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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.
Provides a particle data analysis system for macromolecule electron microscopy (EM). Signature hosts a particle screening module and a particle analysis module. The graphic user interface of the program provides informative data display to facilitate and expedite data processing. The particle screening module supports both automatic and manual operations. The data analysis module provides image processing functions, such as band-pass filtering, intensity normalization and particle classification. Signature aims to create a friendly and flexible computing environment for EM data processing, and therefore to allow the user to concentrate on other important aspects of an EM study, to prepare better specimen grids and to improve the resolution of a structure.
Exploits the advances in high performance computing technology in order to distribute particle picking calculations over multiple nodes of a computer cluster. gEMpicker is a highly parallel correlation-based particle picking tool which uses multiple graphics processor units (GPUs) to accelerate the calculation. The user may define a template particle in one of several ways, and this is then used to pick other similar particles from the micrographs by using a fast Fourier transform (FFT) to calculate the correlation score at each pixel between the template and the micrograph. Multiple micrographs may be processed in parallel.
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