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.

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.