Particle filtering for multiple object tracking in dynamic fluorescence microscopy images: Application to microtubule growth analysis

IEEE Transactions on Medical Imaging

Volumn 27, Issue 6, 2008, Pages 789-804

  Smal, Ihor ^b   Draegestein, Katharina ^b   Galjart, Niels ^b   Niessen, Wiro ^a,b   Meijering, Erik ^a,b  

^a IEEE

^b ERASMUS MEDICAL CENTER   (Netherlands)

Author keywords

Bayesian estimation; Fluorescence microscopy; Microtubule dynamics; Molecular bioimaging; Multiple object tracking; Particle filtering (PF); Sequential Monte Carlo

Indexed keywords

FLUORESCENCE MICROSCOPY; IMAGE ANALYSIS; MOLECULAR BIOLOGY; MONTE CARLO METHODS; OBJECT RECOGNITION;

BAYESIAN ESTIMATION; MICROTUBULE DYNAMICS; MOLECULAR BIOIMAGING; PARTICLE FILTERING (PF);

BAYESIAN NETWORKS;

ALGORITHM; ARTICLE; ARTIFICIAL INTELLIGENCE; AUTOMATED PATTERN RECOGNITION; CELL PROLIFERATION; COMPUTER ASSISTED DIAGNOSIS; FLUORESCENCE MICROSCOPY; IMAGE ENHANCEMENT; METHODOLOGY; MICROTUBULE; MOVEMENT (PHYSIOLOGY); PHYSIOLOGY; REPRODUCIBILITY; SENSITIVITY AND SPECIFICITY; ULTRASTRUCTURE;

ALGORITHMS; ARTIFICIAL INTELLIGENCE; CELL PROLIFERATION; IMAGE ENHANCEMENT; IMAGE INTERPRETATION, COMPUTER-ASSISTED; MICROSCOPY, FLUORESCENCE; MICROTUBULES; MOVEMENT; PATTERN RECOGNITION, AUTOMATED; REPRODUCIBILITY OF RESULTS; SENSITIVITY AND SPECIFICITY;

EID: 44449160376     PISSN: 02780062     EISSN: None     Source Type: Journal    
DOI: 10.1109/TMI.2008.916964     Document Type: Article

References (72)

