Electron microscopy guide


TEM alignment

STEM alignment

Wave interference


Diffractive imaginging


Learn about alignment and shift

The next thing you should do is learn about what’s called ‘shifting the beam’ and aligning an aperture. As an experimental electron microscopist, you will spend many happy hours of your life shifting beams and aligning apertures.

Ask the demonstrator: To set up the microscope with no specimen, condenser system aligned, but now put in and align a small condenser aperture. Show me how to shift the beam.

You will be shown two knobs, which will probably be labelled ‘shift x’ and ‘shift y’. They are sometimes simply referred to as the ‘electrical shifts’. Focus C2 so that you can see a tiny in-focus image of the filament as before.

Experiment: Now over-focus C2 (turn the brightness knob clockwise) until there is a small circle on the phosphor screen. Try turning the shift knobs. The circle moves around the place. The two shift knobs refer to the two Cartesian co-ordinates of the image plane, and they should be at right-angles to each other. (The movements may not be perfectly at right angles, for reasons which are too complicated to explain at this stage).

Try changing the focus of C2 while the beam is shifted to one edge of the phosphor screen. It should behave exactly as before, but just shifted in position. Easy.

Ask the demonstrator: To show me how to move the condenser aperture.

You will be shown two mechanical screw adjustments on a block sticking out of the electron microscope. The thing is called an ‘aperture mechanism’ or ‘aperture assembly’ and it controls the position of a tiny hole (typically 10-500 microns in diameter) which is supposed to sit on the centre-line of the whole microscope.

The centre line of the entire microscope is called the ‘optic axis’, and it is essential that unless you are deliberately ‘tilting the beam’ (which we will come to later), all the lenses and apertures of the microscope are centred on the optic axis.

There are three aperture mechanisms on the column. For the time being, lets just understand the condenser aperture, which is the one at the top of the column.

Before touching the condenser alignments, slightly over- focus C2, as before, and use the shifts to get the disc into the very centre of the phosphor screen.

Now try moving the condenser aperture: the disc shifts. In fact the disc is the shadow cast by the condenser aperture. Shift the disc by moving the aperture right to one side of the phosphor screen.

Use the ‘shift’ knobs - the electrical knobs you have just learnt about - to move the disc back to the centre of the screen.

Now change C2. What’s happening? The disc moves and comes in and out of focus. You’ll find that you can easily ‘lose the beam’ - that is, get into a situation where you can’t see anything on the phosphor screen at all, no matter how much you change the position of the aperture or the beam shifts. This is good way of annoying the demonstrator, if you are in that sort of mood...

Ask the demonstrator: To get the beam back as it was before.

You should now have a few moments to think about what’s going on.

Theory: The useful part of an electron lens is extremely small – only the centre tens of microns of an electron lens is any good at focussing electrons. For this reason, we have to use apertures. We can think of the condenser aperture sitting immediately below the lens we have been playing with, C2.

When the demonstrator set up the microscope, this is what the ray diagram looked like:

Picture of condenser aperture aligned

Beams come out of the filament in a huge range of angles, but only a few of these get through the condenser aperture and onto the phosphor screen. When you moved the aperture to one side, this is what happened:

Picture of condenser aperture misaligned

Now what happens when you change the focus of C2? Well, the focal point of the lens moves up and down vertically, as before. But because the aperture is so offset to one side, the place where the beam hits the phosphor moves laterally, as well as going in and out of focus. It seems complicated when you see it happen: in fact its very simple when you think of the ray diagram.

Experiment: Play around with the condenser aperture and C2 focus to see if you can understand the ray diagram in the figure above.

Let us spend a little time thinking about the ‘shift x’ and ‘shift y’. You will use these knobs all the time when you use the electron microscope. It is pretty important to understand how they (and similar controls you will encounter later) work.

Because the useful part of an electron lens is so tiny, it is essential that each lens is aligned with the optic axis (the very centre line of the microscope), preferable within a few microns. It is virtually impossible to do this mechanically (like we moved the condenser aperture), because electron lenses are so heavy and unwieldy.

Supposing we have two halves of an electron microscope. Both halves contain a number of lenses, all of which are neatly lined up with another inside each half. Unfortunately, the two halves are misaligned with respect to each other, like this

shift misalignment

It is easy to bend an electron beam by applying an electric or magnetic field across the beam. Electric fields are sometimes used in electron microscopes to deflect beams, but usually a pair of magnetic coils are used, mounted opposite one another. The same method is used in a television to scan the electron beam over the surface of the screen. Such coils are called ‘deflection’ or ‘alignment’ coils, and we can draw them in a ray diagram by a pair of curly lines either side of the beam. We could try to counteract the misalignment shown above by using a pair coils thus

shift with single coils

But we will quickly see that although the beam now passes from the first half of the electron microscope column into the second half, it now goes into the second half at a rather extreme angle. This is called a ‘tilt’. It has the same effect as if the alignment coils did not exist, but the column had been put together physically like this:

physical shift

It turns out that sometimes we want to tilt the beam. However, how do we solve the first problem of the physically shifted column? The answer is to have two sets of coils, like this:

double deflection coils

The first coils bend the beam to the left, the second bend it back again by exactly the same amount. The net effect corrects the original alignment fault. Later you will learn that the we sometimes have to adjust the ratio of these bending coils to make sure that they achieve exactly what we want. (This adjustment is sometimes called changing the ‘rocking point’ of the deflection coils.) In a typical transmission electron microscope there are about three or more sets of such coils, which are usually called ‘double deflection coils’. Of course, in reality each set of coils have both x- and y-components, so that we can adjust the two dimensions of possible misalignment.

