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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Microscope Automation Software
10.14293/APMC13-2025-0021
TEM
Extension of TEM/STEM Function by using Python®† scripting
E. Okunishi, D. Maekawa, M. Nishikawa, O. Hirahara, I. Ishikawa
Extension of TEM/STEM Function by using Python®† scripting
2025

The study demonstrates how Python scripting can extend the functionality of TEM and STEM instruments. Customized automation routines allow researchers to streamline acquisition and analysis tasks.

Simulation Software
10.2172/2567047
X-ray
Flexible Integration of Diverse HVAC Technologies in EnergyPlus via Python-Enabled Workflows
Energy Efficiency Office. Building Technologies Office USDOE Office of Energy Efficiency and Renewable Energy (EERE), USDOE Laboratory Directed Research and Development (LDRD) Program, Copeland, US General Services Administration, Wells Fargo Innovation Incubator, Golden, CO (United States) National Renewable Energy Laboratory (NREL), Eric Bonnema, Amy Allen, Edwin Lee, Matt Mitchell, Ryan Meyer
2025

The study demonstrates Python-enabled workflows for integrating diverse HVAC technologies within EnergyPlus simulations. The framework improves flexibility for building-performance and energy-efficiency analyses.

Data Analysis Software
10.1117/12.3050983
SEM
Foundation deep learning model for accurate SEM image segmentation for CD-SEM measurements
Eva Seknazi, Elad Yoshai, Angela Kravstov, Rotem Mor Yosef, Anna Levant
Metrology, Inspection, and Process Control XXXIX
2025

The paper presents a foundation deep-learning model for accurate SEM image segmentation in critical-dimension metrology. The approach improves measurement precision and robustness for semiconductor inspection applications.

AI and Autonomous Microscopy Software
10.2139/ssrn.5199919
TEM
Generative AI-generated Synthetic Medical Data for Training AI Models
Ajit Singh
2025

This work examines the use of generative AI to create synthetic medical datasets for training artificial intelligence systems. The approach aims to improve data availability while addressing privacy and accessibility challenges.

Data Analysis Software
10.1101/2025.10.03.680389
TEM
Helical Reconstruction of Amyloids in cryoSPARC
Jan-Hannes Schäfer, Robert T. O’Neill, Joseph P. Donnelly, Evan T. Powers, Jeffery W. Kelly, Gabriel C. Lander
2025

This work describes cryoSPARC methods for helical reconstruction of amyloid filaments. The workflow facilitates detailed structural characterization of disease-related fibrillar assemblies.

4D-STEM Software
10.62753/ctp.2025.02.4.4
TEM
In-situ TEM heating of FeNiCr/C coatings for hydrogen evolution reaction
Jerzy Morgiel, Łukasz Maj, Tomasz Suszko, Małgorzata Pomorska, Ewa Dobruchowska, Witold Gulbiński
COMPOSITES THEORY AND PRACTICE
2025

The authors use in-situ TEM heating to study FeNiCr/C coatings developed for hydrogen evolution reactions. The observations reveal thermal stability and microstructural changes relevant to catalytic performance.

Data Analysis Software
10.1007/978-3-031-68897-3_13
TEM
Inverse Source Estimation Tools in SDynPy, an Open-Source Python Package
Steven Carter, Daniel Rohe
Dynamic Substructures, Vol. 4
2025

SDynPy introduces open-source tools for inverse source estimation within structural dynamics workflows. The package helps identify excitation sources and supports advanced vibration analysis studies.

Microscope Automation Software
10.1109/MSR66628.2025.00091
TEM
Jupyter Notebook Activity Dataset
Tomoki Nakamaru, Tomomasa Matsunaga, Tetsuro Yamazaki
2025 IEEE/ACM 22nd International Conference on Mining Software Repositories (MSR)
2025

This dataset captures activity patterns associated with Jupyter Notebook usage. The resource supports software engineering research focused on computational workflows and interactive programming practices.

Tomography Software
10.1016/j.softx.2025.102251
X-ray
Marimba: A Python framework for structuring and processing FAIR scientific image datasets
Christopher J. Jackett, Kevin Barnard, Franziska Althaus, Nicolas Mortimer, David Webb, Candice Untiedt, Aaron Tyndall, Ian Jameson, Bec Gorton, Carlie Devine, Joanna Strzelecki, Peter H. Thrall, Ben Scoulding
SoftwareX
2025

Marimba is a Python framework for structuring and processing FAIR scientific image datasets. The platform promotes data discoverability, accessibility, interoperability, and reusability in research workflows.

