A novel multiple hypothesis based particle tracking method for clathrin mediated endocytosis analysis using fluorescence microscopy

IEEE Transactions on Image Processing

Volumn 23, Issue 4, 2014, Pages 1844-1857

  Liang, Liang ^a   Shen, Hongying ^b   De Camilli, Pietro ^b   Duncan, James S ^a  

^a Yale University   (United States)

^b YALE UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

clathrin mediated endocytosis; fluorescence microscopy; multiple hypothesis; Particle tracking

Indexed keywords

CLATHRINS; DATA ASSOCIATION PROBLEM; GAUSSIAN MIXTURE MODEL; MULTIPLE HYPOTHESIS; MULTIPLE HYPOTHESIS TRACKING; PARTICLE TRACKING; PARTICLE-TRACKING METHOD; TOTAL INTERNAL REFLECTION MICROSCOPY;

FLUORESCENCE MICROSCOPY; REFRACTIVE INDEX; TRAJECTORIES;

MOLECULAR BIOLOGY;

CLATHRIN; FLUORESCENT DYE;

CHEMISTRY; CYTOLOGY; ENDOCYTOSIS; FLUORESCENCE MICROSCOPY; IMAGE PROCESSING; METABOLISM; MOLECULAR IMAGING; PARTICLE SIZE; PHYSIOLOGY; PROCEDURES;

CLATHRIN; CYTOLOGICAL TECHNIQUES; ENDOCYTOSIS; FLUORESCENT DYES; IMAGE PROCESSING, COMPUTER-ASSISTED; MICROSCOPY, FLUORESCENCE; MOLECULAR IMAGING; PARTICLE SIZE;

EID: 84897831100     PISSN: 10577149     EISSN: None     Source Type: Journal    
DOI: 10.1109/TIP.2014.2303633     Document Type: Article

References (61)

