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
10.1007/s00216-011-4913-7
X-ray
Synchrotron radiation phase-contrast X-ray CT imaging of acupuncture points
Dongming Zhang, Xiaohui Yan, Xinyi Zhang, Chenglin Liu, Ruishan Dang, Tiqiao Xiao, Peiping Zhu
Analytical and Bioanalytical Chemistry
2011

This paper applies synchrotron phase-contrast X-ray computed tomography to visualize acupuncture points and surrounding biological structures. The method provides non-destructive three-dimensional imaging with enhanced soft-tissue contrast.

Data Analysis Software
10.1117/12.892688
X-ray
The xraylib library for x-ray-matter interaction cross sections: new developments and applications
Tom Schoonjans, Antonio Brunetti, Bruno Golosio, Manuel Sanchez Del Rio, Vicente Armando Solé, Claudio Ferrero, Laszlo Vincze
2011

This article describes new developments in the xraylib library for calculating X-ray–matter interaction cross sections. The software provides accurate physical data and computational tools for spectroscopy, imaging, and materials characterization applications.

Data Analysis Software
10.1063/1.3463256
X-ray
areaDetector: Software for 2-D Detectors in EPICS
Mark L. Rivers, R. Garrett, I. Gentle, K. Nugent, S. Wilkins
2010

areaDetector is a software framework for integrating two-dimensional detectors with EPICS-based control systems. The platform enables efficient acquisition, control, and processing of detector data in scientific facilities.

Data Analysis Software
10.1109/ASMS-SPSC.2010.5586889
TEM
Blind source separation of hyperspectral images in DCT-domain
Emna Karray, Med Anis Loghmari, Med Saber Naceur
2010 5th Advanced Satellite Multimedia Systems Conference and the 11th Signal Processing for Space Communications Workshop
2010

This research explores blind source separation of hyperspectral images within the DCT domain. The technique isolates mixed spectral components and improves interpretation of complex imaging data.

In-Situ TEM Software
10.1017/S1431927610054929
TEM
In-Situ TEM studies of Lithium Ion Battery
Cm Wang, W Xu, B Arey, Lv Saraf, Dw Choi, J Liu, Zg Yang, Jg Zhang, S Thevuthasan, Dr Baer
Microscopy and Microanalysis
2010

The study employs in-situ TEM to investigate structural and electrochemical processes occurring in lithium-ion batteries. Direct observation enables a deeper understanding of electrode behavior during operation.

Data Analysis Software
10.1107/S0021889809045701
X-ray
<i>xia2</i> : an expert system for macromolecular crystallography data reduction
G. Winter
Journal of Applied Crystallography
2010

xia2 is an expert system that automates macromolecular crystallography data reduction. The software streamlines processing workflows from raw diffraction images to merged datasets.

Data Analysis Software
10.4028/www.scientific.net/SSP.160.63
SEM
Texture Analysis with MTEX – Free and Open Source Software Toolbox
F. Bachmann, Ralf Hielscher, Helmut Schaeben
Solid State Phenomena
2010

MTEX is a free open-source toolbox for crystallographic texture analysis. The software assists researchers in interpreting orientation data obtained from diffraction and electron backscatter measurements.

10.1016/j.nima.2009.01.224
TEM
Differential phase contrast and dark field neutron imaging
M. Strobl, A. Hilger, N. Kardjilov, O. Ebrahimi, S. Keil, I. Manke
Nuclear Instruments and Methods in Physics Research Section A: Accelerators, Spectrometers, Detectors and Associated Equipment
2009

The paper introduces differential phase contrast and dark-field methods for neutron imaging applications. These techniques provide additional structural and scattering information beyond conventional transmission-based measurements.

In-Situ TEM Software
10.1017/S1431927609093738
TEM
In-Situ TEM Observation of Domain Behavior in Multiferroic Structures Under Applied DC Bias
C Winkler, L Martin, C Johnson, M Taheri
Microscopy and Microanalysis
2009

This work examines domain behavior in multiferroic structures subjected to applied electrical bias. In-situ TEM observations reveal how domain configurations evolve in response to external stimuli.

Data Analysis Software
10.1109/IVCNZ.2009.5378364
SEM
Red blood cell segmentation from SEM images
Joost Vromen, Brendan McCane
2009 24th International Conference Image and Vision Computing New Zealand
2009

This work presents segmentation methods for identifying red blood cells in SEM images. Automated image analysis improves efficiency and consistency in microscopy-based biological studies.

