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, model refinement, validation	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
ChimeraX	modelling, visualization	Goddard et al 2018
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	model refinement, validation	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, visualization
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	Stalling et al 2005 | (pdf)
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
crYOLO	particle picking	Wagner et al 2019
cryoEF	analyse orientation distribution	Naydenova 2017
JADAS	data acquisition
LAFTER	local filtering, noise reduction	Ramlaul et al 2019
MAPQ/Q-score	map-model fit per atom	Pintilie et al 2020
Isolde	model building in cryo-EM maps	Croll 2018
DeepTracer	automated model building in cryo-EM maps	Pfab et al. 2020
Haruspex	neural network-based segmentation	Mostosi et al. 2020
SPoC	False Discovery Rate FSC	Beckers and Sachse 2020
EMDA	EM Map/Model Manipulation tools	MRC Murshudov Group
SBEMimage	Data acquisition and monitoring, serial SEM	Titze et al 2018
cryoDRGN	reconstruction	Zhong et al 2021
DAQ	model validation	Terashi et al 2022
CryoREAD	modeling	Wang Terashi Kihara 2023
emClarity	tomography	Himes & Zhang 2018