Centers & Labs

RIKEN Center for Advanced Photonics

Image Processing Research Team

Team Leader: Hideo Yokota (D.Eng.)
Hideo  Yokota(D.Eng.)

Our goal is to develop original RIKEN data processing technology and multidimensional measurement technology in order to contribute to understanding biological phenomena. We are especially contributing to the fields of mathematical biology, bio-medical simulations as well as medical diagnostic and treatment technology by researching and developing new data and image processing technologies and establishing new tools for quantification of biological phenomena, intended for researchers both inside and outside RIKEN.

Main Research Field


Related Research Fields



  • Multi dimensional image processing
  • Multi dimensional imaging
  • Bioengineering
  • Image analysis
  • Medical engineering

Selected Publications

  1. A. Sakane, S. Yoshizawa, M. Nishimura, Y. Tsuchiya, N. Matsushita, K. Miyake, K. Horikawa, I. Imoto, C. Mizuguchi, H. Saito, T. Ueno, S. Matsushita, H. Haga, S. Deguchi, K. Mizuguchi, H. Yokota, T. Sasaki,
    "Conformational plasticity of JRAB/MICAL-L2 provides 'law and order' in collective cell migration",
    Article in Molecular Biology of the Cell, 27, 3095-3108, August 2016, DOI: 10.1091/mbc.E16-05-0332
  2. N. Yamashita, M. Morita, W. R. Legant, B.-C. Chen, E. Betzig, H. Yokota, and Y. Mimori-Kiyosue, "Three-dimensional tracking of plus-tips by lattice light-sheet microscopy permits the quantification of microtubule growth trajectories within the mitotic apparatus",
    J. Biomedical Optics, 20(10):101206:1-18, 2015.
  3. T. Ijiri, S. Yoshizawa, H. Yokota, and T. Igarashi,
    "Flower Modeling via X-ray Computed Tomography",
    ACM Transactions on Graphics, Vol. 33(4):48:1-10, (Proc. of SIGGRAPH'14), 2014.
  4. M. Morita, T. Tawara, M. Nishimura, S. Yoshizawa, B. Chou, I. Kuroki, T. Ijiri, Y. Tsujimura, R. Himeno, and H. Yokota,
    "Communication Platform for Image Analysis and Sharing in Biology",
    International Journal of Networking and Computing, Vol. 4, No. 2, pp. 369-391, 2014.
  5. E. A. Susaki, K. Tainaka, D. Perrin, F. Kishino, T. Tawara, T. M. Watanabe, C. Yokoyama, H. Onoe, M. Eguchi, S. Yamaguchi, T. Abe, H. Kiyonari, Y. Shimizu, A. Miyawaki, H. Yokota, and H. R. Ueda,
    "Whole-Brain Imaging with Single-Cell Resolution Using Chemical Cocktails and Computational Analysis", Cell, Vol. 157(3), pp. 726-739, 2014.
  6. T. Ijiri, S. Yoshizawa, Y. Sato, M. Ito, and H. Yokota:
    "Bilateral Hermite Radial Basis Functions for Contour-based Volume Segmentation"
    Computer Graphics Forum (Proc. of EUROGRAPHICS’13), Vo. 32(2), pp. 123-132, 2013.
  7. S. Hihara, C.-G. Pack, K. Kaizu, T. Tani, T. Hanafusa, T. Nozaki, S. Takemoto, T. Yoshimi, H. Yokota, N. Imamoto, Y. Sako, M. Kinjo, K. Takahashi, T. Nagai, and K. Maeshima:
    "Local Nucleosome Dynamics Facilitate Chromatin Accessibility in Living Mammalian Cells"
    Cell Reports, Vol. 2(6), pp. 1645-1656, 2012.
  8. S. Yoshizawa, A. Belyaev, and H. Yokota:
    "Shape and Image Interrogation with Curvature Extremalities"
    Journal for Geometry and Graphics, Vol. 16, No. 1, pp. 81-95, 2012.
  9. Y. Okamura-Oho, K. Shimokawa, S. Takemoto, A. Hirakiyama, S. Nakamura, Y. Tsujimura, M. Nishimura, T. Kasukawa, K. Masumoto, I. Nikaido, Y. Shigeyoshi, H. Ueda, G. Song, J. Gee, R. Himeno, and H. Yokota:
    "Transcriptome tomography for brain analysis in the web-accessible anatomical space"
    PLOS ONE, Vol. 7(9), e45373:1-10, 2012.
  10. T. Ijiri, T. Ashihara, N. Umetani, T. Igarashi, R. Haraguchi, H. Yokota, and K. Nakazawa:
    "A Kinematic Approach for Efficient and Robust Simulation of the Cardiac Beating Motion"
    PLoS ONE, Vol. 7(5), pp. e36706:1-9, 2012

Lab Members

Principal Investigator

Hideo Yokota
Team Leader

Core Members

Shin Yoshizawa
Senior Scientist
Satoko Takemoto
Research Scientist
Masahiko Morita
Postdoctoral Researcher
Norio Yamashita
Postdoctoral Researcher
Toshiharu Mukai
Visiting Scientist
Soichiro Morishita
Visiting Scientist
Takashi Ijiri
Visiting Scientist
Sakiko Nakamura
Technical Staff I
Yuki Tsujimura
Technical Staff I
Masaomi Nishimura
Technical Staff I