Electro-optic Photonic Circuits pp 19-31 | Cite as
Introduction to Microscopy
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Abstract
In this chapter we describe the basics and the state of the art of optical microscopy, the governing equation, the diffraction limit, image formation and the main criteria used for the analysis of imaging systems. In this framework, we also introduce the main concepts of super resolution, methods that can overcome the resolution limit using physical or numerical techniques, structured illumination microscopy, in which the sample is illuminated under different spatially inhomogeneous light fields and fluorescence microscopy, that images specific chemical components of a sample thanks to a selective staining using fluorophores.
References
- 1.Jackson JD (1975) Electrodynamics. Wiley Online LibraryGoogle Scholar
- 2.Mansuripur M (1998) Abbe’s sine condition. Opt Photon News 9(2):56–60ADSCrossRefGoogle Scholar
- 3.Alberto D (2001) Confocal and two-photon microscopy: foundations, applications and advances. Wiley-VCH. ISBN 0-471-40920-0, https://doi.org/10.1117/1.601121
- 4.Rayleigh L (1879) Xxxi. investigations in optics, with special reference to the spectroscope. Philos Mag 8(49):261–274CrossRefGoogle Scholar
- 5.George Biddell Airy (1835) On the diffraction of an object-glass with circular aperture. Trans Camb Phil Soc 5:283Google Scholar
- 6.Michelson AA (1995) Studies in optics. Courier CorporationGoogle Scholar
- 7.Georges N (1960) Interferential polarizing device for study of phase objects. US Patent 2,924,142 9 Feb 1960Google Scholar
- 8.Zernike F (1942) Phase contrast, a new method for the microscopic observation of transparent objects. Physica 9(7):686–698ADSCrossRefGoogle Scholar
- 9.Zernike F (1942) Phase contrast, a new method for the microscopic observation of transparent objects part ii. Physica 9(10):974IN1981IN3983–980982986ADSCrossRefGoogle Scholar
- 10.Stelzer EHK (1998) Contrast, resolution, pixelation, dynamic range and signal-to-noise ratio: fundamental limits to resolution in fluorescence light microscopy. J Microsc 189(1):15–24CrossRefGoogle Scholar
- 11.Luisier F, Blu T, Unser M (2011) Image denoising in mixed poisson-gaussian noise. IEEE Trans Image Process 20(3):696–708ADSMathSciNetzbMATHCrossRefGoogle Scholar
- 12.Swedlow JR (2007) Quantitative fluorescence microscopy and image deconvolution. Methods Cell Biol 81:447–465Google Scholar
- 13.De Micheli E, Viano GA (2009) Inverse optical imaging viewed as a backward channel communication problem. JOSA A 26(6):1393–1402Google Scholar
- 14.Di Toraldo Francia G (1969) Degrees of freedom of an image. JOSA 59(7):799–804Google Scholar
- 15.Pierri R, Soldovieri F (1998) On the information content of the radiated fields in the near zone over bounded domains. Inverse Prob 14(2):321ADSMathSciNetzbMATHCrossRefGoogle Scholar
- 16.Piestun R, Miller DAB (2000) Electromagnetic degrees of freedom of an optical system. JOSA A 17(5):892–902ADSMathSciNetCrossRefGoogle Scholar
- 17.Sementilli PJ, Hunt BR, Nadar MS (1993) Analysis of the limit to superresolution in incoherent imaging. JOSA A 10(11):2265–2276ADSCrossRefGoogle Scholar
- 18.Gelles J, Schnapp BJ, Sheetz MP (1988) Tracking kinesin-driven movements with nanometre-scale precision. Nature 331(6155):450–453ADSCrossRefGoogle Scholar
