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X-windows based microscopy image processing package (Xmipp) is a specialized suit of image processing programs, primarily aimed at obtaining the 3D reconstruction of biological specimens from large sets of projection images acquired by transmission electron microscopy. This public-domain software package was introduced to the electron microscopy field eight(More)
The experimental process of collecting images from macromolecules in an electron microscope is such that it does not allow for prior specification of the angular distribution of the projection images. As a consequence, an uneven distribution of projection directions may occur. Concerns have been raised recently about the behavior of 3D reconstruction(More)
In this work, a powerful parametric spectral estimation technique, 2D-auto regressive moving average modeling (ARMA), has been applied to contrast transfer function (CTF) detection in electron microscopy. Parametric techniques such as auto regressive (AR) and ARMA models allow a more exact determination of the CTF than traditional methods based only on the(More)
Measuring the quality of three-dimensional (3D) reconstructed biological macromolecules by transmission electron microscopy is still an open problem. In this article, we extend the applicability of the spectral signal-to-noise ratio (SSNR) to the evaluation of 3D volumes reconstructed with any reconstruction algorithm. The basis of the method is to measure(More)
Xmipp is a specialized software package for image processing in electron microscopy, and that is mainly focused on 3D reconstruction of macromolecules through single-particles analysis. In this article we present Xmipp 3.0, a major release which introduces several improvements and new developments over the previous version. A central improvement is the(More)
Three-dimensional (3D) electron microscopy (3DEM) aims at the determination of the spatial distribution of the Coulomb potential of macromolecular complexes. The 3D reconstruction of a macromolecule using single-particle techniques involves thousands of 2D projections. One of the key parameters required to perform such a 3D reconstruction is the orientation(More)
In the process of three-dimensional reconstruction of single particle biological macromolecules several hundreds, or thousands, of projection images are taken from tens or hundreds of independently digitized micrographs. These different micrographs show differences in the background grey level and particle contrast and, therefore, have to be normalized by(More)
We present a novel algorithm for the registration of 2D image sequences that combines the principles of multiresolution B-spline-based elastic registration and those of bidirectional consistent registration. In our method, consecutive triples of images are iteratively registered to gradually extend the information through the set of images of the entire(More)
Three-dimensional electron microscopy (3D-EM) is a powerful tool for visualizing complex biological systems. As with any other imaging device, the electron microscope introduces a transfer function (called in this field the contrast transfer function, CTF) into the image acquisition process that modulates the various frequencies of the signal. Thus, the 3D(More)
One of the main applications of electrophoretic 2-D gels is the analysis of differential responses between different conditions. For this reason, specific spots are present in one of the images, but not in the other. In some other occasions, the same experiment is repeated between 2 and 12 times in order to increase statistical significance. In both(More)