4.3 Common Mistakes to Avoid When Using a Petrographic Microscope

It is necessary to understand the parts and proper use of a petrographic microscope.  In practice, however, not everything goes as planned.  This is especially true if there are multiple users of the same microscope, either in the same class or across different classes which may be using the microscopes in different ways during the same semester or term.

In this module, we explore ways to troubleshoot issues that may arise while using the petrographic microscope.

Learning Objectives

Create and test hypotheses for the causes of problems experienced while using a petrographic microscope.

Prior Knowledge and Skills

4.2 Parts of a Petrographic Microscope; some hands-on experience with using a microscope is helpful.

Key Terms

No new terms – they are defined in Parts of a Petrographic Microscope

Guided Inquiry

4.3.1 Using your knowledge of the parts of a petrographic microscope, list at least three ways that a petrographic microscope could be altered or “messed up” so that it did not work properly.

Concept Checks

For each scenario described below, provide at least one testable explanation for the observation.

Concept Check 4.3.1

There is no light passing through the microscope.

Concept Check 4.3.2

It looks like something circular is partially blocking the field of view of the microscope.

Concept Check 4.3.3

The cross-polarized view of your thin section looks “funny”- the colors seem wrong for the minerals in the thin section.

Concept Check 4.3.4

The thin section is in focus at low magnification (4x at JMU), but it is not possible to focus it at higher magnification (63x at JMU).

If you are unsure of your answers to the Concept Checks, then please read the Summary and revisit the Concept Checks as needed.


Top 10 reasons why your microscope isn’t working correctly

This section is written in countdown style- with the number one most encountered reason (at JMU, at least) listed last.

  1. The bottom polarizer is rotated out of its proper position (on our microscopes, 0 degrees should be aligned with the dot), or there is an accessory plate inserted into the microscope. These will create abnormal colors in crossed-polarized light- which is fine if you meant to do so with the accessory plate, if you realize it is there!
  2. One of the objectives or the condenser are misaligned. This rarely happens on good-quality microscopes that are regularly maintained. Misalignment often means that someone has been forceful in using the microscope resulting in the optics being thrown out of alignment.
  3. The nosepiece is not fully rotated so that an objective aligns with the substage condenser. This will produce an incomplete image.

Figure 4.3.1: Nosepiece out of alignment.

  1. The condenser settings are not appropriate for the objective lens you are using, or the purpose for which you are using the microscope. Check the magnification on the condenser aperture diaphragm.
  2. The crosshairs are not vertical and horizontal in the field of view. The orientation of the crosshairs can be adjusted in the right eyepiece.  Simply lift and rotate to the proper orientation.

Figure 4.3.2A: Eyepiece oriented with crosshairs horizontal/vertical.

Figure 4.3.2B: Horizontal/vertical crosshairs.

Figure 4.3.2C: Eyepiece oriented with crosshairs diagonal.

Figure 4.3.2D: Diagonal crosshairs.

  1. One or both of the eyepieces are not focused for your eyes, or you are using a binocular microscope and you cannot see the entire field of view.

Rotate the focus adjustments on the eyepieces themselves until you can see clearly.  Most binocular microscopes have a way to adjust the distance between the eyepieces to fit your eyes.  For our microscopes, gently pull the eyepiece tubes apart or push together gently until you can see the field of view out of both eyes.

  1. Something is in the way (or partially in the way) of the view. If the analyzer or an accessory plate is only partially inserted, part of the view will be obstructed or darkened. If the field diaphragm is closed too far for the chosen objective, a dark ring will block light on the outside of your field of view.

If the Bertrand lens is in, but you are at low magnification, you will get a fuzzy view or a very constricted view of an optical interference figure.

Figure 4.3.3A: Accessory plate partially obscuring the view of a thin section.

Figure 4.3.3B: Field diaphragm partially blocking the field of view.

  1. The illuminator is on its minimum setting, producing a dark or almost dark field of view. Rarely, a light bulb will die, but since we regularly maintain our microscopes, this has only happened once in 10 years during a lab.
  2. The electrical outlet has reset or the plug is not firmly attached to the microscope, resulting in a lack of power to the illuminator (or camera, if your microscope has one).

This is a very common occurrence at JMU because all the power outlets are the type that are typically used for hair dryers in a bathroom (they have ground fault circuit interrupters (GFCI)).  Turn off the microscope power button, make sure the cord is firmly attached to the microscope and the plug is completely in the outlet, then push the “test” and “reset” buttons on the outlet. Try turning the microscope on again.

And the number one issue I see in my petrology course is…

  1. The thin section is upside down. The thin slice of rock on the thin section should be on TOP of the glass slide. Remember that not all thin section labels will be on the top side of the thin section – this is especially true for thin sections used in research.

At low magnification, for example when the 4x objective is used, the focal range of the objective can accommodate the height difference between having the rock slice above the glass, or the glass above the rock section.  However, at higher magnifications the narrow focal region makes it necessary for the rock slice to sit on top of the glass slide to be focused.

Figure 4.3.4A: A thin section right side up on the stage.  Note you can see the edge of the cover slip and top layer of epoxy all the way around the top edge of the thin section.

Figure 4.3.4B: A thin section upside down on the stage.  Only the clean edge of the glass slide can be seen around the top edge. Note that sample labels are not always placed on the top side of thin sections.


Other Related Issues

  1. Do you observe smudges or specks interfering with your view?

The microscope eyepieces, and perhaps the objective lenses, could be coated with dust or oils from human contact.  Our microscopes are heavily used by multiple classes, so cleaning the eyepieces with an approved lens wipe on a regular basis is a good way to keep the field of view clear (and is also hygienic).

If the objective lens is indeed dirty, it is advisable to ask an instructor for help with cleaning.  Make sure to use the correct type of lens wipe and cleaner and take care not to scratch the lens!

  1. It doesn’t matter which microscope I use, I don’t see the colors of the minerals the same way that other people in the class are describing them.

It is possible you could have a type of color blindness. Color blindness is common, and can be tested online: https://www.aao.org/eye-health/diseases/how-color-blindness-is-tested.  One of the test options is here: https://colormax.org/color-blind-test/

Do not be discouraged if you cannot see or can only partially distinguish some colors – many petrologists have partial or total color blindness, including the person who taught the petrology course at JMU for 36 years before I replaced him.  There are many observations which can be used to identify minerals using the petrographic microscope, and color tends to be among the least reliable.  If you need help reading birefringence colors or interpreting accessory plate tests, just ask your instructor.

Licenses and Attributions

Text written by Elizabeth A. Johnson, James Madison University (JMU).
Figures created by Elizabeth Johnson, JMU.
CC-by License