Microtubule dynamics analysis using kymographs and variable-rate particle filters

IEEE Transactions on Image Processing

Volumn 19, Issue 7, 2010, Pages 1861-1876

  Smal, Ihor ^a   Grigoriev, Ilya ^a   Akhmanova, Anna ^a   Niessen, Wiro J ^b   Meijering, Erik ^a  

^a ERASMUS MEDICAL CENTER   (Netherlands)

^b DELFT UNIVERSITY OF TECHNOLOGY   (Netherlands)

Author keywords

Bayesian estimation; Biological microscopy; Microtubule dynamics; Motion analysis; Multiscale trend analysis; Variable rate particle filters

Indexed keywords

BAYESIAN ESTIMATIONS; BIOLOGICAL MICROSCOPY; MICROTUBULE DYNAMICS; MOTION ANALYSIS; MULTISCALES; PARTICLE FILTER; TREND ANALYSIS; VARIABLE RATE;

BAYESIAN NETWORKS; DYNAMICS; ESTIMATION; IMAGE SEGMENTATION; NONLINEAR FILTERING;

TRACKING (POSITION);

ALGORITHM; ARTICLE; BAYES THEOREM; BIOMECHANICS; ELECTROKYMOGRAPHY; IMAGE PROCESSING; METABOLISM; METHODOLOGY; MICROTUBULE; MOLECULAR DYNAMICS; PHASE CONTRAST MICROSCOPY;

ALGORITHMS; BAYES THEOREM; BIOMECHANICS; IMAGE PROCESSING, COMPUTER-ASSISTED; KYMOGRAPHY; MICROSCOPY, INTERFERENCE; MICROTUBULES; MOLECULAR DYNAMICS SIMULATION;

EID: 77953693054     PISSN: 10577149     EISSN: None     Source Type: Journal    
DOI: 10.1109/TIP.2010.2045031     Document Type: Article

References (58)

