Electron Microprobe Operation


J E Patterson


This document is a simplified manual for the operation and setup of the JEOL 733 electron microprobe. It is not a replacement for the hardware and software documentation. It is useful for day to day operations.


This section deals with checking that the software is operating and that the P-10 gas for the X-ray counters is flowing - no gas means no counts and no analyses.

  1. Ensure the Moran WDS software is running on the right hand computer (front keyboard). If not double click on the MS-Startup icon. A welcome screen should appear.
  2. Click on the Wavelength Dispersive Analyser button.
  3. Check that the appropriate analysis program is running, e.g. silicates. Look at the top left of the WDS Control window for (usually) "c:\mseds\user\silicate" or "c:\mseds\user\tephra". Change, if necessary by clicking on Files and Read Analysis File from Disk.
  4. Click on the rightmost button on the toolbar to get an element selection window.
  5. Click individual elements to select for analysis. A tick should show for the selected elements.
  6. The digital imaging program, Image Slave, should also be running on the left hand computer (back keyboard). If not double click on the Image Slave icon. File, New should produce an image screen. Right click to stop the scan. Select View, Full Scale and expand the blank image using the window maximise icon at the top right. To view an image that is showing on the microprobe viewing screen click the 6th button from the top left. It looks a bit like a small TV. To capture a slow scan image with reduced noise press the PHOTO button twice on the microprobe SCAN GENERATOR panel.
  7. Ensure P10 gas (10% CH4 /Ar) is slowly flowing through bubbler attached to the channel l spectrometer. The bubbler contains glycerol which should not evaporate. The other chamber prevents suck back which may occur if a counter window is leaking inside a spectrometer. About one bubble a second or so should be observed. The valve adjustment on the gas bottle regulator is critical so take care. It rarely requires any adjustment.


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You need an electron beam to see the sample on the screen and to make X-rays which are representative of the samples composition.

Normally the Gun Filament knob is set to a standby position of about 12 o'clock. The actual setting depends on the age of the filament. If it is off then the following three instructions apply.

  1. The vacuum, using button 2, on the DYNAVAC gauge, should be better than 10-4 TORR before turning the filament on. You will be prevented from doing so if the pressure is too high.
  2. Select the appropriate KV setting, usually 15 or 25 (10 or 20 on the pushbutton and 5 on the thumbwheel switch). Gun bias is set to 3.
  3. Ensure the Gun Filament knob is fully anti-clockwise, and switch the On-Off toggle to the On position.
  4. Slowly turn the Gun Filament knob clockwise while observing the AEM meter , pass the first peak and adjust until the meter reading plateaus. Repeat to check you have the right setting. The plateau setting indicates the filament is saturated and the electron emission is now being automatically controlled by the electronics. Further increase in the current through the filament will not cause any further increase in beam current but it will shorten the life of the filament markedly. The normal position of the Gun Filament knob starts at about the 3 o'clock position with a fresh filament reduces to as little as 1 o'clock as the filament ages. The filament gets thinner and needs less current to maintain it's operating temperature.
  5. Adjust the X and Y tilt knobs on the Electron Optical system alternatively to maximise current. Adjust the condenser lens Fine knob until required beam current is obtained. If it is necessary to go to the Coarse knob at this stage, the beam alignment is probably out or the previous instructions have not been carried out correctly. It may be necessary to re-adjust the Saturation and Tilt settings during warm up. Refer to the JEOL manual for details.


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Because the microprobe uses crystal spectrometers to separate and detect X-rays the centring of the electron beam on the sample is important to preserve the angular relationships established during calibration. It also means the electron beam is coincident with the optical view of the sample.

