We present an implemented method for automated quantification of neuronal beading. Beading is the "morphological hallmark" of axonal injury and is present in many neurological disease conditions as well. In vitro models of injury result in beading which has previously been difficult to quantify, and therefore difficult to use as a measurement of the degree of axonal injury. The beading program was designed to quantify beading intensity in single axons and output a unitless beading number that represents the size and number of beads in relation to the length and width of the axon. The program was used to analyze a sample set of images and was successful in demonstrating a quantifiable difference between injured neurons and sham controls. Bland-Altman analysis was used to assess agreement between the number of beads counted by the program and those counted manually.