Sholl

Use this analysis to obtain the quantity of objects or the total length within shells in virtual/anatomical regions. It can be performed on trees or markers on the trees. You can rotate the Sholl spheres along with the tracings in 3D by dragging the mouse.

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

 

ClosedWhat is a shell?

A shell is the volume contained out to the given radius, but does not include the volume of any smaller shells. This means that the smallest radius row is a sphere of the given radius.

ClosedHow does the Sholl analysis work?

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

The center point of the Sholl analysis is the center of the cell body. The center is found by examining all of the cell bodies and finding the centroid of each. The average of all of the centroids is then used as the center point.

ClosedWhat 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.

ClosedProcedure
  1. Select at least one cell body and one process/group of processes (or a group of markers).
  2. Select Analyze>Neuron data>Spatial>Sholl analysis.
    • Enter radius values for the spheres.
    • Analyses: 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 File>Preferences>Ordering.

 

To hide the Sholl spheres, click Analyze>Remove analysis graphics.

ClosedReferences

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

Analysis results

Axons / Dendrites / Apical Dendrites report

ClosedRadius

Each radius corresponds to a shell.

Closed Intersections

Number of intersections between process and sphere at the given radius.

ClosedLength

Total length of all processes passing through a shell.

Branch Order report

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

Markers report

Displays the number of markers in each shell (represented by the radius) for each marker type.