TY - JOUR T1 - A combined pipeline for quantitative analysis of human brain cytoarchitecture JF - bioRxiv DO - 10.1101/2020.08.06.219444 SP - 2020.08.06.219444 AU - Irene Costantini AU - Giacomo Mazzamuto AU - Matteo Roffilli AU - Filippo Castelli AU - Mattia Neri AU - Giovanni Lughi AU - Andrea Simonetto AU - Annunziatina Laurino AU - Erica Lazzeri AU - Luca Pesce AU - Christophe Destrieux AU - Ludovico Silvestri AU - Valerio Conti AU - Renzo Guerrini AU - Francesco S. Pavone Y1 - 2020/01/01 UR - http://biorxiv.org/content/early/2020/08/06/2020.08.06.219444.abstract N2 - The 3D analysis of the human brain architecture at cellular resolution is still a big challenge. In this work, we propose a pipeline that solves the problem of performing neuronal mapping in large human brain samples at micrometer resolution. First, we introduce the SWITCH/TDE protocol: a robust methodology to clear and label human brain tissue. Then, we implement the 2.5D method based on a Convolutional Neural Network, to automatically detect and segment all neurons. Our method proved to be highly versatile and was applied successfully on specimens from different areas of the cortex originating from different subjects (young, adult and elderly, both healthy and pathological). We quantitatively evaluate the density and, more importantly, the mean volume of the thousands of neurons identified within the specimens. In conclusion, our pipeline makes it possible to study the structural organization of the brain and expands the histopathological studies to the third dimension.Competing Interest StatementM.R. is CEO of Bioretics srl while G.L., M.N., and A.S. are employees. The ALIQUIS framework and the LAIRA application are products of Bioretics srl. ER -