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Transmission electron microscopy (TEM) can be used to determine the 3D structure of biological samples with the help of techniques such as electron microscope tomography and single-particle reconstruction. While single-particle reconstruction can examine macromolecules and macromolecular complexes in vitro conditions only, tomography permits the study of cell components or small cells in vivo.
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Updated: Mar 1, 2026

High-resolution Single Particle Analysis from Electron Cryo-microscopy Images Using SPHIRE

High-resolution Single Particle Analysis from Electron Cryo-microscopy Images Using SPHIRE

Published on: May 16, 2017

High-resolution Single Particle Analysis from Electron Cryo-microscopy Images Using SPHIRE.

Toshio Moriya¹, Michael Saur¹, Markus Stabrin¹

¹Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology.

Journal of Visualized Experiments : Jove

|June 2, 2017

Summary

This summary is machine-generated.

SPARX for High-Resolution Electron Microscopy (SPHIRE) software enables semi-automated processing of cryo-electron microscopy (cryo-EM) data. This user-friendly tool helps novice researchers obtain near-atomic resolution structures with minimal intervention.

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Last Updated: Mar 1, 2026

High-resolution Single Particle Analysis from Electron Cryo-microscopy Images Using SPHIRE

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Cryo-EM and Single-Particle Analysis with Scipion

Cryo-EM and Single-Particle Analysis with Scipion

Published on: May 29, 2021

Area of Science:

Structural Biology
Biophysics
Computational Biology

Background:

Single particle electron cryo-microscopy (cryo-EM) is a powerful technique for determining macromolecular structures.
Processing cryo-EM data can be complex and requires specialized expertise.
There is a need for user-friendly tools to streamline the cryo-EM structure determination pipeline.

Purpose of the Study:

To introduce SPHIRE (SPARX for High-Resolution Electron Microscopy), a novel open-source software suite.
To provide a detailed protocol for semi-automated processing of cryo-EM data for near-atomic resolution structure determination.
To enable novice users to obtain high-quality structural models with minimal intervention.

Main Methods:

Development of the SPHIRE software suite with a graphical user interface.
Implementation of a semi-automated workflow for single particle analysis from cryo-EM movies.
Application of the SPHIRE protocol to determine the structure of a macromolecular complex.

Main Results:

A near-atomic resolution (3.5 Å) structure of the TcdA1 Tc toxin complex was obtained.
The structure was derived from a small dataset of only 9500 single particles.
The SPHIRE protocol demonstrated minimal user intervention and high efficiency.

Conclusions:

SPHIRE provides a user-friendly and streamlined approach to cryo-EM data processing.
The software facilitates the determination of high-resolution structures for researchers with limited experience.
SPHIRE enables the acquisition of noise-free, unbiased atomic models of macromolecular complexes in their native state.