Automated pipelines for rapid evaluation during cryoEM data acquisition - PubMed

Review

Automated pipelines for rapid evaluation during cryoEM data acquisition

Joshua H Mendez et al. Curr Opin Struct Biol. 2023 Dec.

Abstract

Cryo-electron microscopy (cryoEM) has become a popular method for determining high-resolution structures of biomolecules. However, data processing can be time-consuming, particularly for new researchers entering the field. To improve data quality and increase data collection efficiency, several software packages have been developed for on-the-fly data processing with various degrees of automation. These software packages allow researchers to perform tasks such as motion correction, CTF estimation, 2D classification, and 3D reconstruction in real-time, with minimal human input. On-the-fly data processing can not only improve data collection efficiency but also increase the productivity of instrumentation in high demand. However, the various software packages available differ in their performance, computational requirements, and levels of automation. In this review, we describe the minimal metrics used to assess data quality during data collection, outline the features of an ideal on-the-fly data processing software systems, and provide results from using three of these systems.

Conflict of interest statement

Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.

Similar articles

• Automated data collection in single particle electron microscopy.

  Tan YZ, Cheng A, Potter CS, Carragher B. Tan YZ, et al. Microscopy (Oxf). 2016 Feb;65(1):43-56. doi: 10.1093/jmicro/dfv369. Epub 2015 Dec 15. Microscopy (Oxf). 2016. PMID: 26671944 Free PMC article. Review.

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

  DiIorio MC, Kulczyk AW. DiIorio MC, et al. J Vis Exp. 2022 Jan 31;(179). doi: 10.3791/63387. J Vis Exp. 2022. PMID: 35104261

• Asynchronous data acquisition and on-the-fly analysis of dose fractionated cryoEM images by UCSFImage.

  Li X, Zheng S, Agard DA, Cheng Y. Li X, et al. J Struct Biol. 2015 Nov;192(2):174-8. doi: 10.1016/j.jsb.2015.09.003. Epub 2015 Sep 11. J Struct Biol. 2015. PMID: 26370395 Free PMC article.

• Focus: The interface between data collection and data processing in cryo-EM.

  Biyani N, Righetto RD, McLeod R, Caujolle-Bert D, Castano-Diez D, Goldie KN, Stahlberg H. Biyani N, et al. J Struct Biol. 2017 May;198(2):124-133. doi: 10.1016/j.jsb.2017.03.007. Epub 2017 Mar 23. J Struct Biol. 2017. PMID: 28344036

• Strategies for Automated CryoEM Data Collection Using Direct Detectors.

  Cheng A, Tan YZ, Dandey VP, Potter CS, Carragher B. Cheng A, et al. Methods Enzymol. 2016;579:87-102. doi: 10.1016/bs.mie.2016.04.008. Epub 2016 Jun 22. Methods Enzymol. 2016. PMID: 27572724 Review.

Cited by

• Cryo-EM sample preparation for high-resolution structure studies.

  Wang L, Zimanyi CM. Wang L, et al. Acta Crystallogr F Struct Biol Commun. 2024 Apr 1;80(Pt 4):74-81. doi: 10.1107/S2053230X24002553. Epub 2024 Mar 26. Acta Crystallogr F Struct Biol Commun. 2024. PMID: 38530656

• RNA sample optimization for cryo-EM analysis.

  Chen X, Wang L, Xie J, Nowak JS, Luo B, Zhang C, Jia G, Zou J, Huang D, Glatt S, Yang Y, Su Z. Chen X, et al. Nat Protoc. 2024 Nov 15. doi: 10.1038/s41596-024-01072-1. Online ahead of print. Nat Protoc. 2024. PMID: 39548288 Review.

Publication types

MeSH terms