Sholl analysis 

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

Select one cell body that you want to use as the center for the analysis

Select one or more process/group of processes, puncta, and/or markers to be analyzed in relation to the cell body

Trace cell body contour and branching from the cell body in continuous mode

Go to Analyze-> Neuron data -> Spatial and click SHOLL ANALYSIS

Spheres: Choose the starting radius (0µm) and radius increment (10µm) for the spheres

Analyses: Choose the analyses that you want to include (e.g branching)

Analyze at least fifteen cells per animal (randomly selected from 3 serial coronal sections/animal) and subsequently average all data for each animal

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 and sphere at the given radius

• Length: Total length in µm of all processes passing through a shell
• Nodes: Total number of nodes in the shell
• Endings: Total number of endings in the shell