Neuron-occupied areas (Supplementary Figure S2, A-II and B-II) were extracted from 2D KB and TH stained images (Supplementary Figure S2, A-I and B-I, respectively, 100×, 0.6836 μm2 per pixel) using black and brown colour information for the quantification of Nissl-positive neurons and TH-positive neurons, respectively. Black colour information in blue KB stained sections was extracted by thresholding blue channel information and dark brown colour information in TH-stained sections was extracted by manually selecting the brown-colour-range of the synthetic image from all three colour channels (red channel × max image intensity2 + green channel × max image intensity + blue channel). The number of pixels occupied by neurons for each 10 × 10 pixel block was then recorded to generate a density map (% occupied by neurons), as shown in Supplementary Figure S2, D-II (TH case only). Similarly, iron pigments (Supplementary Figure S2, C-III) and unstained pigmented NM (Supplementary Figure S2, C-II) were also extracted from 2D Perl-stained images (Supplementary Figure S2, C-I, the same two figures) to obtain iron and NM density maps (blue and brown, respectively). Blue-coloured iron information was extracted by thresholding the synthetic image that emphasizes the blue colour (blue channel – red channel/2 – green channel/2) and brown-coloured NM information was obtained by thresholding the sum image of all colour channels to distinguish brown-coloured pigments from the white-coloured background. These density images (10×, 6.836 μm2 per pixel) were then registered to the closest KB-stained image (10×, 6.836 μm2 per pixel) using the previously obtained alignment information. In Supplementary Figure S2, the TH-positive neuron density image (D-II), ranging from 0 to 100%, was registered to the closest KB-stained image to yield the aligned density image (E-II) using the same warp transformation information from the original TH-stained image (D-I) to the aligned image (E-I). Next, all registered MR images and density map (neuron, NM, and iron) images (10×, 6.836 μm2 per pixel) were down-sampled to smaller images after twice blurring using a 10 × 10 moving average kernel so that low resolution images (683.6 μm2 per pixel) were obtained for a voxel-wise statistical analysis. Histograms of the T2* distribution were generated for the respective thresholded binary stained images of iron pigments (blue), NM (brown), and reference tissue regions from the Perl-stained images (10×, 6.836 μm2 per pixel). Mean and standard deviation of each T2* distribution was obtained and compared to one other.