High-Speed and Scalable Whole-Brain Imaging in Rodents and Primates

Seiriki, Kaoru; Kasai, Atsushi; Hashimoto, Takeshi; Schulze, W; Niu, Misaki; Yamaguchi, Shun; Nakazawa, Takahiro; Inoue, Ken; Uezono, Shiori; Takada, Masahiko; Naka, Yuichiro; Igarashi, Hisato; Tanuma, Masato; Waschek, James A.; Ago, Yukio; Tanaka, Kenji F.; Hayata‐Takano, Atsuko; Nagayasu, Kazuki; Shintani, Norihito; Hashimoto, Ryota; Kunii, Yasuto; Hino, Mizuki; Matsumoto, Junya; Yabe, Hirooki; Nagai, Takeharu; Fujita, Katsumasa; Matsuda, Takehisa; Takuma, Kazuhiro; Baba, Akemichi; Hashimoto, Hitoshi

doi:10.1016/j.neuron.2017.05.017

Cited by 115 publications

(109 citation statements)

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“…Several alternative microscopy methods that enable automated collection of large volume datasets at high-resolution have been developed by integrating whole-mount fluorescence imaging and mechanical sectioning of the imaged top portion of the tissue, starting with serial two-photon tomography (STPT) that integrates two-photon microscopy and vibratome-based sectioning (Economo et al, 2016; Ragan et al, 2012), two-photon fluorescence micro-optical sectioning tomography system (2p-fMOST) integrating two-photon microscopy and microtome-based sectioning (Zheng et al, 2013), brain-wide precision imaging system (BPS) integrating wide-field fast structured illumination microscopy and microtome-based sectioning (Gong et al, 2016), block-face serial microscopy tomography (FAST) integrating Nipkow spinning disk-based confocal microscopy and vibratome sectioning (Seiriki et al, 2017), and most recently oblique light-sheet tomography (OLST) integrating light-sheet microscopy and vibratome-based sectioning developed by the Osten group (unpublished). These methods can achieve micron or even submicron voxel resolution throughout the whole mouse brain, enabling automated and standardized collection of serial section datasets with the spatial resolution needed for detailed anatomical studies.…”

Section: Anatomy and Connectivitymentioning

confidence: 99%

The BRAIN Initiative Cell Census Consortium: Lessons Learned toward Generating a Comprehensive Brain Cell Atlas

Ecker

Geschwind

Kriegstein

et al. 2017

Neuron

245

198

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A comprehensive characterization of neuronal cell types, their distributions and patterns of connectivity is critical for understanding the properties of neural circuits and how they generate behaviors. Here we review the experiences of the BRAIN Initiative Cell Census Consortium – ten pilot projects funded by the U.S. BRAIN Initiative – in developing, validating and scaling up emerging genomic and anatomical mapping technologies for creating a complete inventory of neuronal cell types and their connections in multiple species and during development. These projects lay the foundation for a larger and longer-term effort to generate whole-brain cell atlases in species including mice and humans.

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Section: Anatomy and Connectivitymentioning

confidence: 99%

The BRAIN Initiative Cell Census Consortium: Lessons Learned toward Generating a Comprehensive Brain Cell Atlas

Ecker

Geschwind

Kriegstein

et al. 2017

Neuron

245

198

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“…However, the low throughput of this approach makes whole-brain data reconstruction and analysis a tedious task. Several techniques with automated serial sectioning and imaging methods were developed to overcome this problem 9-15 . Recent advances along this line was able to push the imaging speed to ~3 days per mouse brain at synaptic resolution 14 , or ~2.4 hours per mouse brain but at a reduced resolution 15 .…”

Section: Figurementioning

confidence: 99%

“…Several techniques with automated serial sectioning and imaging methods were developed to overcome this problem 9-15 . Recent advances along this line was able to push the imaging speed to ~3 days per mouse brain at synaptic resolution 14 , or ~2.4 hours per mouse brain but at a reduced resolution 15 . Still, it is highly desirable to be able to obtain high resolution images at very high speed for high volume tasks such as whole brain mapping of many animals or of large primates.…”

Section: Figurementioning

confidence: 99%

Scalable volumetric imaging for ultrahigh-speed brain mapping at synaptic resolution

