title: Detecting circular and rectangular particles based on geometric feature detection in electron micrographs.
abstract: Accurate and automatic particle detection from cryo-electron microscopy (cryo-EM images) is very important for high-resolution reconstruction of large macromolecular structures. In this paper, we present a method for particle picking based on shape feature detection. Two fundamental concepts of computational geometry, namely, the distance transform and the Voronoi diagram, are used for detection of critical features as well as for accurate location of particles from the images or micrographs. Unlike the conventional template-matching methods, our approach detects the particles based on their boundary features instead of intensities. The geometric features derived from the boundaries provide an efficient way for locating particles quickly and accurately, which avoids a brute-force searching for the best position/orientation. Our approach is fully automatic and has been successfully applied to detect particles with approximately circular or rectangular shapes (e.g., KLH particles). Particle detection can be enhanced by multiple sets of parameters used in edge detection and/or by anisotropic filtering. We also discuss the extension of this approach to other types of particles with certain geometric features.
authors.affiliation: The Center of Computational Visualization, Department of Computer Sciences and Institute of Computational Engineering and Sciences, The University of Texas at Austin, Austin, TX 78712, USA. zeyun@cs.utexas.edu
authors.forename: Zeyun
authors.initials: Z
authors.lastname: Yu
authors.forename: Chandrajit
authors.initials: C
authors.lastname: Bajaj
mesh_terms: D000465:Algorithms; D000818:Animals; D016880:Anisotropy; D020285:Cryoelectron Microscopy / Q000379:methods*; D003627:Data Interpretation, Statistical; D001330:Electronic Data Processing / Q000379:methods; D006433:Hemocyanins / Q000737:chemistry / Q000648:ultrastructure; D007089:Image Enhancement / Q000379:methods; D007091:Image Processing, Computer-Assisted / Q000379:methods*; D008968:Molecular Conformation; D008974:Mollusca; D010316:Particle Size; D010363:Pattern Recognition, Automated
chemical_list: D006433:Hemocyanins; C032808:keyhole-limpet hemocyanin