8.6.100 - Released: 2025年12月01日 - Content: 284227 cells
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.