Recent breakthroughs in magnetic resonance imaging (MRI) enabled quantitative relaxometry and diffusion-weighted imaging with sub-millimeter resolution.Combined with biophysical models of MR contrast the emerging methods promise in vivo mapping of cyto- and myelo-architectonics, i.e., in vivo histology using MRI (hMRI) in humans. The hMRI methods require histological reference data for model building and validation. This is currently provided by MRIon post mortem human brain tissue in combination with classical histology on sections. However, this well-established approach is limited to qualitative 2D information, while a systematic validation of hMRI requires quantitative 3D information on macroscopic voxels. I will demonstrate how advanced histological methods such as CLARITY and analytical microscopy can be used for informing and validating hMRI. I will present application of this method for mapping of intracortical and subcortical fibers, and mapping of dopaminergic neurons in substantia nigra.