  1. Position Benetoite under the cross-hairs and carefully focus optically. To do this press click on the Go to Position button in the WDS control window.
  2. Select BEN and click on Go To .
  3. Turn the illumination down slightly.
  4. Ensure the KV is set to required value (usually 15 or 25). Click the beam control button [><]. It will change to [> <] indicating the electron beam can pass through to the sample. A light blue spot should be observed in the centre of the optical microscope field.
  5. Minimise the size of the circular image (focus) using the objective lens M knob on the ELECTRON OPTICAL SYSTEM panel. When the focus is adjusted the spot image should expand and contract symmetrically and should be circular. You may also need to re-check the optical focus.
  6. Ensure that the green FINE SHIFT button on the magnification unit is pressed in and adjust the X and Y fine shift knobs below until the focused spot image is perfectly in the centre of the cross-hairs.
  7. While watching the spot image, decrease the condenser lens coarse setting from normal position 5 to 4 , the image should expand concentrically without shifting. You may need to reduce the RANGE setting on the AEM panel.
  8. While in position 4 maximise beam current using X and Y SHIFT knobs (next to TILT knobs on E.O. system.). At the maximum point the beam image should be central on the cross-hairs and will be about 3-4 microns in diameter.
  9. Return condenser lens knob to position 5 and range setting to 3 x 10-8 A. The idea here is to avoid a spot shift while switching through the apertures, from 4 to 6.
  10. Check the image again. Switch off the beam and adjust tilt knobs for maximum current.
  11. Use condenser lens FINE knob to adjust the current to 1.2 x 10-8 A. Some silicates glasses and calcites may require settings as low as 6 x 10-9 A with a defocused beam to avoid sample damage. Sulphide analyses at 25 kV is usually done at 1.5 x 10-8 A.

You may need to cycle through these adjustments to obtain a perfect state.


To get your sample into the microprobe you often have to get someone else's out first. You need to centre the sample stage and rotate it 180 degrees to position 1 in order to do this.

  1. Click the WDS control window to make it active, the banner at the top will change colour.
  2. Press Ctrl T . The stage should move to X=16000, Y=16000 and Z=11000.
  3. Ensure the transmitted light source mirror arm is swung out of position. Use the knob at the side of the probe and turn anticlockwise from SET to OFF if necessary.
  4. To rotate the stage to position 1 click on the 3 above ROTATE in the stage control window. You will be reminded about the transmitted light mirror.
  5. Click OK . If you make a mistake here, by leaving the transmitted light mirror in, make it twice to re-establish the relationship between the computer and rotate knob setting.
  6. Change 3 to 1 and click OK . The stage will rotate.
  7. Pull off the airlock cap.
  8. Fit the changing rod adaptor onto the air lock with WD11 at the top.
  9. While holding the adaptor firmly in place press the red button to the right of the air lock.
  10. When the illuminated red button goes out (airlock evacuated) wait 30 seconds and pull out airlock knob. Pull this knob out firmly without bending it from side to side as a vacuum loss may result. The knob will click into the open position.
  11. Slowly push in the rod and screw it into the specimen holder, slowly withdraw specimen back into the airlock.
  12. Push the airlock knob in firmly, a "click" should be heard and the airlock will be automatically vented. The rod and specimen can be removed immediately.
  13. Replace the airlock cap.

Note that moving the mouse over a button causes the function of that button to be displayed near the top of the window.


Your sample finally makes it into the microprobe.

The sample slide or block mount needs to be coated with a 25 nm thickness of carbon. If a polished brass plate goes into the coater with the samples it will gain a deep blue interference colour if the carbon thickness is correct. With the existing settings, 6 firings gives the correct thickness. The pump down time is about 30 minutes - more if the samples degas.

The slide is held in a special slide holder with conductive rubber clamps. The sample holder is then screwed onto the carrier, ready for insertion.

Block mounts are inserted into a special spring loaded holder which then fits into a carrier. The sample should be level with the rim of the carrier.

Conductive tape and inks can be used but these have largely been replaced by using these holders.

