MicroscopyBasicsLite PDF
MicroscopyBasicsLite PDF
Chapter 1
                                        Parts
       Figure 1.1 illustrates the parts of an upright compound microscope and indicates the
terminology that I use in these notes.
    Stand
        The Stand is the solid support for the optics and mechanical parts of the
microscope. Over the years manufacturers have adopted many different configurations for
the stand. Regardless of the exact style, there are two basic types: The upright stand has
the objective lenses facing downward. The inverted stand has the objective lenses facing
upward.
   Illumination System
       The old microscopists believed that the best illumination came from the north sky. It
was focused on the specimen by use of a concave mirror. It was a beautiful light with a
remarkably constant color. It had drawbacks. The light did fluctuate in intensity, especially
on cloudy days, and you couldn't work at night. Artificial light sources are more
convenient and these are the types I will discuss.
   Illumination Methods
       The quality of light, its color and intensity, and the way it is brought to the
specimen, whether as diverging, converging, or parallel rays, greatly influences the
appearance and resolution of the specimen.
       Köhler Illumination
       In the late 1800’s, August Köhler invented an illumination technique that was so
profound it is still the standard method used today. Modern microscopes are designed to
use Köhler illumination. Köhler illumination uses optics that place the image of the filament
in the back focal plane of the objective lens. This results in the light source being
completely out of focus in the observer’s eye. A small, inhomogeneous, coiled filament can
therefore be used as the light source.
        Critical Illumination
         Köhler illumination is not the only method of illumination. A very different method,
which was popular in the 1930’s and 40’s, is called Critical Illumination or Nelsonian
Illumination after its inventor. Critical illumination forms a real image of the light source in
the specimen plane. In so doing, the specimen acts as if it were a “self luminous” object.
This has certain theoretical advantages when the physical optics of the microscope system
are considered. I will discuss this further in the chapter on confocal laser scanning
microscopy. One problem with critical illumination is that it requires a large light source
that is very homogeneous since the image of the light source is in focus along with that of
the specimen. A wide, ribbon-like filament was used for this propose. The practical
advantage of a small coiled filament far outweighs any theoretical advantage in image
improvement due to critical illumination.
    Lamps
    There are several types of lamps used in modern microscopes. Table 1.1 lists and
compares these. The tungsten-halogen lamp has become a standard because it maintains its
brightness and color temperature throughout its lifetime. Some illuminators use a concave
mirror behind the lamp to increase the intensity of light.
        The lamp housing can contain centering controls for the lamp and for the concave
mirror. Access to these controls is usually through holes in the lamp housing.
        WARNING: Never touch a lamp with your bare fingers. Many lamps have a
quartz envelope that may brake do to uneven heating caused by contamination from fingers.
    Collector Lens
    The collector lens sits directly in front of the lamp. In some illuminators, such as the
mercury-vapor type, this lens is adjustable. It focuses an image of the lamp's filament onto
the front focal plane of the field lens or of the condenser if there is no field lens.
   Diffuser
   The diffuser serves to break up the image of the filament. It may be built in and non-
removable. In modern research level instruments, it should be removable. The ability to
remove the diffuser is important in aligning the filament for phase contrast microscopy.
    Filters
        A series of filters may be present in the illumination system. A heat absorbing
filter is used to reduce the amount of infrared light that passes into the rest of the optical
system. This filter usually has a light blue color and can affect color micrographs. Various
colored filters may be present. These are used to affect contrast and color temperature of
the light for photomicrography, and to set the proper wavelength for phase contrast
microscopy. Neutral density filters may also be present. These filters are used to alter
the intensity of light without changing its color. For high precision polarization
microscopy, a light scrambler may be incorporated into the illuminator. This device,
which consists of a coiled quartz optical fiber, insures that light leaving the illuminator
shows no hint of uneven brightness or polarization.
     45° Mirror
     The 45° mirror directs light into the field lens. This is a flat, first-surface mirror. It is
easily damaged. A mirror is used, rather than a prism, because it introduces no refractive
artifacts.
    Field Iris
    The field iris, or radiant field diaphragm, is also an important item in Köhler
illumination. It serves to limit the area on the specimen that is illuminated.
