Pre-release of IJ2 tools for Neuroanatomy



Simple Neurite Tracer (now simply SNT) and Sholl Analysis are the most popular Fiji plugins for semi-automated segmentation and analysis of neuronal structures. I am excited to announce that both these programs have evolved to more complete tools, that are now IJ2-aware.

If you want to use these improvements, you can do so by subscribing to the Neuroanatomy update site (bugs are likely to exist, please report them). Importantly, the development of the current versions of these programs, i.e., those bundled by default with Fiji, has stalled, and will be deemed deprecated in the future.

For those of you interested, here are some of the highlights of the features already implemented:


  • Support for multidimensional images (including multichannel, and those with a time axis)
  • Paths can now be edited. The new Path Manager allows for paths to be tagged, searched and filtered
  • Multi-threaded tracing, including a new option to perform background tracing on a second, non-displayed image
  • Tracing can be interleaved with image processing routines
  • SNT plugins: SNT now features a plugin mechanism for more functionality: Currently there are plugins for conversion of tracings into ROIs, generation of masks from traces, and statistical analysis of morphometric measurements
  • New GUI with extensive options and shortcuts
  • Preliminary support for sub-pixel accuracy, and many other optimizations


  • Interactive prompt with more control over curve fitting: Including settings for determination of ‘best fit’ and fits to polynomial of arbitrary degree
  • More export options, including ROIs
  • Significant optimizations for 3D images

And here is a shy snapshot of a tracing session in the new SNT:

How to save only the overlays without the image?
Automize labelling of segments in simple neurite tracer plugin
Neurite tracer plugin
Image J SNT, converting to RGB
Sholl Analysis Help