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Optics Express

Optics Express

  • Editor: C. Martijn de Sterke
  • Vol. 20, Iss. 1 — Jan. 2, 2012
  • pp: 403–413

Quantitative sectioning and noise analysis for structured illumination microscopy

Nathan Hagen, Liang Gao, and Tomasz S. Tkaczyk  »View Author Affiliations

Optics Express, Vol. 20, Issue 1, pp. 403-413 (2012)

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Structured illumination (SI) has long been regarded as a nonquantitative technique for obtaining sectioned microscopic images. Its lack of quantitative results has restricted the use of SI sectioning to qualitative imaging experiments, and has also limited researchers’ ability to compare SI against competing sectioning methods such as confocal microscopy. We show how to modify the standard SI sectioning algorithm to make the technique quantitative, and provide formulas for calculating the noise in the sectioned images. The results indicate that, for an illumination source providing the same spatially-integrated photon flux at the object plane, and for the same effective slice thicknesses, SI sectioning can provide higher SNR images than confocal microscopy for an equivalent setup when the modulation contrast exceeds about 0.09.

© 2011 OSA

OCIS Codes
(100.3010) Image processing : Image reconstruction techniques
(100.6640) Image processing : Superresolution
(110.4280) Imaging systems : Noise in imaging systems
(180.0180) Microscopy : Microscopy
(180.6900) Microscopy : Three-dimensional microscopy

ToC Category:

Original Manuscript: September 20, 2011
Revised Manuscript: December 9, 2011
Manuscript Accepted: December 13, 2011
Published: December 21, 2011

Virtual Issues
Vol. 7, Iss. 3 Virtual Journal for Biomedical Optics

Nathan Hagen, Liang Gao, and Tomasz S. Tkaczyk, "Quantitative sectioning and noise analysis for structured illumination microscopy," Opt. Express 20, 403-413 (2012)