The above diagram represents what we call a ‘pure shift’. You should be warned that quite often knobs that are meant to be ‘shift’ knobs also introduce of bit of ‘tilt’ - or vice versa, depending on the exact geometry of the coils relative to the lenses.

Back to the experiment:

Now that we know what an aperture is and how the shift coils work, can we understand what was going on in the previous experiment? Well, a particular combination of beam shift and aperture shift could result in ray diagrams that look like this:

shift misalignment shift misalignment

We have a source, a lens, an aperture and a pair of deflection coils between the aperture and the phosphor screen which we can use to shift the beam.

In the first diagram, the source, the lens and the aperture are all aligned with respect to one another, but the place where the beam hits the phosphor screen has been shifted by the shift coils. If we change the focus of the lens, the disc of the aperture will go in and out on its own axis, but this axis is not the same as the centre of the phosphor screen.

The only difference between the first and the second diagram, is that in the second diagram the aperture has been moved, so its circle appears to hit the phosphor screen in the middle. But now both the aperture and the phosphor screen (the electrical shifts) are out of line. The beam is going through the side of the condenser lens.

It is very, very bad news when a beam goes through the side of an electron lens; whenever possible, as many beams as possible should pass beside the very centre of an electron lens. This is because of another important difference between optical lens and electron lenses; electron lenses suffer from terrible ‘aberration’, which seriously degrades any image we obtain, and which very quickly gets very bad as the angle of a beam through a lens increases.

Luckily, though, it is very easy to tell that an electron lens is not lined up properly. As a general rule, if you change the strength of any lens in the system and the image (or diffraction pattern, whatever you’re looking at) moves, then that lens is not lined up properly.

By now the demonstrator should have re-aligned the condenser aperture.

Experiment: With the condenser aperture aligned, change C2. See that the beam goes in and out of focus symmetrically: the condenser is well-aligned - or at least it should be if the demonstrator has done a good job. Now physically shift the aperture (using the condenser aperture mechanism) say by about its own diameter (the apparent diameter will depend on the setting of C2). Shift the beam back to centre of the phosphor screen using the beam shifts.

Looking at the circle on the phosphor screen like this, could anyone tell whether or not the condenser aperture was lined up? The answer is ‘no’ unless they are allowed to alter C2.

Remember: If you want to test the alignment of a single lens, alter its setting (i.e. its strength or excitation) and see if anything moves.

Try it. Change C2 and you will see the centre of the shadow of the aperture moves. That’s how you know that the condenser aperture is not aligned.

Can you work out a way of re-aligning the condenser aperture without asking the demonstrator? Look at the ray diagrams and think about it. If you find a good way of doing it, then you have learnt about half of everything you need to know about electron beam alignment.

Most people learn to use electron microscopes by following recipes or lists of commands or rules. You will never be a truly good electron microscopist if you need a list of commands. However, to get on quickly the next section, the list of commands for aligning the condenser aperture is this:

  1. Turn up the brightness knob until the illumination reaches the edge of the phosphor screen.
  2. Shift the condenser aperture to the centre of the phosphor screen using the mechanical shifts on the condenser aperture assembly.
  3. Turn down the brightness knob until you see a focussed spot, or until the illumination reaches the edge of the phosphor screen.
  4. Alter the electrical shifts to put the beam onto the centre of the phosphor screen.
  5. Repeat from (1) until the illumination appears to expand and contract around the centre of the phosphor screen.

Here’s another set of rules, which looks almost the same, but doesn’t work at all:

  1. Turn up the brightness knob until the illumination reaches the edge of the phosphor screen.
  2. Alter the electrical shifts to put the beam onto the centre of the phosphor screen.
  3. Turn down the brightness knob until you see a focussed spot, or until the illumination reaches the edge of the phosphor screen.
  4. Shift the condenser aperture to the centre of the phosphor screen using the mechanical shifts on the condenser aperture assembly.
  5. Repeat from (1) until the illumination appears to expand and contract around the centre of the phosphor screen.

You would do well to draw the ray diagrams to work out why one of these schemes works and the other doesn’t. But you can do this at your leisure. In the meantime, the demonstrator is anxious to get on with the lesson.

So far we have learnt about 5 variables: the focus of C2, the electrical ‘x-shift’, the electrical ‘y-shift’, and two controls on the condenser aperture assembly that control the position of the aperture in two-dimensions.

In fact, you’ve now learnt nearly everything you need to know about a single electron lens. The problem we tackle next is how to put several electron lenses on top of one another, and get them to work together.

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Copyright J M Rodenburg