TY - JOUR T1 - A multimodal computational pipeline for 3D histology of the human brain JF - bioRxiv DO - 10.1101/2020.02.10.941948 SP - 2020.02.10.941948 AU - Matteo Mancini AU - AdriĆ  Casamitjana AU - Loic Peter AU - Eleanor Robinson AU - Shauna Crampsie AU - David L. Thomas AU - Janice L. Holton AU - Zane Jaunmuktane AU - Juan Eugenio Iglesias Y1 - 2020/01/01 UR - http://biorxiv.org/content/early/2020/02/11/2020.02.10.941948.abstract N2 - Ex vivo imaging enables analysis of the human brain at a level of detail that is not possible in vivo with MRI. In particular, histology can be used to study brain tissue at the microscopic level, using a wide array of different stains that highlight different microanatomical features. Complementing MRI with histology has important applications in ex vivo atlas building and in modeling the link between microstructure and macroscopic MR signal. However, histology requires sectioning tissue, hence distorting its 3D structure, particularly in larger human samples. Here, we present an open-source computational pipeline to produce 3D consistent histology reconstructions of the human brain. The pipeline relies on a volumetric MRI scan that serves as undistorted reference, and on an intermediate imaging modality (blockface photography) that bridges the gap between MRI and histology. We present results on 3D histology reconstruction of a whole human hemisphere. ER -