Difference between revisions of "SNT: Analysis"

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<li style="display:inline-block;"> [[Image:Snt-Sholl-Precise-Step-1.png|none|thumb|200px|1) Select path]] </li>
 
<li style="display:inline-block;"> [[Image:Snt-Sholl-Precise-Step-1.png|none|thumb|200px|1) Select path]] </li>
 
<li style="display:inline-block;"> [[Image:Snt-Sholl-Precise-Step-2.png|none|thumb|200px|2) Snap cursor to node]] </li>
 
<li style="display:inline-block;"> [[Image:Snt-Sholl-Precise-Step-2.png|none|thumb|200px|2) Snap cursor to node]] </li>
<li style="display:inline-block;"> [[Image:Snt-Sholl-Precise-Step-3.png|none|thumb|146px|3) Press "Alt+Shift+A"]] </li>
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<li style="display:inline-block;"> [[Image:Snt-Sholl-Precise-Step-3.png|none|thumb|146px|3) Sholl dialog]] </li>
 
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Revision as of 22:31, 12 December 2019

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Sholl Analysis

Initiating Sholl Analysis: coarse method

To initiate Sholl Analysis, 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. 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
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