One of the ways that technology has boosted science is by helping researchers observe objects that are normally too small or too far away to see. You won’t be using telescopes or binoculars to study plants, but microscopes can help you explore the cellular world. You can get a close look at the tissues inside seeds, stems, or leaves. You might be able to watch fern spores germinate, tell apart different species of pollen, or figure out which plant cells are used for photosynthesis, starch storage, or water transport. Some very tiny plants, such as duckweed or single-celled algae, are best observed with microscopes!

How a Microscope Works

A compound microscope’s frame has several parts that line up the lenses, light source, and specimen (see Figure 1, next page). The base acts as a sturdy foundation to which an upright arm is firmly attached. Thestagemakesasolid,flatsurface,usuallywithtwostageclipstoholdaslideinplace.

To learn how a microscope works, we can follow the path of a beam of light. The light source is a lamp or illuminator below the stage that shines upwards. As the light travels towards the stage, it passes through a hole with an adjustable opening, the iris diaphragm. The amount of light passing through can be changed by moving a lever at the front of the diaphragm. Next, the light passes through a condenser lens below or inside the stage. This focuses the light onto the specimen.

After passing through the specimen, the light enters into one of two to four objective lenses mounted on a revolving nosepiece. Each objective has been made to give a specific magnification with the best possible clarity of detail. The magnification of each objective is marked on its side, e.g., 4X, 10X, or 40X. Objective lenses are expensive, so you should handle them carefully! The coarse focus knob and the fine focus knob, found on the arm of the microscope, are used to improve the overall clarity or focus on different layers within a specimen.

The image of the object has now been magnified by one of the objective lenses, and this image is carried by light inside the tube. An additional lens, the ocular or eyepiece, now acts just like a magnifying glass, enlarging the image more just before it reaches your eye. The ocular usually has a magnification of 10X. The total magnification of the image you see is the magnification of the ocular multiplied by the magnification of the objective you are using.

tube

illuminator

Caring for a Microscope

Figure 1. The Parts of a Compound Microscope

The microscope is a precision instrument and should be handled with care. Always use two hands when carrying a microscope, and carry it in an upright position. Support the base with one hand while holding onto the arm with your other hand. Your instructor will show you the proper way to remove the microscope from its cabinet and carry it.

Keep the microscope clean – especially the lenses. Your instructor will show you how to clean the ocular lens. Sincelensesareexpensive,useonlyspeciallenspapertocleanthem.

You will also need to use the objective lenses and focus knobs carefully to prevent scratching the objectives against your slides. Always begin your viewing with the lowest power objective, because these have the most leeway to move. You can focus with the coarse focus knob at first, then use the fine focus knob to make smaller adjustments to get the clearest view of your specimen.

Once you have positioned the specimen well for viewing and can see basic details, you can increase the magnification by rotating the nosepiece to the next highest power. Microscopes are built so that a subject in focus with a low power objective should still be nearly in focus at the next higher power. It is best to limit the use of the coarse focus when using higher-power objectives, and never use it with the 40X objective. With this objective in place, you should only adjust the lens upwards unless you are watching from the side to be sure that the tip of the lens does not touch the specimen or slide.

Caring for Your Eyes

Most microscopes are monocular – they have only one eyepiece. The disadvantage here is that you can only look at specimens with one eye. However, this can also be an advantage:

• you can reduce eyestrain by switching eyes every few minutes,

• you can observe and draw the object at the sametime, and

• you don't have to adjust the microscope to account for differences between your eyes.

  Get into the habit of keeping both eyes open when using a monocular microscope. This will let you take advantage of the points outlined above. It also reduces eyestrain. A second way to reduce eyestrain is to periodically look up from the microscope and focus on a distant object for a few seconds. Third, use the iris diaphragm to lower the light intensity just below what seems right before you begin. Setting the light too bright can strain your eyes if you are making observations for a long time.

  Some microscopes are binocular; these have two ocular lenses. Especially for dissecting microscopes, this can allow a more three-dimensional view of specimens. It is still important to reduce eyestrain by looking up from the microscope occasionally when using a binocular microscope. In addition, the two ocular lenses need to be adjusted relative to each other so that you can see the specimen with the same clarity in both eyes. If the adjustment is incorrect, eyestrain will set in much sooner.

