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Laboratory Exercise Instructor Notes
Basic Microscopy


One of the problems facing students in introductory plant pathology courses is that many of them have not learned how to use a microscope properly. This laboratory exercise was developed to provide students with rudimentary skills for setting up a microscope and focusing on material such as prepared slides. Completing this exercise in the first laboratory saves a lot of time later in the semester since students are generally better able to focus on microscopic material. You do not hear, "I can't find anything on this slide," nearly as often, and you do not see students with the objectives two inches above the slide.

This exercise is often paired with an exercise involving the preparation of slides of fungal structures such as cleistothecia or hyphae for viewing on a compound microscope. It is also good to have some fruit or vegetables covered with fungal growth to view under the dissecting microscope. Living nematodes are another specimen which is good for observation using both compound and dissecting microscopes. Nematodes also may be more interesting to students since they can see that they are alive and moving.

Microscopes in teaching laboratories often vary in their components - such as the objectives, magnification of the eyepieces, auxiliary magnification lenses on dissecting microscopes, and types of light sources used with dissecting microscopes. Owing to these differences the instructor may want to provide students with a diagram or picture of the models of microscopes in their laboratory. This exercise was developed to be general rather than specific due to differences in equipment in different laboratories.

Preparation of "e" for observation
Using "e's" for observation provides students with a familiar object to observe. The "e" should be typed in a 6-point font and then printed on a white piece of paper. You could also print it on two different types of printers (laser and inkjet printers) so students can observe the differences between the two printers. Once you have a group of "e's" printed on white paper, this page should be photocopied onto a clear transparency reducing their size 50% in the process. This will provide "e's" which you can still tell the top from the bottom but the student will not be able to see much detail (approximate size 0.6 x 0.45 mm). A clear transparency is used so that the "e's" can be placed on slides and viewed using the compound microscope. Students find it interesting to note how messy and unclear the type is when viewed under the microscope, as compared to how clear it appears with the naked eye.

Guidelines for Microscope Storage and Use
Additional guidelines should be addressed by the instructor. Every laboratory has differences in where and how microscopes are stored, what must be done when students have completed exercises, etc. The following are some guidelines that I have used for students but they may be different in other situations.


  1. Keep microscopes clean. Clean the lenses with lens paper only. Inform students where lens paper is located
  2. The initial focus should always be obtained with the low power objective, then if desired you can change to higher power objectives.
  3. When observing specimens using higher power lenses, only use the fine adjustment.
  4. When carrying the microscope be sure to put a hand under the base and a hand on the arm and carry it in an upright position. On some dissecting microscopes the glass stage plate is not permanently attached and it can be dislodged if the microscope is not carried in an upright position.
  5. Make sure that your work area is well organized. Make sure that power cords are not placed anywhere that someone may trip over them or the microscope or light could be inadvertently pulled off the table.
  6. If you have used any immersion oil for observations, make sure that all immersion oil is removed from the objective using lens paper.
  7. When you are finished for the day, put the microscope back into the storage area after: removing slides from the stage, putting the low power objective in position, and moving the tube down.
  8. Clean all prepared slides prior to placing them back in storage areas. Use lens paper to remove any oil. If the slides are still dirty, please contact the instructor.
  9. If you have any problems, please contact the laboratory instructor. Do not attempt to disassemble the microscopes or repair them.

Orientation of Materials on Slide
The orientation of material on the slide is important for students to note. When viewing materials under a microscope, students often have to move these materials and it helps for students to realize which direction materials on the slide will move as they move their slide. It is also important to note the direction of movement if the students need to look at a structure with the naked eye for comparison. For example, when looking at a fungus growing on the surface of a vegetable, an unidentified structure may be observed under the dissecting microscope. In order to transfer this structure to a slide the student needs to understand where the structure is located on the specimen in relation to what they see through the microscope. It is also important for students to realize that this orientation may vary with the type of microscope being used.

It is helpful for students to draw materials that can be used for comparisons by having them draw specimens in relation to the field of view and include the magnification on their drawings. If students draw a circle to represent their field of view and then draw a grid within the circle (3 lines across and 3 lines down) this will provide an area in which to draw. Students will be able to draw specimens at a relatively correct scale which will be useful later for comparison with other materials. Make sure that students put the magnification used on drawings or comparisons will not be possible. In some cases a half or quarter circle may be an adequate size drawing.​