Image Processing for Electron Microscopy Single-Particle Analysis Using XMIPP

Nat Protoc. 2008;3(6):977-90. doi: 10.1038/nprot.2008.62.

Abstract

We describe a collection of standardized image processing protocols for electron microscopy single-particle analysis using the XMIPP software package. These protocols allow performing the entire processing workflow starting from digitized micrographs up to the final refinement and evaluation of 3D models. A particular emphasis has been placed on the treatment of structurally heterogeneous data through maximum-likelihood refinements and self-organizing maps as well as the generation of initial 3D models for such data sets through random conical tilt reconstruction methods. All protocols presented have been implemented as stand-alone, executable python scripts, for which a dedicated graphical user interface has been developed. Thereby, they may provide novice users with a convenient tool to quickly obtain useful results with minimum efforts in learning about the details of this comprehensive package. Examples of applications are presented for a negative stain random conical tilt data set on the hexameric helicase G40P and for a structurally heterogeneous data set on 70S Escherichia coli ribosomes embedded in vitrified ice.

Publication types

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

MeSH terms

  • Algorithms
  • Image Processing, Computer-Assisted / statistics & numerical data*
  • Imaging, Three-Dimensional / statistics & numerical data
  • Microscopy, Electron / statistics & numerical data*
  • Software
  • Software Design
  • User-Computer Interface