XMIPP: a new generation of an open-source image processing package for electron microscopy.

By Carlos Oscar Sánchez Sorzano, Roberto Marabini, Javier A. Velázquez-Muriel, Jose-Roman Bilbao-Castro, Sjors H. W. Scheres, J. M. Carazo, Alberto Domingo Pascual-Montano. Journal of Structural Biology, 2004

481 citations recorded by the source corpus.

Subfields: Radiation, Structural Biology, Surfaces, Coatings and Films

View Paper: https://www.semanticscholar.org/paper/da9c34db11bb87327bc75734998561c35338faab

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Citations in the corpus

DNSN-1 recruits GINS for CMG helicase assembly during DNA replication initiation in C. elegans (2023, unknown): “Model-to-map FSCs were plotted usingXmipp (76), after weusedEMAN’s pdb2mrc (77) to generate amap fromourmodel and removed solvent density from the relevant full- and half-maps using multiplication in RELION’s relion_image_handler (77).”
Gctf: Real-time CTF determination and correction (2015, methodology): “There are currently several programs available for CTF determination(Ludtke et al., 1999; Mallick et al., 2005; Mindell and Grigorieff, 2003; Penczek et al., 2014; Shaikh et al., 2008; Sorzano et al., 2004; Vargas et al., 2013; Voortman et al., 2011).”
EMAN2: an extensible image processing suite for electron microscopy. (2007, methodology): “…FREALIGN (GrigorieV, 1998), EM (Hegerl, 1996), IMIRS (Liang et al., 2002), SUPRIM (Schroeter and Bretaudiere , 1996), IMOD (Kremer et al., 1996), PHOELIX (Carragher et al., 1996), PFT (Baker and Cheng, 1996), the MRC reconstruction tools (Crowther et al., 1996) and Xmipp (Sorzano et al., 2004).”
SPARX, a new environment for Cryo-EM image processing. (2007, methodology): “, 1996) and Xmipp (Sorzano et al., 2004).”
RELION: Implementation of a Bayesian approach to cryo-EM structure determination (2012, methodology): “for dealing with symmetry, Euler angle operations and image I/O, were copied and/or adapted from the open-source packages XMIPP (Sorzano et al., 2004) and BSOFT (Heymann and Belnap, 2007), and all Euler angle and symmetry conventions are in accordance with the 3DEM standard conventions (Heymann et a”
A Bayesian View on Cryo-EM Structure Determination (2012, methodology): “All other image processing operations were performed in the XMIPP package.(18) Prior to refinement, all data setswere normalized using previously described procedures.”
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].”
3D architecture of DNA Pol α reveals the functional core of multi-subunit replicative polymerases (2009, unknown): “…and Grigorieff, 2003) and corrected using Bsoft (Heymann, 2001); 12 913 side-view images of the complex were manually extracted using XMIPP (Sorzano et al, 2004) and 2D reference-free classification of the data was performed using EMAN (Ludtke et al, 1999) and 2D maximum-likelihood methods…”