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SNT1 is ImageJ’s framework for tracing, visualization, quantitative analyses and modeling of neuronal morphology. For tracing, SNT supports modern multidimensional microscopy data, semi-automated and automated routines, and options for editing traces. For data analysis, SNT features advanced visualization tools, access to all major morphology databases, and support for whole-brain circuitry data.

SNT is available through Fiji and is based on publications. If you use it successfully for your research please be so kind as to cite our work!


SNT is toolbox for tracing and analyzing neuronal morphologies imaged using light microscopy. It aims to be as complete as possible, while remaining efficient to use. It can be used as a desktop application, or a scripting library. It supersedes the original Simple Neurite Tracer software, and aggregates other tools previously scattered across the Fiji ecosystem of plugins, including Sholl2 and Strahler plugins.

The source repository contains more details about the project, including a list of features, and implementation details


SNT is currently distributed through Fiji’s Neuroanatomy update site. The first time you start SNT from Fiji’s menu structure (PluginsNeuroanatomySNT), you should be prompted for automatic subscription and download of required dependencies. If not:

  1. Run the Fiji Updater (HelpUpdate…, the penultimate entry in the Help menu)
  2. Click Manage update sites
  3. Select the Neuroanatomy checkbox
  4. Click Apply changes and restart Fiji.

Optional: For sciview and Cx3D functionality, you need to install sciview. See the official sciview documentation for details.


SNT’s documentation is extensive. Please use the navigation bar on top of the page to access the different sections, organized as follows:

Section Contents
Analysis Overview of GUI-based analyses
Extending Resources for developers interested in extending SNT or parsing TRACES files
FAQ Frequently asked questions
Key Shortcuts List of SNT shortcuts (keyboard cheatsheet)
Machine Learning Semantic segmentation: Labkit and TWS integration
Manual User guide for main interface and tracing operations
Metrics Cheatsheet for common measurements
Modeling Cx3D integration
Reconstruction Viewer SNT’s entry point for visualization of pre-existing data. If you are analyzing neuronal reconstructions you may want to start here
Screencasts Video tutorials. If you are using SNT for the first time you probably want to start here
Scripting Details on how to use SNT as a scripting library
Walk-throughs Detailed step-by-step instructions for specific tasks