2009Sorzano MachineLearning

Citation

Sorzano, C. O. S.; Recarte, E.; Alcorlo, M.; Bilbao-Castro, J. R.; San-Martín, C.; Marabini, R. & Carazo, J. M. Fast automatic particle selection from electron micrographs using machine learning techniques J. Structural Biology, 2009, 167, 252-260

Abstract

The 3D reconstruction of biological specimens using Electron Microscopy is currently capable of achieving subnanometer resolution. Unfortunately, this goal requires gathering tens of thousands of projection images that are frequently selected manually from micrographs. In this paper we introduce a new automatic particle selection that learns from the user which particles are of interest. The training phase is semi-supervised so that the user can correct the algorithm during picking and specifically identify incorrectly picked particles. By treating such errors specially, the algorithm attempts to minimize the number of false positives. We show that our algorithm is able to produce datasets with fewer wrongly selected particles than previously reported methods. Another advantage is that we avoid the need for an initial reference volume from which to generate picking projections by instead learning which particles to pick from the user. This package has been made publicly available in the open-source package Xmipp.

Keywords

Single particles; Automatic particle picking; Machine learning; Classification algorithms; Rotational invariants

Links

Article http://www.ncbi.nlm.nih.gov/pubmed/19555764

Related software

Xmipp http://xmipp.cnb.csic.es/twiki/bin/view/Xmipp/Mark