OSA's Digital Library

Biomedical Optics Express

Biomedical Optics Express

  • Editor: Joseph A. Izatt
  • Vol. 5, Iss. 6 — Jun. 1, 2014
  • pp: 1822–1838

Image simulation for biological microscopy: microlith

Shalin B. Mehta and Rudolf Oldenbourg  »View Author Affiliations


Biomedical Optics Express, Vol. 5, Issue 6, pp. 1822-1838 (2014)
http://dx.doi.org/10.1364/BOE.5.001822


View Full Text Article

Enhanced HTML    Acrobat PDF (2915 KB)





Browse Journals / Lookup Meetings

Browse by Journal and Year


   


Lookup Conference Papers

Close Browse Journals / Lookup Meetings

Article Tools

Share
Citations

Abstract

Image simulation remains under-exploited for the most widely used biological phase microscopy methods, because of difficulties in simulating partially coherent illumination. We describe an open-source toolbox, microlith (https://code.google.com/p/microlith), which accurately predicts three-dimensional images of a thin specimen observed with any partially coherent imaging system, as well as images of coherently illuminated and self-luminous incoherent specimens. Its accuracy is demonstrated by comparing simulated and experimental bright-field and dark-field images of well-characterized amplitude and phase targets, respectively. The comparison provides new insights about the sensitivity of the dark-field microscope to mass distributions in isolated or periodic specimens at the length-scale of 10nm. Based on predictions using microlith, we propose a novel approach for detecting nanoscale structural changes in a beating axoneme using a dark-field microscope.

© 2014 Optical Society of America

OCIS Codes
(110.2990) Imaging systems : Image formation theory
(110.4980) Imaging systems : Partial coherence in imaging
(170.0180) Medical optics and biotechnology : Microscopy
(170.3880) Medical optics and biotechnology : Medical and biological imaging
(350.5030) Other areas of optics : Phase

ToC Category:
Microscopy

History
Original Manuscript: January 31, 2014
Revised Manuscript: March 26, 2014
Manuscript Accepted: April 18, 2014
Published: May 13, 2014

Citation
Shalin B. Mehta and Rudolf Oldenbourg, "Image simulation for biological microscopy: microlith," Biomed. Opt. Express 5, 1822-1838 (2014)
http://www.opticsinfobase.org/boe/abstract.cfm?URI=boe-5-6-1822


