This is an archive of the old MediaWiki-based ImageJ wiki. The current website can be found at imagej.net.
Neuroanatomy:External Resources
This page lists Open Source resources that complement SNT.
Online Tools
| Online Tools (Visualization) | ||
| SharkViewer | http://janeliascicomp.github.io/SharkViewer/ | Simple but fast morphology viewer (WebGL-based). |
| MPDL SWC service | https://servicehub.mpdl.mpg.de/swc/ | Morphology viewer based on SharkViewer implemented as a RESTful web service. Can analyze traces using L-Measure. |
| HBP Morphology Viewer | https://neuroinformatics.nl/HBP/morphology-viewer/ | WebGL-based viewer. Allows customizable rendering. Well integrated with NeuroMorpho.org and Allen Cell Types. Parses some closed-source file formats. SVG/PNG export. Can be used for SWC+ export. |
| Online Tools (Analysis) | ||
| Remod | http://remod.gr | Abandoned. No longer available. |
| L-measure (applet) | http://cng.gmu.edu:8080/Lm/Lmeasure.html | Morphometry tool also available for offline usage |
Desktop Tools
| Visualization and Analysis of Tracings | ||
| Py3DN | https://sourceforge.net/projects/py3dn/ | Blender based. Written in Python. Cross platform. |
| NeuroMorph | https://github.com/ajorstad/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 | http://jefferis.github.io/nat/ | Written in R. |
| Analysis of Tracings | ||
| L-measure | http://cng.gmu.edu:8080/ | Written in Java. Used by http://neuromorpho.org |
| btmorph | http://btmorph.readthedocs.io/en/latest/ | Python library |
Tracing Tools
Software packages for neuronal tracing not based on ImageJ: Neuromantic, NeuronStudio, neuTube, Vaa3D
