Centers & Labs

RIKEN Quantitative Biology Center

Laboratory for Comprehensive Bioimaging

Team Leader: Tomonobu Watanabe (Ph.D.)
Tomonobu  Watanabe(Ph.D.)

Cells can be thought of as complex systems in a dynamic equilibrium between multiple states that fluctuate stochastically. Our aim is to construct a numerical model that describes the common mechanisms regulating high-order function in complex biological systems. To understand the behavior of these systems, it is necessary to observe state transitions while at the same time quantitatively describing their dynamics. We are developing novel imaging systems that combine three major techniques to achieve this aim: 1) imaging systems which measure protein position, dynamics and the surrounding environment , 2) novel cell culture systems which can control and perturb the chemical/mechanical environment, and 3) custom designed biochemical/inorganic sensors that can visualize the status of the cell. The developed techniques will provide significant insight on the regulation of tissues, immunity, metabolism and aging by understanding the fundamental mechanisms that give rise to these disparate and complex systems. In turn, the information gained will significantly improve our ability to diagnose and treat diseases and advance the design of new medicines.


  • Quantitative measurement
  • Optical microscope
  • Fluorescent protein

Selected Publications

  1. Germond A, Kumar V, Ichimura T, Moreau J, Furusawa C, Fujita H, Watanabe TM.
    "Raman spectroscopy as a tool for ecology and evolution"
    J. R. Soc. Interface, 14: 20170174 (2017)
  2. Ichimura T, Chiu L, Fujita K, Machiyama H, Yamaguchi T, Watanabe TM & Fujita H.
    "Non-label immune cell state prediction using Raman spectroscopy"
    Sci. Rep. 6, 37562 (2016)
  3. Morikawa TJ, Fujita H, Kitamura A, Horio T, Yamamoto J, Kinjo M, Sasaki A, Machiyama H, Yoshizawa K, Ichimura T, Imada K, Nagai T, Watanabe TM.
    "Dependence of fluorescent protein brightness on protein concentration in solution and enhancement of it. "
    Sci. Rep. 6, 22342 (2016)
  4. Germond A, Fujita H, Ichimura T, Watanabe TM.
    "Design and development of genetically encoded fluorescent sensors to monitor intracellular chemical and physical parameters. "
    Biophys Rev. 8, 121-138 (2016)
  5. Kaneshiro J, Watanabe TM, Fujita H, Ichimura T.
    "Full control of polarization state with a pair of electro-optic modulators for polarization-resolved optical microscopy. "
    Applied Optics, 55, 1082-1089 (2016)
  6. Ichimura, T., Chiu, L., Fujita, K., Machiyama, H., Kawata, S., et al.:
    "Visualizing the appearance and disappearance of the attractor of differentiation using Raman spectral imaging"
    Sci. Rep. 5, 11358 (2015)
  7. Fujita, H., Esaki, T., Masujima, T., Hotta, A., Kim, S. H., et al.:
    "Comprehensive chemical secretory measurement of single cells trapped in a micro-droplet array with mass spectrometry"
    RSC Adv. 5, 16968-16971 (2015)
  8. Higuchi, S., Watanabe, T. M., Kawauchi, K., Ichimura, T. & Fujita, H.:
    "Culturing of mouse and human cells on soft substrates promote the expression of stem cell markers"
    J. Biosci. Bioeng. 117, 749-755 (2014)
  9. Ichimura, T., Chiu, L., Fujita, K., Kawata, S., Watanabe, T. M., et al.:
    "Visualizing Cell State Transition Using Raman Spectroscopy"
    PLoS One 9 (2014)
  10. Watanabe TM, Fujii F, Jin T, Umemoto E, Miyasaka M, Fujita H, Yanagida T.
    "Four-dimensional spatial nanometry of single particles in living cells using polarized quantum rods. "
    Biophys J. 105, 555-564 (2013)

Lab Members

Principal Investigator

Tomonobu Watanabe
Team Leader

Core Members

Taro Ichimura
Senior Scientist
Junichi Kaneshiro
Special Postdoctoral Researcher
Kazuko Okamoto
Postdoctoral Researcher
Ryota Mizushima
Postdoctoral Researcher
Arnaud Germond
Postdoctoral Researcher
Brit Gracy David
International Program Associate
Yulia Rozanova
International Program Associate
Keiko Yoshizawa
Technical Staff I