Placing markers for Sholl analysis of vessels

Available with the Neurolucida 360 Ultra package only. Click here for more information.

Purpose

Neurolucida 360 Explorer software (the freely available companion software for Neurolucida 360) includes Sholl analysis, which generates a set of nested concentric spheres beginning at a defined center. This analysis is used to quantify the number of objects (markers) or total length of objects (vessels) within volumes defined by these concentric spheres—the shells described below.

How it works

The set of nested concentric spheres created with Sholl analysis creates a series of shells. The volume reported for each shell is the volume contained out to a given radius that does not include the volume of any smaller shells.

  • Define the center of these concentric spheres by placing and selecting markers for Sholl analysis.

  • The coordinates of a single marker can be used to set the center or you can select a group of markers as the center point for Sholl analysis and Vesselucida Explorer will use the coordinates of the middle point of the area created by the group of markers as the center.

Procedure

  1. Open the data file in which you want to conduct Sholl analysis.

  2. Place the marker(s) that will define the center for the analysis using marker tools in either the 2D window or in the 3D Environment:

    • In the 2D window: Choose a marker from the marker panel, then click in the display to place the marker(s) at the location you want as the center for Sholl analysis.

      Be sure to consider the z-depth when placing your marker(s).

    • In the 3D Environment: Click the Marker button, then choose a marker from the list and click in the image to place the marker(s) where you want the Sholl center location.

      Note that when the Image Display is set to the default 3D Volume mode, Neurolucida 360 uses image data to determine the Z-position for marker placement. If you attempt to place a marker and the software cannot recognize a visible structure at that location, no marker is placed. In this case, you would need to follow the instructions for Placing markers at locations without visible structures.

  3. Save and view your data file in Neurolucida 360 Explorer to run Sholl analysis.