SNT1 is ImageJ’s framework for tracing, visualization, quantitative analyses and modeling of neuronal morphology. For tracing, SNT supports modern multi-dimensional 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 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.
SNT is currently distributed through Fiji’s Neuroanatomy update site. The first time you start SNT from Fiji’s menu structure (Plugins › Neuroanatomy › SNT, you should be prompted for automatic subscription and download of required dependencies. If not:
- Run the Fiji Updater (Help › Update.., the penultimate entry in the Help menu)
- Click Manage update sites
- Select the Neuroanatomy checkbox
- Click Apply changes and restart Fiji.
SNT’s documentation is extensive. Please use the navigation bar on top of the page to access the different sections, organized as follows:
|Manual||SNT’s user guide for tracing operations|
|Walk-throughs||Detailed step-by-step instructions for specific tasks|
|Screencasts||Video tutorials. If you are using SNT for the first time you probably want to start here|
|Reconstruction Viewer||SNT’s entry point for visualization of pre-existing data. If you are analyzing neuronal reconstructions you may want to start here|
|Analysis||Overview of all analysis commands, accessible in either the tracing interface or Reconstruction Viewer|
|Scripting||Details on how to use SNT as a scripting library|