on Biomedical Imaging: From Nano to Macro (ISBI’2006), Washington, DC, pp. 530–533. Huber, 1981 Huet, 2006, Model selection for estimating the non zero component of a Gaussian vector, ESAIM P and S, 10, 164, 10.1051/ps:2006004 Ieng, S.-S., Tarel, J.-P., Charbonnier, P., 2004. Evaluation of robust fitting based detection. In: Proceedings of the 8th European Conference on Computer Vision, ECCV’2004, vol. 2, Prague, Czech Republic, pp. 341–352. Jacob, 2004, Design of steerable filters for feature detection using canny-like criterion, IEEE Transactions on Pattern Analysis and Machine Intelligence, 26, 1007, 10.1109/TPAMI.2004.44 Kervrann, 2006, Optimal spatial adaptation for patch-based image denoising, IEEE Transactions on Image Processing, 15, 2866, 10.1109/TIP.2006.877529 Lepski, 1991, Asymptotically minimax adaptive estimation 1: upper bounds, SIAM Journal Theory of Probability and Application, 36, 654 Li, K., Chen, M., Kanade, T., 2007. Cell population tracking and lineage construction with spatiotemporal context. In: Proceedings of the 10th International Conference on Medical Image Computing and Computer Assisted Intervention, Brisbane, Australia, pp. 295–302. Maurizot, M., Bouthemy, P., Delyon, B., Iouditski, A., Odobez, J.-M., 1995. Determination of singular points in 2D deformable flow fields. In: Proceedings of the IEEE International Conference on Image Processing (ICIP’1995), vol. 3, Washington, DC, pp. 488–491. Nédélec, 2001, Computer simulations reveal motor properties generating stable antiparallel microtubule interactions, Journal of Cell Biology, 158, 1005, 10.1083/jcb.200202051 Portilla, 2003, Image denoising using scale mixtures of Gaussians in the wavelet domain, IEEE Transactions on Image Processing, 12, 1338, 10.1109/TIP.2003.818640 Pécot, T., Boulanger, J., Kervrann, C., Bouthemy, P., 2007. Network tomography for trafficking simulation and analysis in fluorescence microscopy imaging. In: Proceedings of the IEEE International Symposium on Biomedical Imaging: From Nano to Macro (ISBI’07), Washington, DC, pp. 268–271. Pécot, T., Kervrann, C., Bouthemy, P., 2008. Minimal paths and probabilistic models for origin-destination traffic estimation in live cell imaging. In: Proceedings of the IEEE International Symposium on Biomedical Imaging: From Nano to Macro (ISBI’08), Paris, France. Racine, V., Hertzog, A., Jouaneau, J., Salamero, J., Kervrann, C., Sibarita, J.-B., 2006. Multiple target tracking of 3D fluorescent objects based on simulated annealing. In: Proceedings of the IEEE International Symposium on Biomedical Imaging: From Nano to Macro (ISBI’2006), Washington, DC, pp. 1020–1023. Ruckstuhl, 2001, Baseline subtraction using robust local regression estimation, Journal of Quantitative Spectroscopy and Radiative Transfer, 68, 179, 10.1016/S0022-4073(00)00021-2 Sbalzarini, 2005, Feature point tracking and trajectory analysis for video imaging in cell biology, Journal of Structural Biology, 151, 182, 10.1016/j.jsb.2005.06.002 Sibarita, J.-B., Magnin, H., De Mey, J.R., 2002. Ultra-fast 4D microscopy and high throughput distributed deconvolution. In: Proceedings of the IEEE International Symposium on Biomedical Imaging: From Nano to Macro (ISBI’2002), Washington, DC, pp. 769–772. Sibarita, J.-B., Racine, V., Salamero, J., 2006. Quantification of membrane trafficking on a 3D cytoskeleton network in living cells. In: Proceedings of the IEEE International Symposium on Biomedical Imaging: From Nano to Macro (ISBI’2006), Washington, DC, pp. 263–266. Smal, I., Draegestein, K., Galjart, N., Niessen, W., Meijering, E., 2007. Rao-blackwellized marginal particle filtering for multiple object tracking in molecular bioimaging. In: IPMI, pp. 110–121. Soatto, S., Doretto, G., Wu, Y.N., Jul. 2001. Dynamic textures. In: Proceedings of the 8th IEEE International Conference on Computer Vision (ICCV’2001), vol. 2, Vancouver, Canada, pp. 439–446. Steger, 1998, An unbiased detector of curvilinear structures, IEEE Transactions on Pattern Analysis and Machine Intelligence, 20, 113, 10.1109/34.659930 Surrey, 2001, Physical properties determining self-organization of motors and microtubules, Science, 292, 1167, 10.1126/science.1059758 Thomann, 2003, Automatic fluorescent tag localization II: improvement in super-resolution by relative tracking, Journal of Microscopy, 211, 230, 10.1046/j.1365-2818.2003.01223.x Wang, Y., Zhu, S.C., 2003. Modeling textured motion: particle, wave and sketch. In: Proceedings of the 9th IEEE International Conference on Computer Vision (ICCV’2003), pp. 213–220. White, 1999, Rab6 coordinates a novel golgi to ER retrograde transport pathway in live cells, The Journal of Cell Biology, 147, 743, 10.1083/jcb.147.4.743 Zhang, B., Enninga, J., Olivo-Marin, J.-C., Zimmer, C., 2006. Automated super-resolution detection of fluorescent rods in 2D. In: Proceedings of the IEEE International Symposium on Biomedical Imaging: From Nano to Macro (ISBI’2006), Washington, DC, pp. 1296–1299.