Sort:  Author  |  Year  |  Journal  |  Reset  

References

  1. S. B. Mehta, M. Shribak, and R. Oldenbourg, “Polarized light imaging of birefringence and diattenuation at high resolution and high sensitivity,” J. Opt.15(9), 094007 (2013). [CrossRef] [PubMed]
  2. R. Oldenbourg, “Polarization microscopy with the LC-Polscope,” in Live Cell Imaging, R. D. Goldman and D. L. Spector, eds. (CSHL Press, 2005), pp. 205–37.
  3. F. Zernike, “The concept of degree of coherence and its application to optical problems,” Physica5(8), 785–795 (1938). [CrossRef]
  4. D. G. Voelz, Computational Fourier Optics: a Matlab Tutorial (SPIE Press, 2011).
  5. H. Kirshner, F. Aguet, D. Sage, and M. Unser, “3-D PSF fitting for fluorescence microscopy: implementation and localization application,” J. Microsc.249(1), 13–25 (2013). [CrossRef] [PubMed]
  6. H. Ishiwata, M. Itoh, and T. Yatagai, “A new method of three-dimensional measurement by differential interference contrast microscope,” Opt. Commun.260(1), 117–126 (2006). [CrossRef]
  7. M. R. Arnison, K. G. Larkin, C. J. R. Sheppard, N. I. Smith, and C. J. Cogswell, “Linear phase imaging using differential interference contrast microscopy,” J. Microsc.214(1), 7–12 (2004). [CrossRef] [PubMed]
  8. F. Pfeiffer, T. Weitkamp, O. Bunk, and C. David, “Phase retrieval and differential phase-contrast imaging with low-brilliance X-ray sources,” Nat. Phys.2(4), 258–261 (2006). [CrossRef]
  9. S. B. Mehta and C. J. R. Sheppard, “Quantitative phase-gradient imaging at high resolution with asymmetric illumination-based differential phase contrast,” Opt. Lett.34(13), 1924–1926 (2009). [CrossRef] [PubMed]
  10. T. E. Gureyev, A. Roberts, and K. A. Nugent, “Phase retrieval with the transport-of-intensity equation: matrix solution with use of Zernike polynomials,” J. Opt. Soc. Am. A.12(9), 1932–1942 (1995). [CrossRef]
  11. H. Su, Z. Yin, S. Huh, and T. Kanade, “Cell segmentation in phase contrast microscopy images via semi-supervised classification over optics-related features,” Med. Image Anal.17(7), 746–765 (2013). [CrossRef] [PubMed]
  12. S. I. Lee, K. C. Ng, T. Orimoto, J. Pittenger, T. Horie, K. Adam, M. Cheng, E. H. Croffie, Y. Deng, F. E. Gennari, T. V. Pistor, G. Robins, M. V. Williamson, B. Wu, L. Yuan, and A. R. Neureuther, “LAVA web-based remote simulation: enhancements for education and technology innovation,” Proc. SPIE4346, 1500–1506 (2001). [CrossRef]
  13. S. B. Mehta, “microlith: Image simulation for microscopy and lithography systems,” https://code.google.com/p/microlith/ .
  14. C. J. Sheppard and S. B. Mehta, “Three-level filter for increased depth of focus and Bessel beam generation,” Opt. Express20(25), 27212–27221 (2012). [CrossRef] [PubMed]
  15. C. J. R. Sheppard, S. B. Mehta, and R. Heintzmann, “Superresolution by image scanning microscopy using pixel reassignment,” Opt. Lett.38(15), 2889–2892 (2013). [CrossRef] [PubMed]
  16. R. Oldenbourg, S. Inoué, R. Tiberio, A. Stemmer, G. Mei, and M. Skvarla, “Standard test targets for high-resolution light microscopy,” in Nanofabrication and Biosystems: Integrating Materials Science, Engineering, and Biology, H. C. Hoch, L. W. Jelinski, and H. G. Craighead, eds. (Cambridge University Press, 1996), p. 123.
  17. A. Köhler, “Ein neues Beleuchtungsverfahren für mikrophotographische Zwecke,” Z. Für Wiss. Mikrosk. Für Mikrosk. Tech.10, 433–440 (1893).
  18. H. H. Hopkins, “On the diffraction theory of optical images,” Proc. R. Soc. Lond.217(1130), 408–432 (1953). [CrossRef]
  19. S. B. Mehta and C. J. R. Sheppard, “Phase-space representation of partially coherent imaging systems using the Cohen class distribution,” Opt. Lett.35(3), 348–350 (2010). [CrossRef] [PubMed]
  20. H. Gamo, “Matrix treatment of partial coherence,” in Progress in Optics, E. Wolf, ed. (Elsevier, 1964), Vol. Volume 3, pp. 187–332.
  21. N. B. Cobb, “Fast optical and process proximity correction algorithms for integrated circuit manufacturing,” Ph.D. Thesis, UC Berkeley (1998).
  22. Y. C. Pati and T. Kailath, “Phase-shifting masks for microlithography: Automated design and mask requirements,” J. Opt. Soc. Am.11(9), 2438–2452 (1994). [CrossRef]
  23. E. Wolf, “New spectral representation of random sources and of the partially coherent fields that they generate,” Opt. Commun. 38(1), 3–6 (1981).
  24. B. J. Davis and R. W. Schoonover, “Computationally efficient coherent-mode representations,” Opt. Lett.34(7), 923–925 (2009). [CrossRef] [PubMed]
  25. K. Yamazoe, “Two matrix approaches for aerial image formation obtained by extending and modifying the transmission cross coefficients,” J. Opt. Soc. Am. A27(6), 1311–1321 (2010). [CrossRef] [PubMed]
  26. H. E. Keller, “Objective lenses for confocal microscopy,” in Handbook of Biological Confocal Microscopy, 3rd ed. (Springer, 2006.), pp. 145–160.
  27. R. Oldenbourg, E. D. Salmon, and P. T. Tran, “Birefringence of single and bundled microtubules,” Biophys. J.74(1), 645–654 (1998). [CrossRef] [PubMed]
  28. C. W. McCutchen, “Generalized source and the van Cittert-Zernike theorem: A study of the spatial coherence required for interferometry,” J. Opt. Soc. Am.56(6), 727–732 (1966). [CrossRef]
  29. C. W. McCutchen, “Generalized aperture and the three-dimensional diffraction image,” J. Opt. Soc. Am.54(2), 240 (1964). [CrossRef]
  30. C. J. F. Böttcher, O. C. van Belle, P. Bordewijk, and A. Rip, Theory of Electric Polarization: Dielectrics in Static Fields, 2nd ed. (Elsevier, Netherlands, 1993).
  31. H. Lodish, A. Berk, P. Matsudaira, C. A. Kaiser, M. Krieger, M. P. Scott, S. L. Zipursky, and J. Darnell, Molecular Cell Biology, 5th ed. (W.H. Freeman, 2003).
  32. D. Nicastro, C. Schwartz, J. Pierson, R. Gaudette, M. E. Porter, and J. R. McIntosh, “The molecular architecture of axonemes revealed by cryoelectron tomography,” Science313(5789), 944–948 (2006). [CrossRef] [PubMed]
  33. K. Wakabayashi, Y. Sugimoto, H. Tanaka, Y. Ueno, Y. Takezawa, and Y. Amemiya, “X-ray diffraction evidence for the extensibility of actin and myosin filaments during muscle contraction,” Biophys. J.67(6), 2422–2435 (1994). [CrossRef] [PubMed]
  34. C. B. Lindemann and D. R. Mitchell, “Evidence for axonemal distortion during the flagellar beat of Chlamydomonas,” Cell Motil. Cytoskeleton64(8), 580–589 (2007). [CrossRef] [PubMed]
  35. H. M. Sakakibara, Y. Kunioka, T. Yamada, and S. Kamimura, “Diameter oscillation of axonemes in sea-urchin sperm flagella,” Biophys. J.86(1), 346–352 (2004). [CrossRef] [PubMed]
  36. H. Sato, G. W. Ellis, and S. Inoué, “Microtubular origin of mitotic spindle form birefringence. Demonstration of the applicability of Wiener’s equation,” J. Cell Biol.67(3), 501–517 (1975). [CrossRef] [PubMed]
  37. E. W. Weisstein, “Logarithmic Spiral–from Wolfram MathWorld,” http://mathworld.wolfram.com/LogarithmicSpiral.html .
  38. H. C. van de Hulst, Light Scattering by Small Particles (Dover Publications, 1981).

Cited By

Alert me when this paper is cited

OSA is able to provide readers links to articles that cite this paper by participating in CrossRef's Cited-By Linking service. CrossRef includes content from more than 3000 publishers and societies. In addition to listing OSA journal articles that cite this paper, citing articles from other participating publishers will also be listed.

Supplementary Material


» Media 1: MOV (311 KB)     
» Media 2: MOV (504 KB)     

« Previous Article  |  Next Article »

OSA is a member of CrossRef.

CrossCheck Deposited