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
10.11922/11-6035.csd.2025.0243.zh
X-ray
A dataset of synchrotron small-angle X-ray scattering and wide-angle X-ray diffraction
Jiabao Yuan, Jiang Zhu, Huili Cao, Jing Ye, Xiaoyun Li, Haojun Cai, Wen Wen, Chunpeng Wang, Sepe Alessandro
China Scientific Data
2026

This dataset provides synchrotron small-angle X-ray scattering and wide-angle X-ray diffraction measurements. The collection supports methodological development, benchmarking, and materials characterization research.

Data Analysis Software
10.1051/epjconf/202634501030
SEM
Comparative analysis of microstructural segmentation techniques on SEM and optical micrographs
Katika Harikrishna
EPJ Web of Conferences
2026

The study compares segmentation techniques applied to SEM and optical micrographs for microstructural characterization. The analysis evaluates the effectiveness of different methods for extracting material features.

In-Situ TEM Software
10.21203/rs.3.rs-9468966/v1
TEM
Impedance microscopy for imaging solid-state battery interfaces
Yuji Yamagishi, Hirotada Gamo, Zyun Siroma, Naoya Ishida, Yasushi Maeda, Tetsu Kiyobayashi, Nobuhiko Takeichi, Kentaro Kuratani, Hikaru Sano
2026

This work introduces impedance microscopy for spatially resolved imaging of solid-state battery interfaces. The technique improves characterization of electrochemical processes that are difficult to isolate using conventional impedance measurements.

In-Situ TEM Software
10.1039/D5NJ04629G
TEM
Liquid-cell TEM study of nanobubble growth kinetics and dynamics in ethanol
Zewen Kang, Yuying Chen, Liangping Xiao, Junyu Zhang
New Journal of Chemistry
2026

This study investigates nanobubble growth and interaction dynamics in ethanol using liquid-cell TEM. The observations provide insight into nucleation mechanisms and gas-liquid behavior at small scales.

Data Analysis Software
10.1093/mictod/qaaf117
TEM
Low-Dose TEM Imaging and Diffraction of a Beam-Sensitive 2D Polymer
Fernando Castro, Benjamin Miller, Cory Czarnik
Microscopy Today
2026

This work presents low-dose TEM imaging and diffraction strategies for highly beam-sensitive two-dimensional polymers. Advanced detector technology enables acquisition of useful structural information while minimizing radiation damage.

Data Analysis Software
10.1016/j.mex.2026.103949
SEM
Open-source satellite image pre-processing and annotation workflows: Stranded whale and dolphin case study
Penny J. Clarke, Hannah C. Cubaynes, Karen A. Stockin, Ellen Bowler, Kris Carlyon, Marie R.G. Attard, Peter T. Fretwell, Aliaksandra Skachkova, Asha De Vos, Kaitlin M. McConnell, Encarni Medina-Lopez, Sergio Lopez Dubon, Jennifer A. Jackson
MethodsX
2026

The authors describe open-source workflows for preprocessing and annotating satellite imagery through a stranded whale and dolphin case study. The framework promotes reproducible image-analysis practices for environmental monitoring applications.

Data Analysis Software
10.1109/CCWC67433.2026.11393891
TEM
Optimizing Big Data Workflows Using AI and Machine Learning
Sujit Murumkar, Chitiz Tayal
2026 IEEE 16th Annual Computing and Communication Workshop and Conference (CCWC)
2026

This paper explores the use of artificial intelligence and machine learning to optimize big-data workflows. The proposed strategies improve resource utilization, processing efficiency, and decision support.

Data Analysis Software
10.1117/12.3093426
SEM
Rapid adaptation of SEM image denoising model using conditional normalization
Shumpei Chochi, Aye Chan Myint, Sota Komatsu, Tomoyuki Okuda, Hideaki Sasazawa, Yasutaka Toyoda
Metrology, Inspection, and Process Control XL
2026

The study introduces a conditional-normalization approach for rapidly adapting SEM image denoising models. The method improves image quality while reducing the effort required for retraining.

Simulation Software
10.1107/S205327332509789X
TEM
Reproducible electron diffraction simulations: bridging Bloch wave and multislice simulations with <i>abTEM</i>
M. K. Cabaj, P. B. Klar, J. Madsen, M. Kaur, T. Susi, L. Palatinus
Acta Crystallographica Section A Foundations and Advances
2026

This paper presents reproducible diffraction simulation workflows within abTEM, linking Bloch wave and multislice approaches. The framework promotes transparent comparisons and consistent computational experiments.

Data Analysis Software
10.1016/j.softx.2026.102700
X-ray
Shimexpy: A python package for spatial harmonic imaging
Jorge Luis Beltran Diaz, Danays Kunka
SoftwareX
2026

Shimexpy is a Python package developed for spatial harmonic imaging applications. The software provides tools for image analysis, processing, and research in advanced imaging techniques.

