Connectome Analysis Unit

RIKEN Center for Brain Science

Demo of our 3D Brain/Atlas Viewer

About US

Our research focuses on mapping and analyzing the neuronal connectivity (connectome) of the brain. The challenge is how to automatically process and understand diverse experimental data of ever-increasing size and complexity. We are therefore developing  digital brain atlases, connectome based brain simulation, and a comprehensive neuroimaging database platform. As a member of the Brain/MINDS project (, our group applies these solutions to study the brain of the common marmoset monkey. Analyzing connectomes across species and healthy vs. diseased brains will help to create new disease treatments and cures and lead the way to new artificial intelligence and autonomous agents.

We are currently recruiting Research Scientist and Technical Staff.

Research Topics

Segmentation using AI

We use U-net to segment tracer signals from NanoZoomer images.

Machine Learning

Brain Atlasing

Atlasing of Marmoset brain regions.



Marmoset brain simulation using TVB (The Virtual Brain).


Image Processing Pipeline

Processing pipeline for Brain/MINDS experiment image data.

Data Processing Pipeline


Database to manage and analysis Brain/MINDS experiment data


Unit Leader

Alexander woodward

Unit Leader

Unit Members

Rui Gong

Research Scientist

Itsuko Ishii

Technical Staff

Masahide Maeda

Technical Staff

Takuto Okuno

Research Scientist

Frederic Papazian

Technical Staff



  • Woodward, A. Brain Atlasing and Databasing in the Brain/MINDS Project. Neuroinformatics 2019.
  • Woodward, A. Computational techniques for 3D brain atlas construction of the Common Marmoset. 5th Eu-Japan Workshop on Neurorobotics/Cognitive Systems.

Journal Publications

  • Woodward, A., Hashikawa, T., Maeda, M., Kaneko, T., Hikishima, K., Iriki, A., et al. (2018). The Brain/MINDS 3D Digital Marmoset Brain Atlas. Scientific Data, 5, 180009.
  • Woodward, A., Gong, R., Abe, H., Nakae, K., Hata, J., Skibbe, H., Yamaguchi, Y., Ishii, S., Okano, H., Yamamori, T., Ichinohe, N.
    The NanoZoomer Connectomics Pipeline for Tracer Injection Studies of the Marmoset Brain. bioRxiv 748376;


  • Woodward, A, Gong, R., Abe, H., Skibbe, H., Nakae, K., Gutierrez, C. E., Tsukada, H., Maeda, M., Ichinohe, N, Yamaguchi, Y, (2019). Large-Scale Automatic Tracer Segmentation in Brain Section Fluorescence Images Using Artificial Intelligence. NEURO2019.
  • Woodward, A, Gong R, Yamaguchi, Y, (2018). Marmoset Brain Atlasing Techniques in the Brain/MINDS Project, Japan Society for Marmoset Research Meeting 2019.
  • Gong, R, Woodward, A, Nakae, K, Ichinohe, N, Watakabe, A, Yamamori, T, Yamaguchi, Y, (2018). The Brain/MINDS Cortical Flap Map for Visualize Neuroimaging Data. AINI2018.