1. A. L. Mattheyses, S. M. Simon, and J. Z. Rappoport, "Imaging with total internal reflection fluorescence microscopy for the cell biologist," J. Cell Sci., vol. 123, pp. 3621-3628, Nov. 2010.
2. V. I. Slepnev and P. D. Camilli, "Accessory factors in clathrin-dependent synaptic vesicle endocytosis," Nature Rev. Neurosci., vol. 1, no. 3, pp. 161-172, 2000.
3. T. Kirchhausen, "Imaging endocytic clathrin structures in living cells," Trends Cell Biolo., vol. 20, no. 1, pp. 596-605, 2009.
4. H. Shen, et al., "Constitutive activated Cdc42-associated kinase (Ack) phosphorylation at arrested endocytic clathrin-coated pits of cells that lack dynamin," Molecular Biol. Cell, vol. 22, no. 4, pp. 493-502, 2011.
5. Y. Saheki and P. D. Camilli, "Synaptic vesicle endocytosis," Cold Spring Harbor Perspect. Biol., vol. 4, no. 9, pp. 1-30, 2012.
6. I. Milosevic, et al., "Recruitment of endophilin to clathrin-coated pit necks is required for efficient vesicle uncoating after fission," Neuron, vol. 72, no. 4, pp. 587-601, 2011.
7. D. Harold, et al., "Genome-wide association study identifies variants at CLU and PICALM associated with Alzheimer's disease, and shows evidence for additional susceptibility genes," Nature Genet., vol. 41, no. 10, pp. 1088-1093, 2009.
8. S. Züchner, et al., "Mutations in the pleckstrin homology domain of dynamin 2 cause dominant intermediate charcot-marie-tooth disease," Nature Genet., vol. 37, no. 3, pp. 289-294, 2005. (Pubitemid 41716256)
9. A. Sorkin and M. von Zastrow, "Endocytosis and signalling: Intertwining molecular networks," Nature Rev. Molecular Cell Biol., vol. 10, no. 9, pp. 609-622, 2009.
10. D. Leto and A. R. Saltiel, "Regulation of glucose transport by insulin: Traffic control of GLUT4," Nature Rev. Molecular Cell Biol., vol. 13, no. 6, pp. 383-396, 2012.
11. B. Brandenburg and X. Zhuang, "Virus trafficking-Learning from single-virus tracking," Nature Rev. Microbiol., vol. 5, no. 3, pp. 197-208, 2007.
12. I. Smal, M. Loog, W. J. Niessen, and E. H. W. Meijering, "Quantitative comparison of spot detection methods in fluorescence microscopy," IEEE Trans. Med. Imag., vol. 29, no. 2, pp. 282-301, Feb. 2010.
13. A. Genovesio, T. Liedl, V. Emiliani, W. J. Parak, M. Coppey-Moisan, and J.-C. Olivo-Marin, "Multiple particle tracking in 3-D+t microscopy: Method and application to the tracking of endocytosed quantum dots," IEEE Trans. Image Process., vol. 15, no. 5, pp. 1062-1070, May 2006.
14. M. Qiu, H.-C. Lee, and G. Yang, "Nanometer resolution tracking and modeling of bidirectional axonal cargo transport," in Proc. IEEE ISBI, Jun. 2012, pp. 992-995.
15. 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 Trans. Image Process., vol. 14, no. 9, pp. 1372-1383, Sep. 2005. (Pubitemid 41430899)
16. W. Godinez, M. Lampe, S. Wörz, B. Müller, R. Eils, and K. Rohr, "Deterministic and probabilistic approaches for tracking virus particles in time-lapse fluorescence microscopy image sequences," Med. Image Anal., vol. 13, no. 2, pp. 325-342, 2009.
17. A. Jaiswal, W. J. Godinez, R. Eils, M. J. Lehmann, and K. Rohr, "Tracking virus particles in fluorescence microscopy images using twostep multi-frame association," in Proc. 9th IEEE Int. Symp. Biomed. Imaging, May 2012, pp. 664-667.
18. I. Smal, K. Draegestein, N. Galjart, W. J. Niessen, and E. H. W. Meijering, "Particle filtering for multiple object tracking in dynamic fluorescence microscopy images: Application to microtubule growth analysis," IEEE Trans. Med. Imaging, vol. 27, no. 6, pp. 789-804, Jun. 2008. (Pubitemid 351760851)
19. K. Jaqaman, et al., "Robust single-particle tracking in live-cell timelapse sequences," Nature Methods, vol. 5, no. 8, pp. 695-702, 2008.
20. B. C. Carter, G. T. Shubeita, and S. P. Gross, "Tracking single-particles: A user-friendly quantitative evaluation," Phys. Biol., vol. 2, no. 1, pp. 60-72, 2005. (Pubitemid 41238219)
21. M. K. Cheezum, W. F. Walker, and W. H. Guilford, "Quantitative comparison of algorithms for tracking single fluorescent particles," Biophys. J., vol. 81, no. 4, pp. 2378-2388, 2001. (Pubitemid 32917184)
