Unsupervised particle sorting for high-resolution single-particle cryo-EM

DOI10.1088/1361-6420/AB5EC8MaRDI QIDQ5000566zbMATH OpenOpenAlexFDO

Authors Ye Zhou, Amit Moscovich, Tamir Bendory, Alberto Bartesaghi

Publication date 14 July 2021

Published in Inverse Problems (Search for Journal in Brave)

Full work available at URL https://arxiv.org/abs/1910.10051

zbMATH Keywords

image analysiscryo-electron microscopysingle particle analysishigh-resolution microscopyunsupervised image sorting

Mathematics Subject Classification ID

Biomedical imaging and signal processing (92C55)

Abstract: Single-particle cryo-Electron Microscopy (EM) has become a popular technique for determining the structure of challenging biomolecules that are inaccessible to other technologies. Recent advances in automation, both in data collection and data processing, have significantly lowered the barrier for non-expert users to successfully execute the structure determination workflow. Many critical data processing steps, however, still require expert user intervention in order to converge to the correct high-resolution structure. In particular, strategies to identify homogeneous populations of particles rely heavily on subjective criteria that are not always consistent or reproducible among different users. Here, we explore the use of unsupervised strategies for particle sorting that are compatible with the autonomous operation of the image processing pipeline. More specifically, we show that particles can be successfully sorted based on a simple statistical model for the distribution of scores assigned during refinement. This represents an important step towards the development of automated workflows for protein structure determination using single-particle cryo-EM.

Recommendations

• Toward Single Particle Reconstruction without Particle Picking: Breaking the Detection Limit
• A max-cut approach to heterogeneity in cryo-electron microscopy
• Cryo-EM reconstruction of continuous heterogeneity by Laplacian spectral volumes
• Reconstruction from limited single-particle diffraction data via simultaneous determination of state, orientation intensity, and phase
• Rapid solution of the cryo-EM reconstruction problem by frequency marching

Cites work

• Angular synchronization by eigenvectors and semidefinite programming
• Three-dimensional structure determination from common lines in cryo-EM by eigenvectors and semidefinite programming

Cited in

(3)

• A max-cut approach to heterogeneity in cryo-electron microscopy
• Reconstruction from limited single-particle diffraction data via simultaneous determination of state, orientation intensity, and phase
• An automatic particle picking method based on generative adversarial network

Describes a project that uses

Uses Software

• EMan
• DeepPicker
• CTFFIND
• RELION
• cisTEM
• IMAGIC
• cryoSPARC
• Leginon
• MAPPOS
• MotionCor2
• crYOLO

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