Launch of the Neuroanatomy update site

A new Neuroanatomy update site has been made available earlier this week. The goal of the Neuroanatomy update site is to aggregate in a single subscription curated plugins tailored to the analysis of neuronal imagery that complement existing capabilities of ImageJ. Importantly, the utility of this update site goes beyond the neurosciences as it is extendable to the processing of many tree-like structures as found in e.g., Botany, Hydrology or Zoology.

The plugins in this initial release include:

  • Strahler Analysis. First released as a BAR script, Strahler grew in complexity and had to be converted into a compiled plugin. It will no longer be distributed through the BAR update site. The new release fixes several issues that did not allow for batch processing of images (discussed e.g., here and here). The new implementation will also allow for better functionality
  • Utilities to summarize skeletonized trees
  • Utilities to render SWC files (a commonly used format by tracing software) as image stacks

The update site is backed up by the hIPNAT repository (hIPNAT: Image Processing for Neuro Anatomy and Tree-like structures). Detailed documentation will start appearing on

Importantly, Iā€™d like to use this opportunity to encourage all of you to participate in this effort by providing suggestions, criticisms, bug reports and code contributions either in this Forum or on Github.


Awesome! Thank you so much for all your efforts in providing these tools!