NeurphologyJ can identify neurites that lie in close proximity to each other. Mouse hippocampal neurons immunofluorescence stained were analyzed using NeurphologyJ and NeuriteTracer. Neurite tracings are shown in white and the original image is shown in green in merged images. Note that NeuriteTracer falsely identifies the area outside the nucleus as neurites (red arrowhead) and is unable to detect neurites in bundles (white arrows). The scale bar represents 50 μm.