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
10.1038/s41598-020-78102-x
TEM
UV induced resistive switching in hybrid polymer metal oxide memristors
Spyros Stathopoulos, Ioulia Tzouvadaki, Themis Prodromakis
Scientific Reports
2020

The paper explores ultraviolet-light-induced resistive switching in hybrid polymer metal-oxide memristors. The approach demonstrates optical control of resistance states for advanced electronic devices.

Data Analysis Software
10.1109/BIBM49941.2020.9312978
SEM
Weakly Supervised Instance Segmentation of SEM Image via Synthetic Data
Yunfeng Wang, Xiaoqin Tang, Jingchuan Fan, GuoQiang Xiao
2020 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)
2020

This research applies weakly supervised learning and synthetic datasets to instance segmentation of SEM images. The methodology reduces annotation requirements while maintaining effective object identification performance.

Data Analysis Software
10.21105/joss.02381
X-ray
xrdfit: A Python package for fitting synchrotron X-ray diffraction spectra
Peter Crowther, Christopher Daniel
Journal of Open Source Software
2020

xrdfit is a Python package developed for fitting synchrotron X-ray diffraction spectra. The software enables reproducible and efficient analysis of diffraction peaks and structural parameters.

Simulation Software
10.1017/S1431927619009747
TEM
3D Electron Ptychography
Si Gao, Zhiyuan Ding, Xiaoqing Pan, Angus I. Kirkland, Peng Wang
Microscopy and Microanalysis
2019

This paper explores three-dimensional electron ptychography for volumetric imaging of materials. The method reconstructs internal structure with high resolution by combining information from multiple diffraction measurements.

Data Analysis Software
10.1080/08940886.2019.1608121
X-ray
Bluesky's Ahead: A Multi-Facility Collaboration for an <i>a la Carte</i> Software Project for Data Acquisition and Management
Daniel Allan, Thomas Caswell, Stuart Campbell, Maksim Rakitin
Synchrotron Radiation News
2019

Bluesky is a collaborative software project for scientific data acquisition and management across research facilities. Its modular architecture enables flexible experiment control and reproducible data workflows.

In-Situ TEM Software
10.1016/j.micron.2018.09.009
TEM
Dynamic behavior of nanoscale liquids in graphene liquid cells revealed by in situ transmission electron microscopy
Jiwoong Yang, Sardar B. Alam, Lei Yu, Emory Chan, Haimei Zheng
Micron
2019

The study explores the behavior of nanoscale liquids confined within graphene liquid cells using in-situ TEM. Observations reveal fluid dynamics, interfacial phenomena, and particle interactions at high spatial resolution.

In-Situ TEM Software
10.11159/tann19.4
TEM
Failure Mechanics of 2D Materials
Tobin Filleter
2019

This work examines the failure mechanics of two-dimensional materials. The discussion explores fracture, defect interactions, and mechanical reliability in atomically thin structures.

Simulation Software
10.1109/IMaRC45935.2019.9118748
TEM
GPU accelerated FDTD based Open-source SAR Simulator
Vidhi Katkoria, Pratik Ghosh, Bhaskar Chaudhury
2019 IEEE MTT-S International Microwave and RF Conference (IMARC)
2019

This work describes an open-source synthetic aperture radar simulator accelerated using GPU-based FDTD computations. The platform delivers faster simulations while maintaining accuracy for radar imaging studies.

Data Analysis Software
10.1038/s41592-019-0582-9
SEM
ilastik: interactive machine learning for (bio)image analysis
Stuart Berg, Dominik Kutra, Thorben Kroeger, Christoph N. Straehle, Bernhard X. Kausler, Carsten Haubold, Martin Schiegg, Janez Ales, Thorsten Beier, Markus Rudy, Kemal Eren, Jaime I Cervantes, Buote Xu, Fynn Beuttenmueller, Adrian Wolny, Chong Zhang, Ullrich Koethe, Fred A. Hamprecht, Anna Kreshuk
Nature Methods
2019

ilastik combines interactive machine learning with user-friendly image-analysis workflows. The software enables rapid segmentation, classification, and object identification without requiring extensive programming expertise.

4D-STEM Software
10.1017/S1431927619010523
TEM
Improved 4D-STEM Strain Mapping Precision Using Patterned Probes
Steven E. Zeltmann, Alexander Müller, Karen C. Bustillo, Benjamin H. Savitzky, Andrew M Minor, Colin Ophus
Microscopy and Microanalysis
2019

This work enhances strain mapping precision in 4D-STEM through the use of patterned electron probes. The technique increases measurement sensitivity and enables more reliable characterization of nanoscale lattice distortions.