22. Y. Kalaidzidis, "Intracellular objects tracking," Eur. J. Cell Biol., vol. 86, no. 9, pp. 569-578, 2007. (Pubitemid 47233378)
23. L. Feng, Y. Xu, Y. Yang, and X. Zheng, "Multiple dense particle tracking in fluorescence microscopy images based on multidimensional assignment," J. Structural Biol., vol. 173, no. 2, pp. 219-228, 2011.
24. S. T. Acton and N. Ray, Biomedical Image Analysis: Tracking. San Mateo, CA, USA: Morgan & Claypool, 2005.
25. M. S. Arulampalam, S. Maskell, N. Gordon, and T. Clapp, "A tutorial on particle filters for online. nonlinear/non-Gaussian Bayesian tracking," IEEE Trans. Signal Process., vol. 50, no. 2, pp. 174-188, Feb. 2002. (Pubitemid 34291500)
26. Q. Wen, J. Gao, and K. Luby-Phelps, "Multiple interacting subcellular structure tracking by sequential Monte Carlo method," in Proc. IEEE Int. Conf. Bioinformat. Biomed., Nov. 2007, pp. 437-442.
27. O. Greß and S. Posch, "Trajectory retrieval from Monte Carlo data association samples for tracking in fluorescence microscopy images," in Proc. 9th IEEE Int. Symp. Biomed. Imaging, May 2012, pp. 374-377.
28. C. Hue, J.-P. L. Cadre, and P. Pérez, "Sequential Monte Carlo methods for multiple target tracking and data fusion," IEEE Trans. Signal Process., vol. 50, no. 2, pp. 309-325, Feb. 2002. (Pubitemid 34291512)
29. A. Basden, C. Haniff, and C. Mackay, "Photon counting strategies with low light level CCDs," Monthly Notices R. Astronomical Soc., vol. 345, no. 3, pp. 985-991, 2003. (Pubitemid 37417073)
30. M. S. Robbins and B. J. Hadwen, "The noise performance of electron multiplying charge-coupled devices," IEEE Trans. Electron Devices, vol. 50, no. 5, pp. 1227-1232, May 2003.
31. D. B. Reid, "An algorithm for tracking multiple targets," IEEE Trans. Autom. Control, vol. 24, no. 6, pp. 843-854, Dec. 1979.
32. N. Chenouard, I. Bloch, and J.-C. Olivo-Marin, "Multiple hypothesis tracking in microscopy images," in Proc. IEEE Int. Symp. Biomed. Imaging, From Nano Macro, Jul. 2009, pp. 1346-1349.
33. G. Yang, A. Matov, and G. Danuser, "Reliable tracking of large-scale dense particle motion for fluorescent live cell imaging," in Proc. IEEE Comput. Soc. Conf. Comput. Vis. Pattern Recognit. Workshops, Jun. 2005, pp. 130-138.
34. A. B. Poore, "Some assignment problems arising from multiple target tracking," Math. Comput. Model., vol. 43, nos. 9-10, pp. 1074-1091, 2006.
35. K. Shafique and M. Shah, "A noniterative greedy algorithm for multiframe point correspondence," IEEE Trans. Pattern Anal. Mach. Intell., vol. 27, no. 1, pp. 51-65, Jan. 2005. (Pubitemid 40195897)
36. O. Al-Kofahi, R. J. Radke, S. K. Goderie, Q. Shen, S. Temple, and B. Roysam, "Automated cell lineage construction: A rapid method to analyze clonal development established with murine neural progenitor cells," Cell Cycle, vol. 5, no. 3, pp. 327-335, 2006. (Pubitemid 43213505)
37. D. Padfield, J. Rittscher, and B. Roysamb, "Coupled minimumcost flow cell tracking for high-throughput quantitative analysis," Medical Image Anal., vol. 15, no. 4, pp. 650-668, 2011.
38. D. Thomann, D. R. Rines, P. K. Sorger, and G. Danuser, "Automatic fluorescent tag detection in 3D with super-resolution: Application to the analysis of chromosome movement," J. Microscopy, vol. 208, no. 1, pp. 49-64, 2002. (Pubitemid 35365582)
39. R. Xu and D. W. II, "Survey of clustering algorithms," IEEE Trans. Neural Netw., vol. 16, no. 3, pp. 645-678, May 2005. (Pubitemid 40718010)
40. M. A. Figueiredo and A. K. Jain, "Unsupervised learning of finite mixture models," IEEE Trans. Pattern Anal. Mach. Intell., vol. 24, no. 3, pp. 1-16, Mar. 2002.
41. A. Genovesio and J.-C. Olivo-Marin, "Split and merge data association filter for dense multi-target tracking," in Proc. 17th Int. Conf. Pattern Recognit., Aug. 2004, pp. 677-680.
42. L. Liang, H. Shen, P. D. Camilli, and J. S. Duncan, "Tracking clathrin coated pits with a multiple hypothesis based method," Med. Image Comput. Comput Assist. Intervent., vol. 13, pp. 315-322, Jan. 2010.
