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Conventional Light Microscopy

Eric S. Cole1

1St. Olaf College, Northfield, Minnesota

Unit Number: 
Unit 9.1
DOI: 
10.1002/9780470089941.et0901s00
Online Posting Date: 
October, 2008
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Abstract

In this molecular day and age, microscopy seems to be a neglected field of instruction. Too often professors, who themselves are strangers to the use of the light microscope, may hurry through a laboratory exercise designed to familiarize students with its uses. This chapter is designed to serve as a useful reference for instructors, perhaps demystifying some features of the microscope, and making their applications more user-friendly and exciting.

Keywords: microscopy; lens; magnification; focus; resolution; refraction; phase-contrast

     
 
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Table of Contents

  • Parts of the Light Microscope
  • Care and Maintenance
  • Basic Principles and Definitions
  • Magnification Versus Resolution
  • Getting Comfortable
  • Finding the Object to be Viewed
  • Marking the location of an Object: Secrets of the Microscope Stage
  • A Quick Guide to Choosing from Various Optical Techniques
  • Köhler Illumination: Secrets of the Substage Condenser
  • Oil Immersion
  • Dark-Field, Rheinberg, Polarized-Light, Phase-Contrast, and DIC Microscopy
  • Acknowledgements
  • Literature Cited
  • Figures
  • Tables
     
 
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Figures

  • Figure 9.1.1
    A typical compound light microscope used in many teaching laboratories. Not shown are the on/off toggle switch and the illuminator rheostat that controls the intensity of illumination.

  • Figure 9.1.2
    Diagram of the major component parts and centering screws for a research upright light microscope. Originally published in Current Protocols in Microbiology Unit 2A.1 (Salmon et al., 2005).

  • Figure 9.1.3
    This figure illustrates the refraction of light as it passes from air to water (A) or water to air (B). Air is shown with refractive index n1, and water with n2. In general, light passing from a low- to high-density medium (A) bends towards an imaginary line drawn perpendicular to the interface. Conversely, light bends away from such a line as it passes from a high- to low-density medium (B).

  • Figure 9.1.4
    Building on Figure 9.1.3, this illustrates the principle of a prism in which light passes through two interfaces: air to glass (A), glass to air (B), and a combination found in a prism (C). Light passing through such an object is refracted towards the base of the prism.

  • Figure 9.1.5
    When prisms are stacked as in this illustration, the compound effect is to refract light in such a way that it converges at a single point, the focal point (f ). This is due to the increasingly acute angles of each prism as one moves away from the center of the lens. This is the principle behind a simple biconvex lens (a lens that curves “outward” on both surfaces).

  • Figure 9.1.6
    This figure illustrates two points. First the ray diagram in panel (A) traces the path of three particular rays of light. “1” represents the path of light from the object that strikes the lens at right angles to its optical axis. Such light will be refracted through the focal point (f¢). The light represented by “2” from the object that strikes the lens dead-center will not change trajectory, but pass straight through. The light represented by “3” from the object that passes through the “back focal plane” (f ) will emerge from the lens perpendicular to the optical axis. All light emanating from f will be focused into a parallel beam as it emerges from the lens (the principle behind the Fresnel lens used in early lighthouse designs). Panels (B) to (D) illustrate the consequences of moving the object progressively closer to the lens.

  • Figure 9.1.7
    This line drawing illustrates the fundamental design of a compound microscope. The object is placed at less than 2 × f1 in front of the objective lens, so that its image is magnified (as in Fig. 9.1.6B). This real image is projected onto a plane that lies inside the focal distance f2 for the ocular lens. Consequently, as light from this real image passes through the ocular lens, its light diverges (as in Fig. 9.1.6D). Your eye collects this divergent light and creates a real image on the retina. This produces the effect of a virtual image.

