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

Transmission Electron Microscopy01:15

Transmission Electron Microscopy

5.6K
In 1931, physicist Ernst Ruska—building on the idea that magnetic fields can direct an electron beam just as lenses can direct a beam of light in an optical microscope—developed the first prototype of the electron microscope. This development led to the development of the field of electron microscopy. In the transmission electron microscope (TEM), electrons are produced by a hot tungsten element and accelerated by a potential difference in an electron gun, which gives them up to 400...
5.6K
Electron Microscope Tomography and Single-particle Reconstruction01:07

Electron Microscope Tomography and Single-particle Reconstruction

2.4K
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...
2.4K
Overview of Electron Microscopy01:25

Overview of Electron Microscopy

9.2K
The wavelengths of visible light ultimately limit the maximum theoretical resolution of images created by light microscopes. Most light microscopes can only magnify 1000X, and a few can magnify up to 1500X. Electrons, like electromagnetic radiation, can behave like waves, but with wavelengths of 0.005 nm, they produce significantly greater resolution up to 0.05 nm as compared to 500 nm for visible light. An electron microscope (EM) can create a sharp image that is magnified up to 2,000,000X.
9.2K
Scanning Electron Microscopy01:07

Scanning Electron Microscopy

4.3K
A scanning electron microscope (SEM) is used to study the surface features of a sample by using an electron beam that scans the sample surface in a two-dimensional manner. Typically, areas between ~1 centimeter to 5 micrometers in width can be imaged. SEM can be used to image bacteria, viruses, tissues as well as larger samples like insects. Conventional SEM gives a magnification ranging from 20X to 30,000X and spatial resolution of 50 to 100 nanometers.
Fundamental Principles
Accelerated...
4.3K
Overview of Microscopy Techniques01:22

Overview of Microscopy Techniques

10.5K
The early pioneers of microscopy opened a window into the invisible world of microorganisms. In 1830, Joseph Jackson Lister created an essentially modern light microscope. The 20th century saw the development of microscopes that leveraged nonvisible light, such as fluorescence microscopy that uses an ultraviolet light source and electron microscopy that uses short-wavelength electron beams. These advances significantly improved magnification, image resolution, and contrast. By comparison, the...
10.5K
Cryo-electron Microscopy01:28

Cryo-electron Microscopy

3.4K
Conventional electron microscopy (EM) involves dehydration, fixation, and staining of biological samples, which distorts the native state of biological molecules and results in several artifacts. Also, the high-energy electron beam damages the sample and makes it difficult to obtain high-resolution images. These issues can be addressed using cryo-EM, which uses frozen samples and gentler electron beams. The technique was developed by Jacques Dubochet, Joachim Frank, and Richard Henderson, for...
3.4K

You might also read

Related Articles

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

Sort by
Same author

Targeted electron beam creates thousands of atomic crystal defects.

Nature·2026
Same author

Diffraction of helium and hydrogen atoms through single-layer graphene.

Science (New York, N.Y.)·2025
Same author

Ehrenfest dynamics with localized atomic-orbital basis sets within the projector augmented-wave method.

The Journal of chemical physics·2025
Same author

Quantifying phase magnitudes of open-source focused-probe 4D-STEM ptychography reconstructions.

Journal of microscopy·2025
Same author

Linear indium atom chains at graphene edges.

NPJ 2D materials and applications·2024
Same author

GPAW: An open Python package for electronic structure calculations.

The Journal of chemical physics·2024
Same journal

Digital science communication for sustainability literacy: A scoping review.

Open research Europe·2026
Same journal

EUPopLink Country report - Sweden.

Open research Europe·2026
Same journal

ERGA-BGE reference genome of <i>Gambusia holbrooki</i>, a globally invasive freshwater fish.

Open research Europe·2026
Same journal

Protocols for <i>in situ</i> continuous monitoring of water relations/potential in soil and leaf.

Open research Europe·2026
Same journal

Generative AI in education: Process-aware pedagogy, assessment integrity, and institutional governance.

Open research Europe·2026
Same journal

SentinelSphere: An AI-driven cybersecurity platform integrating real-time threat detection with security awareness education.

