Spectral Domain-Optical Coherence Tomography (SD-OCT) is an essential tool to assess the health of ocular tissues in live subjects. The processing of SD-OCT images, in particular from non-mammalian species, is a labor-intensive manual process due to the lack of access to analytical programs. The algorithm presented herein was developed for quantitative analysis of SD-OCT images of live teleost eyes. The algorithm measured the thickness characteristic of the retina present in the input dataset The program was also designed to allow adjustments of the thresholding variables to suit any specific image set. 2D and 3Dheat maps are created alongside the algorithm to plot the SD-OCT image measurements as a colour gradient.