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Open AccessArticle

A Super-Clustering Approach for Fully Automated Single Particle Picking in Cryo-EM

1
Electrical Engineering and Computer Science Department, University of Missouri, Columbia, MO 65211, USA
2
Departments of Biochemistry and Chemistry, University of Missouri, Columbia, MO 65211, USA
3
Informatics Institute, University of Missouri, Columbia, MO 65211, USA
*
Author to whom correspondence should be addressed.
Genes 2019, 10(9), 666; https://doi.org/10.3390/genes10090666
Received: 26 June 2019 / Revised: 4 August 2019 / Accepted: 12 August 2019 / Published: 30 August 2019
Structure determination of proteins and macromolecular complexes by single-particle cryo-electron microscopy (cryo-EM) is poised to revolutionize structural biology. An early challenging step in the cryo-EM pipeline is the detection and selection of particles from two-dimensional micrographs (particle picking). Most existing particle-picking methods require human intervention to deal with complex (irregular) particle shapes and extremely low signal-to-noise ratio (SNR) in cryo-EM images. Here, we design a fully automated super-clustering approach for single particle picking (SuperCryoEMPicker) in cryo-EM micrographs, which focuses on identifying, detecting, and picking particles of the complex and irregular shapes in micrographs with extremely low signal-to-noise ratio (SNR). Our method first applies advanced image processing procedures to improve the quality of the cryo-EM images. The binary mask image-highlighting protein particles are then generated from each individual cryo-EM image using the super-clustering (SP) method, which improves upon base clustering methods (i.e., k-means, fuzzy c-means (FCM), and intensity-based cluster (IBC) algorithm) via a super-pixel algorithm. SuperCryoEMPicker is tested and evaluated on micrographs of β-galactosidase and 80S ribosomes, which are examples of cryo-EM data exhibiting complex and irregular particle shapes. The results show that the super-particle clustering method provides a more robust detection of particles than the base clustering methods, such as k-means, FCM, and IBC. SuperCryoEMPicker automatically and effectively identifies very complex particles from cryo-EM images of extremely low SNR. As a fully automated particle detection method, it has the potential to relieve researchers from laborious, manual particle-labeling work and therefore is a useful tool for cryo-EM protein structure determination. View Full-Text
Keywords: super-clustering; intensity based clustering (IBC); micrograph; cryo-EM; singe particle pickling; protein structure determination; k-means; fuzzy c-means (FCM) super-clustering; intensity based clustering (IBC); micrograph; cryo-EM; singe particle pickling; protein structure determination; k-means; fuzzy c-means (FCM)
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MDPI and ACS Style

Al-Azzawi, A.; Ouadou, A.; Tanner, J.J.; Cheng, J. A Super-Clustering Approach for Fully Automated Single Particle Picking in Cryo-EM. Genes 2019, 10, 666.

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