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Updated: Jun 6, 2026
11:52
Single Particle Cryo-Electron Microscopy: From Sample to Structure
Published on: May 29, 2021
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
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.
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.
