The following public-domain tools can be useful for more detailed analysis, visualization, and modeling of neurons and their morphology.

Main Tools

• Center for Neural Informatics, Structure, and Plasticity
• L-Measure   [online neuromorphometric analysis]
• NeuroMorpho database schema
• Neuromantic   [free neuron reconstruction software]
• Vaa3D
• Trees-Toolbox
• btmorph
• Neuroscience Information Framework
• Resources and tools for 3D reconstructions of neuron morphology   [updated version of Table 1 in Ecosystem of digital reconstructions]

Repositories of neural reconstructions mirrored into NeuroMorpho.Org and corresponding NeuroMorpho.Org archives.

• Allen Institute for Brain Science, Allen Cell Types archive
• Borst Cells (original repository no longer available), Borst archive
• Cell-Centered Database (original repository no longer available), Martone archive
• Destexhe Cells (original repository no longer available), Destexhe archive
• FlyCircuit, Chiang archive
• Gulyas archive/Freund Lab (original repository no longer available), Gulyas archive
• MapZebrain, Baier archive
• MouseLight, MouseLight archive
• Spruston cells, Spruston archive
• Wearne/Hof Cells, Wearne-Hof archive

Other useful Links

• 3D Neuron Viewer  [modified Cvapp code on GitHub]
• Allen Institute for Brain Science
• NeuroMorpho.Org Conference  [recognizing the breakthroughs in neuroscience via digital reconstruction of neuronal morphology]
• Diadem Challenge  [to create algorithmic methods for automated neuronal tracing]
• Ecosystem of digital reconstructions  [a review article and an annotated compilation of currently available resources of digital reconstructions. Updated version of this paper's Table 1 available on the above Main Tools list. Click here for pdf of the article]
• George Mason University
• Genesis   [general purpose simulation platform]
• Krasnow Institute for Advanced Study
• ModelDB
• Neuro ML
• Neurolucida   [commercial neuron reconstruction software]
• Neuronland   [free software for morphology format conversions]
• NEURON   [compartmental modeling and simulation]
• Neuron_morpho plugin   [3D reconstruction from image stacks]
• NeuronStudio   [3D reconstruction from confocal and multi-photon images]
• Worm Atlas  [A database of behavioral and structural anatomy of C. elegans]
• BraVa  [A database of arterial reconstructions]
• BigNeuron.Org
• Xyz2swc - an online universal conversion and standardization tool for SWC files. It also has an API with corresponding documentation.