Data Analysis Software
10.1007/978-3-642-03767-2_72
SEM
SEM Image Analysis for Quality Control of Nanoparticles
S. K. Alexander, R. Azencott, B. G. Bodmann, A. Bouamrani, C. Chiappini, M. Ferrari, X. Liu, E. Tasciotti
Computer Analysis of Images and Patterns
2009

This paper presents SEM image-analysis techniques for nanoparticle quality control. Automated image processing enables quantitative assessment of particle size, shape, and distribution in nanomaterial production.

Tomography Software
10.1007/978-3-642-04772-5_44
TEM
Tomographic Image Reconstruction Using Abstractions
J. A. Alvarez, J. Roca
Computer Aided Systems Theory - EUROCAST 2009
2009

The authors present an abstraction-based framework for tomographic image reconstruction. The approach simplifies algorithm development while supporting flexible implementation of reconstruction workflows.

Data Analysis Software
10.1007/978-3-540-85156-1_299
SEM
3D Sculptures From SEM Images
R. Pintus, S. Podda, M. Vanzi
EMC 2008 14th European Microscopy Congress 1–5 September 2008, Aachen, Germany
2008

This paper explores the creation of three-dimensional sculptures and visual representations derived from SEM imagery. The work demonstrates how microscopy data can be transformed into informative 3D models.

4D-STEM Software
10.1016/j.ejor.2007.08.008
TEM
Adaptive data reduction for large-scale transaction data
Xiao-Bai Li, Varghese S. Jacob
European Journal of Operational Research
2008

The authors propose adaptive techniques for reducing the volume of large-scale transaction datasets. The method preserves analytical value while lowering storage and computational requirements.

In-Situ TEM Software
10.1007/s11431-008-0123-8
TEM
A MEMS device for in-situ TEM test of SCS nanobeam
QinHua Jin, YueLin Wang, Tie Li, XinXin Li, FangFang Xu
Science in China Series E: Technological Sciences
2008

This paper introduces a MEMS-based device designed for in-situ TEM testing of nanobeams. The platform enables controlled mechanical loading while simultaneously observing structural responses.

Data Analysis Software
10.1002/imic.200890065
SEM
Correlative 3D Microscopy: CLSM and FIB/SEM Tomography: A Study of Cellular Entry of Vaccinia Virus
Miriam S. Lucas, Philippe Gasser, Maja M. Günthert, Roger Wepf, Jason Mercer, Ari Helenius, Andreas Schertel
Imaging & Microscopy
2008

This study combines confocal laser scanning microscopy and FIB-SEM tomography to investigate vaccinia virus entry into cells. Correlative three-dimensional imaging reveals structural details of virus-host interactions.

Data Analysis Software
10.1063/1.2937302
SEM
Fractal Image Informatics: from SEM to DEM
K. Oleschko, J.-F. Parrot, G. Korvin, M. Esteves, M. Vauclin, V. Torres-Argüelles, C. Gaona Salado, S. Cherkasov, Klaudia Oleschko, Sergei Cherkasov, José Luís Palacio Prieto, Vianey Torres Argüelles, Claudia I. Gaona Salado, Ana Gabriela Castañeda Miranda, Sergio Aurelio Zamora Castro
AIP Conference Proceedings
2008

The authors investigate fractal image informatics across scales ranging from SEM to digital elevation models. The work explores fractal analysis as a tool for understanding complex natural and engineered structures.

In-Situ TEM Software
10.1007/978-3-540-85156-1_248
TEM
In-situ TEM mechanical testing of a Si MEMS nanobridge
A. J. Lockwood, R. J. T. Bunyan, B. J. Inkson
EMC 2008 14th European Microscopy Congress 1–5 September 2008, Aachen, Germany
2008

The study presents in-situ TEM mechanical testing of a silicon MEMS nanobridge. Direct measurements provide insight into nanoscale deformation and structural integrity under applied stress.

Microscope Automation Software
10.63485/bje0d-mj414
TEM
Open Babel for Python scripts
Peter Suber
Front Matter
2008

This contribution highlights the use of Open Babel within Python scripting environments. The toolkit enables manipulation, conversion, and analysis of chemical data through automated workflows.

Data Analysis Software
10.1109/ISCE.2008.4559573
TEM
Personal television: A synchronized metadata system
Peter Dunker, Uwe Kuhhirt
2008 IEEE International Symposium on Consumer Electronics
2008

This study presents a synchronized metadata system designed for personal television applications. The framework enhances content organization, navigation, and user interaction through coordinated metadata management.

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