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...
Computed Tomography01:10

Computed Tomography

Tomography refers to imaging by sections. Computed tomography (CT) is a non-invasive imaging technique that uses computers to analyze several cross-sectional X-rays to reveal minute details about structures in the body.
The technique was invented in the 1970s and is based on the principle that as X-rays pass through the body, they are absorbed or reflected at different levels. In the technique, a patient lies on a motorized platform while a computerized axial tomography (CAT) scanner rotates...

You might also read

Related Articles

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

Sort by
Same author

AlignPCA-2D: PCA-reduced Euclidean vector alignment for 2D classification in cryo-EM.

Acta crystallographica. Section D, Structural biology·2026
Same author

Rational acquisition of laboratory equipment: an accurate mathematical model to estimate the trade-offs in shared and nonshared equipment.

Acta crystallographica. Section D, Structural biology·2026
Same author

Annexin A2 stabilizes the endoplasmic reticulum and actin cytoskeleton and influences the formation of reovirus factories.

Journal of virology·2025
Same author

How many (distinguishable) classes can we identify in single-particle analysis?

Acta crystallographica. Section D, Structural biology·2025
Same author

Automatic detection of alignment errors in cryo-electron tomography.

Journal of structural biology·2024
Same author

Real-space heterogeneous reconstruction, refinement, and disentanglement of CryoEM conformational states with HetSIREN.

bioRxiv : the preprint server for biology·2024

Related Experiment Video

Updated: Jun 9, 2026

Preparing Lamellae from Vitreous Biological Samples Using a Dual-Beam Scanning Electron Microscope for Cryo-Electron Tomography
07:00

Preparing Lamellae from Vitreous Biological Samples Using a Dual-Beam Scanning Electron Microscope for Cryo-Electron Tomography

Published on: August 5, 2021

XMSF: Structure-preserving noise reduction and pre-segmentation in microscope tomography.

J R Bilbao-Castro1, C O S Sorzano, I García

  • 1Department of Computer Architecture and Electronics, University de Almería, Almería, Spain. jrbcast@ace.ual.es

Bioinformatics (Oxford, England)
|August 31, 2010
PubMed
Summary

Electron tomogram interpretation is challenging due to noise. Microscopy Mean Shift Filtering (XMSF) effectively denoises images while preserving structures, aiding segmentation and analysis.

More Related Videos

3D Imaging of Soft-Tissue Samples using an X-ray Specific Staining Method and Nanoscopic Computed Tomography
07:01

3D Imaging of Soft-Tissue Samples using an X-ray Specific Staining Method and Nanoscopic Computed Tomography

Published on: October 24, 2019

Visualization of Failure and the Associated Grain-Scale Mechanical Behavior of Granular Soils under Shear using Synchrotron X-Ray Micro-Tomography
09:00

Visualization of Failure and the Associated Grain-Scale Mechanical Behavior of Granular Soils under Shear using Synchrotron X-Ray Micro-Tomography

Published on: September 29, 2019

Related Experiment Videos

Last Updated: Jun 9, 2026

Preparing Lamellae from Vitreous Biological Samples Using a Dual-Beam Scanning Electron Microscope for Cryo-Electron Tomography
07:00

Preparing Lamellae from Vitreous Biological Samples Using a Dual-Beam Scanning Electron Microscope for Cryo-Electron Tomography

Published on: August 5, 2021

3D Imaging of Soft-Tissue Samples using an X-ray Specific Staining Method and Nanoscopic Computed Tomography
07:01

3D Imaging of Soft-Tissue Samples using an X-ray Specific Staining Method and Nanoscopic Computed Tomography

Published on: October 24, 2019

Visualization of Failure and the Associated Grain-Scale Mechanical Behavior of Granular Soils under Shear using Synchrotron X-Ray Micro-Tomography
09:00

Visualization of Failure and the Associated Grain-Scale Mechanical Behavior of Granular Soils under Shear using Synchrotron X-Ray Micro-Tomography

Published on: September 29, 2019

Area of Science:

  • Structural biology
  • Microscopy image processing

Background:

  • Electron tomography generates high-resolution 3D images but is hampered by significant noise.
  • Effective noise reduction is crucial for accurate interpretation of tomographic data.

Purpose of the Study:

  • To introduce and evaluate Microscopy Mean Shift Filtering (XMSF) as a denoising tool for electron tomograms.
  • To assess XMSF's ability to preserve structural details during noise reduction.

Main Methods:

  • XMSF applies a 3D extension of a mean shift filtering method.
  • The algorithm utilizes parallel computing for efficient processing on multicore systems.
  • XMSF was tested on various electron tomograms.

Main Results:

  • XMSF successfully filters noise, improving the signal-to-noise ratio in electron tomograms.
  • Structural integrity is preserved during the denoising process.
  • Iterative application of XMSF aids in pre-segmentation of tomographic volumes.

Conclusions:

  • XMSF is a fast, user-friendly denoising application with great potential for electron tomography.
  • The software facilitates subsequent segmentation tasks by providing pre-segmented volumes.
  • Low execution times make XMSF a practical tool for researchers.