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Semi-automated selection of cryo-EM particles in RELION-1.3.

Scheres SH - J. Struct. Biol. (2014)

Bottom Line: Here, a semi-automated particle selection procedure is presented that has been implemented within the open-source software RELION.With only limited user-interaction, the proposed procedure yields results that are comparable to manual particle selection.Together with an improved graphical user interface, these developments further contribute to turning RELION from a stand-alone refinement program into a convenient image processing pipeline for the entire single-particle approach.

View Article: PubMed Central - PubMed

Affiliation: MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge CB2 0QH, UK. Electronic address: scheres@mrc-lmb.cam.ac.uk.

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Schematic representation of the data model. (A) Representation of a micrograph, with coordinate vectors  inside the micrograph, and coordinate vectors  inside each particle image. Vectors  place the ith particle inside the micrograph with an unknown in-plane rotation  with respect to a common frame of reference. Inset (B), mask  which is used for normalisation of the particle images: average and standard deviation of the background pixels are calculated in the white area of this mask. Inset (C), mask  which is used for the particle sorting algorithm: all statistics on the difference images between each particle and its corresponding template are calculated in the white area of this mask.
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f0005: Schematic representation of the data model. (A) Representation of a micrograph, with coordinate vectors inside the micrograph, and coordinate vectors inside each particle image. Vectors place the ith particle inside the micrograph with an unknown in-plane rotation with respect to a common frame of reference. Inset (B), mask which is used for normalisation of the particle images: average and standard deviation of the background pixels are calculated in the white area of this mask. Inset (C), mask which is used for the particle sorting algorithm: all statistics on the difference images between each particle and its corresponding template are calculated in the white area of this mask.

Mentions: The template-based particle picking algorithm proposed employs an additive model with white Gaussian noise in real-space. A micrograph that contains N individual particles i at coordinates in the micrograph is described as follows (also see Fig. 1A):(1)X(r→)=μ(r→)+σ(r→)∗N(r→)+∑i=1NAkiϕi(r→-t→i),where:•


Semi-automated selection of cryo-EM particles in RELION-1.3.

Scheres SH - J. Struct. Biol. (2014)

Schematic representation of the data model. (A) Representation of a micrograph, with coordinate vectors  inside the micrograph, and coordinate vectors  inside each particle image. Vectors  place the ith particle inside the micrograph with an unknown in-plane rotation  with respect to a common frame of reference. Inset (B), mask  which is used for normalisation of the particle images: average and standard deviation of the background pixels are calculated in the white area of this mask. Inset (C), mask  which is used for the particle sorting algorithm: all statistics on the difference images between each particle and its corresponding template are calculated in the white area of this mask.
© Copyright Policy - CC BY
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4318617&req=5

f0005: Schematic representation of the data model. (A) Representation of a micrograph, with coordinate vectors inside the micrograph, and coordinate vectors inside each particle image. Vectors place the ith particle inside the micrograph with an unknown in-plane rotation with respect to a common frame of reference. Inset (B), mask which is used for normalisation of the particle images: average and standard deviation of the background pixels are calculated in the white area of this mask. Inset (C), mask which is used for the particle sorting algorithm: all statistics on the difference images between each particle and its corresponding template are calculated in the white area of this mask.
Mentions: The template-based particle picking algorithm proposed employs an additive model with white Gaussian noise in real-space. A micrograph that contains N individual particles i at coordinates in the micrograph is described as follows (also see Fig. 1A):(1)X(r→)=μ(r→)+σ(r→)∗N(r→)+∑i=1NAkiϕi(r→-t→i),where:•

Bottom Line: Here, a semi-automated particle selection procedure is presented that has been implemented within the open-source software RELION.With only limited user-interaction, the proposed procedure yields results that are comparable to manual particle selection.Together with an improved graphical user interface, these developments further contribute to turning RELION from a stand-alone refinement program into a convenient image processing pipeline for the entire single-particle approach.

View Article: PubMed Central - PubMed

Affiliation: MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge CB2 0QH, UK. Electronic address: scheres@mrc-lmb.cam.ac.uk.

Show MeSH