Image simulation for biological microscopy: Microlith

Biomedical Optics Express

Volumn 5, Issue 6, 2014, Pages 1822-1838

  Mehta, Shalin B ^a   Oldenbourg, Rudolf ^a,b  

^a MARINE BIOLOGICAL LABORATORY   (United States)

^b BROWN UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

IMAGING SYSTEMS; OPEN SYSTEMS;

BIOLOGICAL MICROSCOPY; DARK FIELD IMAGES; IMAGE SIMULATIONS; MASS DISTRIBUTION; OPEN SOURCE TOOLBOXES; PARTIALLY COHERENT ILLUMINATION; PARTIALLY COHERENT IMAGING; THREE DIMENSIONAL IMAGES;

BIOINFORMATICS;

ARTICLE; AXONEME; COMPUTER PREDICTION; COMPUTER SIMULATION; IMAGE ANALYSIS; MATHEMATICAL PARAMETERS; MEASUREMENT ACCURACY; MICROSCOPY; OPTICAL COHERENCE TOMOGRAPHY; PHASE CONTRAST MICROSCOPY; POLARIMETRY; RADIOMETRY; SENSITIVITY ANALYSIS;

EID: 84930823520     PISSN: None     EISSN: 21567085     Source Type: Journal    
DOI: 10.1364/BOE.5.001822     Document Type: Article

References (38)

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).
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," Physica 5(8), 785-795 (1938).
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).
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).
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).
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).
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).
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).
11. H. Su, Z. Yin, S. Huh, and T. Kanade, "Cell Segmentation in Phase Contrast Microscopy Images via Semisupervised Classification Over optics-related Features," Med. Image Anal. 17(7), 746-765 (2013).
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. SPIE 4346, 1500-1506 (2001).
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. Express 20(25), 27212-27221 (2012).
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).
16. R. Oldenbourg, S. Inoué, R. Tiberio, A. Stemmer, G. Mei, and M. Skvarla, "Standard test targets for highresolution 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).
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).
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).
23. E. Wolf, "New spectral representation of random sources and of the partially coherent fields that they generate," Opt. Commun. 38(1) 1-6 (1981).
24. B. J. Davis and R. W. Schoonover, "Computationally efficient coherent-mode representations," Opt. Lett. 34(7), 923-925 (2009).
25. K. Yamazoe, "Two matrix approaches for aerial image formation obtained by extending and modifying the transmission cross coefficients," J. Opt. Soc. Am. A 27(6), 1311-1321 (2010).
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).
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).
29. C. W. McCutchen, "Generalized Aperture and the Three-Dimensional Diffraction Image," J. Opt. Soc. Am. 54(2), 240 (1964).
30. nded. (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," Science 313(5789), 944-948 (2006).
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).
34. C. B. Lindemann and D. R. Mitchell, "Evidence for axonemal distortion during the flagellar beat of Chlamydomonas," Cell Motil. Cytoskeleton 64(8), 580-589 (2007).
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).
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).
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).