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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, The Pennsylvania State University, University Park, PA 16802.

Biorxiv : the Preprint Server for Biology
|June 5, 2026
PubMed
Summary

Accurate cryo-electron microscopy (cryo-EM) requires precise pixel size calibration. WebCalEM is a new, install-free web application that simplifies this process, making routine calibration accessible for all cryo-EM users.

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

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Area of Science:

  • Microscopy
  • Biophysics
  • Computational Biology

Background:

  • Accurate pixel size calibration is essential for quantitative cryo-electron microscopy (cryo-EM).
  • Existing calibration methods are often underutilized due to installation complexities and workflow challenges.
  • Routine calibration is crucial for reliable cryo-EM data analysis.

Purpose of the Study:

  • To develop an accessible web-based application for routine cryo-EM pixel size calibration.
  • To overcome the barriers of installation and workflow complexity associated with traditional calibration methods.
  • To provide a user-friendly tool for accurate magnification calibration in cryo-EM.

Main Methods:

  • Developed WebCalEM, a browser-based, install-free application.
  • Utilizes micrographs of specimens with known crystalline lattices (e.g., gold, graphene-oxide).
  • Processes images client-side with real-time visualization and downloadable statistical outputs.

Main Results:

  • WebCalEM achieves cross-standard consistency between gold and graphene-oxide measurements.
  • Demonstrates a low Bland-Altman bias (-0.005%) with tight limits of agreement ([-0.30%, +0.29%]).
  • Reproduces the precision of established command-line calibration tools.

Conclusions:

  • WebCalEM significantly lowers the barrier to entry for per-dataset magnification calibration in cryo-EM.
  • The application facilitates routine adoption of essential calibration procedures.
  • Enables accurate and accessible pixel size determination for quantitative cryo-EM analyses.