Section 1: TEM parts and functions... 2

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1 Introduction The set of instructions below are written by Charlie Sanabria within the first few sessions of his TEM training process, and are intended for anyone interested in viewing the TEM operation procedure through an inexperienced eye. These instructions were written based on information provided by Dr. Yan Xin during a standard TEM training session, and backed up by some reading of the instrument s User Manual and TEM general information online. Contents Section 1: TEM parts and functions... 2 License. 1) General TEM parts and functions... 2 a) Apertures and lenses... 3 b) A simple TEM... 4 c) Beam alignment and shaping techniques ) JEOL-2011 lenses and apertures... 6 a) Parts above your sample... 6 b) Sample position... 9 c) Parts below your sample... 9 d) Summary ) JEOL-2011 controls (apertures and lenses) a) Parts above your sample b) Sample position c) Parts below your sample ) Other controls of the JEOL a) Changing magnification b) Using the small display screen c) Turning the Gun on d) Using the screen and the binoculars e) Using the vacuum gauge Section 2: Procedure ) Sign in ) Check the HT readiness ) Fill cold trap a) Cover the display b) Fill the dewar and place the ladder in a safe position c) Fill the cold trap until it spills out d) Top the cold trap off ) Load the sample a) Loading sample onto specimen holder b) Check O-rings c) Insert the Specimen holder into the TEM ) Bring the TEM to operating conditions a) Check valves 1 and b) Check vacuum gauge c) Turn the filament on ) Alignment of parts above your sample a) Find a hole in your sample b) Gun and condenser alignment c) Condenser aperture alignment d) Condenser aperture stigmation e) Condenser stigmation (fine adjustment, optional) f) Voltage center adjustment ) Sample position ) Alignment of parts below your sample (focusing) This work is licensed under a Creative Commons Attribution-ShareAlike 4.0 International Based on a work at the National MagLab

2 a) Focusing with z b) Focusing with the Objective Lens c) Increasing contrast with the Objective Aperture d) Focusing further with diffraction pattern (Selected Area Aperture) ) Taking images ) Taking diffraction patterns ) Finishing your session a) Turning the filament off b) Zeroing the stage at all mags c) Taking your sample out d) Logging out and setting microscope idle ) Procedure summary Section 1: TEM parts and functions Before talking about the intricate steps for using and controlling the JEOL-2011 Transmission Electron Microscope, I think it is very important to familiarize ourselves with its most basic parts and their functions (e.g. gun, lenses, apertures, screen, etc.). So in the first section of this document I will remind the reader (to the best of my knowledge) about the technique itself, the physical processed behind it, and the microscope parts that allow us to obtain a TEM image. Then, on the second section of the document, I will go through the steps that should be taken from the moment you enter the TEM room to the moment you leave it. Throughout this document, and especially the second section, I would highly encourage the reader to think about the reason for the steps and the consequences of skipping them instead of following them religiously. This is a high precision instrument which works on very well established principles of physics. It is not magic! Every knob, every setting, every step, and every nuance, has a physical reason behind it. 1) General TEM parts and functions We will deal with the specific parts of the JEOL-2011 in parts 2 and 3 of this section, for now, allow me to explain certain basic concepts about electron optic systems. First off, you have a beam of electrons coming off the gun ; these electrons are accelerated by a voltage, causing them to travel in a wave-like manner. And just like light, they can be focused, diffracted, and/or blocked 1. The problem with electron beams is that many things can deflect them. Let me remind you that electrons are electrically charged 2, therefore even the smallest electric field generated anywhere near the beam of electrons can affect the shape and direction of this beam. Things like the vacuum and the temperature of the chamber, the overall cleanliness of the machine, as well as your specimen 3, and/or the specimen holder, all play a role. Additionally, electrical grounding of the instrument is particularly important, that is because anything that touches the beam in any way, may trap some of the electrons from the beam itself, and if not properly grounded, this can accumulate electric fields also affecting the beam morphology. The electron beam is in fact so sensitive, that even when all precautions are taken and when all conditions are reproduced as closely as possible it still needs to be aligned every time it is used. Furthermore, it must not only be aligned with your sample, but also aligned with the apertures and lenses that shape the beam. 1 Reflection is not in this list. Electron reflection is called backscattering and is much more complex. 2 Duh! 3 TEM samples are often called specimens. 2

3 Finally, as you may have guessed by now, this alignment won t last very long. Soon one or more of the conditions mentioned above will change slightly and your image affected. Please keep this in mind when aligning your beam, and be patient. There is no need to obsess over getting one setting perfectly right since it will most likely be affected by the next step. But most importantly, remember that there is no such thing as the way of getting a TEM image. You will most likely find your own way as you familiarize yourself with the instrument. My hope is that after reading this document you will be able to have enough knowledge to formulate your own approach. a) Apertures and lenses The terms apertures and lenses will come up in this document quite often, so let s get ourselves familiar with what they are and how they work. i Condenser Lenses Electron condenser lenses are not at all like optical lenses, however they do perform a similar (physical) transformation of the beam expand it or contract it. The reason why they can t be made in the same way as optical lenses (e.g. glass), is because electrons don t interact as nicely with matter in the way that light does with transparent objects. Fortunately electrons do interact quite nicely with magnetic fields since they are electrically charged particles. This is why electron microscopes use magnetic lenses to bend and diffract the beam 1. So, all electron microscopes use these magnetic coils (or lenses) to condense or expand the beam just like an optical lens. The issue here is that (as we mentioned above) the beam conditions can vary significantly on a daily basis, therefore the magnetic lenses often squeeze or expand the beam asymmetrically producing images with asymmetrical features that often seem out of focus. This asymmetry is called stigmation or astigmatism and can be corrected by adjusting the lens field (i.e. coil current). Figure 1 a sketch of a simple magnetic lens refracting an electron beam Public domain via Wikipedia Commons 1 Via Lorentz force 3

