BrainSight: Imaging of neural codes over the lifecourse

Lead Research Organisation: University of Bristol
Department Name: Physiology and Pharmacology


All your behaviours, thoughts, feelings and memories are caused by activity within interconnected networks of nerve cells in the brain. Brain activity changes every second, yet can sustain thoughts over minutes, feelings that persist for hours or memories that last for years. How does the brain achieve this? Our goal is to decipher these mechanisms to understand precisely how our brains think. In the long run, this is a necessary step towards understanding how brains go wrong.

To realise this ambition we must be able to record the activities of nerve cells stably and repeatedly over time, throughout the life-course of an individual. While this challenge cannot yet be met in humans, it can now be achieved in laboratory rats and mice using a state-of-the-art technology: head-mounted miniaturised microscopes (HMMM) that can image inside the brain.

HMMMs weigh about half as much as 1 penny but contain all the essential parts of a standard microscope. This small size and low weight allows HMMMs to be temporarily connected to the head of a rat or mouse without impeding its behaviour. As a result, we can use HMMMs to image the activities of nerve cells engineered to produce fluorescent proteins, while the animal is asleep, awake or performing behavioural tasks. Hundreds of nerve cells can be imaged at once, allowing us to capture the scale and complexity of activity throughout brain circuits. Additionally, HMMMs can be removed and returned to exactly the same place, so that changes in the activities of the same cells can be tracked across time, for example as the animal learns a new skill or remembers a past event. Finally, by simply adding an extra LED light source, the HMMM can not only image nerve cells, but also switch on or off groups of cells engineered to produce light activated proteins. In this way, we can record and modify brain activity at precise moments to understand whether changing the structure of brain activity can influence behaviour.

This project will establish a core HMMM facility at the University of Bristol that will be shared between 12 internationally recognised research groups working on complementary aspects of brain function. By harnessing our collective expertise we will be equipped to tackle big questions at the forefront of modern neuroscience. Specific aims of the project include:

Determining the parts of the brain that process different features of event-based memories (i.e. what, where and when).

Understanding how emotions influence decision-making.

Deciphering the purpose of REM sleep.

Defining elements of brain circuits (i.e. types of nerve cell) that regulate brain activity during sleep.

Identifying patterns of activity in that allow us to learn complex movements.

Understanding how the neurochemicals dopamine, noradrenaline and acetylcholine modulate sense of touch, movement and our expectations of the world.

Discoveries by our team and others have shown that these diverse brain functions require communication between multiple brain areas, with each area contributing different information or modulating activity in the other. An overarching goal of this project is to advance understanding of this communication by using multiple HMMMs to record activity within and between interconnected brain circuits. This has not been done before, and will allow us to understand how communication between brain structures is modified across different brain states and behaviours.

Technical Summary

The head-mounted miniature microscopes (HMMM) manufactured by Inscopix weigh less than 2g and are small enough to be carried on the head of a mouse. By imaging fluorescent markers of neural activity (most commonly the calcium indicator GCaMP6), HMMM's allow monitoring of network activity simultaneously from hundreds of neurons and - critically - cell populations identified genetically and anatomically can be resampled repeatedly over days to months. Coupling HMMMs to GRIN lenses enables imaging from deep brain structures and, in rat, 2 HMMMs can be used for dual imaging from pairs of functionally interconnected brain regions.

The central preparation shared by all PIs will be a mouse or rat implanted with 1 or 2 HMMMs targeting pairs of structures including prefrontal cortex, hippocampus, perirhinal cortex, retrosplenial cortex, basal forebrain, locus coeruleus, striatum and cerebellum. Behavioural assays will employ recognition and spatial memory tests, motor learning or sensory perception tasks and, for some experiments, will be coupled with neurochemical sensing or electrophysiology. HMMMs allow optogenetic stimulation, meaning high-resolution activation/inhibition can be applied to imaged cell populations to probe causality.

Integrating HMMMs with our collective expertise in behavioural neuroscience, electrophysiology, neurochemistry, optogenetics and computational methods will therefore enable our team of 12 PIs to tackle major longstanding and fundamentally important questions about the neural bases of memory, emotion, sleep, movement, sensation and neuromodulation. Appending this technology to our existing armoury will make a rapid and enduring change to our ability to interrogate the nervous system, fuelling our individual labs, our collaborative network and training opportunities for postgraduates and postdoctoral researchers at the University of Bristol and the SW region.

Planned Impact

Research from this proposal will impact a wide range of stakeholders spanning societal (general public), commercial (pharmaceutical and technology industries) and educational (primary to tertiary teaching) sectors. Details of how each group will benefit include:


- This project will shed new light on fundamental mechanisms of learning and memory. Based on experience, this is a topic which routinely captures public interest. The next Bristol Neuroscience Festival (Spring 2020) will include an exhibit based around 'mechanisms of learning and memory'. To showcase our work, we will incorporate aspects of our latest findings into a range of hands-on activities, e.g. 'brain training' puzzles.
- Head-mounted miniature microscopes (HMMMs) are a novel technology that considerably advances the 'reduction' and 'refinement' principles of the 3Rs framework for performing more humane animal research. BN members participate in outreach events to increase public understanding of the role and importance of animal research in pre-clinical science. Our work on this project will provide an example of how new technologies are improving animal research standards.


Drug discovery
Many pharmaceutical companies, including current collaborators such as Lilly, operate programmes to develop new treatments for neurodegenerative diseases (e.g. Alzheimer's), neuropsychiatric disorders (e.g. depression, schizophrenia) and movement disorders (e.g. Parkinson's disease). These conditions span the collective research foci of our team. In this regard, we will reach out to current and potential industrial partners to identify opportunities where HMMMs can be incorporated into the drug discovery process.

Technological development
The project will expand use of commercialised HMMM technology to enable fully integrated neural circuit imaging across multiple brain regions. This goal is built on detailed feasibility planning in association with our commercial supplier Inscopix. While we cannot predict whether this will lead to further development of multi brain region imaging systems by Inscopix, our work will pave the way for future imitative application of multi-region HMMM imaging throughout the academic community.


- We expect our research in the areas of learning and memory, motivation and emotional regulation of decision-making to have significant implications for learning strategies in the classroom. We will work with the UoB Neuroeducation Network to ensure that our findings are integrated into teaching practice.
- HMMMs are a cutting-edge technology that have already generated significant scientific impact - approximately 60 % of research papers using HMMMs have been published in top-tier journals of impact factor 10 or higher. Lab-based research projects (undertaken in the 3rd year of study) will allow undergraduates to use this novel technology. This will not only provide a high-quality training opportunity, but also expose students to the capabilities of cutting-edge neuroscience research, inspiring them to pursue research careers.


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