Laboratory for Sensory Circuit Formation
Business picture

The Laboratory for Sensory Circuit Formation (Team Leader: Takeshi Imai, Ph.D.) at RIKEN CDB, Kobe, Japan, started from July, 2010. We study the mouse olfactory system as a model system to understand the development of functional neuronal circuitry.

We have moved to Kyushu University from April, 2017. Please visit a website for our new lab at Kyushu University.

Logic of sensory circuit formation
in the mammalian brain

The mammalian nervous system is composed of enormous numbers of neurons, but how do these cells take on diverse fates and organize and array themselves during development? In recent years, it has become clear that the mouse olfactory system provides an excellent platform for addressing these questions experimentally. In this system, there are 1,000 types of odorant receptors that are capable of detecting and discriminating between odorant molecules. Each olfactory sensory neuron expresses a single type of odorant receptor, and the axons of neurons expressing the same receptor type converge on the same site in the olfactory bulb. Olfactory sensory neurons connect axons to the dendrites of mitral and tufted (M/T) cells in the bulb, where each receives inputs from a single specific type of olfactory sensory neuron.

It has generally been thought that neuronal identities are genetically programmed, and that neuronal connectivity is maintained by molecular “lock and key” mechanisms. The mouse olfactory system, however, is highly adaptive; olfactory neuronal identities are dependent on peripheral inputs, and form the basis for a self-organizing olfactory map. A better understanding of this flexibility may provide new insights into the diversification of function that took place during the evolution of the human brain.

We have been studying how odorant receptors govern the axon guidance of olfactory sensory neurons. We are currently studying how the higher-order olfactory circuits are established in the olfactory bulb based on inputs from peripheral neurons (See our review article). We use mouse genetics, two-photon imaging, calcium imaging, single-cell transcriptome analyses, etc. to understand circuit functions and developmental mechanisms. We are also trying to develop next-generation genetic/imaging tools for better understanding of neuronal circuits in the mammalian brain.

Large-scale fluorescence imaging with SeeDB

We have recently developed a new optical clearing agent, SeeDB (Nat Neurosci, 2013), which is quick (3 days in total) and causes minimal morphological distortions. SeeDB is compatible with various fluorescent dyes, including fluorescent proteins and lipophilic dyes (e.g, DiI). Using conventional confocal microscopy, we could image the adult mouse brain up to ~2 mm depth at cellular resolution, and up to ~1 mm at single fiber resolution. When combined with optimized two-photon microscope setup, we could image the mouse brain from the dorsal to ventral side (~ 6 mm) at cellular resolution. Our technique is very powerful to study neuronal wiring at large scale in 3D.
A step-by-step protocol is available in SeeDB Resources.

High-resolution volumetric imaging with SeeDB2

Tissue clearing is also useful for high-resolution imaging including super-resolution microscopy. We recently reported an index-optimized clearing agent, SeeDB2, in (Cell Reports (2016). We can obtain volumetric data for neuronal circuitry at synaptic-resolution up to 100um scale with SeeDB2. SeeDB2 is useful not only for mouse brain tissues, but also for fly brains, and smaller samples for cell biology applications. A step-by-step protocol and TIPs are available in SeeDB Resources. See also YouTube movies [YouTube(1)] [YouTube(2)] [YouTube(3)]

Selected Publications

  • Ke et al., (2016) Super-resolution mapping of neuronal circuitry with an index optimized clearing agent. Cell Reports. doi:10.1016/j.celrep.2016.02.057
  • Imai. (2014) Construction of functional neuronal circuitry in the olfactory bulb. Seminars in Cell & Developmental Biology. in press. (Review) doi: 10.1016/j.semcdb.2014.07.012
  • Nakashima*, Takeuchi*, Imai*, et al. (2013) Agonist-Independent GPCR Activity Regulates Anterior-Posterior Targeting of Olfactory Sensory Neurons. Cell (*equally contributed) doi:10.1016/j.cell.2013.08.033
  • Ke, Fujimoto, & Imai. (2013) SeeDB: a simple and morphology-preserving optical clearing agent for neuronal circuit reconstruction. Nat Neurosci doi:10.1038/nn.3447 [PDF] [SeeDB Resources]
  • Imai, & Sakano, (2011) Axon-axon interactions in neuronal circuit assembly: lessons from olfactory map formation. Eur J Neurosci. 34, 1647-1654 [PDF]
  • Imai, Sakano, & Vosshall, (2010) Topographic Mapping--The Olfactory System. Cold Spring Harb Perspect Biol. 2(8):a001776.[PDF(preprint)]
  • Imai et al., (2009) Pre-Target Axon Sorting Establishes the Neural Map Topography. Science. 325, 585-60. [PubMed]
  • Imai et al., (2006) Odorant receptor-derived cAMP signals direct axonal targeting. Science. 314, 657-61.[PubMed]

Team Leader

Takeshi Imai, Ph.D.

Laboratory for Sensory Circuit Formation
RIKEN, Center for Developmental Biology
Rm 504-505, Bldg C
2-2-3 Minatojima-minamimachi, Chuo-ku
Kobe 650-0047

E-Mail: imai[at]


  • 4/1/17   We moved to Graduate School of Medical Sciences, Kyushu University. Our new website is here.
  • 10/18/16   Our new paper published in eNeuro.
  • 03/11/16   SeeDB2 paper published in Cell Reports. RIKEN press release
  • 02/15/16   Calls for RIKEN fellowship program and JSPS fellowship program are open. Deadline is April. Kyoto University admission guideline is now open. If you are interested, please contact us early.
  • 07/30/14   A new review article published.
  • 07/23/14   Harish (intern student) joined!
  • 04/01/14   Murai-san and Sakaguchi-san (grad students) joined!
  • 09/01/13   Marcus (postdoct) joined!
  • 06/23/13   A new publication on SeeDB technique in Nature Neuroscience. [press release(RIKEN)] [SeeDB Resources] Featured in ScienceNOW.
  • 04/01/13   Aihara-san (grad student) joined!
  • 10/01/12   Nomura-san (technical staff) joined!
  • 08/10/12   Summer internship program for undergrad students (photo).
  • 04/01/12   Yamashita-san (assistant) joined!
  • 03/08/12   A new review paper in Dev Growth Differ (article).
  • 07/01/11   Fujimoto-san (postdoc) joined!
  • 04/01/11   Iwata-san (postdoc) and Ke-san (grad student) joined!
  • 07/01/10   The Laboratory for Sensory Circuit Formation started at RIKEN Center for Developmental Biology. See RIKEN CDB HP .
  • 10/01/09   Investigator, PRESTO program, JST. See here .


Grad Sch of Biostudies, Kyoto Univ

Last updated May 27, 2017.