  Figuring Out What You’re Looking At

  What Part of the Specimen Am I Seeing?

  With the lowest power objective in place, put a slide containing some newsprint onto the stage. Bring the lettering into clear view using the coarse focus. Is the image you observe right side up or upside down relative to the object on the stage? While you are observing the image, move the slide to the left. Which way does the image move? Now move the slide up. Which way does the image move? Keep these observations in mind as you examine your experimental specimens!

  Magnification and Field of View:

  With your newsprint still in place, switch to a medium power objective. If needed, use the fine focus to produce a clear view. Is the size of the letter image larger or smaller? Is the total area you can see on the slide without moving it – the field of view – larger or smaller? Repeat this process with the high power objective, being sure to use only the fine focus knob with this lens in place! Is the image larger or smaller? What about the field of view? Again, keep your observations in mind when you look at experimental specimens.

Thought Exercise: If you were searching a new slide for a single microscopic organism, would it be faster to scan the entire area using the lowest power or the highest power objective? Why?

How Big Is the Field of View?

Suppose you find during Where Does Pollen Come From? that a grain of pollen reaches halfway across your field of view under the highest power objective. How big is it? Or perhaps you see a row of 13 cells in a C-fern sporophyte stretches entirely across the field at medium power during C-Fern in the Open. How long on average is a single sporophyte cell? You can only find the answers to these questions if you have calibrated the microscope’s field of view!

To carry out this calibration, place a plastic ruler on the microscope stage and focus on it under low power so that you can see the mm markings. Estimating as closely as possible, what is the diameter of your field of view? Record the data in Table 1. Now focus on the ruler under medium power and repeat the estimate. Repeat again under high power. You might not be able to directly measure the diameter of the field of view under high power, but you can calculate an estimate with this formula:

Field Diameter (high power) = [Field Diameter (low power) x magnification (low power) ] magnification (high power)

Next, calculate the area of the field of view at each magnification based on the diameter. Recall that the area of a circle is πr2, with π = 3.14 and r = 1/2 diameter. Put the information into Table 1.

Looking Through Layers:

Place a slide containing three differently-colored, overlapping threads on your microscope and bring them into focus under low power. Can you focus on all three at once? Switch to the medium power objective and refocus using the fine focus knob. Are all three threads simultaneously in focus? Repeat for high power, only using the fine focus. How many threads are in sharp focus at one time? Depth of field is the distance over which objects at different, small distances from the stage can be clearly viewed at a single focus point. How does this relate to the area of the field of view at different magnifications? Return to low power and look at your microscope tube from the side as you rotate the coarse focus knob clockwise. Are you focusing up or down?

Higher magnification creates a smaller depth of field. This means you can focus on a plane thinner than the thickness of some part of the specimen. For example, you may want to look at different layers of cells in a thin cross-section of petiole tissue in The Celery Challenge. Looking at different optical sections can help you figure out the three-dimensional structure of individual cells or tissues.

Can I Directly Measure The Sizes of Things I See?

Once you know the diameter and area of the field of view, you can carry out calculations to determine the approximate size of the spores, cells, or tissues you see under the microscope. By estimating how many cells are in the field or how much of the field is taken up by one cell, you can get a rough estimate of a cell’s size. The standard unit of measure in light microscopy is the micrometer (1 μm = 0.001 mm), so it’s best to describe the field of view and specimen sizes on this basis.

Some objects might still be hard to estimate based on the field of view – perhaps they are still small at the magnification you are using, or maybe they are positioned at tricky angles. Having some finer-scale guide would be helpful for judging size! One solution is using an ocular micrometer or reticle, a disc containingaprecise,uniformscalethatisinsertedintotheocularlens. Insomelenses,thetopelement must be unscrewed before dropping the reticle into the lens, where it rests on a circular annulus. In other lenses, the reticle is directly dropped onto the annulus, but a split ring is used to hold the micrometer in place.

Because the reticle is positioned above the objective lens, the actual distance between marks in an image will depend on the magnification in use. This calibration can be done by comparing the gridlines against those on a stage micrometer, a special microscope slide with a grid scale of precise, known dimensions. For example, a stage micrometer’s scale lines may be 0.1 mm apart. One end of the scale may also be subdivided into even smaller units, such as 0.01 mm.

