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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Data Analysis Software
10.1007/s11340-016-0240-4
SEM
Thermographical Analysis of Paper During Tensile Testing and Comparison to Digital Image Correlation
A. Hagman, M. Nygårds
Experimental Mechanics
2017

The study compares thermographic measurements with digital image correlation during tensile testing of paper. Combining the techniques provides complementary information about deformation and damage evolution.

Data Analysis Software
10.1093/bioinformatics/btx180
SEM
Trainable Weka Segmentation: a machine learning tool for microscopy pixel classification
Ignacio Arganda-Carreras, Verena Kaynig, Curtis Rueden, Kevin W Eliceiri, Johannes Schindelin, Albert Cardona, H Sebastian Seung
Bioinformatics
2017

Trainable Weka Segmentation integrates machine-learning methods into microscopy image analysis. The tool allows users to create custom pixel-classification models that improve segmentation accuracy in complex datasets.

Simulation Software
10.1002/9783527808465.EMC2016.6139
TEM
Accurate and fast electron microscopy simulations using the open source <span style="font-variant:small-caps;">MULTEM</span> program
Ivan Lobato, Sandra Van Aert, Johan Verbeeck
European Microscopy Congress 2016: Proceedings
2016

This work highlights the open-source MULTEM platform for precise electron microscopy simulations. The package incorporates advanced scattering models and delivers rapid calculations suitable for realistic experimental studies.

Tomography Software
10.1016/j.nima.2015.10.013
X-ray
A compressed sensing based reconstruction algorithm for synchrotron source propagation-based X-ray phase contrast computed tomography
Seyed Ali Melli, Khan A. Wahid, Paul Babyn, James Montgomery, Elisabeth Snead, Ali El-Gayed, Murray Pettitt, Bailey Wolkowski, Michal Wesolowski
Nuclear Instruments and Methods in Physics Research Section A: Accelerators, Spectrometers, Detectors and Associated Equipment
2016

The authors propose a compressed-sensing reconstruction algorithm for synchrotron-based X-ray phase-contrast computed tomography. The approach improves image reconstruction quality while reducing data requirements.

In-Situ TEM Software
10.1016/j.corsci.2016.05.041
TEM
Corrosion and passivation of magnesium alloys
Fuyong Cao, Guang-Ling Song, Andrej Atrens
Corrosion Science
2016

The article reviews corrosion and passivation mechanisms in magnesium alloys. Understanding these processes is essential for improving durability and corrosion resistance in structural applications.

Data Analysis Software
10.1016/j.jsb.2016.07.006
TEM
DeepPicker: A deep learning approach for fully automated particle picking in cryo-EM
Feng Wang, Huichao Gong, Gaochao Liu, Meijing Li, Chuangye Yan, Tian Xia, Xueming Li, Jianyang Zeng
Journal of Structural Biology
2016

DeepPicker uses deep learning to automate particle picking in cryo-EM datasets. The method reduces user effort while maintaining reliable detection performance across diverse imaging conditions.

Open-Source TEM Software
10.1038/nmeth.3806
TEM
EMPIAR: a public archive for raw electron microscopy image data
Andrii Iudin, Paul K Korir, José Salavert-Torres, Gerard J Kleywegt, Ardan Patwardhan
Nature Methods
2016

EMPIAR acts as a public repository for raw electron microscopy image datasets. The archive supports data sharing, transparency, benchmarking, and reuse across the microscopy community.

Tomography Software
10.1364/OE.24.025129
TEM
Fast and flexible X-ray tomography using the ASTRA toolbox
Wim Van Aarle, Willem Jan Palenstijn, Jeroen Cant, Eline Janssens, Folkert Bleichrodt, Andrei Dabravolski, Jan De Beenhouwer, K. Joost Batenburg, Jan Sijbers
Optics Express
2016

The ASTRA toolbox provides fast and adaptable tomography algorithms accelerated by modern computing hardware. Its modular architecture supports reconstruction research across a broad range of imaging applications.

4D-STEM Software
10.1002/9783527808465.EMC2016.6221
TEM
Generation of super‐oscillatory electron beams beyond the diffraction limit
Roei Remez, Yuval Tsur, Peng‐Han Lu, Amir H. Tavabi, Rafal E. Dunin‐Borkowski, Ady Arie
European Microscopy Congress 2016: Proceedings
2016

The authors demonstrate the creation of super-oscillatory electron beams capable of achieving features beyond traditional diffraction limits. The technique opens new opportunities for ultra-high-resolution electron imaging and beam shaping.

In-Situ TEM Software
10.1002/jemt.22675
TEM
In situ TEM studies of micron‐sized all‐solid‐state fluoride ion batteries: Preparation, prospects, and challenges
Mohammed Hammad Fawey, Venkata Sai Kiran Chakravadhanula, Munnangi Anji Reddy, Carine Rongeat, Torsten Scherer, Horst Hahn, Maximilian Fichtner, Christian Kübel
Microscopy Research and Technique
2016

This article discusses preparation methods, opportunities, and challenges associated with in-situ TEM studies of all-solid-state fluoride-ion batteries. The work highlights experimental strategies for reliable electrochemical characterization.

