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a package (consisting of a suite of five programs: 2dx_manager, 2dx_image, 2dx_diffraction, 2dx_merger and 2dx_logbrowser) for user-friendly image processing of 2D crystals.
a CTF Estimator. ACE2 is a completely rewritten version of ACE. ACE2 adds the additional feature of robust astigmatism estimation and CTF correction with astigmatism using either a mild Weiner filter (recommended) or phase-flipping. Since ACE2 is written in objective C, it no longer requires MATLAB to work.
an automated image reconstruction system that coordinates the execution of the parallel, numerically-intensive codes P3DR, PCUT, POR, PPFT, PSF and RobEM (a GUI driven program used both for image preprocessing and visualization).
a program for filtering 3D maps and applying B-factors.
a program to convert images saved in FEI's bin format into MRC/CCP4 format.
a collection of programs and a platform for the development of software for image processing of electron micrographs, interpretation of reconstructions, molecular modeling, and general image and molecular processing.
a suite of applications for the analysis of helical structures.
a highly extensible, interactive molecular graphics program for interactive visualization and analysis of molecular structures and related data, including density maps, supramolecular assemblies, sequence alignments, docking results, trajectories, and conformational ensembles. It is often a tool of choice for rendering EM volumes.
a program for cutting sections out of 2D and 3D density maps.
CTFFIND3 and CTFTILT are two programs for finding CTFs of electron micrographs.
a new version of ctffind (a program for finding CTFs of electron micrographs) that should run significantly faster than CTFFIND 3 and may give slightly improved results when processing data from detectors other than scanned photographic film.
a program that sorts particles by size using the radius of a particle; it uses difference of Gaussians (DoG) for picking particles.
a software environment for subtomogram averaging of cryo-EM data.
a program to convert images from/to formats used in the "electron microscopical community" (3DEM)
a suite of scientific image processing tools with a particular focus on single particle reconstruction and which includes Foldhunter and Helixhunter.
EMAN2 is a scientific image processing suite with a particular focus on single particle reconstruction from cryoEM images. EMAN2 is a complete refactoring of the original EMAN1 library and contains the SPARX applications. MPI use : to use MPI-enabled executable in SBGrid's EMAN2, use the mpirun.eman2 executable. This will use the older 1.6.3 version of MPI required by EMAN2/SPARX.
allows sharpening of high resolution information in 3D maps obtained by electron cryomicroscopy according to the Rosenthal and Henderson approach (JMB 333:721-745, 2003). The program accepts 3D maps in any common EM format and accepts FSC curves in the format of most common packages for single particles, cryoEM. As output, the program produces a sharpened map and the Guinier plot that allows assessment ...
(EM Imaging Processing GUI) a Graphical User Interface that collects information from the user and runs existing programs from a variety of different software packages.
determines the detective quantum efficiency (DQE) of a detector.
(Fourier REconstruction and ALIGNment) a program for high-resolution refinement of 3D reconstructions from cryo-EM images of single particles.
a program for the refinement of helical filament reconstructions from cryo electron micrographs. It is primarily used to process images of amyloid fibrils, though it has also been tested on TMV and actin filaments.
a GPU-accelerated program for accurate, fast, flexible and fully automatic particle picking from cryo-EM micrographs with or without templates.
a GPU accelerated program for accurate and robust, real-time CTF determination of EM Micrographs.
a version of FREALIGN modified to run on GPU processors so that the refinement process of single particle 3D reconstruction can be speedup.
a GPU-enhanced version of RELION that dramatically speeds up 2D/3D classification and 3D auto-refine.
an interactive molecular modeling system specifically geared towards cryo-EM and other low resolution structures of macromolecular complexes. The long term goal of the gorgon project is to be able to address to every part of the molecular modeling pipeline starting from the initial volumetric reconstruction of the complex all the way to the final placement of each individual atom.
