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Our goal

How do "brain functions"—such as perception, memory, emotion, and decision-making—arise from a network of nerve cells? To reveal its basic principle, we study the nematode C. elegance, the roundworm with a simple brain.

Our strategy

To understand how the brain functions, it is critical to rigorously quantify sensory stimuli, behavioral responses triggered by the stimuli, and neural activities in between, and to reveal the relationships among them. We measure and analyze those multiple aspects of worm's sensory behavior with the robot and machine learning technologies through collaborations with researchers in the fields.

 

・Measuring dynamic odor gradient formed by volatilization and diffusion in a plate: Yamazoe-Umemoto et al., Bio-protocol 2018

・Simultaneous measurement of behavior and neural activity of a freely behaving worm in a virtual odor gradient: Tanimoto et al., eLife 2017 [F1000Prime] [EurekAlert]

・Single cell-targeted regulation of neural activity of a freely behaving worm by optogenetics: Tanimoto et al., Sci Rep 2016

・A versatile method for analyzing animal trajectory by a hybrid machine learning technique: Yamazaki et al., Front Neurosci 2019 [EurekAlert]

・Imaging whole brain activities of a worm by deep learning-based 3D cell tracking algorithm: Wen et al., eLife 2021​ [eLife digest]

・Analyzing whole brain activities with machine learning-based modeling: Wen and Kimura, Jpn J Appl Phys 2020

Our achievement

Using the methods above, we have found the mechanisms of brain functions that can be conserved in higher animals.

・Odor learning modulated by dopamine signaling: Kimura et al., J Neurosci 2010

・Neuropeptide signaling for memory acquisition and dopamine signaling for memory execution: Yamazoe-Umemoto et al., NSR 2015

・Functional diversification of dopamine neurons: Tanimoto et al., Sci Rep 2016

・Cellular and molecular mechanisms for decision-making: Tanimoto et al., eLife 2017 [F1000Prime]

​For all the publications by the PI, please see Google Scholar and Publons.com.

Collaborators

We are conducting joint research with various research institutes.

Overseas: Columbia University (USA), University of Edinburg (UK), etc.

Domestic: Osaka University, Nagoya University, Nagoya Institute of Technology, Tohoku University, National Institute for Physiological Sciences, National Institute for Basic Biology, RIKEN, etc.

Our education

・ Original research themes using various methods, such as molecular genetics, imaging, programming, electronic circuit

・ Bi-weekly 1:1 meetings

・ Joint meeting with other labs in Nagoya Univ.

Our team

Would you like to join our team with state-of-the-art technologies, such as robotic microscopes, whole brain imaging, and machine learning techniques, at Nagoya, one of the biggest cities in Japan? Please send an email to the PI!

News

2021/9/17

Another crazy collaboration with Prof. Maekawa (Osaka Unv.) was published in Nature Communications: Deep learning with "attention" mechanism revealed behavioral characteristics shared among dopamine-deficient humans (i.e., Parkinson's disease patients), mice, beetles, and worms! [link]

2021/8/18

​An article about our interdisciplinary research project on AI-based analysis of animal behavior (Yamazaki et al., 2019) was published in Nature Index [link]

2021/3/20

​Chentao Wen developed the first deep-learning based 3D tracking pipeline for moving 100-1000 cells, called "3DeeCellTracker", which was published in eLife. We really appreciate the great collaborators in the Hillman lab @ Columbia Univ., the Ishihara lab @ Kyushu Univ., and the Nemoto and Aoki labs @ ExCELLS (NINS)! [article][eLife digest]

2021/1/5

​We published a protocol to precisely regulate the changes in odor concentration under a microscope. [link]

2020/10/21

​As a collaboration with Associate Professor Takuya Maekawa at Osaka Univ., we just published a deep learning technique to extract features of animal behavioral trajectory. [link]

2020/10/1

A new lab tech, Miyu Miyachi, and two 3rd year undergrad, Ryoga Suzuki and Keisuke Maruyama, joined the lab.

2020/7/3

Dr. Jared Young left our lab after a 10-months stay. During the stay, he has done incredibly wonderful work!

2020/3/5

​Chentao Wen wrote an introductory review of mathematical/machine learning analyses of whole brain activity. [link]

2020/1/4

Kotaro Kimura became an Associate Editor of Neuroscience Research.

 

2019/11/22

The web site for CeNeuro 2020 In Vienna is now open! (Kotaro Kimura is serving as a scientific committee member.)

 

2019/9/28​

Collaborative work with the Hillman Lab. at Columbia University was published in Nature Methods [link]. Our robust 3D cell tracking algorithm with deep learning developed by Chentao Wen [preprint] was used for processing the images from the insanely ultra-high speed 3D microscope system SCAPE 2.0.

2019/9/1

Dr. Jared Young, Associate Professor @ Mills College (USA), joined our lab as a sabbatical stay.

 

2019/6/28

From worms in a petri dish to penguins in Antarctica. My grad student Johnny Yamazaki developed a versatile method to estimate behavioral states and to extract features of the state only from animal trajectories. The work was pretty much supported by Prof. Takuya Maekawa @ Osaka U. and other really great collaborators! [link]

 

2018/10/1

Ling Fei Tee joined the Lab as a D1 student supported by the MEXT scholarship.