title: A statistical approach to the initial volume problem in Single Particle Analysis by Electron Microscopy.
abstract: Cryo Electron Microscopy is a powerful Structural Biology technique, allowing the elucidation of the three-dimensional structure of biological macromolecules. In particular, the structural study of purified macromolecules -often referred as Single Particle Analysis(SPA)- is normally performed through an iterative process that needs a first estimation of the three-dimensional structure that is progressively refined using experimental data. It is well-known the local optimisation nature of this refinement, so that the initial choice of this first structure may substantially change the final result. Computational algorithms aiming to providing this first structure already exist. However, the question is far from settled and more robust algorithms are still needed so that the refinement process can be performed with sufficient guarantees. In this article we present a new algorithm that addresses the initial volume problem in SPA by setting it in a Weighted Least Squares framework and calculating the weights through a statistical approach based on the cumulative density function of different image similarity measures. We show that the new algorithm is significantly more robust than other state-of-the-art algorithms currently in use in the field. The algorithm is available as part of the software suite Xmipp (http://xmipp.cnb.csic.es) and Scipion (http://scipion.cnb.csic.es) under the name "Significant".
authors: National Center of Biotechnology (CSIC), c/Darwin, 3, Campus Univ. Autonoma de Madrid, 28049 Cantoblanco, Madrid, Spain; Bioengineering Lab., Univ. San Pablo CEU, Campus Urb. Monteprincipe s/n, 28668 Boadilla del Monte, Madrid, Spain. Electronic address: coss@cnb.csic.es.
authors: C O S
authors: CO
authors: Sorzano
authors: National Center of Biotechnology (CSIC), c/Darwin, 3, Campus Univ. Autonoma de Madrid, 28049 Cantoblanco, Madrid, Spain.
authors: J
authors: J
authors: Vargas
authors: National Center of Biotechnology (CSIC), c/Darwin, 3, Campus Univ. Autonoma de Madrid, 28049 Cantoblanco, Madrid, Spain.
authors: J M
authors: JM
authors: de la Rosa-Trevín
authors: National Center of Biotechnology (CSIC), c/Darwin, 3, Campus Univ. Autonoma de Madrid, 28049 Cantoblanco, Madrid, Spain.
authors: J
authors: J
authors: Otón
authors: National Center of Biotechnology (CSIC), c/Darwin, 3, Campus Univ. Autonoma de Madrid, 28049 Cantoblanco, Madrid, Spain.
authors: A L
authors: AL
authors: Álvarez-Cabrera
authors: National Center of Biotechnology (CSIC), c/Darwin, 3, Campus Univ. Autonoma de Madrid, 28049 Cantoblanco, Madrid, Spain.
authors: V
authors: V
authors: Abrishami
authors: Bioengineering Lab., Univ. San Pablo CEU, Campus Urb. Monteprincipe s/n, 28668 Boadilla del Monte, Madrid, Spain.
authors: E
authors: E
authors: Sesmero
authors: Escuela Politecnica Superior, Univ. Autonoma de Madrid, Campus. Univ. Autonoma de Madrid, 28049 Cantoblanco, Madrid, Spain.
authors: R
authors: R
authors: Marabini
authors: National Center of Biotechnology (CSIC), c/Darwin, 3, Campus Univ. Autonoma de Madrid, 28049 Cantoblanco, Madrid, Spain.
authors: J M
authors: JM
authors: Carazo
mesh_terms: D000465:Algorithms; D018834:Chaperonin 60 / Q000737:chemistry; D020285:Cryoelectron Microscopy / Q000379:methods*; D003627:Data Interpretation, Statistical; D007091:Image Processing, Computer-Assisted / Q000379:methods*; D021621:Imaging, Three-Dimensional / Q000379:methods; D016018:Least-Squares Analysis; D016013:Likelihood Functions; D046911:Macromolecular Substances / Q000737:chemistry; D012270:Ribosomes / Q000737:chemistry
chemical_list: D018834:Chaperonin 60; D046911:Macromolecular Substances
keywords: 3D reconstruction; Initial volume