High-definition imaging using line-illumination modulation microscopy

Zhong, Qiuyuan; Li, Anan; Jin, Rui; De-jie, Zhang; Li, Xiangning; Jia, Xueyan; Ding, Zhangheng; Luo, Pan; Zhou, Can; Jiang, Chenyu; Feng, Zuren; Zhang, Zhihong; Gong, Hui; Yuan, Jing; Luo, Qi

doi:10.1038/s41592-021-01074-x

Cited by 84 publications

(53 citation statements)

References 24 publications

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“…Other recent technological advances provide the resolution and throughput to analyse whole-brain neuronal morphology and comprehensive projection mapping 18,19 . Imaging-based single-cell transcriptomics and its combination with functional imaging, and integration of electrophysiology and single-cell sequencing, enable mapping of the spatial organization and key phenotypic properties of molecularly defined cell types [20][21][22][23][24] .…”

Section: Articlementioning

confidence: 99%

A multimodal cell census and atlas of the mammalian primary motor cortex

Callaway¹,

Dong²,

Ecker³

et al. 2021

Nature

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330

128

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Here we report the generation of a multimodal cell census and atlas of the mammalian primary motor cortex as the initial product of the BRAIN Initiative Cell Census Network (BICCN). This was achieved by coordinated large-scale analyses of single-cell transcriptomes, chromatin accessibility, DNA methylomes, spatially resolved single-cell transcriptomes, morphological and electrophysiological properties and cellular resolution input–output mapping, integrated through cross-modal computational analysis. Our results advance the collective knowledge and understanding of brain cell-type organization1–5. First, our study reveals a unified molecular genetic landscape of cortical cell types that integrates their transcriptome, open chromatin and DNA methylation maps. Second, cross-species analysis achieves a consensus taxonomy of transcriptomic types and their hierarchical organization that is conserved from mouse to marmoset and human. Third, in situ single-cell transcriptomics provides a spatially resolved cell-type atlas of the motor cortex. Fourth, cross-modal analysis provides compelling evidence for the transcriptomic, epigenomic and gene regulatory basis of neuronal phenotypes such as their physiological and anatomical properties, demonstrating the biological validity and genomic underpinning of neuron types. We further present an extensive genetic toolset for targeting glutamatergic neuron types towards linking their molecular and developmental identity to their circuit function. Together, our results establish a unifying and mechanistic framework of neuronal cell-type organization that integrates multi-layered molecular genetic and spatial information with multi-faceted phenotypic properties.

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Section: Articlementioning

confidence: 99%

A multimodal cell census and atlas of the mammalian primary motor cortex

Callaway¹,

Dong²,

Ecker³

et al. 2021

Nature

Self Cite

330

128

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“…Different from conventional HiLo microscopy, the two images required to reconstruct an optical-sectioning image, namely uniform illumination image and structured illumination image (denoted as

and

, respectively, where

is 2D spatial coordinate), were obtained in one-time imaging. We took the Gaussian intensity distribution of illumination line as a naturally structured modulation, as demonstrated in wide-field, single-photon fluorescence microscopy [ 30 , 31 , 32 ]. As shown in Figure 2 , we achieved uniform illumination image and structured illumination image by sampling the camera recorded images in different ways.…”

Section: Methodsmentioning

confidence: 99%

“…Moreover, the effects of distortion of the illumination patterns are not so severe in HiLo method, as it does not need well-defined patterns to modulate in-focus information [ 30 ]. However, the temporal resolutions in these techniques are scarified, as more than two images are generally required to reconstruct an optical-sectioning image [ 30 , 31 , 32 ].…”

Section: Introductionmentioning

confidence: 99%

HiLo Based Line Scanning Temporal Focusing Microscopy for High-Speed, Deep Tissue Imaging

et al. 2021

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High-speed, optical-sectioning imaging is highly desired in biomedical studies, as most bio-structures and bio-dynamics are in three-dimensions. Compared to point-scanning techniques, line scanning temporal focusing microscopy (LSTFM) is a promising method that can achieve high temporal resolution while maintaining a deep penetration depth. However, the contrast and axial confinement would still be deteriorated in scattering tissue imaging. Here, we propose a HiLo-based LSTFM, utilizing structured illumination to inhibit the fluorescence background and, thus, enhance the image contrast and axial confinement in deep imaging. We demonstrate the superiority of our method by performing volumetric imaging of neurons and dynamical imaging of microglia in mouse brains in vivo.

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“…Significant efforts have been made in the past decade to map large numbers of neurons to better understand the network in the whole brain ( Economo et al, 2016 ; Ni et al, 2021 ; Zhong et al, 2021 ). Recently, there has been an increasing interest in optimizing methods for volume imaging of molecularly labeled structures in large, cleared tissue samples ( Pan et al, 2016 ; Park et al, 2018 ; Cai et al, 2019 ; Qi et al, 2019 ).…”

Section: Introductionmentioning

confidence: 99%

High-Throughput Strategy for Profiling Sequential Section With Multiplex Staining of Mouse Brain

Chen

Liu

et al. 2021

Front. Neuroanat.

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The brain modulates specific functions in its various regions. Understanding the organization of different cells in the whole brain is crucial for investigating brain functions. Previous studies have focused on several regions and have had difficulty analyzing serial tissue samples. In this study, we introduced a pipeline to acquire anatomical and histological information quickly and efficiently from serial sections. First, we developed a serial brain-slice-staining method to stain serial sections and obtained more than 98.5% of slices with high integrity. Subsequently, using the self-developed analysis software, we registered and quantified the signals of imaged sections to the Allen Mouse Brain Common Coordinate Framework, which is compatible with multimodal images and slant section planes. Finally, we validated the pipeline with immunostaining by analyzing the activity variance in the whole brain during acute stress in aging and young mice. By removing the problems resulting from repeated manual operations, this pipeline is widely applicable to serial brain slices from multiple samples in a rapid and convenient manner, which benefits to facilitate research in life sciences.

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High-definition imaging using line-illumination modulation microscopy

Cited by 84 publications

References 24 publications

A multimodal cell census and atlas of the mammalian primary motor cortex

A multimodal cell census and atlas of the mammalian primary motor cortex

HiLo Based Line Scanning Temporal Focusing Microscopy for High-Speed, Deep Tissue Imaging

High-Throughput Strategy for Profiling Sequential Section With Multiplex Staining of Mouse Brain

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