- 19.Gur A, Fixler D, Micó V, Garcia J, Zalevsky Z (2010) Linear optics based nanoscopy. Opt Express 18(21):22222–22231ADSCrossRefGoogle Scholar
- 20.Heintzmann R (2007) Estimating missing information by maximum likelihood deconvolution. Micron 38(2):136–144CrossRefGoogle Scholar
- 21.Harris JL (1964) Diffraction and resolving power. JOSA 54(7):931–936ADSCrossRefGoogle Scholar
- 22.Saleh B (1977) A priori information and the degrees of freedom of noisy images. JOSA 67(1):71–76ADSCrossRefGoogle Scholar
- 23.Bailey B, Farkas DL, Taylor DL, Lanni F (1993) Enhancement of axial resolution in fluorescence microscopy by standing-wave excitation. Nature 366(6450):44–48ADSCrossRefGoogle Scholar
- 24.Gustafsson MGL (2000) Surpassing the lateral resolution limit by a factor of two using structured illumination microscopy. J Microsc 198(2):82–87CrossRefGoogle Scholar
- 25.Gustafsson MGL, Shao L, Carlton PM, Rachel Wang CJ, Golubovskaya IN, Zacheus Cande W, Agard DA, Sedat JW (2008) Three-dimensional resolution doubling in wide-field fluorescence microscopy by structured illumination. Biophys J, 94(12):4957–4970ADSCrossRefGoogle Scholar
- 26.Schermelleh L, Carlton PM, Haase S, Shao L, Winoto L, Kner P, Burke B, Cardoso MC, Agard DA, Gustafsson MGL et al (2008) Subdiffraction multicolor imaging of the nuclear periphery with 3d structured illumination microscopy. Science 320(5881):1332–1336ADSCrossRefGoogle Scholar
- 27.Müller CB, Enderlein J (2010) Image scanning microscopy. Phys Rev Lett 104(19):198101Google Scholar
- 28.Sandeau N, Wawrezinieck L, Ferrand P, Giovannini H, Rigneault H (2009) Increasing the lateral resolution of scanning microscopes by a factor of two using 2-image microscopy. J Eur Opt Soc Rapid Publ 4:09040CrossRefGoogle Scholar
- 29.Wicker K, Heintzmann R (2007) Interferometric resolution improvement for confocal microscopes. Opt Express 15(19):12206–12216ADSCrossRefGoogle Scholar
- 30.Dorn R, Quabis S, Leuchs G (2003) Sharper focus for a radially polarized light beam. Phys Rev Lett 91(23):233901Google Scholar
- 31.Sheppard CJR, Hegedus ZS (1988) Axial behavior of pupil-plane filters. JOSA A 5(5):643–647ADSCrossRefGoogle Scholar
- 32.Fujita K, Kobayashi M, Kawano S, Yamanaka M, Kawata S (2007) High-resolution confocal microscopy by saturated excitation of fluorescence. Phys Rev Lett 99(22):228105ADSCrossRefGoogle Scholar
- 33.Lemoult F, Lerosey G, de Rosny J, Fink M (2010) Resonant metalenses for breaking the diffraction barrier. Phys Rev Lett 104(20):203901ADSCrossRefGoogle Scholar
- 34.Sentenac A, Chaumet PC (2008) Subdiffraction light focusing on a grating substrate. Phys Rev Lett 101(1):013901Google Scholar
- 35.Van Putten EG, Akbulut D, Bertolotti J, Vos WL, Lagendijk A, Mosk AP (2011) Scattering lens resolves sub-100 nm structures with visible light. Phys Rev Lett 106(19):193905Google Scholar
- 36.Wang Z, Guo W, Li L, Luk’yanchuk B, Khan A, Liu Z, Chen Z, Hong M (2011) Optical virtual imaging at 50 nm lateral resolution with a white-light nanoscope. Nat Commun 2:218ADSCrossRefGoogle Scholar
- 37.Heintzmann R, Cremer C (1999) Laterally modulated excitation microscopy: improvement of resolution by using a diffraction grating. In: Proceedings of SPIE, vol 3568, p 15Google Scholar
- 38.Shaner NC, Steinbach PA, Tsien RY (2005) A guide to choosing fluorescent proteins. Nat Methods 2(12):905–909CrossRefGoogle Scholar
