Current models of the marmoset brain

Hashikawa, Tsutomu; Nakatomi, Reiko; Iriki, Atsushi

doi:10.1016/j.neures.2015.01.009

Cited by 64 publications

(65 citation statements)

References 29 publications

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“…The primary modality of the template is a Nissl-stained volume, which can be virtually cross-sectioned in any plane. The main noticeable difference from the previously available histology-based templates (Hashikawa et al, 2015;Majka et al, 2016;Woodward et al, 2018) is its isotropic nature. The averaging resulted in suppression of the artifacts and noise inherent to the histological processing of the individual hemispheres used to generate the template, in particular those related to the separation between sections (Fig.…”

Section: Discussionmentioning

confidence: 97%

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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Section: Discussionmentioning

confidence: 97%

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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“…Hikishima et al, 2011 ) while other attempt to combine imaging techniques with traditional histology (e.g. Hashikawa et al, 2015 ). Using a population-based brain atlas as a template may increase the normalization accuracy in the present technique, and make further quantitative analyses, particularly with respect to the margin of error of the procedure, more reliable.…”

Section: Limiting Factors and Proposed Future Developmentsmentioning

confidence: 98%

Towards a comprehensive atlas of cortical connections in a primate brain: Mapping tracer injection studies of the common marmoset into a reference digital template

Majka

Chaplin

et al. 2016

J of Comparative Neurology

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The marmoset is an emerging animal model for large-scale attempts to understand primate brain connectivity, but achieving this aim requires the development and validation of procedures for normalization and integration of results from many neuroanatomical experiments. Here we describe a computational pipeline for co-registration of retrograde tracing data on connections of cortical areas into a 3-dimensional marmoset brain template, generated from Nissl-stained sections. The procedure results in a series of spatial transformations that are applied to the coordinates of labeled neurons in the different cases, bringing them into common stereotaxic space. We have applied this procedure to 17 injections, placed in the frontal lobe of 9 marmosets as part of earlier studies. Visualizations of cortical patterns of connections revealed by these injections are supplied as supplementary materials. Comparison between the results of the automated and human-based processing of these cases reveals that the centers of injection sites can be reconstructed, on average, to within 0.6 mm of coordinates estimated by an experienced neuroanatomist. Moreover, cell counts obtained in different areas by the automated approach are highly correlated (r = 0.83) with those obtained by an expert, who examined in detail histological sections for each individual. The present procedure enables comparison and visualization of large data sets, which in turn opens the way for integration and analysis of results from many animals. Its versatility, including applicability to archival materials, may reduce the number of additional experiments required to produce the first detailed cortical connectome of a primate brain.

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“…A computational routine was established to perform this process automatically for all brain sections (Lee, Tward, et al, 2018). Briefly, in 6 animals where ex vivo pre-sectioning MRI of the brains were available, the Nissl stack was reconstructed by a series of jointly optimized rigid motions using the MRI as a guide, and the resulting reconstructed stack was diffeomorphically registered to the marmoset brain atlas (Hashikawa et al, 2015). In the 2 animals (M820, M822) where MRI guidance was unavailable, reconstruction was performed using the atlas as a shape prior and accounting for intrinsic shape differences (Lee, Lin, et al, 2018).…”

Section: Cross-modality Registrationmentioning

confidence: 99%

Continuity between koniocellular layers of dorsal lateral geniculate and inferior pulvinar nuclei in common marmosets

Huo

Zeater

Lin

et al. 2018

Preprint

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The koniocellular (K) layers of the dorsal lateral geniculate nucleus (LGN) and the calbindinrich subdivisions of the inferior pulvinar nucleus are considered part of a thalamic matrix system which projects diffusely to superficial cortical layers. Activity in the matrix system is proposed to coordinate oscillatory activity in thalamocortical loops. Here we studied connections of LGN K layers and IPul in marmosets following injections of retrograde tracer, Fast Blue, in V1 and V2. We adopted a high-throughput neuro-histology pipeline, which enabled simultaneous brain region identification based on cytoarchitecture and fluorescent tracer localization. A computational routine was established to automatically cross-register fluorescent neurons to individual subdivisions of LGN and IPul. We found that both V1 and V2 receive inputs from K layers and IPul, whereas dominant outputs of magnocellular and All rights reserved. No reuse allowed without permission.

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Current models of the marmoset brain

Cited by 64 publications

References 29 publications

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

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

Towards a comprehensive atlas of cortical connections in a primate brain: Mapping tracer injection studies of the common marmoset into a reference digital template

Continuity between koniocellular layers of dorsal lateral geniculate and inferior pulvinar nuclei in common marmosets

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