Dr. Probe - High-resolution (S)TEM image simulation software

 

 

Screenshot: Dr. Probe - STEM simulation graphical user interface.

[Screenshot: Dr. Probe - STEM simulation graphical user interface.]

 

The Dr. Probe software is a tool package for multi-slice image simulations in high-resolution scanning and imaging transmission electron microscopy. It comprises a graphical user interface version for direct visualization of STEM image calculations, as well as a bundle of command-line modules for more comprehensive calculation tasks. While the graphical user-interface version is primarily designed to make quick simulation setups with intuitive parameter input and to check meaningful setups for experiment or intensive calculations, the command-line version modules allow you to script calculations with parameter variations for time-consuming image calculations. The programs have been written using Visual C++, Fortran 90 and Perl, and are available as executable binaries for Microsoft Windows 32-bit and 64-bit operating systems. For intensive calculations of HAADF STEM images, a 64-bit system with 8 GB working memory is recommended.

The image calculations consider the elastic scattering of the primary electrons using either the frozen lattice approximation for high-angle scattering or Debye-Waller factors for bright-field calculations to include the effects of thermal vibrations. A time-efficient approach is implemented for the averaging over variations of frozen lattice configurations with no further approximation.

The calculations require structure information data in form of simple text files, which specify atom coordinates and thermal vibration parameters. The Dr. Probe package contains tools to generate and manipulate such files. These tools allow you also to create complex structure models from scratch or from more commonly used formats like CIF. Another tool is provided to generate the phase grating data for multi-slice calculations. The actual scattering calculations are done by an implementation of the multislice algorithm and generate either electron wavefunction output or STEM images. For HR-TEM image simulations another tool is provided to calculate the image intensity distribution from a given electron wavefunction including the effects of coherent imaging aberrations as well as of partially coherent and incoherent contrast dampening effects.

 

Content of the software package

Dr. Probe GUI

Graphical user interface program for straightforward STEM image simulation including direct visualization. Example simulations of STEM images and simulations of the electron probe propagation using the graphical user interface are documented on this website.

BuildCell

Perl script compiled as Windows 32-bit executable that converts and creates super-cell files (CEL) from crystallographic data for later image simulations with Dr. Probe.

CellMuncher

Perl script compiled as Windows 32-bit executable that converts super-cell files and that manipulates the atom list in many ways. It uses an internal list representation. Super-cell data can be supplied in two different formats used by popular electron microscopy image simulation packages, namely MacTempas and EMS . The same formats are supported for export, besides CIF and VRML format and formats for the structure-viewer programs VESTA, CrystalMaker and JSV.
An example procedure for the creation of atomic structure data using BuildCell and CellMuncher is documented on this website.

CELSLC

Command-line tool that calculates phase gratings for multislice calculations from slices of a super-cell structure for TEM in imaging or scanning mode.

MSA

Command-line tool with an implementation of the multislice algorithm for the calculation of STEM images and electron wave functions for a given atomic structure model.

WAVIMG

Command-line tool that calculates high-resolution TEM images for a given electron wavefunction.

Documentation

Documentation files are included either as PDF files for BuildCell and CellMuncher, or as text files for the usage of CELSLC, MSA, and WAVIMG. The documentation for the Dr. Probe GUI version is located on this web page.

 

Availability of the Dr. Probe software

The Dr. Probe software package is distributed freely via download in form of an installer or a ZIP archive. The installation procedure is simple and can be performed by following the download and installation instructions available on this website. Using the Dr. Probe STEM simulation graphical user interface requires a registration of the installation. The registration is free of charge.

The Dr. Probe software package is updated regularly. A mailing list exists which notifies on new updates and provdies download links to people interested in using the software.

The freeware program Dr. Probe Light is focused on the simulation of STEM probes and ronchigrams and is designed as a training tool for students as well as experts who want to learn the basic and high-level aspects of probe aberration tuning.

 

Development

This software package has been developed by Juri Bartheland Lothar Houben.

Current version:

Program

Version

Dr. Probe GUI

1.5.2

BuildCell

1.0

CellMuncher

1.5

CELSLC

0.34b

MSA

0.62b

WAVIMG

0.57b

 

Publications with contributions by Dr. Probe simulations

  1. M. Bar-Sadan, et al., "Direct Imaging of Single Au Atoms in GaAs Nanowires", Nano Lett. 12 (2012) 2352-2356. [doi]
  2. J. Barthel, "Time-efficient frozen phonon multislice calculations for image simulations in high-resolution STEM", Proc. of the 15th Euro. Microsc. Cong. (2012). [weblink]
  3. C.L. Jia, et al., "Atomic-Scale Measurement of Structure and Chemistry of a Single-Unit-Cell Layer of LaAlO3 Embedded in SrTiO3", Microscopy and Microanalysis 19 (2013) 310-318. [doi]
  4. D.G. Stroppa, et al., "Assessment of a nanocrystal 3-D morphology by the analysis of single HAADF-HRSTEM images", Nanoscale Research Letters 8 (2013) 475. [doi]
  5. M. Heidelmann, et al., "Periodic Cation Segregation in Cs0.44[Nb2.54W2.46O14] Quantified by High-Resolution Scanning Transmission Electron Microscopy", Microscopy and Microanalysis 20 (2014) 1453-1462, [weblink] [doi]
  6. D.G. Stroppa, et al., "Analysis of Dopant Atom Distribution and Quantification of Oxygen Vacancies on Individual Gd-Doped CeO2 Nanocrystals", Chemistry - A European Journal 22 (2014) 6288-6293. [doi]
  7. C.L. Jia, et al., "Determination of the 3D shape of a nanoscale crystal with atomic resolution from a single image", Nature Materials (2014) 4087, in press. [weblink] [doi]

 

Link summary

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Last update: Oct 31 2014
Contact by email:
mailto:ju.barthel-at-fz-juelich.de