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Cryo-electron Microscopy

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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Related Experiment Video

Updated: Oct 3, 2025

User-friendly, High-throughput, and Fully Automated Data Acquisition Software for Single-particle Cryo-electron Microscopy

User-friendly, High-throughput, and Fully Automated Data Acquisition Software for Single-particle Cryo-electron Microscopy

Published on: July 29, 2021

IceBreaker: Software for high-resolution single-particle cryo-EM with non-uniform ice.

Mateusz Olek¹, Kevin Cowtan², Donovan Webb³

¹Electron Bio-Imaging Centre, Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK; Department of Chemistry, University of York, York, UK.

Structure (London, England : 1993)

|February 12, 2022

Summary

This summary is machine-generated.

IceBreaker software improves single-particle cryo-electron microscopy (cryo-EM) by estimating and correcting ice thickness variations. This enhances particle picking and data collection efficiency for better structural analysis.

Keywords:

cryo-EM density map ice gradient ice thickness particle picking preferred orientation single particle vitreous ice

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Single Particle Cryo-Electron Microscopy: From Sample to Structure

Single Particle Cryo-Electron Microscopy: From Sample to Structure

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Last Updated: Oct 3, 2025

User-friendly, High-throughput, and Fully Automated Data Acquisition Software for Single-particle Cryo-electron Microscopy

User-friendly, High-throughput, and Fully Automated Data Acquisition Software for Single-particle Cryo-electron Microscopy

Published on: July 29, 2021

A Robust Single-Particle Cryo-Electron Microscopy cryo-EM Processing Workflow with cryoSPARC, RELION, and Scipion

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Published on: January 31, 2022

Single Particle Cryo-Electron Microscopy: From Sample to Structure

Single Particle Cryo-Electron Microscopy: From Sample to Structure

Published on: May 29, 2021

Area of Science:

Structural Biology
Biophysics
Microscopy

Background:

Optimal particle selection remains a challenge in single-particle cryo-electron microscopy (cryo-EM).
Existing particle picking methods often struggle with variations in ice thickness across micrographs.
Inconsistent ice thickness can negatively impact particle identification and data quality.

Purpose of the Study:

To introduce IceBreaker, a novel software tool for addressing ice thickness variations in cryo-EM.
To improve particle picking performance and data collection strategies in cryo-EM.
To enable automated particle selection and quality assessment based on local ice thickness.

Main Methods:

IceBreaker estimates the relative ice gradient across micrographs.
The software equalizes local contrast to flatten the ice gradient.
It introduces a parameter for local ice thickness associated with each picked particle.

Main Results:

IceBreaker effectively differentiates particles from background noise, even with varying ice thickness.
The tool enhances overall particle picking performance and accuracy.
Particles can be grouped and filtered based on their local ice thickness, aiding downstream processing.

Conclusions:

IceBreaker offers a valuable solution for optimizing particle selection in cryo-EM.
The software facilitates on-the-fly processing and automated data collection region selection.
Estimated ice gradient distributions serve as a quality control metric for sample preparation.