Revision as of 14:45, 16 November 2016 by Tiago (talk | contribs) (Update script path)
Neuroanatomy update site (Fiji)
Author Tiago Ferreira
Maintainer Tiago Ferreira
Source on GitHub
Initial release April 2016
Development status Active
Category Plugins, Analysis, Neuroanatomy


The requirements to run the Neuroanatomy suite of plugins are twofold: i) Fiji (i.e., an ImageJ installation subscribed to the Fiji update site) and ii) Java 8 (as part of an active effort to modernize ImageJ). If you are running an older version of Java, you can either i) Download the latest Fiji release (newer releases come pre-bundled with Java 8); or ii) If you have downloaded Fiji while ago and want to keep your existing installation, you will have to download Java 8 and make your Fiji installation aware of it.

Subscribing to the Neuroanatomy update site:

  1. Run Help › Update...
  2. Click Manage update sites
  3. Select the Neuroanatomy checkbox (see also List of update sites)
  4. Click Apply changes and Restart ImageJ.

List of commands

Name Menu Path Description
Topological Skeletons
Strahler classifier Analyze › Skeleton › Strahler Analysis... Described in Strahler Analysis
Summarize Skeleton Analyze › Skeleton › Summarize Skeleton Bulk statistics of skeletonized images
Particles classifier Analyze › Skeleton › Classify Particles Using Skeleton Tags particles according to skeleton features.

Runs Analyze › Analyze › Analyze Particles on one image and clusters detected particles according to their positioning to features (e.g., a junction or end-point, see AnalyzeSkeleton) of a skeletonizable image. A particle is considered to be associated to a skeleton feature if the distance between its centroid and the feature is within a specified cuttoff ("snap to") distance. Implemented as a Python script.

Tracings Importer File › Import › Tracings (Traces/(e)SWC)... Renders traced reconstructions ( .traces - Simple Neurite Tracer's format - and .swc files) in ImageJ's 3D Viewer or as skeletonized image stacks
Traces converter Plugins › NeuroTools › Convert Traces to SWC Batch conversion of Simple Neurite Tracer's native files into SWC
Fractal Trees File › Open Samples › Fractal Tree Synthetic images (L-System Trees) useful for debugging, testing or prototyping

Further information

  • A list of all pages in this wiki related to image processing in the neurosciences can be found here.