You can calibrate a reticle as follows:

1. Put the stage micrometer on the stage, and look through the ocular lens.

2. Using the lowest power objective, bring the micrometer scale into focus.

3. Line up one end of the stage micrometer’s scale exactly with one end of the reticle grid.

4. Find two lines further along that exactly match between the scale and the grid.

5. Count the number of scale units on the reticle from one matching pair to the other.

6. Record the actual, corresponding measurement from the stage micrometer.

7. Divide the measurement by the number of reticle units you counted to find the distance

   between each mark in the reticle grid.

8. The calibration only applies for the objective lens you used for Steps 3-7, so you must repeat

   these steps with the other objective lenses you plan to use.

Analyzing Images:

What can you measure with a calibrated reticle? Just about any interesting part of a specimen! For example, you can more precisely measure the total distance across a cell, set of cells, or a specimen than you could based on a calibrated field of view. Specific methods for this are described in “Visualizing Plant Cells Using a Microscope,” in the Celery Challenge Toolkit and in “Visualizing Plant Cells and Chloroplasts Using a Microscope,” in the Power of Sunlight Toolkit. With a calibrated grid reticle, you can also use point counting techniques to determine the number of cells in a given area, or cell density. For example, you may want to measure the growth of algae cultures exposed to two different types of lightinginThePowerofSunlight. Afterpreparingslidesofeachculture,youwouldsimplycountthe number of algal cells in a predetermined number of “blocks” in the grid. The cell density in a block is the number of cells within it divided by the block’s area.

Newer microscopes can often be connected to digital cameras, which can then record specimen images. You can easily add digital images to reports and presentations. Certain computer programs can also help you analyze the number of cells in the image or estimate the area of a specific cell.

Techniques for Examining Living Cells

Some your investigations may involve closely examining living cells, so learning how to prepare your own slides can be helpful. Some of the most common and useful techniques are described below.

Hand Sectioning:

Hand sectioning is a fast way to make microscope specimens of the cells making up relatively firm tissues. This method involves using a razor blade, so safety is important to consider! Your early attempts may not give perfect results, but even your mistakes will help to you see the three-dimensional relationships in the samples. With practice, you can eventually create excellent samples. This technique is described in detail in the method “Cutting Transverse Sections of Plant Tissues for Microscopy” in the Celery Challenge Toolkit.

“Poor Man’s Microtome”:

Step 1 Step 2 Step 4 Step 5

Figure 2. Holding Plant Material and Razor for Sectioning

Step 3

Step 7

Images: William Welch & Theresa Woods
Figure 3. Using a “Poor Man’s Microtome” to Make Thin Sections of Celery

A microtome is an instrument used to make very thin sections of plant material, which can then be observed under a microscope. Microtomes can be purchased, but they are usually quite expensive. You can make your own much more cheaply to get better results than can be achieved by hand sectioning alone. This technique is fully described in “Cutting Transverse Sections of Plant Tissues for Microscopy” in the Celery Challenge Toolkit, but the photos above will give you an idea of how it works.

Water Mounts:

A water mount is one of the most common ways to prepare specimens that are too small to be moved around by hand. It is easy to do and especially useful when you plan to examine single-celled organisms, such as algae. In general, an organism is grown in or transferred into water. Using an eyedropper, a drop or two of the sample is placed on a slide and protected with a cover slip. This method is also described briefly in “Visualizing Plant Cells and Chloroplasts Using a Microscope,” in the Power of Sunlight Toolkit.

Epidermal Peels and Scrapes:

Single layers of epidermal cells, the outer "skin" of plant parts, contain several kinds of specialized cells that protect the inside of the plant and allow gas exchange and transpiration to occur. This cell layer can be peeled from thick, fleshy plant organs (Figure 4) and water mounted on a slide. This is called creating an epidermal peel.

If the epidermis cannot easily be peeled, individual epidermis cells or small groups of them may be removed by scraping the surface of a leaf or stem with a scalpel, razor, or wooden toothpick. Rinsing the scraping tool in a drop of water can provide a sample to create a water mount. Both the epidermal scrape and epidermal peel technique are described in “Making Epidermal Peels for Microscopy,” in the Celery Challenge Toolkit.

