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


 

icon alert  News

2017-05-23: Minor update of the Dr. Probe GUI to Version 1.7.9.
- Added debug output options and invalid hardware IDs.

2017-03-08: Minor update: Dr. Probe GUI (v1.7.8), CELSLC (v0.55b), MSA (v0.73b)
- Slice files may now contain projected potentials instead of phase gratings. This allows MSA to apply absorption and universal Debye-Waller factors without expensive calculation of the structure factor.

2017-02-16: Minor update: Dr. Probe GUI (v1.7.7)
- Changed how the registration dialogs act on trial licenses. This should be less annoying now.

2016-12-15: Minor update: Dr. Probe GUI (v1.7.6) and CELSLC (v0.54b).
- Corrected the documentation concerning the input of the projection orientation. The orientation must be specified as a real-space lattice vector [uvw].

 

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 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 multislice calculations. The actual scattering calculations are done by an implementation of the multislice algorithm and generate either electron wave function output or STEM images. For HR-TEM image simulations another tool is provided to calculate the image intensity distribution from a given electron wave function 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.

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.

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.

 

Example calculations

 

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.

[Download Dr. Probe]

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.

For fun reading, see here the Dr. Probe registration statistics.

 

Development

This software package has been developed by Juri Barthel and Lothar Houben.

Current version:

Program

Version

Dr. Probe GUI

1.7.9

BuildCell

1.1

CellMuncher

2.4

CELSLC

0.55b

MSA

0.73b

WAVIMG

0.63b

J. Barthel wants to acknowledge funding by the German Research Foundation (DFG) within the core facilities initiative, grant number MA 1280/40-1.

 

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. [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 13 (2014) 1044-1049. [doi]
  8. S.G. Wolf, L. Houben, M. Elbaum, "Cryo-scanning transmission electron tomography of vitrified cells", Nature Methods 11 (2014) 423-428. [doi]
  9. I. MacLaren et al., "On the origin of differential phase contrast at a locally charged and globally charge-compensated domain boundary in a polar-ordered material", Ultramicroscopy 154 (2015) 57-63. [doi]
  10. H. Du et al., "Atomic Structure of Antiphase Nanodomains in Fe-Doped SrTiO3 Films", Adv. Funct. Mater. 25 (2015) 6369-6373. [doi]
  11. A. Stoffers et al., "Complex Nanotwin Substructure of an Asymmetric Σ9 Tilt Grain Boundary in a Silicon Polycrystal", Phys. Rev. Lett. 115 (2015) 235502. [doi]
  12. J.M. Salih et al., "Maghemite-like regions at the crossing of two antiphase boundaries in doped BiFeO3", Mat. Sci. Tech. 32 (2016) 242-247. [doi]
  13. L.S. Panchakarla et al., "Strontium cobalt oxide misfit nanotubes", Chem. Mat. 28 (2016) 9150-9157. [doi]
  14. L. Jin et al., "Surface reconstructions and related local properties of a BiFeO3 thin films", Sci. Rep. 7 (2017) 39698. [doi]
  15. S. Borghardt et al., "Quantitative Agreement between Electron-Optical Phase Images of WSe2 and Simulations Based on Electrostatic Potentials that Include Bonding Effects", Phys. Rev. Lett. 118 (2017) 086101. [doi]
  16. H. Du et al., "Nanosized Conducting Filaments Formed by Atomic-Scale Defects in Redox-Based Resistive Switching Memories", Chem. Mater. 29 (2017) 3164-3173. [doi]
  17. F. Winkler et al., "Quantitative measurement of mean inner potential and specimen thickness from high-resolution off-axis electron holograms of ultra-thin layered WSe2", Ultramicroscopy 176 (2017) 99-107. [doi]
  18. L. Jin et al., "Atomic resolution imaging of YAlO3:Ce in the chromatic and spherical aberration corrected PICO electron microscope", Ultramicroscopy 178 (2017) 38-47. [doi]

 

Link summary

 

Google+

Last update: May 23, 2017
Contact by email:
mailto:ju.barthel-at-fz-juelich.de