Automatic particle selection: results of a comparative study

J Struct Biol. 2004 Jan-Feb;145(1-2):3-14. doi: 10.1016/j.jsb.2003.09.033.


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.

Publication types

  • Comparative Study
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Algorithms*
  • Animals
  • Cryoelectron Microscopy / methods*
  • Electronic Data Processing / methods
  • Hemocyanins / chemistry
  • Hemocyanins / ultrastructure
  • Image Processing, Computer-Assisted / methods*
  • Imaging, Three-Dimensional
  • Mollusca
  • Protein Conformation


  • Hemocyanins
  • keyhole-limpet hemocyanin