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General references to the package

Please cite one of the following papers if Xmipp has been of general use in your research.

• S.H.W. Scheres, R. Nuñez-Ramirez, C.O.S. Sorzano, J.M. Carazo & R. Marabini (2008)
  "Image processing for electron microscopy single-particle analysis using Xmipp"
  Nat. Protoc., 3, 977-990

• C.O.S. Sorzano, R. Marabini, J. Velazquez-Muriel, J.R. Bilbao-Castro, S.H.W. Scheres, J.M. Carazo & A. Pascual-Montano (2004)
  "XMIPP: a new generation of an open-source image processing package for Electron Microscopy"
  J. Struct. Biol. 148(2), 194-204

• R. Marabini, I. M. Masegosa, M. C. San Martín, S. Marco, J. J. Fernández, L. G. de la Fraga, C. Vaquerizo & J. M. Carazo (1996)
  "Xmipp: An image processing package for electron microscopy"
  J. Structural Biology, 116, 237-240

References to specific programs

Xmipp is the result of scientific research by a team of multiple developers, often offering original approaches to difficult tasks in 3D-EM. If one of these approaches has been of specific use in your research, please also cite its corresponding paper.

xmipp_angular_predict

• C.O.S.Sorzano, S. Jonic, C. El-Bez, J.M. Carazo, S. De Carlo, P. Thévenaz, M. Unser. (2004) "A multiresolution approach to orientation assignment in 3-D electron microscopy of single particles." Journal of Structural Biology 146(3): 381-392

xmipp_angular_predict_continuous

• S. Jonic, C.O.S.Sorzano, P. Thévenaz, C. El-Bez, S. De Carlo, M. Unser. (2005) "Spline-Based image-to-volume registration for three-dimensional electron microscopy." Ultramicroscopy, 103: 303-317

xmipp_art

Single particles

• R. Marabini, G. T. Herman & J. M. Carazo. (1998)
  "3D reconstruction in electron microscopy using ART with smooth spherically symmetric volume elements (blobs)."
  Ultramicroscopy, 72, 53-65

Crystals

• R. Marabini, C. O. S. Sorzano, S. Matej, J. J. Fernández, J. M. Carazo and G. T. Herman (2004)
  "3D Reconstruction of 2D Crystals in Real Space"
  IEEE Trans. Img. Process, 13, 549--561

Parallel blobs reconstruction

• J.R. Bilbao-Castro, R. Marabini, C.O.S. Sorzano, I. García, J.M. Carazo, J.J. Fernández
  "Exploiting desktop supercomputing for three-dimensional electron microscopy reconstructions using ART with blobs"
  (In press)

xmipp_assign_CTF

With ARMA estimation

• J.A. Velázquez-Muriel, C.O.S.Sorzano, J.J. Fernández, J.M. Carazo. (2003)
  "A method for estimating the CTF in electron microscopy based on ARMA models and parameter adjusting."
  Ultramicroscopy 96, 1:17-35.

xmipp_denoising (with Bayesian wavelet approach)

• C.O.S.Sorzano, E. Ortiz, M. López, J. Rodrigo. (2006) "Improved Bayesian image denoising based on wavelets with applications to Electron Microscopy." Pattern Recognition, 39: 1205-1213

xmipp_enhance_PSD

• S. Jonic, C.O.S.Sorzano, M. Cottevieille, E. Larquet, N. Boisset. (2007) "A novel method for improvement of visualization of power spectra for classification of cryo-electron micrographs and their local areas." Journal of Structural Biology, 157: 156-167

xmipp_IDR_ART

• C.O.S.Sorzano, R. Marabini, G.T. Herman, Y. Censor, J.M. Carazo. (2004)
  "Transfer function restoration in 3D electron microscopy via iterative data refinement."
  Physics in Medicine & Biology 49: 509-522

xmipp_kerdenSOM

• A. Pascual-Montano, L. E. Donate, M. Valle, M. Bárcena, R. D. Pascual-Marqui & J. M. Carazo (2001)
  "A Novel Neural Network Technique for Analysis and Classification of EM Single-Particle Images"
  J. Struct. Biol. 133(2-3), 233-245

xmipp_ml_align2d

• S.H.W. Scheres, M. Valle, R. Nuñez, R. Marabini, C.O.S. Sorzano, G.T. Herman & J.M. Carazo (2005)
  "Maximum-likelihood multi-reference refinement for electron microscopy images"
  J. Mol. Biol., 348(1), 139-149

• S.H.W. Scheres, M. Valle & J.M. Carazo (2005)
  "Fast maximum-likelihood refinement of electron microscopy images"
  Bioinformatics 21 (Suppl. 2), ii243-ii244

xmipp_ml_refine3d

• S.H.W. Scheres, H. Gao, M. Valle, G.T. Herman, P.P.B. Eggermont, J. Frank & J.M. Carazo (2007)
  "Disentangling Conformational States of Macromolecules in 3D-EM through Likelihood Optimization"
  Nature Methods, 4, 27-29

xmipp_mlf_align2d & xmipp_mlf_refine3d

• S.H.W. Scheres, R. Nuñez-Ramirez, Y. Gomez-Llorente, C. San Martin, P.P.B. Eggermont & J.M. Carazo (2007)
  "Modelling experimental image formation for likelihood-based classification of electron microscopy data"
  Structure, 15, 1167-1177

xmipp_normalize

• C.O.S.Sorzano, L.G. de la Fraga, R. Clackdoyle, J.M.Carazo. (2004) "Normalizing projection images: a study of image normalizing procedures for single particle three-dimensional electron microscopy." Ultramicroscopy 101(2-4): 129-138

xmipp_protocols

• S.H.W. Scheres, R. Nuñez-Ramirez, C.O.S. Sorzano, J.M. Carazo & R. Marabini (2008)
  "Image processing for electron microscopy single-particle analysis using Xmipp"
  Nat. Protoc., 3, 977-990

xmipp_SOM

• R. Marabni and J.J. Carazo (1994)
  "Pattern recognition and classification of images of biological macromolecules using artificial neural networks"
  Biophysical Journal 66: 1804-1814

xmipp_SSNR

• M. Unser, C. O. S. Sorzano, P. Thévenaz, S. Jonic, C. El-Bez, S. De Carlo, J. Conway & B. L. Trus (2005)
  "Spectral Signal-to-Noise Ratio and resolution assessment of 3D reconstructions"
  J. Structural Biology, 149, 243-255

xmipp_Unbend

• D. Gil, J.M. Carazo and R. MarabiniM. (2006)
  "On the Nature of 2D Crystal Unbending"
  J. Structural Biology, 156, 546-555