a user-friendly extension to Ed Egelman's Iterative Helical Real Space Reconstruction (IHRSR) software. It includes all of the original IHRSR functionality plus the capabilities to determine out-of-plane tilt, apply dihedral symmetry, and automatically construct a starting model from the image data. IHRSR++ also contains a number of Perl and Spider scripts for performing common preprocessing and data manipulation tasks such as power spectra ...
a public domain Java image processing program inspired by NIH Image for the Macintosh. It can display, edit, analyze, process, save and print 8-bit, 16-bit and 32-bit images. It can read many image formats including TIFF, GIF, JPEG, BMP, DICOM, FITS and "raw". It supports "stacks", a series of images that share a single window. It is multithreaded, so time-consuming operations such as image ...
a set of image processing, modeling and display programs used for tomographic reconstruction and for 3D reconstruction of EM serial sections and optical sections.
an efficient tool for flexible fitting of atomic structures into EM maps based on Normal Mode Analysis in internal Coordinates.
mag_distortion_estimate is used to estimate magnification distortions in electron micrographs using images of polycrystalline samples such as gold shadowed diffraction gratings. The measured distortion at a particular magnification can then be corrected in images of the sample using mag_distortion_correct. Both programs read images that are stored in MRC/CCP4 format.
(Multiscale Modeling Tools for Structural Biology) a collection of perl-based user-level utilities as well as programming libraries for multiscale protein structure modeling. Intended applications include protein structure prediction, loop modeling, structure refinement, and structure evaluation/scoring.
a multi-GPU program that corrects beam-induced sample motion on dose fractionated movie stacks. It implements a robust iterative alignment algorithm that delivers precise measurement and correction of both global and non-uniform local motions at single pixel level across the whole frame, suitable for both single-particle and tomographic images. MotionCor2 runs on a Linux platform equipped with one or more advanced NVIDIA GPU cards. It ...
a program that corrects whole frame image motion recorded with dose fractionated image stacks.
determines the structure of macromolecular assemblies. The approach has been to study specimens with some form of symmetry, such as crystals or helical and icosahedral particles, using programs suitable for many kinds of 2-D and 3-D analysis.
a software suite for the modelling of large conformational changes of 3-D protein structures under the constraint of a low resolution electron density map. A typical application for this software is the interpretation of electron microscopy data using atomic scale resolution structural models. The software package provided here should enable the interested user to perform flexible fitting on new cases without encountering major technical ...
a software package for single-particle EM image processing. It provides an integrated computing environment with comprehensive data analysis functions for particle selection, particle classification, 3D reconstruction and model evaluation. In addition, PARTICLE emphasizes on data visualization that enables the user to "see" the data throughout the process.
performs orientation searches and positional refinement of icosahedral viruses.
a software package for image processing of helical macromolecular complexes.
a Python package and simple command-line program to automatically fit high-resolution atomic structures in cryo-EM densities.
the graphical interface to a collection of applications for the analysis and visualization of multidimensional data, with a focus on data from 3D optical microscopy and electron tomography. IVE (Image Visualization environment) is the core set of software libraries that are the foundation for the tools in Priism.
a software toolkit and library of routines for the analysis and manipulation of macromolecular structural models, implemented in the Python programming language.
a small tool to randomize phases of a 3D map in a given resolution zone. The randomization can be used to test bias in the refinement of atomic models into a map.
carries out rigid body, tls, restrained or unrestrained refinement against Xray data, or idealisation of a macromolecular structure. It minimises the coordinate parameters to satisfy either a Maximum Likelihood or Least Squares residual. There are options to use different minimization methods. (At the moment only CGMAT is active.) REFMAC also produces an MTZ output file containing weighted coefficients for SigmaA weighted mFo-DFcalc and 2mFo-DFcalc ...
