02622nas a2200445   4500000000100000000000100001008004100002260001500043653002700058653002300085100002300108700001900131700002100150700001600171700002300187700002000210700002000230700002000250700002000270700001900290700001600309700002000325700001800345700001700363700002400380700001900404700001800423700002000441700001900461700002200480700002100502700002100523700002100544700002600565245007900591856005500670300000800725520142900733022001402162       2025                            d  c2025-11-0510aBiomedical Engineering10aBiophysical models1 aAdrià Casamitjana1 aMatteo Mancini1 aEleanor Robinson1 aLoïc Peter1 aRoberto Annunziata1 aJuri Althonayan1 aShauna Crampsie1 aEmily Blackburn1 aBenjamin Billot1 aAlessia Atzeni1 aOula Puonti1 aYaël Balbastre1 aPeter Schmidt1 aJames Hughes1 aJean C. Augustinack1 aBrian L. Edlow1 aLilla Zöllei1 aDavid L. Thomas1 aDorit Kliemann1 aMartina Bocchetta1 aCatherine Strand1 aJanice L. Holton1 aZane Jaunmuktane1 aJuan Eugenio Iglesias00aA probabilistic histological atlas of the human brain for MRI segmentation  uhttps://www.nature.com/articles/s41586-025-09708-2  a1-83 aIn human neuroimaging, brain atlases are essential for segmenting regions of interest (ROIs) and comparing subjects in a common coordinate frame. State-of-the-art atlases derived from histology1–3 provide exquisite three-dimensional cytoarchitectural maps but lack probabilistic labels throughout the whole brain: that is, the likelihood of each location belonging to a given ROI. Here we present NextBrain, a probabilistic histological atlas of the whole human brain. We developed artificial intelligence-enabled methods to align roughly 10,000 histological sections from five whole brain hemispheres into three-dimensional volumes and to produce delineations for 333 ROIs on these sections. We also created a companion Bayesian tool for automatic segmentation of these ROIs in magnetic resonance imaging (MRI) scans. We showcase two applications of the atlas: segmentation of ultra-high-resolution ex vivo MRI and volumetric analysis of Alzheimer’s disease using in vivo MRI. We publicly release raw and aligned data, an online visualization tool, the atlas, the segmentation tool, and ground truth delineations for a high-resolution ex vivo hemisphere used in validation. By enabling researchers worldwide to automatically analyse brain MRIs at a higher level of granularity, NextBrain holds promise to increase the specificity of findings and accelerate our quest to understand the human brain in health and disease.  a1476-4687