We present a biophysical model that quantitatively describes gradient and spin echo relaxation in substantia nigra induced by iron accumulated the neuromelanin of dopaminergic neurons. This model was informed by 3D quantitative microscopic iron distributions obtained from classical histology and Proton-Induced X-ray Emission. It was validated by comparison to quantitative MRI on post mortem human brain tissue. We demonstrate that the total iron content of DN can be extracted analytically from relaxometry in nigrosomes. This results provides an important step toward a highly desired early stage biomarker for detecting dopaminergic neurons depletion in Parkinson's disease.