Computational image analysis of cellular dynamics: A case study based on particle tracking

Cold Spring Harbor Protocols

Volumn 4, Issue 12, 2009, Pages

  Jaqaman, Khuloud ^a   Danuser, Gaudenz ^a  

^a NONE

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; ARTICLE; CELL GRANULE; COMPUTATIONAL FLUID DYNAMICS; COMPUTER SIMULATION; IMAGE ANALYSIS; IMAGE QUALITY; PROCESS MODEL; PROTEIN DETERMINATION; QUALITY CONTROL; QUANTITATIVE ANALYSIS; SAMPLING;

EID: 72149084634     PISSN: None     EISSN: 15596095     Source Type: Journal    
DOI: 10.1101/pdb.top65     Document Type: Article

References (51)

1. Abraham VC, Taylor DL, Haskins JR. 2004. High content screening applied to large-scale cell biology. Trends Biotechnol 22: 15-22.
2. Bakal C, Aach J, Church G, Perrimon N. 2007. Quantitative morphological signatures define local signaling networks regulating cell morphology. Science 316: 1753-1756.
3. Bates M, Huang B, Dempsey GT, Zhuang X. 2007. Multicolor super-resolution imaging with photo-switchable fluorescent probes. Science 317: 1749-1753.
4. Bonneau S, Dahan M, Cohen LD. 2005. Single quantum dot tracking based on perceptual grouping using minimal paths in a spatiotemporal volume. IEEE Trans Image Process 14: 1384-1395.
5. Burkard RE, Çela E. 1999. Linear assignment problems and extensions. In Handbook of combinatorial optimization (eds. D-Z Du and PM Pardalos), Vol. A, pp. 75-149. Kluwer Academic, Dordrecht, Netherlands.
6. Chen X, Murphy RF. 2006. Automated interpretation of protein subcellular location patterns. Int Rev Cytol 249: 193-227.
7. Chetverikov D, Verestóy J. 1999. Feature point tracking for incomplete trajectories. Computing 62: 321-338.
8. Conrad C, Erfle H, Warnat P, Daigle N, Lörch T, Ellenberg J, Pepperkok R, Eils R. 2004. Automatic identification of subcellular phenotypes on human cell arrays. Genome Res 14: 1130-1136.
9. Crocker JC, Grier DG. 1996. Methods of digital video microscopy for colloidal studies. J Colloid Interface Sci 179: 298-310.
10. Danuser G, Waterman-Storer CM. 2006. Quantitative fluorescent speckle microscopy of cytoskeleton dynamics. Annu Rev Biophys Biomol Struct 35: 361-387.
11. Dorn JF, Jaqaman K, Rines DR, Jelson GS, Sorger PK, Danuser G. 2005. Yeast kinetochore microtubule dynamics analyzed by high-resolution three-dimensional microscopy. Biophys J 89: 2835-2854.
12. Dorn JF, Danuser G, Yang G. 2008. Computational processing and analysis of dynamic fluorescence image data. In Fluorescent proteins (ed. KF Sullivan), 2nd ed, pp. 497-538. Elsevier, San Diego, CA.
13. Ehrlich M, Boll W, van Oijen A, Hariharan R, Chandran K, Nibert ML, Kirchhausen T. 2004. Endocytosis by random initiation and stabilization of clathrin-coated pits. Cell 118: 591-605.
14. Eils R, Athale C. 2003. Computational imaging in cell biology. J Cell Biol 161: 477-481.
15. Ewers H, Smith AE, Sbalzarini IF, Lilie H, Koumoutsakos P, Helenius A. 2005. Single-particle tracking of murine polyoma virus-like particles on live cells and artificial membranes. Proc Natl Acad Sci 102: 15110-15115.
16. Fujiwara T, Ritchie K, Murakoshi H, Jacobson K, Kusumi A. 2002. Phospholipids undergo hop diffusion in compartmentalized cell membrane. J Cell Biol 157: 1071-1081.
17. Genovesio A, Olivo-Marin J-C. 2004. Split and merge data association filter for dense multi-target tracking. In Proceedings of the 17th international conference on pattern recognition (eds. J Kittler et al.), Vol. 4, pp. 677-680. IEEE, Piscataway, NJ.
18. Genovesio A, Liedl T, Emiliani V, Parak WJ, Coppey-Moisan M, Olivo-Marin JC. 2006. Multiple particle tracking in 3-D+t microscopy: Method and application to the tracking of endocytosed quantum dots. IEEE Trans Image Process 15: 1062-1070.
19. Ghosh RN, Webb WW. 1994. Automated detection and tracking of individual and clustered cell surface low density lipoprotein receptor molecules. Biophys J 66: 1301-1318.
20. Groc L, Heine M, Cognet L, Brickley K, Stephenson FA, Lounis B, Choquet D. 2004. Differential activity-dependent regulation of the lateral mobilities of AMPA and NMDA receptors. Nat Neurosci 7: 695-696.
21. Huet S, Karatekin E, Tran VS, Fanget I, Cribier S, Henry J-P. 2006. Analysis of transient behavior in complex trajectories: Application to secretory vesicle dynamics. Biophys J 91: 3542-3559.
22. Inoué S, Spring KR. 1997. Video microscopy: The fundamentals. Plenum, New York.
23. Jaqaman K, Loerke D, Mettlen M, Kuwata H, Grinstein S, Schmid SL, Danuser G. 2008. Robust single-particle tracking in live-cell time-lapse sequences. Nat Methods 5: 695-702.