1. E. Meijering, I. Smal, and G. Danuser, "Tracking in molecular bioimaging," IEEE Signal. Process. Mag., vol. 23, no. 3, pp. 46-53, May 2006.
2. W. Tvaruskó, M. Bentele, T. Misteli, R. Rudolf, C. Kaether, D. L. Spector, H. H. Gerdes, and R. Eils, "Time-resolved analysis and visualization of dynamic processes in living cells," Proc. Nat. Acad. Sci. USA, vol. 96, no. 14, pp. 7950-7955, Jul. 1999.
3. D. Gerlich, J. Mattes, and R. Eils, "Quantitative motion analysis and visualization of cellular structures," Methods Enzymol, vol. 29, no. 1, pp. 3-13, Jan. 2003.
4. D. Thomann, D. R. Rines, P. K. Sorger, and G. Danuser, "Automatic fluorescent tag detection in 3-D with super-resolution: Application to the analysis of chromosome movement," J. Microsc., vol. 208, no. 1, pp. 49-64, Oct. 2002.
5. D. Thomann, J. Dorn, P. K. Sorger, and G. Danuser, "Automatic fluorescent tag localization II: Improvement in super-resolution by relative tracking," J. Microsc., vol. 211, no. 3, pp. 230-248, Sep. 2003.
6. I. F. Sbalzarini and P. Koumoutsakos, "Feature point tracking and trajectory analysis for video imaging in cell biology," J. Struct. Biol., vol. 151, no. 2, pp. 182-195, Aug. 2005.
7. D. A. Schiffmann, D. Dikovskaya, P. L. Appleton, I. P. Newton, D. A. Creager, C. Allan, I. S. Näthke, and I. G. Goldberg, "Open microscopy environment and findspots: Integrating image informatics with quantitative multidimensional image analysis," BioTechniques, vol. 41, no. 2, pp. 199-208, Aug. 2006.
8. H. Bornfleth, K. Satzler, R. Eils, and C. Cremet-, "High-precision distance measurements and volume-conserving segmentation of objects near and below the resolution limit in three-dimensional confocal fluorescence microscopy," J. Microsc., vol. 189, no. 2, pp. 118-136, Mar. 1998.
9. 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. 1062-1270, May 2006.
10. D. Chetverikov and J. Verestói, "Feature point tracking for incomplete trajectories," Computing, vol. 62, no. 4, pt., pp. 321-338, Jul. 1999.
11. C. J. Veenman, M. J. T. Reinders, and E. Backer, "Motion tracking as a constrained optimization problem," Pattern Recogn., vol. 36, no. 9, pp. 2049-2067, Sep. 2003.
12. 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, Oct. 2001.
13. 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, Mar. 2005.
14. C. B. Bergsma, G. J. Streekstra, A. W. M. Smeulders, and E. M. M. Manders, "Velocity estimation of spots in 3-D confocal images sequences of living cells," Cytometry A, vol. 43, no. 4, pp. 261-272, Apr. 2001.
15. D. Uttenweiler, C. Veigel, R. Steubing, C. Götz, S. Mann, H. Haussecker, B. Jähne, and R. H. A. Fink, "Motion determination in actin filament fluorescence images with a spatio-temporal orientation analysis method," Biophys. J., vol. 78, no. 5, pp. 2709-2715, May 2000.
16. 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.
17. S. Bonneau, M. Dahan, and L. D. Cohen, "Single quantum dot tracking based on perceptual grouping using minimal paths in a spatiotemporal volume," IEEE Trans. Image Process., vol. 14, no. 9, pp. 1384-1395, Sep. 2005.
18. P. Y. Burgi, A. L. Yuille, and N. M. Grzywacz, "Probabilistic motion estimation based on temporal coherence," Neural Comput., vol. 12, no. 8, pp. 1839-1867, Aug. 2000.
19. A. Doucet, N. de Freitas, and N. Gordon, Sequential Monte Carlo Methods. New York: Springer-Verlag, 2001.
20. M. 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. 174-189, Feb. 2002.
21. S. Blackman and R. Popoli, Design and Analysis of Modern Tracking Systems. Boston, MA: Artech House, 1999.
22. R. Mahler, "Multi-target Bayes filtering via first-order multi-target moments," IEEE Trans. Aerosp. Electron. Syst., vol. 39, no. 4, pp. 1152-1178, Oct. 2003.
23. C. Hue, J.-P. Le Cadre, and P. Perez, "Sequential Monte Carlo methods for multiple target tracking and data fusion," IEEE Trans. Signal Process., vol. 50, no. 2, pp. 309-325, Feb. 2002.
24. W. Ng, J. Li, S. Godsill, and J. Vermaak, "A hybrid method for online joint detection and tracking for multiple targets," in Proc. IEEE Aerosp. Conf., Mar. 2005, pp. 2126-2141.
25. J. Vermaak, N. Ikoma, and S. Godsill, "Extended object tracking using particle techniques," in Proc. IEEE Aerosp. Conf., Mar. 2004, Apr. 2005, Mar. 2004, vol. 3, pp. 1876-1885.
