top of page

Quantitative Analysis

The purpose behind the quantitative analysis is to put “real” concentration numbers in your map data, rather than the tenuous label of “counts”. What the ToolKit herein does is take a measurement based on a standard and convert the “counts” of an element into some form of concentation. There are many caveats to doing a proper quantitative analysis!

At any particular excitation energy (i.e. the energy that the monochromator is set to) there will be a particular amount of absorption by the sample and the various elements therein. The amount of absorption will determine how much fluorescence will be emitted (as you can not have fluorescence without absorption). This amount of absorption will decrease as slowly as the excitation energy goes farther from an absorption edge. Thus, if you want to measure sulfur fluorescence, you should probably not be trying to make the measurement at 18keV! Additionally, the absorption and resultant yield for the sample will be different at various excitation energies, so a calibration measurement at 8keV will be different than one at 12keV.

Additionally, the air path between the sample and the detector will affect the amount of fluorescence observed. If you change detector distances, the calibration measurements will no longer be valid. For harder fluorescence x-rays, this effect will be smaller, but for the lower or squishy x-ray energies, this can be a very large effect.

Most important is the matrix effects of the sample. If you are making measurements in thin sections of tissue, then it is likely that your sample is not having a large effect. If the tissue is thick, then you may need to worry about how much of the excitation x-rays enter the sample (i.e. the penetration depth) and then, how much of the fluorescence x-rays actually escape the sample. Again, for a near homogeneous biological tissue, this may not be too bad. For a soil/rock sample, this is much more difficult. This issues also stress the importance of having a well defined thickness for your sample if you want to do true quantification. The MicroAnalysis Toolkit assumes that you sample is infinitely thin (for now) and make NO thickness corrections. These will hopefully come at a later date. Thus, this procedure is really only semi-quantitative.

Things to remember

  1. Do a calibration for each excitation energy

  2. Do a calibration for each detector distance

  3. Make careful note of the I0 ion chamber gains (particularly if you change the gains)

  4. What do I think about my matrix

  5. What do I think about the thickness

  6. You know, I bet this is really only semi-quantitative (yes!)

How to do it

Standard measurement can/should be done at the beam line. At SSRL, there is a provision of many elements of interest. Each standard is a thin film support with an element of interest deposited on a Mylar film at approximately 50 micrograms per square cm. The label on the case will have the true concentration. If you have a matrix matched standard, or other standard, measure it! You can still follow the procedure below. Measure a small region of your standard with a map of roughly 30×30 pixels and a similar pixel spacing and dwell times as your data collection.

Calibration Setup

First we need to create a calibration file. This is done by loading a data file of the standard film. Often, there can be edge effects in the measurement, so you want to ensure that the field of view of the element you are looking at looks relatively uniform. You can zoom (control-left click and hold and drag over the area to zoom) or use the edge removal tool by right clicking on the map and selecting “Edge Removal”. The edge removal tool does just that - removes one pixel at the edge of the image. You may even do this multiple times to remove a few bad edges.

Next choose “Analyze - Quantification - Add Data to QuantFile” from the menubar. A dialog will appear asking if you want to do this. Click “yes”. Here you will need to provide a file name. If the QuantFile exists, it will APPEND to the end, NOT OVERWRITE.


Next select the channel (or channels) of data that are present in this standard measurement. A dialog appears with data entry fields to characterize the standard. The “Chan Name” field is the data channel name that was selected. The “Element” field is the element that you wish to quantify. The “Std Formula” is for the chemical formula of the standard. “Std Conc” is the concentration of the FORMULA (not the element).


The Toolkit will make corrections for the elemental abundance in the formula. “Cts/I0” should be filled in for you and is the average counts of the element selected divided by the signal in I0STRM. The quantification process will normalize the data to I0 so you will not have to make this correction later.

If you do not have I0STRM (i.e, all pixels in the channel are 0; this will be true for some older data sets), you should select to divide the signal by the I0 channel instead by going to the Analyze menu, selecting, "Set I0 Channel" and selecting "I0". I0STRM measured the actual flux during the course of the measurement, whereas I0 is constant and thus means you are assuming that the flux does not change during the measurement (this is an ok assumption). 

Also note that if you have data from beamline 14-3, you will need to use either I1STRM or I1 instead of I0STRM or I0.


Lastly there is a dropdown menu to select the gain on the I0 ion chamber during the measurement. This is critical if you change the gains throughout the experiment. If you do not change the gains, then this field is NOT important (but should be set to the same value for all your standards and samples!) Once you are done with entering the information, click “Save” and the data will be added to the QuantFile. Repeat these steps for additional elements of interest, selecting the SAME QuantFile each time.


Load data for a Mn standard, Mn.
Chan Name=Mn
Element = Mn
Std Formula = Mn
Std Conc = 47.1 ug/cm2

Load data for a Zn standard, ZnTe
Chan Name=Zn
Element = Zn
Std Formula = ZnTe
Std Conc = 48.3 ug/cm2

Standard Concentration Table

Foil            ug/cm2

GaP           47.0

Co             45

Se              46.4

Rb             I49

SrF            246.3

LaF            347.6

WO           254

AgHg        42.5

Pb             46.1

GdF          353.7

KCl            98.8

CaF           256.8

Mn            47.1

Fe             56.0

CuS          49.7

ZnTe         45.8

Ti              50.4

Cr             49.0

GaAs        47.3

Ni             50.6

The Final Analysis

Now, after all elements of interest are in the QuantFile, the calibration can be applied to a real data file. Load the data file and then select “Analyze - Quantification - Quantitative Analysis” from the menubar. Select the channels you want to quantify (they need to be ones that you have standardized above). You are presented with the Quantitative Analysis dialog, which asks for similar parameters to those you entered in the first steps. If you have them memorized you can type them all in. Better to go to the “File” menu and select your QuantFile which will fill in all the appropriate entry fields. At this point, if you collected your sample data with different I0 gains than the standards, you would select the new values in the “Samp I0 Gain” drop downs. Clicking on the “Quantify” button will complete the process.

In the end, you will find several new data channels, titled “Xx-conc1” where Xx is the element selected. This channel will be normalized to I0 and now in units of concentration, rather than counts (i.e. micrograms per cm2). You can now progress to do further calculations (with Map Math) to normalize to the beam size, make thickness approximations to get grams per volume, etc. You can always examine the range of you data by selecting “Legend - View Colormap” from the menubar.

NOTE: If you want to make a tricolor plot, you will want to have the RANGE of your data go to at least ~100 or so. Make a better plot. You can multiply your data by an appropriate order of 10 for instance to make concentration in nanograms per cm2 (multiplying by 1000) to accommodate this.


  1. Load a data measurement of a standard, then do and edge correction or zoom to find a uniform region.

  2. Add the information to a QuantFile by choosing a file, followed by entering the composition and concentration information.

  3. Repeat steps above as necessary for additional elements of interest.

  4. Load real data file

  5. Select quantification, choose elements of interest, and load the QuantFile.

  6. Adjust gains if necessary and press “Quantify”

bottom of page