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cryo-EM software tools | Bioimaging

Cryo-EM is an important technique in structural biology used to solve large protein complex and subcellular structures.

cryo-EM steps

ROME
Desktop

ROME Refinement and Optimization based on Machine lEarning for cryo-EM

Offers a clustering method for single-particle cryo-EM data. ROME enables…

Offers a clustering method for single-particle cryo-EM data. ROME enables efficient computation of thousands of reference-free class averages in a highly affordable fashion. It can markedly improve…

MotionCorr
Desktop

MotionCorr

Corrects whole frame image motion recorded with dose fractionated image stack.…

Corrects whole frame image motion recorded with dose fractionated image stack. MotionCorr is a bioinformatic software that greatly enhances image quality and data acquisition efficiency - key…

RosettaES
Desktop

RosettaES Rosetta Enumerative Sampling

Automates, improves upon, and expedites de novo model building. RosettaES uses…

Automates, improves upon, and expedites de novo model building. RosettaES uses fragment-based sampling to enumerate a ‘pool’ of possible protein conformations that both possess physically…

cryoSPARC
Desktop

cryoSPARC

Enables rapid, unbiased, and high-throughput structure discovery of proteins…

Enables rapid, unbiased, and high-throughput structure discovery of proteins and molecular complexes from single-particle cryo-EM data. The algorithms underlying cryoSPARC enable high-resolution…

EMRinger
Desktop

EMRinger

A tool that assesses the precise fitting of an atomic model into the map during…

A tool that assesses the precise fitting of an atomic model into the map during refinement and shows how radiation damage alters scattering from negatively charged amino acids. EMRinger is useful for…

Frealign
Desktop

Frealign

Calculates and refines three-dimensional (3D) structures of macromolecular…

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…

MotionCor2
Desktop

MotionCor2

Corrects beam-induced sample motion on dose fractionated movie stacks.…

Corrects beam-induced sample motion on dose fractionated movie stacks. MotionCor2 is a multi-GPU program that implements a robust iterative alignment algorithm that delivers precise measurement and…

FOCUS
Desktop

FOCUS

Interfaces cryo-transmission electron microscopy (cryo-EM) data collection with…

Interfaces 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…

UCSFImage
Desktop

UCSFImage

Facilitates efficient acquisition, on-the-fly motion correction, and CTF…

Facilitates efficient acquisition, on-the-fly motion correction, and CTF analysis of dose fractionated image stacks. UCSFImage is a computer-assisted system for semi-automated electron cryomicroscopy…

Zorro
Desktop

Zorro

Provides robust drift correction for aligning of dose-fractionated…

Provides robust drift correction for aligning of dose-fractionated cryo-electron microscopy image stacks. Zorro uses of an intensity-normalized cross-correlation and logistic noise model to weight…

Dynamo
Desktop

Dynamo

Aims to subtomogram averaging of cryo Electron Tomography (cryo-ET) data with…

Aims to subtomogram averaging of cryo Electron Tomography (cryo-ET) data with three main goals: first, Dynamo allows user-transparent adaptation to a variety of high-performance computing platforms…

Localize.pytom
Web

Localize.pytom

A webserver for the localize module in the PyTom package. Localize.pytom is a…

A webserver for the localize module in the PyTom package. Localize.pytom is a free website and open to all users and there is no login requirement. The server accepts tomograms as they are imaged and…

PowerFit
Desktop

PowerFit

Determines the placement of subunits to perform a full-exhaustive systematic…

Determines the placement of subunits to perform a full-exhaustive systematic cross- correlation search of the three translational and three rotational degrees of freedom of the model in density.…

DeepPicker
Desktop

DeepPicker

Automates particle picking in single-particle electron cryo-microscopy…

Automates particle picking in single-particle electron cryo-microscopy (cryo-EM) structure determination. DeepPicker aims to liberate structural biologists from the time-consuming and laborious task…

UCSF Tomography
Desktop

UCSF Tomography

Collects single-axis tilt series on electron transmission microscopes. UCSF…

Collects single-axis tilt series on electron transmission microscopes. UCSF Tomography is a software that was implemented based upon an approach in which the compustage tilting is modeled as…

DeepEM
Desktop

DeepEM Deep Electronic Microscopy

Permits to detect “good particles” from cryo-electronic microscopy (EM)…

Permits to detect “good particles” from cryo-electronic microscopy (EM) micrographs taken in a variety of situations. DeepEM is based on a convolutional neural network, a multilayered neural…

