Manual neuron tracing is a very labor‐intensive task. In the drug screening context, the sheer number of images to process means that this approach is unrealistic. Moreover, the lack of reproducibility, objectivity, and auditing capability of manual tracing is limiting even in the context of smaller studies. We have developed fast, sensitive, and reliable algorithms for the purpose of detecting and analyzing neurites in cell cultures, and we have integrated them in software called HCA‐Vision, suitable for the research environment. We validate the software on images of cortical neurons by comparing results obtained using HCA‐Vision with those obtained using an established semi‐automated tracing solution (NeuronJ). The effect of the Sez‐6 deletion was characterized in detail. Sez‐6 null neurons exhibited a significant increase in neurite branching, although the neurite field area was unchanged due to a reduction in mean branch length. HCA‐Vision delivered considerable speed benefits and reliable traces. © 2007 International Society for Analytical Cytology.