Key publications, open-source tools, and research directions in TEM automation, 4D-STEM, tomography, and AI-assisted microscopy.

Software is now central to modern transmission electron microscopy. Today’s TEM and STEM workflows depend on automated acquisition, microscope scripting, detector synchronization, tomography reconstruction, 4D-STEM analysis, machine learning, and increasingly autonomous experimental control.

This publication library curates influential papers, software platforms, and research directions that have shaped the software ecosystem for modern electron microscopy.

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In-Situ TEM Software
10.1007/s11340-014-9873-3
TEM
In Situ Measurements of Strains in Composite Battery Electrodes during Electrochemical Cycling
E. M. C. Jones, M. N. Silberstein, S. R. White, N. R. Sottos
Experimental Mechanics
2014

This study measures strain evolution in composite battery electrodes during electrochemical cycling. The results help explain mechanical degradation and performance changes in energy storage systems.

Data Analysis Software
10.1017/S1431927614003432
TEM
In-Situ Quantification of TEM Lamella Thickness and Ga Implantation in the FIB
Matthew Hiscock, Michael Dawson, Christian Lang, Cheryl Hartfield, Peter Statham
Microscopy and Microanalysis
2014

The authors develop methods for quantifying TEM lamella thickness and gallium implantation effects during focused ion beam preparation. Accurate measurements improve sample quality assessment and analytical reliability.

In-Situ TEM Software
10.1017/S1431927614009520
TEM
In-situ TEM Investigation of Reduction-Oxidation Reactions during Densification of Iron Oxide Nanoparticles
Cecile S. Bonifacio, K. Das Gautom, Ian M. Kennedy, Klaus Van Benthem
Microscopy and Microanalysis
2014

The authors investigate reduction and oxidation reactions occurring during densification of iron oxide nanoparticles. In-situ TEM enables direct observation of chemical transformations and microstructural changes during processing.

Data Analysis Software
10.1109/TPAMI.2013.138
TEM
Matching by Tone Mapping: Photometric Invariant Template Matching
Yacov Hel-Or, Hagit Hel-Or, Eyal David
IEEE Transactions on Pattern Analysis and Machine Intelligence
2014

The authors propose a template matching technique that remains robust under varying lighting conditions through tone mapping transformations. The method improves matching reliability in challenging imaging environments.

In-Situ TEM Software
10.1557/mrs.2014.139
TEM
Phase change materials and phase change memory
Simone Raoux, Feng Xiong, Matthias Wuttig, Eric Pop
MRS Bulletin
2014

The authors review phase-change materials and their application in phase-change memory technologies. The discussion explains reversible amorphous-crystalline transformations that enable nonvolatile data storage.

Data Analysis Software
10.1107/S2053273314092031
X-ray
Remote Access of the beamline BL17U at Shanghai Synchrotron Radiation Facility
Qisheng Wang, Bo Sun, Sheng Huang, Zhijun Wang, Jianhua He
Acta Crystallographica Section A Foundations and Advances
2014

The study describes remote-access capabilities for the BL17U beamline at the Shanghai Synchrotron Radiation Facility. The system enables users to conduct crystallography experiments and manage beamline operations from remote locations.

Data Analysis Software
10.1201/b16621-8
X-ray
Soft x-ray scanning transmission spectromicroscopy
Julie Cosmidis, Karim Benzerara
Biomineralization Sourcebook
2014

This chapter reviews soft X-ray scanning transmission spectromicroscopy as a technique for chemical and structural characterization at the microscale. The method combines imaging and spectroscopy to investigate complex biological and mineralized materials.

Data Analysis Software
10.1016/B978-0-08-095975-7.01415-7
X-ray
Synchrotron x-Ray Spectroscopic Analysis
S.R. Sutton, M. Newville
Treatise on Geochemistry
2014

The authors review synchrotron X-ray spectroscopic techniques used in geochemistry and materials science. These methods enable detailed investigation of elemental composition and chemical environments.

Tomography Software
10.1117/12.2061373
X-ray
TomoPy: A framework for the analysis of synchrotron tomographic data
Doğa Gürsoy, Francesco De Carlo, Xianghui Xiao, Chris Jacobsen
2014

TomoPy is an open-source framework designed for processing and analyzing synchrotron tomographic datasets. The software provides reconstruction, visualization, and data-analysis tools for large-scale imaging experiments.

