The joint registration of multiple microscopy contrasts to MRI in the BigMac dataset

We built a novel pipeline to register 290 high-resolution multi-contrast microscopy sections in the BigMac dataset to post-mortem MRI with sub-millimetre accuracy. The MRI-microscopy alignment is optimised over all microscopy sections jointly, to achieve high-quality co-registration whilst ensuring the slide order and separation is consistent with how the tissue was sectioned. We demonstrate the accuracy of the registration by overlaying FreeSurfer-estimated grey-white matter contours on orthogonal sections of 3D volumetric reconstructions of each microscopy modality. Our pipeline provides an integrated workflow for diffusion-microscopy studies using the BigMac dataset, which is openly available via the Oxford Digital Brain Bank.