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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Simulation Software
10.1007/978-3-540-85156-1_119
TEM
“Phase-scrambling” multislice simulations of precession electron diffraction
T. A. White, A. S. Eggeman, P. A. Midgley
EMC 2008 14th European Microscopy Congress 1–5 September 2008, Aachen, Germany
2008

This work introduces phase-scrambling multislice simulations to examine precession electron diffraction. The method improves understanding of diffraction behavior and supports more realistic modeling studies.

Simulation Software
10.1007/978-3-540-85156-1_47
TEM
Quantitative TEM and STEM Simulations
C. T. Koch
EMC 2008 14th European Microscopy Congress 1–5 September 2008, Aachen, Germany
2008

The article discusses quantitative simulation methods for TEM and STEM experiments. These computational approaches help researchers compare observations with theoretical predictions and improve interpretation accuracy.

Data Analysis Software
10.1007/978-3-540-85226-1_19
TEM
STEM EELS/EDX dopant analysis of nm-scale Si devices
G. Servanton, R. Pantel, M. Juhel, F. Bertin
EMC 2008 14th European Microscopy Congress 1–5 September 2008, Aachen, Germany
2008

The study combines STEM, EELS, and EDX techniques for dopant characterization in nanoscale silicon devices. The integrated workflow provides detailed compositional mapping at technologically relevant dimensions.

Tomography Software
10.1007/978-3-540-85156-1_156
TEM
STEM electron tomography of gold nanostructures
J. C. Hernandez, M. S. Moreno, E. A. Coronado, P. A. Midgley
EMC 2008 14th European Microscopy Congress 1–5 September 2008, Aachen, Germany
2008

This work applies STEM electron tomography to reconstruct three-dimensional gold nanostructures. The technique provides detailed visualization of morphology and internal architecture beyond conventional imaging methods.

Data Analysis Software
10.1007/978-3-540-85156-1_260
SEM
Surface potential and SE detection in the SEM
J. Cazaux
EMC 2008 14th European Microscopy Congress 1–5 September 2008, Aachen, Germany
2008

This study explores the relationship between surface potential and secondary-electron detection in scanning electron microscopy. The findings contribute to improved interpretation of image contrast and charging effects.

Tomography Software
10.1093/acprof:oso/9780199213245.003.0005
X-ray
SYNCHROTRON X-RAY ABSORPTION TOMOGRAPHY
Astrid Haibel
Advanced Tomographic Methods in Materials Research and Engineering
2008

This chapter introduces the principles of synchrotron X-ray absorption tomography for three-dimensional materials characterization. The technique exploits variations in attenuation and density to reveal internal structures with high spatial resolution.

4D-STEM Software
10.1002/9780470444214.ch11
TEM
Texture Changes During Phase Transformations Studied <i>in situ</i> With Neutron Diffraction
Hans‐Rudolf Wenk
Ceramic Transactions Series
2008

This work examines texture evolution during phase transformations through in-situ neutron diffraction measurements. The approach provides insight into crystallographic changes occurring during material processing and transformation.

Data Analysis Software
10.2144/000112257
SEM
CellProfiler™: Free, Versatile Software for Automated Biological Image Analysis
Michael R. Lamprecht, David M. Sabatini, Anne E. Carpenter
BioTechniques
2007

This paper introduces CellProfiler as a free and versatile solution for automated biological image analysis. Its modular workflow design allows researchers to process large imaging datasets efficiently and reproducibly.

In-Situ TEM Software
10.1557/PROC-1036-M05-02
TEM
Electromigration Reliability in Nanoscale Cu Interconnects
C.-K. Hu, L. M. Gignac, B. C. Baker-O'Neal, G. Bonilla, E. G. Liniger, P. L. Flaitz
MRS Proceedings
2007

This research analyzes electromigration reliability in nanoscale copper interconnects. The findings highlight how microstructure and processing conditions influence long-term device durability.

Data Analysis Software
10.1016/j.jsb.2006.05.009
TEM
EMAN2: An extensible image processing suite for electron microscopy
Guang Tang, Liwei Peng, Philip R. Baldwin, Deepinder S. Mann, Wen Jiang, Ian Rees, Steven J. Ludtke
Journal of Structural Biology
2007

EMAN2 provides an extensible image-processing environment for electron microscopy data analysis. The suite supports reconstruction, visualization, and workflow customization for a broad range of structural biology applications.

Open-Source TEM Software
10.1201/b17472-6
TEM
Image Data Formats and Image Compression
Elizabeth Berry
A Practical Approach to Medical Image Processing
2007

This chapter reviews common image file formats and compression techniques used in medical imaging. It explains trade-offs between storage efficiency, image quality, and data accessibility.