In-Situ TEM Software
10.1002/9783527808465.EMC2016.6310
TEM
In situ tensile testing of silica glass membranes in the TEM
Mirza Mačković, Hana Stara, Thomas Przybilla, Christel Dieker, Florian Niekiel, Patrick Herre, Stefan Romeis, Nadine Schrenker, Wolfgang Peukert, Erdmann Spiecker
European Microscopy Congress 2016: Proceedings
2016

This work presents in-situ tensile testing of silica glass membranes inside a TEM. Real-time mechanical characterization reveals deformation and failure behavior at small length scales.

In-Situ TEM Software
10.1017/9781316337455
TEM
Liquid Cell Electron Microscopy
2016

This reference introduces the principles, instrumentation, and applications of liquid-cell electron microscopy. The technique allows visualization of materials and processes in liquid environments with high spatial resolution.

In-Situ TEM Software
10.1017/S1431927616012113
TEM
Liquid Cell Transmission Electron Microscopy for Electrochemical Processes
Frances M. Ross
Microscopy and Microanalysis
2016

The paper reviews liquid-cell TEM methods for studying electrochemical reactions in real time. These approaches provide direct insight into mechanisms governing batteries, corrosion, and related systems.

Data Analysis Software
10.1002/9783527808465.EMC2016.5281
TEM
Precise atomic column position measurements using ISTEM
Karel H W Van Den Bos, Florian F Krause, Armand Béché, Johan Verbeeck, Andreas Rosenauer, Sandra Van Aert
European Microscopy Congress 2016: Proceedings
2016

The authors describe ISTEM-based methods for highly precise atomic column position measurements. The approach improves quantitative structural characterization at atomic resolution.

Simulation Software
10.1016/j.ultramic.2016.06.003
TEM
Progress and new advances in simulating electron microscopy datasets using MULTEM
I. Lobato, S. Van Aert, J. Verbeeck
Ultramicroscopy
2016

This paper reviews developments made within the MULTEM simulation framework. Recent enhancements broaden its capabilities, improve computational efficiency, and support more realistic electron microscopy modelling.

Data Analysis Software
10.1016/j.jsb.2016.04.010
TEM
Scipion: A software framework toward integration, reproducibility and validation in 3D electron microscopy
J.M. De La Rosa-Trevín, A. Quintana, L. Del Cano, A. Zaldívar, I. Foche, J. Gutiérrez, J. Gómez-Blanco, J. Burguet-Castell, J. Cuenca-Alba, V. Abrishami, J. Vargas, J. Otón, G. Sharov, J.L. Vilas, J. Navas, P. Conesa, M. Kazemi, R. Marabini, C.O.S. Sorzano, J.M. Carazo
Journal of Structural Biology
2016

Scipion serves as an integration framework that connects multiple cryo-EM software packages within a unified environment. The platform promotes reproducibility, workflow traceability, and result validation.

Tomography Software
10.1107/S1600577516008018
X-ray
Synchrotron X-ray CT characterization of titanium parts fabricated by additive manufacturing. Part II. Defects
Nicola Vivienne Yorke Scarlett, Peter Tyson, Darren Fraser, Sheridan Mayo, Anton Maksimenko
Journal of Synchrotron Radiation
2016

This article uses synchrotron X-ray computed tomography to characterize defects in additively manufactured titanium components. The analysis reveals internal flaw distributions and supports process-quality assessment.

Open-Source TEM Software
10.1117/12.2238785
X-ray
X-ray microtomography at Shanghai Synchrotron Radiation facility
Rongchang Chen, Honglan Xie, Biao Deng, Guohao Du, Yuqi Ren, Yudan Wang, Guangzhao Zhou, Hai Tan, Yiming Yang, Liang Xu, Tao Hu, Qiao Li, Binggang Feng, Feixiang Wang, Tiqiao Xiao
2016

The paper describes X-ray microtomography capabilities at the Shanghai Synchrotron Radiation Facility. The technique supports detailed three-dimensional imaging of materials and biological specimens.

Tomography Software
10.1016/j.ultramic.2014.10.012
TEM
3D image reconstruction of fiber systems using electron tomography
Osama M. Fakron, David P. Field
Ultramicroscopy
2015

This research reconstructs three-dimensional fiber systems using electron tomography. The technique reveals spatial organization and morphology that are difficult to capture from two-dimensional projections alone.

4D-STEM Software
10.14778/2824032.2824045
TEM
An architecture for compiling UDF-centric workflows
Andrew Crotty, Alex Galakatos, Kayhan Dursun, Tim Kraska, Carsten Binnig, Ugur Cetintemel, Stan Zdonik
Proceedings of the VLDB Endowment
2015

The paper proposes a compilation architecture for data analytics workflows built around user-defined functions. The framework optimizes execution efficiency and simplifies management of complex analytical pipelines.

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