An elemental mapping can be obtained using the 'HYPERMAP' option in the edx application of the SEM. After the application has completed acquiring enough counts to quantify elements, the spectrum could be calculated using manually selecting a specific region using the option highlighted in the red box below. All the options mentioned below can be seen in the bottom right corner of the edx application.
Selecting the option in the red box, allows you to select the region of the captured image to obtain the spectrum from. In general, the whole image is selected to scan for the spectrum.
The option boxed below automatically calculates the 'Maximum Pixel Spectrum' that is the spectrum of the full image with the element of the highest peaked counts. Such an option is beneficial when we calculate the spectrum of a sample with a specific primary element.
After the spectrum has been successfully calculated using either method, click on the 'spectrum' tab to view the spectrum. Then click on the periodic table icon which will display a periodic table of elements. The 'Auto' button on the bottom right corner of the periodic table will display the elements that are present in the spectrum. Manually selecting the spectrum will show you a series of elements that might or might not be present; Check the peaks of the elements by zooming into the spectrum and thereby determine the presence of the element in the sample. Using the 'Maximum Pixel Spectrum', the 'Auto' button will only show one element in the spectrum that is primarily present. Aditional elements can be selected according to peak heights. It is important to press 'Auto' before quantifying data.
The name of the spectrum could be changed for convenience, by double-clicking the name below the spectrum, as shown in the image below;
Prior to saving the spectrum data, the spectrum should be quantified using the 'quantify' button shown below;
Once the spectrum is quantified, the arrow button to the right side of the tabs, shown below, gives you the option to save the raw spectrum data.
Clicking the 'Save' button prompts a dialog to choose a location and filename to save the raw spectrum data. It also provides the option to save the spectrum in three different data formats, that is .xls, .txt and .spx as shown below. The format '.spx' is the data file accepted by the edx application 'Espirit 1.9'. The format '.xls' is the excel data file with the spectrum data that is accepted by the MATLAB code. It is recommended to save the data using both .spx and .xls formats.
Once the excel file has been created through the edx application 'espirit', simply open the '*.xls' excel data file to make sure the file is not corrupt. Almost every time, the data file is corrupt and you will be prompted to recover data as shown below. Click 'yes' and no data will be altered.
Click 'Ok' to the message followed by clicking 'yes' to recover data in the previous message. The excel data file with the spectrum data can be seen after.
Even though no changes were made to the data file, SAVE the file with the "recovered" data so that MATLAB can read the spectrum data without any complications. The MATLAB code for the SEM spectrum and the excel X-ray Characteristic line data file can be found in the google drive link provided below (Log-in using your Siena email);
https://drive.google.com/drive/folders/0B2ACmmug9K_UY2h1ejJNZVdsU0k?usp=sharing