4 ii Deflector lenses Deflector lenses are very similar to condenser lenses except they focus more on shifting the beam without affecting its morphology as much. They are used for basic alignments between the gun, the condenser lenses, the apertures, and the screen because they move the beam as a hole. iii Apertures Apertures in electron microscopy work very similarly to optical apertures. They are small holes through which the beam passes and gets partially blocked. You may be wondering: Why would you want to block the beam? Well, just like for light optics 1, a smaller aperture provides a sharper image (finer detail) which is obviously desirable but there is a price to pay since there is smaller amount of electrons (or light) passing through, and results in a dimmer image. A large aperture on the other hand, focuses only on a very shallow region (and it can easily go out of focus) nonetheless it provides a larger signal, which is often beneficial. Finding the balance between sharpness, contrast, and signal strength can be done through a correct choice of aperture. Figure 2 An aperture can be as simple as a pinhole in a piece of metal. The image above is a sketch of an array of apertures that can be changed by simply inserting the piece further in (or out). iv Phosphor Screen The phosphor screen is essentially the detector of this instrument and is what allows us to see an image. It is located at the bottom of the microscope, and it s made of a phosphorus layer that glows when electrons hit it. If you think about it, the light reaching your eyes is not coming off the gun above; it is generated by the phosphor screen when the transmitted electrons from the gun excite other electrons on the screen. In other words, the green tint that is projecting this image into your eyes is not present inside the TEM column 2. b) A simple TEM Figure 3 shows a very basic and general sketch of a TEM column. Notice that there are several apertures and lenses. Above your sample, you have the condenser lenses and condenser apertures which do precisely that condense the beam onto your sample. This sketch doesn t show them, but there should also be some beam deflector lenses which (as I mentioned above) can shift the beam as to align it better with the other components. Now, after the beam passes through the specimen region, there are two kinds of aperture/lens combinations which manipulate the transmitted electron beam. One is the objective aperture/objective lens combination, used to obtain a better contrast from the image formed, and the other one is the diffraction aperture, 1 This term is redundant. 2 I had to stop and think about this one for a second. It s very revealing. 4

5 sometimes called intermediate aperture or selected area aperture (not present in Figure 3), which restrict the beam to a very small region and allows for a diffraction pattern to be formed (more on this later). c) Beam alignment and shaping techniques Figure 3 A simple view of. Public domain via Wikipedia Commons Each one of the parts mentioned above interacts with the beam differently, and therefore have their own alignment methods. i Beam shifting The deflector lenses are aligned by increasing or decreasing the current in the coils, which physically moves the beam. They usually work in pairs, one that predominantly moves the beam in the x direction and another one moves the beam in the y direction. ii Beam shaping Condenser lenses have a larger magnetic field region than deflector lenses and affect the morphology of the beam instead of its position only. They also work in pairs of x and y effects which often don t shape the beam symmetrically, and therefore need to be adjusted every time. This asymmetry can often be spotted by stretched circles (ellipses) whenever a perfect circle is to be observed, therefore its effects are more easily seen when the beam is condensed close to a single point (small circle). However, when condensing the beam to a single point is not an option, the asymmetry effects can be seen as distortion of the image in a preferred direction often in the shape of streaks (almost smearing the view). iii Partially blocking the beam Apertures are physically moved into the beam s way using mechanical knobs to match the center of the beam in order to block the beam partially perhaps to increase contrast. iv Wobbling Wobbling is a technique that helps us see more clearly any misalignment of lenses or apertures. While in wobbling mode, the gun voltage is oscillated slightly, and if there is any misalignment, the image should rock sideways. While in wobbling mode, the user has to move the aperture around or adjust the lens current to stop the image from rocking sideways. 5

6 2) JEOL-2011 lenses and apertures The four basic alignment techniques described above need to be done in different ways and to different parts of the JEOL-2011 TEM. Below I will try to paint a better picture on what is happening when each one of the alignment steps are done to which lens or aperture. The specific controls (and knobs) used for these alignments will be discussed in part 3 of this section, for now let s look at the components inside the microscope and what they do. In Figure 4 you can see a simple sketch of the JEOL-2011 TEM highlighting the most relevant parts. Notice they are separated in two groups, those above your sample and those below your sample. Figure 4 Simple sketch of the JEOL-2011 emphasizing on those parts which become relevant during alignment a) Parts above your sample Let s start with the parts that sit above your sample i Brightness coil The Brightness coil on the JEOL-2011 is one of the coils that you will be adjusting the most. This is a condenser lens, therefore expands or contracts the beam that shines on your sample, and consequently the width of the signal on the phosphor screen. It can go from a very wide (and perhaps dim) signal that goes beyond the size of the phosphor screen (at which point you are wasting precious electrons), to a single point focus which might not be very useful for imaging but certainly very useful for centering the beam and spotting stigmation. Ideally, when centering the beam, you want the beam to be as close to a point. On the other hand, when imaging or centering apertures you want it to cover the phosphor screen completely. Figure 5 shows the effects of the Brightness coil. 6

7 Figure 5 Left: An example of a wide beam covering a large part of the phosphor screen, a situation which can be used to center the aperture. Right: a very condensed beam which can be used to center the beam. The Brightness coil is responsible for this drastic change. ii Gun Shift coils As observed in Figure 4, these Gun Shift coils are located closest to the gun, and the effects of these deflector lenses or beam deflector coils are most easily noticed when the beam is in its largest Spot Size (see spot change below). Their purpose is the same as all deflector lenses, center the beam. This is done by condensing the beam into a single point (using the Brightness coil) and then adjusting the current of these Gun Shift coils to move the beam around in the x or the y direction to put it in the center of the phosphor screen. There might be some stigmation associated with these coils, and as it will be seen later, you will also have to adjust for this. I m not sure if this stigmation is done via separate coils or simply a different adjustment on these coils but either way, this adjustment is called Gun Def instead of Gun Shift. iii Mechanical adjustments of the Condenser Aperture This Condenser Aperture is recommended in the largest setting possible (meaning the largest hole, see Figure 2). To center the Condenser Aperture, you want to make the beam as wide as the phosphor screen. When you do this, you may find that the beam is not centred with the phosphor screen as seen in Figure 6. Using the mechanical knobs on the side of the microscope column, you may move the Condenser Aperture around to center it 1. 1 I think is worth mentioning that the beam is not moving here, only your aperture. 7

