HELP ! Dust in the microscope !

Sometimes (even in the best of families), the day comes when some dust becomes visible in the field of view of the microscope. The first thing (after panicking) is to find out exactly where that dust is, so that it can be removed. The notes below refer to one of our typical fission track systems, based on a Zeiss microscope. The method of finding the offending dust particles will be very similar for other brands of microscopes, though a few of the details may differ.

The easiest place to check (and the best place to start with) is the camera. If the camera is rotated and the spots stay exactly where they are, then the dust is on the camera chip (or in the operator's eyes, of course. But we'll assume that this possible source has been eliminated). In that case, it will be necessary to take off the camera and very carefully blow the dust off the camera chip. The dust will often be easily visible in reflected light.

It's not a good idea to use anything to rub the dust off, since the camera sensor is very fragile. And it's also a bad idea to use ordinary paper tissues, as they are quite abrasive. They contain clay, and they also drop lint particles. The best thing to use is a special lens cloth of the type sold to clean camera lenses. Camera shops also sell special blower brushes and spray-cans of compressed air. With the blower brush, it is important never to touch the brush part with the fingers, as this is guaranteed to transfer oils from the skin on to the brush hairs. These will then cause smears on anything cleaned with it afterwards.

As for solvents, many people use isopropyl alcohol (isopropanol). This material is good because it does not leave a residue. It is often possible to buy little wipes in foil packets, pre-impregnated with isopropanol, and these are very popular. Methylated spirits (denatured wood alcohol) is also used, but often leaves a residue. Distilled water is good in some cases for rinsing. Harsher solvents, such as mineral turpentine, petroleum and stronger materials, are not good. In severe cases, they may even damage the glues between layers of lenses, or the plastic finishes on components, or their constituent parts. For further advice, the best thing to do is to consult people who are either experts with microscopes, cameras or telescopes (or laboratory technicians, of course). There may also be some information about cleaning optical glass components on the internet.

If the spots move as the camera is rotated, then the dust is not on the camera. This means that it will be necessary to check each element (starting from the camera) on the way down to the light source.
In order these are typically :

1. The glass prism just underneath the camera, which splits the light so that some goes to the camera and some to the eye-pieces. It should be possible to take off the camera and look down into the tube on the top of the microscope - any large dust particles would probably be visible to the naked eye. It is important to avoid leaving this aperture open without protection, as dust will quickly find its way in, and may be difficult to remove. It is a good idea to immediately put a spare plastic cap (or even sticky tape) on the hole to prevent dust falling in.
2. Of course, the next suspects are the eyepieces themselves. The best method is to remove them both, one at a time, and to look up into the light against a plain background. Any dust in there should be pretty evident and would not be too difficult to remove.
3. If the dust is only visible when the microscope is set to REFLECTED light, then the dust is probably on the mirror cube. This item sits in the revolving chamber just above the objectives. The semi-mirrored cube reflects the light which comes from the bulb at the rear of the microscope, and sends it downwards onto the sample, through the objectives. When the light is then returned after being reflected off the sample, it goes straight up (again through the mirror cube) to the eye and the camera.
4. For both reflected and transmitted light, there is a possibility that there is an unwanted object on the LED, on the diaphragm (which closes down to focus the beam, and also slightly reduces the amount of light) or on one of the neutral-density filters (which cut the light down by measured amounts). But these would usually be out of focus, and would have to be pretty big to be noticeable. The diaphragms and filters for both the transmitted and reflected light paths can be pulled out for ease of cleaning.
5. Next is the set of objectives. If there is dust on an objective, the spot it causes will only be visible for that objective. So if the objective is changed and the spot is still there, it's not on an objective.
6. After that, for TRANSMITTED light only, there is the condenser. It quickly builds up dust on its top surface, and may need cleaning. There is also often a swing-out lens. This means that there are actually TWO horizontal dust-catching surfaces. At worst, it may be necessary to pull the condenser out to clean it.
7. Finally, there is the lens at the bottom of the microscope, under the condenser. This is again only a problem for TRANSMITTED light, but is often a bad offender. It is the reason why the Zeiss people have supplied the large black rubber disk. The idea is to put that on at night (but not to forget to take it off when you start work in the morning. Otherwise - no transmitted light !)

Cleaning a microscope is one of those things that just comes with the territory, but the first time is always the hardest. Very few labs are entirely dust-free, and some are REALLY bad offenders !

There is actually a very interesting document here :$FILE/50-1-0025_the_clean_microscope_e.pdf (Please copy and paste into your browser to download the document. It is called "The Clean Microscope", and contains a lot of very valuable information in addition to my quick outline above).