title: Alignment of direct detection device micrographs using a robust Optical Flow approach.
abstract: The introduction of direct detection devices in cryo-EM has shown that specimens present beam-induced motion (BIM). Consequently, in this work, we develop a BIM correction method at the image level, resulting in an integrated image in which the in-plane BIM blurring is compensated prior to particle picking. The methodology is based on a robust Optical Flow (OF) approach that can efficiently correct for local movements in a rapid manner. The OF works particularly well if the BIM pattern presents a substantial degree of local movements, which occurs in our data sets for Falcon II data. However, for those cases in which the BIM pattern corresponds to global movements, we have found it advantageous to first run a global motion correction approach and to subsequently apply OF. Additionally, spatial analysis of the Optical Flow allows for quantitative analysis of the BIM pattern. The software that incorporates the new approach is available in XMIPP (http://xmipp.cnb.csic.es).
authors: Biocomputing Unit, Centro Nacional de Biotecnología-CSIC, C/ Darwin 3, 28049 Madrid, Spain.
authors: Vahid
authors: V
authors: Abrishami
authors: Biocomputing Unit, Centro Nacional de Biotecnología-CSIC, C/ Darwin 3, 28049 Madrid, Spain.
authors: Javier
authors: J
authors: Vargas
authors: School of Life Sciences, Tsinghua University, Beijing 100084, China.
authors: Xueming
authors: X
authors: Li
authors: The Keck Advanced Microscopy Laboratory, Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158-2517, USA.
authors: Yifan
authors: Y
authors: Cheng
authors: Escuela Politécnica Superior, Universidad Autónoma de Madrid, C/ Francisco Tomás y Valiente, 28049 Cantoblanco, Madrid, Spain.
authors: Roberto
authors: R
authors: Marabini
authors: Biocomputing Unit, Centro Nacional de Biotecnología-CSIC, C/ Darwin 3, 28049 Madrid, Spain.
authors: Carlos Óscar Sánchez
authors: CÓ
authors: Sorzano
authors: Biocomputing Unit, Centro Nacional de Biotecnología-CSIC, C/ Darwin 3, 28049 Madrid, Spain. Electronic address: carazo@cnb.csic.es.
authors: José María
authors: JM
authors: Carazo
mesh_terms: D000465:Algorithms; D019843:Archaeal Proteins / Q000737:chemistry; D003198:Computer Simulation; D020285:Cryoelectron Microscopy / Q000295:instrumentation* / Q000379:methods*; D007091:Image Processing, Computer-Assisted / Q000379:methods*; D009975:Orthomyxoviridae / Q000737:chemistry; D046988:Proteasome Endopeptidase Complex / Q000737:chemistry; D012261:Ribonucleoproteins / Q000032:analysis / Q000737:chemistry; D012270:Ribosomes / Q000737:chemistry
chemical_list: D019843:Archaeal Proteins; D012261:Ribonucleoproteins; D046988:Proteasome Endopeptidase Complex
keywords: Beam induced motion; Direct detection devices; Electron microscopy; Single particle analysis