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Electron Microscope Tomography and Single-particle Reconstruction

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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.
Electron Tomography
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Updated: Mar 24, 2026

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

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High resolution single particle refinement in EMAN2.1.

James M Bell¹, Muyuan Chen¹, Philip R Baldwin²

¹Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA.

Methods (San Diego, Calif.)

|March 3, 2016

Summary

This summary is machine-generated.

EMAN2.1 offers automated, high-resolution single particle analysis for transmission electron microscopy. This pipeline refines structures, estimates resolution using gold standard FSC, and reduces model bias for accurate results.

Keywords:

3-D reconstruction CryoEM Image processing Single particle analysis Structural biology

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Last Updated: Mar 24, 2026

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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

Area of Science:

Microscopy and Imaging
Computational Biology
Structural Biology

Background:

Quantitative analysis of grayscale images is crucial in microscopy.
Transmission electron microscopy (TEM) requires advanced image processing for structural determination.
Existing methods may lack comprehensive workflows for complex analyses.

Purpose of the Study:

To provide a detailed description of the EMAN2.1 high-resolution single particle analysis pipeline.
To explain the underlying philosophy of the reconstruction approach.
To introduce automated refinement and validation methods.

Main Methods:

High-resolution single particle analysis (SPA) pipeline.
Automated refinement using adaptive heuristics.
Gold standard Fourier Shell Correlation (FSC) for resolution estimation.
CTF correction and optimal filtering.
Model bias reduction and cross-validation techniques.

Main Results:

The EMAN2.1 pipeline automates high-resolution single particle reconstruction.
Automatic gold standard FSC provides robust resolution estimates.
Optimized filtering of corrected structures enhances map quality.
Methods for reducing model bias and enabling cross-validation are implemented.

Conclusions:

EMAN2.1 provides a robust and automated solution for high-resolution single particle analysis in TEM.
The described pipeline ensures accurate structural determination and reliable resolution estimation.
The software facilitates advanced quantitative image analysis in structural biology.