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This page describes content relating to the Fiji distribution of ImageJ. Click the logo for details.

Neuroanatomy update site

The Neuroanatomy update site is Fiji’s update site for the distribution of SNT and related plugins.

Subscribing to the Neuroanatomy update site

  1. Run HelpUpdate…
  2. Click Manage update sites
  3. Select the Neuroanatomy checkbox (see also list of update sites)
  4. Click Apply changes
  5. 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
PluginsNeuroanatomyNeuroanatomy Shortcut Window A centralized hub to access all neuroanatomy commands, including SNT, Sholl, Strahler, demos, and scripts
PluginsNeuroanatomyReconstruction Plotter… Starts Reconstruction Plotter
PluginsNeuroanatomyReconstruction Viewer Starts Reconstruction Viewer
PluginsNeuroanatomySNT… Starts SNT
PluginsNeuroanatomySholl Starts Sholl analyses without running SNT
AnalyzeSkeletonSummarize Skeleton Bulk statistics of skeletonized images
AnalyzeSkeletonClassify 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
FileOpen SamplesFractal Tree Synthetic image (L-System Tree) useful for debugging, testing or prototyping
FileOpen SamplesddaC 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 ImageShow Info… to know more about this cell type

Script Editor

Command Description
TemplatesNeuroanatomy 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.