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
10.4018/978-1-7998-3591-2.ch004
SEM
Heterogeneous Large-Scale Distributed Systems on Machine Learning:
Karthika Paramasivam, Prathap M., Hussain Sharif
Advances in Bioinformatics and Biomedical Engineering
2020

The article reviews large-scale heterogeneous distributed systems used for machine learning workloads. It highlights frameworks such as TensorFlow and discusses scalable computing architectures for AI applications.

Data Analysis Software
10.1017/S1431927620022540
X-ray
High Speed SEM Elemental Mapping with Micro-XRF-EDS
Andrew Menzies, Stephan Boehm, John Mastovich
Microscopy and Microanalysis
2020

This work presents high-speed elemental mapping in SEM through the integration of micro-XRF and EDS technologies. The combined approach improves compositional imaging speed and analytical coverage.

In-Situ TEM Software
10.3390/cryst10010041
TEM
In Situ TEM Crystallization of Amorphous Iron Particles
Andrea Falqui, Danilo Loche, Alberto Casu
Crystals
2020

The authors explore crystallization processes in amorphous iron particles using in-situ TEM. Real-time observations reveal structural transitions and thermal stability characteristics at the nanoscale.

In-Situ TEM Software
10.1017/S1431927620018061
TEM
In Situ TEM Investigation on the Thermal Stability of Hydroxyapatite Nanobelts
Mei-li Qi, Shengkun Yao, Zhennan Huang, Yu-peng Lu, Tolou Shokuhfar
Microscopy and Microanalysis
2020

This paper evaluates the thermal stability of hydroxyapatite nanobelts through in-situ TEM experiments. The results provide insight into morphological and structural changes occurring during heating.

Data Analysis Software
10.1109/XLOOP51963.2020.00010
X-ray
Interactive Parallel Workflows for Synchrotron Tomography
Dilworth Y. Parkinson, Harinarayan Krishnan, Daniela Ushizima, Matthew Henderson, Shreyas Cholia
2020 IEEE/ACM 2nd Annual Workshop on Extreme-scale Experiment-in-the-Loop Computing (XLOOP)
2020

The authors develop interactive parallel workflows for synchrotron tomography experiments. The framework accelerates data processing and enables near real-time analysis of large imaging datasets.

Simulation Software
10.1107/S1600576720010985
X-ray
<i>PyNX</i> : high-performance computing toolkit for coherent X-ray imaging based on operators
Vincent Favre-Nicolin, Gaétan Girard, Steven Leake, Jerome Carnis, Yuriy Chushkin, Jerome Kieffer, Pierre Paleo, Marie-Ingrid Richard
Journal of Applied Crystallography
2020

PyNX is a high-performance computing toolkit for coherent X-ray imaging and simulation. GPU-based processing supports advanced imaging reconstruction and analysis workflows.

Data Analysis Software
10.21105/joss.02006
TEM
LiberTEM: Software platform for scalable multidimensional data processing in transmission electron microscopy
Alexander Clausen, Dieter Weber, Karina Ruzaeva, Vadim Migunov, Anand Baburajan, Abijith Bahuleyan, Jan Caron, Rahul Chandra, Sayandip Halder, Magnus Nord, Knut Müller-Caspary, Rafal Dunin-Borkowski
Journal of Open Source Software
2020

LiberTEM provides a high-performance framework for analyzing large electron microscopy datasets. Its distributed architecture enables rapid data exploration and supports real-time scientific workflows across multiple computing environments.

Data Analysis Software
10.1016/j.icarus.2019.113441
TEM
Mapping the zonal structure of Titan's northern polar vortex
Jason Sharkey, Nicholas A. Teanby, Melody Sylvestre, Dann M. Mitchell, William J.M. Seviour, Conor A. Nixon, Patrick G.J. Irwin
Icarus
2020

This study maps the zonal structure of Titan’s northern polar vortex using atmospheric observations and modeling. The analysis reveals circulation patterns that improve understanding of climate dynamics on Saturn’s largest moon.

In-Situ TEM Software
10.1021/acsomega.0c04711
TEM
Mitigating Damage to Hybrid Perovskites Using Pulsed-Beam TEM
Elisah J. VandenBussche, Catherine P. Clark, Russell J. Holmes, David J. Flannigan
ACS Omega
2020

The paper demonstrates the use of pulsed-beam TEM to reduce radiation damage in hybrid perovskite materials. The approach helps preserve specimen integrity while maintaining imaging performance.

