Alignment of direct detection device micrographs using a robust Optical Flow approach

J Struct Biol. 2015 Mar;189(3):163-76. doi: 10.1016/j.jsb.2015.02.001. Epub 2015 Feb 12.


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 (

Keywords: Beam induced motion; Direct detection devices; Electron microscopy; Single particle analysis.

MeSH terms

  • Algorithms
  • Archaeal Proteins / chemistry
  • Computer Simulation
  • Cryoelectron Microscopy / instrumentation*
  • Cryoelectron Microscopy / methods*
  • Image Processing, Computer-Assisted / methods*
  • Orthomyxoviridae / chemistry
  • Proteasome Endopeptidase Complex / chemistry
  • Ribonucleoproteins / analysis
  • Ribonucleoproteins / chemistry
  • Ribosomes / chemistry


  • Archaeal Proteins
  • Ribonucleoproteins
  • Proteasome Endopeptidase Complex