Supported Applications

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Name Description Links
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 tool for quantifying directional resolution and density isotropy of cryoEM maps using a 3D Fourier Shell Correlation (FSC) algorithm.
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.
(Collaborative Computational Project for Electron cryo-Microscopy) a software framework and resulting software suite that includes tools for project and data management along with a focus on building and refinement of atomic models into cryo-EM reconstructions. The framework allows easy access to various programs and utilities from collaborators via Python task wrappers and a user-friendly graphical user interface or a command-line interface suitable for scripting.
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.
automatic 2d class selection tool based on a deep learning network to separate 2D classes from .hdf / .mrcs files into good and bad classes. Cinderella uses the same deep neural network as crYOLO and was pretrained on a set good / bad classes.
(Computational Imaging System for Transmission Electron Microscopy) processes cryo-EM images of macromolecular complexes and obtains high-resolution 3D reconstructions with tools to process image data including movies, micrographs and stacks of single-particle images, implementing a complete “pipeline” of processing steps to obtain high-resolution single-particle reconstructions.
a program for cutting sections out of 2D and 3D density maps.
an open-source software package for robust analysis of the orientation distribution of cryoelectron microscopy data.
a graphical user interface for identification of proteins from cryo-EM maps.
a novel automated particle picking software based on the deep learning object detection system 'You Only Look Once' (YOLO). CrYOLO is available as standalone program under http://sphire.mpg.de/ and will be part of the image processing workflow in SPHIRE.
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.

Neil Voss wrote: I use a dual license of the both GPL and Apache license, user choice.

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 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.
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).
(enhanced macromolecular classification and alignment for high-resolution in situ tomography) a GPU-accelerated image processing software for high-resolution cryo-electron tomography and subtomogram averaging and classification.
(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.
(geometrically optimized CTF determination for single-particle cryo-EM) a program explicitly designed to determine the focus gradient in single-particle cryo-EM using a novel geometrically optimized approach. The goCTF software is built on the open-source code of CTFFIND4.
A Neural Network for the Automatic Identification of Oligonucleotides and Protein Secondary Structure in Cryo‐EM Maps
a user-friendly extension to Ed Egelman's Iterative Helical Real Space Reconstruction (IHRSR) software that includes the original IHRSR functionality but can also determine out-of-plane tilt, apply dihedral symmetry, and automatically construct a starting model from the image data Perl and Spider scripts allow users to perform common tasks: power spectra calculations, CTF corrections, image stack generation, image centering, and tube diameter determination.

Timothy S. Baker, UCSD

an efficient tool for flexible fitting of atomic structures into EM maps based on Normal Mode Analysis in internal Coordinates.
uses rotationally averaged reference amplitudes from a refined atomic model to locally scale (sharpen) amplitudes of the Fourier transform of a cryo-EM potential map, keeping the phases constant.
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.
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. Norma is used to interpret electron microscopy data using atomic scale resolution structural models and perform flexible fitting on new cases without encountering major technical difficulties.
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.
Python modules and command-line utilities for electron microscopy of biological samples.
unifies standard tomogram processing steps in a single python-based toolbox. For subtomogram averaging, we implemented an adaptive adjustment of scoring and sampling that clearly improves the resolution of averages compared to static strategies.
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. REFMAC also produces an MTZ output file containing weighted coefficients for SigmaA weighted mFo-DFcalc and 2mFo-DFcalc maps, where missing data have been restored.
(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.

Professor Maofu Liao, Liao Lab, Cell Biology, HMS.

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.
a tool for mitigating local over-fitting during single particle reconstruction.
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).
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) for cryoEM using statistical resampling to attain quality assessment and result reproducibility. 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 up to the 3-D sorting of different conformational states based …
(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.
a particle-filter framework for robust cryoEM 3D reconstruction.
an open source suite of classes and programs implemented in C++ for single particle electron microscopic image processing.
programs for cryo-tomography tilt-series alignment and subsequent tomographic reconstruction that take into consideration beam-induced sample motion, modeled by means of polynomial surfaces. TomoAlign comprises: 1) tomoalign, for alignment, to determine the basic parameters of the images (rotation, magnification, tilt) along with the polynomial coefficients that model the motion; 2) tomorec to calculate the tomogram from the tilt-series and takes into account the motion estimated …
TomoEED is an optimized software tool for fast feature-preserving noise filtering of large three-dimensional (3D) tomographic volumes on CPUs and GPUs. The tool is based on the anisotropic nonlinear diffusion method. It has been developed with special emphasis in the reduction of the computational demands by using different strategies, from the algorithmic to the high performance computing perspectives. TomoEED manages to filter large volumes …
Topaz is a pipeline for particle detection in cryo-electron microscopy images using convolutional neural networks trained from positive and unlabeled examples.  Topaz includes methods for micrograph denoising using deep denoising models.
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 boxing program developed by James Conway.
(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.