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The purpose of the study was to create a standardised protocol for choroidal thickness measurements and to determine whether choroidal thickness measurements made on images obtained by spectral domain optical coherence tomography (SD-OCT) and swept source (SS-) OCT from patients with healthy retina are interchangeable when performed manually or with an automatic algorithm.36 grid cell measurements for choroidal thickness for each volumetric scan were obtained, which were measured for SD-OCT and SS-OCT with two methods on 18 eyes of healthy volunteers. Manual segmentation by experienced retinal graders from the Vienna Reading Center and automated segmentation on >6300 images of the choroid from both devices were statistically compared.Model-based comparison between SD-OCT/SS-OCT showed a systematic difference in choroidal thickness of 16.26±0.725 μm (p<0.001) for manual segmentation and 21.55±0.725 μm (p<0.001) for automated segmentation. Comparison of automated with manual segmentations revealed small differences in thickness of −0.68±0.513 μm (p=0.1833). The correlation coefficients for SD-OCT and SS-OCT measures within eyes were 0.975 for manual segmentation and 0.955 for automatic segmentation.Choroidal thickness measurements of SD-OCT and SS-OCT indicate that these two devices are interchangeable with a trend of choroidal thickness measurements being slightly thicker on SD-OCT with limited clinical relevance. Use of an automated algorithm to segment choroidal thickness was validated in healthy volunteers.