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Related Concept Videos

Electron Microscope Tomography and Single-particle Reconstruction01:07

Electron Microscope Tomography and Single-particle Reconstruction

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
Electron tomography can be performed either in TEM or STEM (scanning transmission...
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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Related Experiment Video

Updated: Jul 12, 2026

Single-Particle Cryo-EM Data Collection with Stage Tilt using Leginon
04:52

Single-Particle Cryo-EM Data Collection with Stage Tilt using Leginon

Published on: July 1, 2022

Using spIsoNet to address the preferred-orientation problem in cryoEM reconstructions.

Hongcheng Fan, Yun-Tao Liu, Z Hong Zhou

    Biorxiv : the Preprint Server for Biology
    |July 10, 2026
    PubMed
    Summary

    This study introduces spIsoNet, a deep-learning tool to address preferred orientation in cryo-electron microscopy (cryoEM) data. It corrects reconstruction artifacts and improves particle alignment for higher resolution structures.

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    A Robust Single-Particle Cryo-Electron Microscopy (cryo-EM) Processing Workflow with cryoSPARC, RELION, and Scipion
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    Strategies for Optimization of Cryogenic Electron Tomography Data Acquisition
    08:16

    Strategies for Optimization of Cryogenic Electron Tomography Data Acquisition

    Published on: March 19, 2021

    Area of Science:

    • Structural Biology
    • Biophysics
    • Computational Biology

    Background:

    • Cryo-electron microscopy (cryoEM) is crucial for determining biological macromolecule structures at high resolution.
    • Preferred orientation of specimens on cryoEM grids leads to uneven data sampling and anisotropic reconstruction artifacts.
    • These issues can hinder particle alignment and limit the success of near-atomic resolution cryoEM studies.

    Purpose of the Study:

    • To present a practical protocol for using the self-supervised deep-learning method, spIsoNet, to mitigate preferred orientation problems in cryoEM.
    • To offer two workflows: map Anisotropy Correction and particle Misalignment Correction, for improving cryoEM reconstructions.
    • To provide guidance for applying spIsoNet to experimental cryoEM data.

    Main Methods:

    • Implementation of spIsoNet, a self-supervised deep-learning approach.
    • Development of two complementary workflows: map Anisotropy Correction and particle Misalignment Correction.
    • Integration of spIsoNet with RELION external reconstruction for enhanced particle pose estimation.

    Main Results:

    • Demonstration of spIsoNet workflows on influenza hemagglutinin (HA) trimer datasets with varying degrees of preferred orientation bias.
    • Successful correction of anisotropic artifacts in cryoEM maps.
    • Improved particle pose estimation, leading to better cryoEM reconstructions.

    Conclusions:

    • The spIsoNet software effectively mitigates preferred orientation issues in cryoEM reconstructions.
    • The presented workflows provide a robust method for enhancing cryoEM data quality and enabling higher resolution structure determination.
    • This protocol offers a valuable resource for researchers facing orientation bias challenges in cryoEM studies.