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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AI and Autonomous Microscopy Software
10.1016/j.compbiomed.2024.108112
TEM
A Review of deep learning methods for denoising of medical low-dose CT images
Ju Zhang, Weiwei Gong, Lieli Ye, Fanghong Wang, Zhibo Shangguan, Yun Cheng
Computers in Biology and Medicine
2024

The authors review deep learning approaches for denoising low-dose CT images. These techniques improve image quality while helping reduce radiation exposure during medical imaging procedures.

In-Situ TEM Software
10.1051/bioconf/202412908013
TEM
Development of simple image processing for in-situ TEM toward live processing
Junbeom Park, Hongyu Sun, Janghyun Jo, Eva Jodat, André Karl, Shibabrata Basak, Rüdiger-A. Eichel
BIO Web of Conferences
2024

The paper develops lightweight image-processing methods for in-situ TEM experiments with an emphasis on live analysis. These tools enable faster interpretation of dynamic processes during data acquisition.

In-Situ TEM Software
10.1093/mam/ozae044.714
TEM
Dynamics of Beam Interaction and Damage within a Thin TEM Specimen
Ray Egerton, Peter Rez, Yimei Zhu
Microscopy and Microanalysis
2024

The authors examine how electron beams interact with and damage thin TEM specimens during imaging. The work provides insights into radiation effects and strategies for preserving sample integrity.

Open-Source TEM Software
10.22477/9788570131959
TEM
Fair Principles Applied to research Data Management: Brazilian Experiences
2024

The publication surveys Brazilian initiatives implementing FAIR principles for research data management. It documents practical experiences and promotes broader adoption of open and reusable data practices.

4D-STEM Software
10.1016/j.ultramic.2024.113938
TEM
Framework of compressive sensing and data compression for 4D-STEM
Hsu-Chih Ni, Renliang Yuan, Jiong Zhang, Jian-Min Zuo
Ultramicroscopy
2024

This paper presents a framework for reducing storage and acquisition burdens in 4D-STEM through compressive sensing and data compression. The method preserves valuable information while lowering dataset size requirements.

In-Situ TEM Software
10.1093/mam/ozae044.542
TEM
In Situ Gas Phase Environmental Transmission Electron Microscopy
Dan Zhou
Microscopy and Microanalysis
2024

This work explores environmental TEM techniques for observing materials under gas-phase conditions. The approach enables direct study of reactions, phase changes, and catalytic processes under realistic environments.

In-Situ TEM Software
10.1051/bioconf/202412908018
TEM
In situ TEM holder for liquid cell research with combined electrochemical and thermal stimuli control
Yevheniy Pivak, Hongyu Sun, Vasilis Papadimitriou, Christian Deen-van-Rossum, Andres Alvarez, Merijn Pen, Joseph Patterson, Hugo Perez
BIO Web of Conferences
2024

The paper presents a liquid-cell TEM holder capable of simultaneously applying electrochemical and thermal stimuli. The platform expands opportunities for studying complex dynamic processes under controlled experimental conditions.

Open-Source TEM Software
10.1051/bioconf/202412910024
TEM
Introducing a FAIR RDM infrastructure for electron microscopy and other materials science data
Christoph Koch, Markus Kühbach, Sherjeel Shabih, Sandor Brockhauser, Erdmann Spiecker, Markus Scheidgen, Lauri Himanen, Ádám Fekete, José A. Márquez, Heiko Weber, Claudia Draxl
BIO Web of Conferences
2024

This work introduces a FAIR research data management infrastructure tailored for electron microscopy and materials science. The framework improves data discoverability, accessibility, interoperability, and long-term reuse.

Data Analysis Software
10.1038/s41377-024-01530-1
X-ray
Metalenses phase characterization by multi-distance phase retrieval
Bowen Liu, Jialuo Cheng, Maoxiong Zhao, Jin Yao, Xiaoyuan Liu, Shaohu Chen, Lei Shi, Din Ping Tsai, Zihan Geng, Mu Ku Chen
Light: Science & Applications
2024

The study presents a multi-distance phase-retrieval method for characterizing metalens phase modulation. Accurate phase measurements support the optimization and performance evaluation of advanced optical devices.

Simulation Software
10.1051/bioconf/202412905024
TEM
Mitigation of beam damage on MoS2 using electrostatic beam blanking in TEM
Joakim Kryger-Baggesen, Noopur Jain, Mark Van Rijt, Ruud Krijnen, Marteen Wirix, Pritam Banerjee, Joachim Dahl Thomsen, Jakob Kibsgaard, Christian Damsgaard, Joerg Jinschek, Stig Helveg
BIO Web of Conferences
2024

This study investigates electrostatic beam blanking as a strategy for reducing beam damage in MoS2 during TEM analysis. The technique preserves specimen integrity while maintaining useful imaging performance.

