title: 3D BrainCV: simultaneous visualization and analysis of cells and capillaries in a whole mouse brain with one-micron voxel resolution.
abstract: Systematic cellular and vascular configurations are essential for understanding fundamental brain anatomy and metabolism. We demonstrated a 3D brainwide cellular and vascular (called 3D BrainCV) visualization and quantitative protocol for a whole mouse brain. We developed a modified Nissl staining method that quickly labeled the cells and blood vessels simultaneously in an entire mouse brain. Terabytes 3D datasets of the whole mouse brains, with unprecedented details of both individual cells and blood vessels, including capillaries, were simultaneously imaged at 1-μm voxel resolution using micro-optical sectioning tomography (MOST). For quantitative analysis, we proposed an automatic image-processing pipeline to perform brainwide vectorization and analysis of cells and blood vessels. Six representative brain regions from the cortex to the deep, including FrA, M1, PMBSF, V1, striatum, and amygdala, and six parameters, including cell number density, vascular length density, fractional vascular volume, distance from the cells to the nearest microvessel, microvascular length density, and fractional microvascular volume, had been quantitatively analyzed. The results showed that the proximity of cells to blood vessels was linearly correlated with vascular length density, rather than the cell number density. The 3D BrainCV made overall snapshots of the detailed picture of the whole brain architecture, which could be beneficial for the state comparison of the developing and diseased brain.
authors.affiliation: Britton Chance Center for Biomedical Photonics, Huazhong University of Science and Technology - Wuhan National Laboratory for Optoelectronics, Wuhan 430074, China; MoE Key Laboratory for Biomedical Photonics, Department of Biomedical Engineering, Huazhong University of Science and Technology, Wuhan 430074, China.
authors.forename: Jingpeng
authors.initials: J
authors.lastname: Wu
authors.affiliation: Britton Chance Center for Biomedical Photonics, Huazhong University of Science and Technology - Wuhan National Laboratory for Optoelectronics, Wuhan 430074, China; MoE Key Laboratory for Biomedical Photonics, Department of Biomedical Engineering, Huazhong University of Science and Technology, Wuhan 430074, China.
authors.forename: Yong
authors.initials: Y
authors.lastname: He
authors.affiliation: Britton Chance Center for Biomedical Photonics, Huazhong University of Science and Technology - Wuhan National Laboratory for Optoelectronics, Wuhan 430074, China; MoE Key Laboratory for Biomedical Photonics, Department of Biomedical Engineering, Huazhong University of Science and Technology, Wuhan 430074, China.
authors.forename: Zhongqin
authors.initials: Z
authors.lastname: Yang
authors.affiliation: Britton Chance Center for Biomedical Photonics, Huazhong University of Science and Technology - Wuhan National Laboratory for Optoelectronics, Wuhan 430074, China; MoE Key Laboratory for Biomedical Photonics, Department of Biomedical Engineering, Huazhong University of Science and Technology, Wuhan 430074, China.
authors.forename: Congdi
authors.initials: C
authors.lastname: Guo
authors.affiliation: Britton Chance Center for Biomedical Photonics, Huazhong University of Science and Technology - Wuhan National Laboratory for Optoelectronics, Wuhan 430074, China; MoE Key Laboratory for Biomedical Photonics, Department of Biomedical Engineering, Huazhong University of Science and Technology, Wuhan 430074, China.
authors.forename: Qingming
authors.initials: Q
authors.lastname: Luo
authors.affiliation: Britton Chance Center for Biomedical Photonics, Huazhong University of Science and Technology - Wuhan National Laboratory for Optoelectronics, Wuhan 430074, China; MoE Key Laboratory for Biomedical Photonics, Department of Biomedical Engineering, Huazhong University of Science and Technology, Wuhan 430074, China.
authors.forename: Wei
authors.initials: W
authors.lastname: Zhou
authors.affiliation: Britton Chance Center for Biomedical Photonics, Huazhong University of Science and Technology - Wuhan National Laboratory for Optoelectronics, Wuhan 430074, China; MoE Key Laboratory for Biomedical Photonics, Department of Biomedical Engineering, Huazhong University of Science and Technology, Wuhan 430074, China.
authors.forename: Shangbin
authors.initials: S
authors.lastname: Chen
authors.affiliation: Britton Chance Center for Biomedical Photonics, Huazhong University of Science and Technology - Wuhan National Laboratory for Optoelectronics, Wuhan 430074, China; MoE Key Laboratory for Biomedical Photonics, Department of Biomedical Engineering, Huazhong University of Science and Technology, Wuhan 430074, China.
authors.forename: Anan
authors.initials: A
authors.lastname: Li
authors.affiliation: Britton Chance Center for Biomedical Photonics, Huazhong University of Science and Technology - Wuhan National Laboratory for Optoelectronics, Wuhan 430074, China; MoE Key Laboratory for Biomedical Photonics, Department of Biomedical Engineering, Huazhong University of Science and Technology, Wuhan 430074, China.
authors.forename: Benyi
authors.initials: B
authors.lastname: Xiong
authors.affiliation: Britton Chance Center for Biomedical Photonics, Huazhong University of Science and Technology - Wuhan National Laboratory for Optoelectronics, Wuhan 430074, China; MoE Key Laboratory for Biomedical Photonics, Department of Biomedical Engineering, Huazhong University of Science and Technology, Wuhan 430074, China.
authors.forename: Tao
authors.initials: T
authors.lastname: Jiang
authors.affiliation: Britton Chance Center for Biomedical Photonics, Huazhong University of Science and Technology - Wuhan National Laboratory for Optoelectronics, Wuhan 430074, China; MoE Key Laboratory for Biomedical Photonics, Department of Biomedical Engineering, Huazhong University of Science and Technology, Wuhan 430074, China. Electronic address: huigong@mail.hust.edu.cn.
authors.forename: Hui
authors.initials: H
authors.lastname: Gong
mesh_terms: D000818:Animals; D001921:Brain / Q000648:ultrastructure*; D002196:Capillaries / Q000648:ultrastructure*; D007090:Image Interpretation, Computer-Assisted / Q000379:methods*; D021621:Imaging, Three-Dimensional / Q000379:methods*; D008297:Male; D051379:Mice; D009457:Neuroglia / Q000648:ultrastructure*; D009474:Neurons / Q000648:ultrastructure*
keywords: 3D BrainCV; 3D Brainwide Cellular and Vascular; Cells and blood vessels; FrA; M1; MOST; Micro-optical sectioning tomography; Mouse brain; Nissl staining; One-micron resolution; PMBSF; V1; micro-optical sectioning tomography; the frontal association cortex; the posteromedial barrel subfield; the primary motor cortex; the primary visual cortex