Image processing for electron microscopy single-particle analysis using XMIPP

By Sjors H. W. Scheres, Rafael Núnez-Ramírez, Carlos Oscar Sánchez Sorzano, J. M. Carazo, Roberto Marabini. Nature Protocols, 2008

344 citations recorded by the source corpus.

Subfields: Materials Chemistry, Structural Biology, Surfaces, Coatings and Films

View Paper: https://www.semanticscholar.org/paper/1403c7022b5c8d41b94b15b745cfe5869f12fab4

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Materials Chemistry

1. Sjors H. W. Scheres
2. G. Murshudov
3. Dari Kimanius
4. Erik Lindahl
5. Tom Burnley
6. Björn Forsberg
7. Martyn D. Winn
8. Colin M. Palmer

In Structural Biology

1. Sjors H. W. Scheres
2. Dari Kimanius
3. Erik Lindahl
4. G. Murshudov
5. Björn Forsberg
6. Tom Burnley
7. G. McMullan
8. Shaoxia Chen

In Surfaces, Coatings and Films

1. Sjors H. W. Scheres
2. Dari Kimanius
3. Erik Lindahl
4. Björn Forsberg
5. G. Murshudov
6. G. McMullan
7. Shaoxia Chen
8. R. Henderson

Citations in the corpus

• Appion: an integrated, database-driven pipeline to facilitate EM image processing (2009, unknown): “For example, functions from SPIDER, EMAN, Frealign, Imagic, FindEM, Xmipp and Matlab have all been incorporated into the Appion pipeline by Python wrappers (Frank et al., 1996; Grigorieff, 2007; Ludtke et al., 1999; Mallick et al., 2005; Roseman, 2003; Scheres et al., 2008; van Heel et al., 1996).”
• High-resolution noise substitution to measure overfitting and validate resolution in 3D structure determination by single particle electron cryomicroscopy (2013, methodology): “Image processing of the particle stacks to produce 3D maps was carried out using the standard single particle iterative procedure of parameter determination and 3D structure calculation, following the normal protocols in each case, as for example with Frealign [9], Relion [10] or Xmipp [53].”
• Recent developments in the CCP-EM software suite (2017, methodology): “The MRC file format is one of the principal formats for cryo-EM data, and is used in common programs such as RELION (Scheres et al., 2008) and for the deposition of experimental volumes in the EMDB (Tagari et al., 2002; Lawson et al., 2016).”
• Revisit of reconstituted 30-nm nucleosome arrays reveals an ensemble of dynamic structures (2018, methodology): “Scheres SH, Nunez-Ramirez R, Sorzano CO, Carazo JM, Marabini R. Image processing for electron microscopy single-particle analysis using XMIPP.”
• Accelerated cryo-EM structure determination with parallelisation using GPUs in RELION-2 (2016, background): “, 2007), FREALIGN (Grigorieff, 2007), XMIPP (Scheres et al., 2008), RELION (Scheres, 2012a), or SIMPLE (Elmlund and Elmlund, 2012).”
• A Bayesian View on Cryo-EM Structure Determination (2012, methodology): “The initial map was first subjected to conventional refinement as implemented in the XMIPP package.(24) This implementation merely represents one of many other available implementations for cryo-EM reconstruction and is not expected to perform significantly better or worse than most of them.”