Robust Single-particle Tracking in Live-cell Time-lapse Sequences

Overview

Journal Nat Methods

Specialties Biomedical Engineering
Pathology

Date 2008 Jul 22

PMID 18641657

Citations 852

Authors

Khuloud Jaqaman

Dinah Loerke

Marcel Mettlen

Hirotaka Kuwata

Sergio Grinstein

Sandra L Schmid

Gaudenz Danuser

Affiliations

Soon will be listed here.

Abstract

Single-particle tracking (SPT) is often the rate-limiting step in live-cell imaging studies of subcellular dynamics. Here we present a tracking algorithm that addresses the principal challenges of SPT, namely high particle density, particle motion heterogeneity, temporary particle disappearance, and particle merging and splitting. The algorithm first links particles between consecutive frames and then links the resulting track segments into complete trajectories. Both steps are formulated as global combinatorial optimization problems whose solution identifies the overall most likely set of particle trajectories throughout a movie. Using this approach, we show that the GTPase dynamin differentially affects the kinetics of long- and short-lived endocytic structures and that the motion of CD36 receptors along cytoskeleton-mediated linear tracks increases their aggregation probability. Both applications indicate the requirement for robust and complete tracking of dense particle fields to dissect the mechanisms of receptor organization at the level of the plasma membrane.

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References

Kalaidzidis Y . Intracellular objects tracking. Eur J Cell Biol. 2007; 86(9):569-78. DOI: 10.1016/j.ejcb.2007.05.005. View

Thomann D, Rines D, Sorger P, Danuser G . Automatic fluorescent tag detection in 3D with super-resolution: application to the analysis of chromosome movement. J Microsc. 2002; 208(Pt 1):49-64. DOI: 10.1046/j.1365-2818.2002.01066.x. View

Ehrlich M, Boll W, van Oijen A, Hariharan R, Chandran K, Nibert M . Endocytosis by random initiation and stabilization of clathrin-coated pits. Cell. 2004; 118(5):591-605. DOI: 10.1016/j.cell.2004.08.017. View

Manley S, Gillette J, Patterson G, Shroff H, Hess H, Betzig E . High-density mapping of single-molecule trajectories with photoactivated localization microscopy. Nat Methods. 2008; 5(2):155-7. DOI: 10.1038/nmeth.1176. View

Sako Y, Minoghchi S, Yanagida T . Single-molecule imaging of EGFR signalling on the surface of living cells. Nat Cell Biol. 2000; 2(3):168-72. DOI: 10.1038/35004044. View

Cheezum M, Walker W, Guilford W . Quantitative comparison of algorithms for tracking single fluorescent particles. Biophys J. 2001; 81(4):2378-88. PMC: 1301708. DOI: 10.1016/S0006-3495(01)75884-5. View

Schmidt T, Schutz G, Baumgartner W, Gruber H, Schindler H . Imaging of single molecule diffusion. Proc Natl Acad Sci U S A. 1996; 93(7):2926-9. PMC: 39736. DOI: 10.1073/pnas.93.7.2926. View

Febbraio M, Hajjar D, Silverstein R . CD36: a class B scavenger receptor involved in angiogenesis, atherosclerosis, inflammation, and lipid metabolism. J Clin Invest. 2001; 108(6):785-91. PMC: 200943. DOI: 10.1172/JCI14006. View

Ghosh R, Webb W . Automated detection and tracking of individual and clustered cell surface low density lipoprotein receptor molecules. Biophys J. 1994; 66(5):1301-18. PMC: 1275851. DOI: 10.1016/S0006-3495(94)80939-7. View

10.

Genovesio A, Liedl T, Emiliani V, Parak W, Coppey-Moisan M, Olivo-Marin J . Multiple particle tracking in 3-D+t microscopy: method and application to the tracking of endocytosed quantum dots. IEEE Trans Image Process. 2006; 15(5):1062-70. DOI: 10.1109/tip.2006.872323. View

11.

Macia E, Ehrlich M, Massol R, Boucrot E, Brunner C, Kirchhausen T . Dynasore, a cell-permeable inhibitor of dynamin. Dev Cell. 2006; 10(6):839-50. DOI: 10.1016/j.devcel.2006.04.002. View

12.

Tvarusko W, Bentele M, Misteli T, Rudolf R, Kaether C, Spector D . Time-resolved analysis and visualization of dynamic processes in living cells. Proc Natl Acad Sci U S A. 1999; 96(14):7950-5. PMC: 22168. DOI: 10.1073/pnas.96.14.7950. View

13.

Jiang S, Zhou X, Kirchhausen T, Wong S . Tracking molecular particles in live cells using fuzzy rule-based system. Cytometry A. 2007; 71(8):576-84. DOI: 10.1002/cyto.a.20411. View

14.

Merrifield C, Perrais D, Zenisek D . Coupling between clathrin-coated-pit invagination, cortactin recruitment, and membrane scission observed in live cells. Cell. 2005; 121(4):593-606. DOI: 10.1016/j.cell.2005.03.015. View

15.

Merrifield C, Feldman M, Wan L, Almers W . Imaging actin and dynamin recruitment during invagination of single clathrin-coated pits. Nat Cell Biol. 2002; 4(9):691-8. DOI: 10.1038/ncb837. View

16.

Goulian M, Simon S . Tracking single proteins within cells. Biophys J. 2000; 79(4):2188-98. PMC: 1301109. DOI: 10.1016/S0006-3495(00)76467-8. View

17.

Racine V, Sachse M, Salamero J, Fraisier V, Trubuil A, Sibarita J . Visualization and quantification of vesicle trafficking on a three-dimensional cytoskeleton network in living cells. J Microsc. 2007; 225(Pt 3):214-28. DOI: 10.1111/j.1365-2818.2007.01723.x. View

18.

Bonneau S, Dahan M, Cohen L . Single quantum dot tracking based on perceptual grouping using minimal paths in a spatiotemporal volume. IEEE Trans Image Process. 2005; 14(9):1384-95. DOI: 10.1109/tip.2005.852794. View

19.

Shafique K, Shah M . A noniterative greedy algorithm for multiframe point correspondence. IEEE Trans Pattern Anal Mach Intell. 2005; 27(1):51-65. DOI: 10.1109/TPAMI.2005.1. View

20.

Fujiwara T, Ritchie K, Murakoshi H, Jacobson K, Kusumi A . Phospholipids undergo hop diffusion in compartmentalized cell membrane. J Cell Biol. 2002; 157(6):1071-81. PMC: 2174039. DOI: 10.1083/jcb.200202050. View