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Systems Neuroscience

Laboratory of Neurocomputation

Picture of Professor Matsui
Teppei Matsui, Ph.D.

We can see and recognize the surrounding environment with our eyes, interpret situations, and take flexible actions such as driving a car while avoiding obstacles. Whereas the brain accomplishes these actions with ease, implementing the same functionality in artificial intelligence remains a challenging task. In our laboratory, we would like to clarify the principle of flexible information processing by neural circuits, focusing mainly on visual perception.

Other than visual perception, we focus on the spontaneous activity of the brain. Unlike a computer, the brain is restlessly active even when the animal is at rest and has no sensory input. Such spontaneous activity is thought to be useful for the formation of neural circuits in the early developmental stages, but its relationships with cognitive functions as well as diseases remain unknown. In our laboratory, we would like to clarify the spatio-temporal structure and dynamics of spontaneous brain activity and understand their relationships with cognitive functions and diseases.

We will use both animal experiments and data science researches to answer these questions. In experimental research, we mainly use optical imaging and molecular biological techniques to measure and manipulate neural circuit activities. In data science researches, we apply the latest AI and statistical methods to large-scale neuroscience databases.

Research topics

  1. Principles of visual information processing by the brain
  2. Functions of spontaneous brain activity during development, adulthood and pathology
  3. Large-scale neural data analysis using AI and data science techniques
  4. Neural circuit analysis using molecular biology and optical techniques

Selected publications

  1. Matsui, T., Koyano, K. W., Koyama, M., Nakahara, K., Takeda, M., Ohashi, Y., Naya, Y., Miyashita, Y. (2007) MRI-based localization of electrophysiological recording site within the cerebral cortex at single-voxel accuracy. Nature Methods 4(2), 161-168.
  2. Matsui, T., Tamura, K., Koyano, K. W., Takeuchi, D., Adachi, Y., Osada, T., Miyashita, Y. (2011) Direct comparison of spontaneous functional connectivity and effective connectivity evoked by intracortical microstimulation: an fMRI study in macaque monkeys. Cerebral Cortex 21(10), 2348-2356.
  3. Matsui, T., Ohki, K., (2013) Target dependence of orientation and direction selectivity of corticocortical projection neurons in the mouse V1. Frontiers in Neural Circuit 7, 143.
  4. Matsui , T., Murakami, T., Ohki, K. (2016) Transient neuronal coactivations embedded in globally propagating waves underlie resting-state functional connectivity. Proceedings of the National Academy of Sciences 113(23), 6556-6551.
  5. Matsui, T., Murakami, T., Ohki, K. (2018) Neuronal basis of the temoral dynamics of spontaneous BOLD activity correlation. Cerebral Cortex 29(4), 1496-1508.
  6. Nishiyama M., Matsui, T., Murakami, T., Hagihara, K., Ohki, K*. (2019) Cell-Type Specific Thalamocortical Inputs Constrain Direction Map Formation in the Visual Cortex. Cell Reports 26(5), 1082-1088 e3.
  7. Matsui, T., Taki M., Pham, TQ., Chikazoe, J., Jimura, K. (2021) Counterfactual Explanation of Brain Activity Classifiers Using Image-To-Image Transfer by Generative Adversarial Network. Frontiers in Neuroinfomatics 15, 802938.
  8. Matsui, T., Hattori, Y., Tsumura, K., Aoki, R., Takeda, M., Nakahara, K., Jimura, K. (2022) Executive control by fronto-parietal activity explains counterintuitive decision behavior in complex value-based decision-making. Neuroimage 249, 118892.
  9. Matsui, T., Pham, TQ., Jimura, K., Chikazoe, J. (2022) On co-activation pattern analysis and non-stationarity of resting brain activity. Neuroimage 249, 118904.
  10. Murakami, T., Matsui, T., Uemura, M., Ohki, K. (2022) Modular strategy for development of the hierarchical visual network in mice. Nature 608(7923), 578-585.


Teppei Matsui, Ph.D. (Principal investigator, Professor)
Kenji Hayashi, Ph.D. (Research associate professor)



3F Hochikan, 1-3 Tatara Miyakodani, Kyotanabe-shi, Kyoto 610-0394 Japan
Telephone: +81-774-65-7182
E-mail : tematsui@mail.doshisha.ac.jp