Instructions for Use of the Scanning Electron Microscope (SEM)

Collecting and Saving Quantitative Mineral Chemistry with EDAX-Genesis

For quantitative mineral chemistry, we use the LEO controls (left side) to set SEM conditions, save images, and select spots. We use the EDAX controls (right side) to collect and save the chemistry.


  • Center beam and saturate filament as necessary
  • Obtain focused BSE image at 20kv and WD ~20mm
  • Print BSE image
  • Adjust spot size to obtain 1000-2500CPS on EDAX.
  • In spot mode, put spot on point desired for analysis, and mark spot # on printout.


  • Clear spectra window and collect new spectra for 120 live seconds
  • Expand Peak ID and add the following elements: Si Al K Ca Na Mg Fe Mn Ti Cr (see Standards step if using standards)
  • Minimize Peak ID
  • You'll want to use a standard if you have a sample that's similar in composition to one of the available standards (rhyolitic glass, 2 garnets, biotite, and wollastonite).
    • Open standard file (File > Open > C:\EDS\USR\(filename). Select file type Quant Method File, .qzf).
    • Your Peak ID list must match the standard element list. Edit the Peak ID list if it doesn't already match. You may need to reopen the standard .qzf file.
  • Option: In LEO hit scroll lock to stop beam in order to minimize sample damage.
  • Save Spectra in Sequence
    • File > Save in Sequence
    • Check 'Save in Sequence'
    • Filename > My Documents (and sub folder if desired) > Use sample # (and possibly mineral name) as file name
    • Highlight A: and name if desired (e.g. mineral or sample #)
    • Click the double floppy disk icon to save in sequence
  • Quantification
    • Expand Quant panel
    • Click ZAF: confirm all desired elements are selected (O should not be selected)
    • Results: Should read % Conc
    • Check 'Multiple'
    • To right of Q button, right click Type - Check 'Oxy by Diff'
    • Click Type (raised button below ZAF) - Check 'O in Chem. Formula', enter # O appropriate for mineral analyses (see Deer, Howie and Zussman, 1992) for appropriate number of O for given mineral.
    • Click Quant; in Quantification Results select Page Set Up: Under Quantification as a minimum Multiple results, at% and wt% should be selected. Preferable to select all.
    • You will have first displayed "Chem" the formula units (# ions on the basis of given #O as determined by Oxy by Diff)
    • To right of Q button, right click Type - Check 'Oxides'
    • Reclick Quant/show: You will now display the wt% by element oxide (e.g. SiO2) in addition to the previously displayed chem. (e.g. Si)
  • LEO: Move spot to next point and repeat
  • When finished with analyses hit save (in Quant panel). Save to My Documents. The name of the file should include the sample #.
  • The saved file is a .csv and may be opened in Excel. In Excel, reformat the data into a table that displays the elements in a row, and the wt % elements in a column, under this column should be the formula units (chem.).