The NanoZoomer artificial intelligence connectomics pipeline for tracer injection studies of the marmoset brain

Woodward, Alexander; Gong, Rui; Abe, Hiroshi; Nakae, Ken; Hata, Junichi; Skibbe, Henrik; Yamaguchi, Yoko; Ishii, Shin; Yamamori, Tetsuo; Ichinohe, Noritaka

doi:10.1007/s00429-020-02073-y

Cited by 11 publications

(21 citation statements)

References 33 publications

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“…Vertices connecting the outer and inner surfaces (Fig. S1B, right side) were used to extend the midpoint flatmap (51) to include lamina information (Fig. S1B, left side) (50).…”

Section: Conversion Of Cortex Data Into a Flatmap Stack And Its Normalizationmentioning

confidence: 99%

Local and long-distance organization of prefrontal cortex circuits in the marmoset brain

Watakabe

Skibbe

Nakae

et al. 2021

Preprint

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The primate prefrontal cortex (PFC) has greatly expanded to evolve specialized architecture, but its roles in top-down brain control remain enigmatic. Based on connectomics mapping of the marmoset PFC, we characterized two contrasting features of corticocortical and corticostriatal projections. One is the "focalness" of projections, exemplified by multiple columnar axonal terminations in the cortical layers and the other is the "widespreadness" of weaker projections, whose patterns consisted of several common motifs representing the framework of PFC connectivity. We clarified the topographic rules of distribution for these features, which should constrain how PFC neurons can coordinate to control the target regions as populations. These features are observed only primitively in rodents and are considered critical in understanding the roles of the PFC in neuropsychiatric disorders.

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“…Vertices connecting the outer and inner surfaces (Fig. S1B, right side) were used to extend the midpoint flatmap (51) to include lamina information (Fig. S1B, left side) (50).…”

Section: Conversion Of Cortex Data Into a Flatmap Stack And Its Normalizationmentioning

confidence: 99%

Local and long-distance organization of prefrontal cortex circuits in the marmoset brain

Watakabe

Skibbe

Nakae

et al. 2021

Preprint

Self Cite

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“…Though this method is readily available to most labs, it is difficult to scale up. High-speed slide scanners such as the Nanozoomer (Hamamatsu) can make this method more streamlined and have even been used to achieve brain mapping in many different species including the marmoset (Zheng et al, 2014;Lin et al, 2019;Woodward et al, 2020). However, histological sectioning and mounting on microscopic slides can also present a challenge as these procedures introduce unexpected volume distortion, making 3D reconstruction challenging.…”

Section: Imagingmentioning

confidence: 99%

“…Many previous works have focused on the mouse brain due to the variety of available transgenic animals, the compact size of the mouse brain, and the availability of high-quality 3D atlases. However, similar mapping approaches are also possible in other species such as the non-human primate (NHP) as well as human brains (Woodward et al, 2020;Rapan et al, 2021;Shapson-Coe et al, 2021).…”

Section: Introductionmentioning

confidence: 99%

Seeing the Forest and Its Trees Together: Implementing 3D Light Microscopy Pipelines for Cell Type Mapping in the Mouse Brain

Newmaster

Kronman

et al. 2022

Front. Neuroanat.

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The brain is composed of diverse neuronal and non-neuronal cell types with complex regional connectivity patterns that create the anatomical infrastructure underlying cognition. Remarkable advances in neuroscience techniques enable labeling and imaging of these individual cell types and their interactions throughout intact mammalian brains at a cellular resolution allowing neuroscientists to examine microscopic details in macroscopic brain circuits. Nevertheless, implementing these tools is fraught with many technical and analytical challenges with a need for high-level data analysis. Here we review key technical considerations for implementing a brain mapping pipeline using the mouse brain as a primary model system. Specifically, we provide practical details for choosing methods including cell type specific labeling, sample preparation (e.g., tissue clearing), microscopy modalities, image processing, and data analysis (e.g., image registration to standard atlases). We also highlight the need to develop better 3D atlases with standardized anatomical labels and nomenclature across species and developmental time points to extend the mapping to other species including humans and to facilitate data sharing, confederation, and integrative analysis. In summary, this review provides key elements and currently available resources to consider while developing and implementing high-resolution mapping methods.

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“…This new Brain Structure and Function special issue entitled 'Structural connectivity of the cerebral cortex' aims at providing the reader with a comprehensive understanding of the organisation of the brain's structural connectivity, based on different methods (Lanciego and Wouterlood 2020;Blazquez Freches et al 2020;Huang et al 2020;Oishi et al 2020;Kaneko et al 2020;Woodward et al 2020). The special issue also clarifies the multidimensional concept of structural connectivity by collecting articles that investigate how its variations at different scales affect brain functions (Rockland 2020;Gamberini et al 2020;Andre et al 2020;Ioannucci et al 2020;Rooks et al 2020).…”

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confidence: 99%

“…Lanciego and Wouterlood (2020) (this issue) reviewed a wide range of neuroanatomical tracttracing methods, from classical to modern, and examined their advantages and disadvantages. Woodward et al (2020) (this issue) also proposed a new tracer processing pipeline in marmoset brains. They succeeded at quantifying anterograde tracer signals by using the latest artificial intelligence algorithms.…”

mentioning

confidence: 99%

Perspectives given by structural connectivity bridge the gap between structure and function

Takemura

Schotten

2020

Brain Struct Funct

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The NanoZoomer artificial intelligence connectomics pipeline for tracer injection studies of the marmoset brain

Cited by 11 publications

References 33 publications

Local and long-distance organization of prefrontal cortex circuits in the marmoset brain

Local and long-distance organization of prefrontal cortex circuits in the marmoset brain

Seeing the Forest and Its Trees Together: Implementing 3D Light Microscopy Pipelines for Cell Type Mapping in the Mouse Brain

Perspectives given by structural connectivity bridge the gap between structure and function

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