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Biomedical Optics Express

Biomedical Optics Express

  • Editor: Joseph A. Izatt
  • Vol. 2, Iss. 5 — May. 1, 2011
  • pp: 1377–1393

Simultaneous multiple-emitter fitting for single molecule super-resolution imaging

Fang Huang, Samantha L. Schwartz, Jason M. Byars, and Keith A. Lidke  »View Author Affiliations


Biomedical Optics Express, Vol. 2, Issue 5, pp. 1377-1393 (2011)
http://dx.doi.org/10.1364/BOE.2.001377


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Abstract

Single molecule localization based super-resolution imaging techniques require repeated localization of many single emitters. We describe a method that uses the maximum likelihood estimator to localize multiple emitters simultaneously within a single, two-dimensional fitting sub-region, yielding an order of magnitude improvement in the tolerance of the analysis routine with regards to the single-frame active emitter density. Multiple-emitter fitting enables the overall performance of single-molecule super-resolution to be improved in one or more of several metrics that result in higher single-frame density of localized active emitters. For speed, the algorithm is implemented on Graphics Processing Unit (GPU) architecture, resulting in analysis times on the order of minutes. We show the performance of multiple emitter fitting as a function of the single-frame active emitter density. We describe the details of the algorithm that allow robust fitting, the details of the GPU implementation, and the other imaging processing steps required for the analysis of data sets.

© 2011 OSA

OCIS Codes
(100.3010) Image processing : Image reconstruction techniques
(100.6640) Image processing : Superresolution
(180.2520) Microscopy : Fluorescence microscopy

ToC Category:
Microscopy

History
Original Manuscript: January 31, 2011
Revised Manuscript: April 9, 2011
Manuscript Accepted: April 14, 2011
Published: April 29, 2011

Citation
Fang Huang, Samantha L. Schwartz, Jason M. Byars, and Keith A. Lidke, "Simultaneous multiple-emitter fitting for single molecule super-resolution imaging," Biomed. Opt. Express 2, 1377-1393 (2011)
http://www.opticsinfobase.org/boe/abstract.cfm?URI=boe-2-5-1377


