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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 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.
(Alignment and Reconstruction for Electron Tomography) is a GPU-accelerated software package that provides an integrated solution to both fiducial-free alignment and reconstruction for cryoEM tomography.
(Alignment and Reconstruction for Electron Tomography 2) is a GPU-accelerated software package that provides an integrated solution to both fiducial-free alignment and reconstruction for cryoEM tomography.
an assembly line of macromolecular assemblies, Assembline is a multi-step protocol for integrative structural modeling of macromolecular complexes based on electron microscopy, cross-linking mass spectrometry and other data.
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 sequence assignment validation tool for in cryo-EM models
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.
the next-generation molecular visualization program from the Resource for Biocomputing, Visualization, and Informatics (RBVI), following UCSF Chimera. Compared to Chimera, ChimeraX has improved graphics (e.g. interactive ambient shadows); faster handling of large structures (millions of atoms); and a more modern, single-window user interface.
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 automatic pipeline for cryo-EM data preprocessing and assessment using a combination of deep learning and image analysis tools.
PIP package memory efficient implementation of cryoCARE (Content-Aware Image Restoration for Cryo-Transmission Electron Microscopy Data), is a restoration method that dramatically increases contrast in cryo-TEM images, improving the interpretability of the acquired data.
a neural network based algorithm for heterogeneous cryo-EM reconstruction. In particular, the method models a continuous distribution over 3D structures by using a neural network based representation for the volume.
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 a standalone program under and is part of the image processing workflow in SPHIRE.
a computational tool using deep learning to automatically build full DNA/RNA atomic structure from cryo-EM map.
an advanced software solution designed for particle sorting/sieving in single particle analysis (SPA) for Cryogenic Electron Microscopy (cryo-EM).
Toolkit for interfacing with CryoSPARC.
A simple utility that wraps around to convert particle positions from Cryosparc JOB directories into a RELION-ready directory.
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 computational tool using deep learning that can estimate the residue-wise local quality for protein models from cryo-Electron Microscopy (EM) maps.
(Deep cryo-EM Map Enhancer) a python package designed to perform non-linear post-processing of cryo-EM maps for local sharpening, automatic masking and denoising. Systems using cuda 11+ should use the 20210511 version of deepEMhancer, and the modified models distributed in /programs/share/deepemhancer/20210511/deepEMhancerModels/production_checkpoints/
a de novo modeling protocol to build an entire protein 3D model directly from near-atomic (up to about 5 Angstrom) resolution EM map.
(Dynamics Extraction From cryo-em Map) provides an implementation of a dynamics prediction from a cryo-EM density map.
a program that sorts particles by size using the radius of a particle; it uses difference of Gaussians (DoG) for picking particles.
a tool for nucleic acid sequence identification, assignment and validation for cryo-EM and crystal structure models.
a software environment for subtomogram averaging of cryo-EM data.
a small set of tools providing a bidirectional interface between the subtomogram averaging software Dynamo and the Warp-RELION-M pipeline.
a collection of tools for subtomogram averaging in dynamo.
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.
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.
a computational tool using deep learning that can accurately identify structures, alpha helices, beta sheets, other(coils/turns) and DNA/RNA, in cryo-EM maps of medium to low resolution.
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.
improves the quality and interpretability of cryo-EM maps by local and non-local deep learning
a deep learning based automated RNA modeling from cryo-EM maps.
a Python package for detecting and erasing gold fiducials in cryo-EM images.
determines the detective quantum efficiency (DQE) of a detector.
an interface for cryo-transmission electron microscopy (cryo-EM) data collection with computer image processing. Focus creates a user-friendly environment to import and manage data recorded by direct electron detectors and perform elemental image processing tasks in a high-throughput manner, while new data is being acquired at the microscope.
(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.
GCtfFind robustly estimates the contrast transfer function (CTF) of cryoET tilt series and cryoEM micrographs, essential information needed for cryoET subtomogram averaging and cryoEM single-particle reconstruction.
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.
superimposes molecular subunits into the density map of their complex. To reduce computational costs for the superimposing, both subunits and complexes are transformed into GMM (Gaussian Mixture Model) using the gmconvert program. Although designed to superimpose multiple atomic models of subunits into a low-resolution 3D density map, gmfit can also be applied to superimposing two 3D density maps or two atomic models.
(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.
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 neural network for the automatic identification of oligonucleotides and protein secondary structure in cryo‐EM maps.
software for ice gradient estimation and removal on cryoEM micrographs.
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.
a Java image processing program inspired by NIH Image that 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" and supports "stacks", a series of images that share a single window. It is multithreaded, so time-consuming operations can be performed in parallel with other operations.
a set of image processing, modeling and display programs used for tomographic reconstruction and for 3D reconstruction of EM serial sections and optical sections.
A tool reading IMOD points, obtaining particles' info and generating .star file for RELION.
an efficient tool for flexible fitting of atomic structures into EM maps based on Normal Mode Analysis in internal Coordinates.
(Image Processing Library & Toolbox) a 2D Crystallography Suite developed by Andreas Schenk.
an immersive environment designed to ease the task of building high quality macromolecular models into low to medium resolution experimental maps, where the experimental information alone is insufficient to place individual atoms precisely. ISOLDE is implemented as a plugin to ChimeraX and can be conveniently installed via its built-in Tool Shed.
(ISOtropic reconstructioN of Electron Tomography) trains deep convolutional neural networks to reconstruct meaningful contents in the missing wedge for electron tomography, and to increase signal-to-noise ratio, using the information learned from the original tomogram.
