=================================================================================
Tables 3669a3669d lists some software and program examples for EMrelated 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 EMrelated Simulations.
Software 
Function 
CASINO 
= CArlo
SImulation of electroN trajectory in sOlids, which is Monte Carlo simulation software to simulate the interactions between the incident ebeam
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 
SHRLI 
Software for multislice simulation. By M. A. O'Keefe, 1978. 
JMULTIS 
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. 
HREMResearch 
Software for multislice simulation. Kazuo Ishizuka, 2001. 
NUMIS 
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. 
NCEMSS 
Multislice and HRTEM simulation,
By M. A. O'Keefe & R. Kilaas, 1988. 
JEMS 
Java based electron microscopy simulation program, for the multislice simulations. By Pierre Stadelmann, 2004. Platform: Windows. 
TEMSIM 
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 welldocumented 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 
SRIM 
Calculation of penetration depth and vacancy density in FIB milling and ion implantation 
TEMPAS 
Software for multislice simulation. By R. Kilaas, 1987. 
MacTempasX 
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 
Acqlong 
Collects
EELS data from samples while monitoring sample drift
and energy resolution; Corrects background,
dark current, channeltochannel 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. 
TIA 
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. 
DTSA 
A free software package for Xray spectrum (e.g. EDS) manipulation/simulation. Authors: Chuck Fiori, Carol SwytThomas, 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 plugin 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) 203215. Link. 
QSTEM 
Simulation of Z contrast in STEM image and quantitative analysis of alloying in real space with atomic resolution (Link) [2] 
Wien2k 
Calculating band structure and transport properties 
VESTA 
Atomic models for STEM simulations [5] 
ASAC^{TM}

Measure the shift of HOLZ lines to quantitatively evaluate strains in a crystal. 
GPA plugin 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 
EDAX SWTHIN program 
Integrate peak counts and subtract background in EDS measurements 
Monte Carlo simulation 
Compute both secondary and backscatter yields as a
function of energy [11] 
DeConvEELS 
A DigitalMicrograph Plugin for EELS deconvolution by using a Maximum Entropy Method (MEM) or the RichardsonLucy Algorithm. [8] 
Table 3669b. Software for electron diffraction Simulations.
Software 
Function 
Websites 
www.globalsino.com/EM/page1474.html 
IdealMicroscope 
Macintosh program helps index diffraction patterns, find excitation errors and structure factors, draw crystal structures, Klines, stereograms, CBED geometry, etc. Contact: sharon@emlabsoftware.com. 
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 labmade Software for EMs.
Software 
Function Examples 
SciLab (INRIAENPC) 
Calculations of rockingcurve intensity oscillations within CBED using dynamical electron diffraction approach (twobeam 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 cleanup procedures in DREAM.3D [7] 
TRIMDYN 
Dynamic MonteCarlo
program for simulation of gallium
implantation in FIB milling [3, 4] 
Table 3669d. Other Software.
Software 
Introduction 
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 25 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, Selforganized Sr leads to solid state twinning in nanoscaled 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.257269, 1980.
[4] J.P. Biersack, “Computer simulations of sputtering”,
Nucl. Instr. Methods in Phys. Res., B27, 99. 2136,
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. http://dx.doi.org/10.1186/2193977235.
[8] www.hremresearch.com/Eng/download/documents/EELScatE2.html.
[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)
