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Related Concept Videos

Electron Microscope Tomography and Single-particle Reconstruction01:07

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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
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Overview of Electron Microscopy01:25

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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.
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Transmission Electron Microscopy01:15

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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...
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Preparation of Samples for Electron Microscopy01:20

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To be visualized by an electron microscope, either transmission or scanning, biological samples need to be fixed (stabilized) so the electron beam does not destroy them and dried thoroughly (desiccated/dehydrated) so the vacuum does not affect them. Fixation needs to be done as quickly as possible because the sample properties will start changing as soon as it is removed from its natural environment. For example, in a tissue sample, the oxygen levels begin decreasing, causing an altered...
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Immunogold Electron Microscopy01:20

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Immunoelectron microscopy utilizes immunogold labeling of endogenous proteins with specific antibodies to detect and localize these proteins in cells and tissues. The procedure provides insights into the distribution and quantification of protein under different stimulation conditions offering clues about their functions. Conjugating highly electron-dense gold particles with primary or secondary antibodies allow antigen detection on and within cells, with high resolution and specificity.
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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...
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Updated: Aug 19, 2025

Imaging Replicative Domains in Ultrastructurally Preserved Chromatin by Electron Tomography
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EMPIAR: the Electron Microscopy Public Image Archive.

Andrii Iudin1, Paul K Korir1, Sriram Somasundharam1

  • 1European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK.

Nucleic Acids Research
|November 28, 2022
PubMed
Summary
This summary is machine-generated.

The Electron Microscopy Public Image Archive (EMPIAR) archives raw cryo-EM image data and 3D reconstructions. It supports validation, software development, and training, now holding over 2 petabytes of data.

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Area of Science:

  • Structural Biology
  • Biophysics
  • Data Science

Background:

  • Established archives like PDB and EMDB exist for atomic models and cryo-EM reconstructions.
  • A community need for raw cryo-EM image data archiving was identified for validation and development.
  • Growth in 3D imaging techniques (vEM, XT) created demand for archiving their data.

Purpose of the Study:

  • To establish a public archive for raw cryo-EM image data.
  • To archive 3D reconstructions from volume EM and X-ray tomography.
  • To provide resources for data validation, software development, and training.

Main Methods:

  • Development of the EMPIAR public archive.
  • Implementation of deposition system, entry pages, and search/download facilities.
  • Provision of a REST API for programmatic metadata access.

Main Results:

  • EMPIAR now hosts over a thousand entries.
  • The archive contains over 2 petabytes of structural biology data.
  • Resources facilitate searching, visualization, and downloading of datasets.

Conclusions:

  • EMPIAR successfully addresses the need for archiving raw cryo-EM and 3D imaging data.
  • The archive's success presents challenges in managing data volume growth and enhancing reusability.
  • Future efforts will focus on scaling resources and improving data accessibility.