  1. Follow the same procedure as removal to insert a specimen. In this case the slide or block mount holder is fitted to the end of the rod first. Note that the slide holder gap faces the rod end. It won't fit in the air lock the other way round, nor will it engage properly with the rod end.
  2. While holding the adaptor firmly in place press the red button to the right of the air lock.
  3. When the illuminated red button goes out (airlock evacuated) wait 30 seconds and pull out airlock knob. Pull this knob out firmly without bending it from side to side as a vacuum loss may result. The knob will click into the open position.
  4. With the air lock open insert the sample. Keep it level and engage it with the stud on the stage surface. Don't collide with the stage edge. You may need to lift the sample slightly to compensate for sag.
  5. Push in the rod until there is a firm spring like resistance.
  6. Release the rod pressure.
  7. Rotate the rod anticlockwise to release it from the sample holder.
  8. Withdraw the rod.
  9. Close the gate valve until a click is heard.
  10. Remove the changing rod adaptor and replace the cap.
  11. After checking the spot position on Benetoite and doing any necessary standard analyses you are ready for analysis.


Now the sample is ready for analysis. Hopefully a map exists otherwise you may spend a long time looking.

  1. Click the WDS control window to make it active, the banner at the top will change to blue.
  2. Press Ctrl T . The stage should move to X=16000, Y=16000 and Z=11000.
  3. The spectrometers can also be set to their reference positions (10000) by by pressing Ctrl P.
  4. Re- check that the transmitted light source mirror arm is swung out of position. Use the knob at the side of the probe and turn anticlockwise from SET to OFF if necessary.
  5. To rotate the stage to position 3 click on the 1 above ROTATE in the stage control window. You will be reminded about the transmitted light mirror.
  6. Click OK . If you make a mistake here, make the mistake twice to re-establish the correct relationship between the computer and rotate knob setting.
  7. Change 1 to 3 and click OK . The stage will rotate. You will be positioned on the upper part of the slide on the centre line. From this point, if the slide is properly marked up, you can move to the first analysis spot.
  8. Switch to BRIGHT UP and turn the beam on.[ | |] to view the image.
  9. Re-open the Joystick control. You need to close it every time you want to turn the beam on or off.
  10. View the image and locate a smooth area for analysis using the joystick for x,y movement. You can click Fast or Slow to move more efficiently to the next location. You may need to focus with the z control as well if the image is not sharp.
  11. Raise the magnification to well above 400 times to prevent spot movement during analysis.
  12. Re-position the sample slide if necessary to avoid cracks, scratches and inclusions.
  13. Turn the beam off. [U] and re-enable the joystick.
  14. Switch to SPOT mode.
  15. Turn the incident light on. The switch is second from the right at knee height. It has three positions, up for incident light, down for transmitted light and neutral for off. The right hand switch controls an electron trap and should always be down - check it. There is also a brightness knob which controls both the incident anad transmitted light.
  16. Use the Sony video screen to check the focus. Adjust it using the Z control switch below the joystick control. The image gets brighter as you approach the focus. On this screen you are seeing an optical image of the slide surface magnified about 1300 times.
  17. Turn the light off.
  18. Close the Joystick control.
  19. Check the required elements are selected.
  20. If you want a larger beam diameter to avoid sample heating, set it now using the PROBE DIAMETER switch and continuous ADJ control. 10 - 20 microns is often chosen for glass, mica or calcite analyses.
  21. Click on the analyse icon.
  22. Enter a name for the slide, circle and the position within the circle.
  23. Check that your user name is entered. Change "oldname.res" to "yourname.res" . Use 8 or fewer letters here. Next time round just check that nothing has changed. The default is the last name used or "auto.res".
  24. Click OK and the analysis will begin
  25. After the analysis turn the PROBE DIAMETER switch to off.
  26. Repeat from step 8 for the next spot.


  1. It might help if a printed image of the slide is used for reference. A digital camera or a negative scanner can be used to create an image directly from the slide. You can also capture an image from each circle using ImageSlave. Print it and mark analysis points.
  2. You can use ImageSlave to get an image on the computer screen. Click on the IMAGE tab and select VISUAL. The computer image will scan at the same rate as the microprobe screen.
  3. If you want to capture and save an image press the PHOTO button twice.
  4. Add a scale by clicking on text and type |------|. The number of dashes required corresponds to the magnification times 1.35 for a 1000 micron marker, divided by 10 for a 100 micron marker and divided by 10 again for a 10 micron marker. The marker can be placed anywhere on the image. You can also add text to the marker such as beam energy in kV, detector type, slide identification and position. Save the image with a unique name.


