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Head: Winfried Wiegraebe

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Cleaning Your Microscope

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Cleaning Issues

Materials Bottom

MicrographiaSubstances used in experiments frequently end up on the microscope and its optical surfaces. Media, airborne oils, fingerprints and skin particles are typical contaminants of day-to-day use.

Even when the microscope is not in use, dust accumulates on optical surfaces causing artifacts and degrading image quality. This image from Micrographia shows specks of dirt on a coated lens surface. The halos around some are caused by oil.

Cleaning frequency is the first issue we consider. Optical surfaces should be considered delicate and protected from contact as much as possible. On the other hand, any dirt on an optical surface is going to degrade your image. Here are three guidelines to help establish your cleaning schedule:

Post experiment clean-up should be a part of every protocol. Locate materials before they dry on the microscope or contaminate other experiments. If immersion oil is used for oil objectives, it should be removed when finished and before applying more. Do not mix immersion oils.

Daily inspection is appropriate for heavily used microscopes. To ensure the best images, or preparing for publications, check the objective for dirt before your begin.

Clean optical surfaces only when needed. The least contact with optical surfaces is preferable, so inspect often, but clean only when dirt is present.

Where to clean is the second issue. We present a list of critical areas on the microscope, and a simple steps to clean them below in Safe Cleaning of Optical Surfaces. But first, check out the safe materials in the next section to find what you need for the best care of your lenses.

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Web Links:
Optical Microscopy Primer: Cleaning, Care, and Maintenance of Microscopes
Microscopy-UK: Lens Cleaning - Best Practice Review

The Clean Microscope (Carl Zeiss)Download PDF
Illumination: Cleaning & maintenance (Olympus)Download PDF

Image source: Micrographia TOC Top
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Safe Materials for Optical Surfaces

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Put cool picture hereSome cleaning materials can damage sensitive optical surfaces. For example, lens coatings can be degraded or destroyed by certain common solvents that may not harm an other lenses. Another consideration is that certain cleaners are more effective for particular kinds of dirt. Different labs recommend various favorite cleaning materials but there is little agreement. The favorite materials of one lab may be forbidden in another.

Here are the basic tools you will need:

  • Air blower
  • Cleaner and swabs
  • Lens tissue

Each of these is presented in greater detail below, with links to sources for more information or convenient purchasing.


Image source: Zeiss Cleaning Top
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Air Blower

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Dust blowerA blower, or puffer, is the safest cleaning tool and should be the first, and most frequent cleaning method you use. There are numerous kinds available, but your selection should have these features:

  • A "chalk-free" type.
  • Plastic sleeve-tip at the bottom to prevent scratches.
  • One-way inlet valve at the top preventing air and dirt from being drawn back through the tip.

A blower is preferred to a lens brush, since the latter can retain dirt and subsequently reapply it and possibly be a source of scratches. Consider keeping a blower beside the microscope to reduce the temptation to blow away dust by mouth.

Warn Avoid canned air. Cans emit propellant when shaken or tilted, leaving your lens with a bigger mess than when you started. Compressed air can be very cold when released.

Web Links:
VWR: Dust'it Blower

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Cleaners & Swabs

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The cleaner you use depends in part on whether you are removing dry dirt or greasy dirt. Here are three, beginning with the mildest.

Distilled water is the safest and preferred solvent to apply to dirt that is not oil or grease based. It is also the easiest and most convenient since you can tap in to your lifetime supply of it by open-mouth exhaling directly to the lens. The moisture from your lungs will condense on the lens surface. You can also use filtered or de-ionized water from lab dispensers.

Cleaners Manufacturer's recommended cleaner is needed when there are greasy smears or persistent dirt. Optical surfaces can be sensitive to solvents or chemicals in some cleaners, so it is important to know what the manufacturer recommends to clean your particular equipment. For example, ammonia and acid will harm some anti-reflective coatings. Strong organic solvents can dissolve the black anti-reflex surfaces on the front of some objectives, or erode lens mounting cement.

