Fig 2:

NextBrain workflow. (A) Photograph of formalin-fixed hemisphere. (B) High-resolution (400 μm) ex vivo MRI scan, FreeSurfer segmentation, and extracted pial surface (parcellated with FreeSurfer). (C) Tissue slabs and blocks, before and after paraffin embedding. (D) Section stained with H&E and LFB. (E) Semi-automated labelling of 333 ROIs on sections using an Al method [5]. (F) Initialization of affine alignment of tissue blocks using a custom registration algorithm that minimises overlap and gaps between blocks. (G) Refinement of registration with histology and nonlinear transform, using a combination of Al and Bayesian techniques [9,10]. (H) Orthogonal slices of 3D probabilistic atlas. (I) Automated Bayesian segmentation of an in vivo scan into 333 ROIs using the atlas.