Hearing lose affects 360 million people worldwide and a largely preventable contributor is excessive noise. Exposure to loud noise damages the delicate hair cells of the cochlea. The mechanism by which this damage occurs has been linked to overproduction of reactive oxygen species in hair cell mitochondria. In this capstone project we demonstrate the use of both ImageJ open-source software and commercially available Imaris® software to characterize mitochondria in cochlear hair cells. The application of available image analysis software to today’s multidimensional high-resolution imaging data is crucial to understanding the role of mitochondrial changes in noise-induced hearing loss.