8 Figure 6 Left: a beam which (when spread) does not match the circle of the phosphor screen. Right: an adequately centred aperture where the beam is concentric with the screen and spreads to cover it completely (without going over on any edge). iv Spot change In the JEOL-2011 there is another setting ruling the aperture assembly that helps to center the beam, it is called the Spot Size and it s adjusted using an electronic switch (as opposed to the mechanical movement of the apertures explained above). There are five different spot sizes that you can switch around regardless of what the rest of the settings are. Spot Size number 1 is the largest and number 5 is the smallest. It will be useful to keep in mind that the larger sizes are influenced more strongly by the Gun Shift coils (which we already talked about) and that the smaller sizes are more sensitive to the Beam Shift coils (see below). In Figure 7 the relative sizes of the spots 1 and 5 are seen. v Beam Shift coils The Beam Shift coils are a pair of beam deflector lenses 1 which (unlike the Gun Shift coils) have a stronger influence on the smaller spot sizes. vi Beam Def coils The Beam Def coils adjust for any stigmation that has been introduced by the Beam Shift coils. In Figure 7 two very nice small circles are seen when the beam is condensed using the Brightness coil, but often you will find that these are slightly elliptical (very hard to see in picture) which means an adjustment on the stigmation needs to be done. 1 Just like the Gun Shift 8

9 Figure 7 Two cases where the beam has been condensed to its smallest size using the Brightness coil, on the left we can appreciate a very sharp and small spot (5) and on the right a slightly wider spot (1). To center the beam on the left you want to rely more on the Beam Shift coil while to center the beam on the right use the Gun Shift. vii Summary of parts above the specimen So that is what we have above your sample: 1. The most important thing is the Brightness coil, which can condense the beam down to a point or spread it to the size of the phosphor screen (or bigger). 2. A Condenser Aperture, which you want to center by spreading the beam to the size of the phosphor screen and manually turn the aperture knobs. 3. Two separate pairs of beam deflector lenses, the Gun Shift coils and the Beam Shift coils; which help you match the beam center with the phosphor screen. At its largest Spot Size (1), the position of the condensed beam is highly influenced by the Gun Shift coils, and as the size is decreases the position is more influenced by the Beam Shift coils. 4. And, each of these two groups of coils (Gun Shift coils and the Beam Shift coils) have a corresponding pair of condenser lenses (Gun Def and Beam Def) to account for any stigmation. b) Sample position All of the alignment done above should be done without the sample interfering with the beam. Once you have done such alignment, you may move your sample (in the x and y) so that the beam hits it. Once the sample is in view, you want to focus it, and you should be able to see a pretty good image already (if your specimen was adequately prepared). To focus your image you need to find the correct z position, this is done by wobbling the beam (see page 5 for a definition of wobbling). As the beam wobbles, your sample will seem to split in two images. Moving the stage in the z position will allow you to merge these splitting images into one. Once this is done, your sample will be focused well enough and your image should be looking even better. c) Parts below your sample And now for the parts below your sample 9

10 i High contrast aperture As I mentioned earlier, a smaller aperture provides a sharper image. So at this point (once the beam has already passed through your sample) you can still take advantage of this effect and increase the contrast of your image by inserting the High Contrast Aperture. There are several sizes you may choose from, but make sure you don t sacrifice signal for sharpness. ii Objective lens If you look at Figure 4, you can see that right below the High Contrast Aperture there are two beam condenser lenses called the Objective Lens coils. These two (one in the x and one in the y, I assume) can help you focus your image even more. However you should always adjust z to get in the ball park of a good focus before fine tuning this Objective Lens coils. Now, just like any other lens, it would be a good idea to check for stigmation. Again, we will talk about the specific knobs and buttons later, but for now just keep in mind that we are looking for the same thing as any other stigmation adjustment: minimize asymmetries by shrinking any elongated features although in this case we don t have a point sample, so instead of looking at the elliptical shape of the beam we are going to have to guide ourselves by what the sample looks like 1. iii Selected area aperture The Selected Area Aperture is even smaller than the High Contrast Aperture. This is used to limit the beam to a very small area so that when the microscope is switched to Diffraction Mode, we know that the diffraction pattern is coming from that (very) specific place. However this Selected Area Aperture in Diffraction Mode also has other uses. Since the image that a diffraction pattern produces is supposed to be a bunch of small dots, fine focusing misalignments can be detected much more easily. Any asymmetries in the Objective Lens coils can be adjusted further in scattering mode by minimizing the fuzziness of the scattering points. iv Other lenses The rest of the lenses in Figure 4 are not influential enough to have to be adjusted every time you use the microscope. Therefore I won t go into their calibration. d) Summary Alright, we have covered the most influential parts of the microscope. The first thing we need to keep in mind is that before the beam hits your sample, it must be aligned with the microscope itself. This is done with your sample out of the way of the beam, and using the Gun Shift and the Beam Shift to center it on the phosphor screen. The influence of these two coils is most easily seen when the beam is condensed to a single spot (using the Brightness coil). And it is important to remember that these two coil groups influence different Spot Sizes. Another thing that is done before putting your sample in the way of the beam is 1 Very often stigmation manifests itself with streaks that distort your sample in a preferred direction. 10

11 centering the Condenser Aperture, which is done mechanically and is most easily done when the beam is as wide as the phosphor screen. Once the beam is aligned, you may move your sample so that the beam hits it, and adjust the sample s z position to bring it to focus. Wobbling helps this process. Then, for a finer focus, you may adjust the Objective Lens. And for an even finer focus, you could help yourself using the diffraction pattern. This diffraction pattern is obtained by inserting the Selected Area Aperture and switching the microscope to Diffraction Mode. Finally, to improve contrast of your image (before or after you have adjusted the focus completely) you may insert use the High Contrast Aperture, remember that a smaller aperture increases detail, but your signal may become weak, or smaller than the phosphor screen. One last thing, all lenses are prone to stigmation! Which means you may have to adjust the stigmation of the Gun Shift, the Beam Shift, and the Objective Lens coils 1. 3) JEOL-2011 controls (apertures and lenses) Now that we are familiar with the basic mechanisms that allow you to align the beam and obtain an image, let s go through them one more time, but this time pointing out the knobs and controls on the panels of the JEOL Below, I will show you the knobs and controls for the things we have already talked about (apertures and lenses). Then Part 2 will talk about the rest of the JEOL-2011 components and controls that you need to be familiar with. I should also add that in this section of the document (Section 1: TEM parts and functions) we will not be relating the knob adjustment to any particular image on the phosphor screen; we will save this for the next section of the document (Section 2: Procedure) in which we will combine all this knowledge to operate the microscope 2. With that said, the two images below show an overview of the TEM highlighting its most important parts. Figure 8 Overview of TEM and components (one of two) 1 I m not sure why the Brightness coil doesn t have a stigmation adjustment. 2 I apologize for the slow learning process but I believe is an efficient way to build a strong foundation for using this instrument. 11

