SwarmPS: Rapid, semi-automated single particle selection software

Woolford, David, Ericksson, Geoffery, Rothnagel, Rosalba, Muller, David, Landsberg, Michael, Pantelic, Radosav, McDowall, Alasdair, Pailthorpe, Bernard, Young, Paul, Hankamer, Ben, & Banks, Jasmine (2007) SwarmPS: Rapid, semi-automated single particle selection software. Journal of Structural Biology, 157(1), pp. 174-188.

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Abstract

Single particle analysis (SPA) coupled with high-resolution electron cryo-microscopy is emerging as a powerful technique for the structure determination of membrane protein complexes and soluble macromolecular assemblies. Current estimates suggest that ∼104–105 particle projections are required to attain a 3 Å resolution 3D reconstruction (symmetry dependent). Selecting this number of molecular projections differing in size, shape and symmetry is a rate-limiting step for the automation of 3D image reconstruction. Here, we present SwarmPS, a feature rich GUI based software package to manage large scale, semi-automated particle picking projects. The software provides cross-correlation and edge-detection algorithms. Algorithm-specific parameters are transparently and automatically determined through user interaction with the image, rather than by trial and error. Other features include multiple image handling (∼102), local and global particle selection options, interactive image freezing, automatic particle centering, and full manual override to correct false positives and negatives. SwarmPS is user friendly, flexible, extensible, fast, and capable of exporting boxed out projection images, or particle coordinates, compatible with downstream image processing suites.

Impact and interest:

18 citations in Scopus
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18 citations in Web of Science®

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ID Code: 45505
Item Type: Journal Article
Refereed: Yes
Keywords: Electron microscopy, Electron cryomicroscopy, Cryoelectron microscopy, Single particle analysis, Automatic particle detection, Particle selection, Particle picking, Software
DOI: 10.1016/j.jsb.2006.04.006
ISSN: 1047-8477
Subjects: Australian and New Zealand Standard Research Classification > BIOLOGICAL SCIENCES (060000) > BIOCHEMISTRY AND CELL BIOLOGY (060100)
Divisions: Past > QUT Faculties & Divisions > Faculty of Science and Technology
Deposited On: 29 Aug 2011 04:11
Last Modified: 29 Feb 2012 14:27

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