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Author: Mikael Häggström [note 1]

Microscopy settings

Usual parts of a microscope.

Generally the condenser is placed in its highest position or just slightly lower. At low magnification objectives (mainly 4x and 10x objectives), the opening of the condenser (or iris) diaphragm should be wide open. This corresponds to turning away or "lowering" the condenser on microscopes where the condenser apparatus can be turned to the side (and is shown as "without condenser" in images below). For high-dry (40x) and oil-immersion objectives (100x), the diaphragm should be closed slowly while looking at a sharply focused section until the level of illumination is just slightly reduced, in order to attain optimal contrast and resolution (and corresponds to "with condenser" in images below).[1]

Low magnification has a greater span of focus compared to high magnification, so it is normal to need to focus if you're increasing magnification. However, if you find that you need to change focus even if going from high to low magnification, try the following (if you can adjust the eye piece):

  1. Use high magnification and focus on a specimen using the main focus knob.
  2. Switch to low magnification, and focus using the eye piece adjustment.

If there's a constant visual artifact, even after you've cleaned the eye piece and objective lenses with lens tissue, try raising or lowering the condenser if you can, and the artifact may disappear out of focus.

Main steps

  • Preferably, look up past medical history of the patient, mainly past cancers that could possibly appear in the current specimen.
  • Look at each microscopy slide by plain eye, to plan the microscopy screening so as to not miss peripheral fragments.
  • Have a systematic direction of screening through microscopy slides, such as from top left to bottom right as seen in the microscope. When the microscope makes what you see two-way mirrored, the starting position is with the objective pointing at the bottom right of the glass slide.
  • Look in particular for whatever is requested or suspected on the requisition form or equivalent.

While learning, you will generally focus relatively more on high magnification features with high specificity, but still have a habit of learning how your cases look at low magnification as well. In time, you will increasingly correlate diseases and conditions with their overall low magnification patterns - patterns that may require 1000 words to describe and thus cannot conveniently be part of written criteria, but will nevertheless allow you to make quicker and more accurate diagnoses.

Complete your evaluation even if you encounter a finding, as there may be additional findings as well.


In microscopy, an artifact is an apparent structural detail that is caused by the processing of the specimen and is thus not a legitimate feature of the specimen. Major artifacts to account for include:

Differential diagnoses of artifacts are mainly:

  • Foreign bodies. In contrast to contamination, these conform more naturally to the surrounding tissue.
  • Organisms, to be particularly considered when there are multiple objects of the same size.

Order recuts from the same paraffin-embedded tissue if artifacts significantly impairs your diagnostic evaluation of the glass slide. However, artifacts caused by gross processing may affect recuts as well.

General patterns

Following are major patterns that often help in making a diagnosis.

Architectural patterns

Cellular patterns

Nuclear patterns

When feasible, classify nuclei as follows:

Other patterns


Measuring distances

There are also eye pieces that show a ruler in the field of view, but make sure you match it with the correct objective and other settings to make the measurement valid.

Counts per mm2

There are multiple situations where a finding will be quantified in terms of amount per mm2. To make such calculations, you need to know the size of the area you see in the microscope. It is usually possible to look up what theoretically would be the area, but the most reliable way of knowing is to use a calibration slide to measure the diameter of your view. The area is then calculated as:

  • Area in mm2 ≈ (diameter in mm)2 x 0.79

Sometimes "high power field" (HPF) is used for area, but it has a substantially different area for different microscopes, for example:

Microscope type Area per HPF
  • Olympus BX43 with 10x eyepiece
0.096 mm2 [3]
AO with 10x eyepiece 0.12 mm2 [3]
Nikon Eclipse E400 with 10x eyepiece and 40x objective 0.25 mm2
Leitz Ortholux 0.27 mm2 [3]
Leitz Diaplan 0.31 mm2 [3]

When your instructions are to count a specific number of HPFs, one HPF can be assumed to be 0.2 mm2.[4] If the view area in your microscope significantly differs from this area, calculate how many views you need to count as:

Views = HPFs required x 0.2
Your microscope area (in mm2)

For example, if your instruction is to count 10 HPFs and each view in your microscope shows 0.096 mm2, you should count in this many views:

10 x 0.2 ≈ 21

Subsequently, if your microscope area is significantly different from 0.2 mm2 and you need to state your result in terms of count/HPF, use:

Count/HPF = Average count in your view x 0.2
Area of your view in mm2

For example, if you have counted an average of 10 cells (or other object of interest) in each of your views, and the area of your view is 0.096 mm2, then your count/HPF is:

10 x 0.2 ≈ 21

Micrography and telepathology

Unless you have more specific equipment for taking microscopic images and showing cases to remote colleagues, you can perform these tasks as follows:

  • With a stationary computer, you can connect to a microscopy camera. For telepathology, you can start a videoconferencing session with your senior, then share the screen while showing a micrograph, or the live view so that you can move around.
  • With a mobile phone:
You can send micrographs to your senior, but it is technically difficult to keep the focus while moving the glass slide.


In cytology samples, or any sample with scattered cells rather than coherent tissue, also evaluate the following:

  • Adequacy of specimen. There may be too few cells to make a proper diagnosis.
  • Background, mainly if it is clear or dirty
  • Overall cellularity
General notes edit

Further reading:



Main page


  1. Patrice F Spitalnik. Histology Laboratory Manual, Vagelos College of Physicians & Surgeons Columbia University. Retrieved on 2021-09-20.
  2. 2.0 2.1 2.2 Taqi, SyedAhmed; Sami, SyedAbdus; Sami, LateefBegum; Zaki, SyedAhmed (2018). "A review of artifacts in histopathology ". Journal of Oral and Maxillofacial Pathology 22 (2): 279. doi:10.4103/jomfp.JOMFP_125_15. ISSN 0973-029X. 
  3. 3.0 3.1 3.2 3.3 . Infiltrating Ductal Carcinoma of the Breast (Carcinoma of No Special Type). Stanford University School of Medicine. Retrieved on 2019-10-02.
  4. Klimstra, David S.; Modlin, Irvin R.; Coppola, Domenico; Lloyd, Ricardo V.; Suster, Saul (2010). "The Pathologic Classification of Neuroendocrine Tumors ". Pancreas 39 (6): 707–712. doi:10.1097/MPA.0b013e3181ec124e. ISSN 0885-3177. 

Image sources