Version 7.7 - Released: 04/08/2019 - Content: 107395 neurons

Resources and tools of 3D reconstructions of neuron morphology: Unabridged collection of essential pointers and literature references, originally published here.

  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 www.bitplane.com/go/products/filamenttracer
Amira* WML EGDA N/A S.Hupert www.fei.com/software/amira-extensions
Neuron 3DMA* L DA Koh et al 2002 W.Lindquist www.ams.sunysb.edu/~lindquis/3dma/3dma_neuron/3dma_neuron.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/body_index.php
KNOSSOS-EM and LM reconstruction WL EGTDA Helmstaedter et al 2014 J.Kornfeld, F. Svara www.knossostool.org
Filament Editor WL E Vincent et al 2014 H. Hege www.zib.de/en/visual/software/neuronreconstruction.html
neuTube MWL GTDA Feng et al 2014 T. Zhao, L. Feng neutracing.com
Neural Circuit Tracer W EGT Gala et al 2014 A. Stepanyants neurogeometry.net
VolRoverN M EGTD Edwards et al 2014 C.Bajaj cvcweb.ices.utexas.edu/cvcwp/?page_id=2089
WIS-NeuroMath W EGT Rishal et al 2013 M.Galun www.weizmann.ac.il/vet/IC/software/wis-neuromath
Volumetric RGC WML (O) EG Sümbül et al 2014 U.Sümbül github.com/uygarsumbul/rgc
Tubular Geodesics LM ETA Türetken et al 2013 E.Turetken  cvlab.epfl.ch/research/medical/lm#software
Tubularity Flow Field** WM (O) EDA Mukherjee et al 2015 Scot T. Acton viva-lab.ece.virginia.edu/suvadip_docs/Neuron/research_neuron.html
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 neuron.duke.edu/cells/download.html
L-Measure WML (CJ) FGDA Scorcioni et al 2008 G.Ascoli cng.gmu.edu:8080/Lm
4D SPA WM EGT Lee et al 2013 P.Lee, H.He people.cs.nctu.edu.tw/~percycat/4DSPA
Dendrite Length Quantifier WML EGT Smafield et al 2015 Zhou Group faculty.cs.niu.edu/~zhou/tool/dlq
NEMO W E Billeci et al 2010 B.Lucia, M.Chiara, G.Pioggia, A.Ahluwalia www.centropiaggio.unipi.it/content/nemo-neuron-morphological-analysis-tool
Py3DN WL EDA Aguiar et al 2013 P.Aguiar sourceforge.net/projects/py3dn
btmorph WML(O) GTA Torben-Nielsen et al 2014 B.Torben-Nielsen btmorph.readthedocs.org/en/latest
Bonfire WML(O) EG Langhammer et al 2010 B.Firestein firesteinlab.cbn.rutgers.edu/tools.html
NeuroM WML(O) EGTA Shillcock et al 2016 G.Shillcock github.com/BlueBrain/NeuroM
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 surf-hippo.neurophysics.eu
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
N2A W EGDA Rothganger et al 2014 F.Rothganger code.google.com/p/n2a/wiki/Installation
morphforge*** W EGLDA Hull et al 2014 M.Hull morphforge.readthedocs.org/en/latest
NeuroMac*** WML (P) EDA Torben-Nielsen et al 2014 B.Torben-Nielsen groups.oist.jp/cnu/neuromac
REMOD WML(O) E Bozelos et al 2015 Y.Poirazi remod.gr
Database NeuroMorpho.Org WML EGDA Ascoli et al 2007 G.Ascoli neuromorpho.org
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: *Commercial; **Free, not open source; 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
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