EMHP
Desktop

EMHP Electron Microscopy Hole Punch

Allows users to focus on streamlining this preprocessing stage. EMHP works on…

Allows users to focus on streamlining this preprocessing stage. EMHP works on image assessment, masking, and pick filtering in preparation for single particle analysis. This tool contains an…

EMAN
Desktop

EMAN

Focuses on single particle reconstruction from cryoEM images. EMAN is a broadly…

Focuses on single particle reconstruction from cryoEM images. EMAN is a broadly based greyscale scientific image processing suite with a primary focus on processing data from transmission electron…

SubspaceEM
Desktop

SubspaceEM

Accelerates maximum-likelihood reconstructions. The speedup is by orders of…

Accelerates maximum-likelihood reconstructions. The speedup is by orders of magnitude, and the SubspaceEM algorithm produces similar quality reconstructions compared to the traditional…

lm-bfgs
Desktop

lm-bfgs

Allows for individual <1 MDa particle images to be aligned without frame…

Allows for individual <1 MDa particle images to be aligned without frame averaging or linear trajectories. The lm-bfgs algorithm maximizes the overall correlation of the shifted frames with the…

PyTom
Desktop

PyTom

Provides the essential tools for the analysis of subtomograms obtained by cryo…

Provides the essential tools for the analysis of subtomograms obtained by cryo electron tomography. PyTom covers a processing pipeline of tomogram reconstruction, localization of macromolecular…

RELION
Desktop

RELION REgularised LIkelihood OptimisatioN

Employs an empirical Bayesian approach to refinement of (multiple) 3D…

Employs an empirical Bayesian approach to refinement of (multiple) 3D reconstructions or 2D class averages in electron cryo-microscopy (cryo-EM). RELION is implemented as a stand-alone program, and…

EM-SURFER
Web

EM-SURFER

A web-based tool for real-time comparison and analysis of electron microscopy…

A web-based tool for real-time comparison and analysis of electron microscopy (EM) density maps. EM-SURFER compares the shape of EM map isosurfaces, generated using author-recommended contour values.…

3DEMBenchmark
Web

3DEMBenchmark 3D Electron Microscopy Benchmark

Compares several algorithms using a variety of datasets and a wide range of…

Compares several algorithms using a variety of datasets and a wide range of analysis tools. 3DEMBenchmark is also used to set open challenges aiming at obtaining the lastest and most up-to-date view…

PHOELIX
Desktop

PHOELIX

Provides an efficient and reliable method for reconstructing a…

Provides an efficient and reliable method for reconstructing a three-dimensional density map from specimens with helical symmetry. PHOELIX was developed to provide a time-efficient and semi-automated…

Appion
Desktop

Appion

Processes and analyses electron microscopy (EM) images. Appion is integrated…

Processes and analyses electron microscopy (EM) images. Appion is integrated with Leginon data acquisition but can also be used stand-alone after uploading images (either digital or scanned…

SIMPLE
Desktop

SIMPLE Single-particle IMage Processing Linux Engine

Provides data analysis methods for single-particle cryo-electron microscopy…

Provides data analysis methods for single-particle cryo-electron microscopy (cryo-EM). SIMPLE addresses the problem of obtaining 3D reconstructions from 2D projections only, without using an input…

SPARX
Desktop

SPARX

Provides an image processing environment with a particular emphasis on…

Provides an image processing environment with a particular emphasis on transmission electron microscopy (TEM) structure determination. SPARX includes a graphical user interface that provides a…

gEMpicker
Desktop

gEMpicker

Exploits the advances in high performance computing technology in order to…

Exploits the advances in high performance computing technology in order to distribute particle picking calculations over multiple nodes of a computer cluster. gEMpicker is a highly parallel…

FSC
Web

FSC Fourier Shell Correlation

Calculates and plots the Fourier Shell Correlation (FSC) curve from two 3D…

Calculates and plots the Fourier Shell Correlation (FSC) curve from two 3D reconstructions. FSC is a web application that uses the EMAN2 package for the FSC calculation.

SwarmPS
Desktop

SwarmPS

Accelerates the process of particle selection and facilitates particle…

Accelerates the process of particle selection and facilitates particle selection across multiple images. SwarmPS permits to manage large scale particle selection projects. It incorporates…

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