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Related Concept Videos

Cryo-electron Microscopy01:28

Cryo-electron Microscopy

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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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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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Scanning Electron Microscopy01:07

Scanning Electron Microscopy

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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.
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Transmission Electron Microscopy01:15

Transmission Electron Microscopy

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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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Immunogold Electron Microscopy01:20

Immunogold Electron Microscopy

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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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Preparation of Samples for Electron Microscopy01:20

Preparation of Samples for Electron Microscopy

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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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Updated: Feb 5, 2026

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CryoJAX: a cryo-electron microscopy image-simulation library in JAX.

Michael J O'Brien1, David Silva-Sánchez2, Geoffrey Woollard3

  • 1Department of Physics, Harvard University, Cambridge, MA 02143, USA.

Acta Crystallographica. Section D, Structural Biology
|February 3, 2026
PubMed
Summary

Cryo-electron microscopy (cryo-EM) is expanding beyond molecular resolution. A new JAX-based library, cryoJAX, simplifies computationally intensive cryo-EM data analysis for intracellular organization studies.

Keywords:
automatic differentiationbiophysicscryo-EMimage simulationsoftware library

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Author Spotlight: Enhancing Cryo-Electron Microscopy by Automated Data Collection and Analysis Techniques
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Area of Science:

  • Structural Biology
  • Computational Biology
  • Biophysics

Background:

  • Cryo-electron microscopy (cryo-EM) excels at atomic resolution of biomolecular complexes.
  • Advancements enable cryo-EM for intracellular organization and heterogeneous molecular states.
  • Computational demands of cryo-EM data analysis pose a significant challenge.

Purpose of the Study:

  • To develop advanced computational tools for cryo-EM data analysis.
  • To leverage scientific computing frameworks for statistical analysis in cryo-EM.
  • To introduce cryoJAX, a cryo-EM image-simulation library within the JAX ecosystem.

Main Methods:

  • Development of cryoJAX, a Python library for cryo-EM image simulation.
  • Integration of cryoJAX with the JAX numerical computing framework.
  • Utilizing JAX's automatic differentiation and vectorization capabilities for statistical inference.

Main Results:

  • CryoJAX provides a flexible modeling language for cryo-EM image formation.
  • The library supports a wide range of downstream data analysis applications.
  • Enables development and deployment of algorithms for diverse cryo-EM applications.

Conclusions:

  • CryoJAX facilitates computationally demanding cryo-EM data analysis.
  • The library supports the expansion of cryo-EM applications into intracellular organization.
  • Integration with JAX accelerates algorithm development for advanced cryo-EM studies.