Many labs recommend acetone or Sparkle®. These may be fine for cover slips, but we suggest using only the manufacturer's cleaner or the recipe given below for cleaning your microscope's optical surfaces.

If your manufacturer recommends other solvents, be sure to consult the appropriate Material Safety Data Sheets (MSDM) before using them.

Sometimes you will need to remove all traces of immersion solution from an objective front lens, such as when crystals begin to form or when changing to a different immersion solution. In this case it is more effective (and requires less wiping of the lens surface) to use an ether-alcohol formulation.


Optical Cleaning Solution L (from Carl Zeiss®)

  • 85% petroleum ether
  • 15% isopropanol

This ether-alcohol mixture has the favorable characteristic of quick evaporation. This automatically limits the time it has contact with the optical surface.


Swabs need to be soft, absorbent, disposable and compatible (does not dissolve) with solvents. There are two acceptable types, the cotton tips, and absorbent polyester. Whichever you prefer, keep them covered so that dust will not get on them.

Absorbent polyester swabs from Textwipe® are extremely clean, fiber free, and compatible with the cleaners recommended here. Two of the most useful sizes are the 13 mm and 3 mm pictured here.



Pure cotton (ophthalmology grade) has been and remains a good choice for applying cleaner. Objectives with extreme concave or convex surfaces may be more effectively reached with cotton swabs.



Warn Do not use Q-Tips. They are not pure cotton, but contain synthetic fibers too harsh for optical surfaces.

Web Links:
Texwipe: TX761 (long)
Texwipe: TX759B (small)
Texwipe: Wrapped Cotton Swab

The Clean Microscope (Carl Zeiss)Download PDF

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Lens Tissue

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Whatman pictureLens tissue is mainly used to remove immersion solution from objectives. It must be very soft to avoid scratching the optical surface. It must also be absorbent, free of fibers and free of any of the chemical additives commonly found in cosmetic tissues. Our choice is Whatman Lens Cleaning Tissue 105.

Hard lens paper does not absorb immersion solution quickly enough. However, it is a good choice for dust-free storage of lenses and filters.

Kim Wipes are fine for wiping the stage and microscope body, but they are not for optical surfaces. They leave particulate behind.


Web Links:
Whatman 105

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Safe Cleaning of Optical Surfaces

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There are risks involved when coming into contact with optical surfaces, even when safe materials are used.

For example, wiping without first blowing loose particles off the surface is a hazardous practice. Allowing strong cleaners or solvents to remain on a lens is another. Our first concern is protecting the exposed optical surfaces. Expert cleaning is part of that protection plan.

Warn TIP: Keep your microscope protected with a plastic cover when you're not using it.

Note these exposed optical surfaces, listed in order of their influence on image quality. Users should inspect them and clean only when needed:

  • Back of slide & cover slip
  • Objective front lens
  • Oculars (eyepiece)
  • Condenser front lens

The objective front lens will have the greatest effect on your image quality and requires the most caution. Keep these recommendations in mind when cleaning any lens:

Inspect regularly. Magnification is needed to inspect objectives. A flashlight held at a glancing angle can expose dirt on larger optical surfaces. Clean only when dirt is observed.

Minimize contact with optical surfaces. The overall goal of these cleaning procedures is to use as little pressure and contact as possible. This includes minimizing the time cleaners remain on the surfaces.

Only use safe materials as described in the Safe Materials section.

Objectives may be removed for cleaning, but as a rule, none of these procedures involve disassembling the microscope. Cleaning that requires accessing the interior of the microscope should be left to manufacturer's technical support.

Please be careful when cleaning optical surfaces!

Stowers Links:
Building Blocks of a Light Microscope


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Cleaning Oculars

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Objectives Bottom

startSpiralUse the air blower first. This minimal contact method is the safest and simplest way to clean optical surfaces. If the particles disappear, you are done!