  • Figure 9.1.8
    This illustration helps define the acceptance angle of an objective lens. (A) The numerical aperture of a lens is defined as NA = nsin, where is ½ the acceptance angle for a lens. Lenses with larger numerical apertures (NA) have better resolution. Panel (B) illustrates a lens with a lower acceptance angle (and hence lower NA) and panel (C) illustrates a lens with a higher acceptance angle (and hence higher NA). In panel B, only three light rays are admitted, whereas the lens shown in panel C can accept five of the rays indicated.

  • Figure 9.1.9
    The microscope stage often has two sets of coordinates (x and y) that can be used to record the location of a specific object on a microscope slide. This figure illustrates the appearance of the x coordinate designating a location at 112.6. See text for details.

  • Figure 9.1.10
    The condenser diaphragm is an essential piece with which to become familiar. (A) Condenser diaphragm closed down. The edges of the iris diaphragm appear as a polygon through the ocular light tube. (B) When adjusted for Köhler illumination (bright-field microscopy), the diaphragm should be open 75% as shown here. For dark-field, the diaphragm should be opened all the way to allow the greatest collection of tangential light (and the condenser should be racked all the way up, nearly touching the microscope slide).

  • Figure 9.1.11
    Establishing Köhler illumination. This illustrates the two major steps in establishing Köhler illumination. First, panel (A) shows how (after focusing the microscope on an object), one should focus the substage condenser using its own focusing knob in order to bring the image of the collector lens into focus. This can be done in one of three ways. (1) If the microscope has a field diaphragm, simply close the field diaphragm down and focus on the edges of the diaphragm polygon. Next, open the diaphragm back up until its image expands just beyond the field of view. (2) If the microscope doesn't have a field diaphragm, drop a clear plastic disk onto the illuminator marked with an “X,” and focus on that, or (3) bring the ground glass of the diffuser into focus and then slightly defocus (the ground glass image can be too subtle for some to catch). Panel (B) shows the step (see step 7 under Logistics of Köhler Illumination) in which one adjusts the condenser diaphragm to the 75% image seen in Figure 9.1.10B.

  • Figure 9.1.12
    This illustrates the effect of oil immersion. Panel (A) indicates a total of six interfaces between glass and air, each of which is an opportunity for light to be refracted and information lost. Panel (B) shows that an appropriate oil (n = 1.501), establishes a light path with far fewer interfaces for light to be refracted through. The oil, glass, and mounting medium all share the same refractive index. Panels (C) and (D) illustrate how oil immersion helps a lens to capture more of the light from an illuminated object.

  • Figure 9.1.13
    A cartoon of the diffraction pattern of light as it passes through a tiny aperture or is diffracted around some tiny microscopic object. The central light disk is referred to as the Airy disk and contains ~84% of the light. It is referred to as the zero-order light. The concentric rings of light represent the first-order, second-order diffracted light, etc., and are of decreasing intensity. All microscopic images can be modeled as a collection of such diffraction patterns and the composite interference pattern that occurs through their interaction.

  • Figure 9.1.14
    Images of a plant stem (Tilia sp.) at 400× magnification (a 40× objective lens and a 10× ocular). Panel (A) shows the image with a 40× dry lens. Panel (B) shows the same image with a 40× oil immersion lens. Cell walls and internal cytoplasmic inclusions appear crisper. Panel (C) shows the same image with polarized light. The polarizer and analyzer are not quite at right angles, so that background light is not fully extinguished. Polymers of lignin appear bright. Panel (D) shows a DIC (Nomarski) image of the same. A sense of topological relief is produced as steep gradients in refractive index are converted into changes in light intensity.

  • Figure 9.1.15
    Dark-field microscopy. Panel (A) shows the light-path from a typical bright-field microscope. Most of the image is created by direct, undeviated light. Diffracted light is collected, but its signal is swamped by the undeviated light. Panel (B) shows the effect of placing a dark-field stop into the center of the light path between the illuminator and specimen. Only tangential light passes through the specimen pane. Having no specimen with which to interact, this tangential light misses the objective lens completely and the image is black. (C) When an object passes into the path of this hollow cone of light, light is diffracted, and that diffracted light will be collected by the objective lens. The result is a bright image against a dark background. (See Fig. 9.1.16B for an example).

