Sholl analysis

Vessel reconstruction and analysis is available with the Neurolucida 360 Ultra package only. Click here for more information.

Purpose

Use Sholl analysis to evaluate neuronal processes emanating from the cell body (soma) that you specify. Sholl Analysis reports length, surface area, volume, and diameter of the processes; as well as the numbers of nodes, endings and spines in "shells" that represent a specific distance from the soma designated as the center point of the analysis. The number of intersections with each shell is also reported.

You can also use Sholl analysis to quantify vessel length, surface area, volume, and diameter in "shells" that represent a specific distance from the marker(s) that you designate as the center point of the analysis. The number of vessel intersections with each shell is also reported.

You can also obtain the numbers of markers and/or puncta that are located within each "shell".

You can rotate the Sholl spheres along with the tracings in 3D by clicking and dragging the mouse.

Analyze one neuron per data file. If your file contains two or more neurons, select just one cell body before performing the Sholl analysis.

The Sholl Analysis generates a set of nested concentric spheres centered at a selected cell body or marker(s). The smallest sphere has a radius of 0. The spheres increase in size by a constant change in radius (r) that you specify. Neurolucida Explorer determines the largest sphere so that it is large enough to enclose everything selected for the analysis.

The center point of the Sholl analysis is the center of the cell body or marker(s). If you select more than a single marker, the centroid of the markers is calculated and used as the center point.

What is a centroid?

The centroid is the balance point. Imagine placing a pencil point at the centroid; the cell body tracing would balance on the pencil tip. If the cell body has been traced at several different focal planes, several centroids are calculated. The average of the centroids is the average of each coordinate.

What is a shell?

A shell is the volume contained out to the given radius; it does not include the volume of any smaller shells. This means that the smallest radius row in the results represents a sphere of the given radius.

Procedure

  1. Select the center for the analysis and the structures or markers to be compared:

    1. Select one cell body, or one or more markers, that you want to use as the center for the analysis.

    2. Select one or more process/group of processes, puncta, and/or markers to be analyzed in relation to the cell body, or vessels in relation to the marker(s).

  2. Select Sholl Analysis from the Spatial drop-down menu on the Analyze ribbon.

    • Spheres: Choose the starting radius and radius increment for the spheres, as well as line thickness and color.

    • Analyses: Choose the analyses that you want to include.

      If you select Branch Order, an additional report is generated with centrifugal branch order results and any additional order you may have selected.

      To select an additional branch order, go to Preferences in the File menu and select Ordering.

  3. Click Display to view result tables.

    The Sholl spheres will also be displayed in the main Neurolucida Explorer window.

    • To hide the Sholl spheres, click Remove analysis graphics; find the button on the View and Analyze ribbons.

Analysis results

Axons / Dendrites / Apical Dendrites / Vessels report

Radius: Each radius corresponds to a shell. The number shown is the position of the shell in µm from the designated center point.

Intersections: Number of intersections between process or vessel and sphere at the given radius.

Length: Total length in µm of all processes or vessels passing through a shell.

SArea: Total surface area in µm2 of all processes or vessels passing through a shell.

Volume: Total volume in µm3 of all processes or vessels passing through a shell.

Avg. Diameter: Average Diameter in µm of all processes or vessels passing through a shell.

Nodes: Total number of nodes in the shell.

Endings: Total number of endings in the shell.

Spines: Total number of spines modeled in the shell.

None Spine, Thin Spine, Stubby Spine, etc.: If the spines in the data file were classified as spine types, the numbers of each spine type in the shell are reported in individual columns.

Automatic Varicosities: Total number of varicosities detected and modeled in the shell.

Branch Order report

Reports the length and number of intersections of the processes for each shell by branch order.

Markers report

Displays the number of markers in each shell for each marker type.

Puncta report

Displays the number of puncta in each shell.

 

References

Sholl, D. A. (1953). Dendritic organization in the neurons of the visual and motor cortices of the cat. J. Anat. 87, 387-406.

Rodger J., Drummond E.S., Hellström M., Robertson D., Harvey A.R .(2012). Long-Term Gene Therapy Causes Transgene-Specific Changes in the Morphology of Regenerating Retinal Ganglion Cells. PLoS ONE 7(2): e31061. doi:10.1371/journal.pone.0031061