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

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...

You might also read

Related Articles

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

Sort by
Same author

Molecular mechanism of transition-state inhibitors of bacterial antibiotic efflux pumps.

npj antimicrobials and resistance·2026
Same author

copick: An open dataset interface and toolkit for collaborative annotation and analysis of cryo-electron tomography data.

Protein science : a publication of the Protein Society·2026
Same author

The native human glomerulus features a slit diaphragm resembling a densely interwoven fishnet.

JCI insight·2026
Same author

Conformational plasticity across phylogenetic clusters of RND multidrug efflux pumps and its impact on substrate specificity.

Nature communications·2025
Same author

In situ structure of a gap junction-stomatin complex.

Science advances·2025
Same author

How does <i>Mycoplasma pneumoniae</i> scavenge lipids from its host membranes?

Science advances·2025
Same journal

MLAC: MicroED-assisted ligand structure analysis in complexes and its application to hERG-ligand complexes.

Journal of structural biology·2026
Same journal

Ultrastructural evidence of autophagy-related processes and mitochondrial remodeling in the myxozoan parasite Henneguya piaractus.

Journal of structural biology·2026
Same journal

Architecture and dynamics of a supramolecular oxygen transport system in human homogentisate 1,2-Dioxygenase.

Journal of structural biology·2026
Same journal

Connecting pathways between mineralized fibrocartilage and bone at the Achilles tendon insertion.

Journal of structural biology·2026
Same journal

Structural and functional characterization of thermostable EstS1 esterase for BHET degradation.

Journal of structural biology·2026
Same journal

Following the white rabbit: multiscale 2D3D correlative imaging of bone structure.

Journal of structural biology·2026
See all related articles

Related Experiment Video

Updated: Jul 2, 2026

From Voxels to Knowledge: A Practical Guide to the Segmentation of Complex Electron Microscopy 3D-Data
12:08

From Voxels to Knowledge: A Practical Guide to the Segmentation of Complex Electron Microscopy 3D-Data

Published on: August 13, 2014

A visualization and segmentation toolbox for electron microscopy.

Sabine Pruggnaller1, Matthias Mayr, Achilleas S Frangakis

  • 1Department of Computational and Structural Biology, European Molecular Biology Laboratory, Meyerhofstr 1, 69117 Heidelberg, Germany. pruggnal@embl.de

Journal of Structural Biology
|August 12, 2008
PubMed
Summary
This summary is machine-generated.

A new toolbox for three-dimensional (3D) electron microscopy (EM) in Amira streamlines image analysis. This package offers integrated denoising, segmentation, and ray-tracing for enhanced data visualization and interpretation in EM research.

More Related Videos

Correlative Confocal and 3D Electron Microscopy of a Specific Sensory Cell
08:00

Correlative Confocal and 3D Electron Microscopy of a Specific Sensory Cell

Published on: July 19, 2015

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

Related Experiment Videos

Last Updated: Jul 2, 2026

From Voxels to Knowledge: A Practical Guide to the Segmentation of Complex Electron Microscopy 3D-Data
12:08

From Voxels to Knowledge: A Practical Guide to the Segmentation of Complex Electron Microscopy 3D-Data

Published on: August 13, 2014

Correlative Confocal and 3D Electron Microscopy of a Specific Sensory Cell
08:00

Correlative Confocal and 3D Electron Microscopy of a Specific Sensory Cell

Published on: July 19, 2015

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

Area of Science:

  • Microscopy and Imaging Science
  • Computational Biology
  • Data Visualization

Background:

  • Three-dimensional (3D) image analysis is crucial for interpreting complex biological data.
  • Electron microscopy (EM) generates large 3D datasets requiring specialized analysis tools.
  • Existing workflows often involve multiple software packages, complicating the process.

Purpose of the Study:

  • To develop an integrated toolbox for 3D electron microscopy (EM) data analysis within the Amira software environment.
  • To provide a user-friendly interface for essential 3D EM image processing tasks.
  • To enhance the visualization capabilities of 3D EM data through advanced rendering techniques.

Main Methods:

  • Development of a specialized toolbox integrated into the commercial Amira software package.
  • Implementation of functions for input-output, filtering, segmentation, and visualization.
  • Inclusion of ray-tracing capabilities for photo-realistic rendering.
  • Features for direct data interaction, including sub-tomogram extraction and interactive segmentation selection.

Main Results:

  • The toolbox offers a comprehensive suite of tools for 3D EM analysis directly within Amira.
  • Users can perform denoising and segmentation without external software.
  • Photo-realistic visualization with ray-tracing is achievable.
  • Interactive data manipulation, such as sub-tomogram extraction, is supported.

Conclusions:

  • The developed Amira toolbox provides a fast, reliable, and intuitive solution for 3D EM image analysis.
  • It simplifies complex workflows, enabling efficient data interpretation and visualization.
  • The package enhances the utility of Amira for researchers in the field of electron microscopy.