Contrast transfert function estimation/correction software tools | Cryo-electron microscopy image analysis

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.

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.

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.

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.

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.

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.

Assesses contrast transfer function (CTF) parameters in electron microscope (EM) images. FitCTF is a standalone Python script that is based on the EMAN software CTF model. The application integrates three different approaches for investigating the focus values and allows users to list micrographs with large inconsistencies, classified by decreasing level. The program is also part of the jspr software.

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.

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.

Facilitates efficient acquisition, on-the-fly motion correction, and CTF analysis of dose fractionated image stacks. UCSFImage is a computer-assisted system for semi-automated electron cryomicroscopy (cryoEM) image acquisition that implements an asynchronous data acquisition scheme. It has a simple interface and can work with different types of cameras, including scintillator-based cameras and direct detection cameras, such as K2 Summit and DE cameras.

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.

Determines the defocus and astigmatism parameters of a given micrograph. FASTDEF automates the accurate processing of large quantities of data, including the individual treatment of multiple subareas of a micrograph. It is based on a fully non-parametric evaluation. This tool considers the contrast transfer function (CTF) as a fringe pattern where a two-dimensional phase is modulated by a sine function. It is useful for high throughput study.

Allows users to perform cryo-electron microscopy (Cryo-EM). TranSPHIRE is supposed to help with the cryo-EM data collection.

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.

Allows access to cryo electron microscopy (cryo-EM) with the goal of quality assessment and result reproducibility by statistical resampling. SPHIRE is a software suited for cryo-EM novices, and users can find an array of programs which guide through the complete process.