12 Figure 9 Overview of TEM and components (two of two) Seeing all these knobs and buttons can be very overwhelming at first, so let s break things down and build on top of the TEM knowledge we already have. The panels you will be using to control your apertures and lenses are the Left Upper Panel, the Right Upper Panel and the Right Lower Panel shown in Figure 8. Close-ups of these panels are shown in Figure 10, Figure 11, and Figure 12 below. Figure 10 The Left Upper Panel. 12

13 Figure 11 The Right Upper Panel. Figure 12 The Right Lower Panel. Notice this panel is inside the keyboard drawer. a) Parts above your sample To continue with the same order that we established in part (2), I will be talking about the apertures and lenses above your sample first. i The Brightness coil As I ve said before, the Brightness coil is probably the one that you will adjust the most because it alters the width of your beam 1. You can find the Brightness coil in the Left Upper Panel (Figure 10) and it will be on your left-hand side when operating the microscope. One thing you need to keep in mind is that after you have condensed the beam to a single point, you want to always expand it by turning the knob in the clockwise direction 2. We had already seen the effects of turning this knob in Figure 5. You can also see in Figure 10 that there is a line that comes out of the Brightness knob and goes to a button that says CRS, this stands for Coarse and when you press it, it will light up, activating the Coarse 1 The width of your beam will vary depending on the magnification you are in. 2 For reasons I haven t figured out but this is apparently very important. 13

14 mode for that particular knob. In this Coarse mode, the effect of each knob turn (or knob click) will be much larger than without the Coarse mode. ii Gun Shift and Gun Def coils The knobs for the Gun Shift coils are located in the Right Lower Panel (Figure 12). You have to pull out the keyboard that is inside this drawer to reveal the Right Lower Panel. To engage the Gun Shift knobs in Figure 12 you need to engage the button with the word GUN on it (all of the buttons in the TEM light up when engaged). Also, in the same way as above, the CRS button activates the Coarse mode for these two knobs (despite there not being a line joining the button and the knobs). Let me remind you that what you want to do here is to condense the beam to a point (using the Brightness coil) and centering it using the Gun Shift coils which are most effective for large Spot Sizes. The Gun Def knobs below the Gun Shift knobs also get engaged when the GUN button is lit up and they are used to correct any stigmation of the beam. In other words make the beam spot a perfect circle instead of an ellipsis. Don t worry about the rest of the buttons in this Right Lower Panel, they are not used very often and those that are used rarely will be covered in Section 2. iii Mechanical adjustment of the Condenser Aperture As you may recall, the apertures are adjusted manually, Figure 13 shows the relevant knobs for inserting and adjusting the Condenser Aperture. To change aperture size, rotate the Size Selector so that the white dots lineup with the Size Marker. To center the aperture you need to spread the beam close to the size of the screen (using the Brightness coil CLOCKWISE), this will allow you to center it using the outermost knob (Adjust x in Figure 13) and the smaller knob on the side (Adjust y) 1. Figure 13 The Condenser Aperture assembly showing the relevant knobs for inserting and adjusting it. Aligning the Size Selector with the dots (sizes) in the Insert knob selects the aperture size. 1 These are local axes; they are not necessarily aligned with the axes of the coils or the specimen holder. 14

15 iv Electronic adjustment of the aperture assembly To change the Spot Size you want to use the switch above the Brightness knob (see Figure 10). Flipping this switch to the left changes to a larger Spot Size (more suitable for Gun Shift changes) while moving the switch to the right changes to a smaller Spot Size (more suitable for Beam Shift coils). 1 v Beam Shift coils The goal of the Beam Shift coils is to center the beam at smaller Spot Sizes. The Shift X and Shift Y knobs for this coil are located on either side of the microscope, seen on the right side of Figure 10 and on the left side of Figure 11. The Coarse button for these two is the same as the Coarse button for the Brightness knob. vi Beam Def coils These two coils correct for stigmation and their goal is to make an elliptical spot into a circular one. Their knobs are also located on either side of the microscope right below the Shift X and Shift Y knobs, they are labeled as DEF X and DEF Y. Their Coarse button is also located below the Coarse button of the Beam Shift coils. However, in order to engage these knobs to the right coils (Beam Def coils) you have to press the button labeled COND STIG for Condenser Stigmation, as long as this button is lit up, the DEF knob will be engaged to the Beam Def coils (this is because, as it will be shown below, these same knobs can control something else if you press OBJ STIG instead). b) Sample position Since all the alignment mentioned above has to be done on a part of your sample holder (or sample) that is empty, you are going to need to move your sample around in the x and the y directions. The x and y sample position controls (shown in Figure 14) are located right next to the Left Upper Panel. You may also use the wheel (next to these controllers, not in picture) to move the sample more freely. Notice the Coarse button right next to these buttons. Figure 14 The sample position controls 1 This switch returns to the center after it is flipped. So each time you flip it you either increase or decrease the spot size number. 15

