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Image processing for electron microscopy single-particle analysis using XMIPP

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.

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Figure 1: A generalized XMIPP processing workflow.
Figure 2: Micrograph selection.
Figure 3: Example of class selection from a self-organizing map of rotational spectra.
Figure 4: Anticipated results for the G40P case.
Figure 5: Anticipated results for the ribosome case.

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Acknowledgements

We thank Haixiao Gao and Joachim Frank for providing the ribosome data, and we thank the Barcelona Supercomputing Center (Centro Nacional de Supercomputación) for providing computer resources. This work was funded by the European Union (FP6-502828 and UE-512092), the US National Institutes of Health (HL740472), the Spanish Comisión Interministerial de Ciencia y Tecnología (BFU2004-00217), the Spanish Ministerio de Educacioón y Ciencias (CSD2006-0023, BIO2007-67150-C03-01 and -03), the Spanish Fondo de Investigación Sanitaria (04/0683) and the Comunidad de Madrid (S-GEN-0166-2006).

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Correspondence to Sjors H W Scheres.

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Scheres, S., Núñez-Ramírez, R., Sorzano, C. et al. Image processing for electron microscopy single-particle analysis using XMIPP. Nat Protoc 3, 977–990 (2008). https://doi.org/10.1038/nprot.2008.62

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