Simulation Software
10.26868/25222708.2013.1271
TEM
Automation Of Common Building Energy Simulation Workflows Using Python
Clayton Miller, Christian Hersberger, Marcus Jones
IBPSA
2013

The paper demonstrates how Python can automate common building energy simulation workflows. The framework reduces manual effort, increases reproducibility, and accelerates building performance studies.

Tomography Software
10.1016/j.ultramic.2013.03.019
TEM
Compressed sensing electron tomography
Rowan Leary, Zineb Saghi, Paul A. Midgley, Daniel J. Holland
Ultramicroscopy
2013

The paper demonstrates compressed sensing techniques for electron tomography. By exploiting data sparsity, the method improves three-dimensional reconstruction quality while reducing acquisition demands.

Simulation Software
10.1109/CoASE.2013.6653991
SEM
Fine registration of SEM and AFM images using Monte Carlo simulations
Christian Geldmann
2013 IEEE International Conference on Automation Science and Engineering (CASE)
2013

This study presents a method for precise registration of SEM and AFM images using Monte Carlo simulations. Improved image alignment enables more accurate multimodal analysis and data interpretation.

4D-STEM Software
10.1107/S0021889813003531
X-ray
<i>GSAS-II</i> : the genesis of a modern open-source all purpose crystallography software package
Brian H. Toby, Robert B. Von Dreele
Journal of Applied Crystallography
2013

GSAS-II is an open-source crystallography software suite designed for diffraction data reduction, structure solution, and refinement. The package supports both neutron and X-ray diffraction experiments across a wide range of research applications.

In-Situ TEM Software
10.1021/nl3044508
TEM
In Situ TEM of Two-Phase Lithiation of Amorphous Silicon Nanospheres
Matthew T. McDowell, Seok Woo Lee, Justin T. Harris, Brian A. Korgel, Chongmin Wang, William D. Nix, Yi Cui
Nano Letters
2013

This study examines the two-phase lithiation behavior of amorphous silicon nanospheres using in-situ TEM. Real-time imaging reveals structural changes relevant to high-capacity battery anode materials.

Data Analysis Software
10.1088/1742-6596/430/1/012007
X-ray
Larch: An Analysis Package for XAFS and Related Spectroscopies
Matthew Newville
Journal of Physics: Conference Series
2013

Larch is an analysis package for XAFS and related spectroscopic methods. The software offers data-processing, modeling, and visualization capabilities for spectroscopy research.

Simulation Software
10.1109/TMAG.2013.2247410
TEM
MALTS: A Tool to Simulate Lorentz Transmission Electron Microscopy From Micromagnetic Simulations
Stephanie K. Walton, Katharina Zeissler, Will R. Branford, Solveig Felton
IEEE Transactions on Magnetics
2013

MALTS provides a simulation tool that generates Lorentz TEM images from micromagnetic models. The software helps researchers investigate magnetic domain structures and compare simulations with experiments.

Tomography Software
10.1016/j.jsb.2013.02.004
TEM
Marker-free dual-axis tilt series alignment
Hanspeter Winkler, Kenneth A. Taylor
Journal of Structural Biology
2013

This work introduces a marker-free approach for aligning dual-axis tilt series. The technique avoids reliance on fiducial particles while maintaining accurate registration of tomography datasets.

Data Analysis Software
10.1167/13.15.54
X-ray
pyarbus: a Python library for eye tracking data analysis
P. Ivanov
Journal of Vision
2013

pyarbus is a Python library developed for eye-tracking data analysis. The package provides tools for processing gaze information and conducting quantitative behavioral studies.

4D-STEM Software
10.1017/S0885715613000924
X-ray
PyFAI: a Python library for high performance azimuthal integration on GPU
J. Kieffer, J.P. Wright
Powder Diffraction
2013

PyFAI is a high-performance Python library for azimuthal integration of diffraction data. GPU acceleration enables rapid processing of one-dimensional and two-dimensional scattering measurements.

Data Analysis Software
10.1016/j.radphyschem.2013.03.033
SEM
Quantification by SEM–EDS in uncoated non-conducting samples
V. Galván Josa, G. Castellano, S.R. Bertolino
Radiation Physics and Chemistry
2013

The study examines SEM-EDS quantification methods for uncoated non-conductive samples. The approach addresses analytical challenges associated with specimen charging while maintaining compositional accuracy.

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