Quantifying mesoscale neuroanatomy using X-ray microtomography

• Type of Material: Article
• Authors: Eva Dyer, Emory University; William Gray Roncal, The Johns Hopkins University Applied Physics Laboratory; Judy A. Prasad, University of Chicago; Hugo L. Fernandes, Northwestern University; Doga Gürsoy, Argonne National Laboratory; Vincent De Andrade, Argonne National Laboratory; Kamel Fezzaa, Argonne National Laboratory; Xianghui Xiao, Argonne National Laboratory; Joshua T. Vogelstein, Johns Hopkins University; Chris Jacobsen, Argonne National Laboratory; Konrad P. Körding, University of Pennsylvania; Narayanan Kasthuri, University of Chicago
• Language: English
• Date: 2017-09-01
• Publisher: Society for Neuroscience
• Publication Version: Final Published Version
• Copyright Statement: © 2017 Dyer et al.
• License: Creative Commons Attribution 4.0 International
• Final Published Version (URL): http://dx.doi.org/10.1523/ENEURO.0195-17.2017
• Title of Journal or Parent Work: eNeuro
• ISSN: 2373-2822
• Volume: 4
• Issue: 5
• Start Page: ENEURO.0195-17.2017
• End Page: ENEURO.0195-17.2017
• Grant/Funding Information: Support was provided by NIH U01MH109100 (E.L.D., H.L.F., D.G., X.X., C.J., N.K., and K.P.K.), the IARPA MICRONS project under IARPA Contract D16PC0002 (N.K.), an educational Fellowship from the Johns Hopkins University Applied Physics Laboratory (W.G.R.), the Defense Advanced Research Projects Agency (DARPA) SIMPLEX program through SPAWAR contract N66001-15-C-4041, and DARPA GRAPHS N66001-14-1-4028.; This research used resources from the US Department of Energy (DOE) Office of Science User Facilities operated for the DOE Office of Science by Argonne National Laboratory under contract no. DE-AC02-06CH11357.
• Keywords: cs.CV; q-bio.QM
• Research Categories: Engineering, Biomedical

Abstract

Methods for resolving the three-dimensional (3D) microstructure of the brain typically start by thinly slicing and staining the brain, followed by imaging numerous individual sections with visible light photons or electrons. In contrast, X-rays can be used to image thick samples, providing a rapid approach for producing large 3D brain maps without sectioning. Here we demonstrate the use of synchrotron X-ray microtomography (μCT) for producing mesoscale (~1 μm 3 resolution) brain maps from millimeter-scale volumes of mouse brain. We introduce a pipeline for μCT-based brain mapping that develops and integrates methods for sample preparation, imaging, and automated segmentation of cells, blood vessels, and myelinated axons, in addition to statistical analyses of these brain structures. Our results demonstrate that X-ray tomography achieves rapid quantification of large brain volumes, complementing other brain mapping and connectomics efforts.