Abstract
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.
Highlights
Background & SummaryA brain atlas provides a reference for the anatomical brain regions of a particular species of study
The emergence of digital brain atlasing provides a number of benefits over the traditional book form; we can generate arbitrary cutting planes through the data, no longer limited to a presentation in 2D along some predetermined anatomical plane, and a digital atlas is amenable to computational processing and transformation, forming a critical component of quantitative analysis pipelines on 3D brain data
In this data report we present a new 3D digital atlas of the non-human primate, common marmoset (Callithrix jacchus), a new world monkey that has become an increasingly popular research species within biology and neuroscience as a brain disease model Okano et al.1. (Throughout this article ‘marmoset’ shall refer to the common marmoset.) The atlas was constructed as part of Japan’s Brain/MINDS project which aims to map the marmoset brain connectome at micro, meso, and macro-scales, from both structural and functional perspectives—see Okano et al.1. for an overview
Summary
A brain atlas provides a reference for the anatomical brain regions of a particular species of study. The second important aspect of this data release is that the atlas is provided in the common NIfTI format, with separate volumes for the MRI, Nissl and region segmentation (parcellation), whereas the previous work was in a proprietary format that could only be loaded into custom software. This atlas can be loaded and integrated into neuroscience tools and pipelines, or directly manipulated via programming languages such as Python or Matlab. The data can be downloaded as individual files or together as one.zip file
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