Software and Program Examples for EM-related Simulations
- Practical Electron Microscopy and Database -
- An Online Book -  




Table 3669a. Software Examples for Some EM-related Simulations.

FTSR scripts
Electron image series reconstruction for TEM images
TEM, STEM and SEM imaging and analysis, and EELS, EFTEM and EDS processing and analysis
Java based electron microscopy simulation program, for the multislice simulations
Calculation of penetration depth and vacancy density in FIB milling and ion implantation
E. J. Kirkland, "Advanced Computing in Electron Microscopy", Plenum, New York, 1998
This book contains a CD of software and source code. Multiple scattering calculations for STEM and TEM images, including phonon scattering.
Electron Microdiffraction. Spence and Zuo, 1992

Contains well-documented Fortran listings for programs to simulate CBED patterns by Block Wave method, and multislice. Indexed patterns shown with HOLZ to speed indexing.

A general microscopy analysis and simulation package for OSX (written by former NCEM staffer Roar Kilaas). Can perform exit wave reconstruction, symmetry analysis, peak position measurements, geometric phase analysis and many more analysis methods.
A general TEM image processing software provided by Gatan Inc. Various plugins available, including geometric phase analysis (GPA) for measuring strain in micrographs.

Analysis software for STEM data provided by FEI.

IDL 3D Tomographic Reconstruction
A 3D reconstruction algorithm and GUI developed by Peter.
MATLAB Focal Series Reconstruction
Code for reconstructing HRTEM exit wave phase with high accuracy, written by Colin.
A free software package for X-ray spectrum (e.g. EDS) manipulation/simulation. Authors: Chuck Fiori, Carol Swyt-Thomas, and Bob Myklebust. Platform: Mac classic. Citation: C.E. Fiori C.R. Swyt and R.L. Myklebust, NIST/NIH Desk Top Spectrum Analyzer, public domain software available from the National Institute of Standards and Technology Gaithersburg, MD. (Link), 1992.
Gatan EELS Advisor
A commercialized plug-in package for EELS spectrum simulation in Gatan DigitalMicrograph. Commercialized package. Platform: Windows. Citation: N.K. Menon and O.L. Krivanek, "Synthesis of Electron Energy Loss Spectra for the Quantification of Detection Limits", Microsc. Microanal. 8 (2002) 203-215. Link.
Simulation of Z contrast in STEM image and quantitative analysis of alloying in real space with atomic resolution (Link) [2]

Calculating band structure and transport properties

Atomic models for STEM simulations [5]
Measure the shift of HOLZ lines to quantitatively evaluate strains in a crystal.
GPA plug-in for DigitalMicrograph

Generates fully quantitative deformation and strain maps from standard HREM images (Link: Commercial) [2]

Argonne National Lab software library for EM Free programs for everything you need related to TEM and SEM.
Stripe Removal
Simulation of parasitic stripes (streaks) in electron diffraction pattern [6]


Table 3669b. Software for electron diffraction Simulations.


Macintosh program helps index diffraction patterns, find excitation errors and structure factors, draw crystal structures, K-lines, stereograms, CBED geometry, etc. Contact:

MATLAB Multislice Simulations
Custom software routines for simulating images and diffraction patterns in TEM and STEM using a large number of scripts developed by Colin. Methods are given in Earl Kirkland’s textbook “Advanced Computing in Electron Microscopy,” second edition. Can be used to simulate virtually any scale of problem and vary any structural, chemical or optical parameter.

Table 3669c. Other lab-made Software for EMs.

Function Examples
Calculations of rocking-curve intensity oscillations within CBED using dynamical electron diffraction approach (two-beam approximation) [1]
Dynamic Monte-Carlo program TRIM-DYN
Simulation of gallium implantation in FIB milling [3, 4]

Table 3669d. Other Software.

SciFinder Scholar
Produced by Chemical Abstracts Service (CAS), is the most comprehensive database for the chemical literature, searchable by topic, author, substances by name or CAS Registry Number, OR use the editor to draw chemical structures, substructures, or reactions. It's a core research tool for chemistry, biochemistry, chemical engineering, materials science, nanotechnology, physics, environmental science and other science and engineering disciplines.










[1] Microscopy of Semiconducting Materials 2007: Proceedings of the 15th Conference 2-5 April 2007, Cambridge, UK, Edited by A. G. Cullis and P. A. Midgley.
[2] M. Albu, A. Pal, C. Gspan, R. C. Picu, F. Hofer & G. Kothleitner, Self-organized Sr leads to solid state twinning in nano-scaled eutectic Si phase, Scientific Reports at Nature, Link.
[3] J.P. Biersack, L.G. Haggmark, “A Monte Carlo computer program for the transport of energetic ions in amorphous targets”, Nucl. Instr. Methods, vol. 174, pp.257-269, 1980.
[4] J.P. Biersack, “Computer simulations of sputtering”, Nucl. Instr. Methods in Phys. Res., B27, 99. 21-36, 1987.
[5] Momma, K.; Izumi, F. J. Appl. Crystallogr. 2008, 41, 653−658.
[6] Francesco Scattarella, Liberato De Caro, Dritan Siliqi and Elvio Carlino, Effective Pattern Intensity Artifacts Treatment for Electron Diffractive Imaging, Crystals, 7, 186 (2017).