The Neuroanatomy update site is Fiji’s update site for the distribution of SNT and related plugins.
Subscribing to the Neuroanatomy update site
- Run Help › Update…
- Click
- Select the Neuroanatomy checkbox (see also list of update sites)
- Click
- Restart ImageJ
Installed Commands
Main ImageJ Window
| Command | Description |
|---|---|
| Neuroanatomy Shortcuts Tool | A ImageJ macro tool (SNT icon, installed next to the “» More Tools” switch) to toggle the visibility of the Neuroanatomy Shortcut Window |
| Plugins › Neuroanatomy › Neuroanatomy Shortcut Window | A centralized hub to access all neuroanatomy commands, including SNT, Sholl, Strahler, demos, and scripts |
| Plugins › Neuroanatomy › Reconstruction Plotter… | Starts Reconstruction Plotter |
| Plugins › Neuroanatomy › Reconstruction Viewer | Starts Reconstruction Viewer |
| Plugins › Neuroanatomy › SNT… | Starts SNT |
| Plugins › Neuroanatomy › Sholl | Starts Sholl analyses without running SNT |
| Analyze › Skeleton › Summarize Skeleton | Bulk statistics of skeletonized images |
| Analyze › Skeleton › Classify Particles Using Skeleton | Tags particles according to skeleton features. Detects maxima on a masked image and clusters detected maxima using features of the skeletonized mask. A maxima is considered to be associated to a skeleton feature (e.g., a junction or end-point, see AnalyzeSkeleton) if the distance between its centroid and the feature is less than or equal to a cutoff (“snap to”) distance |
| File › Open Samples › Fractal Tree | Synthetic image (L-System Tree) useful for debugging, testing or prototyping |
| File › Open Samples › ddaC Neuron | Binary image (2D) of a Drosophila class IV ddaC sensory neuron in which dendrites have been segmented. Useful for debugging, testing or prototyping. Run Image › Show Info… to know more about this cell type |
Script Editor
| Command | Description |
|---|---|
| Templates › Neuroanatomy | Demo scripts exemplifying SNT usage |
Further information
A list of all ImageJ extensions related to the neurosciences can be found on the list of extensions page, by filtering to the Neuroanatomy category.