Data Analysis Software
10.1016/j.neucom.2026.133286
SEM
Torchmil: A PyTorch-based library for deep multiple instance learning
Francisco M. Castro-Macías, Francisco J. Sáez-Maldonado, Pablo Morales-Álvarez, Rafael Molina
Neurocomputing
2026

Torchmil is a PyTorch-based library designed for deep multiple-instance learning applications. The framework simplifies development of advanced machine learning models for complex data analysis tasks.

Data Analysis Software
10.1016/j.ultramic.2026.114374
TEM
Unsupervised denoising of STEM images for enhanced atomic quantification
Yucong Wu, Ziyang Huang, Honglue Chen, Bohua He, Meng Qi, He Zheng, Peili Zhao, Shuangfeng Jia, Jianbo Wang
Ultramicroscopy
2026

The authors develop an unsupervised denoising approach for STEM images that preserves atomic-scale information. The method improves image quality and strengthens the accuracy of quantitative structural measurements.

Data Analysis Software
10.21105/joss.07533
SEM
Algorithms for SEM-EDS Mineral Dust Classification
Austin M. Weber
Journal of Open Source Software
2025

This article presents algorithms for classifying mineral dust particles using SEM-EDS data. The open-source approach supports automated identification of particle types and improves analysis efficiency for environmental and materials studies.

Data Analysis Software
10.1109/QPAIN66474.2025.11172204
SEM
An Enhanced Malware Family Classification Approach with Balancing, Feature Optimization, and Explainable AI Insights
Muhaimen Khan, Md. Sarowar Hossain Rana, Mahbub Hasan, Md. Ferdous Bin Hafiz
2025 International Conference on Quantum Photonics, Artificial Intelligence, and Networking (QPAIN)
2025

The authors propose an enhanced malware family classification framework that combines data balancing, feature optimization, and explainable AI methods. The methodology improves classification accuracy while providing interpretable insights into model behavior.

Simulation Software
10.1109/CASE58245.2025.11163870
TEM
Benchmarking Population-Based Reinforcement Learning across Robotic Tasks with GPU-Accelerated Simulation
Asad Ali Shahid, Yashraj Narang, Vincenzo Petrone, Enrico Ferrentino, Ankur Handa, Dieter Fox, Marco Pavone, Loris Roveda
2025 IEEE 21st International Conference on Automation Science and Engineering (CASE)
2025

The authors benchmark population-based reinforcement learning techniques across robotic applications using GPU-accelerated simulation. The evaluation highlights scalability and performance differences among training strategies.

In-Situ TEM Software
10.1038/s42254-025-00896-4
TEM
Cryogenic electron microscopy and tomography for beam-sensitive materials
Yi Cui, Zewen Zhang, Robert Sinclair, Wah Chiu, Yi Cui
Nature Reviews Physics
2025

The paper discusses cryogenic electron microscopy and tomography approaches for characterizing beam-sensitive materials. Cryogenic conditions reduce radiation damage and enable preservation of delicate structural information.

In-Situ TEM Software
10.1016/j.carbon.2025.120444
TEM
Detailed in situ TEM/EELS analysis of laser-induced reduction of graphene oxide
Israt Ali, Huiyu Lei, Shuhui Sun, Kenneth R. Beyerlein
Carbon
2025

The authors perform detailed in-situ TEM and EELS analysis of laser-induced reduction processes in graphene oxide. The results clarify structural and chemical transformations occurring during reduction.

4D-STEM Software
10.1038/s41598-025-21638-7
TEM
Electron fourier ptychography for phase reconstruction
Jingjing Zhao, Chen Huang, Ali Mostaed, Amirafshar Moshtaghpour, James M. Parkhurst, Ivan Lobato, Marcus Gallagher-Jones, Judy S. Kim, Mark Boyce, David Stuart, Elena A. Andreeva, Jacques-Philippe Colletier, Angus I. Kirkland
Scientific Reports
2025

This paper presents electron Fourier ptychography as a phase reconstruction technique for transmission electron microscopy. The method recovers detailed structural information from diffraction measurements while supporting both beam-sensitive and radiation-resistant specimens.

Data Analysis Software
10.1093/mam/ozaf048.1045
SEM
Elemental Analysis of Fine Particles by SEM-EDS
R Ramirez-Leal, A Alvarado-Castro, H Estuardo-Moreno, M E Cruz-Campas
Microscopy and Microanalysis
2025

This article investigates elemental analysis of fine particles using SEM-EDS techniques. The method enables chemical characterization of small-scale particulates for materials and environmental studies.

Data Analysis Software
10.1016/j.micron.2024.103774
TEM
ETSpy: A HyperSpy extension package for electron tomography data processing and reconstruction
Andrew A. Herzing, Joshua A. Taillon
Micron
2025

ETSpy extends the HyperSpy ecosystem with dedicated tools for electron tomography reconstruction and analysis. The package supports preprocessing, alignment, and volumetric interpretation within a reproducible workflow environment.

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