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Frealign
Calculates and refines three-dimensional (3D) structures of macromolecular assemblies that are calculated from images collected on an electron microscope. Frealign provides a fast and accurate projection matching algorithm, and calculates 3D reconstructions that are fully corrected for the contrast transfer function (CTF) of the microscope. Other features include refinement of microscope defocus and magnification, correction for the Ewald sphere curvature, processing of helical particles, 3D classification, and density masking. Furthermore, algorithms and run scripts were developed to take advantage of parallel computing environments to speed up processing.
Xmipp / X-Window-based Microscopy Image Processing Package
Provides a suite of programs for image processing in electron microscopy. Xmipp is mainly focused on 3D reconstruction of macromolecules through single-particles analysis. Xmipp last release introduces the concept of a project that stores the entire processing workflow from data import to final results. It is possible to monitor, reproduce and restart all computing tasks as well as graphically explore the complete set of interrelated tasks associated to a given project. The graphical tools, such as data visualization, particle picking and parameter ‘‘wizards’’, allow the visual selection of some key parameters. Many standard image formats are transparently supported for input/output from all programs. Additionally, results are standardized, facilitating the interoperation between different Xmipp programs.
cisTEM / Computational Imaging System for Transmission Electron Microscopy
Permits the treatment of cryo-electron microscopy (cryo-EM) images of macromolecular complexes. cisTEM is able to extract high-resolution 3D reconstructions form these images. It can deal with movies, micrographs and stacks of single-particle images, implementing a complete pipeline of processing steps. This tool is based on a maximum-likelihood algorithm. Users can define a combination of particle image stack, alignment parameters and a 3D reference structure.
ACE / Automated CTF Estimation
Provides a completely automated method for the estimation of the contrast transfer function (CTF), the envelope function and the noise spectrum parameters of an image taken using transmission electron microscopy. The ACE method incorporates a way of estimating astigmatism, and reduces the problem of CTF estimation to a truly 1D estimation problem using elliptical averaging. The accuracy of the algorithm was demonstrated using images of carbon support film as well as on large datasets of single particles embedded in ice.
Eos / Extensible Object-oriented System
Allows users to analyze different types of images. Eos is an image analysis environment that allows users to study images of electron micrographs. It supports four types of analyze images: (1) a group of small tools for image analysis and three-dimensional reconstruction of objects with helical symmetry; (2) integration tools such as ‘‘Display2’’ and examples of ‘‘makefile’’; (3) tools for development such as ‘‘maketool’’; and (4) object-oriented libraries for development of new tools.
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