Image processing for electron microscopy single-particle analysis using XMIPP.
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.
Centro Nacional de Biotecnología CSIC, Unidad de Biocomputación, Cantoblanco, 28049 Madrid, Spain.
Sjors H W
SH
Scheres
Rafael
R
Núñez-Ramírez
Carlos O S
CO
Sorzano
José María
JM
Carazo
Roberto
R
Marabini
D000465:Algorithms; D007091:Image Processing, Computer-Assisted / Q000706:statistics & numerical data*; D021621:Imaging, Three-Dimensional / Q000706:statistics & numerical data; D008854:Microscopy, Electron / Q000706:statistics & numerical data*; D012984:Software; D012985:Software Design; D014584:User-Computer Interface