  • Figure 9.1.16
    At 200× magnification, a plant stem in cross section is imaged with (A) bright-field and (B) dark-field illumination.

  • Figure 9.1.17
    Phase-contrast microscopy. The upper figure illustrates the basic design of the phase-contrast microscope. A phase annulus lies just below the condenser lens, illuminating the specimen with a hollow cone of light, similar to the dark-field model, yet different. The hollow cone of direct (undeviated) light has a more acute angle, so that its light is collected by the objective lens and contributes to formation of the image. Within the objective lens, there is a phase plate through which the direct, undeviated cone of light is transmitted. In the model illustrated, this phase plate has a raised annulus of glass that is coated with a neutral-density filter to dim the undeviated light. The height of this raised ring is such that light passing through it is phase-delayed by ¼ (see lower diagram). Deviated light, i.e., light that has passed through a diffraction object in the specimen, passes through the unraised center of the phase plate. When light is diffracted, it is also phase delayed by ¼ . Hence, in this design, the deviated light and the undeviated light are brought back in phase with one another, and will interfere positively to create regions of brightness in the image. Since diffraction is the result of light interfering with edges and tiny particles, these are the objects that become highlighted in the final image. Other models of phase microscopes etch the glass of the phase plate, reducing its effective light path so that the direct, undeviated light is advanced ¼ with respect to the deviated (diffracted) light. The net effect is that deviated light is now ½ delayed with respect to undeviated light, and the deviated and undeviated light interfere negatively, producing areas of shadow around edges and particles.

  • Figure 9.1.18
    Nomarski or differential interference contrast (DIC) microscopy. This figure illustrates the basic design of the DIC microscope. Two features are familiar: the polarizer and analyzer, two pieces of cross-polarizing material that extinguish most light. The new features are the two Wollaston prisms, one located below the condenser lens and the other above the objective lens. Polarized light enters the first Wollaston prism and is split. Each ray is split into two rays that are cross-polarized and travel parallel (yet very close) paths. These split rays probe the specimen. When sharp gradients in refractive index are encountered (subcellular compartments with different chemical compositions), one of the twin rays passes through the lower-refractive-index medium, while the other passes through the higher-refractive-index medium. This results in a phase shift between the initially in-phase, cross-polarized beams. The second Wollaston prism recombines the “split rays.” If a pair of split rays never encounter a difference in refractive index as they passed through the specimen, they are recombined exactly as they were, and their light is extinguished as it passes through the analyzer. If two rays do encounter differences in refractive index and become out-of-phase, when recombined by the second Wollaston prism, the resultant light has a component that vibrates at angle to the initial, polarized beam. This can then pass through the analyzer and form an image. This microscope turns steep gradients of refractive index (in an otherwise transparent object) into a landscape of contrast.

