Objective comparison of particle tracking methods

Nature Methods

Volumn 11, Issue 3, 2014, Pages 281-289

  Chenouard, Nicolas ^a,b,c   Smal, Ihor ^d   De Chaumont, Fabrice ^a   Maška, Martin ^e,f   Sbalzarini, Ivo F ^g   Gong, Yuanhao ^g   Cardinale, Janick ^g   Carthel, Craig ^h   Coraluppi, Stefano ^h   Winter, Mark ⁱ   Cohen, Andrew R ⁱ   Godinez, William J ^j,k   Rohr, Karl ^j,k   Kalaidzidis, Yannis ^g,l   Liang, Liang ^m   Duncan, James ^m   Shen, Hongying ⁿ   Xu, Yingke ^o   Magnusson, Klas E G ^p   Jaldén, Joakim ^p   Blau, Helen M ^q   Paul Gilloteaux, Perrine ^r   Roudot, Philippe ^s   Kervrann, Charles ^s   Waharte, François ^r   Tinevez, Jean Yves ^t   Shorte, Spencer L ^t   Willemse, Joost ^u   Celler, Katherine ^u   Van Wezel, Gilles P ^u   Dan, Han Wei ^v   Tsai, Yuh Show ^v   De Solórzano, Carlos Ortiz ^e   Olivo Marin, Jean Christophe ^a   Meijering, Erik ^d   more..

^a CNRS   (France)

^b EPFL   (Switzerland)

^c NEW YORK UNIVERSITY SCHOOL OF MEDICINE   (United States)

^d ERASMUS MEDICAL CENTER   (Netherlands)

^e UNIVERSITY OF NAVARRA   (Spain)

^f MASARYK UNIVERSITY   (Czech Republic)

^g MAX PLANCK INSTITUTE OF MOLECULAR CELL BIOLOGY AND GENETICS   (Germany)

^h Compunetix Inc   (United States)

ⁱ Drexel University   (United States)

^j UNIVERSITY OF HEIDELBERG   (Germany)

^k GERMAN CANCER RESEARCH CENTER DKFZ   (Germany)

^l MOSCOW STATE UNIVERSITY   (Russian Federation)

^m Yale University   (United States)

ⁿ YALE UNIVERSITY SCHOOL OF MEDICINE   (United States)

^o ZHEJIANG UNIVERSITY   (China)

^p ROYAL INSTITUTE OF TECHNOLOGY   (Sweden)

^q STANFORD UNIVERSITY SCHOOL OF MEDICINE   (United States)

^r INSTITUT CURIE   (France)

^s INRIA   (France)

^t INSTITUT PASTEUR   (France)

^u LEIDEN UNIVERSITY   (Netherlands)

^v CHUNG YUAN CHRISTIAN UNIVERSITY   (Taiwan)

more..

Author keywords

[No Author keywords available]

Indexed keywords

ANALYTIC METHOD; ARTICLE; COMPARATIVE STUDY; COMPETITION; CONFOCAL MICROSCOPY; FLUORESCENCE MICROSCOPY; HUMAN; IMAGE ANALYSIS; INFORMATION PROCESSING; PARTICLE TRACKING METHOD; PERFORMANCE MEASUREMENT SYSTEM; PRIORITY JOURNAL; QUANTITATIVE ANALYSIS; TIME SERIES ANALYSIS;

IMAGE INTERPRETATION, COMPUTER-ASSISTED; MICROSCOPY, FLUORESCENCE;

EID: 84895512107     PISSN: 15487091     EISSN: 15487105     Source Type: Journal    
DOI: 10.1038/nmeth.2808     Document Type: Article

References (62)

