The ImageJ framework for semi-automated tracing of neurons and tubular structures
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README.md

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 http://imagej.net/SNT

Development

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)

Tracing:

  • 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

Analysis:

  • 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