In spite of dramatic advancement in biomedical imaging technologies, non-invasive visualization of anatomic detail of the spinal cord has remained a major challenge. Here, a novel color-coded contrast method for magnetic resonance imaging (MRI) which provides superb resolution of the spinal cord in live animals, comparable to that of histological preparations, is described. The method, referred to here as three dimensional anisotropy (3DAC) contrast MRI, displays cross-sectional images in the full visible color spectrum, encoding directional information regarding intravoxel anisotropic water motion in space. Since neuronal fibers, especially axons, possess significantly higher intravoxel anisotropic water motion compared with other elements in the nervous system, 3DAC is highly sensitive to axonal direction and density. Axonography of the spinal cord of rats obtained using this technique showed anatomic detail at a resolution hitherto unobtainable in live animals.