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

 

Documentation pages

General information

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 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. Input of atomic structure models is possible in the CIF file format. The electron diffraction is calculated by the multislice algorithm and resulting in either electron wave functions or STEM images. For HR-TEM images can be calculated from exit-plane wave functions by an additional tool considering the effects of coherent imaging aberrations as well as of partially coherent and incoherent contrast dampening effects.

 

Documentation of individual tools

Documentation files are included either as PDF files for the atomic structure manipulation tools BuildCell and CellMuncher, or as text files for the simulation tools of CELSLC, MSA, and WAVIMG. A documentation of the Dr. Probe graphical user interface (GUI) is given in this website.

Links to individual documentation pages are given in the following table.

Dr. Probe GUI

Graphical user interface program for straightforward STEM image simulation including direct visualization.

BuildCell

Perl script compiled as Windows 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 executable that converts super-cell files and manipulates the atom list in many ways.

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 from electron wave functions.

 


Last update: August 1, 2017

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