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References

  1. S. W. Hell, “Far-field optical nanoscopy,” Science 316, 1153–1158 (2007). [CrossRef] [PubMed]
  2. K. R. Chi, “Microscopy: ever-increasing resolution,” Nature 462, 675–678 (2009). [CrossRef] [PubMed]
  3. B. Huang, M. Bates, and X. W. Zhuang, “Super-resolution fluorescence microscopy,” Annu. Rev. Biochem. 78, 993–1016 (2009). [CrossRef] [PubMed]
  4. G. Patterson, M. Davidson, S. Manley, and J. Lippincott-Schwartz, “Superresolution imaging using single-molecule localization,” Annu. Rev. Phys. Chem. 61, 345–367 (2010). [CrossRef] [PubMed]
  5. L. Schermelleh, R. Heintzmann, and H. Leonhardt, “A guide to super-resolution fluorescence microscopy,” J. Cell Biol. 190, 165–175 (2010). [CrossRef] [PubMed]
  6. K. A. Lidke, B. Rieger, T. M. Jovin, and R. Heintzmann, “Superresolution with quantum dots: enhanced localization in fluorescence microscopy by exploitation of quantum dot blinking,” Biophys. J. 88, 346a–346a (2005).
  7. B. C. Lagerholm, L. Averett, G. E. Weinreb, K. Jacobson, and N. L. Thompson, “Analysis method for measuring submicroscopic distances with blinking quantum dots,” Biophys. J. 91, 3050–3060 (2006). [CrossRef] [PubMed]
  8. E. Betzig, G. H. Patterson, R. Sougrat, O. W. Lindwasser, S. Olenych, J. S. Bonifacino, M. W. Davidson, J. Lippincott-Schwartz, and H. F. Hess, “Imaging intracellular fluorescent proteins at nanometer resolution,” Science 313, 1642–1645 (2006). [CrossRef] [PubMed]
  9. S. T. Hess, T. P. K. Girirajan, and M. D. Mason, “Ultra-high resolution imaging by fluorescence photoactivation localization microscopy,” Biophys. J. 91, 4258–4272 (2006). [CrossRef] [PubMed]
  10. M. J. Rust, M. Bates, and X. W. Zhuang, “Sub-diffraction-limit imaging by stochastic optical reconstruction microscopy (storm),” Nat. Methods 3, 793–795 (2006). [CrossRef] [PubMed]
  11. J. Vogelsang, C. Steinhauer, C. Forthmann, I. H. Stein, B. Person-Skegro, T. Cordes, and P. Tinnefeld, “Make them blink: probes for super-resolution microscopy,” Chemphyschem 11, 2475–2490 (2010). [CrossRef] [PubMed]
  12. S. W. Hell and J. Wichmann, “Breaking the diffraction resolution limit by stimulated-emission—stimulated-emission-depletion fluorescence microscopy,” Opt. Lett. 19, 780–782 (1994). [CrossRef] [PubMed]
  13. S. Hell and E. H. K. Stelzer, “Fundamental improvement of resolution with a 4pi-confocal fluorescence microscope using 2-photon excitation,” Opt. Commun. 93, 277–282 (1992). [CrossRef]
  14. M. G. L. Gustafsson, “Nonlinear structured-illumination microscopy: Wide-field fluorescence imaging with theoretically unlimited resolution,” Proc. Natl. Acad. Sci. U. S. A. 102, 13081–13086 (2005). [CrossRef] [PubMed]
  15. A. R. Small, “Theoretical limits on errors and acquisition rates in localizing switchable fluorophores,” Biophys. J. 96, L16–L18 (2009). [CrossRef] [PubMed]
  16. S. Ram, E. S. Ward, and R. J. Ober, “Beyond rayleigh’s criterion: A resolution measure with application to single-molecule microscopy,” Proc. Natl. Acad. Sci. U.S.A. 103, 4457–4462 (2006). [CrossRef] [PubMed]
  17. J. Chao, S. Ram, E. S. Ward, and R. J. Ober, “A comparative study of high resolution microscopy imaging modalities using a three-dimensional resolution measure,” Opt. Express 17, 24377–24402 (2009). [CrossRef]
  18. J. A. Högbom, “Aperture synthesis with a non-regular distribution of interferometer baselines,” Astron. Astrophys. Suppl. 15, 417 (1974).
  19. A. Serge, N. Bertaux, H. Rigneault, and D. Marguet, “Dynamic multiple-target tracing to probe spatiotemporal cartography of cell membranes,” Nat. Methods 5, 687–694 (2008). [CrossRef] [PubMed]
  20. X. H. Qu, D. Wu, L. Mets, and N. F. Scherer, “Nanometer-localized multiple single-molecule fluorescence microscopy,” Proc. Natl. Acad. Sci. U.S.A. 101, 11298–11303 (2004). [CrossRef] [PubMed]
  21. M. P. Gordon, T. Ha, and P. R. Selvin, “Single-molecule high-resolution imaging with photobleaching,” Proc. Natl. Acad. Sci. U.S.A. 101, 6462–6465 (2004). [CrossRef] [PubMed]
  22. B. Zhang, J. Zerubia, and J. C. Olivo-Marin, “Gaussian approximations of fluorescence microscope point-spread function models,” Appl. Opt. 46, 1819–1829 (2007). [CrossRef] [PubMed]
  23. S. Stallinga and B. Rieger, “Accuracy of the gaussian point spread function model in 2d localization microscopy,” Opt. Express 18, 24461–24476 (2010). [CrossRef] [PubMed]
  24. A. Van den Bos and C. Ebooks, Parameter Estimation for Scientists and Engineers (Wiley Online Library, 2007).
  25. C. S. Smith, N. Joseph, B. Rieger, and K. A. Lidke, “Fast, single-molecule localization that achieves theoretically minimum uncertainty,” Nat. Methods 7, 373–U52 (2010). [CrossRef] [PubMed]
  26. R. J. Ober, S. Ram, and E. S. Ward, “Localization accuracy in single-molecule microscopy,” Biophys. J. 86, 1185–1200 (2004). [CrossRef] [PubMed]
  27. P. Stoica and T. L. Marzetta, “Parameter estimation problems with singular information matrices,” IEEE Trans. Sig. Process. 49, 87–90 (2001). [CrossRef]
  28. C. L. L. Hendriks, L. J. van Vliet, B. Rieger, G. M. P. van Kempen, and M. van Ginkel, “Dipimage: a scientific image processing toolbox for MATLAB,” Quantitative Imaging Group, Faculty of Applied Sciences, Delft University of Technology, Delft, The Netherlands (1999).
  29. NVIDIA, “Compute unified device architecture (CUDA),” http://www.nvidia.com/object/cuda_home.html (2007).
  30. W. H. Press, S. L. A. Teukolsky, B. N. P. Flannery, and W. M. T. Vetterling, Numerical Recipes: FORTRAN (Cambridge University Press, 1990).
  31. M. Heilemann, S. van de Linde, M. Schuttpelz, R. Kasper, B. Seefeldt, A. Mukherjee, P. Tinnefeld, and M. Sauer, “Subdiffraction-resolution fluorescence imaging with conventional fluorescent probes,” Angew. Chem. Int. Ed. 47, 6172–6176 (2008). [CrossRef]

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