Towards whole-brain, quantitative characterisation of microscopy-derived microstructure in the BigMac dataset

The BigMac dataset is an open access resource combining in vivo MRI, postmortem MRI and multi-contrast microscopy data in a single, whole macaque brain. Here we perform data-driven segmentation of the BigMac histology slides to extract quantitative microscopy metrics for myelin, cell density, and cellular morphology (e.g. soma size and packing). Utilising high-quality MRI-microscopy registrations, we work towards building 3D volumes of quantitative microscopy derived metrics obtained at high resolution. This “ground truth” atlas of how cellular distributions vary across the brain is then directly related to co-registered diffusion MRI acquired in the same tissue.