26. J. Wolf, W. Burgard, and H. Burkhardt, "Robust vision-based localization by combining an image-retrieval system with Monte Carlo localization," IEEE Trans. Robot., vol. 21, no. 2, pp. 208-216, Apr. 2005.
27. P. Perez, J. Vermaak, and A. Blake, "Data fusion for visual tracking with particles," Proc. IEEE, vol. 92, no. 3, pp. 495-513, Mar. 2004.
28. C. Chang, P. Ansari, and A. Khokhar, "Efficient tracking of cyclic human motion by component motion," in IEEE Signal Process. Lett., Dec. 2004, vol. 11, no. 12, pp. 941-944.
29. Y. Wu, J. Lin, and T. S. Huang, "Analyzing and capturing articulated hand motion in image sequences," IEEE Trans. Pattern Anal. Mach. Intell., vol. 27, no. 12, pp. 1910-1922, Dec. 2005.
30. M. Pantic and I. Patras, "Dynamics of facial expression: Recognition of facial actions and their temporal segments from face profile image sequences," IEEE Trans. Syst. Man Cybern. B, vol. 36, no. 2, pp. 433-449, Apr. 2006.
31. M. Isard and A. Blake, "Condensation-conditional density propagation for visual tracking," Int. J. Comput. Vis., vol. 29, no. 1, pp. 5-28, Aug. 1998.
32. J. MacCormick and A. Blake, "Probabilistic exclusion and partitioned sampling for multiple object tracking," Int. J. Comput. Vis., vol. 39, no. 1, pp. 57-71, Aug. 2000.
33. K. Li, E. Miller, L. Weiss, P. Campbell, and T. Kanade, "Online tracking of migrating and proliferating cells imaged with phase-contrast microscopy," in 2006 Conf. Comput. Vision Pattern Recognit. Workshop (CVPRW06), New York, Jun. 2006, pp. 65-72.
34. H. Shen, G. Nelson, S. Kennedy, D. Nelson, J. Johnson, D. Spiller, M. R. H. White, and D. B. Kell, "Automatic tracking of biological cells and compartments using particle filters and active contours," Chem. Intell. Lab. Syst., vol. 82, no. 1-2, pp. 276-282, May 2006.
35. Q. Wen, J. Gao, A. Kosaka, H. Iwaki, K. Luby-Phelps, and D. Mundy, "A particle filter framework using optimal importance function for protein molecules tracking," in Proc. IEEE Int. Conf. Image Process., Sep. 2005, vol. 1, pp. 1161-1164.
36. I. Smal, W. Niessen, and E. Meijering, "Bayesian tracking for fluorescence microscopic imaging," in 2006 3rd IEEE Int. Symp. Biomed. Imag.: Macro Nano, Arlington, VA, Apr. 2006, pp. 550-553.
37. I. Smal, W. Niessen, and E. Meijering, "Particle filtering for multiple object tracking in molecular cell biology," in Proc. Nonlinear Stat. Signal Process. Workshop, Sep. 2006, pp. 44.1-44.4.
38. A. Desai and T. J. Mitchison, "Microtubule polymerization dynamics," Ann. Rev. Cell Develop. Biol., vol. 13, pp. 83-117, 1997.
39. H. Flyvbjerg, T. E. Holy, and S. Leibler, "Microtubuledynamics: Caps, catastrophes, and coupled hydrolysis," Phys. Rev. E, vol. 54, no. 5, pp. 5538-5560, Nov. 1996.
40. F. Verde, J. C. Labbe, M. Doree, and E. Karsenti, "Regulation of microtubule dynamics by cdc2 protein kinase in cell-free extracts of xenopus eggs," Nature, vol. 343, no. 6255, pp. 233-238, Jan. 1990.
41. F. Verde, M. Dogterom, E. Stelzer, E. Karsenti, and S. Leibler, "Control of microtubule dynamics and length by cyclin A- and cyclin b-dependent kinases in xenopus egg extracts," J. Cell Biol., vol. 118, no. 5, pp. 1097-1108, Sep. 1992.
42. S. C. Schuyler and D. Pellman, "Microtubule "plus-end-tracking proteins": The end is just the beginning," Cell, vol. 105, no. 4, pp. 421-424, May 2001.
43. G. Lansbergen and A. Akhmanova, "Microtubule plus end: A hub of cellular activities," Traffic, vol. 7, no. 5, pp. 499-507, May 2006.
44. A. Akhmanova and C. C. Hoogenraad, "Microtubule plus-end-tracking proteins: Mechanisms and functions," Curr. Opin. Cell Biol., vol. 17, no. 1, pp. 47-54, Feb. 2005.
45. J. Howard and A. A. Hyman, "Dynamics and mechanics of the microtubule plus end," Nature, vol. 422, no. 6933, pp. 753-758, Apr. 2003.
46. F. Perez, G. S. Diamantopoulos, R. Stalder, and T. E. Kreis, "CLIP-170 highlights growing microtubule ends in vivo," Cell, vol. 96, no. 4, pp. 517-527, Feb. 1999.
47. S. Hadjidemetriou, J. S. Duncan, D. Toomre, and D. Tuck, "Automatic quantification of microtubule dynamics," in 2004 2nd IEEE Int. Symp. Biomed. Imag.: Macro Nano, Arlington, VA, Apr. 2004, pp. 656-659.
48. K. Y. Kong, A. I. Marcus, J. Y. Hong, P. Giannakakou, and M. D. Wang, "Computer assisted analysis of microtubule dynamics in living cells," in 2005 27th Annu. Int. Conf. IEEE Eng. Med. Biol. Soc., China, Sep. 2005, pp. 3982-3985.