1. P. Bieling, L. Laan, H. Schek, L. E. Munteanu, L. Sandblad, M. Dogterom, D. Brunner, and T. Surrey, "Reconstitution of a microtubule plus-end tracking system in vitro," Nature, vol.450, no.7172, pp. 1100-1105, 2007.
2. E. L. Munteanu, "Dynamics and Regulation at the Tip: A High Resolution View on Microtubule Assembly," Ph.D. dissertation, Inst. Atomic Molec. Phys. (AMOLF), Amsterdam, The Netherlands, 2008.
3. Q. Wu, F. A. Merchant, and K. R. Castleman, Microscope Image Processing. New York: Elsevier, 2008.
4. D. J. Stephens and V. J. Allan, "Light microscopy techniques for live cell imaging," Science, vol.300, no.5616, pp. 82-86, 2003.
5. J. B. Pawley, Handbook of Biological Confocal Microscopy, 3rd ed. New York: Springer, 2006.
6. 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, 2002.
7. 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, 2003.
8. 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.
9. 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, 2005.
10. K. Jaqaman, D. Loerke, M. Mettlen, H. Kuwata, S. Grinstein, S. Schmid, and G. Danuser, "Robust single-particle tracking in live-cell time-lapse sequences," Nature Methods, vol.5, no.8, pp. 695-702, 2008.
11. E. Meijering, I. Smal, and G. Danuser, "Tracking in molecular bioimaging," IEEE Signal Process. Mag., vol.23, no.3, pp. 46-53, May 2006.
12. E. Meijering, I. Smal, O. Dzyubachyk, and J.-C. Olivo-Marin, "Time-lapse imaging," in Microscope Image Processing, Q. Wu, F. A. Merchant, and K. R. Castleman, Eds. New York: Elsevier, 2008, pp. 401-440.
13. I. Smal, K. Draegestein, N. Galjart, W. Niessen, and E. Meijering, "Particle filtering for multiple object tracking in dynamic fluorescence microscopy images: Application to microtubule growth analysis," IEEE Trans. Med. Imag., vol.27, no.6, pp. 789-804, Jun. 2008.
14. I. Smal, E. Meijering, K. Draegestein, N. Galjart, I. Grigoriev, A. Akhmanova, M. E. van Royen, A. B. Houtsmuller, and W. Niessen, "Multiple object tracking in molecular bioimaging by Rao-Blackwellized marginal particle filtering," Med. Image Anal., vol.12, no.6, pp. 764-777, 2008.
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.
16. 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.
17. Y. Sato, J. Chen, R. Zoroofi, N. Harada, S. Tamura, and T. Shiga, "Automatic extraction and measurement of leukocyte motion in microvessels using spatiotemporal image analysis," IEEE Trans. Biomed. Eng., vol.44, no.4, pp. 225-236, Apr. 1997.
18. B. Hinz, W. Alt, C. Johnen, V. Herzog, and H.-W. Kaiser, "Quantifying lamella dynamics of cultured cells by SACED, a new computer-assisted motion analysis," Exper. Cell Res., vol.251, no.1, pp. 234-243, 1999.
19. J. C. Bulinski, D. J. Odde, B. J. Howell, T. D. Salmon, and C. M. Waterman-Storer, "Rapid dynamics of the microtubule binding of ensconsin in vivo," J. Cell Sci., vol.114, no.21, pp. 3885-3897, 2001.
20. J. E. Bear, T. M. Svitkina, M. Krause, D. A. Schafer, J. J. Loureiro, G. A. Strasser, I. V. Maly, O. Y. Chaga, J. A. Cooper, G. G. Borisy, and F. B. Gertler, "Antagonism between Ena/VASP proteins and actin filament capping regulates fibroblast motility," Cell, vol.109, no.4, pp. 509-521, 2002.
21. V. Racine, M. Sachse, J. Salamero, V. Fraisier, A. Trubuil, and J. B. Sibarita, "Visualization and quantification of vesicle trafficking on a three-dimensional cytoskeleton network in living cells," J. Microsc., vol.225, pp. 214-228, 2007.
22. A. Desai and T. J. Mitchison, "Microtubule polymerization dynamics," Annu. Rev. Cell Development. Biol., vol.13, pp. 83-117, 1997.
23. E. Nogales, M. Whittaker, R. Milligan, and K. Downing, "Highresolution model of the microtubule," Cell, vol.96, no.1, pp. 79-88, 1999.
24. J. Howard and A. A. Hyman, "Dynamics and mechanics of the microtubule plus end," Nature, vol.422, no.6933, pp. 753-758, 2003.
25. T. Mitchison and M. Kirschner, "Dynamic instability of microtubule growth," Nature, vol.312, no.5991, pp. 237-242, 1984.
26. 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, 2001.
27. P. Carvalho, J. S. Tirnauer, and D. Pellman, "Surfing on microtubule ends," Trends Cell Biol., vol.13, no.5, pp. 229-237, 2003.
28. A. Akhmanova and M. O. Steinmetz, "Tracking the ends: A dynamic protein network controls the fate of microtubule tips," Nature Rev. Molec. Cell Biol., vol.9, no.4, pp. 309-322, 2008.
29. A. Akhmanova and C. C. Hoogenraad, "Microtubule plus-end-tracking proteins: Mechanisms and functions," Current Opin. Cell Biol., vol.17, no.1, pp. 47-54, 2005.
30. R. Walker, E. O'Brien, N. Pryer, M. Soboeiro, W. Voter, H. Erickson, and E. Salmo, "Dynamic instability of individual microtubules analyzed by video light microscopy: Rate constants and transition frequencies," J. Cell Biol., vol.107, no.4, pp. 1437-1448, 1988.
