The Brain/MINDS 3D digital marmoset brain atlas

Woodward, Alexander; Hashikawa, Tsutomu; Maeda, Masami; Kaneko, Takaaki; Hikishima, Keigo; Iriki, Atsushi; Okano, Hideyuki; Yamaguchi, Yoko

doi:10.1038/sdata.2018.9

Cited by 84 publications

(91 citation statements)

References 18 publications

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“…Furthermore, eFLASH can facilitate studies of animal models with limited access to genetic labeling methodologies. The Common Marmoset is an emerging primate model for social behaviors with many experimental advantages 51,52 , and thus much effort has been undertaken to construct marmoset brain atlases in diverse modalities [53][54][55] . Unfortunately, numerous hurdles remain in translating existing genetic labeling approaches for rodents to marmosets.…”

Section: Discussionmentioning

confidence: 99%

Ultrafast immunostaining of organ-scale tissues for scalable proteomic phenotyping

Yun

Park

Cho

et al. 2019

Preprint

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Studying the function and dysfunction of complex biological systems necessitates comprehensive understanding of individual cells. Advancements in three-dimensional (3D) tissue processing and imaging modalities have enabled rapid visualization and phenotyping of cells in their spatial context. However, system-wide interrogation of individual cells within large intact tissue remains challenging, low throughput, and error-prone owing to the lack of robust labeling technologies.Here we introduce a rapid, versatile, and scalable method, eFLASH, that enables complete and uniform labeling of organ-scale tissue within one day. eFLASH dynamically modulates chemical transport and reaction kinetics to establish system-wide uniform labeling conditions throughout the day-long labeling period. This unique approach enables the same protocol to be compatible with a wide range of tissue types and probes, enabling combinatorial molecular phenotyping across different organs and species. We applied eFLASH to generate quantitative maps of various cell types in mouse brains. We also demonstrated multidimensional cell profiling in a marmoset brain block. We envision that eFLASH will spur holistic phenotyping of emerging animal models and disease models to help assess their functions and dysfunctions.

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Section: Discussionmentioning

confidence: 99%

Ultrafast immunostaining of organ-scale tissues for scalable proteomic phenotyping

Yun

Park

Cho

et al. 2019

Preprint

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“…The Brain/MINDS atlas is a multi-modal atlas with individual MRI T2WI and co-registered Nissl histology data Woodward et al (2018a). Anatomical regions were delineated in original high-resolution Nissl image data which was then computationally mapped into the 3D shape of the MRI T2WI.…”

Section: Common Brain Space Using a Population Average Mri T2wi And Amentioning

confidence: 99%

“…We quantitatively evaluated the registration of fluorescence images since they were the most challenging image type to register, often having weakly visible brain structures in the auto-fluorescence signal to drive image registration. The set of landmarks were based on the definitions in Woodward et al (2018a). The landmarks and registration error are listed in Table. 2.…”

Section: Flat Map Warpmentioning

confidence: 99%

The NanoZoomer Connectomics Pipeline for Tracer Injection Studies of the Marmoset Brain

Woodward

Gong

Abe

et al. 2019

Preprint

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We describe our connectomics pipeline for processing tracer injection data for the brain of the common marmoset (Callithrix jacchus). Brain sections were imaged using a batch slide scanner (NanoZoomer 2.0-HT) and we used artificial intelligence to precisely segment the anterograde tracer signal from the background in the fluorescence images. The shape of each brain was reconstructed by reference to a block-face and all data was mapped into a common 3D brain space with atlas and 2D cortical flat map. To overcome the effect of using a single template atlas to specify cortical boundaries, each brain was cytoarchitectonically annotated and used for making an individual 3D atlas. Registration between the individual and common brain cortical boundaries in the flat map space was done to absorb the variation of each brain and precisely map all tracer injection data into one cortical brain space. We describe the methodology of our pipeline and analyze tracer segmentation and brain registration accuracy. Results show our pipeline can successfully process and normalize tracer injection experiments into a common space, making it suitable for large-scale connectomics studies with a focus on the cerebral cortex.

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“…Toarmino et al, 2017;Atapour et al, 2019;Ghahremani et al, 2019;Hori et al, 2020;Liu et al, 2019;Majka et al, 2019Majka et al, , 2020. However, most atlases are based on single individuals, with the brains processed using histological techniques (Majka et al, 2016;Woodward et al, 2018) or imaged with high field magnetic resonance imaging (MRI; Liu et al, 2018). All of these templates have adopted the scheme of parcellation first proposed by Paxinos et al (2012).…”

Section: Introductionmentioning

confidence: 99%

Histology-based average template of the marmoset cortex with probabilistic localization of cytoarchitectural areas

Majka

Bednarek

Chan

et al. 2020

Preprint

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Highlights• A 3D template of the marmoset cortex representing the average of 20 individuals.• The template is based on Nissl stain and preserves information about cortical layers.• Probabilistic mapping of areas, cortical thickness, and layer intensity profiles.• Includes spatial transformations to other marmoset brain atlases. AbbreviationsFor a list of areas and their abbreviations see Table S2. AbstractThe rapid adoption of marmosets in neuroscience has created a demand for three dimensional (3D) atlases of the brain of this species to facilitate data integration in a common reference space. We report on a new open access template of the marmoset cortex (the Nencki-Monash, or NM template), representing a morphological average of 20 brains of young adult individuals, obtained by 3D reconstructions generated from Nissl-stained serial sections. The method used to generate the tem plate takes into account morphological features of the individual brains, as well as the borders of clearly defined cytoarchitectural areas. This has resulted in a resource which allows direct estimates of the most likely coordinates of each cortical area, as well as quantification of the margins of error involved in assigning voxels to areas, and preserves quantitative information about the laminar structure of the cortex. We provide spatial transformations between the NM and other available marmoset brain templates, thus enabling integration with magnetic resonance imaging (MRI) and tracer-based connectivity data. The NM template combines some of the main advantages of histology-based atlases (e.g. information about the cytoarchitectural structure) with features more commonly associated with MRI-based templates (isotropic nature of the dataset, and probabilistic analyses). The underlying workflow may be found useful in the future development of brain atlases that incorporate information about the variability of areas in species for which it may be impractical to ensure homogeneity of the sample in terms of age, sex and genetic background.

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The Brain/MINDS 3D digital marmoset brain atlas

Cited by 84 publications

References 18 publications

Ultrafast immunostaining of organ-scale tissues for scalable proteomic phenotyping

Ultrafast immunostaining of organ-scale tissues for scalable proteomic phenotyping

The NanoZoomer Connectomics Pipeline for Tracer Injection Studies of the Marmoset Brain

Histology-based average template of the marmoset cortex with probabilistic localization of cytoarchitectural areas

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