In-Situ TEM Software
10.1016/S1369-7021(07)70051-2
TEM
In situ nanoindentation in the TEM
Oden L. Warren, Zhiwei Shan, S.A. Syed Asif, Eric A. Stach, J.W. Morris, Andrew M. Minor
Materials Today
2007

This article reviews in-situ nanoindentation techniques performed inside a transmission electron microscope. The approach combines mechanical testing with direct imaging to reveal deformation mechanisms at nanometer scales.

Data Analysis Software
10.1186/1471-2105-8-288
TEM
TomoJ: tomography software for three-dimensional reconstruction in transmission electron microscopy
Cédric MessaoudiI, Thomas Boudier, Carlos Oscar Sanchez Sorzano, Sergio Marco
BMC Bioinformatics
2007

TomoJ offers a software suite for three-dimensional reconstruction from transmission electron tomography experiments. The platform integrates alignment, reconstruction, and visualization functions to reveal cellular and material structures.

Data Analysis Software
10.63485/x8tt8-2215
X-ray
Access to scientific data
Peter Suber
Front Matter
2006

The article discusses issues surrounding access to scientific data and the importance of data sharing within the research community. It highlights challenges and opportunities related to openness, accessibility, and collaboration.

Data Analysis Software
10.1186/gb-2006-7-10-r100
SEM
CellProfiler: image analysis software for identifying and quantifying cell phenotypes
Anne E Carpenter, Thouis R Jones, Michael R Lamprecht, Colin Clarke, In Han Kang, Ola Friman, David A Guertin, Joo Han Chang, Robert A Lindquist, Jason Moffat, Polina Golland, David M Sabatini
Genome Biology
2006

CellProfiler provides automated image-analysis capabilities for identifying and quantifying cellular phenotypes. The software enables high-throughput biological experiments by reducing the need for manual image evaluation.

Data Analysis Software
10.1017/S1431927606069066
SEM
Considerations for Automated Multi-Frame Particle Sizing in the SEM
G Fritz, P Camus, D Rohde
Microscopy and Microanalysis
2006

The study examines practical considerations for automated multi-frame particle sizing in scanning electron microscopy. The approach aims to improve throughput, reliability, and statistical robustness in particle characterization.

Data Analysis Software
10.1145/1182807.1182844
X-ray
Data analysis tools for sensor-based science
Stuart Ozer, Jim Gray, Alex Szalay, Andreas Terzis, Razvan Musaloiu-E, Katalin Szlavecz, Randal Burns, Josh Cogan
Proceedings of the 4th international conference on Embedded networked sensor systems
2006

The paper presents data-analysis tools designed for sensor-based scientific research. The framework assists in managing, processing, and interpreting large volumes of data generated by distributed sensor networks.

In-Situ TEM Software
10.1016/j.nimb.2005.08.158
TEM
Grain growth in Zr–Fe thin films during in situ ion irradiation in a TEM
D. Kaoumi, A.T. Motta, R.C. Birtcher
Nuclear Instruments and Methods in Physics Research Section B: Beam Interactions with Materials and Atoms
2006

The study examines grain growth in zirconium-iron thin films exposed to ion irradiation inside a TEM. Observations reveal how radiation influences microstructural development and material stability.

Data Analysis Software
10.1117/12.671232
X-ray
Performance characterization of hard x-ray imaging instruments at synchrotron radiation facility SPring-8
Yasushi Ogasaka, Keisuke Tamura, Ryo Shibata, Akihiro Furuzawa, Tomokazu Nakamura, Masataka Naitou, Takuya Miyazawa, Kenta Shimoda, Katsuhiko Onishi, Yoshihiro Fukaya, Tomonaga Iwahara, Yasushi Kanou, Hideyo Kunieda, Koujun Yamashita, Emi Miyata, Kenji Mukai, Kazuhiro Ikegami, Michihiko Aono, Hiroshi Tsunemi, Kentaro Uesugi, Yoshio Suzuki
2006

This work characterizes the performance of hard X-ray imaging instruments at the SPring-8 synchrotron facility. The evaluation provides insight into imaging quality, resolution, and instrument capabilities.

Simulation Software
10.1109/MILCOM.2006.302437
TEM
Reliability Simulation of Large-Scale Networks using Sampling-Scale
Jack McCann, Lynn Carlson, Kristy Casella
MILCOM 2006
2006

This work presents a sampling-based framework for evaluating reliability in large-scale communication networks. The approach estimates network performance characteristics without exhaustive simulation.

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