16 To control the z position of your sample you need to use the two buttons on the upper left corner of the Right Upper Panel (Figure 11). c) Parts below your sample i High contrast aperture The High Contrast Aperture may be inserted after you have focused your sample adequately in order to increase the contrast of your projected image. In the similar way as the Condenser Aperture, you can aligning the Size Marker by rotating the Size Selector to obtain different aperture sizes. Notice that in this case there is a red dot, which corresponds to the position where the aperture is not in at all (as seen in Figure 15). Figure 15 The High Contrast Aperture assembly ii Objective lens As long as your sample is well focused using the z sample movement, you may improve your focus using the Objective Lens coil whose knob is located in the Right Upper Panel (Figure 11). Notice there is a coarse and fine knob as well as a Coarse button. There might also be some stigmation associated with this lens, and this can be fixed by engaging the DEF knobs (the same ones that controlled the Beam Def coils earlier), but this time you want to press the button labeled OBJ STIG (for Objective Stigmation) instead of the one labeled Condenser Stigmation button. Same Coarse buttons apply here. iii Selected area aperture The Selected Area Aperture works just like the High Contrast Aperture except it tends to block a larger part of the beam, leaving you with a very small and specific region of your sample in the image, but this is done precisely so that the diffraction pattern comes from this specific place. Once the small region is selected, you want to switch the microscope into Diffraction Mode using the DIFF button on the Right Upper Panel. We will come back to this later once we have learned the rest of the microscope controls and parts in Part (4). 16

17 4) Other controls of the JEOL-2011 Figure 16 The Selected Area Aperture assembly In this section we will talk about other JEOL-2011 controls that I have not mentioned previously such as changing magnification, using the small display screen, turning the GUN on, using the binoculars, and using the vacuum gauge. a) Changing magnification The JEOL-2011 has two magnification modes, Low Mag, which goes from 50X to 6000X and High Mag (which has two options or placeholder values called Mag 1 and Mag 2) from 2000X to 1.5 MX. There is not much mystery to these, Low Mag is used often to find your sample and make quick movements across your sample while Mag 1 and Mag 2 are for finding specific spots. These two have the convenience of being independent, so you can have one set to overlook a certain area of your sample and the other one focused much closer to see more detail. But perhaps even more useful, each one of these has their own sample position memories, meaning you can have Mag 1 be focused in a certain area of your sample while Mag 2 focused on a different one. You can exchange between these three modes using the Right Upper Panel (Figure 11) by pressing the buttons with their respective labels, and you can increase or decrease magnification for each one of these settings using the SELECTOR switch (also in the Right Upper Panel) moving it to the right (to increase magnification) or to the left (to decrease magnification). b) Using the small display screen The small display screen 1 is where you can view most of the microscope status information. It s located to the right of the chamber (see Figure 8) and has five different windows (or pages) providing information about the microscope status. As shown in Figure 17, these are: 1. TEM status and sample position information 2. Specimen position 3. Pumping system 4. User s comment 5. Lens 1 If the small screen is off you may turn it on with the switch on its back. See Figure

18 Figure 17 the different pages of the small display screen You will most likely use only pages 1 and 3, and you may switch between pages by pressing p + (number) + Enter on the keyboard, where the number corresponds to each page above. The keyboard is located in the lower right panel as shown in Figure 18 below. Figure 18 Lower right panel (keyboard) opened i Page 1 Page 1 displays some TEM status and sample position information. On this Page, you will be able to see the x, y, z positions and the x, y tilt values of the sample holder as is shown in Figure 19. It is important that you remember that when unloading and loading your sample, all the axis of the sample must be on their neutral positions, which are zero for the x, y, positions as well as the x, y tilt values, but a value of 7 for the 18

19 z position (although the number fluctuates quite a bit when at 7). From this Page (see Figure 19), the only things you really need to pay attention to are: 1. MAG: it allows you to know at what magnification you currently are. Also when in Diffraction Mode (which we haven t talked about much) it will show the camera lens focal length in cm. 2. TEM: this will let you know which mag option you are on, Mag 1, Mag 2 or Low Mag. 3. Specimen: these are the x, y, z positions of your sample, notice it says 8 but this is close enough, besides it will fluctuate from 7 quite a bit even after you have set it to Tilt: If you are using the double-tilt holder you will be able to change these values, if not they stay as they are. 5. And DV, which is related to the focusing done with the Objective Lens coil. This one is particularly important when focusing your sample because if you recall, the z position has the strongest influence on focusing, and the Objective Lens coil (the DV value) only helps improve the focus. Therefore, you want this to stay as close to zero as possible, if you have a very large number (lager than 10 or lower than -10) you may be better off if you adjust the z value slightly and try adjusting this DV (Objective Lens) again. Figure 19 sample position information. And the on/off button of the small display screen. ii Page 3 By pressing p Enter, the small display screen will go into the valve status information. This allows you to see the pressure map inside the TEM and know when operation conditions or sample exchange conditions are optimal. Notice all the bowtie symbols; they represent open valves when solid white and closed valves when outlined. Valves 1 and 2 (V1 and V2) are the most important and they should both be open (solid white) when the GUN is on (microscope operation) and closed (outlined) when exchanging your sample. Opening and closing them is done through the steps taken to load and unload your sample, which will be talked about later on Section 2 of this document. 19

20 Figure 20 valve status information c) Turning the Gun on To turn the Gun on, you may use the button that says ON below the filament light in the Left Upper Panel of Figure 10. Once on, you can slowly ramp up the filament power with the knob below it. The ramping should be done smooth and gradual manner, and should take you about 4 minutes to reach full power. Notice the stopper around 6 that is full power d) Using the screen and the binoculars The window to the phosphor screen has a plastic cover that you must remove when using the TEM, and through the glass you will be able to see the phosphor screen. This is what you will use to determine the width of your beam, your sample position, your stigmation, etc. For very fine adjustments such as the Objective Lens coil focus, or the Condenser Stigmation of small Spot Sizes, you may want to use the binoculars and the small phosphor screen. You can see the binoculars in Figure 9. You can swing these in or out of your way to look closer at your beam and be able to discern the details much better. However, the binoculars are not aiming to the main phosphor screen, there is a small lever to the right of the screen window that you can move up or down which brings a small phosphor screen (about an inch in diameter) at which the binoculars are aiming. This small phosphor screen is what you will use in conjunction with the binoculars to make the fine details of TEM operation. e) Using the vacuum gauge The last thing we need to familiarize ourselves with is the vacuum gauge seen at the bottom of Figure

