EM software
Below is a list of software programs for generation, fitting, and analysis of 3D maps from electron microscopy images. See also: EM software wiki page. Please send corrections/additions to help@emdataresource.org.| Program | Type | Reference |
|---|---|---|
Focus (successor to 2dx) |
General Package | Biyani et al 2017 |
|
EMBFACTOR |
Bfactor correction | Fernandez et al 2008 |
|
TomoAlign |
Image alignment, Tomography | Fernandez et al 2018 |
|
ACE/ACE2 |
CTF correction | Mallick et al 2005 |
|
ctffind/ctftilt |
CTF correction | Rohou & Grigorieff 2015 |
|
EMCTF/TOMOCTF |
CTF correction | Fernandez & Crowther 2006 |
|
Leginon |
data acquisition | Suloway et al 2005 |
|
UCSF Tomography |
data acquisition, tomography | Zheng et al 2004 |
|
TOMOAND/TOMOBFLOW |
denoising | Fernandez & Li 2003 |
|
Bsoft |
reconstruction | Heymann 2018 |
|
cisTEM |
reconstruction | Grant et al 2018 |
CryoSPARC |
reconstruction | Punjani et al 2017 |
|
EMAN/EMAN2 |
reconstruction | Bell et al 2018 |
|
Eos |
reconstruction | |
|
IMAGIC |
reconstruction | van Heel et al 1996 |
|
IPLT |
reconstruction | Schenk et al 2013 |
|
CCP-EM |
reconstruction | Burnley et al 2017 |
|
Simple |
reconstruction | Reboul et al 2018 |
|
Sparx |
reconstruction | Behrmann et al 2012 |
|
Spider |
reconstruction | Leith et al 2012 |
|
Suprim |
reconstruction | |
|
SPHIRE |
reconstruction | Moriya et al 2017 |
|
Xmipp |
reconstruction | de la Rosa-Treví et al 2013 |
|
IHRSR |
helical | Egelman 2010 |
|
Phoelix |
helical | Carragher et al 1996 |
|
Ruby-Helix |
helical | Metlagel et al 2007 |
|
Spring |
helical | Desfosses et al 2014 |
|
AUTO3DEM |
icosahedral | Yan et al 2007 |
|
em2em |
map conversion | van Heel et al 1996 |
|
ADP_EM |
modelling | Garzon et al 2007 |
|
UCSF Chimera |
modelling, visualization | Petterson et al 2004 |
|
COOT |
modelling, visualization | Brown et al 2015 |
|
DireX |
modelling | Wang & Schroeder 2012 |
|
EMfit |
modelling | Rossmann et al 2001 |
|
Flex-EM |
modelling | Joseph et al 2016 |
|
Gorgon |
modelling | Baker et al 2012 |
|
iMODFIT |
modelling | Lopéz-Banco & Chacon 2013 |
|
MDFF |
modelling | Trabuco et al 2009 |
NMFF |
modelling | Tama et al 2004 |
|
NORMA |
modelling | Suhre et al 2006 |
|
Phenix |
modelling | Afonine et al 2018 |
|
REFMAC |
modelling | Brown et al 2015 |
|
Rosetta for cryoEM |
modelling | Wang et al 2016 |
|
Situs |
modelling | Kovacs et al 2018 |
|
TEMPy |
modelling, model validation | Farabella et al 2015 |
|
VMD |
modelling, visuallization |
EMRinger |
model validation | Barad et al 2015 |
|
Molprobity |
model validation | Williams et al 2018 |
|
SamViewer |
particle picking | |
|
Signature |
particle picking | Chen & Grigorieff 2007 |
|
FSC |
resolution estimation | van Heel et al 1996 |
|
rmeasure |
resolution estimation | Sousa & Grigorieff 2007 |
|
Frealign |
reconstruction | Lyumkis et al 2013 |
|
PFT3DR |
reconstruction | |
|
RELION |
reconstruction | Scheres 2012 |
|
Dynamo |
tomography | Castano-Diez et al 2012 |
|
EM3D |
tomography | Ress et al 2004 |
|
IMOD |
tomography | Mastronarde & Held 2017 |
|
protomo |
tomography | Winkler & Taylor 2006 |
|
SerialEM |
data acquisition, tomography | Mastronarde 2005 |
|
TOM |
tomography | Nickell et al 2005 |
|
Amira-Avizo |
visualization | |
|
CCP4mg |
visualization | McNicholas et al 2011 |
|
RIVEM |
visualization | Xiao and Rossmann 2007 |
|
Appion |
workflow | Lander et al 2009 |
|
Scipion |
workflow | de la Rosa-Trevin 2016 |
|
motioncor2 |
movie frame alignment | Zheng et al 2017 |
|
Gautomatch |
particle picking | |
|
Gctf |
CTF correction | Zhang 2016 |
|
ResMap |
Local Resolution Estimation | Kucukelbir et al 2014 |
|
Unblur/Summovie |
movie frame alignment | Grant & Grigorieff 2015 |
|
FragFit |
modelling server | Tiemann et al 2018 |
|
Powerfit |
modelling server | Zundert et al 2017 |
|
Samuel |
workflow scripts | |
|
ASPIRE |
reconstruction | |
|
APPLE-Picker |
particle picking | Heimowitz et al 2018 |
|
Topaz |
particle picking | Bepler et al 2018 |
|
CDMD |
modelling | Igaev et al 2019 |