Data Analysis Software
10.1107/S0108767320097810
TEM
Neural network particle picking and denoising in cryoEM with <i>Topaz</i>
Alex Noble, Tristan Bepler, Bonnie Berger
Acta Crystallographica Section A Foundations and Advances
2020

Topaz employs neural networks for both particle identification and image denoising in cryo-EM workflows. The framework improves data quality and enhances downstream structural reconstruction tasks.

Data Analysis Software
10.1117/12.2573154
SEM
Open-source software for SEM metrology
Iacopo Mochi, Michaela Vockenhuber, Timothée P. Allenet, Yasin Ekinci
Photomask Technology 2020
2020

The authors present open-source software tools developed for SEM metrology applications. The framework improves accessibility, reproducibility, and measurement capabilities for microscopy-based dimensional analysis.

Simulation Software
10.3390/proceedings2020059006
TEM
Predicting Airplane Go-Arounds Using Machine Learning and Open-Source Data
Benoit Figuet, Raphael Monstein, Manuel Waltert, Steven Barry
8th OpenSky Symposium 2020
2020

This study uses machine learning models and openly available aviation datasets to predict aircraft go-around events. The approach supports operational analysis and improved understanding of flight safety factors.

Data Analysis Software
10.1088/1757-899X/891/1/012002
SEM
Processing and indexing of electron backscatter patterns using open-source software
H W Ånes, J Hjelen, B E Sørensen, A T J Van Helvoort, K Marthinsen
IOP Conference Series: Materials Science and Engineering
2020

The authors describe open-source methods for processing and indexing electron backscatter diffraction patterns. Principal component analysis and related techniques are used to enhance signal quality and improve EBSD data interpretation.

Tomography Software
10.1017/S1431927620017572
X-ray
Processing X-ray Fluorescence Tomography Data With XRFtomo
Fabricio Marin, Si Chen, Francesco De Carlo, Arthur Glowacki, Olga Antipova, Lu Xi Li
Microscopy and Microanalysis
2020

This work presents XRFtomo, a software tool for processing X-ray fluorescence tomography data. The package supports reconstruction, visualization, and analysis of elemental imaging datasets.

Data Analysis Software
10.1016/j.matchar.2020.110506
SEM
Secondary phase area fraction determination using SEM-EDS quantitative mapping
Minshi Wang, Yulung Chiu, Dominique Flahaut, Ian P. Jones, Zhu Zhang
Materials Characterization
2020

This work presents a method for determining secondary-phase area fractions using quantitative SEM-EDS mapping. Automated compositional analysis improves the assessment of multiphase material microstructures.

Simulation Software
10.1007/978-3-030-38435-7_13
TEM
Simulated Reconstruction Based on Virtual Imaging
Kyoji Matsushima
Introduction to Computer Holography
2020

The chapter describes virtual imaging methods for simulating holographic reconstructions. The framework explains how computational models can generate and analyze reconstructed wavefronts from synthetic data.

Data Analysis Software
10.5940/jcrsj.62.10
X-ray
Sparse Phase Retrieval Algorithm for Coherent X-ray Diffraction Imaging
Yuichi Yamasaki
Nihon Kessho Gakkaishi
2020

This article introduces a sparse phase-retrieval algorithm for coherent X-ray diffraction imaging. The method improves reconstruction quality while leveraging sparse representations of the sample structure.

Data Analysis Software
10.1017/S143192762002334X
TEM
STEMTooL: An Open Source Python Toolkit for Analyzing Electron Microscopy Datasets
Debangshu Mukherjee, Raymond Unocic
Microscopy and Microanalysis
2020

STEMTooL provides an open-source collection of Python utilities for processing electron microscopy datasets. The framework simplifies image handling, quantitative measurements, and custom analytical workflows for researchers.

Data Analysis Software
10.31031/AMMS.2020.05.000606
X-ray
Synchrotron-(XRF, XRD, XAFS) Techniques in Advanced Mineralogy
Garg Nandini
Aspects in Mining & Mineral Science
2020

This review highlights the applications of synchrotron XRF, XRD, and XAFS methods in advanced mineralogy. These techniques provide complementary information about composition, structure, and chemical states.

In-Situ TEM Software
10.1017/S1431927620013331
TEM
Understanding Radiation Damage in Beam-Sensitive TEM Specimens
Ray Egerton
Microscopy and Microanalysis
2020

The article reviews radiation damage mechanisms in beam-sensitive TEM specimens. Understanding these effects helps researchers optimize imaging conditions and preserve delicate materials.

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