- 39.Eisenstein M (2006) Helping cells to tell a colorful tale. Nat Methods 3(8):647–655CrossRefGoogle Scholar
- 40.Suzuki T, Matsuzaki T, Hagiwara H, Aoki T, Takata K (2007) Recent advances in fluorescent labeling techniques for fluorescence microscopy. Acta Histochem Cytoc 40(5):131–137CrossRefGoogle Scholar
- 41.Coling D, Kachar B (2001) Theory and application of fluorescence microscopy. Curr Protoc Neurosci 2–1Google Scholar
- 42.Hibbs AR (2004) Confocal microscopy for biologists. Springer Science & Business Media, SpringerGoogle Scholar
- 43.Pawley JB (2006) Fundamental limits in confocal microscopy. In: Handbook of biological confocal microscopy, pp. 20–42. Springer, BerlinCrossRefGoogle Scholar
- 44.Diaspro A, Bianchini P, Vicidomini G, Faretta M, Ramoino P, Usai C (2006) Multi-photon excitation microscopy. Biomed. Eng. Online 5(1):36CrossRefGoogle Scholar
- 45.Svoboda K, Yasuda R (2006) Principles of two-photon excitation microscopy and its applications to neuroscience. Neuron 50(6):823–839CrossRefGoogle Scholar
- 46.Kellner RR, Baier CJ, Willig KI, Hell SW, Barrantes FJ (2007) Nanoscale organization of nicotinic acetylcholine receptors revealed by stimulated emission depletion microscopy. Neuroscience 144(1):135–143CrossRefGoogle Scholar
- 47.Willig KI, Rizzoli SO, Westphal V, Jahn R, Hell SW (2006) Sted microscopy reveals that synaptotagmin remains clustered after synaptic vesicle exocytosis. Nature 440(7086):935–939ADSCrossRefGoogle Scholar
- 48.Strickler SJ, Berg RA (1962) Relationship between absorption intensity and fluorescence lifetime of molecules. J Chem Phys 37(4):814–822ADSCrossRefGoogle Scholar
- 49.Song L, Hennink EJ, Ted Young I, Tanke HJ (1995) Photobleaching kinetics of fluorescein in quantitative fluorescence microscopy. Biophys J 68(6):2588–2600ADSCrossRefGoogle Scholar
- 50.Betzig E, Patterson GH, Sougrat R, Lindwasser OW, Olenych S, Bonifacino JS, Davidson MW, Lippincott-Schwartz J, Hess HF (2006) Imaging intracellular fluorescent proteins at nanometer resolution. Science 313(5793):1642–1645ADSCrossRefGoogle Scholar
- 51.Hess ST, Girirajan TPK, Mason MD (2006) Ultra-high resolution imaging by fluorescence photoactivation localization microscopy. Biophys J 91(11):4258–4272ADSCrossRefGoogle Scholar
- 52.Rust MJ, Bates M, Zhuang X (2006) Sub-diffraction-limit imaging by stochastic optical reconstruction microscopy (storm). Nat Methods 3(10):793–796CrossRefGoogle Scholar
- 53.Dertinger T, Colyer R, Iyer G, Weiss S, Enderlein J (2009) Fast, background-free, 3d super-resolution optical fluctuation imaging (sofi). Proc Natl Acad Sci 106(52):22287–22292ADSCrossRefGoogle Scholar
- 54.Chance RR, Prock A, Silbey R (1974) Lifetime of an emitting molecule near a partially reflecting surface. J Chem Phys 60(7):2744–2748ADSCrossRefGoogle Scholar
- 55.Rahmani A, Chaumet PC, de Fornel F, Girard C (1997) Field propagator of a dressed junction: fluorescence lifetime calculations in a confined geometry. Phys Rev A 56(4):3245ADSCrossRefGoogle Scholar
- 56.Pearson H (2007) The good, the bad and the ugly. Nature 447(7141):138–140ADSCrossRefGoogle Scholar
- 57.Demos SG, Alfano RR (1997) Optical polarization imaging. Appl Opt 36(1):150–155ADSCrossRefGoogle Scholar
- 58.Morgan SP, Khong MP, Somekh MG (1997) Effects of polarization state and scatterer concentration on optical imaging through scattering media. Appl Opt 36(7):1560–1565ADSCrossRefGoogle Scholar
