BDR researchers coming from diverse research fields are working together to achieve higher goals.

Seminars & Symposia

Seminars & Symposia

BDR hosts annual symposium and regular seminars inviting international scientists in life science.

Careers & Study

Careers & Study

BDR embraces people from diverse backgrounds, and strives to create an open and supportive setting for research.



BDR communicates the appeal and significance of our research to society through the use of various media and activities.



From research, events, people and everything in between, find out what’s going on at RIKEN BDR.

About Us

About Us

Exploring the scientific foundations of life through interdisciplinary approaches to address society’s problems.

Photo of Team leder, Tomonobu Watanabe

Team Leader
Tomonobu Watanabe Ph.D.

Laboratory for Comprehensive Bioimaging

Location :Kobe / Developmental Biology Buildings, Hiroshima


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Recruiting graduate students

Exploring the potential of light and changing biology

Light has been an essential modality in medical and life science for 400 years because of the availability of living specimens. When light passes through the biomaterial or when light emanates from the biomaterial, the light is modified/modulated by information inside the biomaterial. Our developmental aim is extract the biological information from the fluorescence or scattering light. We are also trying to apply the developed measurement technology to various fields such as medicine and agriculture. For example, Raman scattering light contains all the molecular information constituting a substance, and the Raman scattered light spectrum of the cell is very complicated. We exploit this complexity to make Raman scattered light spectrum into a cellular fingerprint that identifies the type and state of cells. In addition, this "cell fingerprinting technology" is developed as an evaluation method applicable without touching or damaging cells or tissues. We are conducting research and development on as many innovation seeds as possible by simultaneously developing both basic measurement principles and practical application techniques. We believe that these technologies support many biological research fields and contribute to industries and revitalize the community.

Research Theme

  • Stem cell research by utilizing single molecule measurement for transcription factors.
  • Development and application of cellular fingerprinting based on Raman spectroscopy
  • Development and application of protein structural analysis based on second harmonic generation microscopy
  • Development of whole tissue imaging
  • The others

Selected Publications

Kawai T, Mihara Y, Morita M, et al.
Quantitation of Cell Membrane Permeability of Cyclic Peptides by Single-Cell Cytoplasm Mass Spectrometry.
Analytical chemistry 93(7), 3370-3377 (2021) doi: 10.1021/acs.analchem.0c03901

Germond A, Panina Y, Shiga M, et al.
Following Embryonic Stem Cells, Their Differentiated Progeny, and Cell-State Changes During iPS Reprogramming by Raman Spectroscopy.
Analytical Chemistry 92, 14915-14923 (2020) doi: 10.1021/acs.analchem.0c01800

Kakizuka T, Takai A, Yoshizawa K, et al.
An improved fluorescent protein-based expression reporter system that utilizes bioluminescence resonance energy transfer and peptide-assisted complementation
Analytical chemistry 56, 3625-3628 (2020) doi: 10.1039/C9CC08664A

David BG, Fujita H, Yasuda K, et al.
Linking substrate and nucleus via actin cytoskeleton in pluripotency maintenance of mouse embryonicstem cells.
Nat Protoc. 41, 101614 (2019) doi: 10.1016/j.scr.2019.101614

Matsumoto K, Mitani TT, Horiguchi SA, et al.
Advanced CUBIC tissue clearing for whole-organ cell profiling
Nat Protoc. 14, 3506-3537 (2019) doi: 10.1038/s41596-019-0240-9.

Kaneshiro J, Okada Y, Shima T, et al.
Second harmonic generation polarization microscopy as a tool for protein structure analysis.
Biophys Physicobiol. 16, 147-157 (2019) doi: 10.2142/biophysico.16.0_147

Germond A, Ichimura T, Horinouchi T, et al.
Raman spectral signature reflects transcriptomic features of antibiotic resistance.
Communications Biology 1, 85 (2018) doi: 10.1038/s42003-018-0093-8

Okamoto K, Germond A, Fujita H, et al.
Single cell analysis reveals a biophysical aspect of collective cell-state transition in embryonic stem cell differentiation.
Sci Rep. 8, 11965 (2018) doi: 10.1038/s41598-018-30461-2

Morikawa TJ, Fujita H, Kitamura A, et al.
Dependence of fluorescent protein brightness on protein concentration in solution and enhancement of it.
Scientific Reports 6, 22342 (2016) doi: 10.1038/srep22342

Ichimura T, Chiu L, Fujita K, et al.
Visualizing the appearance and disappearance of the attractor of differentiation using Raman spectral imaging.
Scientific Reports 5, 11358 (2015) doi: 10.1038/srep11358


Tomonobu Watanabe

Team Leader

Yasuhiro Maeda

Technical Scientist

Go Shioi

Technical Scientist

Junya Ichinose

Research Scientist

Michiko Inoue

Technical Staff I

Yuki Tano