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Humboldt-Universität zu Berlin - Mathematisch-Naturwissen­schaft­liche Fakultät - Nanoscale Processes - Time-resolved X-ray scattering

Downloads

Some scientific software we wrote, that you might find useful:

 

1) Trofit - Fitting Anti-Bragg Growth oscillations with the reduced Trofimov rate equations (graphical user interface)

We routinely use this program to fit Anti-Bragg X-ray growth oscillations. The program uses the kinematical approximation, that is a lattice sum approach. It allows one to fit many parameters such as changing lattice constant, phase between substrate and adlayer etc. Here is a very short description with some screenshots: 

readme.pdf 

Here the self extracting archive with all program files and test data for verification of installation and for practising fits:

TroFit 0.7.9.exe 

In case of questions email us. If you find the program useful do Paul Beyer, who wrote the program, a favor and cite his publication: 

P. Beyer, T. Breuer, S. Ndiaye, A. Zykov, A. Viertel, M. Gensler, J. P. Rabe, S. Hecht, G. Witte, S. Kowarik “Commensurability as the determining factor for molecular tilt and multilayer growth: In-situ and real-time growth study of the nanographene HBC on SiO2 and HOPG” ACS Applied Materials & Interfaces, 6, 21484 (2014)

 

 2) ImageJ plugins to simplify data analysis of large area x-ray pixel detectors

Especially when dealing with pixel data from various synchrotron light sources with differing detectors ImageJ has proven to be a powerful tool. To adopt it to our needs we have developed this collection of plugins to simplify our workflow:

- A plugin to import stacks of EDF files (e.g. used by MaxiPix detectors at ESRF) into ImageJ that makes use of metadata in the file header such as motor positions, absorber - and counter values

- A plugin to stitch together images that result from GIXD scans to reciprocal space maps

- A plugin that shifts the xy-position of an region of interest (ROI) as a function of the stack depth z. This plugin can e.g. be used to recover ascan values from a2scan datasets

All plugins and a brief description how to install and use the plugins are included in the following zip file:

hu_berlin_xray_imagej-plugins.zip 


In case of questions email us. If you find the program useful do Linus Pithan, who wrote the plugins, a favor and cite his publication:

L. Pithan, C. Cocchi, H. Zschiesche, C. Weber, A. Zykov, S. Bommel, S. J. Leake, P. Schäfer, C. Draxl, S. Kowarik, “Light control of polymorphism in thin films of Sexithiophene”, Crystal Growth and Design, 15 (3), 1319-1324, (2015).