21 Figure 21 vacuum gauge The vacuum gauge allows you to check the pressure inside the column, which should be below Pa when using the microscope. This gage has several ranges, and when operating the TEM you want have it set to the 10-5 Pa as highlighted and selected in Figure 22. However when not using the TEM, because the fluctuations can be much larger than 10-5 Pa, you want to protect the gage by always leaving it in the 10-3 Pa position (also highlighted in Figure 22). Figure 22 Picture of vacuum gauge during TEM operating conditions below Pa (blue numbers) 21

22 Section 2: Procedure Now that we are familiar with how the TEM parts are adjusted, let s dive into the procedure step-by-step. Keep in mind that your safety and the health of the instrument are the Laboratory s priority, therefore some of the steps like sample insertion, and microscope preparation (which I have not talked about yet), should be followed very carefully and consciously. 1) Sign in For record keeping and in order to identify situations when the microscope is behaving abnormally, make sure you write down your name, date, time and material examined in the user log-book as well as any comments regarding the microscope s functionality. The log-in time starts right before you start filling the cold trap, and the log-out time ends right after you are done putting the microscope in idle mode. 2) Check the HT readiness Before you start, make sure you check the high tension readiness (i.e. the beam current or HT for short) displayed on the beam current window on Left Upper Panel. It should be at 103. If it is not, contact a TEM technician. 3) Fill cold trap The cold trap protects the chamber (and your sample) from contamination, and it needs to be filled with nitrogen before you start. You can see the cold trap and the heater to the left of the TEM column in Figure 23. Figure 23 Cold trap 22

23 Figure 24 Cold trap miscellaneous items a) Cover the display During this process you will most likely spill some nitrogen, so make sure you cover the display using a lab coat (there should always be one in the TEM room) as seen in Figure 25. Figure 25 Display covered by lab coat b) Fill the dewar and place the ladder in a safe position There is a dewar and a ladder in this room, make sure you fill the dewar (about a third of the way) with nitrogen using the adequate personal protective equipment (show in Figure 26). Place the ladder in front of the microscope in a safe position. 23

24 Figure 26 Dewar and PPE c) Fill the cold trap until it spills out Remove the heater from the cold trap by gently pulling it upwards (as shown in Figure 27), and placing the funnel on the cold trap opening fill the cold trap (as seen in Figure 28) until nitrogen spills out of it. Figure 29 shows the heater lying on the desk. Figure 27 Removing the heater 24

25 Figure 28 Filling process Figure 29 Heater d) Top the cold trap off After the initial fill, you may put the Teflon cap back on for a few seconds (up to a couple of minutes). It will take some time for the nitrogen to stabilize at which point a burst of steam will come out of the cold trap followed by a much calmer flow. See the difference in Figure 30 and Figure

26 Figure 30 Normal flow of steam Figure 31 Burst of steam right before the nitrogen stabilizes Top the cold trap off and make sure you put the Teflon cap back on. Return the ladder, PPE and dewar to their respective places. 26

27 4) Load the sample This is the step that requires the most attention from you. Make sure you know what you are doing before doing any of these steps. Figure 32 shows the sample holder box as it should be when you open it with the sample holder inside. Figure 33 shows the sample holder out of the box once the protective sleeve is removed. Figure 32 Non-rotating sample holder Figure 33 Non-rotation sample holder out of the box a) Loading sample onto specimen holder Make sure you wear gloves at all times when manipulating the sample holder and do not touch the holder beyond the O-rings. Using the optical microscope when needed (seen to the right of Figure 32), load your sample and make sure it is held adequately as show in Figure 34 and Figure 35. Also, when tightening any screws make sure you apply a finger-tight torque on it and never over-tighten any screws. To separate the stage from the sample holder you can insert the screwdriver into the stage clamp orifice and use it as a lever to open the clamp. 27

28 Figure 34 Loading sample Figure 35 Adequately loaded sample b) Check O-rings Sometimes the O-rings can pick up dust or hairs which may induce vacuum leaks, check under the optical microscope and remove any debris using your gloved finger. c) Insert the Specimen holder into the TEM Insert the specimen holder by aligning the pin with the guide groove until it stops. At this moment you should hear a clicking noise inside the column and if you check the small display screen, you should see that valve 1 has opened (solid white). Allow a few seconds to pass and flip the switch onto the pump position. Wait for the green light to turn on as shown in Figure

29 Figure 36 Picture of the switch and the sample holder in. Green light ON. Once the green light is on, turn the sample clockwise until it reaches a stop (rotational stop). Make sure you hold the sample as it may be suctioned by the TEM vacuum. After that rotational stop, you will notice that the sample can be pushed in a few millimeters in, before it reaches another stop (linear stop), at which point you may turn clockwise again until it stops yet again (rotational stop). Finally the sample holder should be able to be pushed in completely. Keep holding it and insert slowly until it stops. Your sample is ready! The steps are seen graphically in Figure 37. Figure 37 Sketch of the sample motion. After the first insertion, the switch must be flipped to the pump position and you must wait for the green light to turn on. 5) Bring the TEM to operating conditions Keeping in mind all the parts, functionality, and controls of the TEM explained in Section 1, follow the steps below to bring the microscope to operating conditions. a) Check valves 1 and 2 Use the keyboard to navigate to the valve status information (Figure 20) and check the valve status in the small display screen. Valves 1 and 2 should be open (solid white). 29