In-Situ TEM Software
10.1007/978-3-319-91989-8_83
TEM
Nanodiffraction Strain Mapping of Metallic Glasses During In Situ Deformation
Christoph Gammer, Thomas C. Pekin, Colin Ophus, Andrew M. Minor, Jürgen Eckert
Proceedings of the First International Conference on Theoretical, Applied and Experimental Mechanics
2019

The authors use nanodiffraction strain mapping to investigate metallic glasses during in-situ deformation. The technique reveals local strain distributions and deformation pathways with high spatial resolution.

Data Analysis Software
10.1017/S1431927619000333
SEM
Reflector Selection for the Indexing of Electron Backscatter Diffraction Patterns
Stuart I. Wright, Saransh Singh, Marc De Graef
Microscopy and Microanalysis
2019

The paper proposes strategies for selecting reflectors used in EBSD pattern indexing. Improved ranking of diffraction features enhances indexing reliability and crystallographic analysis accuracy.

Data Analysis Software
10.1017/S1431927619001454
SEM
Semantic SEM Image Segmentation of Concrete with Contextual Labels
Authors: Peter Bajcsy, Steve Feldman, Mary Brady, Kenneth Snyder
Microscopy and Microanalysis
2019

This study presents a semantic segmentation approach for SEM images of concrete using contextual labels. The method improves identification of material phases and supports automated microstructural characterization.

10.1109/MTV48867.2019.00015
TEM
Smarter Disk Space Management for Silicon Workflows
Jigar Kuverji Savla
2019 20th International Workshop on Microprocessor/SoC Test, Security and Verification (MTV)
2019

This work proposes strategies for optimizing disk space utilization in semiconductor workflow environments. The framework helps organizations reduce storage overhead while maintaining efficient access to engineering data.

Microscope Automation Software
Electron tomography, tilt series, montaging, automated acquisition, cryo-EM.
10.1093/micmic/ozad067.338
TEM
Software Tools for Automated Transmission Electron Microscopy
Schorb, Haberbosch, Hagen, Schwab, Mastronarde
Microscopy and Microanalysis
2019

This review describes software tools used to automate transmission electron microscopy acquisition. It explains how image analysis, microscope control, targeting, navigation, and data handling can be combined into practical automated workflows.

4D-STEM Software
10.1063/1.5113761
TEM
Strain analysis of a Ge micro disk using precession electron diffraction
Aneeqa Bashir, Ross W. Millar, Kevin Gallacher, Douglas J. Paul, Amith D. Darbal, Robert Stroud, Andrea Ballabio, Jacopo Frigerio, Giovanni Isella, Ian MacLaren
Journal of Applied Physics
2019

This work uses precession electron diffraction to map strain and crystal orientation within a germanium microdisk device. The analysis reveals local deformation patterns relevant to semiconductor and photonic applications.

Tomography Software
10.1149/MA2019-04/2/86
X-ray
Synchrotron Operando x-Ray Computed Tomography of Battery Pouch Cells
Iryna V. Zenyuk, Annalisa DeBari, Wei Han Lim, Dilworth Y. Parkinson, Xianghui Xiao
ECS Meeting Abstracts
2019

The study applies operando synchrotron X-ray computed tomography to battery pouch cells. Three-dimensional imaging enables direct observation of structural changes during battery operation.

4D-STEM Software
10.1117/12.2508451
TEM
Ultrafast linear array detector for real-time imaging
Michele Caselle, Lorenzo Rota, Andreas Kopmann, Suren Chilingaryan, Meghana Mahaveer Patil, Weijia Wang, Erik Bründermann, Stefan Funkner, Michael Nasse, Gudrun Niehues, Matthias Balzer, Marc Weber, Anke-Susanne Mueller, Serge Bielawski
Optical Data Science II
2019

This study introduces an ultrafast linear array detector designed for real-time imaging applications. The system enables rapid data acquisition while supporting high temporal resolution measurements.

Data Analysis Software
10.1016/j.tice.2018.09.006
SEM
Volume microscopy in biology: FIB-SEM tomography
Caroline Kizilyaprak, York-Dieter Stierhof, Bruno M. Humbel
Tissue and Cell
2019

The article reviews FIB-SEM tomography as a powerful volume microscopy technique in biological research. The approach enables three-dimensional visualization of cellular and tissue architecture with nanometer-scale detail.

Data Analysis Software
10.1126/sciadv.aav0282
X-ray
X-ray Fourier ptychography
Klaus Wakonig, Ana Diaz, Anne Bonnin, Marco Stampanoni, Anna Bergamaschi, Johannes Ihli, Manuel Guizar-Sicairos, Andreas Menzel
Science Advances
2019

This study introduces X-ray Fourier ptychography as a high-resolution imaging approach. The technique increases image resolution and sensitivity by combining multiple diffraction measurements computationally.

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