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  1. D. Karadaglić and T. Wilson, “Image formation in structured illumination wide-field fluorescence microscopy,” Micron 39, 808–818 (2008). [CrossRef]
  2. M. A. A. Neil, R. Juškaitis, and T. Wilson, “Method of obtaining optical sectioning by using structured light in a conventional microscope,” Opt. Lett. 22, 1905–1907 (1997). [CrossRef]
  3. L. Schermelleh, P. M. Carlton, S. Haase, L. Shao, L. Winoto, P. Kner, B. Burke, M. C. Cardoso, D. A. Agard, M. G. L. Gustafsson, H. Leonhardt, and J. W. Sedat, “Subdiffraction multicolor imaging of the nuclear periphery with 3D structured illumination microscopy,” Science 320, 1332–1336 (2008). [CrossRef] [PubMed]
  4. V. C. Cogger, G. P. McNerney, T. Nyunt, L. D. DeLeve, P. McCourt, B. Smedsrød, D. G. L. Couteur, and T. R. Huser, “Three-dimensional structured illumination microscopy of liver sinusoidal endothelial cell fenestrations,” J. Struct. Biol. 171, 382–388 (2010). [CrossRef] [PubMed]
  5. P. Kner, B. B. Chhun, E. R. Griffis, L. Winoto, and M. G. L. Gustafsson, “Super-resolution video microscopy of live cells by structured illumination,” Nat. Met. 6, 339–344 (2009). [CrossRef]
  6. G. Best, R. Amberger, D. Baddeley, T. Ach, S. Dithmar, R. Heintzmann, and C. Cremer, “Structured illumination microscopy of autofluorescent aggregations in human tissue,” Micron 42, 330–335 (2011). [CrossRef]
  7. P. J. Keller, A. D. Schmidt, A. Santella, K. Khairy, Z. Bao, J. Wittbrodt, and E. H. K. Stelzer, “Fast, high-contrast imaging of animal development with scanned light sheet-based structured-illumination microscopy,” Nat. Meth. 7, 637–645 (2010). [CrossRef]
  8. N. Bozinovic, C. Ventalon, T. Ford, and J. Mertz, “Fluorescence endomicroscopy with structured illumination,” Opt. Express 16, 8016–8026 (2008). [CrossRef] [PubMed]
  9. R. Heintzmann and C. Cremer, “Laterally modulated excitation microscopy: improvement of resolution by using a diffraction grating,” in EUROPTO Conference on Optical Microscopy, Proc. SPIE 3568, 185–196 (1999). [CrossRef]
  10. M. G. L. Gustafsson, “Surpassing the lateral resolution limit by a factor of two using structured illumination microscopy,” J. Microsc. 198, 82–87 (2000). [CrossRef] [PubMed]
  11. L. M. Hirvonen, K. Wicker, O. Mandula, and R. Heintzmann, “Structured illumination microscopy of a living cell,” Eur. Biophys. J. 38, 807–813 (2009). [CrossRef] [PubMed]
  12. J. M. Murray, P. L. Appleton, J. R. Swedlow, and J. C. Waters, “Evaluating performance in three-dimensional fluorescence microscopy,” J. Microsc. 228, 390–405 (2007). [CrossRef] [PubMed]
  13. L. Gao, N. Bedard, N. Hagen, R. T. Kester, and T. S. Tkaczyk, “Depth-resolved image mapping spectrometer (IMS) with structured illumination,” Opt. Express 19, 17439–17452 (2011). [CrossRef] [PubMed]
  14. M. G. Somekh, K. Hsu, and M. C. Pitter, “Resolution in structured illumination microscopy: a probabilistic approach,” J. Opt. Soc. Am. A 25, 1319–1329 (2008). [CrossRef]
  15. M. G. Somekh, K. Hsu, and M. C. Pitter, “Stochastic transfer function for structured illumination microscopy,” J. Opt. Soc. Am. A 26, 1630–1637 (2009). [CrossRef]
  16. K. M. Kedziora, J. H. M. Prehn, J. Dobruck, and T. Bernas, “Method of calibration of a fluorescence microscope for quantitative studies,” J. Microsc. 244, 101–111 (2011). [CrossRef] [PubMed]
  17. J. C. Waters, “Accuracy and precision in quantitative fluorescence microscopy,” J. Cell Biol. 1858, 1135–1148 (2009). [CrossRef]
  18. A. Esposito, S. Schlachter, G. S. Schierle, A. D. Elder, A. Diaspro, F. S. Wouters, C. F. Kaminski, and A. I. Iliev, “Quantitative fluorescence microscopy techniques,” Methods Mol. Biol. 586, 117–142 (2009). [CrossRef] [PubMed]
  19. R. Heintzmann and P. A. Benedetti, “High-resolution image reconstruction in fluorescence microscopy with patterned excitation,” Appl. Opt. 45, 5037–5045 (2006). [CrossRef] [PubMed]
  20. M. A. A. Neil, T. Wilson, and R. Juškaitis, “A light efficient optical sectioning microscope,” J. Microsc. 189, 114–117 (1998). [CrossRef]
  21. M. J. Cole, J. Siegel, S. E. D. Webb, R. Jones, K. Dowling, M. J. Dayel, D. Parsons-Karavassis, P. M. W. French, M. J. Lever, L. O. D. Sucharov, M. A. A. Neil, R. Juvskaitis, and T. Wilson, “Time-domain whole-field fluorescence lifetime imaging with optical sectioning,” J. Microsc. 203, 246–257 (2001). [CrossRef] [PubMed]
  22. L. H. Schaefer, D. Schuster, and J. Schaffer, “Structured illumination microscopy: artefact analysis and reduction utilizing a parameter optimization approach,” J. Microsc. 216, 165–174 (2004). [CrossRef] [PubMed]
  23. L. G. Krzewina and M. K. Kim, “Single-exposure optical sectioning by color structured illumination microscopy,” Opt. Lett. 31, 477–479 (2006). [CrossRef] [PubMed]
  24. A. L. Barlow and C. J. Guerin, “Quantization of widefield fluorescence images using structured illumination and image analysis software,” Microsc. Res. Tech. 70, 76–84 (2007). [CrossRef]
  25. F. Chasles, B. Dubertret, and A. C. Boccara, “Optimization and characterization of a structured illumination microscope,” Opt. Express 15, 16130–16141 (2007). [CrossRef] [PubMed]
  26. S. D. Konecky, A. Mazhar, D. Cuccia, A. J. Durkin, J. C. Schotland, and B. J. Tromberg, “Quantitative optical tomography of sub-surface heterogeneities using spatially modulated structured light,” Opt. Express 17, 14780–14790 (2009). [CrossRef] [PubMed]
  27. M. F. Langhorst, J. Schaffer, and B. Goetze, “Structure brings clarity: structured illumination microscopy in cell biology,” Biotechnol. J. 4, 858–865 (2009). [CrossRef] [PubMed]
  28. T. A. Erickson, A. Mazhar, D. Cuccia, A. J. Durkin, and J. W. Tunnell, “Lookup-table method for imaging optical properties with structured illumination beyond the diffusion theory regime,” J. Biomed. Opt. 15, 036013 (2010). [CrossRef] [PubMed]
  29. K. Wicker and R. Heintzmann, “Single-shot optical sectioning using polarization-coded structured illumination,” J. Opt. 12, 084010 (2010). [CrossRef]
  30. T. Wilson, “Optical sectioning in fluorescence microscopy,” J. Microsc. 242, 111–116 (2010). [CrossRef] [PubMed]
  31. S. Gruppetta and S. Chetty, “Theoretical study of multispectral structured illumination for depth resolved imaging of non-stationary objects: focus on retinal imaging,” Biomed. Opt. Express 2, 255–263 (2011). [CrossRef] [PubMed]
  32. M. A. A. Neil, R. Juškaitis, and T. Wilson, “Real time 3D fluorescence microscopy by two beam interference illumination,” Opt. Commun. 153, 1–4 (1998). [CrossRef]
  33. V. Poher, H. X. Zhang, G. T. Kennedy, C. Griffin, S. Oddos, E. Gu, D. S. Elson, M. Girkin, P. M. W. French, M. D. Dawson, and M. A. A. Neil, “Optical sectioning microscopes with no moving parts using a micro-stripe array light emitting diode,” Opt. Express 15 (2007). [CrossRef] [PubMed]
  34. L. Mortara and A. Fowler, “Evaluations of charge-coupled device (CCD) performance for astronomical use,” in Solid state imagers for astronomy, Proc. SPIE 290, 28–33 (1981).

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