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Disinfecting microscopes

Submitted by sat on 21 May 2020

Answer reviewed 30 Jan 2023

Microscope purchase, repair and servicing

Microscopes used in school science laboratories have traditionally been of two basic types; compound or bright field (high power), and stereo or dissecting (low power). Technology has advanced over the last few decades to produce digital microscopes and affordable options for capturing images and videos.

When choosing a microscope consideration needs to be given to the application, skill level of staff and students and budget. Microscopes range in quality and price and are used for different purposes.

See our information sheet AIS: Microscope choices for schools

Other considerations for purchasing new microscopes are:

Microscopes are precision instruments. The vital parts are fragile lenses, lamps and fine optics. Microscopes used in schools are exposed to different rigours than industry or medical laboratories. It is vital microscopes are treated gently and kept maintained. Routine maintenance is best carried out annually. Further details for simple maintenance is available from SOP: Use and care of the compound light microscope. However, from time to time, repairs are required. Microscopes that are not working or are difficult to focus result in students quickly losing interest in microscopy or biology.

Schools should consider if repairs of microscopes are worth the cost, or if replacing them is a better option.

Science ASSIST recognises the difficulties of schools located in regional and remote areas. Therefore, we have compiled a list of microscope service providers, which can be found on our site under School science suppliers They were contacted to see if they were able to repair microscopes in the Northern Territory (for example). Responses received indicate that these companies generally service their own states and perhaps an adjoining state and that they would be prepared to travel to service and repair microscopes in the Northern Territory if the cost of a trip was feasible.

Therefore, if you have a number of microscopes which need repairing, we suggest that you do the following.

  1. List makes, models and quantity of microscopes that need repairs.
  2. Contact the supplier or manufacturer of the microscopes, if possible, to see if they have a repair and service department, or an agreement with an Australian provider. If this is not possible:
    1. See our list of School science suppliers for companies that provide microscope servicing adjacent to your state; and
    2. Consider approaching other schools to see if there is a larger need for this service, which may help create a sufficient demand for a microscope repair company to travel to your state. (We suggest that you approach other schools via your teacher's or technician's network).

Microscope lenses and the use of immersion oil

Immersion oil and which one to use?

Immersion oil is utilised to increase the optical resolving power of the microscope. It is used by placing a small amount between the coverslip of a specimen and the front lens of an oil immersion objective. There are many different types of immersion oils, all with different properties and it is generally best to use the immersion oil recommended by the manufacturer of the objective. Immersion oil properties are usually matched to the objective lens properties to give optimal image quality. The refractive index of the immersion oil is an important parameter, and it is typically 1.515 at 23° C, close to that of glass to obtain optimal results. As the refractive index is similar to that of glass, light rays leaving the microscope slide and passing into the oil continue unrefracted or are refracted less than if they are passed from glass to air. Using immersion oil increases the resolution so that smaller objects can be seen.

As basic light microscopy is routinely used in school science laboratories, the difference in image quality will not be evident, so any manufacturer’s immersion oil will be suitable as long as the refractive index is correct. Immersion oil is available from many scientific suppliers, see the Science ASSIST School science suppliers list.

The choice of immersion oil for many years was Cedar Wood Oil, until the manufacture of synthetic alternatives in the 1940s. Cedar Wood oil is still available but has many disadvantages: it goes yellow with age, and if not cleaned up properly, will penetrate and damage the cement in the lens. The modern synthetic versions used today are inert, more colour stable and can be obtained in various viscosities.

Other fluids such as glycerine, and also mineral and vegetable oils work, but their refractive indices and dispersive powers vary somewhat from that of glass, and hence cannot be expected to elicit the best imagery from the specimen.

Immersion oil should only be used sparingly with an oil immersion objective lens. It should never be used with any of the other dry objectives, as it will damage them. Immersion oil is best stored at room temperature.

Microscope cleaning and disinfection

Shared equipment such as microscopes should be cleaned and disinfected between each use. If it is possible to allocate each student their own microscope in a lesson this will avoid the need for disinfecting during a lesson. Note that the use of safety glasses is not recommended, as they are not needed when using a microscope and they may introduce new risks such as additional face touching.

Here are some general guidelines formulated from the microscope manufacturer references noted below:


Body of microscope

Eyepiece (oculars) plus rubber eyepiece shades:

Note: It is not recommended to clean the internal surfaces of lenses.

