Sholl analysis validation parameters

In pictures where the axon is only visible and the soma is far away from the arbor (eg. NMJ), it is absolutely necessary to divide the arbor in half or have a focal point exactly at the center (or near) in order for Sholl to be valid?


Dear Ivan,

In short: No its not. Although widespread, the idea that Sholl sampling starts at the soma is just a misconception. The center of analysis (the focal point of sampling shells) can be any part of the arbor. In fact, in the original 1953 paper, Sholl used distinct focal points when, e.g., analyzing pyramidal cells: the soma for basal dendrites and the main apical ramification for apical dendrites. The documentation of the Sholl Analysis plugin also includes an example of a non-somatic center: See axonal arbor of a Drosophila olfactory neuron, also in the supplementary information of the Sholl Analysis manuscript).

Also, note that the hemisphere/hemicircle option can be useful in these cases, as it can be used to exclude sections of the arbor not stemming directly from the chosen center. Feel free to post a representative image of your NMJ axons, if you need further help.


@tferr Thanks for the reply!, I really appreciate it.