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
10.1017/S1431927606067894
TEM
Screening of Individual Nanostructures with STEM-EELS and EFTEM Spectral Imaging
I Anderson, J Scott, K Klein, A Melechko, M Simpson
Microscopy and Microanalysis
2006

The paper demonstrates STEM-EELS and EFTEM spectral imaging for screening individual nanostructures. The combined methodology delivers spatially resolved chemical and electronic characterization at the nanoscale.

Data Analysis Software
10.2352/ISSN.2169-4451.2006.22.1.art00037_1
SEM
Toner Particle Shape Characterization by FE-SEM Image Analysis
Dustin M. Earnhardt, Mark R. Cummings, Kenzo Ogata
NIP & Digital Fabrication Conference
2006

The authors apply FE-SEM image analysis techniques to characterize toner particle shape and morphology. Quantitative measurements provide insight into particle properties that influence printing performance.

4D-STEM Software
10.4028/www.scientific.net/SSP.105.37
TEM
Advances in Automatic TEM Based Orientation Mapping
Jean-Jacques Fundenberger, Adam Morawiec, Emmanuel Bouzy
Solid State Phenomena
2005

The paper reviews advances in automatic orientation mapping based on transmission electron microscopy. The methodology enables efficient crystallographic characterization and supports detailed microstructural analysis.

In-Situ TEM Software
10.1017/S1431927605504057
TEM
Cryo-FIB for Thinning Cryo-TEM samples and Evading Ice During Cryo-Transfer
W J MoberlyChan, M Marko, C-E Hsieh
Microscopy and Microanalysis
2005

The authors present cryo-focused ion beam methods for thinning cryo-TEM specimens while minimizing ice contamination during transfer. The technique improves sample quality and supports high-resolution cryogenic imaging.

Simulation Software
10.1002/sia.2115
SEM
EBSD geometry in the SEM: simulation and representation
Andrew Deal, Xiaodong Tao, Alwyn Eades
Surface and Interface Analysis
2005

This work investigates the geometry of electron backscatter diffraction within a scanning electron microscope. Simulations and visual representations help clarify signal generation and detector configuration effects.

4D-STEM Software
10.1016/j.tsf.2005.01.038
TEM
Phase segregation in laser crystallized polycrystalline SiGe thin films
M. Weizman, N.H. Nickel, I. Sieber, W. Bohne, J. Röhrich, E. Strub, B. Yan
Thin Solid Films
2005

The paper investigates phase segregation phenomena in laser-crystallized polycrystalline SiGe thin films. The findings improve understanding of compositional redistribution and microstructural evolution during processing.

Data Analysis Software
10.3182/20050703-6-CZ-1902.01814
SEM
PLANT DATA VISUALIZATION USING NON-NEGATIVE MATRIX FACTORIZATION
J. Tapson, J.R. Greene
IFAC Proceedings Volumes
2005

The paper explores visualization techniques for plant data using non-negative matrix factorization. The approach extracts meaningful patterns and supports interpretation of complex biological datasets.

Data Analysis Software
10.1107/S0021889805006059
X-ray
Quantitative Rietveld texture analysis of zirconium from single synchrotron diffraction images
Gloria Ischia, Hans-Rudolf Wenk, Luca Lutterotti, Florian Berberich
Journal of Applied Crystallography
2005

This study applies Rietveld texture analysis to synchrotron diffraction images of zirconium. Quantitative orientation distributions are extracted from a single diffraction image to characterize preferred crystallographic textures.

Open-Source TEM Software
10.1016/S0168-9002(04)01713-9
X-ray
Silicon-based photon counting X-ray detector for synchrotron applications
A Fant, M French, P Murray, P Seller, S Manolopoulos, S Thomas
Nuclear Instruments and Methods in Physics Research Section A: Accelerators, Spectrometers, Detectors and Associated Equipment
2004

The paper presents a silicon-based photon-counting X-ray detector developed for synchrotron applications. The technology improves detection efficiency, counting accuracy, and measurement sensitivity.

4D-STEM Software
10.1016/S1369-7021(04)00578-4
TEM
Three-dimensional X-ray diffraction microscopy
Materials Today
2004

This article reviews three-dimensional X-ray diffraction microscopy as a tool for non-destructive characterization of crystalline materials. The method provides insight into grain structures, orientations, and internal defects within bulk samples.