There are a few actions that can cause damage or a big waste of time.

  1. Don't attempt to turn stage controls by hand while the system is under computer control, use the joystick control.
  2. Don't bend the right side airlock knob toward or away from yourself while operating it. A loss of vacuum may occur via the O ring seal.
  3. Don't bend the changing rod. Centre X and Y automatically to 16000 microns by clicking on the WDS control window and keying in control T.
  4. Don't rotate the holder around on the end of the rod while it is in the chamber, it is very easy to hit and damage the edge of the backscattered electron detector.
  5. Don't try to adjust the aperture alignment, this is very sensitive and a little tricky to use. It should not be adjusted until other alignments such as TILT and SHIFT are done. All adjustments are interactive and they may need to be cycled through several times. Refer to the JEOL manual.


Images are often used to mark analysis positions on. We mainly use backscattered electron images as they contain analytical information. A bright area implies the average atomic number is high, eg calcite, titanomagnetite, pyrite etc while a darker area might show quartz, feldspar or mica.

  1. It is possible to generate several types of images giving a variety of information on composition and surface features. For details of these the user must consult the JEOL-733 manual. The following is a brief description for generating secondary electron images (SEI) and backscattered electron images (BEI). The procedures described do not necessarily result in optimum image quality and are intended purely as an aid for use with routine analysis work.
  2. All the room lights should be off to make viewing easier. Ensure the specimen is in optical focus.
  3. Set the selector switch on the scan-generator unit to PICTURE. Turn the BRIGHTNESS and CONTRAST knobs beneath the screen fully clockwise and check the NORMAL pushbutton is in. Press the RAPID 1 button on the scan generator. Press SEI on the left-hand column of buttons on the image selector. Select a suitable magnification using the coarse push buttons and fine control on the magnification unit. (400x will give an image on the screen about the same size as that viewed down the optical microscope). The selected magnification is displayed with LEDs on the display board.
  4. Press the PROBE SCAN button on the magnification unit, switch up the SEI/BEI toggle switch to the SEI position and press the probe detector button on the tall left-hand instrument rack.
  5. At this stage you should be greeted by some kind of image on the screen but the brightness and contrast will probably not be satisfactory.


  1. The BEI is a little more difficult to set up correctly but having done so it provides a wealth of information and is especially useful in examining composition variations in minerals. Select the SLOW l pushbutton (BEI can only be used with slow scan speeds) and press the COMPO button on the left-hand column on the image selector. You may or may not obtain some sort of image.
  2. Adjusting the BEI image - this is similar to the SEI above but is more critical. Select the WAVEFORM MONITOR button and using the GAIN , DC SUPPRESS and BRIGHTNESS knobs on the BEI unit (next to the screen) set the wavy lines to fit approximately inside the upper and lowermost horizontal lines. The setting of the DC SUPPRESS knob is very critical and even slight changes in its setting may make the image disappear or be too bright. You can use the COMPO knob as a fine control for this.
  3. For accurate analysis of very small areas one should use the spot mode and scanning images of at least 1000 times. Before analysing please ensure that the specimen is in perfect optical focus (as should be the case for normal analytical procedure).
  4. Switch from PICTURE to SPOT using the selector on the scan generator unit. Using the X and Y position knobs below, position the very fine spot on the screen to the analysis position. Do not stray more than a few centimetres from the centre of the screen at this magnification level. Try to get to the analysis position using the joystick control as the X and Y errors may slowly accumulate.


Press the WAVEFORM MONITOR button (below screen) and adjust the BRIGHTNESS and CONTRAST knobs on the secondary electron image panel so that the wavy signal lines on the screen sit inside the upper and lowermost horizontal lines. Select the NORMAL pushbutton again and the image should be satisfactory.


