title: Automatic particle selection: results of a comparative study.
abstract: Manual selection of single particles in images acquired using cryo-electron microscopy (cryoEM) will become a significant bottleneck when datasets of a hundred thousand or even a million particles are required for structure determination at near atomic resolution. Algorithm development of fully automated particle selection is thus an important research objective in the cryoEM field. A number of research groups are making promising new advances in this area. Evaluation of algorithms using a standard set of cryoEM images is an essential aspect of this algorithm development. With this goal in mind, a particle selection "bakeoff" was included in the program of the Multidisciplinary Workshop on Automatic Particle Selection for cryoEM. Twelve groups participated by submitting the results of testing their own algorithms on a common dataset. The dataset consisted of 82 defocus pairs of high-magnification micrographs, containing keyhole limpet hemocyanin particles, acquired using cryoEM. The results of the bakeoff are presented in this paper along with a summary of the discussion from the workshop. It was agreed that establishing benchmark particles and using bakeoffs to evaluate algorithms are useful in promoting algorithm development for fully automated particle selection, and that the infrastructure set up to support the bakeoff should be maintained and extended to include larger and more varied datasets, and more criteria for future evaluations.
authors.affiliation: Center for Integrative Molecular Biosciences and Department of Cell Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.
authors.forename: Yuanxin
authors.initials: Y
authors.lastname: Zhu
authors.forename: Bridget
authors.initials: B
authors.lastname: Carragher
authors.forename: Robert M
authors.initials: RM
authors.lastname: Glaeser
authors.forename: Denis
authors.initials: D
authors.lastname: Fellmann
authors.forename: Chandrajit
authors.initials: C
authors.lastname: Bajaj
authors.forename: Marshall
authors.initials: M
authors.lastname: Bern
authors.forename: Fabrice
authors.initials: F
authors.lastname: Mouche
authors.forename: Felix
authors.initials: F
authors.lastname: de Haas
authors.forename: Richard J
authors.initials: RJ
authors.lastname: Hall
authors.forename: David J
authors.initials: DJ
authors.lastname: Kriegman
authors.forename: Steven J
authors.initials: SJ
authors.lastname: Ludtke
authors.forename: Satya P
authors.initials: SP
authors.lastname: Mallick
authors.forename: Pawel A
authors.initials: PA
authors.lastname: Penczek
authors.forename: Alan M
authors.initials: AM
authors.lastname: Roseman
authors.forename: Fred J
authors.initials: FJ
authors.lastname: Sigworth
authors.forename: Niels
authors.initials: N
authors.lastname: Volkmann
authors.forename: Clinton S
authors.initials: CS
authors.lastname: Potter
mesh_terms: D000465:Algorithms; D000818:Animals; D020285:Cryoelectron Microscopy / Q000379:methods*; D001330:Electronic Data Processing / Q000379:methods; D006433:Hemocyanins / Q000737:chemistry / Q000648:ultrastructure; D007091:Image Processing, Computer-Assisted / Q000379:methods*; D021621:Imaging, Three-Dimensional; D008974:Mollusca; D011487:Protein Conformation
chemical_list: D006433:Hemocyanins; C032808:keyhole-limpet hemocyanin