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 based on publications. Please cite SNT in your own research!
Overview
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.
Overview of SNT components & SNT functionality
Semi-automated tracing: Support for multi-channel and timelapse images
Fully automated tracing of segmented images
Scripted routines co-exist with graphical user interface operations
Scripting in any of Fiji’s supported languages facilitated by SNT’s Script Recorder
Scripting in native python through pyimagej
Delaunay tesselation: Tracings can be used in image processing routines
Density maps for group(s) of cells obtained from built-in scripts
Quantitative and publication quality visualizations
Data-rich 3D visualizations
Routines to summarize innervation patterns
Routines to summarize data from projectomes and connectomics
Glia analysis: Bulk characterization (width and length) of astrocytic processes (use case)
Not only neurons: SNT can be used to analyze many types of filamentous structures
Installation
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
- Search for Neuroanatomy (or SNT) and activate the Neuroanatomy checkbox
- Click Apply changes and restart Fiji
Optional: For sciview and Cx3D functionality, you need to install sciview. See the official sciview documentation for details.
Documentation
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 |
| Contributing | How to contribute to SNT |
| 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 | Definition of metrics |
| 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 |
