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Image processing for electron microscopy single-particle analysis using XMIPP

AuthorsScheres, Sjors H. W.; Núñez-Ramírez, Rafael ; Sánchez Sorzano, Carlos Óscar; Carazo, José M.; Marabini, Roberto
KeywordsBiomedical imaging
Image processing
Computational and theoretical biology
Spectroscopy and structural analysis
Issue Date15-May-2008
PublisherNature Publishing Group
CitationNature Protocols 3: 977-990 (2008)
AbstractWe 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.
Description14 pages.-- PMID: 18536645 [PubMed].
Publisher version (URL)http://dx.doi.org/10.1038/nprot.2008.62
Appears in Collections:(CNB) Artículos
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