Literature Cited

Literature Cited
    Abramowitz, M. 1985. Contrast Methods in Microscopy. Vol. 2. Olympus America Inc., Center Valley, Pa.
    Allen, R.D., David, G.B., and Nomarski, G. 1969. The Zeiss-Nomarski differential interference equipment for transmitted-light microscopy. Z. Wiss. Mikrosk. 69:193-221.
    Cole, E.S., Stuart, K.R., Marsh, T.C., Aufderheide, K., and Ringlien, W. 2002. Confocal fluorescence microscopy for Tetrahymena thermophila. Meth. Cell Biol. 70:337-359.
    Köhler, A. 1893. A new system of illumination for photomicrographic purposes. Z. Wiss. Mikroskopie 10:433-440. Translated in Royal Microscopical Society-Köehler Illumination Centenary, 1994.
    Murphy, D.B. 2001. Fundamentals of Light Microscopy and Electronic Imaging. Wiley-Liss, New York.
    Newton, R.H., Haffagee, J.P., and Ho, M.W. 1998. Creating color contrast in light microscopy of living organisms. J. Biol. Education 32:29-33.
    Nomarski, G. 1955. Microinterféromètre différentiel à ondes polarisées. J. Phys. Radium 16:9S-11S.
    Omoto, C.K. and Folwell, J.A. 1999. Using darkfield microscopy to enhance contrast: An easy and inexpensive method. American Biol. Teacher 61:621-624.
    Padawer, J. 1968. The Nomarski interference-contrast microscope. An experimental basis for image interpretation. J. Royal Microscopical Society 88:305-349.
    Salmon, E.D., von Lackum, K., and Canman, J.C. 2005. Proper alignment and adjustment of the light microscope. Curr. Protoc. Microbiol. 0:2A.1.1-2A.1.31.
    Zernicke, F. 1955. How I discovered phase contrast. Science 121:345-349.
 Key References
    Barker, K. 2005. At the Bench: A Laboratory Navigator. Updated Edition. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.

A useful (brief) practical guide.

    Murphy, 2001. See above.

A recent book (the best in my opinion, which does a good job discussing practical microscopy and its theoretical underpinnings.

 Internet Resources
 General Microscopy Resource Sites
    http://micro.magnet.fsu.edu/primer/
    http://micro.magnet.fsu.edu/primer/java/components/characteristicrays/index.html
    http://www.olympusmicro.com/primer/index.html
    http://web.uvic.ca/ail/techniques/scope_basics.html
    http://www.ou.edu/research/electron/mirror/
 Resolution and Numerical Aperture
    http://www.microscopyu.com/articles/formulas/formulasresolution.html
    http://micro.magnet.fsu.edu/primer/anatomy/numaperture.html
 Köhler Illumination
    http://micro.magnet.fsu.edu/primer/anatomy/kohler.html
    http://www.aecom.yu.edu/aif/instructions/koehler/koehler.htm
    http://www.emlab.ubc.ca/pKoehler.htm
 Specialized Microscopy (Overviews)
    http://micro.magnet.fsu.edu/primer/techniques/index.html
    http://www.pirx.com/droplet/microscopes.html
 Dark-Field Microscopy
    http://www.ruf.rice.edu/~bioslabs/methods/microscopy/dfield.html
    http://micro.magnet.fsu.edu/primer/techniques/dark-fieldindex.html
    http://www.microscopyu.com/articles/stereomicroscopy/stereodark-field.html
    http://www.olympusmicro.com/primer/techniques/dark-fieldindex.html
    http://www.olympusmicro.com/primer/java/dark-field/cardioid/index.html
 Rheinberg
    http://micro.magnet.fsu.edu/primer/techniques/rheinberg.html
    http://www.microscopy-uk.org.uk/mag/indexmag.html http://www.microscopy-uk.org.uk/mag/artnov02/diydic.html
 Polarized-Light Microscopy
    http://www.microscopyu.com/articles/polarized/polarizedintro.html
    http://www.microscopy.fsu.edu/primer/java/polarizedlight/waveform3d
    http://www.microscopyu.com/articles/polarized/polarizedintro.html
    http://www.olympusmicro.com/primer/techniques/polarized/polarizedhome.html
    http://micro.magnet.fsu.edu/primer/techniques/polarized/polmicroalignment.html
 Phase-Contrast Microscopy
    http://www.microscopyu.com/articles/phasecontrast/phasemicroscopy.html
    http://www.microscopyu.com/tutorials/java/phasecontrast/microscopealignment/index.html
    http://micro.magnet.fsu.edu/primer/techniques/phasecontrast/phaseindex.html
 DIC Microscopy
    http://www.olympusmicro.com/primer/java/dic/wavefrontrelationships
    http://micro.magnet.fsu.edu/primer/java/dic/wollastonwavefronts/index.html
    http://www.microscopyu.com/articles/dic/dicindex.html
     
 
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