Wang

Zhu

Ding

et al. 2017

Preprint

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2We describe a new light-sheet microscopy method for fast, large-scale and imaging methods were developed to overcome this problem [9][10][11][12][13][14][15] . Recent 50 advances along this line was able to push the imaging speed to ~3 days per 51 . CC-BY-NC-ND 4.0 International license not peer-reviewed) is the author/funder. It is made available under aThe copyright holder for this preprint (which was . http://dx.doi.org/10.1101/240770 doi: bioRxiv preprint first posted online Dec. 29, 2017; 3 mouse brain at synaptic resolution 14 , or ~2.4 hours per mouse brain but at a 52 reduced resolution 15 . Still, it is highly desirable to be able to obtain high 53 resolution images at very high speed for high volume tasks such as whole 54 brain mapping of many animals or of large primates. 56The past decade has also seen various tissue clearing techniques that 57 greatly improve the transparency of brain samples 16 The basic configuration of our system consists of an illumination objective 91 through which a scanning light-beam enters a thick slice sample at a 45-92 degree angle to the sample surface, and an imaging objective positioned 93 perpendicular to the illumination plane (Fig. 1a,b (Supplementary Fig. 1). The geometry and working distance of 98 the objectives constrain the imageable sample thickness to ~300 µm (Fig. 1b). 99The light path is configured such that the effective imaging area on the object 100 plane (corresponding to half of the camera sensor, ~1000 X 2000 pixels) 101covers an oblique section of ~420 µm X 1000 µm using a 20X imaging 102 objective with system magnification reduced to ~13X (Fig. 1c). 104To achieve fast volumetric imaging over a large range, we configured the (Fig. 1c, d). This approach has also been used in the we eliminate virtually all motion blur and achieve high image quality 118 indistinguishable from stationary imaging, with dendritic spines of cortical 119 neurons clearly visible ( Fig. 1e-g). In principle, motion blur can also be 120 reduced using strobe light illumination in a regular light-sheet configuration. 121This however requires much higher light power to achieve similar illumination. 122The synchronized beam scan is thus also optimized in light efficiency. Supplementary Fig. 2a). 134We also developed a system to automatically detect the edges of all mounted 135 brain slices, so that the imaging system can directly move to the target based color VISoR imaging and cell counting in different brain areas (Fig. 3). In the 174 paraventricular nucleus (PVN) of hypothalamus where CRH neurons were 175 observed to form a dense cluster (Fig. 3a,b), more than half of these neurons (Fig. 3b,c, Supplementary Video 6). This is consistent with the role of CRH 180 neurons of the PVN in stress response 28 . Interestingly, in the medial 181 amygdala (MeA) where CRH neurons were more dispersed (Fig. 3d), the . 29, 2017; 9 stimulated animal, with 104 CRH neurons being activated out of 1018 total 184 CRH neurons and 569 total activated neurons (Fig. 3d,e, Supplementary 1...

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“…Using this method, it takes nearly 1 week to obtain the image of a whole mouse brain at a voxel size of 0.3 × 0.3 × 1 μm. Very lately, block‐face serial microscopy tomography (FAST), consisting of a spinning disk‐based confocal microscope with a microslicer, was developed . It can obtain the image of a mouse brain within 2.4 hours at a voxel size of 0.7 × 0.7 × 5 μm.…”

Section: Introductionmentioning

confidence: 99%

High‐throughput light sheet tomography platform for automated fast imaging of whole mouse brain

Yang

Zhang

Huang

et al. 2018

Journal of Biophotonics

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Acquiring information of the neural structures in the whole-brain level is vital for systematically exploring mechanisms and principles of brain function and dysfunction. Most methods for whole brain imaging, while capable of capturing the complete morphology of neurons, usually involve complex sample preparation and several days of image acquisition. The whole process including optical clearing or resin embedding is time consuming for a quick survey of the distribution of specific neural circuits in the whole brain. Here, we develop a high-throughput light-sheet tomography platform (HLTP), which requires minimum sample preparation. This method does not require optical clearing for block face light sheet imaging. After fixation using paraformaldehyde, an aligned 3 dimensional image dataset of a whole mouse brain can be obtained within 5 hours at a voxel size of 1.30 × 1.30 × 0.92 μm. HLTP could be a very efficient tool for quick exploration and visualization of brain-wide distribution of specific neurons or neural circuits.

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High-Speed and Scalable Whole-Brain Imaging in Rodents and Primates

Cited by 115 publications

References 50 publications

The BRAIN Initiative Cell Census Consortium: Lessons Learned toward Generating a Comprehensive Brain Cell Atlas

The BRAIN Initiative Cell Census Consortium: Lessons Learned toward Generating a Comprehensive Brain Cell Atlas

Scalable volumetric imaging for ultrahigh-speed brain mapping at synaptic resolution

High‐throughput light sheet tomography platform for automated fast imaging of whole mouse brain

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