Automated specimen search in cryo-TEM observation with DIFF-defocus imaging

J Electron Microsc (Tokyo). 2010;59(4):299-310. doi: 10.1093/jmicro/dfq009. Epub 2010 Mar 30.


We have developed an automated specimen search algorithm for cryo-electron microscopy imaging of ice-embedded single particles suspended across regularly spaced holes. To maximize the particle visibility under a low electron exposure rate condition, specimen searching is carried out in diffraction mode. However, images in diffraction mode contain significant pincushion distortion, making it difficult to computationally predict the locations of the regularly spaced holes. We have implemented a distortion-correction mechanism to restore the primitive distortion-free image and a correlation-based algorithm to accurately determine the periodicity of the holes. A stage-shift method to optimize positional reproducibility is also implemented. Addition of our algorithms to the JADAS software for automated transmission electron microscopy data acquisition has significantly improved the accuracy of specimen search.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms*
  • Automation
  • Cryoelectron Microscopy / instrumentation
  • Cryoelectron Microscopy / methods*
  • Image Enhancement / methods
  • Image Processing, Computer-Assisted / methods*
  • Microscopy, Electron, Transmission / instrumentation
  • Microscopy, Electron, Transmission / methods*
  • Software