Epidermal Impressions:

Figure 4. Making an Epidermal Peel

Making peels or scrapes from thin leaves, or small stems or roots can be difficult. Sometimes you may also want to make repeated observations of the same cells, so destructive techniques like peeling or cutting plant tissues will not be helpful. In such cases, a good option is making an impression of the cells in another material, such as nail polish, then examining the impression under a microscope. To do this, paint a small area of the tissue to be studied with nail polish. After it has dried completely, use a fine forceps to peel off the hardened polish. This impression has recorded the outline of the cells to which it was applied, and it can be mounted on a slide for observation just like living tissue. “Visualizing and Counting Stomata Using the Impression Method” describes this technique in more detail, and it is found in both the Power of Sunlight Toolkit and the Celery Challenge Toolkit.

Bringing Out Interesting Features

Sometimes it can be tricky to identify certain parts of a cell, or to figure out whether different cells in a tissue are the same type or a different type. For example, in the Power of Sunlight, you may want to know which plant cells store the starch made from the sugars created during photosynthesis, and where in the cells the starch is stored. A number of simple stains can be used to determine the presence and location of specific kinds of molecules in cells. In the example above, stains that bind specifically to starch would be helpful. Below, several common stains are briefly described. Detailed methods for preparing and using them are provided in “Plant Cell Staining Techniques” in the Celery Challenge Toolkit. The preparation and use of Lugol’s solution is also described in “Identifying Starch in Plant Leaves Using an Iodine Staining Method” in the Power of Sunlight Toolkit.

Lugol’s Solution:

Lugol’s solution is a stain made from potassium and iodine. It binds to starch and produces slightly different brown, purple, or black colors depending on how long the starch molecules are. Since longer starch molecules take more time for a plant cell to build, this stain can provide hints about how old the starch is in the cells you are observing.

Toluidine Blue:

Toluidine Blue is a stain that reacts with a variety of cell components to produce different colors. This is a good stain to quickly tell apart tissue regions, identify different cell types, and find specific cell structures. Toluidine blue stains proteins, DNA, and RNA when in an alkaline solution (pH 10), so it can be helpful in examining thin sections or observing mitosis.

Phloroglucinol:

Phloroglucinol is mixed in a dilute solution of hydrochloric acid. The acid reacts with lignin, a polymer found in plants’ secondary cell walls, to break specific bonds. These free chemical groups then react with the phloroglucinol stain to produce a red color.

Sudan IV:

Sudan IV stain is prepared in ethylene glycol or propylene glycol, and it binds with waxes, fats, and oils to produce a red color. This is helpful in identifying structures like oil bodies inside cells, the waxy cuticle outside the epidermis, or the Casparian strip outside the vascular bundles in a stem or petiole.

Special Types of Microscopes

Dissecting Microscope:

Suppose you want to look closely at the colors and shapes of seeds as a part of an experiment in The Wonder of Seeds. You would need magnification, but it probably would not need to be as strong as that of a compound microscope. A dissecting microscope is used mainly for this sort of purpose and for dissecting small objects. Like a compound microscope, it consists of an objective lens and an ocular lens. While the ocular lens is usually 10X, the objective lens is a lower power, often able to zoom from 1X to 6X. The total magnification is determined by multiplying the magnification of both lenses. Unlike in a compound microscope, the image is not inverted. Overall, a dissecting scope is a bit like a powerful magnifying glass that you don’t need to hold in your hand!

Polarizing Microscopes:

Transparent crystalline materials can often bend (refract) the light
that passes through them to move at different angles relative to
the incoming light. Cell walls, starch, the spindle apparatus, and
crystals all exhibit this property, so it can be used to study cell
structure. To observe this, special filters are needed. A polarizing
filter will absorb all light waves except those moving exactly
perpendicular to the plane of the filter. If a second polarizing filter, called the analyzer, is placed so that its polarization is rotated 90o relative to the first filter, it will absorb the light that passed through the first. At this precise orientation, the polarizing filters are crossed, and the condition of maximum darkness is called extinction. The interesting part is that materials that can refract incoming light can still be seen with crossed polarizing filters (Figure 5)!