Data Analysis Software
10.1063/1.1650034
X-ray
THz near-field imaging employing synchrotron radiation
U. Schade, K. Holldack, P. Kuske, G. Wüstefeld, H.-W. Hübers
Applied Physics Letters
2004

This work demonstrates terahertz near-field imaging using coherent synchrotron radiation. The approach achieves sub-diffraction-limited spatial resolution for advanced spectroscopy and imaging applications.

Data Analysis Software
10.1016/j.jsb.2004.06.006
TEM
XMIPP: a new generation of an open-source image processing package for electron microscopy
C.O.S. Sorzano, R. Marabini, J. Velázquez-Muriel, J.R. Bilbao-Castro, S.H.W. Scheres, J.M. Carazo, A. Pascual-Montano
Journal of Structural Biology
2004

XMIPP introduces an open-source image-processing package designed for electron microscopy research. The software includes tools for classification, alignment, reconstruction, and quantitative image analysis.

Microscope Automation Software
10.1017/S1431927603033002
TEM
Signal Extraction and Visualization of Biological Structures from Electron Tomograms
Reiner Hegerl, Ariane Briegel
Microscopy and Microanalysis
2003

This work describes methods for extracting and visualizing biological structures from electron tomograms. The techniques enhance interpretation of complex cellular datasets and three-dimensional features.

Data Analysis Software
10.1007/0-387-23814-X_13
TEM
Transmission Electron Microscopy and Spectroscopy
Handbook of Nanophase and Nanostructured Materials
2003

This chapter provides an overview of transmission electron microscopy and spectroscopy techniques. The discussion outlines imaging, diffraction, and spectroscopic methods used to investigate nanoscale materials.

In-Situ TEM Software
10.1016/S0927-0256(01)00231-2
TEM
Dislocation nucleation and propagation during thin film deposition under compression
W.C. Liu, S.Q. Shi, Hanchen Huang, C.H. Woo
Computational Materials Science
2002

The authors investigate dislocation nucleation and propagation during compressive thin-film deposition. Computational analysis helps explain defect formation and stress-relief mechanisms in growing films.

4D-STEM Software
10.1017/S1431927602106428
TEM
Misorientation Mapping for Visualization of Plastic Strain Via Electron Back-Scattered Diffraction
L.N. Brewer, M.A. Othon, , L.M. Young, T.M. Angeliu
Microscopy and Microanalysis
2002

This research presents misorientation mapping techniques based on EBSD for visualizing plastic deformation. The approach highlights strain localization patterns and supports quantitative assessment of material response.

Data Analysis Software
10.1016/S0168-1273(00)30005-8
TEM
Chapter 188 Crystal chemistry of superconducting rare-earth cuprates
B. Raveau, C. Michel, M. Hervieu
Handbook on the Physics and Chemistry of Rare Earths
2000

This chapter reviews the crystal chemistry of superconducting rare-earth cuprates. The discussion links atomic structure, composition, and superconducting behavior in these technologically important materials.

Data Analysis Software
10.1017/S1431927600034395
SEM
Comparison of Particle Size Analyses from FEG-SEM and TEM Images
S Lanteri, D Gendt, P Barges, G Petitgand
Microscopy and Microanalysis
2000

This paper compares particle-size measurements obtained from field-emission SEM and TEM images. The analysis evaluates consistency between techniques and highlights factors affecting measurement accuracy.

Microscope Automation Software
10.1006/jsbi.2000.4314
TEM
Leginon: An Automated System for Acquisition of Images from Vitreous Ice Specimens
Bridget Carragher, Nick Kisseberth, David Kriegman, Ronald A. Milligan, Clinton S. Potter, James Pulokas, Amy Reilein
Journal of Structural Biology
2000

Leginon automates image acquisition from cryogenic electron microscopy specimens. The system improves data collection efficiency, consistency, and throughput while reducing manual intervention.

Tomography Software
10.6009/jjrt.KJ00001356956
X-ray
Monochromatic X-ray CT Using Synchrotron Radiation
Fukai Toyofuku
Japanese Journal of Radiological Technology
2000

The authors discuss monochromatic X-ray computed tomography performed with synchrotron radiation sources. The approach provides high image quality and improved quantitative characterization compared with conventional methods.

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