Ultrafast, accurate, and robust localization of anisotropic dipoles

Protein and Cell

Volumn 4, Issue 8, 2013, Pages 598-606

  Zhang, Yongdeng ^a,b   Gu, Lusheng ^a,b   Chang, Hao ^b,c   Ji, Wei ^b   Chen, Yan ^b,d   Zhang, Mingshu ^b   Yang, Lu ^e   Liu, Bei ^a,b   Chen, Liangyi ^e   Xu, Tao ^a,b  

^a HUAZHONG UNIVERSITY OF SCIENCE AND TECHNOLOGY   (China)

^b INSTITUTE OF BIOPHYSICS   (China)

^c UNIVERSITY OF SCIENCE AND TECHNOLOGY OF CHINA   (China)

^d UNIVERSITY OF CHINESE ACADEMY OF SCIENCES   (China)

^e PEKING UNIVERSITY   (China)

Author keywords

artificial neural network; point spread function; restricted mobility; super resolution imaging

Indexed keywords

ACCURACY; ALGORITHM; ANISOTROPY; ARTICLE; ARTIFICIAL NEURAL NETWORK; DIPOLE; IMAGE ANALYSIS; IMMUNOFLUORESCENCE TEST; KERNEL METHOD; MICROSCOPY; OPTICAL RESOLUTION; PHYSICAL PARAMETERS; POINT SPREAD FUNCTION; PRIORITY JOURNAL; PROCESS DEVELOPMENT; STOCHASTIC OPTICAL RECONSTRUCTION MICROSCOPY; THREE DIMENSIONAL IMAGING; VALIDATION PROCESS;

EID: 84880847417     PISSN: 1674800X     EISSN: 16748018     Source Type: Journal    
DOI: 10.1007/s13238-013-3904-1     Document Type: Article

References (27)

