EM Software

Listed here are software programs used in the generation, analysis, and fitting of 3D maps from electron microscopy images. Look here for an example of how metadata for software programs are archived. The starting point for the list was the EM software wiki page. Please send corrections/additions to help@emdatabank.org.

Click on the Program and Type table headers to change the sort order.

ProgramTypeWebSite
2dx2D crystalhttp://2dx.org/

EMBFACTORBfactor correctionhttp://www.ual.es/~jjfdez/SW/embfactor.html
ACECTF correctionhttp://nramm.scripps.edu/software/ace/
ctffindCTF correctionhttp://emlab.rose2.brandeis.edu/grigorieff/downloads.html
ctftiltCTF correctionhttp://emlab.rose2.brandeis.edu/grigorieff/downloads.html
EMCTFCTF correctionhttp://www.ual.es/~jjfdez/SW/emctf.html
TOMOCTFCTF correctionhttp://www.ual.es/~jjfdez/SW/tomoctf.html
UCSF Tomographydata acquisitionhttp://www.msg.ucsf.edu/em/EMNEW2/tomography_page.html
Leginondata acquisitionhttp://leginon.scripps.edu/
SerialEMdata acquisitionhttp://bio3d.colorado.edu/SerialEM/
TOMOANDdenoisinghttp://www.ual.es/~jjfdez/SW/tomoand.html
TOMOBFLOWdenoisinghttp://www.ual.es/~jjfdez/SW/tomobflow.html
BsoftGeneral packagehttp://lsbr.niams.nih.gov/bsoft/bsoft.html
CyclopsGeneral packagehttp://www.bfsc.leidenuniv.nl/software/Cyclops/
EMANGeneral packagehttp://blake.bcm.edu/EMAN/
EMStudioGeneral packagehttp://emlab.rose2.brandeis.edu/grigorieff/downloads/EMStudio

IMAGICGeneral packagehttp://www.imagescience.de/imagic/index.htm
SparxGeneral packagehttp://macro-em.org/sparxwiki/SparxWiki
IPLTGeneral packagehttp://www.iplt.org/wiki
MDPPGeneral packagehttp://gcrc.med.nyu.edu/mdpp/
MRCGeneral packagehttp://www2.mrc-lmb.cam.ac.uk/image2000.html

Additional Documentation: Helical Crystals, 2D Crystals
SpiderGeneral packagehttp://www.wadsworth.org/spider_doc/spider/docs/spider.html
SuprimGeneral packagehttp://nramm.scripps.edu/software/suprim/
XmippGeneral packagehttp://xmipp.cnb.csic.es/
pyappionGeneral packagehttp://code.google.com/p/appion/
IHRSRhelical
Phoelixhelicalhttp://nramm.scripps.edu/software/phoelix/
Ruby-Helixhelicalhttp://structure.biophys.kyoto-u.ac.jp/software/software.html
AUTO3DEMicosahedralhttp://cryoem.ucsd.edu/programs.shtm
IMIRSicosahedralhttp://www.eicn.ucla.edu/imirs
em2emmap conversionhttp://www.imagescience.de/em2em/index.htm
Chimeramodellinghttp://www.cgl.ucsf.edu/chimera/
DireXmodellinghttps://simtk.org/home/direx/
EMfitmodellinglink to Rossmann Lab software
Gorgonmodellinghttp://www.cs.wustl.edu/~ssa1/gorgon/
NMFFmodellinghttp://mmtsb.org/software/nmff.html
NORMAmodellinghttp://www.elnemo.org/NORMA/
Situsmodellinghttp://situs.biomachina.org/
UROXmodellinghttp://sites.google.com/site/xsiebert/urox
VMDmodellinghttp://www.ks.uiuc.edu/Research/vmd/
YUP.SCXmodellinghttp://rumour.biology.gatech.edu/YammpWeb/userman/yupscx/intro.shtml
Signatureparticle selectionhttp://emlab.rose2.brandeis.edu/grigorieff/downloads/signature
SwarmPSparticle selectionhttp://www.imb.uq.edu.au/index.html?page=44665
Appion Tilt Pickerparticle selectionhttp://code.google.com/p/appion/
FSCresolution estimationhttp://www.imagescience.de/fsc/index.htm
rmeasureresolution estimationhttp://emlab.rose2.brandeis.edu/grigorieff/download_r.html
Seggersegmentationhttp://ncmi.bcm.edu/ncmi/software/segger/
Frealignsingle particlehttp://emlab.rose2.brandeis.edu/grigorieff/downloads.html
PFT2DRsingle particlehttp://people.chem.byu.edu/belnap/pft3dr
IMODtomographyhttp://bio3d.colorado.edu/imod/
protomotomographyhttp://www.electrontomography.org/
SerialEMtomographyhttp://bio3d.colorado.edu/SerialEM/
TOMtomographyhttp://www.biochem.mpg.de/tom///
EM3Dtomographyhttp://em3d.stanford.edu/index.html
Chimeravisualizationhttp://www.cgl.ucsf.edu/chimera/
RIVEMvisualizationlink to Rossmann lab software
UROXvisualizationhttp://sites.google.com/site/xsiebert/urox
amiravisualizationhttp://www.amira.com/
VMDvisualizationhttp://www.ks.uiuc.edu/Research/vmd/