To practice using polarizing filters, you can make a water mount of a small bit of starch. First observe your preparation under a typical compound microscope. Make a sketch of two or three grains, as observed with the high power objective, in your lab notebook. Next, convert the microscope to a polarizing microscope by placing a polarizer filter between the light source and the specimen. Hold the analyzer between your eye and the ocular lens. Rotate the analyzer until you achieve extinction, and observe your starch grains. Make a second sketch of the same grains as observed with polarized light. Do you see a difference? How might this approach be useful for observing your experimental samples?

Dark Field Microscopy:

Image: Wikimedia Commons

Dark field microscopy helps the viewer see more detail in small objects by making them light against a dark background. Some of the light entering the condenser is blocked with a field stop, a special filter with a blackened circle in the center. No light passes directly through the specimen; instead, it is illuminated from the sides. Small parts of the specimen refract or reflect light into the objective, appearing to produce their own light against a dark background (Figure 6). Dark field microscopy is especially helpful in examining algal cultures, pond water, or other samples in which small objects are distributed throughout a liquid.

To practice using a dark field microscope, place a drop of pond water on a

slide and add a coverslip. Observe your specimen under the usual bright field, sketching two or three different organisms in your lab notebook. To convert your microscope into a dark field microscope, place a field stop in the filter holder. Next, adjust the iris diaphragm so that the field holder appears black. Reexamine your specimen and make new sketches of the same organisms in

dark field. Is any more detail visible? How might this be useful in your own experiment?

Figure 5. Starch Crystals Under

a Polarizing Microscope.

Image: Wikimedia Commons

Figure 6. Dark Field Microscopy

Additional Resources

Videos: Confocalandmultiphotonmicroscopy–WellcomeImageAwards2009,byWellcomeCollection. Learn about how high-tech research labs use laser microscopes to generate 3D images. http://www.youtube.com/watch?v=g5U-n4Toq60

Dark Field Microscopy, On the Cheap, by Bruce Taylor. This video shows a simple way to carry out dark field microscopy without using a field stop, then shows what the results look like. http://www.youtube.com/watch?v=Mkqi3fL84sg

Different Kinds of Microscopes, by Donna Forward. This general presentation shows differences among light microscopes, dissecting microscopes, electron microscopes, and ion field microscopes. http://www.youtube.com/watch?v=eUQzE_UX23Y

Fluorescent Microscope by Sarah, by Medical Ignorance. A cancer researcher describes how fluorescent molecules can be attached to certain molecules or organelles to clearly view cellular processes. http://www.youtube.com/watch?v=O6JVAUgz0MU

PartsofaCompoundLightMicroscope,byAndrewPiper(everythingPiper). Thisvideobrieflyreviews the names and uses of different parts of a light microscope. http://www.youtube.com/watch?v=RKA8_mif6-E

Polarized Light Microscopy Reveals Hidden Beauty, by Gary Barker. Learn how to convert a light microscope to a polarizing microscope, and see examples of crystals viewed using polarizing filters. http://www.youtube.com/watch?v=ulNZ3u7_J5I

Web Pages:
Eukaryotic Cell Interactive Animation, by Cells Alive! These interactive models of a plant and an animal cell highlight the organelles if you move the cursor over parts of the image or over the organelle name. If you click the image or the name, you can read a description of the organelle and its function. http://www.cellsalive.com/cells/cell_model.htm

Selected staining methods for plant microtechnique, by Steven E. Ruzin with the CNR Biological Imaging Facility at the University of California Berkeley. This online selection from Ruzin’s microscopy book gives tips and recipes for a few plant stains and includes references for other staining methods. http://microscopy.berkeley.edu/Resources/instruction/staining.htm

Books and Articles:
Matsumoto, B. 2010. Practical Digital Photomicrography: Photography Through the Microscope for the

Life Sciences. Santa Barbara, California: Rocky Nook, Inc. 184 pp.

Ruzin, S.E. 1999. Plant Microtechnique and Microscopy. New York, New York: Oxford University Press USA. 336 pp.

Yeung, E.C. 1998. A Beginner’s Guide to the Study of Plant Structure. In S.J. Karcher, Ed. Tested Studies for Laboratory Teaching, Vol. 19: Proceedings of the 19th Workshop/Conference of the Association for Biology Laboratory Education (ABLE), pp. 125-142.