Picking images of particles in cryo-electron micrographs is an important step in solving the 3D structures of large macromolecular assemblies. However, in order to achieve sub-nanometre resolution it is often necessary to capture and process many thousands or even several millions of 2D particle images. Thus, a computational bottleneck in reaching high resolution is the accurate and automatic picking of particles from raw cryo-electron micrographs.
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.
Reconstructs single particle from electron cryo-microscopy (cryoEM) images. EMAN is capable of processing large data sets and focuses on processing data from transmission electron microscopes. The application is mainly dedicated to single particle rebuilding but includes more than 40 functionalities allowing users to perform helical reconstruction or single particle tomography as well as interacting with external software such as Frealign or Relion.
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.
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.
Assists users in addressing the problem of picking unknown particles from images. DoG Picker is a general, particle picker based on the Difference of Gaussians (DoG) image transform. The software can function (1) alone as a reference-free particle picker with the unique ability to sort particles based on size, and (2) as a way to bootstrap the creation of templates or training datasets for other particle pickers. It is also implemented within the TiltPicker program.
Consists of a local correlation function particle picker. FindEM is a program based on projection matching using local real-space correlation with a series of templates. The software is also wrapped up in the Appion software.