43. L. Liang, Y. Xu, H. Shen, P. D. Camilli, D. Toomre, and J. S. Duncan, "Automatic detection of subcellular particles in fluorescence microscopy via feature clustering and Bayesian analysis," in Proc. IEEE Workshop Math. Methods Biomed. Image Anal., Jan. 2012, pp. 161-166.
44. L. Liang, H. Shen, P. Rompolas, V. Greco, P. D. Camilli, and J. S. Duncan, "A multiple hypothesis based method for particle tracking and its extension for cell segmentation," in Proc. 23rd Int. Conf. Inf. Process. Med. Imaging, 2013, pp. 98-109.
45. X. R. Li and V. P. Jilkov, "Survey of maneuvering target tracking. Part I. Dynamic models," IEEE Trans. Aerosp. Electron. Syst., vol. 39, no. 4, pp. 1333-1364, Oct. 2003.
46. X. R. Li and V. P. Jilkov, "Survey of maneuvering target tracking. Part V. Multiple-model methods," IEEE Trans. Aerosp. Electron. Syst., vol. 41, no. 4, pp. 1255-1321, Jan. 2005. (Pubitemid 43033916)
47. K. Smith, A. Carleton, and V. Lepetit, "General constraints for batch multiple-target tracking applied to large-scale videomicroscopy," in Proc. IEEE Conf. Comput. Vis. Pattern Recognit., Jun. 2008, pp. 1-8.
48. H. A. Blom and Y. Bar-Shalom, "The interacting multiple model algorithm for systems with Markovian switching coefficients," IEEE Trans. Autom. Control, vol. 33, no. 8, pp. 780-783, Aug. 1988.
49. K. Li, M. Chen, T. Kanade, E. Miller, L. Weiss, and P. Campbell, "Cell population tracking and lineage construction with spatiotemporal context," Med. Image Anal., vol. 12, no. 5, pp. 546-566, Oct. 2008.
50. B. Zhang, J. Zerubia, and J.-C. Olivo-Marin, "Gaussian approximations of fluorescence microscope point-spread function models," Appl. Opt., vol. 46, no. 10, pp. 1819-1829, 2007. (Pubitemid 46659549)
51. T. Y. Kong and A. Rosenfeld, Topological Algorithms for Digital Image Processing. New York, NY, USA: Elsevier, 1996.
52. K. Stock, R. Sailer, W. S. L. Strauss, M. Lyttek, R. Steiner, and H. Schneckenburger, "Variable-angle total internal reflection fluorescence microscopy (VA-TIRFM): Realization and application of a compact illumination device," J. Microscopy, vol. 211, no. 1, pp. 19-29, 2003. (Pubitemid 41709848)
53. A. Rohrbach, "Observing secretory granules with a multiangle evanescent wave microscope," Biophys. J., vol. 78, no. 5, pp. 2641-2654, 2000. (Pubitemid 30313822)
54. Q. Yang, A. Karpikov, D. Toomre, and J. S. Duncan, "3-D reconstruction of microtubules from multi-angle total internal reflection fluorescence microscopy using Bayesian framework," IEEE Trans. Image Process., vol. 20, no. 8, pp. 2248-2259, Aug. 2011.
55. L. Liang, H. Shen, Y. Xu, P. D. Camilli, D. Toomre, and J. S. Duncan, "A Bayesian method for 3D estimation of subcellular particle features in multi-angle TIRF microscopy," in Proc. 9th IEEE Int. Symp. Biomed. Imaging, May 2012, pp. 984-987.
56. R. Kasturi, et al., "Framework for performance evaluation of face, text, and vehicle detection and tracking in video: Data, metrics, and protocol," IEEE Trans. Pattern Anal. Mach. Intell., vol. 31, no. 2, pp. 319-336, Feb. 2009.
57. S. Rodal, G. Skretting, O. Garred, F. Vilhardt, B. van Deurs, and K. Sandvig, "Extraction of cholesterol with methyl-beta-cyclodextrin perturbs formation of clathrin-coated endocytic vesicles," Mol Biol Cell, vol. 10, no. 4, pp. 961-974, 1999. (Pubitemid 29193724)
58. A. Subtil, I. Gaidarov, K. Kobylarz, M. Lampson, J. Keen, and T. McGraw, "Acute cholesterol depletion inhibits clathrin-coated pit budding," Proc. Nat. Acad. Sci. United States Amer., vol. 96, no. 12, pp. 6775-6780, 1999. (Pubitemid 29274959)
59. R. Zoncu, et al., "Loss of endocytic clathrin-coated pits upon acute depletion of phosphatidylinositol 4,5-bisphosphate," Proc. Nat. Acad. Sci. United States Amer., vol. 104, no. 10, pp. 3793-3798, 2007. (Pubitemid 47181533)
60. D. Loerke, et al., "Cargo and dynamin regulate clathrin-coated pit maturation," PLoS Biol., vol. 7, no. 3, p. e1000057, 2009.
61. S. Saffarian, E. Cocucci, and T. Kirchhausen, "Distinct dynamics of endocytic clathrin-coated pits and coated plaques," PLoS Biol., vol. 7, no. 9, pp. 1-18, 2009.