Quantifying Mesoscale Neuroanatomy Using X-Ray Microtomography

ENeuro
Eva L DyerNarayanan Kasthuri

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.

Citations

Feb 9, 2018·Scientific Reports·Xiaogang YangDoğa Gürsoy
Sep 16, 2020·Nature Neuroscience·Aaron T KuanWei-Chung Allen Lee
Mar 13, 2020·Nature Methods·Mihail Ivilinov TodorovAli Ertürk
Aug 17, 2020·Scientific Reports·Matteo ManciniJuan Eugenio Iglesias
Sep 27, 2018·Scientific Reports·Ali ShahbaziWalter J Scheirer
Jun 20, 2018·Proceedings of the National Academy of Sciences of the United States of America·Mareike TöpperwienTim Salditt
Jul 4, 2018·Molecular Imaging and Biology : MIB : the Official Publication of the Academy of Molecular Imaging·J AlbersC Dullin
Nov 15, 2019·Development·Todd A SchoborgNasser M Rusan
Aug 9, 2020·Frontiers in Cell and Developmental Biology·David L Bernstein, Slava Rom
Jul 25, 2018·Journal of Colloid and Interface Science·Timothy J LeeCraig R Forest
Apr 6, 2021·Frontiers in Neuroscience·Paulla Vieira RodriguesMatheus de Castro Fonseca
May 7, 2021·Journal of Applied Crystallography·Ming DuChris Jacobsen

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Methods Mentioned

BETA
X-ray
electron microscopy
dissection
transgenic
biopsies
pulls down
light microscopy

Software Mentioned

ITK Snap
Python
Blender
GridRec
ilastik
ITK
Matlab
Fiji
Snap
LONI Pipeline

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