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Neuroanatomy update site




Tiago Ferreira


Tiago Ferreira


on GitHub




Plugins, Analysis, Neuroanatomy

The Neuroanatomy update site is used for distribution of SNT. A few other (legacy) plugins for Image Processing for NeuroAnatomy and Tree-like Structures are also included.


The requirements to run the Neuroanatomy suite of plugins are twofold: i) Fiji (i.e., an ImageJ installation subscribed to the Fiji update site) running at least Java 8. 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 HelpUpdate…
  2. Click Manage update sites
  3. Select the Neuroanatomy checkbox (see also list of update sites)
  4. Click Apply changes and Restart ImageJ


SNT has its own documentation. The list of Image Processing for NeuroAnatomy and Tree-like Structures (source) is as follows:


Menu Path


Topological Skeletons

Strahler classifier

AnalyzeSkeletonStrahler Analysis...

Described in Strahler Analysis. Implemented as a Java plugin.

Summarize Skeleton

AnalyzeSkeletonSummarize Skeleton

Bulk statistics of skeletonized images. Implemented as a Java plugin.

Particles classifier

AnalyzeSkeletonClassify Particles Using Skeleton

Tags particles according to skeleton features. Detects maxima on a masked image and clusters detected maxima using features of the skeletonized mask. A maxima is considered to be associated to a skeleton feature (e.g., a junction or end-point, see AnalyzeSkeleton) if the distance between its centroid and the feature is less than or equal to a cutoff ("snap to") distance. Implemented as a Python script.


Fractal Trees

FileOpen SamplesFractal Tree

Synthetic images (L-System Trees) useful for debugging, testing or prototyping. Implemented as a Java plugin.

Further information

  • A list of all ImageJ extensions related to the neurosciences can be found on the list of extensions page, by filtering to the Neuroanatomy category.