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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Simulation Software
10.1063/1.4927172
TEM
Atomic vapor spectroscopy in integrated photonic structures
Ralf Ritter, Nico Gruhler, Wolfram Pernice, Harald Kübler, Tilman Pfau, Robert Löw
Applied Physics Letters
2015

This research investigates atomic vapor spectroscopy implemented within integrated photonic devices. The platform combines waveguides and atomic interactions to enable compact spectroscopic applications.

In-Situ TEM Software
10.1093/jmicro/dfv224
TEM
B12-P-04Fabrication of in-situ TEM Biasing and Heating Holder: New Opportunities of Battery Characterization
Mu-Tung Chang, Shen-Chuan Lo, Ming-Wei Lai, Cheng-Yu Hsieh, Ren-Fong Cai
Microscopy
2015

The paper introduces an in-situ TEM holder that combines electrical biasing and heating capabilities for battery characterization. The platform enables direct observation of electrochemical and thermal processes.

Data Analysis Software
10.1016/j.jsb.2015.08.008
TEM
CTFFIND4: Fast and accurate defocus estimation from electron micrographs
Alexis Rohou, Nikolaus Grigorieff
Journal of Structural Biology
2015

CTFFIND4 provides rapid and accurate estimation of microscope defocus parameters from electron micrographs. The tool supports essential image correction steps in cryo-EM processing pipelines.

In-Situ TEM Software
10.1017/S1431927615003943
TEM
In-Situ Liquid Cell TEM Observations of Silicate Mineral Dissolution
Donovan N. Leonard, Raymond R. Unocic, Roland Hellmann
Microscopy and Microanalysis
2015

The paper uses liquid-cell TEM to monitor dissolution processes in silicate minerals. The approach provides direct evidence of reaction pathways and mineral-fluid interactions under realistic conditions.

In-Situ TEM Software
10.1016/j.matlet.2015.03.105
TEM
In-situ TEM mechanical testing of nanocrystalline zirconium thin films
Baoming Wang, Vikas Tomar, Aman Haque
Materials Letters
2015

The authors perform in-situ TEM mechanical testing on nanocrystalline zirconium thin films. Real-time observations reveal deformation mechanisms and structural responses at the nanoscale under applied loads.

Simulation Software
10.1016/j.ultramic.2015.04.016
TEM
MULTEM: A new multislice program to perform accurate and fast electron diffraction and imaging simulations using Graphics Processing Units with CUDA
I. Lobato, D. Van Dyck
Ultramicroscopy
2015

MULTEM introduces CUDA-based acceleration for multislice electron microscopy simulations. By leveraging GPUs, the software dramatically reduces computation time while preserving high-fidelity diffraction and imaging results.

Simulation Software
10.18358/np-25-1-i7682
X-ray
Software toolkit for the education in X-ray fluorescence analysis
Institute of Chemistry, Saint-Petersburg, RF Saint-Petersburg State University, Sergey Konstantinovich Savelyev, Kaliningrad, RF Immanuel Kant Baltic Federal University, A. V. Bakhtiarov, Institute of Chemistry, Saint-Petersburg, RF Saint-Petersburg State University, V. G. Semenov, Institute of Chemistry, Saint-Petersburg, RF Saint-Petersburg State University, N. B. Klimova, Kaliningrad, RF Immanuel Kant Baltic Federal University
NAUCHNOE PRIBOROSTROENIE
2015

This work introduces an educational software toolkit for teaching X-ray fluorescence analysis. The platform helps students understand analytical principles through interactive computational tools and simulations.

Tomography Software
10.1016/j.ultramic.2015.05.002
X-ray
The ASTRA Toolbox: A platform for advanced algorithm development in electron tomography
Wim Van Aarle, Willem Jan Palenstijn, Jan De Beenhouwer, Thomas Altantzis, Sara Bals, K. Joost Batenburg, Jan Sijbers
Ultramicroscopy
2015

The ASTRA Toolbox provides a platform for developing advanced electron-tomography reconstruction algorithms. The software supports flexible experimentation with imaging and computational techniques.

In-Situ TEM Software
10.1149/MA2015-03/2/428
TEM
Understanding Nanoscale Battery Processes By Operando (Scanning) Transmission Electron Microscopy
Nigel D Browning, B. Layla Mehdi, Eric Jensen, Patricia Abellan, Lucas Parent, Andrew Stevens, James E Evans, Chiwoo Park, Wu Xu, Chongmin Wang, Jason Zhang, Jie Xiao, Karl T Mueller
ECS Meeting Abstracts
2015

The authors use operando TEM and STEM techniques to investigate nanoscale processes occurring within battery systems. Real-time observations reveal dynamic structural and chemical changes during device operation.

