This is an archive of the old MediaWiki-based ImageJ wiki. The current website can be found at

Neuroanatomy:External Resources

This page lists Open Source resources that complement SNT.

Online Tools

Online Tools (Visualization)
SharkViewer Simple but fast morphology viewer (WebGL-based).
MPDL SWC service Morphology viewer based on SharkViewer implemented as a RESTful web service. Can analyze traces using L-Measure.
HBP Morphology Viewer WebGL-based viewer. Allows customizable rendering. Well integrated with and Allen Cell Types. Parses some closed-source file formats. SVG/PNG export. Can be used for SWC+ export.
Online Tools (Analysis)
Remod Abandoned. No longer available.
L-measure (applet) Morphometry tool also available for offline usage

Desktop Tools

Visualization and Analysis of Tracings
Py3DN Blender based. Written in Python. Cross platform.
NeuroMorph Blender based. Written in Python. Cross platform. Designed specifically for the morphological analysis of 3D objects derived from SEM. Some of its functionality can be applied to reconstructions of single neurons.
nat Written in R.
Analysis of Tracings
L-measure Written in Java. Used by
btmorph Python library

Tracing Tools

Software packages for neuronal tracing not based on ImageJ: Neuromantic, NeuronStudio, neuTube, Vaa3D