       Modern microscopes may have more than one illuminator attached to the stand. In
addition to the transmitted light (diascopic) illuminator there may be an epi-illuminator
(episcopic) that is used for fluorescence or reflected light microscopy.
    Focus Knobs
        The ability to focus a microscope in very fine increments has been a goal long
sought by manufacturers. Today’s microscopes have focusing mechanisms that are more
precise than the resolution of the microscope itself. Course, fine, and sometimes medium
focusing knobs are present. Focusing can be achieved by moving either the specimen stage
or the objective lens. A mechanical focus mechanism usually has some means to tightening
and loosen it. Mechanical focus mechanisms need periodic servicing. Their lubricant dries
out, they become dirty and hard to operate, and they begin to drift. Servicing is best left to
a qualified service engineer. Appendix B lists USA contacts for microscope manufacturers.
    Condenser
        The condenser is the bully of the microscope. It ultimately limits the resolution of
the entire optical system; it provides the proper kind of light for Köhler illumination; it
carries optical elements necessary for dark field, phase contrast, and differential
interference contrast. The condenser iris (or aperture iris) controls the amount of contrast
and the depth of field seen in bright field. Centering knobs are available for aligning an
image of the field iris in the optical path. Movable lenses may be associated with the
condenser. These lenses adapt the condenser for different objective lens magnifications.
Usually they must be inserted for objective lens magnifications 10 X and above. These
lenses also affect the numerical aperture of the condenser.
   Stage
       The stage carries the specimen. On some microscopes it is the stage that moves
when focus is adjusted. Stages are often equipped with mechanical devices for holding and
moving the specimen. Special rotateable stages are available for polarization microscopy.
Special specimen holders are made for stages on inverted microscopes.
    Objective Lens
        The beauty of modern microscopes rests in the objective lenses. The theoretical
limits of resolution have been reached largely through the design of objective lenses. These
are the jewels of the microscope. This chapter will tell you how to care for them. Later
chapters will cover their characteristics and proper use.
    Nosepiece
       The nosepiece is a revolving turret that carries the objective lenses. On some
microscopes it is the nosepiece that moves when focus is adjusted. The thread size of the
nosepiece positions is an international standard enabling objectives from any manufacturer
to be mounted. It is not, however, a good idea to mix and match objective lenses. This will
be discussed in Chapter 7. The arrangement of objective lenses on the nosepiece is
    Binocular Tubes
        On microscopes equipped for binocular viewing, the eyepieces are connected to the
stand by a binocular tube. There are two types of binocular tubes and they differ in the way
they should be used. Figure 1.3 illustrates these rotational and translational types. Each
microscopist must adjust the interpupillary distance of Figure 1.3 Rotational Tubes
the binocular tubes to achieve a unified circular field of
view. Then, each tube and/or eyepiece is adjusted to
make a diopter correction for the microscopist’s
vision. Over time the prisms in binocular tubes can
become misaligned making it difficult for the
microscopist to see one circular field of view.
Realignment of the prisms should be done by a
qualified service engineer.
        Automatic Tubes
        On some microscopes, correction is done automatically – the binocular tubes move
in or out as the interpupillary distance is adjusted. One tube or eyepiece will be focusable.
Adjust the interpupillary distance to achieve a circular field of view. Focus the microscope
carefully on a specimen while viewing through the fixed tube, then adjust the focusable
tube or eyepiece for your other eye.
microscope while viewing through the fixed tube and finally adjust the focusable eyepiece
for your other eye.
        With rotational binocular tubes, the oculars may be independently focusable and
their adjustment depends on the type of instrument. In some instruments of both rotational
and translational types, a built in reticule is brought into sharp focus for one or both eyes
by adjusting the ocular(s). This assures coincidence of focus on the microscopist's retina
and on the film plane of attached cameras. Other microscopes work as follows: Set one or
both of the oculars to the 0 diopter position. This may be indicated by scale lines or by a
single line encircling the ocular. Adjust the microscope for fine focus using your dominant
eye (or using the fixed ocular if only one is focusable). Adjust the other ocular for fine
focus for the other eye.
