NeuriteQuant is a freely available open-source tool that enables automated analysis of neuronal morphologies . It enables both analysis of individual experiments, as well as large-scale high-content screens. The analysis pipeline is particularly optimized to quantify the effect of experimental manipulations on physiologically relevant neuronal cultures that display a high degree of overlap among neurites, such as those that are derived from primary neurons, stem cells or brain sections.
The open-source software is provided as an ImageJ plugin and available here:
 Dehmelt L, Poplawski G, Hwang E, Halpain S (2011)
NeuriteQuant: an open source toolkit for high content screens of neuronal morphogenesis.
BMC Neurosci 12:100