1. Aquino, D., Schonle, A., Geisler, C., Middendorff, C. V., Wurm, C. A., Okamura, Y., Lang, T., Hell, S. W., and Egner, A. (2011). Two-color nanoscopy of three-dimensional volumes by 4Pi detection of stochastically switched fluorophores. Nat Methods 8, 353-359.
2. Backlund, M. P., Lew, M. D., Backer, A. S., Sahl, S. J., Grover, G., Agrawal, A., Piestun, R., and Moerner, W. E. (2012). Simultaneous, accurate measurement of the 3D position and orientation of single molecules. Proc Natl Acad Sci U S A 109, 19087-19092.
3. Betzig, E., Patterson, G. H., Sougrat, R., Lindwasser, O. W., Olenych, S., Bonifacino, J. S., Davidson, M. W., Lippincott-Schwartz, J., and Hess, H. F. (2006). Imaging intracellular fluorescent proteins at nanometer resolution. Science 313, 1642-1645.
4. Born, M., and Wolf, E. (1999). Principles of optics: electromagnetic theory of propagation, interference and diffraction of light, 7th expanded edn (Cambridge; New York, Cambridge University Press).
5. Cartwright, H. M. (2008). Artificial neural networks in biology and chemistry: the evolution of a new analytical tool. Methods Mol Biol 458, 1-13.
6. Chang, H., Zhang, M., Ji, W., Chen, J., Zhang, Y., Liu, B., Lu, J., Zhang, J., Xu, P., and Xu, T. (2012). A unique series of reversibly switchable fluorescent proteins with beneficial properties for various applications. Proc Natl Acad Sci U S A 109, 4455-4460.
7. Dale, R. E., Hopkins, S. C., and der Heide, U. A., Marszalek, T., Irving, M., and Goldman, Y. E. (1999). Model-independent analysis of the orientation of fluorescent probes with restricted mobility in muscle fibers. Biophys J 76, 1606-1618.
8. Enderlein, J., Toprak, E., and Selvin, P. R. (2006). Polarization effect on position accuracy of fluorophore localization. Opt Express 14, 8111-8120.
9. Engelhardt, J., Keller, J., Hoyer, P., Reuss, M., Staudt, T., and Hell, S. W. (2011). Molecular orientation affects localization accuracy in superresolution far-field fluorescence microscopy. Nano Lett 11, 209-213.
10. Ha, T., Laurence, T. A., Chemla, D. S., and Weiss, S. (1999). Polarization spectroscopy of single fluorescent molecules. Phy Chem 103, 6839-6850.
11. Hess, S. T., Girirajan, T. P., and Mason, M. D. (2006). Ultra-high resolution imaging by fluorescence photoactivation localization microscopy. Biophys J 91, 4258-4272.
12. Irving, M. (1996). Steady-state polarization from cylindrically symmetric fl uorophores undergoing rapid restricted motion. Biophys J 70, 1830-1835.
13. Juette, M. F., Gould, T. J., Lessard, M. D., Mlodzianoski, M. J., Nagpure, B. S., Bennett, B. T., Hess, S. T., and Bewersdorf, J. (2008). Threedimensional sub-100 nm resolution fluorescence microscopy of thick samples. Nat Methods 5, 527-529.
14. McKinney, S. A., Murphy, C. S., Hazelwood, K. L., Davidson, M. W., and Looger, L. L. (2009). A bright and photostable photoconvertible fluorescent protein. Nat Methods 6, 131-133.
15. Mortensen, K. I., Churchman, L. S., Spudich, J. A., and Flyvbjerg, H. (2010). Optimized localization analysis for single-molecule tracking and super-resolution microscopy. Nat Methods 7, 377-381.
16. Ober, R. J., Ram, S., and Ward, E. S. (2004). Localization accuracy in single-molecule microscopy. Biophys J 86, 1185-1200.
17. Ohmachi, M., Komori, Y., Iwane, A. H., Fujii, F., Jin, T., and Yanagida, T. (2012). Fluorescence microscopy for simultaneous observation of 3D orientation and movement and its application to quantum rodtagged myosin V. Proc Natl Acad Sci U S A 109, 5294-5298.
18. Quirin, S., Pavani, S. R., and Piestun, R. (2012). Optimal 3D singlemolecule localization for superresolution microscopy with aberrations and engineered point spread functions. Proc Natl Acad Sci U S A 109, 675-679.
19. Riedl, J., Crevenna, A. H., Kessenbrock, K., Yu, J. H., Neukirchen, D., Bista, M., Bradke, F., Jenne, D., Holak, T. A., Werb, Z., et al. (2008). Lifeact: a versatile marker to visualize F-actin. Nat Methods 5, 605-607.
20. Rust, M. J., Bates, M., and Zhuang, X. (2006). Sub-diffraction-limit imaging by stochastic optical reconstruction microscopy (STORM). Nat Methods 3, 793-795.
21. Schoen, I., Ries, J., Klotzsch, E., Ewers, H., and Vogel, V. (2011). Binding-activated localization microscopy of DNA structures. Nano Lett 11, 4008-4011.
22. Shtengel, G., Galbraith, J. A., Galbraith, C. G., Lippincott-Schwartz, J., Gillette, J. M., Manley, S., Sougrat, R., Waterman, C. M., Kanchana-wong, P., Davidson, M. W., et al. (2009). Interferometric fluorescent super-resolution microscopy resolves 3D cellular ultrastructure. Proc Natl Acad Sci U S A 106, 3125-3130.
23. Smith, C. S., Joseph, N., Rieger, B., and Lidke, K. A. (2010). Fast, single-molecule localization that achieves theoretically minimum uncertainty. Nat Methods 7, 373-375.
24. Stallinga, S., and Rieger, B. (2010). Accuracy of the Gaussian Point Spread Function model in 2D localization microscopy. Opt Express 18, 24461-24476.
25. Testa, I., Schonle, A., von Middendorff, C., Geisler, C., Medda, R., Wurm, C. A., Stiel, A. C., Jakobs, S., Bossi, M., Eggeling, C., et al. (2008). Nanoscale separation of molecular species based on their rotational mobility. Opt Express 16, 21093-21104.
26. Thompson, R. E., Larson, D. R., and Webb, W. W. (2002). Precise nanometer localization analysis for individual fluorescent probes. Biophys J 82, 2775-2783.
27. Zhang, M., Chang, H., Zhang, Y., Yu, J., Wu, L., Ji, W., Chen, J., Liu, B., Lu, J., Liu, Y., et al. (2012). Rational design of true monomeric and bright photoactivatable fluorescent proteins. Nat Methods 9, 727-729.