(REgularised LIkelihood OptimisatioN) a stand-alone computer program for Maximum A Posteriori (MAP) refinement of (multiple) 3D reconstructions or 2D class averages in cryo-electron microscopy.
converts PDB files between PDBv2.3 and PDBv3.2 formats. It can accurately and rapidly convert in either direction: old to new OR new to old. Atom records of type ATOM, HETATM, TER, ANISOU, SIGATM, SIGUIJ, and LINK are converted, as are DNA residue names (e.g., A, C, T, G of v2.3 cf. DA, DC, DT, DG of v3.2).
a 2D image display and analysis program, specifically designed for single-particle EM.
an image processing framework to obtain 3D models of macromolecular complexes using 3D EM that allows you to execute workflows combining different software tools, while taking care of formats and conversions.
an automated particle selection system for electron microscopy. The application was written by James Chen in Niko Grigorieff laboratory at Brandeis.
(Single-particle IMage Processing Linux Engine) does ab initio 3D reconstruction (programs cluster & origami), heterogeneity analysis (programs cluster, origami & cycler), and high-resolution refinement (programs align, reconstruct, automask & cycler).The SIMPLE back-end consists of an object-oriented numerical library with a single external dependency - the Fastest Fourier Transform in the West (FFTW). The SIMPLE front-end consists of a few standalone, interoperable components developed according to the 'Unix ...
a program package for modeling of atomic resolution structures into low-resolution density maps. The software supports both rigid-body and flexible docking using a variety of fitting strategies.
(single particle analysis for resolution extension) an image processing environment with a particular emphasis on transmission electron microscopy (TEM) structure determination. It includes a graphical user interface that provides a complete graphical programming environment.
(SParx for HIgh Resolution Electron microscopy) is designed for easy access to cryo-electron microscopy using statistical resampling to attain quality assessment and result reproducibility. The SPHIRE pipeline includes movie frame alignments (movie), CTF estimation of raw electron micrographs (cter), picking/stack creation (window), reproducible 2-D classification (isac), reproducible initial model generation (viper), automatic gold-standard 3-D refinement (meridien), local resolution estimation and filtering (localres), and ...
(System for Processing Image Data from Electron microscopy and Related fields) a large image processing suite for electron microscopy.
a graphical user interface for executing SPIDER batch files and other programs, Spire offers a way to manage and organize the many output files created by SPIDER during reconstruction projects.
(Single Particle Reconstruction from Images of kNown Geometry) a single-particle based helical reconstruction package for electron cryo-micrographs used to determine 3D structures of either highly ordered or less ordered specimens.
uses the alignment results from the software application Unblur to calculate movie frame sums.
a flexible, modular software package intended primarily for the processing of transmission electron micrographs. One of several applications developed by Automated Molecular Imaging Group at The Scripps Research Institute.
an open source suite of classes and programs implemented in C++ for single particle electron microscopic image processing.
a graphical user interface for picking particles from image tilt pairs for such applications as random conical tilt (RCT) and orthogonal tilt reconstruction (OTR). TiltPicker borrows its interface from Leginon and re-implements many of the tilt picking features of SPIDER WEB that can be run on modern computers.
a collection of software tools for computational analysis of cryo-EM images developed by John Rubinstein/U Toronto
used to align the frames of movies recorded on an electron microscope to reduce image blurring due to beam-induced motion. It reads stacks of movies that are stored in MRC/CCP4 format and generates frame sums that can be used in subsequent image processing.
designed for interactive fitting of high-resolution X-Ray crystallography models into Electron Microscopy reconstructions. It can also be used to fit two maps together (e.g., in tomography) or to perform Normal-modes calculations. UROX is deprecated, a new version named VEDA should be used instead.
a slightly vectorized (AVX & SSE instructions) version of the original RELION 1.4 code by Dmitry Tegunov of the Max Planck Institute.
a boxing program developed by James Conway.
used for processing electron diffraction data. Previously available only on DEC Alpha.
(X-Window-based Microscopy Image Processing Package) a suite of image processing programs primarily aimed at single-particle 3D electron microscopy.
a tool for analyzing and manipulating images, especially those generated for electron microscopy. Zephyr is scriptable in Python, easy to extend, and easy to link to other programs. Zephyr was written (is being written) by Alex Stewart and Donald J. Olbris in the laboratories of Prof. David J. DeRosier and Prof. Niko Grigorieff at the Rosenstiel Basic Medical Sciences Research Center at Brandeis University ...
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