How to Keep Your Microscope Clean

Maintain the image quality and cleanliness of your microscope

Clean optics are essential for successful microscopy and perfect images. The choice of cleaning methods depends on the nature of the optical surface concerned and the type of dirt to be removed.

Additionally, microscope systems are commonly shared by several users. Therefore, they bear the risk of being contaminated with microorganisms. Also microorganisms themselves can serve as specimens which are observed with the microscope system.

Here you will find a brief overview with recommendations on how to use, clean, and transport your ZEISS microscope so that you can benefit from the outstanding image quality and performance for a long time*.

Keeping Your Microscope Clean & Properly Adjusted

Preventing your microscope from being contaminated and keeping it perfectly adjusted is an important first step to maintain its image quality. Below, find working steps to support you with this*.

How to Transport and Store Your Microscope

Binocular Viewing Tubes

The openings of the binocular viewing tubes must always be closed. Unless the eyepieces are in, use dust stoppers.


After cleaning the objective lens with solvent, the objective should only be mounted in the objective capsule after a few minutes to allow solvent residues to evaporate completely.


Microscopes can be transported in styrofoam or a dedicated transport case if available.


Use dust cover when your microscope is turned off and not in use. Please make sure that HAL lamp housing is no longer hot before you put the cover on.

For long-term storage, microscopes should be kept with a dust cover, if possible in a cabinet. Microscopes should not be kept in styrofoam boxes for a long time.

Never locate the microscope in a place where it could be affected by corrosive acidic or alkaline vapors.

Detecting Dirt on Optical Surfaces

In order to recognize dirt on optical surfaces, you should have an idea of the best result you can expect from a specific microscopy method and a specific application. If you then compare your expectation with the visual image in terms of maximum definition, best contrast, and cleanness, you will immediately recognize whether or not your microscope is soiled anywhere.

If the sharpness or contrast of the image is less than optimum, there is a high probability that your microscope optics are not clean. Here are the steps to locate the dirt*.

Types of Soiling

In a next step, it is necessary to differentiate between dust particles (e.g. glass abraded from specimen slides or flakes of the microscopist's skin) and other kinds of soiling (e.g. liquid or dried-up embedding or immersion media).

Dust may either rest loosely on optical surfaces or sticks less to them. Other dirt may be soluble in water or need organic solvents for complete removal.

Find an overview of selected types of soiling here*.

Solving Image Blur & Poor Contrast

A blurred image may not always be due to dirt. Using an objective with a large numerical aperture in conjunction with a cover slip of the wrong thickness may result in blurred images (spherical aberration). However, if the image still appears blurred, cleaning the objective can solve the issue*:

* Disclaimer

This document/webpage summarizes general decontamination and disinfecting methods and recommendations without being meant to replace a scientists expertise nor medical or professional advice. ZEISS shall not be held responsible for and makes no representation as to the suitability or effectiveness of any method and/or disinfectant mentioned. ZEISS shall not be held responsible for any damage resulting from the disinfecting of the Microscope System outside of this document/webpage. The use of methods which deviate from the recommended ones is at the own risk and sole responsibility of the user and voids the warranty.

Filter cubes of microscopes and internal optical components must be cleaned only by service technicians, who are authorized by Carl Zeiss Microscopy GmbH. For cleaning IT equipment, please follow the guidance of your local IT department. Do not use abrasive compounds or cleaners as they can scratch surfaces and negatively affect protective coatings of the parts of your microscope.