Microscope objectives

It is best to consult the manufacturer’s guidelines as to the best cleaning method and fluid for your particular microscope.

Generally, the choice of cleaning method and fluid depends on the optical surface that requires cleaning and the substance to be removed. The surface of the optics of a microscope are easily damaged and therefore require extra care in their maintenance. Any cleaning fluid used should not damage any part of the microscope, including the lenses, and it should not leave any residue.

General advice for cleaning objectives:

Removal of immersion oil from the external surface of the oil immersion lens

Image quality is dependent on having clean, damage-free optics. Immersion oil should be removed immediately after use and not be allowed to remain on the objective lens. The risk of leaving immersion oil on an objective lens can result in the contamination of other parts of the microscope and the possibility of the oil moving into the objective itself causing irreversible damage.

Good hygiene

With regard to COVID-19: Good hygiene should be strictly observed such as is stated in the Australian Health Protection Principal Committee (AHPPC) statements, see

As the information is being frequently updated it is good to check the latest advice. As of (24th April 2020) the latest advice for schools can be found at

In particular, see the sections on hygiene, routine care and environmental cleaning. The general hygiene advice is

Record keeping

This is not mandated; however, it is a good idea to keep records in a microscope maintenance log to demonstrate that disinfection has taken place. We don’t have a proforma for you to use, but you could make one up to suit your school circumstances, which would include as a minimum the date; microscope identification, and which class (or student) used the microscope. It could also be used to identify where there is another issue with a specific microscope such as needing a replacement part (e.g., globe) or servicing (e.g., poor focusing or dirty lenses).

Microscope Alternatives

An eyepiece microscope camera can be used to view images projected from the microscope onto a smart board. or computer screen.


Nikon Instruments. (2009, April). Immersion oil and the microscope FAQs. Retrieved from MVI Micro video instruments, inc: (Accessed 30 Jan 2023)

James, P. (2002, March). The oil immersion objective. Retrieved from Microscopy UK: (Accessed 30 Jan 2023)

Rottenfusser, R., Wilson, E. Erin., & Davidson, W. Michael. (n.d.). Microscope cleaning and maintenance. Retrieved from ZEISS: (Accessed 30 Jan 2023)

Murphy, B. Douglas., & Davidson, W. Michael. (2013). Fundamentals of Light Microscopy and Electronic Imaging. Retrieved from Google Books: (Accessed 30 Jan 2023)

Christoph, Greb. (2020, April 3). How to Sanitize a Microscope. Retrieved from Leica Microsystems: (Accessed 30 Jan 2023)

Government of South Australia, SA Health. (2022, December 23). COVID-19: Information for health professionals – COVID-19 Health System Response. Retrieved from Government of South Australia, SA Health: (Accessed 30 Jan 2023)

Abramowitz, Mortimer., & Davidson W. Michael. (n.d.). Immersion Media. Retrieved from Evident: (Accessed 30 Jan 2023)

Australian Government, Department of Health and Aged Care. (2023, January 17). Australian Health Protection Principal Committee (AHPPC). Retrieved from Australian Government, Department of Health and Aged Care: (Accessed 30 Jan 2023)

Cargille, J. John. (1985). Immersion oil and the microscope. New York Microscopical Society Yearbook, 1964, 1-6. (Accessed 30 Jan 2023)

Evident. (n.d.). Microscopy Resource Center - Basic Concepts in Optical Microscopy. Retrieved from Evident: (Accessed 30 Jan 2023)

Nikon. (2020, April 16). Recommended Handling and Disinfecting Procedures for Nikon Microscope products to reduce spread of infectious agents including SARS-CoV-2 (Coronavirus). Retrieved from Nikon: (Accessed 30 Jan 2023)

Ogama, Takeo. (2020, April 13). How to Clean and Sterilize Your Microscope. Retrieved from Evident Discovery Blog: (Accessed 30 Jan 2023)

Rottenfusser, R., Dragoo, Tadja., & Davidson, W. Michael. (n.d.). Education in Microscopy and Digital Imaging, Oil Immersion and Refractive Index. Retrieved from Zeiss: (Accessed 30 Jan 2023)

Science ASSIST. (2015). SOP: Use and care of the compound light microscope. Retrieved from Science ASSIST: (Accessed 30 Jan 2023)

Zeiss. (n.d.). Recommendations for Disinfection of Microscope Components and Objectives. Retrieved from Carl Zeiss Microscopy, LLC: (Accessed 30 Jan 2023)