Marmoset Reference Brain

Multi-modal Nissl & MRI 3D brain atlas

The current Brain/MINDS Marmoset Reference Brain is a multi-modal Nissl & MRI 3D brain atlas where the Nissl histology data has been normalized to the MRI shape. The brain region annotation is now version 6.2, revised from the Hashikawa et. al (2015). The atlas contains over 200 cortical and sub-cortical annotations per hemisphere and improves upon the work of Hashikawa et al. (2015). State-of-the-art registration algorithms were used to register the different data modalities to one another and to remove noise and artifacts. The original Nissl and parcellation data (for one hemisphere only) have been warped to match the ex-vivo MRI data, then mirrored across the sagittal plane. The brain atlas can be used for tasks such as brain region identification and data analysis, such as connectomics.

Contributors: Alexander Woodward, Tsutomu Hashikawa, Masahide Maeda and Yoko Yamaguchi

Ver. 1.0 : Released on November 22, 2017 by adding the physical coordinate in RAS coordinate along AC-PC line together with minor revision of ZAViewer;
Ver. 0.9: Released on March 21, 2017;

Neuroinformatics Japan Center (NIJC), RIKEN BSI


  • Download Page

    Download the marmoset brain reference atlas dataset. NEW!

  • By Zooming Atlas Viewer

    Reference brain in the zooming atlas viewer (ZAViewer).

  • Viewer Operation Quick Guide

    How to use the zooming atlas viewer.

  • Infographic

    Summary of reference brain construction and surface rendering.