    Eyepieces or Oculars
        Oculars provide the second level of magnification in the microscope. They finish
lens aberration corrections begun in the objective lens. They define the diameter of the field
of view. Oculars are also used to make diopter corrections for individual microscopists and
they can contain reticules for photomicrography or morphometry. Chapter 7 covers the
various types of oculars.
Exercises
1) Locate the parts shown in figure 1, or their equivalents, on your microscope.
2) Inspect the lamp in your illuminator. What are its type and wattage? Is it discolored?
3) Observe the frosted end of a slide under low power. What happens to the color of the
illumination as you decrease the lamp’s voltage from full to minimum? The color of the
light is very important in photomicrography.
5) If you have an arc lamp, note the type of lamp and power supply. Is there a way of
timing the number of hours the lamp has burned? Arc lamps degrade over time.
6) Write down the information printed on each of your condensers, objectives, and oculars.
This information will be needed later on.
7) Determine your dominant eye: Cut a hole about 2 inches square in a sheet of paper. Hold
the paper at arms length directly in front of your face. Look with both eyes through the hole
in the paper at some distant object. Close one eye and see if you are looking through the
hole or at the paper. Try the other eye. The eye that is seeing through the hole is your
dominant eye. Knowing which eye is dominant is helpful in correctly adjusting the oculars.
                                     Chapter 2
                                     Alignment
         Figure 2.1 is an image of striated muscle taken with a misaligned microscope and
figure 2.2 is with a properly aligned microscope. In 2.1 the illumination is uneven and
artificial fringes have been added to the image. In 2.2, the illumination is even, there are no
artificial fringes, and resolution is higher.
6)    Adjust the binocular tubes for your interpupillary distance. You should see one big
      circle of light.
8)    Adjust the eyepieces and / or binocular tube to correct for your vision. See the section
      on binocular tubes in Chapter 1.
9) While observing the specimen close the field iris until its shadow appears.
10) Focus the field iris using the condenser focus knob. Try for a thin purple fringe at the
    edge of the iris. If you can’t focus on the field iris, check the condenser for flip-in
    lenses and find the configuration that lets you focus on the field iris. If the iris moves
    out of the field of view as it is focused, bring it back into the field of view with the
    condenser centering screws.
11) Center the field iris with the condenser centering screws.
12) Open the field iris just to the edge of the field of view.
13) Pull out an eyepiece (you could instead insert a phase telescope or Bertrand lens –
    Chapter 10).
14) Remove the diffuser. (Some diffusers are not removable. If this is your case, go to
    step 17).
15) While looking down the empty tube, focus and center the filament image using the
    adjustment screws on the lamp housing. You should see neither the top nor bottom
    edge of the coiled filament nor its ends. Some illuminators have no adjustments.
17) While looking down the empty tube close the condenser iris to cover 10% to 50% of
    the full bright circle.
19) When you change objectives, repeat steps 9 - 12, 17 and 18.
Tip:
    When changing a lot between objectives, align the field iris for the lowest
magnification and the condenser iris for the highest and forget repeating steps 9 - 18.
Exercises
1) Align your microscope for Köhler illumination. Include the bulb centering procedure if
you can remove the diffuser. If you do not have a Bertrand lens or phase telescope for
observing the objective’s back focal plane, make a pinhole in some aluminum foil and use
this as a cap over the eyepiece tube to improve this image.
                       Chapter 11
     Differential Interference Contrast Microscopy
        Many microscopic specimens are colorless, nearly transparent, and relatively thick,
such as whole cells. Thick specimens do not give a clear phase contrast image. This chapter
presents a method for producing contrast in this type of specimen. The resulting image is
one that has a very topographic appearance. It looks as though you are looking down on
the specimen while it is being lit strongly from one side. Figure 11.1 is a DIC image of
cheek epithelial cells.
History of DIC
        We owe the current method of DIC to the work of Georges Nomarski (figure 11.1)
who developed it in the 1960’s. It is based on an older method of interferometery
microscopy. Nomarski was able to produce a modified Wollaston prism that he used with
high magnification, high NA objectives. He altered the older method by using two of these
prisms.
