Quantifying spatial organization in point-localization superresolution images using pair correlation analysis

Nature Protocols

Volumn 8, Issue 2, 2013, Pages 345-354

  Sengupta, Prabuddha ^a   Jovanovic Talisman, Tijana ^a,b   Lippincott Schwartz, Jennifer ^a  

^a EUNICE KENNEDY SHRIVER NATIONAL INSTITUTE OF CHILD HEALTH AND HUMAN DEVELOPMENT   (United States)

^b UNIVERSITY OF HAWAII   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

GREEN FLUORESCENT PROTEIN; MEMBRANE PROTEIN;

ALGORITHM; ARTICLE; CELL COMPARTMENTALIZATION; CONTROLLED STUDY; CORRELATION ANALYSIS; MATHEMATICAL COMPUTING; MATHEMATICAL MODEL; MICROSCOPY; MOLECULAR IMAGING; PHOTOACTIVATION; POINT LOCALIZATION SUPERRESOLUTION IMAGING; PRIORITY JOURNAL; PROTEIN BLOOD LEVEL; PROTEIN LOCALIZATION; QUANTITATIVE ANALYSIS; STRUCTURE ANALYSIS;

ALGORITHMS; GREEN FLUORESCENT PROTEINS; IMAGE PROCESSING, COMPUTER-ASSISTED; INTRACELLULAR SPACE; MEMBRANE PROTEINS; MICROSCOPY;

EID: 84873350446     PISSN: 17542189     EISSN: 17502799     Source Type: Journal    
DOI: 10.1038/nprot.2013.005     Document Type: Article

References (40)

