Data descriptor

The Brain/MINDS 3D digital marmoset brain atlas

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

Research output: Contribution to journalArticle

8 Citations (Scopus)

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.

Original languageEnglish
Article number180009
JournalScientific data
Volume5
DOIs
Publication statusPublished - 2018 Feb 13
Externally publishedYes

Fingerprint

Atlas
Descriptors
Brain
brain
Histology
Magnetic resonance imaging
Segmentation
Region Segmentation
Visualization
Pipelines
Lighting
Neuroscience
Hemisphere
neurosciences
visualization
Illumination
artifact
Integrate
Simulation Study
simulation

ASJC Scopus subject areas

  • Statistics and Probability
  • Information Systems
  • Education
  • Computer Science Applications
  • Statistics, Probability and Uncertainty
  • Library and Information Sciences

Cite this

Woodward, A., Hashikawa, T., Maeda, M., Kaneko, T., Hikishima, K., Iriki, A., ... Yamaguchi, Y. (2018). Data descriptor: The Brain/MINDS 3D digital marmoset brain atlas. Scientific data, 5, [180009]. https://doi.org/10.1038/sdata.2018.9

Data descriptor : The Brain/MINDS 3D digital marmoset brain atlas. / Woodward, Alexander; Hashikawa, Tsutomu; Maeda, Masahide; Kaneko, Takaaki; Hikishima, Keigo; Iriki, Atsushi; Okano, Hideyuki; Yamaguchi, Yoko.

In: Scientific data, Vol. 5, 180009, 13.02.2018.

Research output: Contribution to journalArticle

Woodward, A, Hashikawa, T, Maeda, M, Kaneko, T, Hikishima, K, Iriki, A, Okano, H & Yamaguchi, Y 2018, 'Data descriptor: The Brain/MINDS 3D digital marmoset brain atlas', Scientific data, vol. 5, 180009. https://doi.org/10.1038/sdata.2018.9
Woodward A, Hashikawa T, Maeda M, Kaneko T, Hikishima K, Iriki A et al. Data descriptor: The Brain/MINDS 3D digital marmoset brain atlas. Scientific data. 2018 Feb 13;5. 180009. https://doi.org/10.1038/sdata.2018.9
Woodward, Alexander ; Hashikawa, Tsutomu ; Maeda, Masahide ; Kaneko, Takaaki ; Hikishima, Keigo ; Iriki, Atsushi ; Okano, Hideyuki ; Yamaguchi, Yoko. / Data descriptor : The Brain/MINDS 3D digital marmoset brain atlas. In: Scientific data. 2018 ; Vol. 5.
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