Cryo-EM images are usually collected in defocused condition for increased phase contrast. These images are modulated in frequency space by the phase CTF (Contrast Transfer Function). Image CTF must be estimated for later deconvolution. Currently, several software for CTF estimation is available (e.g. ctffind, gctf, e2ctf.py).
Permits surface rendering, multivariate statistical analysis (MSA), automatic classification, projection matching, angular reconstitution, automatic particle selection. IMAGIC can be employed for real data processing run for educational or testing purposes. This tool can exploit the properties of cheap graphic processors. It is useful for 4D analysis at atomic resolution or for refining towards multiple 3D structures.
Determines defocus parameters from images of untitled specimens, as well as defocus and tilt parameters from images of tilted specimens. CTFFIND is a package that uses images collected using modern technologies such as dose fractionation and phase plates. Defocus parameters are estimated by fitting a model of the microscope’s contrast transfer function (CTF) to an image’s amplitude spectrum.
Describes the reconstruction of biological molecules from the electron micrographs of single particles. SPIDER is an open source project that manages computation using the image-processing software and can also using a graphical user interface (GUI), termed the SPIDER Reconstruction Engine. These two approaches are described to obtain an initial reconstruction: random-conical tilt and common lines.
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.
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.
Allows particle picking and contrast transfer function (CTF) estimation from cryo-electron microscopy data (cryo-EM). e2boxer.py includes several features: Interactive particle picking, automated particle picking using Gauss convolution method, command-line (batch) automated particle picking (no GUI) using Gauss convolution method and CTF estimation in both GUI and command-line mode.
Predicts, refines and corrects contrast transfer function (CTF). Gctf offers four customizable parameters: resolution range, astigmatism, box size and B-factors. It can serve to identify local defocus variation that can be useful to find abnormal micrographs. This tool simplifies the cryogenic electron microscopy (cryoEM) image processing. It can be employed to improve the final resolution of 3D cryoEM reconstructions.