A multimodal computational pipeline for 3D histology of the human brain

Published in Scientific reports - Nature Publishing Group, 2020

Authors: Adrià Casamitjana, Verónica Vilaplana, Santi Puch, Asier Aduriz, Carlos López, Grégory Operto, Raffaele Cacciaglia, Carles Falcón, José Luis Molinuevo, Juan Domingo Gispert



Ex vivoimaging enables analysis of the human brain at a level of detail that is not possibleinvivowith MRI. In particular, histology can be used to study brain tissue at the microscopiclevel, using a wide array of different stains that highlight different microanatomical features.Complementing MRI with histology has important applications inex vivoatlas building andin modeling the link between microstructure and macroscopic MR signal. However, histologyrequires sectioning tissue, hence distorting its 3D structure, particularly in larger human samples.Here, we present an open-source computational pipeline to produce 3D consistent histologyreconstructions of the human brain. The pipeline relies on a volumetric MRI scan that serves asundistorted reference, and on an intermediate imaging modality (blockface photography) thatbridges the gap between MRI and histology. We present results on 3D histology reconstructionof a whole human hemisphere.