31. D. Murphy, Fundamentals of Light Microscopy and Digital Imaging. New York: Wiley, 2001.
32. N. Caudron, I. Arnal, E. Buhler, D. Job, and O. Valiron, "Microtubule nucleation from stable tubulin oligomers," J. Biol. Chem., vol.227, no.52, pp. 50973-50979, 2002.
33. M. Sonka, V. Hlavac, and R. Boyle, Image Processing, Analysis, and Machine Vision, 2nd ed. Boston, MA: PWS-Kent, 1999.
34. Y. S. Fong, C. A. Pomalaza, and X. H. Wang, "Comparison study of nonlinear filters in image processing applications," Opt. Eng., vol.28, no.7, pp. 749-760, 1989.
35. C. Tomasi and R. Manduchi, "Bilateral filtering for gray and color images," in Proc. 6th Int. Conf. Computer Vision, 1998, pp. 839-846.
36. D. Comaniciu and P. Meer, "Mean shift: A robust approach toward feature space analysis," IEEE Trans. Pattern Anal. Mach. Intell., vol.24, no.5, pp. 603-619, May 2002.
37. P. Perona and J. Malik, "Scale-space and edge detection using anisotropic diffusion," IEEE Trans. Pattern Anal. Mach. Intell., vol.12, no.7, pp. 629-639, Jul. 1990.
38. B. M. ter Haar Romeny, Front-End Vision and Multi-Scale Image Analysis. New York: Springer, 2003.
39. J. F. Canny, "A computational approach to edge detection," IEEE Trans. Pattern Anal. Mach. Intell., vol.PAMI-8, no.6, pp. 679-698, Nov. 1986.
40. S. 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. 174-188, Feb. 2002.
41. B. Ristic, S. Arulampalam, and N. Gordon, Beyond the Kalman Filter: Particle Filters for Tracking Applications. Norwood, MA: Artech House, 2004.
42. A. Doucet, N. de Freitas, and N. Gordon, Sequential Monte Carlo Methods in Practice. New York: Springer-Verlag, 2001.
43. S. Godsill and J. Vermaak, "Variable rate particle filters for tracking applications," in Proc. IEEE/SP 13th Workshop Statistical Signal Processing, 2005, pp. 1280-1285.
44. S. Godsill, J. Vermaak, K.-F. Ng, and J.-F. Li, "Models and algorithms for tracking of manoeuvring objects using variable rate particle filters," Proc. IEEE, vol.95, no.5, pp. 925-952, May 2007.
45. Y. Bar-Shalom, X. R. Li, and T. Kirubarajan, Estimation With Applications to Tracking and Navigation. New York: Wiley, 2001.
46. N. M. Haan and S. J. Godsill, "A time-varying model for DNA sequencing data submerged in correlated noise," in Proc. IEEEWorkshop Statistical Signal Processing, Aug. 2001, pp. 245-248.
47. M. Schaap, I. Smal, C. Metz, T. van Walsum, and W. J. Niessen, "Bayesian tracking of elongated structures in 3-D images," in Proc. 20th Int. Conf. Information Processing in Medical Imaging, 2007, pp. 74-85.
48. M. Schaap, R. Manniesing, I. Smal, T. van Walsum, A. van der Lugt, and W. J. Niessenc, "Bayesian tracking of tubular structures and its application to carotid arteries in CTA," in Proc. Medical Image Computing and Computer-Assisted Intervention, 2007, pp. 562-570.
49. I. Zaliapin, A. Gabrielov, and V. Keilis-Borok, "Multiscale trend analysis," Fractals, vol.12, no.3, pp. 275-292, 2004.
50. I. Zaliapin, I. Semenova, A. Kashina, and V. Rodionov, "Multiscale trend analysis of microtubule transport in melanophores," Biophys. J., vol.88, no.6, pp. 4008-4016, 2005. (Pubitemid 40991113)
51. W. Ng, J. Li, S. Godsill, and J. Vermaak, "A hybrid approach for online joint detection and tracking for multiple targets," in Proc. IEEE Aerospace Conf., 2005, pp. 2126-2141.
52. W. S. Rasband, ImageJ: Image Processing and Analysis in Java [Online]. Available: http://rsb.info.nih.gov/ij/
53. E. Meijering, M. Jacob, J.-C. F. Sarria, P. Steiner, H. Hirling, and M. Unser, "Design and validation of a tool for neurite tracing and analysis in fluorescence microscopy images," Cytometry, vol.58A, no.2, pp. 167-176, 2004. (Pubitemid 38509178)
54. Y. Boykov, O. Veksler, and R. Zabih, "Fast approximate energy minimization via graph cuts," IEEE Trans. Pattern Anal. Mach. Intell., vol.23, no.11, pp. 1222-1239, Nov. 2004. (Pubitemid 33137959)
55. Y. Boykov and V. Kolmogorov, "An experimental comparison of min-cut/max-flow algorithms for energy minimization in vision," IEEE Trans. Pattern Anal. Mach. Intell., vol.26, no.9, pp. 1124-1137, Sep. 2004.
56. J. Malcolm, Y. Rathi, and A. Tannenbaum, "Multi-object tracking through clutter using graph cuts," in Proc. IEEE Int. Conf. Computer Vision, 2007, pp. 1-5.
57. G.Winkler, Image Analysis, Random Fields and Markov Chain Monte Carlo Methods: A Mathematical Introduction (Stochastic Modelling and Applied Probability). New York: Springer-Verlag, 2006.
58. Y. Komarova, C. O. de Groot, I. Grigoriev, S. M. Gouveia, E. L. Munteanu, J. M. Schober, S. Honnappa, R. M. Buey, C. C. Hoogenraad, M. Dogterom, G. G. Borisy, M. O. Steinmetz, and A. Akhmanova, "Mammalian end binding proteins control persistent microtubule growth," J. Cell Biol., vol.184, no.5, pp. 691-706, 2009.