1. Saxton, M.J. & Jacobson, K. Single-particle tracking: applications to membrane dynamics. Annu. Rev. Biophys. Biomol. Struct. 26, 373-399 (1997).
2. Akhmanova, A. & Steinmetz, M.O. Tracking the ends: a dynamic protein network controls the fate of microtubule tips. Nat. Rev. Mol. Cell Biol. 9, 309-322 (2008).
3. Berginski, M.E., Vitriol, E.A., Hahn, K.M. & Gomez, S.M. High-resolution quantification of focal adhesion spatiotemporal dynamics in living cells. PLoS ONE 6, e22025 (2011).
4. Brandenburg, B. & Zhuang, X. Virus trafficking-learning from single-virus tracking. Nat. Rev. Microbiol. 5, 197-208 (2007).
5. Jandt, U. & Zeng, A.-P. Modeling of intracellular transport and compartmentation. Adv. Biochem. Eng. Biotechnol. 127, 221-249 (2012).
6. Sinha, B. et al. Dynamic organization of chromatin assembly and transcription factories in living cells. Methods Cell Biol. 98, 57-78 (2010).
7. Agarwal, S. et al. ATP-dependent and independent functions of Rad54 in genome maintenance. J. Cell Biol. 192, 735-750 (2011).
8. Stephens, D.J. & Allan, V.J. Light microscopy techniques for live cell imaging. Science 300, 82-86 (2003).
9. Ji, N., Shroff, H., Zhong, H. & Betzig, E. Advances in the speed and resolution of light microscopy. Curr. Opin. Neurobiol. 18, 605-616 (2008).
10. Shaner, N.C., Steinbach, P.A. & Tsien, R.Y. A guide to choosing fluorescent proteins. Nat. Methods 2, 905-909 (2005).
11. Giepmans, B.N.G., Adams, S.R., Ellisman, M.H. & Tsien, R.Y. The fluorescent toolbox for assessing protein location and function. Science 312, 217-224 (2006).
12. Saxton, M.J. Single-particle tracking: connecting the dots. Nat. Methods 5, 671-672 (2008).
13. Genovesio, A. et al. 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 (2006).
14. Smal, I., Draegestein, K., Galjart, N., Niessen, W. & Meijering, E. Particle filtering for multiple object tracking in dynamic fluorescence microscopy images: application to microtubule growth analysis. IEEE Trans. Med. Imaging 27, 789-804 (2008).
15. Kalaidzidis, Y. Multiple objects tracking in fluorescence microscopy. J. Math. Biol. 58, 57-80 (2009).
16. Meijering, E., Dzyubachyk, O. & Smal, I. Methods for cell and particle tracking. Methods Enzymol. 504, 183-200 (2012).
17. Meijering, E., Smal, I. & Danuser, G. Tracking in molecular bioimaging. IEEE Signal Process. Mag. 23, 46-53 (2006).
18. Kalaidzidis, Y. Intracellular objects tracking. Eur. J. Cell Biol. 86, 569-578 (2007).
19. Dorn, J.F., Danuser, G. & Yang, G. Computational processing and analysis of dynamic fluorescence image data. Methods Cell Biol. 85, 497-538 (2008).
20. Meijering, E., Dzyubachyk, O., Smal, I. & van Cappellen, W.A. Tracking in cell and developmental biology. Semin. Cell Dev. Biol. 20, 894-902 (2009).
21. Jaqaman, K. & Danuser, G. Computational image analysis of cellular dynamics: a case study based on particle tracking. Cold Spring Harb. Protoc. 2009, pdb.top65 (2009).
22. Rohr, K. et al. Tracking and quantitative analysis of dynamic movements of cells and particles. Cold Spring Harb. Protoc. 2010, pdb.top80 (2010).
23. Blackman, S. & Popoli, R. Design and Analysis of Modern Tracking Systems (Artech House, Norwood, Massachusetts, USA, 1999).
24. Sonka, M., Hlavac, V. & Boyle, R. Image Processing, Analysis, and Machine Vision 3rd edn. (Cengage Learning, Florence, Kentucky, USA, 2007).
25. Cheezum, M.K., Walker, W.F. & Guilford, W.H. Quantitative comparison of algorithms for tracking single fluorescent particles. Biophys. J. 81, 2378-2388 (2001).
26. Carter, B.C., Shubeita, G.T. & Gross, S.P. Tracking single particles: a user-friendly quantitative evaluation. Phys. Biol. 2, 60-72 (2005).
27. Smal, I., Loog, M., Niessen, W. & Meijering, E. Quantitative comparison of spot detection methods in fluorescence microscopy. IEEE Trans. Med. Imaging 29, 282-301 (2010).
28. Ruusuvuori, P. et al. Evaluation of methods for detection of fluorescence labeled subcellular objects in microscope images. BMC Bioinformatics 11, 248 (2010).
29. Godinez, W.J. et al. Deterministic and probabilistic approaches for tracking virus particles in time-lapse fluorescence microscopy image sequences. Med. Image Anal. 13, 325-342 (2009).
30. Gillette, T.A., Brown, K.M., Svoboda, K., Liu, Y. & Ascoli, G.A. DIADEMchallenge.org: a compendium of resources fostering the continuous development of automated neuronal reconstruction. Neuroinformatics 9, 303-304 (2011).
31. Anonymous. Going for algorithm gold. Nat. Methods 5, 659 (2008).
32. Sbalzarini, I.F. & Koumoutsakos, P. Feature point tracking and trajectory analysis for video imaging in cell biology. J. Struct. Biol. 151, 182-195 (2005).
