3D BrainCV: Simultaneous visualization and analysis of cells and capillaries in a whole mouse brain with one-micron voxel resolution

Wu, Jingpeng; He, Yong; Yang, Zhongqin; Guo, Congdi; Luo, Qingming; Zhou, Wei; Chen, Shangbin; Li, Anan; Xiong, Binbin; Jiang, Tao; Gong, Hui

doi:10.1016/j.neuroimage.2013.10.036

Cited by 112 publications

(147 citation statements)

References 53 publications

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“…It was demonstrated that Nissl staining could be used to identify the barrels according to the cell density variation (Woolsey and Van der 1970), and a modified Nissl staining was proved to distinguish the cells and blood vessels simultaneously (Ramos et al 2008;Wu et al 2014). Moreover, our home-made microoptical sectioning tomography (MOST) system (Li et al 2010) enabled whole mouse brain visualization with a 1-μm voxel resolution, which is sufficient to resolve both cells and capillaries.…”

Section: Introductionmentioning

confidence: 99%

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Direct 3D Analyses Reveal Barrel-Specific Vascular Distribution and Cross-Barrel Branching in the Mouse Barrel Cortex

Guo

Chen

et al. 2014

Cereb. Cortex

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Jingpeng Wu and Congdi Guo contributed equally to this work.Whether vascular distribution is spatially specific among cortical columns is a fundamental yet controversial question. Here, we have obtained 1-μm resolution 3D datasets that cover the whole mouse barrel cortex by combining Nissl staining with micro-optical sectioning tomography to simultaneously visualize individual cells and blood vessels, including capillaries. Pinpointing layer IV of the posteromedial barrel subfield, direct 3D reconstruction and quantitative analysis showed that (1) penetrating vessels preferentially locate in the interbarrel septa/barrel wall (75.1%) rather than the barrel hollows, (2) the branches of 70% penetrating vessels only reach the neighboring but not always all the neighboring barrels and the other 30% extend beyond the neighboring barrels and may provide cross-barrel blood supply or drainage, (3) the branches of 59.6% penetrating vessels reach all the neighboring barrels, while the rest only reach part of them, and (4) the length density of microvessels in the interbarrel septa/barrel wall is lower than that in the barrel hollows with a ratio of 0.92. These results reveal that the penetrating vessels and microvessels exhibit a barrel-specific organization, whereas the branches of penetrating vessels do not, which suggests a much more complex vascular distribution pattern among cortical columns than previously thought.

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Section: Introductionmentioning

confidence: 99%

“…Thus, we combined the modified Nissl staining with MOST to investigate the structural organization of blood vessels among barrels in the mouse barrel cortex. Based on this approach, we recently developed a 3D brainwide cellular and vascular analysis protocol, 3D BrainCV (Wu et al 2014), which provides a solid technical base for our study.…”

Section: Introductionmentioning

confidence: 99%

Direct 3D Analyses Reveal Barrel-Specific Vascular Distribution and Cross-Barrel Branching in the Mouse Barrel Cortex

Guo

Chen

et al. 2014

Cereb. Cortex

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“…An accurate mechanical positioning stage (X-axis: ABL20020, Y-axis: ANT130, Z-axis: AVL125, Aerotech) was used to ensure the natural and accurate registration of all the images. 3D reconstruction of the images was implemented using previously reported methods [28][29][30][31][32]. Fig.…”

Section: Successive High-resolution Stage-scanning Block-face Imagingmentioning

confidence: 99%

Plastic embedding immunolabeled large-volume samples for three-dimensional high-resolution imaging

Gang¹,

Liu²,

Wang³

et al. 2017

Biomed. Opt. Express

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High-resolution three-dimensional biomolecule distribution information of large samples is essential to understanding their biological structure and function. Here, we proposed a method combining large sample resin embedding with iDISCO immunofluorescence staining to acquire the profile of biomolecules with high spatial resolution. We evaluated the compatibility of plastic embedding with an iDISCO staining technique and found that the fluorophores and the neuronal fine structures could be well preserved in the Lowicryl HM20 resin, and that numerous antibodies and fluorescent tracers worked well upon Lowicryl HM20 resin embedding. Further, using fluorescence MicroOptical sectioning tomography (fMOST) technology combined with ultra-thin slicing and imaging, we were able to image the immunolabeled large-volume tissues with high resolution. Miyawaki, "Scale: a chemical approach for fluorescence imaging and reconstruction of transparent mouse brain," Nat. Neurosci. 14(11), 1481-1488 (2011). 11. J. Sharpe, U. Ahlgren, P. Perry, B. Hill, A. Ross, J. Hecksher-Sørensen, R. Baldock, and D. Davidson, "Optical projection tomography as a tool for 3D microscopy and gene expression studies," Science 296 (

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“…Currently, the user can select between three tracing methods, APP2 14 , MOST 21 , and Neutube 22 The data collected here utilized Neutube as the base tracer.…”

Section: S2 Software and Code Availabilitymentioning

confidence: 99%

SmartScope2: Simultaneous Imaging and Reconstruction of Neuronal Morphology

Long

Zhou

Çetin

et al. 2017

Preprint

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Quantitative analysis of neuronal morphology is critical in cell type classification and for deciphering how structure gives rise to function in the brain. Most current approaches to imaging and tracing neuronal 3D morphology are data intensive. We introduce SmartScope2, the first open source, automated neuron reconstruction machine integrating online image analysis with automated multiphoton imaging. SmartScope2 takes advantage of a neuron's sparse morphology to improve imaging speed and reduce image data stored, transferred and analyzed. We show that SmartScope2 is able to produce the complex 3D morphology of human and mouse cortical neurons with six-fold reduction in image data requirements and three times the imaging speed compared to conventional methods.

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3D BrainCV: Simultaneous visualization and analysis of cells and capillaries in a whole mouse brain with one-micron voxel resolution

Cited by 112 publications

References 53 publications

Direct 3D Analyses Reveal Barrel-Specific Vascular Distribution and Cross-Barrel Branching in the Mouse Barrel Cortex

Direct 3D Analyses Reveal Barrel-Specific Vascular Distribution and Cross-Barrel Branching in the Mouse Barrel Cortex

Plastic embedding immunolabeled large-volume samples for three-dimensional high-resolution imaging

SmartScope2: Simultaneous Imaging and Reconstruction of Neuronal Morphology

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