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Cleaning Your Microscope

- Discussing Best Practices -

In order to protect your microscope, it requires a regular cleaning schedule to ensure your images remain crisp and artifact free. 

Of course cleaning your microscope does depend on the quality of your microscope's optics as well as that of the electronic and mechanical components.  Also, when deciding on the protocol for cleaning your microscope, you must consider how much a microscope is used and by whom. 

Students in a lab are less likely to be as clean and prudent as an experienced hobbyist or professional microscopist. Furthermore, it's probably best to not allow a student to clean the microscope after use except in the case of cleaning up after their immersion oil microscopy with the appropriate lens paper.

Dust and debris accumulate on microscopes that are left uncovered or are not regularly used.  The use of the microscope's cover helps to protect from any airborne contaminants. 

Also, contaminants can be transferred to the microscope from users themselves (skin oils from hands, moisture from breathing) and from the general environment even over a short period of time.  

Artifacts can noteably appear in images infecting the optics as a result of poor cleaning and maintenance. 

To best protect your microscope you need to make sure your working environment is a place where there would be less environmental contamination with a constant temperature (little humidity) and that your microscope sits on a solid work station to decrease vibration.

Be Careful with Solvents

First of all it is imperative that you adhere to your microscope manufacturer's recommendations and instructions regarding the cleaning products you use when cleaning your microscope. Using a cleaning agent that is not recommended may cause damage to the coating of optical surfaces. 

It is not necessary to clean the optics after each use.  If you are able to see dust and debris then imaging will be impaired so a cleaning is necessary but keep in mind that each cleaning comes with the risk of scratching the optics.

The use of solvents is generally not recommended.  Often times too much solvent is used.  Your microscope's lens construction and mechanical components can be damaged by your unintentional seeping of solvents onto these surfaces. 

When solvents come in contact with the cement used in lens assembly, you end up with corrosion and separation.  Another important point is the risk to your health when touching and breathing in solvents. 

Liquid window cleaners and eyeglass cleaners are not meant for your microscope's delicate optics. 

First try removing surface dirt/dust with a shot of air from a squeeze bulb. Simply using distilled water is a good and safe first choice when a cleaning agent is needed. Otherwise 90% and more pure isopropyl alcohol is next. Place a drop or two of the alcohol on your cloth and cover and hold against the debris for a few seconds.  This will help to dissolve the culprit and then remove with a gentle wipe.

Kimberley Clark Kimwipes are recommended:

Immersion Oil

Oil immersion microscopy is a major culprit in that the improper cleaning and use of the immersion oil leads to debris that attaches to the residual oil as it accumulates. 

Irreparable damage can occur to the optics and mechanical components with its misuse and improper clean-up.  Lens paper can be used to remove immersion oil wiping gently/softly.

Also, pay special attention to the age of the oil and its change in viscosity over time as these can make it more difficult to remove.


Your microscope's performance relies on its optics, lenses, filters and prisms being kept free from any contaminants. Unplug your microscope prior to cleaning it.

Anywhere the user naturally touches to operate the microscope like for example, the body tube; knobs; levers; interocular eyepiece as well as the stage, deposits oil from skin contact and so will attract dust.  These areas need frequent attention.

A moistened cloth with the recommended surface cleaner followed by a dry cloth for drying the area should be sufficient

The Optics: 

Special Note:  Never clean the internal lens surfaces. Image sharpness will be affected.  This should only be done by a qualified service center. 

The top portion of the eyepiece tube and the ocular rims should not be cleaned with any moistened cloth but a dry cotton cloth instead while not touching the optics themselves. 

Hard particulates can be present on cleaning cloths that you might naturally gravitate towards to use in cleaning your microscope.  Like for instance facial tissues or paper towels, these are soft to the touch but can leave contaminants.  Special lens cloths are recommended instead. 

It is possible to reuse lens cloths only when you are sure they are clean but it's better to use a new one. To be 100% positive, it's best to use lens cleaners and cloths specifically marketed for microscopy lab use. 

Clean the optics with cotton cloths and not with lens paper as in the case of removing immersion oil. As well, clean optics only when necessary as each time you disassemble you run the risk of introducing more contaminants. 

With the help of a magnifier or loupe, you can see the amount and type of contaminants.  The front elements of the objectives can be removed for external cleaning but rear elements should not be touched.

Always be light-handed in cleaning, excessive pressure can damage objectives.  Re-inspect to be sure of particle removal. 

Elements for phase contrast, polarizing or DIC as well component parts of the condenser body should not be removed.  Only the top lens of the condenser can be removed and cleaned with the optical lens cleaning procedure. 

Eyepieces can be cleaned externally including the lower field lens surface.  The interior of eyepieces generally remain clean as they are sealed during manufacturing. 

Your microscope can last for many years with proper and regular cleaning and maintenance.  The microscope must be used correctly as well.  What a fun and worthwhile investment into your hobby and/or profession. Enjoy your microscope but remember in cleaning your microscope to be light-handed and careful. 

** is not responsible for any damages to your microscope as a result of your cleaning techniques and/or product use.

Of interest:  Basic Microscope Ergonomics

Check out MicroscopeMaster’s online help:

Basics of a Compound Microscope

Diagram/Parts/Functions of a Compound Microscope

Beginner Microscope Experiments

Microscope Slides Preparations-Styles and Techniques

Prepared Microscope Slides - Benefits and Recommendations

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