Microscope Automation Software
10.1002/jemt.70011
TEM
PyCCAPT: A Python Package for Open‐Source Atom Probe Instrument Control and Data Calibration
Mehrpad Monajem, Benedict Ott, Jonas Heimerl, Stefan Meier, Peter Hommelhoff, Peter Felfer
Microscopy Research and Technique
2025

PyCCAPT introduces an open-source Python platform for atom probe instrument control and data calibration. The package expands experimental flexibility and promotes reproducible workflows in atom probe tomography.

4D-STEM Software
10.1093/mam/ozaf048.289
TEM
Quantitative Analysis of Battery Cathode Nanoparticles using 4D-STEM and EELS
Chu-Yun Hwang, Oliver Lin, Jian-Min Zuo, Qian Chen
Microscopy and Microanalysis
2025

The authors combine 4D-STEM and EELS techniques to analyze battery cathode nanoparticles quantitatively. The workflow links structural and chemical information to support advanced energy materials research.

AI and Autonomous Microscopy Software
10.1016/j.commatsci.2024.113400
TEM
SAM-I-Am: Semantic boosting for zero-shot atomic-scale electron micrograph segmentation
Waqwoya Abebe, Jan Strube, Luanzheng Guo, Nathan R. Tallent, Oceane Bel, Steven Spurgeon, Christina Doty, Ali Jannesari
Computational Materials Science
2025

SAM-I-Am introduces a semantic boosting framework for zero-shot segmentation of atomic-scale electron microscopy images. The method improves feature recognition without requiring extensive task-specific training data.

Data Analysis Software
10.17504/protocols.io.14egnrwb6l5d/v1
SEM
SEM Analysis of Sclerotial Morphology v1
Md Sahadat Ali, Jonathon D. Eisenback, Fatima Tuz Zohora Mony
2025

This protocol describes SEM-based analysis of sclerotial morphology and specimen preparation procedures. The workflow enables detailed examination of structural changes in fungal samples.

Data Analysis Software
10.1016/j.advengsoft.2025.104043
SEM
SUN-DIC: A Python-based open-source software tool for Digital Image Correlation
Gerhard Venter, Melody Neaves
Advances in Engineering Software
2025

SUN-DIC is an open-source Python software package for digital image correlation analysis. The tool enables accurate full-field displacement and strain measurements from image data in engineering applications.

In-Situ TEM Software
10.1093/mam/ozaf048.752
TEM
TemCompanion: An Open-Source Multi-Platform GUI Program for TEM Image Processing and Analysis
Tao Ma
Microscopy and Microanalysis
2025

TemCompanion is an open-source graphical application for TEM image processing and analysis across multiple operating systems. The software provides an accessible environment for visualization, measurement, and workflow management in electron microscopy.

Tomography Software
10.1145/3712256.3726365
TEM
Tomographic Reconstruction with Real-time a priori Acquisition
Muhammad Wishal Khan, Hooman Oroojeni M. J., Bal Sanghera, Tim Blackwell, Mohammad Majid al-Rifaie
Proceedings of the Genetic and Evolutionary Computation Conference
2025

The authors propose a tomographic reconstruction strategy that incorporates real-time prior information during data acquisition. The method aims to improve reconstruction efficiency and decision-making while imaging.

Data Analysis Software
10.1145/3734436.3734439
X-ray
Towards Explainable Access Control [BlueSky Paper]
Gelareh Hasel Mehri, Charles Morisset, Nicola Zannone
Proceedings of the 30th ACM Symposium on Access Control Models and Technologies
2025

This paper explores explainable approaches to access-control systems within the BlueSky framework. The work aims to improve transparency and user understanding of authorization decisions in complex security environments.

Data Analysis Software
10.3233/FAIA251487
SEM
Towards Explaining SEM Defect Image Classification
Vahidin Hasić, Corinna Kofler, Senka Krivić
Frontiers in Artificial Intelligence and Applications
2025

This study explores explainable artificial intelligence techniques for SEM defect image classification in semiconductor manufacturing. The approach improves model transparency and helps experts understand the reasoning behind automated defect detection decisions.

Tomography Software
10.1093/mam/ozaf048.865
TEM
Towards Time-Resolved Electron Tomography and 4D-STEM
Michael Yannai, Ido Kaminer
Microscopy and Microanalysis
2025

This article discusses emerging approaches toward time-resolved electron tomography and four-dimensional STEM. The techniques aim to capture both spatial and temporal information from dynamic nanoscale systems.

In-Situ TEM Software
10.1016/j.bmi.2025.100025
TEM
Ultrafast polymerase chain reaction on MEMS microheater
Hongjun Liu, Yu Liu, Rongyue Liu, Rifei Chen, Weihao Li, Qin Luo, Zijun Chen, Ji Tae Kim, Zhong-Ren Chen, Xing Cheng
Biomedical Instrumentation
2025

The paper presents an ultrafast polymerase chain reaction platform based on a MEMS microheater. The technology enables rapid thermal cycling and improves the speed of molecular diagnostics workflows.

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