The Brain/MINDS 3D digital marmoset brain atlas

We present a new 3D digital brain atlas of the non-human primate, common marmoset monkey (Callithrix jacchus), with MRI and coregistered Nissl histology data. To the best of our knowledge this is the first comprehensive digital 3D brain atlas of the common marmoset having normalized multi-modal data...

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Bibliographic Details
Published inScientific data Vol. 5; no. 1; p. 180009
Main Authors Woodward, Alexander, Hashikawa, Tsutomu, Maeda, Masahide, Kaneko, Takaaki, Hikishima, Keigo, Iriki, Atsushi, Okano, Hideyuki, Yamaguchi, Yoko
Format Journal Article
LanguageEnglish
Published England Nature Publishing Group 13.02.2018
Subjects
Animals
Atlases as Topic
Brain - cytology
Brain - diagnostic imaging
Callithrix
Callithrix jacchus
Connectome
Cortex
Data Descriptor
Histology
Image processing
Magnetic Resonance Imaging
Nervous system
NMR
Nuclear magnetic resonance
Segmentation
Substantia alba
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Summary:We present a new 3D digital brain atlas of the non-human primate, common marmoset monkey (Callithrix jacchus), with MRI and coregistered Nissl histology data. To the best of our knowledge this is the first comprehensive digital 3D brain atlas of the common marmoset having normalized multi-modal data, cortical and sub-cortical segmentation, and in a common file format (NIfTI). The atlas can be registered to new data, is useful for connectomics, functional studies, simulation and as a reference. The atlas was based on previously published work but we provide several critical improvements to make this release valuable for researchers. Nissl histology images were processed to remove illumination and shape artifacts and then normalized to the MRI data. Brain region segmentation is provided for both hemispheres. The data is in the NIfTI format making it easy to integrate into neuroscience pipelines, whereas the previous atlas was in an inaccessible file format. We also provide cortical, mid-cortical and white matter boundary segmentations useful for visualization and analysis.
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M.M. extracted the brain region boundaries from the TIF files along with providing files for the region and color naming information. T.K. generated the csf/gray, gray/white and mid-cortical segmentations. H.O. and Y.Y. organized and facilitated the development of this brain atlas. A.W. performed all of the data-processing steps described in the text except for the manual editing of the mid-cortical segmentations which were completed collaboratively with T.K. T.H. and A.I created the Nissl stained images and drew the original brain region boundaries in the TIF files. K.H. created the MRI T2 data.
ISSN:2052-4463
2052-4463
DOI:10.1038/sdata.2018.9