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Related Concept Videos

Cryo-electron Microscopy01:28

Cryo-electron Microscopy

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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Single Particle Cryo-Electron Microscopy: From Sample to Structure
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WebCalEM: a browser-based tool for routine and accurate pixel-size calibration in cryo-EM.

Lan Dang1, Zhiqing Wang2, Sung Hyun Joseph Cho2

  • 1Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, State College, PA 16802, USA.

Acta Crystallographica. Section F, Structural Biology Communications
|July 15, 2026
PubMed
Summary

WebCalEM simplifies cryo-electron microscopy calibration. This web application makes accurate pixel size determination accessible for routine quantitative analysis, overcoming previous workflow complexities.

Keywords:
cryo-electron microscopyfast Fourier transformgold latticegraphene oxidemagnification calibrationpixel sizeweb applications

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Area of Science:

  • Cryo-electron microscopy
  • Image analysis
  • Scientific instrumentation

Background:

  • Accurate pixel size determination is crucial for quantitative cryo-electron microscopy (cryo-EM).
  • Existing calibration methods are often under-utilized due to installation barriers and complex workflows.
  • Routine adoption of calibration procedures is hindered by practical implementation challenges.

Purpose of the Study:

  • To develop an accessible web-based application, WebCalEM, for routine cryo-EM pixel size calibration.
  • To transform specialized calibration procedures into an accessible practice for core facilities.
  • To lower the barrier for documented per-dataset magnification calibration in cryo-EM.

Main Methods:

  • Developed WebCalEM, a self-contained HTML file running client-side in any modern web browser.
  • Users upload micrographs of specimens with known crystalline lattices (e.g., gold, graphene oxide).
  • Real-time visualization and downloadable statistical outputs are provided without server-side computation.

Main Results:

  • WebCalEM processes micrographs entirely client-side, suitable for isolated workstations.
  • Cross-standard consistency was achieved between gold and graphene oxide measurements.
  • Measurements across two microscopes and ten magnifications showed a Bland-Altman bias of -0.005% with limits of agreement [-0.30%, +0.29%].

Conclusions:

  • WebCalEM effectively lowers practical barriers to magnification calibration in routine cryo-EM.
  • The application facilitates accessible and documented per-dataset calibration.
  • This tool promotes wider adoption of essential quantitative analysis practices in cryo-EM.