    Polarization Angle
        In Nomarski DIC, unpolarized light from the lamp is first plane polarized. Usually
a dichroic material such as Polaroid does this. Dichroic materials absorb light. The amount
absorbed depends on the light’s vibration axis (i.e., polarization angle) relative to the major
transmission and absorption axes of the polarizer. Light vibrating in the Polaroid’s major
absorption axis will be nearly all absorbed whereas light vibrating at 90 degrees to this axis
will be nearly all transmitted. Light vibrating at other angles will be partially absorbed and
partially transmitted. All transmitted light will have the same vibration orientation as the
polarizer’s major transmission axis. An important property of polarized light as used in
DIC is that interference can not occur between beams of polarized light that have different
polarization angles. Figure 11.2 illustrates the action of a polarizer. The polarizer’s major
transmission axis (vibration axis) is shown vertical; its major absorption axis horizontal.
5) Strain free plan achromatic objectives – A DIC objective lens must not affect the
polarization of light. This can happen if the glass elements of the lens have been subjected
to stresses that cause slight variations in the refractive index. It is difficult to manufacture
an apochromatic lens that is strain free because of the large number of lens elements. Thus,
most DIC lenses are achromats. Treat your strain free lenses very gently. One jolt can ruin
them.
6) Second modified Wollaston prism – A second prism is placed above the objective
lenses. The location of the interference fringes of this Wollaston prism must coincide with
the back focal plane of the objective. The back focal plane of middle and high power
objectives is inside the objective. The Wollaston prism therefore has its interference fringes
located outside the prism. Specific prisms are matched to specific lenses. It is therefore
unlikely that any objective lens you might have will function in a DIC system. Rather you
should buy prisms and objectives that are made for DIC. Manufacturers usually indicate
DIC on the barrel of these objectives. The upper modified Wollaston prism(s) will be
movable in a lateral direction. Moving this prism horizontally affects the optical path
difference between the two beams and therefore the amplitude contrast in the final image. It
emphasizes optical path differences introduced by the specimen.
7) Analyzer – This is a second polarizer placed after the second modified Wollaston prism.
This polarizer has its major transmission axis at right angles to the lower polarizer.
8) Eyepiece – Interference of the two modified beams occurs in the intermediate image
plane forming a real image that is further magnified by the eyepiece.
1) Using a 40 X objective, align the microscope for bright field Köhler illumination.
4) Insert the polarizer and the analyzer – insure that they are right side up. Usually this is
indicated on the mount. If the polarizer and / or analyzer are rotateable, make sure the
polarizer is set to the 0 or 90 degree position and that the analyzer is set to the opposite
position. Usually the polarizer’s major transmission axis is set right to left across the
microscope and the analyzer’s is set front to back.
9) Insert your specimen and adjust the illumination. Move the adjustable Wollaston prism
to achieve the desired DIC effect.
        Because the DIC technique is designed to work at the limits of resolution of the
objective lens, higher image resolution can be achieved than with phase contrast. A
significant advantage of DIC is its ability to produce very clean optical sections compared to
phase contrast.
       Although phase contrast requires additional optical equipment, the DIC apparatus is
more complex and generally more expensive.
        Specimens that alter polarized light, such as birefringent specimens and plastic
culture dishes, are not suitable for DIC. Phase contrast is still the best method for
examining cells in plastic culture dishes. A method called Hoffman Modulation Contrast
can be used to produce an image similar to DIC for specimens in plastic dishes, but this
method is also expensive.
Exercises
1) Set your microscope up for DIC. Note where the following components are located:
polarizer, first Wollaston prism, second Wollaston prism, and analyzer. Make a rough
sketch of their positions.
2) Check the alignment of your DIC system. What method is available for adjusting the
system for crossed polars?
3) Observe cheek cells using DIC. Describe how the image compares to a phase image?
4) Move the adjustable Wollaston prism from one extreme to the other while observing
cheek cells. What happens to the image?
5) Remove one of the DIC optical components while looking at cheek cells. What is the
effect on the image?