Electron microscopy guide


TEM alignment

STEM alignment

Wave interference


Diffractive imaginging


The Vacuum System

There are three main types of vacuum pump: rough pumps, high vacuum pumps which need backing, and high vacuum pumps which don't need backing.

A rough pump can pump down from atmospheric pressure, but can only reach a rather modest vacuum, at best 0.01 mbar (0.00001 of an atmosphere).

High vacuum pumps can reach good or ultra-high vacuum (UHV), between log(-6) - log(-10-11) mbar. A high vacuum pump that needs backing means that it needs another pump (a rough pump) to work on the 'back end of it' (the high-pressure end), to take away from it air that it has pumped out of the vacuum chamber. Examples of such pumps are diffusion pumps and some types of high-vacuum turbo pumps.

Some UHV pumps, like ion pumps, do not need backing: the vacuum they deal with has such a low pressure that the pump can dispose of residual gas atoms simply by accelerating them into the solid walls of the pumping chamber (this seems improbable, but it does work).

Other types of pump include 'getters' (at high vacuum) or 'traps' (at rough vacuum), which simply allow a chemically-reactive surface to adsorb or absorb stray gas atoms. Cryogenic pumps freeze molecules to a surface; many microscopes have a 'cold finger' - a thin, cryogenic pump that is led into the objective pole- piece to keep contaminants away from the specimen, and is cooled down from outside by a dewar of liquid nitrogen.

The main vacuum system on a typical electron microscope has a roughing pump, a diffusion pump and an ion pump.

The roughing pump is a large mechanical contraption which is easy to hear. It is used to pump the chamber from 'air' (atmospheric pressure) when necessary, to pump the specimen transfer chamber (also from atmospheric pressure), and to back the diffusion pump. Because it is used to do so many things, it is usually attached to a 'roughing manifold' - a pipe with lots of other pipes coming off it. By opening and closing various valves off the roughing manifold, the roughing pump can be switched from one role to another.

Ask the demonstrator: To point out the roughing pumping on the schematic diagram on the computer screen. Ask to be shown it in reality.

How many valves come off the roughing manifold? Where do they go and what do they do?

The diffusion pump is usually positioned at the bottom of the column, near the back, and its front end is used to pump the viewing chamber and the photographic film casement. There is usually a large empty volume between the back end of the diffusion pump and the roughing manifold, so that when the microscope is being used, the roughing pump can be switched off (it creates a lot of vibration). The empty volume is very slowly filled with the gas being pumped out of the chamber by the diffusion pump. From time to time (once every few hours), it is necessary to empty the backing line, by pumping it for a short while with the roughing pump. On modern machines, this all happens automatically, although the sound of the roughing pump coming on in a quiet, dark room can be quite surprising.

Ask the demonstrator: To point out the diffusion pump on the schematic diagram of the vacuum system on the computer screen, and also in reality.

The gun and top end of the microscope is often pumped by an ion pump. This section of the microscope is almost entirely separate from the viewing chamber, except for a small aperture (called a 'differential pumping aperture') which is large enough to let the electrons down the column (remember, they are all confined to a few tens of microns width), but which is small enough to maintain a differential pressure. Note that at high vacuum, air does not get sucked through holes like in a domestic vacuum cleaner because the mean- free path of air atoms at low pressure can be many metres, so that they never notice each other. They just ricochet around the chamber and rarely pass through a small aperture. In this way, it is possible to have a poor vacuum in the viewing chamber (say 10-4 mbar) but UHV (10-8 mbar or better) in the gun chamber.

There is often a valve between the top half of the column and lower half, so that the bottom section can be let up to atmospheric in isolation. All this depends on the exact make of microscope.

Pressures in various parts of the vacuum system are measured by gauges. There are several types of gauges, but they fall into two broad categories: low vacuum gauges (usually Pirani gauges) which monitor areas which go up to atmospheric pressure; and high vacuum gauges, which are highly sensitive and are quite often entirely destroyed if they are exposed to atmospheric pressure.

Ask the demonstrator: To point out the vacuum gauges on the schematic diagram of the vacuum system on the computer monitor. To point where their values are displayed.

You don't need to know how the gauges work, but it is worth bearing in mind that the values shown on the computer screen are purely notional, and bear no systematic or linear relationship to the actual pressures in the system. For example, Pirani gauges mounted on various parts of the roughing manifold, are virtually insensitive outside of a range of pressures between about 10-2 mbar and 5mbar: all that they indicate is that a rough vacuum exists or does not exist.

On a modern machine, the computer controls the whole vacuum system, and in general these systems are pretty fail safe. However, as a qualified user of the machine, you must be aware of what the normal behaviour of the vacuum system should be, and what the normal values of the vacuum gauges should read, just in case something goes wrong.

Specimen loading

A side-entry stage normally just requires the user to push in a rod, which is holding the specimen, into the side of the microscope. As the rod enters, you should hear the roughing pump come on; a red light may also show. After a minute or two, the red light extinguishes, and the user must then rotate the rod, and then very carefully let it be sucked right the way into the microscope.

Ask the demonstrator: To show you how to load and unload a specimen, and to supervise you doing it on your own several times.

Pay particular attention to remember at what angle the specimen rod goes into the chamber, how long you have wait before you turn it, and that you are exceedingly careful not to let the rod get sucked in too quickly under the influence of atmospheric pressure pushing it into the column.

Also watch what happens on the vacuum screen of the computer. Do you understand the sequence of valve openings and closings? Remember, the backing line must never go above rough vacuum (letting it do so is a good way of inflicting thousands of pounds of damage to microscope: the oil in the diffusion pump will back-stream into the column).

What happens to the vacuum gauges and why?

The demonstrator should explain whether you must wait until the pressure recovers to a certain value, what that value is, and which gauge monitors it.

Ask the demonstrator: How to load a specimen into the specimen holder.

Note the o-ring, which seals the rod into the column. Never touch the o-ring, or any part of the specimen holder which lies deeper into the microscope than the o-ring. A single fingerprint will torment the next twenty users with terrible specimen contamination.

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Copyright J M Rodenburg