If particles remain, you will need to remove the ocular and swab the lens surface as described in the next step. Never dry wipe a lens, since this increases the risk of scratching the surface.

spiralUse the correct swabbing method. For particles that will not blow away, you will need to gently swab the surface. A safe method consists of the following:

  • Apply the cleaner to the swab, not directly to the lens.
  • Use cleaner sparingly, so as not to flood the lens.
  • Wipe in a spiral pattern, center to edge.
  • Use as little pressure as possible.

Repeat if necessary. Use a new swab each time, since particles picked up by the swab can scratch during repeated wipes.

Before swabbing the lens, consider which cleaner is appropriate, starting with the mildest. Examine the lens to determine if there is only dust or if greasy smears are present. If you observe only dust, fog the lens by exhaling with an open mouth directly onto the surface. Then wipe with a clean swab using the spiral pattern. The moisture that condenses on the lens is the mildest cleaner and the only solvent applied directly to the lens.

When there are smears, fingerprints or smudges, use your manufacturer's cleaner applied to the swab, repeating if necessary. Optical cleaners are formulated to leave no residue, but it is not unusual to observe an evaporation spot or some buildup around the edges. After a cleaner is used, finish by fogging the lens and swabbing as described before. This will help ensure that no residue remains.

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Image source: Zeiss Procedures Top
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Cleaning Objectives

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Condenser Bottom

The cleaning approach to immersion (oil/water/glycerine) objectives differs slightly from air objectives. Immersion solution is always removed with lens tissue immediately after use, which serves as a kind of light cleaning. This is not done with air objectives, but it is a good idea to use a blower on them, while in place, before routine imaging. Regular cleaning or preparing for critical imaging starts with an examination.

Examine the front lens surface. You need magnification to determine if there is a need for thorough cleaning. This usually requires removal of the objective, and placing under a stereoscope. Secure it by threading it into its packing container lid. An alternative is to use a hand lens, or reverse an ocular. If dirt is present, start with the least aggressive method.

Put cool picture here

Immersion objectives: Any excess immersion solution should be removed by drawing a piece of lens tissue across the front lens surface slowly enough to allow the immersion solution to be absorbed.

When a thorough cleaning is needed, such as before storage, or when crystals or dirt remain, you will need to swab oil objectives with ether-alcohol (water for water objectives). Use these best swabbing practices:

  • A safe swab and cleaner
  • A clean swab for each wipe
  • Apply cleaner to the swab, not the lens
  • Just enough cleaner to dampen the swab (shake off excess)
  • Spiral swab pattern if lens area is large enough

Dry objectives: Always use the air blower to gently remove dust and particles first. If particles remain, swab the lens surface using distilled water or exhaled moisture. If smudges or smears are present, swab with a safe cleaner. Use the best swabbing practices above.

Monitor progress after each swab by looking for the light reflection on the surface. Observing the process under a stereomicroscope is ideal. If that is not available, you can use a hand lens or an ocular, inverted to magnify the front lens.

Either type of objective may have dirt that is resistent to a cleaner. In these instances, you may alternate between swabbing with manufacturer's cleaner and ether-alcohol. This could happen when a dry objective is rotated onto an oil-covered slide. The ether-alcohol will work better on oil. With immersion objectives, there are times when ether-alcohol seems to be leave a residue. The manufacturer's cleaner can usually remove this effectively.

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Cleaning Condenser & Filters

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Cleaning filtersMost of the time, exposed filters and polarizers near the top of an inverted microscope will benefit from simply using the air blower. In extreme cases, they may need to be cleaned in the same manner as oculars.

The front lens of the condenser should be inspected regularly and cleaned in the same manner as oculars.

Stowers Links:
Köhler Illumination


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For comments and additional information, please contact Winfried Wiegraebe. Red links are for internal use only. Sorry!