The ImageJ framework for semi-automated tracing of neurons and tubular structures
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Simple Neurite Tracer

The ImageJ framework for semi-automated tracing of neurons and other tube-like structures. It is part of the Fiji distribution of ImageJ. For details, please see


SNT is currently under heavy development. Because the ongoing work does not guaranty full backwards compatibility with previous versions, the latest pre-releases are not yet made available through Fiji's main update site but through the Neuroanatomy update site.

Recent Capabilities of SNT (Scijava branch)


  • Support for multidimensional images (including multichannel, and those with a time axis)
  • A new option to perform background tracing on a second, non-displayed image
  • Manual Mode: Semi-automated tracing can be temporary disabled
  • Pause mode: Tracing can be interleaved with image processing routines
  • Edit mode: Paths can now be edited, i.e., a path can be merged into a existing one, or split into two. Nodes can be moved, deleted, or inserted.
  • Preliminary support for sub-pixel accuracy,
  • New GUI with extensive options and shortcuts


  • Paths can tagged, searched and filtered. Tags can be SWC fields, branch order labels, or a list of arbitrary strings. Analysis can be performed on all paths, or filtered subsets
  • Paths can be color-coded by their properties: e.g., compartment, length, radii or depth
  • Paths can be converted to IJ ROIs
  • Masks can be generated from filled traces in a more efficient way
  • Distribution command retrieves Histogram and Descriptive statistics of selected path properties
  • Quick statistics command calculates common morphometric properties of traced arbors
  • Detailed Horton-Strahler analysis (tabular and plotted results)
  • Traces can be rendered in a rotating plot and exported as SVG/PDF

To Document:

  • ITK bridge
  • Scripting
  • Multi-threading improvements
  • 3D Viewer legacy support