Significance: A data-based calibration method with enhanced depolarization contrast in polarization-sensitive optical coherence tomography (PS-OCT) was developed and demonstrated effective for detecting melanin content in the eye. Aim: We aim to mitigate the dependence between the measured depolarization metric and the intensity signal-to-noise ratio (SNR) for improved visualization of depolarizing tissues, especially in low SNR regions, and to demonstrate the enhanced depolarization contrast to evaluate melanin presence. Approach: A function for calibrating the depolarization metric was experimentally derived from the young albino guinea pig, assuming depolarization free in the retina. A longitudinal study of guinea pigs (9 weeks) was conducted to assess the accumulation of melanin during early eye growth. Furthermore, the melanin content of the sub-macular choroid was compared in eyes with light and dark irides involving 14 human subjects in early middle adulthood. Results: We observed an increase in the improved depolarization contrast, which indicates potential melanin accumulation in the early eye development with age in the pigmented guinea pig eyes. We found a significant difference in melanin content between human eyes with light and dark colors. Conclusions: Our proposed calibration method enhanced the visualization of depolarizing structures in PS-OCT, which can be generalized to all kinds of polarization-sensitive imaging and can potentially monitor melanin in healthy and pathological eyes.