This DigitalMicrograph plugin makes Multivariate Statistical Analysis of STEM EELS or EDX data cubes. The core of the package is Principal Component Analysis (PCA) that extracts several components with the highest variance from raw data. In this way the dimensionality of data is greatly reduced and  data sets are denoised. For better interpretation,  obtained PCA components can be further rotated in the factor space using Varimax or ICA methods. PCA results can also be casted in end-member spectra. These easy-to-interpret spectra are found by the combination of manual adjustment and Alternating Least-Square (ALS) optimization.  For  datasets with the complicated internal topology the package allows clustering data in the factor space.

Lecture introducing into the MSA stuff delivered in the EELS school in July 2019:
Multivariate Statistical Analysis to denoise EELS spectrum-images

How to use temDM MSA:

basic version
advanced version

temDM MSA 1.96:

NEW: import Velox XEDS spectrum-images (basic version),
NEW: correct GIF quadrants (advanced version).
NEW: automatic truncation of components (advanced version).

get advanced version

Example of simulated EELS datacube:

free download

Example – Mag*I*Cal EELS datacube:

free download

Example – Mag*I*Cal XEDS datacube:

free download

Example – Velox XEDS superalloy:

free download

Example – GaAs XEDS datacube:

free download

Example – synthetic STEM XEDS spectrum-images of a CMOS device:

free download

YouTube tutorials

11 Replies to “temDM MSA”

  1. As some temDM MSA users mentioned, the problem with reading Velox 2.4 arised from the changed format of metadata. The problem is fixed in the temDM MSA 1.93 version.

  2. In the meantime I found out that the “img2str” method was creating the problem (FEI changed the metadata field size in x direction from 1 to 2).

  3. Thank you for your message. The importing tool was tested with the version 2.3 only. It seems (not unexpectedly) that a new version makes changes. To tune the tool I would appreciate getting an examplary dataset. It should not be anything critical but must consist of recognizable pattern like C-grid. In case, someone dont mind to share it, please contact through pavel@temdm.com.

  4. It seems that your test data contains only one entry in the “SpectrumStream” branch, whereas in my file there are 4 (“counts”, “net counts”, “wt%” and “at%”, I guess, as it is in the Velox software version 2.4). Not all of them contain data, especially if you haven’t conducted any quantification. The result is that the Graz script is complaining about empty labels in TagGroups. I checked the path names and their names seem unchanged. I think the 4 sub paths create some kind of ambiguity, so that your script does not know which one (“counts”, “net counts”, “wt%” and “at%”) to import.

  5. Indeed, FEI changes their format too often. If this is the only change of path, temDM MSA can acommodate for that:
    Go to DigitalMicrograph Global Info/Global Tags/_temDM-Scripts/MSA/Velox and find there the editable standard pathes.Those should be compared with the actual pathes in your Velox version. The meaning of all pathes is explained in the text of “Read EDX Velox Spectrum-image” script free downloadable at https://www.felmi-zfe.at/dm-script/dm-script-database.
    Alternatively, you might send me your (not-confidential) Velox data and I will try to figure out what goes wrong.

  6. Velox import does work for the test data being provided, however, it doeas not for new acquired data. The script just shows the TagEditor and states “failed or stopped” in the import dialog. Maybe FEI changed the Velox format a bit in the meantime (I use Velox v. 2.4) so that the script is not able to find the correct data location within the Velox file anymore.

  7. temDM MSA tries to remember all your last applied settings. It can happen that your tool window was set at the crazy position last time. A universal solution for such problems: open a new script window and type there MSA112_delete(). Execute the script. All temDM MSA tags will be deleted and the next time the program will start from the default settings.

  8. When I load the Import tool from temdm msa menu it does not appear. Whats wrong?

  9. Barney, you are 100% right. This EELS set was not good because 1) sample was thick 2) some Tridiem and Quantum GIFs degrade at the end of their energy range due to the shifted cross-over (I didnot optimize crossover, it was not my instrument). I need this set just as an example that the slight signal can be enhanced by PCA. Pavel.

  10. Hi Pavel. Your MagiCAL EELS data is of bad quality, The sample should consist of about 80% Si but the Si K edge is almost not seen!

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