SNT: Analysis

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Sholl Analysis

Initiating Sholl Analysis: coarse method

To initiate Sholl Analysis on a tracing in the canvas, you must select a focal point. You can do it coarsely by right-clicking near a node and choosing Sholl Analysis at Nearest Node from the contextual menu (Shortcut: Alt + Shift + A.

Alternatively, for precise positioning of the center of analysis:

  1. Mouse over the path of interest. Press G to activate it.
  2. Press Alt+ Shift to select a node along the path.
  3. Press Alt+ Shift+A to start analysis.
  • 1) Select path
  • 2) Snap cursor to node
  • 3) Sholl dialog

The Sholl dialog created by this approach differs slightly from the dialog created by running the Analyze › Sholl › Sholl Analysis (From Tracings)... plugin in the main Fiji menu. First, the center of analysis is automatically taken from the nearest (or exact) node where the user clicks. In addition to morphology and custom tag filters, the Path filtering drop-down menu provides an additional option to restrict the analysis to the subset of paths selected in the Path Manager. Another advantage is that the display canvas allows the radius step size to be previewed visually. To do this, toggle on the Preview checkbox under the Sampling section and experiment with different step sizes.

  • Step Size = 0
  • Step Size = 5

In addition to the Sholl Profile plot and table, the output of the analysis can be visualized as a color mapping of the reconstruction and as a Sholl Image. To color code the tracing, choose Color coded paths from the Annotations drop-down menu and select a Lut from the Annotations Lut drop-down menu before pressing Run Analysis. To output the Sholl Image, choose 3D viewer labels image from the Annotations drop-down menu and select the desired Lut before running the analysis.

  • Sholl Profile Plot
  • Sholl Profile Table
  • Color Coded Tracing - Ice Lut
  • Sholl Image - Ice Lut

Strahler Analysis

To conduct Strahler Analysis on the current contents of the Path Manager, choose the Utilities › Strahler Analysis command in the main SNT dialog. This command will output the results of the analysis as a table and plot. These figures contains statistics on the group of paths associated with each Horton-Strahler Number. Note that this feature analyzes traced reconstructions. To run Strahler analysis on images, use the Analyze › Skeleton › Strahler Analysis... plugin in the main Fiji dialog.

  • Strahler Analysis table for OP_1
  • Strahler Analysis plot for OP_1

Custom Analyses

It is possible to script your own analysis routines. See SNT:_Scripting for the link to SNT's API as well as script templates demonstrating a range of analysis possibilities.

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