No picture, low or zero analysis totals and no beam current? The filament has blown.

Note: Only experienced operators should do this see John Patterson.

  1. When the electron gun emission decreases or its filament burns out, replace the filament.
  2. A burned-out filament can be detected as follows:
  3. Set the LOAD/FILAMENT switch on the ACCELERATING VOLTAGE unit to FILAMENT and the ON/OFF switch to ON.
  4. The filament is burned out if the LOAD/FILAMENT meter needle does not move when the GUN FILAMENT knob is turned clockwise.
  5. Turn the GUN FILAMENT knob on the ACCELERATING VOLTAGE unit fully counterclockwise and set the ON/OFF switch to OFF . Also check that the POWER switch on the HIGH VOLTAGE unit is OFF.
  6. Push the GUN VENT button on the VACUUM SYSTEM unit. Air automatically goes into the anode chamber.
  7. Push the electron gun assembly backwards to open it.
  8. Wear cotton or nylon gloves from now on.
  9. Turn the Wehnelt unit securing ring counterclockwise with the Wehnelt unit setting tool and remove the Wehnelt unit. The whole Wehnelt unit will be hot immediately after the filament burns out. Place the unit on a metal surface until it cools down so that it can be touched by hand. Cover the anode chamber to protect it from dust. A single sheet of weighing paper is ideal, otherwise use aluminium foil.
  10. Clean the Wehnelt cap, or use the pre-cleaned 2nd cap. The cap can be cleaned in a 50% ammonia-water solution. Remove residual dirt with fine-grained metal polish and rinse with petroleum ether and dry with absorbent cotton. For the best results, use an ultra-sonic washer.
  11. Loosen the filament securing screws with a screwdriver, remove the burned-out filament and replace it.
  12. Place the Wehnelt cap on the Wehnelt unit base and screw it in by turning it clockwise until the tip of the filament can be seen through the cap opening.
  13. Screw in the cap until the tip of the Wehnelt cap and tip of the filament are the same height. Lock the cap by the Wehnelt cap height adjust ring after turning the cap counterclockwise one full turn. Recheck that the tip of the filament is in the centre of the Wehnelt cap opening. Use a stereo microscope. If the filament tip is off centre, re-centre it with the four filament positioning adjustment screws. Use an Allen key for this and ensure the screws are tight after adjustment.
  14. Mount the Wehnelt unit on the high voltage insulator and secure it by turning the Wehnelt unit securing ring clockwise. There is a pin which engages in a hole on the Wehnelt unit. Rotate to engage.
  15. Check that the gun chamber O-ring and O-ring contact surface is clean and scratch free. Lower the electron gun assembly carefully onto the O-ring. Lint or scratches on the O-ring or O-ring contact surface may cause vacuum deterioration.
  16. Push the PUMP DOWN button on the VACUUM SYSTEM unit. The anode chamber and the column will be evacuated.
  17. Upon completion of evacuation (the meter lamp on the ACCELERATING VOLTAGE unit comes ON). Wait as long as possible, about 30 min, this will avoid any arcing problems and allow the column to be properly evacuated.
  18. Set the LOAD/FILAMENT switch to ON . Check that the LOAD/FILAMENT meter needle deflects while gradually turning the GUN FILAMENT knob clockwise. If the filament is properly mounted, the meter indication will increase as the GUN FILAMENT knob is turned clockwise.
  19. Follow the previous instructions to obtain an electron beam.


  1. Turn the GUN FILAMENT knob to 12 O'clock i.e. turn anticlockwise until the beam current falls to zero.
  2. Turn the Brightness and Contrast knobs located below the screen, fully anticlockwise.
  3. Make sure the Stage illumination is off.
  4. Turn off both computer monitors.
  5. Turn off the room lights.
  6. Lock the door.

For a full machine shutdown i.e. nothing running see the JEOL manual.