Software for 3D-EM Image Analysis

Information about image processing and 3D reconstruction programs:

Please visit the comprehensive Wikipedia entry for Software Tools for Molecular Microscopy. The following software is included in the list:

 

General packages

  • Appion
  • Bsoft
  • Cyclops
  • EMAN2
  • EMAN
  • Eos
  • IMAGIC
  • IPLT
  • MDPP
  • MRC IMAGE PROCESSING PACKAGE
  • RELION
  • SIMPLE
  • SPARX
  • SPIDER
  • Suprim
  • Xmipp

    •  


Specific packages

Two-dimensional crystals:

  • 2dx

Icosahedral viruses

  • AUTO3DEM

Helices:

  • BBHP - Burnham-Brandeis Helical Package
  • IHRSR
  • Phoelix
  • Ruby-Helix
  • Stokes Lab Procedures

Single particles:

  • Frealign
  • PFT3DR
  • Search/Refine/Build

Tomography

  • EM3D
  • IMOD
  • protomo
  • PyTom
  • RAPTOR
  • SerialEM
  • TOM Toolbox
  • TomoJ
  • TxBR
  • UCSF Tomography
  • FEI Xplore3D™ Tomography Suite

 

Application tools

Subvolume averaging

  • Dynamo
  • Jsubtomo
  • PEET

Mass measurements

  • MASDET

Data Acquisition

  • Leginon

Particle Selection

  • DoG Picker
  • FindEM
  • Signature
  • SwarmPS
  • TiltPicker
  • TMaCS

CTF Estimation and Correction

  • ACE
  • ACE2
  • ctfEval
  • ctf Explorer
  • CTFfind3 and CTFtilt
  • EMCTF
  • TOMOCTF
  • fitctf
  • FitCTF2v

3D Reconstruction

  • TOMO3D
  • TOMO3Dhybrid

Resolution Estimation

  • FSC
  • RMEASURE

Denoising

  • iMed
  • TOMOAND
  • TOMOBFLOW
  • XMSF

Segmentation

  • CoDiv
  • Population
  • TOMOSEGMEM
  • TomoSegMemTV

 

B-Factor Estimation and Correction

  • bfactor
  • EM-BFACTOR

 

Initial Model Construction

  • ROTAN

 

Visualization and Modeling

  • ADP_EM
  • Amira
  • Automated Segmentation of Actin Networks (Software Package for Amira)
  • CoAn/CoFi
  • UCSF Chimera
  • coloRNA
  • EMDataBank
  • EMfit
  • EMPackage (Electron Tomography Toolbox for Amira)
  • Gorgon
  • iMODFIT
  • NORMA
  • OpenStructure
  • PyMOL
  • RIVEM
  • Sculptor
  • Situsv
  • UROX
  • V3D

 

Utilities

  • BBHP/Suprim add-ons
  • crop
  • diffmap
  • em2em
  • Matlab functions for 3dEM file formats
  • Nexperion Sentinel

Additional information about software and resources are also available:

  • Modeling/Fitting 3DEM Software Descriptions (courtesy of Elizabeth Villa, UCSD).
    From Villa, E. and Lasker, K., (2014) Finding the right fit: chiseling structures out of cryo-electron microscopy maps. Curr Opin Struct Biol 25:118-125. PMID: 24814094

  • National Center for Microscopy and Imaging Research
  • The NIH Image Home Page
  • The Radon Transform Package
  • Synapse Web