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:
Icosahedral viruses
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
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Application tools
Subvolume averaging
Mass measurements
Data Acquisition
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
Resolution Estimation
Denoising
- iMed
- TOMOAND
- TOMOBFLOW
- XMSF
Segmentation
- CoDiv
- Population
- TOMOSEGMEM
- TomoSegMemTV
B-Factor Estimation and Correction
Initial Model Construction
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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
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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