(Karhunen Loeve Transform picker) is a fully automatic EM particle picker and requires only the approximated particle size as an input . It is especially designed to handle low SNR micrographs. It is based on learning a set of optimal templates through the use of multi-variate statistical analysis via the Karhunen Loeve Transform.
a pipeline for simulation assisted interpretation of lipid or lipid-like densities in e.g. cryogenic electron microscopy (cryo-EM) structures of membrane proteins.
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.
a tool for assessing how well atomic model features are resolved in cryoEM maps. A fitted model is used in the analysis. A Q-score is calculated for each atom in the model. Q-scores can then be used to visualize how well each residue/atom is resolved and averaged to represent the entire model/map.
Mean curvature motion and levelset motion for cryo-ET
a pipeline for the automated detection of membrane-bound proteins in cryo-electron tomograms. It utilizes the geometry of a pre-segmented membrane to reduce the complexity of the detection task. As a result, MemBrain only requires a small amount of annotated data (even one single annotated membrane can be enough!) and can generalize well to unseen tomograms and membranes.
Membrane segmentation in 3D for cryo-electron tomography (cryo-ET).
(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.
an automatic atomic model building program for cryo-EM maps.
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.
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.
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. 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.
provides 3D-CTF correction for cryo-electron tomography
a fast and simple python module and program to estimate local scaling of cryo-EM maps, to approximate relative occupancy and/or resolution, and optionally to equalize the map according to occupancy while suppressing solvent amplification.
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.
(Particle Estimation for Electron Tomography) a package for aligning and averaging particles in 3-D subvolumes extracted from tomograms. If PEET and IMOD are both installed, most PEET operations are available from the eTomo graphical user interface in IMOD. PEET is written in Matlab and a compiled version is distributed along with the Matlab runtime environment needed to run it.
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.
includes programs and shell scripts for electron tomography of thin specimens, providing an interactive graphical tool for fast initial alignment of a tilt series, shell scripts for the more time consuming refinement, and some other useful image manipulation utilities.
Python modules and command-line utilities for electron microscopy of biological samples.
a Python-based GUI program for indexing power spectra of helical assemblies.
a software toolkit and library of routines for the analysis and manipulation of macromolecular structural models, implemented in the Python programming language.
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 Star Files from RELION 4.0 to Dynamo Table
RELION with block-based reconstruction modifications.
RELION 4 with support for composite masks
simple python script which enables one to follow the progress of 2D/3D classification and refinement in RELION in real time.
additional tools for subtomogram analysis in Relion tomo.
a collection of scripts for cryoEM data collection and analysis
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).
restore is a program for denoising cryogenic electron microscopy images with a convolutional neural network.
(Refinement and Optimization via Machine lEarning for cryo-EM) a parallel computing software system dedicated for high-resolution cryo-EM structure determination and data analysis, which implements advanced machine learning approaches in modern computer sciences and runs natively in an HPC environment.
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.
structure refinement and validation for crystallography and single particle analysis.
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.
a tool designed to correct for the preferred orientation problem in cryoEM by self-supervised deep learning, by recovering missing information from well-sampled orientations in Fourier space.
(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.
a Python implementation of the STAR file format designed principally for compatibility with RELION format STAR files. It allows STAR files to be created and opened easily using a very simple API, exposing data blocks as pandas DataFrame objects.
a package implemented in Python to manipulate Relion star files including counting, modifying, plotting, and sifting the data.
(Subtomogram averaging scripts with TOM toolbox or Subvolume processing scripts with the TOM toolbox) is a collection of scripts for a pipeline for subvolume alignment and averaging of electron cryo-tomography data.
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 pipeline of tools to generate robust open mesh surfaces from voxel segmentations of biological membranes using the Screened Poisson algorithm and calculate morphological features including curvature and membrane-membrane distance using pycurv's vector voting framework with tools to convert these morphological quantities into morphometric insights.
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.
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 package for fast tomographic reconstruction on multicore computers. Full resolution tomograms are generated at high speed on standard computers with no special system requirements.
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 …
a package for noise reduction in electron tomography with Anisotropic Nonlinear Diffusion.
a package for feature-preserving noise filtering in electron tomography.
a package for CTF determination and correction in electron cryotomography.
extends the cryoDRGN framework to cryo-ET by learning heterogeneity from datasets in which each particle is sampled by multiple projection images at different stage tilt angles.
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 …
a software package with a modern graphical user interface to carry out the entire pipeline of cryoET and subtomogram averaging to achieve high resolution.
a software suite intended to assist users in segmenting membranes in tomograms, based on a local differential structure approach and on a Gaussian-like model of membrane profile.
is a software package for segmenting membranes in tomograms. It is based on (1) a Gaussian-like model of membrane profile, (2) a local differential structure approach, and (3) anisotropic propagation of the local structural information using the tensor voting algorithm.
a deep metric learning based particle picking procedure for cryo-ET
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.
Added support for filament start-end coordinate picking (new options -f, -fp and -fl in the extract command in Topaz, for subsequent helical reconstruction in RELION.
a collection of software tools for computational analysis of cryo-EM images developed by John Rubinstein/U Toronto
a software package for fully automated processing of cryo-EM data sets during data acquisition. TranSPHIRE transfers data from the microscope, automatically applies the common pre-processing steps, picks particles, performs 2D clustering and 3D refinement parallel to image recording. Importantly, TranSPHIRE introduces a machine learning-based feedback loop to re-train its internally used picking model to adapt to any given data set live during processing. This …
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 computational tool using local vector based algorithm that can accurately identify the global and local alignment of cryo-electron microscopy (EM) maps.
a set of tools for cryo-EM and cryo-ET data processing including, among other tools: Warp, M, WarpTools, MTools, MCore, and Noise2Map.
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.