Shimaoka Lab research
Collaborations | Student research projects | Publications
About Dr Daisuke Shimaoka
Throughout my research career, I’ve focused on systems neuroscience, the study of how populations of neurons in the living brain interact to process functions such as sensation and perception. My longstanding goal is understanding how subjective experience emerges from the physical substrate of neural activity. In other words, how does consciousness arise from mere matter?
My undergraduate training was engineering, and I find the great joy in building things (I’m a great fun of 3D printing). But engineering, as I learned early on, is not just about construction. it's about deeply understanding systems so they can be reconstructed. This philosophy was instilled in me by my first supervisor in Osaka, one of the pioneers in applying engineering principles to neuroscience. I learned this approach to uncover the visual receptive fields of individual neurons.
In Tokyo during my masters and PhD studies, I expanded my focus to dynamical systems theory, it’s the study of how individual physical systems interact to produce collective phenomena such as oscillations. I applied this framework to quantitatively model neural population dynamics underlying visual perception.
During my first postdoc at UCL, I shifted toward more empirical brain research. There, I established the world’s first voltage imaging system in awake mice, enabling direct observation of neural activity at cortex-wide scale. Using this system, I identified how arousal modulates not just a single region but at cortex-wide scale.
Up to this point, my research was conducted under highly constrained experimental conditions, where animals were either immobilized or trained to perform stereotyped behaviors. At Monash, I transitioned to studying neuronal encoding in more naturalistic settings. I developed an encoding model approach that uses naturalistic conditions, such as movies or spontaneous behaviors during neuronal recordings. In this framework, a mathematical model is fitted to empirical brain signals, allowing us to inspect the model itself to understand what aspects of the stimuli or behavior are encoded in the brain activity.
Collectively, my research has focused on decoding brain signals related to sensory processing and arousal. This 'reading' of the neural code has been a central pursuit in systems neuroscience for decades, advancing our understanding of brain functions. These insights have also laid the foundation for applications like brain-computer interfaces.
In the past 10–15 years, however, a transformative shift has occurred with the emergence of technologies that enables to write to the neural code through optogenetic tools such as channelrhodopsin. These tools enable direct manipulation of neural activity, allowing us to test which patterns of brain activity are causally involved in specific brain functions. Beyond basic science, this capability also opens new possibilities for developing prosthetic devices to restore or enhance human sensation.
To fully realize this potential, it is critical to simultaneously monitor and stimulate the brain. Because without monitoring, we cannot understand how stimulation affects neural dynamics. My group is therefore actively developing this dual capability, both reading and writing the neural code.
By integrating these experimental capabilities with mathematical modelling, my research aims to uncover the principles governing emergent brain functions, including consciousness, through direct interrogation and control of neural dynamics in the living brain.
Our research
Current projects
Research Program 1: Reading and Writing Brain-Wide Dynamics Through Light
Traditionally, neuroscience has relied on electrical and optical recordings to observe brain signals. The advent of optogenetics, genetic tools that allow control of brain activity using light, has revolutionized the field by enabling precise manipulation of neural dynamics.
We are actively developing a system for simultaneous imaging and manipulation of brain activity across the entire brain. Simultaneously, we use it to control brain-wide oscillations during sleep and investigate the causal roles of individual brain regions.
Research Program 2: Modeling the Impact of Brain Geometry on Visual Processing
The human brain is wrinkled: a design thought to maximize the number of neurons packed into the limited space of the skull. But recent AI-driven research (Ribeiro et al 2021 NeuroImage; 2023 eLife) has uncovered a surprising link between the pattern of these wrinkles and how the brain represents visual information.
How could geometry shape brain functions? This project aims to explore that question by using computational modeling and simulation based on real human brain data. We are investigating how the brain’s physical structure influences its functional processing of visual input, through computational modelling of brain wiring using the geometry of the real human brains.
Research Program 3: Decoding and Assisting Visual Perception
We aim to decode how the brain represents naturalistic sensory experiences and to develop neurotechnologies that assist visual perception. Using an encoding modeling framework, we link neural activity to quantitative descriptions of complex, real-world stimuli. Applied to widefield optical imaging, this approach has revealed the functional organization of visual cortical areas in the marmoset brain (Shimaoka et al., 2024 Prog Neurobiol). We are extending this work to naturalistic behaviors, including data with unconstrained eye movements. For example, single-neuron recordings from posterior parietal cortex reveal how individual neurons encode both visual input and eye movements (Shimaoka et al., 2025 bioRxiv). By inverting these models, we aim to decode perceptual states directly from brain activity—a foundational step toward mind reading.
Beyond decoding, we seek to assist perception by intervening in visual processing. Visual information flows hierarchically through cortical areas to form visual perception. We deploy the optogenetics to manipulate specific stages of the visual processing stream to reshape perception. Together, our decoding and intervention strategies aim to advance assistive technologies for individuals with visual or neurological impairments.
Research Program 4: Detecting and Titrating Arousal Levels
We aim to infer arousal level from brain signals. A key insight is that the same anesthetic agents induce loss of consciousness across species with vastly different brain architectures. By comparing brain signals across multiple species, we aim to extract features that are conserved and reliable indicators of arousal level (Shimaoka et al., in principle accepted). This cross-species analysis, powered with highly-comparative time-series analysis, aims to establish a broadly applicable consciousness meter to prevent under and over dosage under general anaesthesia.
Visit Dr Daisuke Shimaoka's Monash research profile to see a full listing of current projects.
Techniques/expertise
- Widefield Optical Imaging
- Optogenetics
- Single-unit Electrophysiology
- Psychophysics
- Dynamical Systems Modeling
- Highly-Comparative Time-Series Analysis
Animal models
- Mouse
- Marmoset
Collaborations
We collaborate with many scientists and research organisations around the world. Some of our more significant national and international collaborators are listed below. Click on the map to see the details for each of these collaborators (and you'll be able to dive into specific publications and outputs).
- Prof Greg Stuart (Monash)
- Prof Marcello Rosa (Monash)
- Prof Alex Fornito (Monash)
- Dr James Pang (Monash)
- Prof Nao Tsuchiya (Monash)
- William Wong (Monash)
- Chikayo Hemmi (ATR)
Student research projects
The Shimaoka Lab offers a variety of Honours, Masters and PhD projects for students interested in joining our group. There are also a number of short term research opportunities available.
Please visit Supervisor Connect to explore the projects currently available in our Lab.
The Shimaoka Lab offers a variety of Honours, Masters and PhD projects for students interested in joining our group. There are also a number of short-term research opportunities available. You are encouraged to contact <<Title First Name Surname>> regarding potential projects that align with the presented research themes.