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Table 3669a. Software Examples for Some EMrelated Simulations.
Software 
Function 
FTSR scripts 
Electron image series reconstruction for TEM images 

TEM, STEM and SEM imaging and analysis, and EELS, EFTEM and EDS processing and analysis 
JEMS 
Java based electron microscopy simulation program, for the multislice simulations 
SRIM 
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 welldocumented Fortran listings for programs to simulate CBED patterns by Block Wave method, and multislice. Indexed patterns shown with HOLZ to speed indexing. 
MacTempasX 
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. 
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. 
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] 
Dynamic MonteCarlo
program TRIMDYN 
Simulation of gallium
implantation in FIB milling [3, 4] 
[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.