- 59.Papaioannou DG, Baselmans JJM, van Gemert MJC et al (1995) Image quality in time-resolved transillumination of highly scattering media. Appl Opt 34(27):6144–6157ADSCrossRefGoogle Scholar
- 60.Wang QZ, Liang X, Wang L, Ho PP, Alfano RR (1995) Fourier spatial filter acts as a temporal gate for light propagating through a turbid medium. Opt Lett 20(13):1498–1500ADSCrossRefGoogle Scholar
- 61.Yadlowsky MJ, Schmitt JM, Bonner RF (1995) Multiple scattering in optical coherence microscopy. Appl Opt 34(25):5699–5707ADSCrossRefGoogle Scholar
- 62.Deng X, Min G (2003) Penetration depth of single-, two-, and three-photon fluorescence microscopic imaging through human cortex structures: monte carlo simulation. Appl Opt 42(16):3321–3329ADSCrossRefGoogle Scholar
- 63.Deng X, Gan X, Min G (2004) Effective mie scattering of a spherical fractal aggregate and its application in turbid media. Appl Opt 43(14):2925–2929ADSCrossRefGoogle Scholar
- 64.Gan X, Min G (2002) Microscopic image reconstruction through tissue-like turbid media. Opt Commun 207(1):149–154ADSCrossRefGoogle Scholar
- 65.Gan XS, Schilders SP, Gu M (1998) Image formation in turbid media under a microscope. JOSA A, 15(8):2052–2058ADSCrossRefGoogle Scholar
- 66.Gu M, Gan X, Xiaoyuan D (2015) Microscopic imaging through turbid media: Monte Carlo modeling and applications. Springer, BerlinCrossRefGoogle Scholar
- 67.Schilders SP, Gan XS, Gu M (1998) Effect of scatterer size on microscopic imaging through turbid media based on differential polarisation-gating. Opt Commun 157(1):238–248ADSCrossRefGoogle Scholar
- 68.Dunn A, DiMarzio C (1996) Efficient computation of time-resolved transfer functions for imaging in turbid media. JOSA A 13(1):65–70ADSCrossRefGoogle Scholar
- 69.de Haller EB (1996) Time-resolved transillumination and optical tomography. J Biomed Opt 1(7)Google Scholar
- 70.De Boer JF, Milner TE, van Gemert MJC, Stuart Nelson J (1997) Two-dimensional birefringence imaging in biological tissue by polarization-sensitive optical coherence tomography. Opt Lett 22(12):934–936Google Scholar
- 71.Gan X, Schilders S, Gu M (1997) Combination of annular aperture and polarization gating methods for efficient microscopic imaging through a turbid medium: theoretical analysis. Microsc Microanal 3(6):495–503ADSCrossRefGoogle Scholar
- 72.Schilders SP, Gan XS, Gu M (1998) Efficient suppression of diffusing photons using polarising annular objectives for microscopic imaging through turbid media. Bioimaging 6(2):92–97CrossRefGoogle Scholar
- 73.Tromberg B, Yodh A, Sevick E, Pine D (1997) Diffusing photons in turbid media: introduction to the feature. Appl Opt 36(1):9–9ADSCrossRefGoogle Scholar
- 74.Denk W, Strickler JH, Webb WW et al (1990) Two-photon laser scanning fluorescence microscopy. Science 248(4951):73–76ADSCrossRefGoogle Scholar
- 75.Gan XS, Gu M (2000) Fluorescence microscopic imaging through tissue-like turbid media. J Appl Phys 87(7):3214–3221ADSCrossRefGoogle Scholar
- 76.Gu M (1996) Principles of three-dimensional imaging in confocal microscopes. World Scientific, SingaporeGoogle Scholar
- 77.Gu M (2000) Advanced optical imaging theory, vol 75. Springer Science & Business Media, BerlinGoogle Scholar
- 78.Wilson T, Sheppard C (1984) Theory and practice of scanning optical microscopy, vol 180. Academic Press, LondonGoogle Scholar
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