4D-STEM Software
10.1107/S205327331409264X
TEM
3D grain orientation mapping of nanocrystalline materials in the TEM
Soeren Schmidt, Peter Larsen, Xiaoxu Huang
Acta Crystallographica Section A Foundations and Advances
2014

This study presents a methodology for three-dimensional grain orientation mapping in nanocrystalline materials using transmission electron microscopy. The approach enables detailed characterization of grain structures that are difficult to resolve with conventional techniques.

Tomography Software
10.1017/S1431927614005698
TEM
Advanced 3-D Reconstruction Algorithms for Electron Tomography
Toby Sanders, John D. Roehling, K. Joost Batenburg, Bruce C. Gates, Alexander Katz, Peter Binev, Ilke Arslan
Microscopy and Microanalysis
2014

The paper evaluates advanced reconstruction algorithms designed for electron tomography applications. These methods improve volumetric accuracy, artifact suppression, and structural detail recovery.

Data Analysis Software
10.1007/s11433-014-5397-1
SEM
A micro-scale strain rosette for residual stress measurement by SEM Moiré method
RongHua Zhu, HuiMin Xie, JianGuo Zhu, YanJie Li, ZhiGang Che, ShiKun Zou
Science China Physics, Mechanics and Astronomy
2014

This article introduces a micro-scale strain rosette for residual stress measurements using the SEM moire method. The technique enables precise local strain and stress characterization at small scales.

Data Analysis Software
10.1117/12.2062917
X-ray
Computational techniques in propagation-based x-ray phase imaging
Jonathan C. Petruccelli, Sajjad Tahir, Sajid Bashir, Adam Pan, Lei Tian, Ling Xu, C. A. MacDonald, George Barbastathis
2014

The authors review computational methods used in propagation-based X-ray phase imaging. These techniques improve phase retrieval, image reconstruction, and quantitative interpretation of phase-contrast measurements.

In-Situ TEM Software
10.1017/S1431927614007855
TEM
Cryogenic FIB Lift-out as a Preparation Method for Damage-Free Soft Matter TEM Imaging
Christopher Parmenter, Michael Fay, Cheryl Hartfield, Gonzalo Amador, Grigore Moldovan
Microscopy and Microanalysis
2014

This work introduces cryogenic FIB lift-out techniques for preparing soft-matter samples for TEM analysis. The method minimizes preparation-induced damage and improves imaging of sensitive materials.

Data Analysis Software
10.1109/MIEL.2014.6842134
X-ray
Dielectric powders X-ray crystallography using rietveld refinement
Lidia Dobrescu
2014 29th International Conference on Microelectronics Proceedings - MIEL 2014
2014

The paper demonstrates the use of Rietveld refinement in the crystallographic analysis of dielectric powders. The approach supports accurate determination of crystal structures and phase compositions.

Data Analysis Software
10.1186/2193-9772-3-5
SEM
DREAM.3D: A Digital Representation Environment for the Analysis of Microstructure in 3D
Michael A Groeber, Michael A Jackson
Integrating Materials and Manufacturing Innovation
2014

DREAM.3D is a software environment for analyzing and manipulating three-dimensional microstructure data. The platform supports segmentation, quantification, visualization, and digital materials characterization workflows.

In-Situ TEM Software
10.1017/S1431927614009490
TEM
Fast Imaging of Carbon Nanotube Nucleation and Growth Processes using Environmental TEM
Dmitri N. Zakharov, Mostafa Bewedy, Cory Czarnik, A. John Hart, Shigeki Misawa, Eric A. Stach
Microscopy and Microanalysis
2014

The paper demonstrates fast environmental TEM imaging of carbon nanotube nucleation and growth. High-speed observations provide valuable insight into the mechanisms governing nanotube formation.

Data Analysis Software
10.1134/S0036024414030212
TEM
Grain boundary segregations in nanocrystalline alloys
I. K. Razumov
Russian Journal of Physical Chemistry A
2014

The paper examines grain-boundary segregation phenomena in nanocrystalline alloys. The analysis explains how solute distribution influences stability, microstructure evolution, and material properties.

In-Situ TEM Software
10.1149/MA2014-02/5/457
TEM
Graphite Particle Cracking as a Failure Mode during Li-Ion Battery Cycling
Kenji Takahashi, Venkat Srinivasan
ECS Meeting Abstracts
2014

This research identifies graphite particle cracking as an important degradation mechanism in lithium-ion batteries. The findings provide insight into factors that influence battery lifetime and reliability.

In-Situ TEM Software
10.1016/j.jnucmat.2014.06.010
TEM
Helium bubble formation in nuclear glass by in-situ TEM ion implantation
G. Gutierrez, S. Peuget, J.A. Hinks, G. Greaves, S.E. Donnelly, E. Oliviero, C. Jégou
Journal of Nuclear Materials
2014

The authors investigate helium bubble formation in nuclear glass through in-situ TEM ion implantation experiments. The findings improve understanding of radiation-induced damage and long-term material stability.

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