Open research Europe·2026
See all related articles

Related Experiment Video

Updated: Jul 17, 2025

Author Spotlight: A Machine-Vision Approach to Transmission Electron Microscopy Workflows, Results Analysis and Data Management
10:23

Author Spotlight: A Machine-Vision Approach to Transmission Electron Microscopy Workflows, Results Analysis and Data Management

Published on: June 23, 2023

2.8K

The abTEM code: transmission electron microscopy from first principles.

Jacob Madsen1, Toma Susi1

  • 1Faculty of Physics, University of Vienna, Vienna, 1090, Austria.

Open Research Europe
|August 30, 2023
PubMed
Summary
This summary is machine-generated.

We developed abTEM, an open-source Python code for simulating transmission electron microscopy (TEM) images. It integrates density functional theory (DFT) to capture valence bonding effects, enabling more accurate analysis of experimental data.

Keywords:
Pythondensity functional theoryelectron scatteringimage simulationmolecular dynamicsopen sourcetransmission electron microscopy

More Related Videos

Preparation and Observation of Thick Biological Samples by Scanning Transmission Electron Tomography
08:04

Preparation and Observation of Thick Biological Samples by Scanning Transmission Electron Tomography

Published on: March 12, 2017

9.3K
Method to Visualize and Analyze Membrane Interacting Proteins by Transmission Electron Microscopy
10:49

Method to Visualize and Analyze Membrane Interacting Proteins by Transmission Electron Microscopy

Published on: March 5, 2017

13.3K

Related Experiment Videos

Last Updated: Jul 17, 2025

Author Spotlight: A Machine-Vision Approach to Transmission Electron Microscopy Workflows, Results Analysis and Data Management
10:23

Author Spotlight: A Machine-Vision Approach to Transmission Electron Microscopy Workflows, Results Analysis and Data Management

Published on: June 23, 2023

2.8K
Preparation and Observation of Thick Biological Samples by Scanning Transmission Electron Tomography
08:04

Preparation and Observation of Thick Biological Samples by Scanning Transmission Electron Tomography

Published on: March 12, 2017

9.3K
Method to Visualize and Analyze Membrane Interacting Proteins by Transmission Electron Microscopy
10:49

Method to Visualize and Analyze Membrane Interacting Proteins by Transmission Electron Microscopy

Published on: March 5, 2017

13.3K

Area of Science:

  • Materials Science
  • Computational Physics
  • Chemistry

Background:

  • Transmission electron microscopy (TEM) simulations are crucial for interpreting experimental data.
  • The independent atom model, commonly used, neglects valence bonding, limiting accuracy.
  • Advanced instrumentation reveals subtle scattering potential details previously unobservable.

Purpose of the Study:

  • To develop an open-source simulation code, abTEM, for advanced TEM image and diffraction pattern analysis.
  • To integrate density functional theory (DFT) calculations for accurate scattering potential determination.
  • To provide a user-friendly, modular, and extensible Python-based tool for researchers.

Main Methods:

  • Developed abTEM, a Python-based simulation code integrating DFT for scattering potential calculations.
  • Implemented a modular software design for flexibility and extensibility.
  • Leveraged open-source libraries like Atomic Simulation Environment and GPAW for performance and functionality.
  • Designed for interactive Python notebooks for a seamless workflow from structure definition to result analysis.

Main Results:

  • Demonstrated abTEM's capability to detect valence bonding in hexagonal boron nitride.
  • Performed 4D-STEM simulations of molybdenum disulfide with ptychographic phase reconstruction.
  • Compared molecular dynamics (MD) and frozen phonon modeling for silicon systems using convergent-beam electron diffraction.
  • Evaluated the performance of the PRISM algorithm implementation for gold nanoparticles.

Conclusions:

  • abTEM provides a powerful, accessible tool for advanced TEM simulations, incorporating valence bonding effects.
  • The code's integration with DFT and modular design facilitates accurate and reproducible materials analysis.
  • abTEM supports various imaging modes and algorithmic developments, enhancing its utility for researchers.