Applications for EPMA

[Probeman]

This topic's purpose is to list and generally discuss free applications that might be useful for EPMA. For detailed discussions of specific applications and their actual usage, please utilize the existing topic for that application (or create a new topic for that application if it does not yet exist).

CalcZAF and Standard Description:
CalcZAF is an off-line EPMA calculation utility for both teaching and research. CalcZAF allows for modeling of intensities from composition and composition from intensities (matrix corrections). CalcZAF includes X-ray and electron range modeling, support for thin film and particle quantitative analysis. It also calculates detection limits for given conditions or conditions for given detection limit. CalcZAF provides 10 different matrix correction models and 6 different mass absorption coefficient tables for rigorous evaluation of accuracy, in addition to compositional searching and matching from multiple standard composition databases. Also calculates any combination of elemental, oxide, element by specification, difference, relative to stoichiometric oxygen or any element, formula, atomic percent, mineral end-member values. CalcZAF also comes with a full featured standard database utility (Standard) that is automatically installed with the PENEPMA 2012 Monte Carlo modeling software to allow advanced modeling with an easy to use GUI for spectrum simulation and secondary fluorescence phase boundary modeling using Penfluor/Fanal (see below for descriptions of Penepma and Penfluor/Fanal). CalcZAF and Standard runs under the Windows OS (or under Parallels on the Mac)

CalcZAF and Standard Download:
http://www.probesoftware.com/download/CalcZAF.msi

CalcZAF and Standard Topic:
http://probesoftware.com/smf/index.php?board=7.0


DTSA II (NISTMonte) Description:
NIST DTSA-II is a freely available software for quantitative energy dispersive x-ray spectroscopy.  DTSA-II has been available for almost a decade and is currently in use all over the world for quantifying x-ray spectra, simulating x-ray spectra and designing better measurements.  Unlike commercial products, you can see inside the black box to better understand how the algorithms work or, if need be, make your own customizations. DTSA-II is Java based on runs on all computer platforms that support Java.

DTSA II (NISTMonte) Download:
http://www.cstl.nist.gov/div837/837.02/epq/dtsa2/index.html

DTSA II (NISTMonte) Topic:
http://probesoftware.com/smf/index.php?board=32.0


Casino2 Description:
Casino is a freeware program for quickly calculating and displaying electron-solid interactions for a variety of beam conditions and sample geometries. It was developed at the University of Sherbrooke, Quebec and McGill University, Canada by Raynald Gauvin, Hendrix Demers and Philippe Pinard. Casino runs under Windows on PCs.

Casino2 Download:
http://www.probesoftware.com/download/CASINO_v2.4.8.1.zip


Penelope/Penepma (2012):
PENEPMA performs simulations of X-ray emission from samples bombarded with electron beams. It is both based on the general-purpose Monte Carlo simulation package PENELOPE, an elaborate system for the simulation of coupled electron-photon transport in arbitrary materials, and on the geometry subroutine package PENGEOM, which tracks particles through complex material structures defined by quadric surfaces. Penepma calculates the complete generated, emitted and backscatter spectra for a given composition at given conditions. For ease of use one should utilize one of the various GUIs such as pyPenelope or Standard (CalcZAF) which includes the Penepma distribution. Penepma is a FORTRAN code that requires compiling under GNU FORTRAN for the specific platform.

Penfluor/Fanal Description:
Penfluor/Fanal a semi-analytical method for the fast calculation of secondary fluorescence in electron probe microanalysis of material couples (phase boundaries). The calculation includes contributions from primary K-, L- and M-shell characteristic x-rays and bremsstrahlung photons. The required physical interaction parameters (subshell partial cross sections, attenuation coefficients, etc) are extracted from the database of the Monte Carlo simulation code system PENELOPE. The calculation makes use of the intensities of primary photons released in interactions of beam electrons and secondary electrons. Since these intensities are not readily available and do not allow analytical calculation, they are generated from short Monte Carlo simulation runs. For ease of use one should utilize the GUI in Standard (CalcZAF) which includes the Penfluor/Fanal distribution. Penfluor/Fanal is a FORTRAN code that requires compiling under GNU FORTRAN for the specific computer platform.


Win X-Ray Description:
Win X-Ray is a Monte Carlo simulation of electron trajectory in solids. The important features in Win X-Ray are: the complete simulation of the x-ray spectrum, the charging effect for insulating specimen. Win X-Ray runs under the Windows platform.

Win X-Ray Download:
http://montecarlomodeling.mcgill.ca/download/winxray-1.4.2.zip

MC X-Ray Description:
MC X-Ray is a new Monte Carlo program that is an extension of the Monte Carlo programs Casino and Win X-Ray since it computes the complete x-ray spectra from the simulation of electron scattering in solids of various types of geometries. MC X-Ray runs under the Windows platform.

MC X-Ray Download:
http://montecarlomodeling.mcgill.ca/download/MCXRayLite_v1.7.0.0.zip


GMRFilm Description:
GMRFILM is a research grade, shareware DOS program for thin film analysis (created by Richard Waldo of General Motors Research Labs). It can be used to estimate film thicknesses using the experimentally determined K-ratios, or to calculate compositions given known thickness and K-ratios.
Thin films are increasingly important in the EPMA lab, e.g. as specific research objects (creating thin film superconductors), AND because many samples have either intentional (conductive) thin films laid down on them, or accidental ones (e.g. oxide coat). It runs on an IBM compatible PC, in a DOS window (command prompt). See http://www.geology.wisc.edu/~johnf/g777/Ex-ThinFilm.pdf for more details.

GMRFilm Download:
ftp://ftp.geology.wisc.edu/johnf/g777/software/PC/WaldoZip.zip

[Ben Buse]

Hi,

A speculative question

Is there a monte carlo package from which you can identify the body from which the x-rays are generated from. I.e. it tells me the amount of Fe x-rays generated and emitted from the inclusion, and the amount of Fe x-rays generated and emitted from the surrounding substrate. A bit like GMRFilm which divides it up into film and substrate. I realise for monte carlo for film its easy from phi-rho-z curve.

Thanks

Ben

[Probeman]

Hi,

A speculative question

Is there a monte carlo package from which you can identify the body from which the x-rays are generated from. I.e. it tells me the amount of Fe x-rays generated and emitted from the inclusion, and the amount of Fe x-rays generated and emitted from the surrounding substrate. A bit like GMRFilm which divides it up into film and substrate. I realise for monte carlo for film its easy from phi-rho-z curve.

Thanks

Ben

Hi Ben,
I thought that is what Penepma is used for?  That it can track photon emissions from each material defined in the .geo file?   I thought that was how it was able to calculate secondary fluorescence effects from one material to another?

I have to admit though, I've never tried to find that information in the output files.  Maybe it's just not output by default.  Have you asked Xavier?

[Philippe Pinard]

Ben,

I don't think there is a out-of-the-box solution.

PENEPMA returns an average dose per "body" but not X-ray intensities per body. It wouldn't be too difficult to modify the code for a one-off geometry. You can add a if-statement after CALL LOCATE and use the global variable IBODY to know in which body the electron is located.

The same can also be done in DTSA2/NISTMonte. In the actionPerformed method of CharacteristicXRayGeneration3 class, you can add another if-statement to check the current region.

I hope this helps...
Philippe

[Ben Buse]

Has anyone tried ScatterJn plugin for ImageJ or Fiji?

Just stumbled across it.

https://openresearchsoftware.metajnl.com/articles/10.5334/jors.89/