Image processing for electron microscopy single-particle analysis using XMIPP (original) (raw)
Henderson, R. Realizing the potential of electron cryo-microscopy. Q. Rev. Biophys.37, 3–13 (2004). ArticleCASPubMed Google Scholar
Subramaniam, S. & Milne, J.L.S. Three-dimensional electron microscopy at molecular resolution. Annu. Rev. Biophys. Biomol. Struct.33, 141–155 (2004). ArticleCASPubMed Google Scholar
Carragher, B . & Smith, P.R. Special issue on Advances in Computational Image Processing for Microscopy. J. Struct. Biol.116, 2–8 (1996). ArticleCASPubMed Google Scholar
Chiu, S.L.A.W. Special Issue on Single Particle Processing (eds. Ludtke, S.J. & Chiu, W.) J. Struct. Biol.173 (2001).
Frank, J. et al. SPIDER and WEB: processing and visualization of images in 3D electron microscopy and related fields. J. Struct. Biol.116, 190–199 (1996). ArticleCASPubMed Google Scholar
Ludtke, S.J., Baldwin, P.R. & Chiu, W. EMAN: semiautomated software for high-resolution single-particle reconstructions. J. Struct. Biol.128, 82–97 (1999). ArticleCASPubMed Google Scholar
Heymann, J.B. & Belnap, D.M. Bsoft: image processing and molecular modeling for electron microscopy. J. Struct. Biol.157, 3–18 (2007). ArticleCASPubMed Google Scholar
van Heel, M., Harauz, G., Orlova, E.V., Schmidt, R. & Schatz, M. A new generation of the IMAGIC image processing system. J. Struct. Biol.116, 17–24 (1996). ArticleCASPubMed Google Scholar
Hohn, M. et al. SPARX, a new environment for Cryo-EM image processing. J. Struct. Biol.157, 47–55 (2007). ArticleCASPubMed Google Scholar
Sorzano, C.O.S. et al. XMIPP: a new generation of an open-source image processing package for electron microscopy. J. Struct. Biol.148, 194–204 (2004). ArticleCASPubMed Google Scholar
Marabini, R. et al. Xmipp: an image processing package for electron microscopy. J. Struct. Biol.116, 237–240 (1996). ArticleCASPubMed Google Scholar
Nickell, S. et al. Automated cryoelectron microscopy of 'single particles' applied to the 26S proteasome. FEBS Lett.581, 2751–2756 (2007). ArticleCASPubMed Google Scholar
Martin-Benito, J. et al. Divergent substrate-binding mechanisms reveal an evolutionary specialization of eukaryotic prefoldin compared to its archaeal counterpart. Structure15, 101–110 (2007). ArticleCASPubMed Google Scholar
Busselez, J. et al. Structural basis for the PufX-mediated dimerization of bacterial photosynthetic core complexes. Structure15, 1674–1683 (2007). ArticleCASPubMed Google Scholar
Tato, I. et al. The ATPase activity of the DNA transporter TrwB is modulated by protein TrwA: implications for a common assembly mechanism of DNA translocating motors. J. Biol. Chem.282, 25569–25576 (2007). ArticleCASPubMed Google Scholar
Agirrezabala, X. et al. Quasi-atomic model of bacteriophage t7 procapsid shell: insights into the structure and evolution of a basic fold. Structure15, 461–472 (2007). ArticleCASPubMed Google Scholar
Nunez-Ramirez, R. et al. Loading a ring: structure of the Bacillus subtilis DnaB protein, a co-loader of the replicative helicase. J. Mol. Biol.367, 764–769 (2007). ArticleCASPubMed Google Scholar
Rivera-Calzada, A., Spagnolo, L., Pearl, L.H. & Llorca, O. Structural model of full-length human Ku70-Ku80 heterodimer and its recognition of DNA and DNA-PKcs. EMBO Rep.8, 56–62 (2007). ArticleCASPubMed Google Scholar
Arias-Palomo, E., Recuero-Checa, M.A., Bustelo, X.R. & Llorca, O. 3D structure of Syk kinase determined by single-particle electron microscopy. Biochim. Biophys. Acta1774, 1493–1499 (2007). ArticleCASPubMedPubMed Central Google Scholar
Van Heel, M. Angular reconstitution: a posteriori assignment of projection directions for 3D reconstruction. Ultramicroscopy21, 111–123 (1987). ArticleCASPubMed Google Scholar
Crowther, R.A. & Amos, L.A. Harmonic analysis of electron microscope images with rotational symmetry. J. Mol. Biol.60, 123–130 (1971). ArticleCASPubMed Google Scholar
Pascual-Montano, A. et al. A novel neural network technique for analysis and classification of EM single-particle images. J. Struct. Biol.133, 233–245 (2001). ArticleCASPubMed Google Scholar
