Neuroanatomy update site (Fiji)
Author Tiago Ferreira
Maintainer Tiago Ferreira
Source on GitHub
Initial release April 2016
Latest version 1.0.10 May 2017 (Changelog)
Development status Active
Category Plugins, Analysis, Neuroanatomy

This is the main documentation page for the hIPNAT (Image Processing for NeuroAnatomy and Tree-like Structures) plugins distributed through the Neuroanatomy update site, released in April 2016. For a list of all pages in this wiki related to Neuroanatomy have a look at Category: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.

Implemented as a Java plugin.

Summarize Skeleton Analyze ▶ Skeleton ▶ Summarize Skeleton Bulk statistics of skeletonized images.

Implemented as a Java plugin.

Particles classifier Analyze ▶ Skeleton ▶ Classify 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 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.

Implemented as a Java plugin.

Traces converter Plugins ▶ NeuroAnatomy ▶ Convert Traces to SWC Batch conversion of Simple Neurite Tracer's .traces files into SWC.

Implemented as a Python script.

Multi-SWC renderer Plugins ▶ NeuroAnatomy ▶ Render Multiple SWC Files Renders multiple SWC files in a single image canvas or a 3D viewer universe.

Implemented as a Python script.

Remote File renderer Plugins ▶ NeuroAnatomy ▶ Render Remote SWC File Exemplifies how to download and access a remote (e)SWC (internet connection required).

Implemented as a Python script.

Fractal Trees File ▶ Open Samples ▶ Fractal Tree Synthetic images (L-System Trees) useful for debugging, testing or prototyping.

Implemented as a Java plugin.

Further information

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