1. Patterson, G., Davidson, M., Manley, S. & Lippincott-Schwartz, J. Superresolution imaging using single-molecule localization. Annu. Rev. Phys. Chem. 61, 345-367 (2010).
2. Toomre, D. & Bewersdorf, J. A new wave of cellular imaging. Annu. Rev. Cell Dev. Biol. 26, 285-314 (2010).
3. Patterson, G.H. Fluorescence microscopy below the diffraction limit. Semin. Cell Dev. Biol. 20, 886-893 (2009).
4. Flors, C. & Earnshaw, W.C. Super-resolution fluorescence microscopy as a tool to study the nanoscale organization of chromosomes. Curr. Opin. Chem. Biol. 15, 838-844 (2011).
5. Sigrist, S.J. & Sabatini, B.L. Optical super-resolution microscopy in neurobiology. Curr. Opin. Neurobiol. 22, 86-93 (2012).
6. Betzig, E. et al. Imaging intracellular fluorescent proteins at nanometer resolution. Science 313, 1642-1645 (2006).
7. Hess, S.T., Girirajan, T.P.K. & Mason, M.D. Ultra-high resolution imaging by fluorescence photoactivation localization microscopy. Biophys. J. 91, 4258-4272 (2006).
8. Rust, M.J., Bates, M. & Zhuang, X.W. Sub-diffraction-limit imaging by stochastic optical reconstruction microscopy (STORM). Nat. Methods 3, 793-795 (2006).
9. Wombacher, R. et al. Live-cell super-resolution imaging with trimethoprim conjugates. Nat. Methods 7, 717-719 (2010).
10. Folling, J. et al. Fluorescence nanoscopy by ground-state depletion and single-molecule return. Nat. Methods 5, 943-945 (2008).
11. Burnette, D.T., Sengupta, P., Dai, Y.H., Lippincott-Schwartz, J. & Kachar, B. Bleaching/blinking assisted localization microscopy for superresolution imaging using standard fluorescent molecules. Proc. Natl. Acad. Sci. USA 108, 21081-21086 (2011).
12. Simonson, P.D., Rothenberg, E. & Selvin, P.R. Single-molecule-based super-resolution images in the presence of multiple fluorophores. Nano Lett. 11, 5090-5096 (2011).
13. Thompson, R.E., Larson, D.R. & Webb, W.W. Precise nanometer localization analysis for individual fluorescent probes. Biophys. J. 82, 2775-2783 (2002).
14. Mortensen, K.I., Churchman, L.S., Spudich, J.A. & Flyvbjerg, H. Optimized localization analysis for single-molecule tracking and super-resolution microscopy. Nat. Methods 7, 377-381 (2010).
15. Kanchanawong, P. et al. Nanoscale architecture of integrin-based cell adhesions. Nature 468, 580-584 (2010).
16. Loschberger, A. et al. Super-resolution imaging visualizes the eightfold symmetry of gp210 proteins around the nuclear pore complex and resolves the central channel with nanometer resolution. J. Cell Sci. 125, 570-575 (2012).
17. Kopek, B.G., Shtengel, G., Xu, C.S., Clayton, D.A. & Hess, H.F. Correlative 3D superresolution fluorescence and electron microscopy reveal the relationship of mitochondrial nucleoids to membranes. Proc. Natl. Acad. Sci. USA 109, 6136-6141 (2012).
18. Sengupta, P. et al. Probing protein heterogeneity in the plasma membrane using PALM and pair correlation analysis. Nat. Methods 8, 969-975 (2011).
19. Gould, T.J., Verkhusha, V.V. & Hess, S.T. Imaging biological structures with fluorescence photoactivation localization microscopy. Nat. Protoc. 4, 291-308 (2009).
20. van de Linde, S. et al. Direct stochastic optical reconstruction microscopy with standard fluorescent probes. Nat. Protoc. 6, 991-1009 (2011).
21. Sengupta, P. & Lippincott-Schwartz, J. Quantitative analysis of photoactivated localization microscopy (PALM) datasets using pair-correlation analysis. Bioessays 34, 396-405 (2012).
22. Annibale, P., Vanni, S., Scarselli, M., Rothlisberger, U. & Radenovic, A. Identification of clustering artifacts in photoactivated localization microscopy. Nat. Methods 8, 527-528 (2011).
23. Annibale, P., Vanni, S., Scarselli, M., Rothlisberger, U. & Radenovic, A. Quantitative photo activated localization microscopy: unraveling the effects of photoblinking. PLoS ONE 6, e22678 (2011).
24. Kiskowski, M.A., Hancock, J.F. & Kenworthy, A.K. On the use of Ripley's K-function and its derivatives to analyze domain size. Biophys. J. 97, 1095-1103 (2009).
25. Owen, D.M. et al. PALM imaging and cluster analysis of protein heterogeneity at the cell surface. J. Biophotonics 3, 446-454 (2010).
26. Williamson, D.J. et al. Pre-existing clusters of the adaptor Lat do not participate in early T cell signaling events. Nat. Immunol. 12, 655-662 (2011).
27. Dickson, R.M., Cubitt, A.B., Tsien, R.Y. & Moerner, W.E. On/off blinking and switching behaviour of single molecules of green fluorescent protein. Nature 388, 355-358 (1997).
28. Schwille, P., Kummer, S., Heikal, A.A., Moerner, W.E. & Webb, W.W. Fluorescence correlation spectroscopy reveals fast optical excitation-driven intramolecular dynamics of yellow fluorescent proteins. Proc. Natl. Acad. Sci. USA 97, 151-156 (2000).
29. Ha, T. & Tinnefeld, P. Photophysics of fluorescent probes for single-molecule biophysics and super-resolution imaging. Annu. Rev. Phys. Chem. 63, 595-617 (2012).
30. Smith, C.S., Joseph, N., Rieger, B. & Lidke, K.A. Fast, single-molecule localization that achieves theoretically minimum uncertainty. Nat. Methods 7, 373-375 (2010).
31. Holden, S.J., Uphoff, S. & Kapanidis, A.N. DAOSTORM: an algorithm for high-density super-resolution microscopy. Nat. Methods 8, 279-280 (2011).
32. Huang, F., Schwartz, S.L., Byars, J.M. & Lidke, K.A. Simultaneous multiple-emitter fitting for single molecule super-resolution imaging. Biomed. Opt. Express 2, 1377-1393 (2011).
33. Quan, T. et al. High-density localization of active molecules using Structured Sparse Model and Bayesian Information Criterion. Opt. Express 19, 16963-16974 (2011).
34. Cox, S. et al. Bayesian localization microscopy reveals nanoscale podosome dynamics. Nat. Methods 9, 195-200 (2012).
35. Wang, Y., Quan, T., Zeng, S. & Huang, Z.L. PALMER: a method capable of parallel localization of multiple emitters for high-density localization microscopy. Opt. Express 20, 16039-16049 (2012).
36. Veatch, S.L. et al. Correlation functions quantify super-resolution images and estimate apparent clustering due to over-counting. PLoS ONE 7, e31457 (2012).
37. Veatch, S.L., Chiang, E.N., Sengupta, P., Holowka, D.A. & Baird, B.A. Quantitative Nanoscale analysis of IgE-Fc RI clustering and coupling to early signaling proteins. J. Phys. Chem. B 116, 6923-6935 (2012).
38. Tanaka, K.A. et al. Membrane molecules mobile even after chemical fixation. Nat. Methods 7, 865-866 (2010).
39. Testa, I., Mazza, D., Barozzi, S., Faretta, M. & Diaspro, A. Blue-light (488 nm)-irradiation-induced photoactivation of the photoactivatable green fluorescent protein. Appl. Phys. Lett. 91, 133902-133904 (2007).
40. Subach, F.V. et al. Photoactivatable mCherry for high-resolution two-color fluorescence microscopy. Nat. Methods 6, 153-159 (2009).