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




Tables 3669a-3669d lists some software and program examples for EM-related simulations and analysis. However, one needs to know that any software can contain some artifacts, which are not always apparent to the end user of commercial software.

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

= CArlo SImulation of electroN trajectory in sOlids, which is Monte Carlo simulation software to simulate the interactions between the incident e-beam and the target materials [10]
FTSR scripts
Electron image series reconstruction for TEM images
TEM, STEM and SEM imaging and analysis, and EELS, EFTEM and EDS processing and analysis
Software for multislice simulation. By M. A. O'Keefe, 1978.
Software for multislice simulation was written in FORTRAN 77 by Dr. J. M. Zuo, while he was a postdoc research fellow at Arizona State University under the guidance of John C. H. Spence. J.M. Zuo and John C. H. Spence, Electron Microdiffraction, 1991.
Software for multislice simulation. Kazuo Ishizuka, 2001.
Multislice simulation. It uses a command line interface (CLI) and is based on UNIX. A structure file must be provided as input to run this code. By Laurence Marks of Northwestern University.
Multislice and HRTEM simulation, By M. A. O'Keefe & R. Kilaas, 1988.
Java based electron microscopy simulation program, for the multislice simulations. By Pierre Stadelmann, 2004. Platform: Windows.
By Kirkland, 1988. See 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

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. By Spence and Zuo, 1992

Calculation of penetration depth and vacancy density in FIB milling and ion implantation
Software for multislice simulation. By R. Kilaas, 1987.
A general microscopy analysis and simulation, e.g. multislice 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. R. Kilaas, 1987.
Simulation for EELS
Collects EELS data from samples while monitoring sample drift and energy resolution; Corrects background, dark current, channel-to-channel gain variations [9]
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.
Used for the calculation of electron energy loss spectra. [13]

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]

Free programs for everything you need related to TEM and SEM.
Stripe Removal
Simulation of parasitic stripes (streaks) in electron diffraction pattern [6]
Tracor Northern (TN)-2000 system
Integrate peak counts and subtract background in EDS measurements
Integrate peak counts and subtract background in EDS measurements
Monte Carlo simulation
Compute both secondary and backscatter yields as a function of energy [11]
A DigitalMicrograph Plug-in for EELS deconvolution by using a Maximum Entropy Method (MEM) or the Richardson-Lucy Algorithm. [8]


Table 3669b. Software for electron diffraction Simulations.

Simulate theoretical diffraction diagram [12]

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]
Python script
Oxford 3D file type (CPR) can be converted to the CTF file type using a Python script provided by Oxford instruments. This 3D CTF file is used for
subsequent reconstruction and clean-up procedures in DREAM.3D [7]
Dynamic Monte-Carlo program for simulation of gallium implantation in FIB milling [3, 4]

Table 3669d. Other Software.

SPIP or Scanning Probe Image Processor
An advanced software package for processing and analyzing microscopic images at nano- and microscale, e.g. for atomic force microscopy (AFM).
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).
[7] M.A. Groeber, M.A. Jackson, DREAM.3D: A Digital Representation Environment for the Analysis of Microstructure in 3D, Integr. Mater. Manuf. Innov. 3 (2014) 5.
[9] Qian, M., Sarikaya, M., Stern, E.A., 1995. Development of the EXELFS technique for high accuracy structural information. Ultramicroscopy 59, 137–147.
[10] Pengyu Yuan, Jason Y. Wu, D. Frank Ogletree, Jeffrey J. Urban, Chris Dames, and Yanbao Ma, Adapting the Electron Beam from SEM as a Quantitative Heating Source for Nanoscale Thermal Metrology, Nano Lett., 20, 3019−3029, 2020.
[11] Joy DC: A model for calculating secondary and backscattered electron yields, J. Microsc 147, 51 (1 987)
[12] H.-D. Bauer, J. Thomas, K. Wetzig, Phys. Stat. Sol. A 150 (1995) 141. 
[13] C. Hébert, Practical aspects of running the WIEN2k code for electron spectroscopy, Micron 38 (2007) 12–28.