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Treat Line Scan

Category: Data Processing and Evaluation – Spectra
Description: Script extracts chemical profiles from the EELS/EDX spectroscopic line scan of the common DM format (energy along X, spatial coordinate along Y). The spectra collected by TIA (ser files) can be also imported. Up to 5 profiles can be extracted at once and plotted together. The EELS background is extrapolated by power-low from the edge-preceeding window. THe EDX background is modeled as linear interpolation between two windows surrounding the line. THe position of an EELS edge is found automatically if deviates insignificantly from the tabulated value. THe width and positions of all windows can be tuned live. THe tuned settings can be stored in the text file and opened later. Step-By-Step Guide. -1- Open the DM file with the spectroscopic line scan (energy along X-axis, spatial coordinates along Y-axis). Alternatively TIA.ser file can by imported by clicking "Import TIA.ser". The appropriate ser file with _1 or _2 ending should be chosen (depending on TIA setting these endings might imply EELS or EDX spectra). -2- Choose which element you would like to extract. Up to 5 elements can be extracted at once. That is called ShortList. Note that there are two separate lists: for EELS and EDX. If the desired element is not in the short list, type it in the ElementField in the format "Element+Space+Series" and click "?" button. The element setting will be loaded from the FullList. The FullList embedded in the script can be printed out in the results window by clicking full list "print". IN CASE YOU FIND THE POSITION OF SOME ELEMENTs IN THE FULL LIST ARE FAR FROM THE OPTIMAL ONES PLEASE INFORM ME! I WISH TO OPTIMIZE IT WITH TIME USING YOUR HELP. -3- Check box for every element which you would like to analyse. Click "->" button for each element to see the appearence of all energy windows (THe data file should be frontmost). THe script would automatically find the spectrum where this element appears to be most intensive. You may tune the positions of all windows manually by keys. The displayed spectra can be also scrolled. To learn the assignment of keys click "keys" button. Note that it is slighly different for EELS and EDX. When satisfied, click "space". If completely out of range, click ESC and analyse the spectrum. -4- The setting for each element is displayed in 6 fields . THe 1st and 2nd fields are position and width of the signal window. The 3rd and 4th fields are position and width of the background window. The 5th field is special. For EELS this shows the distance between the edge onset and maximal derivative of the peak. It is used for automatic detection of the edge position. For EDX the 5th field introduce the assymetry in the location of the left and right background windows. It shows how much the right window is further from the signal than the left window. I recommend to change the 5th field only when strongly neccesary! THe 6th field shows the shift between the found edge/line position and the tabulated one. -5- If you notice the systematic energy shift in all EELS edge positions, it means that your zero-energy is shifted. Click "recal" button and the data will be recalibrated. It is a good idea to store the original data file before. For EDX this option is seldom used. -6- You may save the tuned shortList in the text file by clicking "save". It can be later loaded by "open". -7- Click "extract" button. The script would suggest you to look at all elements which were not already checked. Then the profiles will be extracted and plotted in one display. -8- You might select some region by ROI tool and normilise all profiles such that they count to 100% in this region. This is convenient for combining different profiles in one display. Note that the script is not doing quantification. Instead, all profiles are scaled rather approximatelly. -9- You may merge several profile displays, for instance EELS and EDX profiles by putting these displays to frontmost and secondfront and clicking "...+..." button. THis way you can place an arbitrary number of profiles in one display. Please normalise the profiles to 100% before. Otherwise they might appear of completely different scales! -10- Enjoy the resulted chemical profiles! By clicking "->file" you might print it into the two-collumn text file to treat in other programs.
Acknowledgements: Bernhard Schaffer and Vincent Hou gave a couple of brilliant ideas for this script. As a subroutine, this script incorporates the TIA import script written by Ray Twesten.
Script version: 1.0
DM/GMS version: 3.9.2
Script written as a function: No
Source: Show code
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