4D-STEM Software
10.1093/mam/ozae044.080
TEM
Precession-Assisted 4D-STEM Strain Characterization of Semiconductor Devices
Eduardo Serralta, Tomáš Moravek, Rob Hooley, Narendraraj Chandran
Microscopy and Microanalysis
2024

The paper applies precession-assisted 4D-STEM to improve strain characterization in semiconductor devices. Enhanced diffraction data quality enables more accurate measurement of nanoscale deformation and crystal distortions.

Data Analysis Software
10.1016/bs.mie.2024.10.004
X-ray
Processing serial synchrotron crystallography diffraction data with DIALS
Methods in Enzymology
2024

This article describes the use of DIALS for processing serial synchrotron crystallography diffraction datasets. The workflow streamlines indexing, integration, and analysis of high-throughput crystallographic experiments.

AI and Autonomous Microscopy Software
10.1007/s10462-023-10687-x
TEM
Variational autoencoders for 3D data processing
Szilárd Molnár, Levente Tamás
Artificial Intelligence Review
2024

This review examines variational autoencoders for processing and generating three-dimensional data. The models provide efficient latent representations that support reconstruction, synthesis, and analysis tasks.

Data Analysis Software
10.1002/adts.202300247
TEM
A Processing and Analytics System for Microscopy Data Workflows: The Pycroscopy Ecosystem of Packages
Rama Krishnan Vasudevan, Sai Mani Valleti, Maxim Ziatdinov, Gerd Duscher, Suhas Somnath
Advanced Theory and Simulations
2023

This paper describes the Pycroscopy ecosystem, a collection of software packages for microscopy data analytics. The framework addresses challenges in data management, processing, and knowledge extraction across diverse modalities.

Tomography Software
10.1093/micmic/ozad083
TEM
Autonomous Electron Tomography Reconstruction with Machine Learning
William Millsaps, Jonathan Schwartz, Zichao Wendy Di, Yi Jiang, Robert Hovden
Microscopy and Microanalysis
2023

This work applies machine learning to automate electron tomography reconstruction and parameter selection. The system reduces manual tuning requirements and helps generate high-quality volumetric reconstructions.

4D-STEM Software
10.1016/j.ultramic.2022.113627
TEM
Complementary ADF-STEM: a Flexible Approach to Quantitative 4D-STEM
Bryan D. Esser, Joanne Etheridge
Ultramicroscopy
2023

This study introduces a complementary ADF-STEM methodology for quantitative 4D-STEM analysis. The technique enhances flexibility in signal interpretation and enables reliable extraction of specimen properties.

Data Analysis Software
10.3390/app13105829
X-ray
Data Acquisition System Based on the Bluesky Suite in the Shanghai Synchrotron Radiation Facility
Ying Zhao, Chun Hu, Chunpeng Wang, Jiefeng Cao, Zhaohong Zhang
Applied Sciences
2023

This paper presents a Bluesky-based data-acquisition system developed for the Shanghai Synchrotron Radiation Facility. The platform supports high-throughput experiments and flexible beamline operation.

Data Analysis Software
10.1162/dint_a_00160
X-ray
FAIR Data Point: A FAIR-Oriented Approach for Metadata Publication
Luiz Olavo Bonino Da Silva Santos, Kees Burger, Rajaram Kaliyaperumal, Mark D. Wilkinson
Data Intelligence
2023

The FAIR Data Point architecture provides a standardized framework for publishing machine-actionable metadata. The approach supports FAIR data principles and improves interoperability across scientific repositories.

Data Analysis Software
10.3390/app13063700
SEM
Fiber Orientation Reconstruction from SEM Images of Fiber-Reinforced Composites
Zhouxiang Zhao, Hongwu Wu, Meng Zhang, Shiqiang Fu, Kang Zhu
Applied Sciences
2023

The authors propose methods for reconstructing fiber orientations from SEM images of fiber-reinforced composites. The technique supports quantitative assessment of microstructure and material performance.

In-Situ TEM Software
10.1093/jmicro/dfad025
TEM
In situ pulsed electrical biasing TEM observation of AA7075
Tyler J Grimm, Laine Mears
Microscopy
2023

This study employs pulsed electrical biasing within TEM to examine microstructural responses in AA7075 alloys. The technique provides insight into electrically assisted processing and material behavior.

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