Table 1.

Resources and tools of 3D reconstructions of neuron morphology: Unabridged collection of essential pointers and literature references

	Resource	Platform	Support	Reference	Lead	Web Address
Tracing	Neurolucida	W	EFGTDA	Glaser & Glaser 1990	J.Glaser	mbfbioscience.com/neurolucida
	Filament Tracer	WM	ETDA	N/A	M.Messerli	bitplane.com/go/products/filamenttracer
	Amira	WML	EGDA	N/A	S.Hupert	www.vsg3d.com/amira/skeletonization
	Neuron 3DMA	L	DA	Koh et al 2002	W.Lindquist	www.ams.sunysb.edu/~lindquis/3dma/3dma_neuron/3dma_neuron.html
	NTS/Eutectic	W	G	Capowski 1977	J.Capowski	bellsouthpwp.net/c/a/capowski/NTSPublic.html
	NeuronJ	WML	GNDA	Meijering et al 2004	E.Meijering	imagescience.org/meijering/software/neuronj
	NeuRA	M	G	Broser et al 2004	G. Wittum	neura.org
	NeuronStudio	W	EGA	Wearne et al 2005	A.Rodriguez	research.mssm.edu/cnic/tools-ns.html
	ORION	WL	FGDA	Losavia et al 2008	I.Kakadiaris	cbl.uh.edu/ORION
	Neuron_Morpho	WM (I)	GN	Brown et al 2005	G.D’Alessandro	www.personal.soton.ac.uk/dales/morpho
	Farsight	WML (C)	LTDA	Wang et al 2011	B.Roysam	farsight-toolkit.org/wiki/Open_Snake_Tracing_System
	Trees Toolbox	WML (O)	EGTDA	Cuntz et al 2011	H.Cuntz	treestoolbox.org
	Vaa3D	WML (C)	FGTDA	Peng et al 2010	H.Peng	Vaa3D.org
	Simple Neurite Tracer	WML (I)	EGLTDA	Longair et al 2011	M.Longair	pacific.mpi-cbg.de/wiki/index.php/Simple_Neurite_Tracer
	Neuromantic	W	ETDA	Myatt et al 2012	D.Myatt	reading.ac.uk/neuromantic
Analysis	Neurolucida Explorer	W	EFGTDA	Glaser & Glaser 1990	J.Glaser	mbfbioscience.com/neurolucida
	Neuronland	WM	GLDA	N/A	J.Ogden	neuronland.org/NL.html
	Cvapp	WM (J)	G	Cannon et al 1998	R.Cannon	compneuro.org/CDROM/docs/cvapp.html
	L-Measure	WML (CJ)	FGDA	Scorcioni et al 2008	G.Ascoli	cng.gmu.edu:8080/Lm
Computational modeling	L-Neuron ^*	WL (C)	GNA	Ascoli et al 2001	G.Ascoli	krasnow1.gmu.edu/cn3/L-Neuron
	NeuGen ^*	WML (CJ)	GNDA	Eberhard et al 2006	G.Wittum	neugen.org
	NetMorph ^*	WML (C)	GNDA	Koene et al 2009	A.van Ooyen	netmorph.org
	CX3D ^*	WM (J)	FT	Zubler & Douglas 2009	A.Hauri	www.ini.uzh.ch/~amw/seco/cx3d
	NEURON	WML (C)	FGLTDA	Hines & Carnevale 1997	M.Hines	www.neuron.yale.edu/neuron
	GENESIS	WML (C)	FGLTDA	Bower & Beeman 1998	J.Bower	genesis-sim.org
	NeuronC	ML (C)	GNDA	Smith 1992	R.Smith	retina.anatomy.upenn.edu/~rob/neuronc.html
	Surf-Hippo	L (O)	GL	Borg-Graham 2000	L.Borg-Graham	neurophys.biomedicale.univ-paris5.fr/~graham/surf-hippo.html
	Catacomb	WML	GNDA	Cannon et al 2003	M.Hasselmo	catacomb.org
	neuroConstruct	WML (J)	GTNDA	Gleeson et al 2007	A.Silver	neuroconstruct.org
	Moose	WML (O)	FGDA	Ray & Bhalla, 2008	U.Bhalla	moose.ncbs.res.in
	PSICS	WML (JO)	EFGDA	Cannon et al 2010	M.Nolan	psics.org
Database	NeuroMorpho.Org	WML	EGDA	Ascoli et al 2007	G.Ascoli	neuromorpho.org
	Cercal DB	WML	NDA	Troyer et al 1994	G.Jacobs	apps.montana.edu/cercaldb
	CCDB	WML	GLDA	Martone et al 2008	M.Martone	ccdb.ucsd.edu
	Fly Circuit	WML	EGT	Chiang et al 2011	A-S.Chiang	flycircuit.tw

Resource: Inline graphic ; ; Free;

morphological modeling (as opposed to electrophysiological)

Platform: W: Windows; M: Mac; L: Linux; (C: C/C++; J: Java; I: ImageJ plugin; O: Others, i.e. Matlab, Python, Lisp or Fortran)

Support: E: E-mail; F: Forum; G: Guide (Manual); L: mailing List; N: Newsletter; T: Tutorial; D: ongoing Development; A: Actively maintained