49. M. Saban, A. Altinok, A. Peck, C. Kenney, S. Feinstein, L. Wilson, K. Rose, and B. S. Manjunath, "Automated tracking and modeling of microtubule dynamics," in 2006 3rd IEEE Int. Symp. Biomed Imag.: Macro Nano, Arlington, VA, Apr. 2006, pp. 1032-1035.
50. P. Niethammer, I. Kronja, S. Kandels-Lewis, S. Rybina, P. Bastiaens, and E. Karsenti, "Discrete states of a protein interaction network govern interphase and mitotic microtubule dynamics," PLoS Biol., vol. 5, no. 2, p. e29, Jan. 2007.
51. P. Carvalho, J. S. Tirnauer, and D. Pellman, "Surfing on microtubule ends," Trends Cell Biol., vol. 13, no. 5, pp. 229-237, May 2003.
52. B. D. Ripley, Stochastic Simulation. New York: Wiley, 1987.
53. A. Doucet, S. Godsill, and C. Andrieu, "On sequential Monte Carlo sampling methods for Bayesian filtering," Statist. Comput., vol. 10, no. 3, pp. 197-208, Jul. 2000.
54. B. Ristic, S. Arulampalam, and N. Gordon, Beyond Kalman Filters: Particle Filters For Applications. Norwood, MA: Artech House, 2004.
55. J. Vermaak, A. Doucet, and P. Pérez, "Maintaining multi-modality through mixture tracking," in Proc. 9th IEEE Int. Conf Comput. Vision, Nice, France, Oct. 2003, pp. 1110-1116.
56. Y. Bar-Shalom, X. R. Li, and T. Kirubarajan, Estimation with Applications to Tracking and Navigation. New York: Wiley., 2001.
57. 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.
58. L. Song, E. J. Hennink, I. T. Young, and H. J. Tanke, "Photobleaching kinetics of fluorescein in quantitative fluorescence microscopy," Biophys. J., vol. 68, no. 6, pp. 2588-2600, Jun. 1995.
59. J. P. Rigaut and J. Vassy, "High-resolution three-dimensional images from confocal scanning laser microscopy. Quantitative study and mathematical correction of the effects from bleaching and fluorescence attenuation in depth," Anal. Quant. Cytol Histol., vol. 13, no. 4, pp. 223-232, Aug. 1991.
60. Z. Khan, T. Balch, and F. Dellaert, "MCMC-based particle filtering for tracking a variable number of interacting targets," IEEE Trans. Pattern Anal. Mach. Intell., vol. 27, no. 11, pp. 1805-1819, Nov. 2005.
61. 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, Apr. 2007.
62. S. F. Gibson and F. Lanni, "Experimental test of an analytical model of aberration in an oil-immersion objective lens used in three-dimensional light microscopy," J. Opt. Soc Am. A., vol. 9, no. 1, pp. 154-166, Jan. 1992.
63. Y. Kosuge and T. Matsuzaki, "The optimum gate shape and threshold for target tracking," in Proc. SICE Annu. Conf. Fukui, Fukui, Japan, Aug. 2003, vol. 2, pp. 2152-2157.
64. T. Stepanova, J. Slemmer, C. C. Hoogenraad, G. Lansbergen, B. Dortland, C. I. de Zeeuw, F. Grosveld, G. van Cappellen, A. Akhmanova, and N. Galjart, "Visualization of microtubule growth in cultured neurons via the use of EB3-GFP (end-binding protein 3-green fluorescent protein)," J. Neurosci., vol. 23, no. 7, pp. 2655-2664, Apr. 2003.
65. W. S. Rasband, ImageJ: Image processing and analysis in Java [Online]. Available: http://www.rsb.info.nih.gov/ij/
66. E. Meijering, MTrackJ: A Java program for manual object tracking [Online]. Available: http://www.imagescience.org/meijering/software/ mtrackj/
67. A. Akhmanova, C. C. Hoogenraad, K. Drabek, T. Stepanova, B. Dortland, T. Verkerk, W. Vermeulen, B. M. Burgering, C. I. de Zeeuw, F. Grosveld, and N. Galjart, "Clasps are CLIP-115 and -170 associating proteins involved in the regional regulation of microtubule dynamics in motile fibroblasts," Cell, vol. 104, no. 6, pp. 923-935, Mar. 2001.
68. W. Schroeder, K. Martin, and B. Lorensen, The Visualization Toolkit: An Object-Oriented Approach to 3-D Graphics, 3rd ed. New York: Kitware, 2002.
69. M. D. Abramoff, P. J. Magelhaes, and S. J. Ram, "Image processing with imageJ," Biophotonics Int., vol. 11, pp. 36-42, 2004.
70. G. Rabut and J. Ellenberg, "Automatic real-time three-dimensional cell tracking by fluorescence microscopy," J Microsc., vol. 216, no. 2, pp. 131-137, Nov. 2004.
71. V. Levi, Q. Ruan, and E. Gratton, "3-D Particle tracking in a two-photon microscope: Application to the study of molecular dynamics in cells," Biophys. J., vol. 88, no. 4, pp. 2919-2928, Apr. 2005.
72. T. Ragan, H. Huang, P. So, and E. Gratton, "3-D particle tracking on a two-photon microscope," J. Fluoresc., vol. 16, no. 3, pp. 325-336, May 2006.