The choriocapillaris is a unique vascular plexus located posterior to the retinal pigment epithelium. In recent years, there is an increasing interest in the examination of the interrelationship between the choriocapillaris and eye diseases. We used several techniques to study choroidal perfusion, including laser Doppler flowmetry, laser speckle flowgraphy, and optical coherence tomography angiography (OCTA), but with the latter no standardized algorithm for quantitative analysis has been provided. We analyzed different algorithms to quantify flow voids in non-human primates that can be easily implemented into clinical research. In-vivo, high-resolution images of the non-human primate choriocapillaris were acquired with a swept-source OCTA (SS-OCTA) system with 100kHz A-scan/s rate, over regions of 3 × 3 mm2 and 12 × 12 mm2. The areas of non-perfusion, also called flow voids, were segmented with a structural, intensity adjusted, uneven illuminance-compensated algorithm and the new technique was compared to previously published methods. The new algorithm shows improved reproducibility and may have applications in a wide array of eye diseases including age-related macular degeneration (AMD).