33. Coraluppi, S. & Carthel, C. Recursive track fusion for multi-sensor surveillance. Inf. Fusion 5, 23-33 (2004).
34. Coraluppi, S. & Carthel, C. Multi-stage multiple-hypothesis tracking. J. Adv. Inf. Fusion 6, 57-67 (2011).
35. Olivo-Marin, J.-C. Extraction of spots in biological images using multiscale products. Pattern Recognit. 35, 1989-1996 (2002).
36. Chenouard, N., Bloch, I. & Olivo-Marin, J.-C. Multiple hypothesis tracking in cluttered condition. in Proc. Int. Conf. Image Proc. 3621-3624 (IEEE, 2009).
37. Chenouard, N., Bloch, I. & Olivo-Marin, J.-C. Multiple hypothesis tracking in microscopy images. in Proc. IEEE Int. Symp. Biomed. Imaging 1346-1349 (IEEE, 2009).
38. Winter, M.R., Fang, C., Banker, G., Roysam, B. & Cohen, A.R. Axonal transport analysis using Multitemporal Association Tracking. Int. J. Comput. Biol. Drug Des. 5, 35-48 (2012).
39. Winter, M. et al. Vertebrate neural stem cell segmentation, tracking and lineaging with validation and editing. Nat. Protoc. 6, 1942-1952 (2011).
40. Godinez, W.J., Lampe, M., Eils, R., Müller, B. & Rohr, K. Tracking multiple particles in fluorescence microscopy images via probabilistic data association. in Proc. IEEE Int. Symp. Biomed. Imaging 1925-1928 (IEEE, 2011).
41. Rink, J., Ghigo, E., Kalaidzidis, Y. & Zerial, M. Rab conversion as a mechanism of progression from early to late endosomes. Cell 122, 735-749 (2005).
42. Liang, L., Shen, H., De Camilli, P. & Duncan, J.S. Tracking clathrin coated pits with a multiple hypothesis based method. Med. Image Comput. Comput. Assist. Interv. 6362, 315-322 (2010).
43. Yin, Z., Kanade, T. & Chen, M. Understanding the phase contrast optics to restore artifact-free microscopy images for segmentation. Med. Image Anal. 16, 1047-1062 (2012).
44. Magnusson, K.E.G. & Jaldén, J. A batch algorithm using iterative application of the Viterbi algorithm to track cells and construct cell lineages. in Proc. IEEE Int. Symp. Biomed. Imaging 382-385 (IEEE, 2012).
45. Husain, M., Boudier, T., Paul-Gilloteaux, P., Casuso, I. & Scheuring, S. Software for drift compensation, particle tracking and particle analysis of high-speed atomic force microscopy image series. J. Mol. Recognit. 25, 292-298 (2012).
46. Casuso, I. et al. Characterization of the motion of membrane proteins using high-speed atomic force microscopy. Nat. Nanotechnol. 7, 525-529 (2012).
47. Rao, A.R. & Schunck, B.G. Computing oriented texture fields. CVGIP: Graph. Models Image Process. 53, 157-185 (1991).
48. Hager, G.D., Dewan, M. & Stewart, C.V. Multiple kernel tracking with SSD. in Proc. IEEE Comput. Soc. Conf. Comput. Vis. Pattern Recognit. 790-797 (IEEE, 2004).
49. Rousseeuw, P.J. & Leroy, A.M. Robust Regression and Outlier Detection (Wiley, Hoboken, New Jersey, USA, 2003).
50. Thompson, R.E., Larson, D.R. & Webb, W.W. Precise nanometer localization analysis for individual fluorescent probes. Biophys. J. 82, 2775-2783 (2002).
51. Shafique, K. & Shah, M. A noniterative greedy algorithm for multiframe point correspondence. IEEE Trans. Pattern Anal. Mach. Intell. 27, 51-65 (2005).
52. Jaqaman, K. et al. Robust single-particle tracking in live-cell time-lapse sequences. Nat. Methods 5, 695-702 (2008).
53. Lowe, D.G. Distinctive image features from scale-invariant keypoints. Int. J. Comput. Vis. 60, 91-110 (2004).
54. Crocker, J.C. & Grier, D.G. Methods of digital video microscopy for colloidal studies. J. Colloid Interface Sci. 179, 298-310 (1996).
55. Celler, K., van Wezel, G.P. & Willemse, J. Single particle tracking of dynamically localizing TatA complexes in Streptomyces coelicolor. Biochem. Biophys. Res. Commun. 438, 38-42 (2013).
56. Ku, T.-C. et al. An automated tracking system to measure the dynamic properties of vesicles in living cells. Microsc. Res. Tech. 70, 119-134 (2007).
57. Ku, T.-C., Kao, L.-S., Lin, C.-C. & Tsai, Y.-S. Morphological filter improve the efficiency of automated tracking of secretory vesicles with various dynamic properties. Microsc. Res. Tech. 72, 639-649 (2009).
58. Huth, J. et al. Significantly improved precision of cell migration analysis in time-lapse video microscopy through use of a fully automated tracking system. BMC Cell Biol. 11, 24 (2010).
59. Munkres, J. Algorithms for the assignment and transportation problems. J. Soc. Ind. Appl. Math. 5, 32-38 (1957).
60. Saxton, M.J. Wanted: a positive control for anomalous subdiffusion. Biophys. J. 103, 2411-2422 (2012).
61. de Chaumont, F. et al. Icy: an open bioimage informatics platform for extended reproducible research. Nat. Methods 9, 690-696 (2012).
62. Schindelin, J. et al. Fiji: an open-source platform for biological-image analysis. Nat. Methods 9, 676-682 (2012).