Fig. 1: NextBrain workflow.
From: A probabilistic histological atlas of the human brain for MRI segmentation
a, Photograph of formalin-fixed hemisphere (lateral view). b, High-resolution (400 μm) ex vivo MRI scan, FreeSurfer segmentation and extracted pial surface (parcellated with FreeSurfer). Left, sagittal slice of MRI. Centre, corresponding FreeSurfer segmentation. Right, 3D rendering of reconstructed and parcellated pial surface. c, Tissue slabs and blocks, before and after paraffin embedding. Left, blocked coronal slice of the cerebrum. Right, blockface photo of a cerebral block. d, Histology: coronal section of cerebrum stained with LFB (left) and H&E (right). e, Artificial-intelligence-assisted labelling of 333 ROIs on LFB. Left, cerebrum; centre, brainstem; right, cerebellum28. f, Initialization of affine alignment of tissue blocks using a custom registration algorithm that minimizes overlap and gaps between blocks. g, Refinement of registration with histology and nonlinear transform24,25. Reconstructed coronal slice of LFB (left), H&E (middle) and labels (right), overlaid on MRI, after nonlinear registration with artificial intelligence and robust Bayesian refinement. h, Orthogonal slices of our 3D probabilistic atlas. Left, sagittal; middle, coronal; right, axial. Each voxel is painted with a linear combination the colours of each label, multiplied by their probabilities. i, Automated Bayesian segmentation of an in vivo scan into 333 ROIs using the atlas. The atlas can also be used for segmenting ex vivo MRI and as CCF for population analyses.
