Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

Electron Microscope Tomography and Single-particle Reconstruction01:07

Electron Microscope Tomography and Single-particle Reconstruction

2.6K
Transmission electron microscopy (TEM) can be used to determine the 3D structure of biological samples with the help of techniques such as electron microscope tomography and single-particle reconstruction. While single-particle reconstruction can examine macromolecules and macromolecular complexes in vitro conditions only, tomography permits the study of cell components or small cells in vivo.
Electron Tomography
Electron tomography can be performed either in TEM or STEM (scanning transmission...
2.6K

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

Atomic Evolution of Hydrogen Intercalation Wave Dynamics in Palladium Nanocrystals Revealed by Liquid-Phase Transmission Electron Microscopy.

Journal of the American Chemical Society·2026
Same author

Staging and defect-limited intercalation of FeCl<sub>3</sub> in graphite electrodes.

Nature communications·2026
Same author

Toward Hydrogen Isotope Separations through Strong Hydrogen Adsorption at Open Copper(I) Sites in an Ultramicroporous Metal-Organic Framework.

Journal of the American Chemical Society·2026
Same author

Three-Dimensional Atomic Scale Insights into Unconventional Fragmentation of Two-Dimensional ReS<sub>2</sub> Monolayers into Molecular Clusters.

ACS nano·2026
Same authorSame journal

Unsupervised Segmentation and Clustering Workflow for Efficient Processing of 4D-STEM and 5D-STEM Data.

Microscopy and microanalysis : the official journal of Microscopy Society of America, Microbeam Analysis Society, Microscopical Society of Canada·2026
Same author

Model for Imaging in High-Resolution Secondary Electron Microscopy.

Microscopy and microanalysis : the official journal of Microscopy Society of America, Microbeam Analysis Society, Microscopical Society of Canada·2026
Same journal

Lingual Surface Morphology in Delphinids: Structural Adaptations to Feeding Strategies.

Microscopy and microanalysis : the official journal of Microscopy Society of America, Microbeam Analysis Society, Microscopical Society of Canada·2026
Same journal

A Scalable Pathway for Plan-View TEM of 2D Materials and Surface Layers.

Microscopy and microanalysis : the official journal of Microscopy Society of America, Microbeam Analysis Society, Microscopical Society of Canada·2026
Same journal

Development of an EDS-Based Grain Segmentation Method for MIMAS-MOX Nuclear Fuels.

Microscopy and microanalysis : the official journal of Microscopy Society of America, Microbeam Analysis Society, Microscopical Society of Canada·2026
Same journal

The Fabrication of Atom Probe Tomography Specimens From Mineral Nanoplates by Focused Ion Beam Redeposition.

Microscopy and microanalysis : the official journal of Microscopy Society of America, Microbeam Analysis Society, Microscopical Society of Canada·2026
Same journal

From Bone to Body: Qualitative Evaluation of Collagenous Tissues Using JFRL Staining in Normal and Pathological Conditions.

Microscopy and microanalysis : the official journal of Microscopy Society of America, Microbeam Analysis Society, Microscopical Society of Canada·2026
See all related articles

Related Experiment Video

Updated: Nov 4, 2025

Cryo-Electron Tomography Remote Data Collection and Subtomogram Averaging
08:55

Cryo-Electron Tomography Remote Data Collection and Subtomogram Averaging

Published on: July 12, 2022

5.4K

py4DSTEM: A Software Package for Four-Dimensional Scanning Transmission Electron Microscopy Data Analysis.

Benjamin H Savitzky1, Steven E Zeltmann2, Lauren A Hughes1

  • 1National Center for Electron Microscopy, Molecular Foundry, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA94720, USA.

Microscopy and Microanalysis : the Official Journal of Microscopy Society of America, Microbeam Analysis Society, Microscopical Society of Canada
|May 21, 2021
PubMed
Summary
This summary is machine-generated.

This study introduces py4DSTEM, an open-source Python toolkit for analyzing four-dimensional scanning transmission electron microscopy (4D-STEM) datasets. It simplifies extracting material properties from complex microscopy data, enhancing research standards.

Keywords:
4D-STEMSTEMcalibrationdiffractionopen source

More Related Videos

A 3D Cartographic Description of the Cell by Cryo Soft X-ray Tomography
08:47

A 3D Cartographic Description of the Cell by Cryo Soft X-ray Tomography

Published on: March 15, 2021

4.2K
Visualization of Organelles In Situ by Cryo-STEM Tomography
08:37

Visualization of Organelles In Situ by Cryo-STEM Tomography

Published on: June 23, 2023

2.6K

Related Experiment Videos

Last Updated: Nov 4, 2025

Cryo-Electron Tomography Remote Data Collection and Subtomogram Averaging
08:55

Cryo-Electron Tomography Remote Data Collection and Subtomogram Averaging

Published on: July 12, 2022

5.4K
A 3D Cartographic Description of the Cell by Cryo Soft X-ray Tomography
08:47

A 3D Cartographic Description of the Cell by Cryo Soft X-ray Tomography

Published on: March 15, 2021

4.2K
Visualization of Organelles In Situ by Cryo-STEM Tomography
08:37

Visualization of Organelles In Situ by Cryo-STEM Tomography

Published on: June 23, 2023

2.6K

Area of Science:

  • Materials Science
  • Physics
  • Computational Science

Background:

  • Scanning transmission electron microscopy (STEM) generates rich 4D-STEM datasets offering atomic-scale insights into material properties.
  • Extracting structural, orientational, and electromagnetic information from these datasets is challenging due to complex analysis pipelines and artifacts.

Purpose of the Study:

  • To present py4DSTEM, an open-source Python toolkit designed for robust analysis of 4D-STEM data.
  • To provide standardized algorithms for dataset calibration and material property measurements.
  • To facilitate data handling and promote community contribution in electron microscopy.

Main Methods:

  • Development of py4DSTEM, a Python-based analysis toolkit for 4D-STEM data.
  • Implementation of algorithms for dataset calibration, property measurement, and visualization.
  • Adoption of the HDF5 standard for a universal electron microscopy data file format.

Main Results:

  • Demonstration of py4DSTEM's capability in measuring various material properties from experimental 4D-STEM datasets.
  • Successful implementation of a universal file format for electron microscopy data.
  • Establishment of a robust and accessible platform for 4D-STEM data analysis.

Conclusions:

  • py4DSTEM offers a standardized and efficient approach to analyzing complex 4D-STEM data.
  • The toolkit and its universal file format aim to improve data integrity and computational methods in electron microscopy.
  • Encourages community engagement to further develop and enhance the py4DSTEM project.