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The 3D Sholl Analysis Tool is a classical based on the classic Sholl analysis method to characterize dendritic density and morphology of a neuron by positioning the center of a series of concentric shells (with user-defined distance between shells) on the center of the soma of the neurons, and counting all the intersection between dendrites and concentric shells. The number of dendritic intersections correlated with the distance from the cell body helps to describe morphological characteristics of complex dendritic branching patterns in a quantifiable manner.


On this page:

Table of Contents


The Sholl Analysis Tool is a floating window tool accessible from any image which contains Aivia Neuron objects. To access the tool, you can click on the Analysis menu at the top of the Aivia window, and then select the 3D Sholl Neuron Analysis Tool. You can also access it through either the Spreadsheet or the Relational Spreadsheet by clicking on the icon shown below and to the right.

An example of the Sholl Analysis tool interface is shown below.

The tool’s UI is split into two sections: the top settings section and the bottom table section. These sections are described in the sections to follow.


  • Neuron Set

    • This allows the user to select which Object Set containing Neuron objects to be analyzed and displayed in the tool

  • Shell Count

    • This dictates how many shells to generate and to count intersections for. Each shell is an equal distance apart defined by the following setting

  • Radius Step

    • This dictates the distance between the shells, using the calibration unit set on the loaded image

  • Heatmap

    • This dictates if the table displays a color gradient ranging from Red → Green to highlight the min → max intersection range of cells

    • The Grey color indicates no intersection was found at that shell

  • Refresh

    • Repopulates the data with the current settings displayed in the Settings portion of the UI

  • Export

    • This exports the currently displayed data in the data table of the tool

Sholl Analysis Results Table

  • Distance

    • Indicates the distance at which the shell intersection was evaluated

    • IMPORTANT: The first distance location is not based on the center point of the Soma/Neuron instead the Minimum Volume Enclosing Ellipsoid’s longest axis radii away from the center point

      • Minimum Volume Enclosing Ellipsoid

        • This is a 3D ellipse shaped object which is formed in such a way that it is the smallest it can possibly be while still encapsulating the entire object (in this case the Soma)

      • Longest Axis Radii

        • Of the 3 dimensional axis that the ellipsoid contains, this is the one which spans the most distance

        • In the picture below, the red section 'a' is the longest axis radii

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  • The starting point for any Neuron in the data table uses this longest axis radii distance from the Soma center point as a starting point for the shell intersection count

    • This row is generated via the “Radius” setting in the settings panel

  • Summary

    • This row displays a total count of intersections from all Neurons displayed in the table for that given column

  • Mean

    • This row displays an average count of intersections from all Neurons displayed in the table for that given column

  • Neuron X

    • These rows display the intersections for that given Neuron object (Dendrite and Segment intersections of the shell) at that given shell distance column

    • A color gradient is used from Red → Green ranging from the minimum count of all intersections in the table to maximum count of all intersections in the table (with the exception of no intersections)

    • When no intersections are found the Grey color is used

Calculation of Intersection

To calculate the intersection of a Neuron object with a Shell, the following logic is used:

  1. For any Dendrite Segment in the Neuron Object, collect all point locations along the center line

    1. These center line points can be visually inspected via the 3D viewer under the Dendrite display settings by turning on the “Trace” and being in “Sphere” mode

2. For any of the collected points ], check the state of distance versus all of the shells, identifying greater than or less than the distance of the shell

  1. Example: if the “start distance” → point_i on the segment is greater or less than the Shells defined distance

  2. Using the previously calculated information, if point_i and point_i+1 change from “greater than” to “less than” or visa versa, count this as an intersection for that shell

Visualization of Neurons for Exploration

  • Select “Whole Cell” level for object selection

  • Select the “Soma” set and click on a soma of interest based on the output of the Sholl analysis result in the Spreadsheet. Clicking the soma again in the image visualizes the entire neuron for inspection of the dendritic branches.

Image Credits

Dr. Julien Gasser, Neuroinflammation group, UCB Biopharma SRL, Belgium

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