Scheres, S.H.W. et al. Maximum-likelihood multi-reference refinement for electron microscopy images. J. Mol. Biol.348, 139–149 (2005). ArticleCASPubMed Google Scholar
Radermacher, M., Wagenknecht, T., Verschoor, A. & Frank, J. Three-dimensional reconstruction from a single-exposure, random conical tilt series applied to the 50S ribosomal subunit of Escherichia coli. J. Microsc.146, 113–136 (1987). ArticleCASPubMed Google Scholar
Scheres, S.H.W. et al. Disentangling conformational states of macromolecules in 3D-EM through likelihood optimization. Nat. Methods4, 27–29 (2007). ArticleCASPubMed Google Scholar
Scheres, S.H.W. et al. Modeling experimental image formation for likelihood-based classification of electron microscopy data. Structure15, 1167–1177 (2007). ArticleCASPubMedPubMed Central Google Scholar
Cheng, R.H. et al. Functional implications of quasi-equivalence in a T = 3 icosahedral animal virus established by cryo-electron microscopy and X-ray crystallography. Structure2, 271–282 (1994). ArticleCASPubMedPubMed Central Google Scholar
Penczek, P.A., Grassucci, R.A. & Frank, J. The ribosome at improved resolution: new techniques for merging and orientation refinement in 3D cryo-electron microscopy of biological particles. Ultramicroscopy53, 251–270 (1994). ArticleCASPubMed Google Scholar
Sorzano, C.O.S. et al. A multiresolution approach to orientation assignment in 3D electron microscopy of single particles. J. Struct. Biol.146, 381–392 (2004). ArticleCASPubMed Google Scholar
Jonic, S. et al. Spline-based image-to-volume registration for three-dimensional electron microscopy. Ultramicroscopy103, 303–317 (2005). ArticleCASPubMed Google Scholar
Sorzano, C.O.S., Marabini, R., Herman, G.T., Censor, Y. & Carazo, J.M. Transfer function restoration in 3D electron microscopy via iterative data refinement. Phys. Med. Biol.49, 509–522 (2004). ArticleCASPubMed Google Scholar
Marabini, R., Herman, G.T. & Carazo, J.M. 3D reconstruction in electron microscopy using ART with smooth spherically symmetric volume elements (blobs). Ultramicroscopy72, 53–65 (1998). ArticleCASPubMed Google Scholar
Sorzano, C.O.S. et al. The effect of overabundant projection directions on 3D reconstruction algorithms. J. Struct. Biol.133, 108–118 (2001). ArticleCASPubMed Google Scholar
Jonic, S., Sorzano, C.O.S., Cottevieille, M., Larquet, E. & Boisset, N. A novel method for improvement of visualization of power spectra for sorting cryo-electron micrographs and their local areas. J. Struct. Biol.157, 156–167 (2007). ArticleCASPubMed Google Scholar
Zhu, Y. et al. Automatic particle selection: results of a comparative study. J. Struct. Biol.145, 3–14 (2004). ArticleCASPubMed Google Scholar
Pascual, A., Barcena, M., Merelo, J.J. & Carazo, J.M. Mapping and fuzzy classification of macromolecular images using self-organizing neural networks. Ultramicroscopy84, 85–99 (2000). ArticleCASPubMed Google Scholar
Pascual-Montano, A., Taylor, K.A., Winkler, H., Pascual-Marqui, R.D. & Carazo, J.M. Quantitative self-organizing maps for clustering electron tomograms. J. Struct. Biol.138, 114–122 (2002). ArticleCASPubMed Google Scholar
Scheres, S.H.W., Valle, M. & Carazo, J.M. Fast maximum-likelihood refinement of electron microscopy images. Bioinformatics21 Suppl 2: ii243–ii244 (2005). ArticleCASPubMed Google Scholar
Sorzano, C.O.S., Marabini, R., Herman, G.T. & Carazo, J.M. Multiobjective algorithm parameter optimization using multivariate statistics in three-dimensional electron microscopy reconstruction. Pattern Recognit.38, 2587–2601 (2005). Article Google Scholar
Van Heel, M. Similarity measures between images. Ultramicroscopy21, 95–99 (1987). Article Google Scholar
Unser, M., Aldroubi, A. & Eden, M. The L(2) polynomial spline pyramid. IEEE Trans. Pattern Anal. Mach. Intell.15, 364–379 (1993). Article Google Scholar
Unser, M. et al. Spectral signal-to-noise ratio and resolution assessment of 3D reconstructions. J. Struct. Biol.149, 243–255 (2005). ArticleCASPubMed Google Scholar
Nunez-Ramirez, R. et al. Quaternary polymorphism of replicative helicase G40P: structural mapping and domain rearrangement. J. Mol. Biol.357, 1063–1076 (2006). ArticleCASPubMed Google Scholar