24. Ji L, Danuser G. 2005. Tracking quasi-stationary flow of weak fluorescent signals by adaptive multi-frame correlation. J Microsc 220: 150-167.
25. Jiang S, Zhou X, Kirchhausen T, Wong STC. 2007. Tracking molecular particles in live cells using fuzzy rule-based system. Cytometry A 71A: 576-584.
26. Kalaidzidis Y. 2007. Intracellular objects tracking. Eur J Cell Biol 86: 569-578.
27. Loerke D, Mettlen M, Yarar D, Jaqaman K, Jaqaman H, Danuser G, Schmid SL. 2009. Cargo and dynamin regulate clathrin-coated pit maturation. PLoS Biol 7: e1000057. doi: 10.1371/journal.pbio.1000057.
28. Meijering E, Smal I, Danuser G. 2006. Tracking in molecular bioimaging. IEEE Signal Process Mag 23: 46-53.
29. Neumann B, Held M, Liebel U, Erfle H, Rogers P, Pepperkok R, Ellenberg J. 2006. High-throughput RNAi screening by time-lapse imaging of live human cells. Nat Methods 3: 385-390.
30. Nixon M, Aguado A. 2002. Feature extraction in computer vision and image processing. Butterworth-Heinemann/Newnes, Oxford, UK.
31. Olivo-Marin J-C. 2002. Extraction of spots in biological images using multiscale products. Pattern Recognit 35: 1989-1996.
32. Ponti A, Vallotton P, Salmon WC, Waterman-Storer CM, Danuser G. 2003. Computational analysis of F-actin turnover in cortical actin meshworks using fluorescent speckle microscopy. Biophys J 84: 3336-3352.
33. Ponti A, Matov A, Adams M, Gupton S, Waterman-Storer CM, Danuser G. 2005. Periodic patterns of actin turnover in lamellipodia and lamellae of migrating epithelial cells analyzed by quantitative fluorescent speckle microscopy. Biophys J 89: 3456-3469.
34. Racine V, Sachse M, Salamero J, Fraisier V, Trubuil A, Sibarita J-B. 2007. Visualization and quantification of vesicle trafficking on a three-dimensional cytoskeleton network in living cells. J Microsc 225: 214-228.
35. Reid DB. 1979. An algorithm for tracking multiple targets. IEEE Trans Automat Contr. 24: 843-854.
36. Sage D, Neumann FR, Hediger F, Gasser SM, Unser M. 2005. Automatic tracking of individual fluorescence particles: Application to the study of chromosome dynamics. IEEE Trans Image Process 14: 1372-1383.
37. Sako Y, Minoguchi S, Yanagida T. 2000. Single-molecule imaging of EGFR signalling on the surface of living cells. Nat Cell Biol 2: 168-172.
38. Sbalzarini IF, Koumoutsakos P. 2005. Feature point tracking and trajectory analysis for video imaging in cell biology. J Struct Biol 151: 182-195.
39. Shafique K, Shah M. 2005. A noniterative greedy algorithm for multiframe point correspondence. IEEE Trans Pattern Anal Mach Intell 27: 51-65.
40. Shroff H, Galbraith CG, Galbraith JA, White H, Gillette J, Olenych S, Davidson MW, Betzig E. 2007. Dual-color superresolution imaging of genetically expressed probes within individual adhesion complexes. Proc Natl Acad Sci 104: 20308-20313.
41. Smith C, Eisenstein M. 2005. Automated imaging: Data as far as the eye can see. Nat Methods 2: 547-555.
42. Starck JL, Murtagh F, Bijaoui A. 2000. Image processing and data analysis: The multiscale approach. Cambridge University Press, Cambridge, UK.
43. Stelzer EHK. 2000. Practical limits to resolution in fluorescence light microscopy. In Imaging neurons (eds. R Yuste et al.), pp. 12.11-12.19. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
44. Swedlow JR, Goldberg I, Brauner E, Sorger PK. 2003. Informatics and quantitative analysis in biological imaging. Science 300: 100-102.
45. Thomann D, Rines DR, Sorger PK, Danuser G. 2002. Automatic fluorescent tag detection in 3D with super-resolution: Application to the analysis of chromosome movement. J Microsc 208: 49-64.
46. Tirnauer JS, Salmon ED, Mitchison TJ. 2004. Microtubule plus-end dynamics in Xenopus egg extract spindles. Mol Biol Cell 15: 1776-1784.
47. Tvaruskó W, Bentele M, Misteli T, Rudolf R, Kaether C, Spector DL, Gerdes HH, Eils R. 1999. Time-resolved analysis and visualization of dynamic processes in living cells. Proc Natl Acad Sci 96: 7950-7955.
48. Vallotton P, Ponti A, Waterman-Storer CM, Salmon ED, Danuser G. 2003. Recovery, visualization, and analysis of actin and tubulin polymer flow in live cells: A fluorescence speckle microscopy study. Biophys J 85: 1289-1306.
49. Veenman CJ, Reinders MJT, Backer E. 2001. Resolving motion correspondence for densely moving points. IEEE Trans Pattern Anal Mach Intell 23: 54-72.
50. Yildiz A, Selvin PR. 2005. Fluorescence imaging with one nanometer accuracy: Application to molecular motors. Acc Chem Res 38: 574-582.
51. Zenisek D, Steyer JA, Almers W. 2000. Transport, capture, and exocytosis of single synaptic vesicles at active zones. Nature 406: 849-854.