Start-up/Shut-down Operating Instructions for Sirion SEM


Always adjust your specimen height before closing the chamber door to make sure your specimen will not hit the bottom of the lens; see instructions.

Do not change z after that.

Do not tilt your sample more than ±3º without explicit permission or authorization from the Lab Managers/trainers.

Do not put magnetic samples into the microscope without the same explicit authorization.

Failure to follow these warnings could result in serious damage to the lower lens with a $70,000 replacement cost

The SEM is normally left with the vacuum system ON, the field emission gun (FEG) ON, the high voltage or tension (HT) hardware button ON, but the kV OFF in the software: on hardware panel under scope: "stby", "off", "HT", "vac" buttons are all lit. (It is standard for FEI/Philips microscopes fo rthe "off" button to be lit when the scope is on.)


  1. Log into CORAL and enable the SEM.
  2. Turn monitor on, check "Vac OK" message on screen.
  3. Choose CCD in "Detectors" menu.
  4. Load sample:  in RH vacuum window choose "vent", then venting "OK".  Venting takes about 2 minutes until the front door of the microscope can be opened.
  5. When inserting sample: 
    1. wear gloves
    2. adjust sample height to 5 mm from lens using only the manual knob – clockwise to raise (use eucentric height adjuster or "elephant")
    3. remove elephant from chamber!
    4. turn on "videoscope" by clicking icon on upper left of screen.
    5. close chamber door slowly and carefully partway while watching CCD camera - make sure the highest point on the sample mount is aligned along or a little below the upper dotted line on the screen.
    6. continue to monitor CCD image while closing chamber door completely
    7. do not change z anymore - not with manual control, nor with computer control.
  6. While leaning on the door, click on "pump" command in RH vacuum window.  Wait a couple seconds and then check that the door is sealed by tugging firmly.  Wait until "Vac OK" message appears directly under "pump" command, about 2 min. The chamber should be at or below 1.2E-4 mbar.
  7. Click on "kV" command in RH Beam window to turn on high voltage. 
    IMPORTANT:  "Microscope Confirm focus" pop-up window opens on image screen - do not click "OK" on this window until you obtain an image and focus as instructed (see following).  This tells the computer how far your sample is from the lens.
  8. Choose SE detector in "Detectors" menu.  Choose TV scan rate.  Focus.  Go to 5000X and focus again.  The working distance "WD" at bottom of screen will now read the true distance from the sample to the bottom of the lens.  Click "OK" on pop-up window to calibrate z to WD. 

    If you do not see an image click "ACB" (automatic contrast and brightness).  Aslo check that the beam blanker ("eclipse button") is not active. If still no image, go to lowest mag. At this point you should see something you can focus on.  Only after performing a rough focus, translate to an appropriate feature that you can adjust your focus at 5000x.  Translate using "get", "shift" or "stage track" icons and mouse.  Focus and calibrate z as in previous paragraph.
  9. Proceed with your sample.  Typical imaging parameters are 5 kV, spot size 3, and working distance 5 mm. 
  10. To obtain a good image you must stigmate and focus the image well.  If the image moves noticeably when changing focus, then the lens alignment should also be performed (see a trainer if you don't know what this means).



  1. If in UHR or EDX mode, return to HR mode.
  2. Zero the x and y translates as well as the tilt.
  3. Clear the stage position table, databar legend, and reset anything else you may have changed back to default.
  4. Turn off high voltage by clicking on "kV" command in RH Beam window.
  5. Choose "CCD" detector.
  6. Vent chamber and remove your sample.
  7. Pump chamber down again; make sure you obtain "vac OK" status before leaving.
  8. Straighten up the sample preparation area.
  9. Log out of CORAL.


EDAX Set-Up:

Note:  The specimen interaction volume producing an EDAX spectrum is much larger than the electron beam spot size.  It is on the order of one micron in width and depth, and varies with atomic number and beam energy (kV).

1) Change voltage to 10-15kV.  You can use any voltage, but you won’t get x-ray peaks at energies higher than about two-thirds of the beam energy.  A good x-ray spectrum range is 0-10kV, so use accelerating voltage of 15kV to achieve that range.

2) Open EDAX Genesis software on EDAX computer.

3) Under magn menu choose EDX or UHR mode.

4) Under scan menu choose “spot”.  Position crosshairs by click-and-drag, or by clicking on the area of interest.  You may also use the large or small windows and collect x-rays from the entire scanned area.

5) Press “collect” on RHS of EDAX screen.  Pressing “collect” again stops the collection, and “clear” clears it.

6) Use “Peak ID” to identify peaks.  You may also expand the window (click on up/down arrows in bottom right corner of the window) and enter possible elements in the “Element:” box, and click “add”.

Notes on peak identification:

a)  “Peak ID” tends to pop up an excessive list of elements.  Take this with a grain of salt.  How many of you are actually looking at something that might contain polomium or thulium?  Check if 1) the marker is on something that may be in the noise level and 2) if it is overlapping with a more likely element and 3) if other peaks expected for that element are present. 

b) I find it more useful to enter the expected elements, and then identify remaining peaks using Z-/Z+ to scan up and down the spectrum, or by simply guessing.

c) All the peaks for a given element in a given energy range should be present, and in the relative amounts indicated by the element markers on the spectrum that show up when you click “add”, or click on the element in the list.  For example, if you are using 15kV electrons to identify copper, you should see the CuKa and much smaller Kb at 8.04 and 8.9 keV respectively, and the overlapping CuLa and Lb at about 0.93 keV.  If you only see one or two of these three peaks, it’s not copper. 

d) The exception to this is that the very low energy peaks are more easily absorbed by their surroundings, and therefore more likely to be suppressed if the sample geometry somehow blocks a direct line of sight to the detector.