30 b) Check vacuum gauge When you found the microscope, the gage range on the vacuum gauge should be at 10-3 Pa, please add a note on the log if the previous user didn t leave it as such. However, before ramping the microscope, you want to switch the gage range to 10-5 Pa (see Figure 38) and check that the vacuum is below Pa (blue numbers) 1. Figure 38 Picture of vacuum gauge at OK conditions well below Pa (blue numbers). c) Turn the filament on Before turning the filament on (seen in Figure 10, Left Upper Panel) make sure the filament light is green. This would be a good time to turn the fluorescent room lights off and turn the dimmable incandescent lights. You will be able to see the panel lights much better. Press the button that says ON (below the filament light) and slowly start ramping up the filament power with the knob below it. The ramping should be done smooth and gradual manner, and should take you about 4 minutes to reach full power. Notice the stopper around 6 that is full power. You are ready to locate your sample and align the microscope. Remove the screen cover if you haven t done so. 6) Alignment of parts above your sample At this point you should be getting something on the phosphor screen (perhaps a piece of your sample grid). Go to Low Mag and zoom out using the SELECTOR switch in the Right Upper Panel (Figure 11). If you still don t see anything (or your image is very small you may turn the Brightness knob (CLOCKWISE) to fill the phosphor screen with the electron beam. Sometimes too low of a Mag may not allow you to fill in the phosphor screen even at the highest Brightness setting. If your sample (or the sample grid) is out of focus, you need to use the z button in the Right Upper Panel to get it roughly in focus. The HT wobbling or Image X and Image Y wobbling are very effective here to show you how out of focus you are. Engage any of these buttons and use z to merge the images. 1 If it is higher make sure you wait a few minutes until it stabilizes below Pa 30

31 a) Find a hole in your sample In order to start the whole alignment process you must first find your sample and zoom into a hole within your sample so the beam passes through undisturbed. You may switch to Mag 1 and zoom to about 50kX, the beam should be blank (with no features). b) Gun and condenser alignment If you paid attention when reading Section 1, you may remember that there are two deflector lenses, one that works better at larger spot sizes and one that works better at smaller spot sizes, these are the Gun Shift and the Beam Shift. You may also remember that spot size 1 is largest and spot size 5 is smallest. So increase your magnification to about 100kX, and after focusing the beam to a single point, using the Brightness knob (COUNTER CLOCKWISE), you may use the Gun Shift and the Beam Shift to center the beam. Start with a spot size of 2 perhaps, and try adjusting the Gun Shift first using the Right Lower Panel (Figure 12). This is done by engaging the Gun Shift coils using the GUN button and using the Shift X and Shift Y knobs. Remember using the Corase mode whenever necessary. While still at spot size 2 try now adjusting the Beam Shift using the knobs on both the Right Upper Panel and the Left Upper Panel, don t forget that these settings don t need to be perfect, since you are about to check other spot sizes and they will most likely change your current setting slightly. Now, keeping in mind that Gun Shift dominates lower numbers of Spot Size and the Beam Shift dominates higher numbers of Spot Size, try finding the settings where the beam is completely centered at all spot sizes. c) Condenser aperture alignment While in Spot Size 2 and still 100kX, spread the beam clockwise so that it covers almost to the edge of the phosphor screen. If it doesn t match the phosphor screen circle try adjusting the aperture with the right short knob and the knob on the outside (see Figure 15). You may notice that when condensing the beam back down to a point it is a little off from the center. Try adjusting it again with the Gun Shift and the Beam Shift, hopefully for al spot sizes, and repeat the aperture alignment. Repeat the entire process at 200kX. d) Condenser aperture stigmation Going back to 50kX with a Spot Size of 2, and making sure that everything is still centered, use the Brightness knob to go back and forth between a point and a small circle. If you notice that the circle looks more like an ellipse you may have to adjust the Condenser Stigmation, remember that you have to press the button labeled COND STIG to engage the DEF knob to the Beam Def coils. Use these Beam Def coils to make that small ellipse into a small circle. And once again, just like pretty much every step, some of these changes may have affected previous alignments, make sure they are still ok. e) Condenser stigmation (fine adjustment, optional) This is an optional step that uses the microscope in Diffraction Mode. We have briefly mentioned Diffraction Mode before. It is when you set the microscope to get a diffraction pattern instead of a picture, and instead of magnification in units of X, you will be using the lens focal distance in centimeters. But don t 31

32 despair, this Diffraction Mode also uses similar techniques and knobs we have talked about before to make adjustments during your calibration. The first thing you need to do, is set your magnification to 100kX, then turn the Brightness knob clockwise until it beep (widest beam) at which point you will switch to Diffraction Mode by pressing the DIFF button on the Right Upper Panel 1. Using the magnification SELECTOR, change your focal length to 200 cm (this value will be shown in the small display screen instead of the magnification value). Then, using the knob next to the DIFF button (which says DIFF Focus), bring the beam to as close to a point as you can make it (it should become a small circle with a sharp edge and a funky shape on it). You can also center it using the Right Lower Panel which we had previously used to adjust the Gun Shift coils by engaging the GUN button and using the Shift X and Shift Y knobs, but this time we will engage the PROJ button instead of the GUN button (see Figure 12). And the last thing you want to do also uses the Right Lower Panel (but is something we have not talked about before). If you look at Figure 12 there is a switch to the right of the image which reads COND DEF ADJ, switch this to x and you will see that the circle you previously focused is now flickering back and forth between two positions. Press the button that says Shift (next to the switch), and using both knobs of Shift X and Def X you can merge these two flickering positions. Make sure you do the same for y. f) Voltage center adjustment This final adjustment uses the wobbling technique which we mentioned earlier is very useful to find aperture centers. In this case is the GUN which wobbles (aka the HT). With a magnification higher than 100 kx and a Spot Size of 2 focused to a single point, press the HT wobbler button in the Right Upper Panel and then press the BRT tilt button in the Left Upper Panel. You should be seeing the beam rock slightly. You may actually want to use the binoculars and the small phosphor screen to be able to tell if it is moving. Then, reduce the rocking motion using the Beam Def coils (DEF X and DEF Y which we have used before), but this time engaging the BRIT TILT button instead of the COND STIG. 7) Sample position At this point you should be ready to move your sample into the beam using the x and y sample position controls (Figure 14) or the wheel. You may want to lower your magnification to something like 50 kx and also try widening the beam (using Brightness clockwise) to cover the entire phosphor screen. You want to find a region of interest close to an edge of your sample hopefully with plenty of sharp features to distinguish so the focusing is easier. 8) Alignment of parts below your sample (focusing) a) Focusing with z As I have mentioned before, your z value is the most influential on your sample focusing, therefore you want to find its sweet-spot. To do this, you want to wobble the image. But instead of using the press the HT wobbler button in the Right Upper Panel like we did before, you want to use the SHAM/ROCK button 1 To get out of diffraction mode just press Mag 1 or Mag 2. 32

33 towards the top of the Right Upper Panel (See Figure 11). You will see your sample split into two images back and forth, the goal is to use the z to merge the images together as much as you can. b) Focusing with the Objective Lens Then, while still wobbling, you want to use the next step of focusing which (as we have seen before) is the Objective Lens coil or the OBJ FOCUS knob on the Right Upper Panel (Figure 11). You may also want to use the binoculars for this fine adjustment. When done focusing, check that your DV value is low (it should be if you focused using z first) and depress the SHAM/ROCK button. Try zooming in a little to something like 200 kx, press the SHAM/ROCK button again and use the OBJ FOCUS knob with the binoculars again to focus your sample further. You may also check for stigmation of this Objective Lens coil using the DEF knobs, the OBJ STIG button engaged. Make you depress it when you are done. Finally, go to the closest edge of your sample and slightly over focus it with the fine knob of the OBJ FOCUS knob, doing so you will see a dark line at the edge of the sample which makes it easier to discern. These dark lines are called Fresnel fringes and although it is technically moving away from a perfect focus, it makes the image look much better. c) Increasing contrast with the Objective Aperture At this point, inserting the Objective Aperture may increase the contrast of your image making it look even better. Don t forget to keep in mind the balance between signal and contrast when selecting the aperture size, and always make sure your aperture is centered. d) Focusing further with diffraction pattern (Selected Area Aperture) As I ve mentioned before, you can also insert the Selected Area Aperture to check that your diffraction patterns are sharp, and if they are, your focusing was done well. So find an appropriate location on your sample, insert the Selected Area Aperture, (you may want to take the Objective Aperture out) center it, and switch to Diffraction Mode using the DIFF button. Using the magnification selector you may change the camera lens focal length to fill the phosphor screen with your pattern and use the DIFF FOCUS knob to focus your pattern 1. You can also center this pattern by using the Shift X and Shift Y knobs on the Right Lower Panel with the PROJ button engaged. 9) Taking images You may now go back to transmission mode by pressing Mag 1 or Mag 2 (whichever you had previously chosen) and you picture should be looking very sharp. To take an image you must first log into the external image acquisition computer next to the microscope. Once logged in, flip the switch on the front of the control box sitting by the CPU of this computer. Once the box is switched on, you may open the image acquisition software named AMT 5.4. In the menu bar, go to Correction Diagnostic Tools Suspend Correction and Zero Threshold. After this click the Recall button on the lower right corner of the software window and select the file labeled Tak-ASC. Then, to take an image, wind the camera in using the turning knob shown 1 Make sure you try to focus the pattern not the bright dot in the center. Also if you get a series of rings your sample is amorphous and is very hard to focus. 33

34 in Figure 9 (labeled CCD camera) and go to Correction Acquire Dark Image. Your image should now be on the screen. Make sure you wind the camera out as soon as you are done (to protect the sensor). 10) Taking diffraction patterns To take images of diffraction patterns you must insert the Selected Area Aperture back, and switch back to diffraction mode by pressing the DIFF button. It is also better if you take out the Objective Aperture out. You may want to adjust your Brightness knob to focus the transmitted pattern. Take the image using the AMT 5.4 software just like you did for the step above. Once you are done with the image acquisition software you may close it and turn the control box off. 11) Finishing your session Finishing your session adequately is of paramount importance. Just like starting your session you must be very conscious of all your steps in order to protect the microscope and your sample. The first thing you need to do is take out the Selected Area Aperture and the Objective Aperture and then you must to the following: a) Turning the filament off Turn the filament knob down slowly (on the Left Upper Panel of Figure 10), taking about 30 seconds to reach the minimum value 1. Then, press the ON button (below the filament light), which this time will turn OFF the Gun. b) Zeroing the stage at all mags Now we need to zero all stage values. This happens when you press the N button on the sample position controls (Figure 14), all the stage control values will zero out 2. You must do this for both magnifications. So press Mag 2 followed by this N button and double check on the small display screen that all values went to zero (except for z which should go to 7). Then, press Mag 1 followed by this N button again, and double check again. Take Mag 1 to 100kX and make sure all your apertures are out (i.e. red markers are aligned with the position marker, see Figure 15 and Figure 16) c) Taking your sample out Pull the sample out using the opposite motion to the one you did when you inserted it. See Figure 39 for a graphic representation of the sample holder motion out. Before the last pull, flip the switch onto the air position. The green light should turn off. Wait 30 seconds before take the sample holder out. 1 Not as slow as the ramp up 2 Make sure you have the Coarse mode on or else you will be waiting for a long time for them to zero out 34

35 Figure 39 sample holder motion out. Now make sure you take your sample back and place the holder back where it was in the same way you found it. d) Logging out and setting microscope idle Putting the microscope idle is very important. The first thing you may want to do is press the HT button in the Left Upper Panel (the one with a plastic cover over it) so the light above it turns off. With this, the green light above it will go off and the current will drop to zero. Then, go to the keyboard and type htset followed by a space and the number 100. Press enter. Don t forget to return everything to the places where you found it, this includes the screen cover, the cold trap objects (see Figure 24), and the ACD heater (see Figure 27). There is a drawer on the left side of the microscope that we have not used at all (similar to the Right Lower Panel). In it, press the button that says ACD to activate the heater. Make sure you return the pressure gage back 10-3 Pa (see Figure 38). And last but not least, turn the small display screen off (see Figure 19). 12) Procedure summary 1. Sign in. 2. Check HT readiness, displayed on the beam current window on Left Upper Panel. It should be at 103. If it is not, contact a TEM technician. 3. Fill the cold trap. a) Cover the display with a lab coat. b) Remove the heater by gently pulling it upwards. c) Fill the dewar and place the ladder in a safe position. d) Fill the cold trap until it spills out. e) Put the Teflon cap on and wait for the burst of steam. f) Top the cold trap off. g) Put the Teflon cap back on. h) Return the ladder, PPE and dewar to their respective places. 4. Load the sample a) Take sample holder out of the box and remove the protective sleeve. 35