Scott Lab - Neural circuits and behaviour

Addressing the brain’s complexity

In the Scott Lab, we are interested in the workings of the brain at the level of cells and circuits.  We aim to understand how sensory stimuli are perceived and processed in the brain, and how the brain then interprets these stimuli to produce adaptive behaviours.

Because of the brain’s extraordinary complexity, these questions are difficult to address by looking at individual cells.  The flow of information through the brain relies on the coordinated activity of thousands or millions of cells, and on ensembles of neurons that are active simultaneously.  For this reason, our research involves imaging activity in thousands of cells, and seeking salient patterns of activity across these populations.  In a range of projects, we characterise the neurons and circuits that respond to various visual, auditory, water flow, and vestibular stimuli; that play a role in the integration of information from these modalities; and that filter sensory information to produce behaviour.

Optogenetics in zebrafish

We work in the zebrafish model system because of its strengths in genetics, behaviour, microscopy, and optogenetics.  Specifically, we use transgenic techniques to express genetically encoded calcium indicators (GECIs) or optogenetic proteins in specific parts of the zebrafish brain.  We then use selective plane illumination microscopy (SPIM) to observe the GECIs, which reveal activity across our cells and circuits.  We also use optical physics to produce holograms in the brain for optogenetics in our larval fish.  Gradually, we aim to transition from describing patterns of activity in the brain to manipulating them in targeted ways, and to describing the structures and connectivity of the neurons carrying the information.  This will contribute to a comprehensive understanding of brain function spanning cells, circuits, regions, and the brain as a whole.

A z-series of a volumetric dataset in the larval zebrafish brain 

In a typical experiment, we sample from 50 different depths in the brain, at 5 micron intervals, capturing 2 volumes per second.


Circuits neuroscience

From a broad perspective, this work is part of a burgeoning field of circuits neuroscience. Over the coming decades, neuroscientists will make the leap from understanding how regions of the brain function to describing, in concrete terms, the cellular circuits that underlie perception and behaviour.  Our group hopes to contribute to this effort, specifically in describing how the senses work, how the brain produces a coherent representation of the outside world, and how information from the outside world is translated into appropriate actions.

Vestibular-responsive neurons across the zebrafish larval brain  

The colours reflect different functional profiles that the neurons have during vestibular stimulation.



Lab Head




Opportunities for new researchers

Our lab spans numerous experimental approaches and techniques, and as a result, we need all kinds of expertise.  Historically, most lab members have been trained as biologists, especially neuroscientists, but recently this has diversified as we have adopted new techniques. 

Specifically, as our microscopes have begun producing vast datasets containing activity from tens of thousands of neurons, we have a great need for people who can code solutions for image analysis, data mining, and the detection of salient patterns among these vast data.  As a result, we are particularly eager to bring in mathematicians and bioinformaticians.  We are also building our own microscopes and performing tricks on them like digital holography (see our methods).  This vastly increases our experimental capacities, but it also means that we need capable optical physicists on the team.  Of course, we are still happy to bring in biologists of all varieties.

Positions are available across our research program for undergraduates, honours students, PhD students, and postdocs, and we are happy to entertain new ideas.  If you are interested in joining the lab, please contact Ethan.

Current projects

Anatomical circuit mapping

We are interested in both the physical and the functional connections that underlie brain function, so we use both anatomical and optogenetic approaches for circuit mapping.  Anatomical approaches include imaging the architectures of individual neurons within a brain region of interest.  This allows us to view these brain regions as collections of discernible cell types, which is a prerequisite for explaining how those cells form functional circuits.

A single tectal periventricular neuron labelled the BGUG technique
(adapted from Scott et al, 2007).

A single tectal periventricular neuron labelled the BGUG technique
(adapted from Scott et al., 2009).

Cerebellar projection neurons.  See caption for more explanation.

 Tracings of five cerebellar projection neurons to the tectum, and a spatially registered map of topography between the structures
(adapted from Heap et al, 2013).

We also use targeted photoconversions to resolve patterns of projections between different brain regions.  By illuminating Kaede-expressing neurons with violet light, we can cause Kaede to change from a green to a red fluorophore.  If we target this photoconversion to particular cells and wait for the red Kaede to diffuse into the axons, we can identify these cells’ targets throughout the brain. 

Kaede photoconversions

tectal neuropil from a larva in which both the thalamus and retina are labelled with Kaede

These are images of the tectal neuropil from a larva in which both the thalamus and retina are labelled with Kaede. We have photoconverted Kaede in thalamic, but not retinal, projection neurons, allowing us to determine which layers of the tectal neuropil receive inputs from each. (Heap et al, 2018 )


Sensory processing and integration

We are interested in addressing how the brain perceives and integrates information about the outside world, and we have expanded our experiments to cover as many sensory modalities as possible.  Most of these projects have been based around calcium imaging in large populations of neurons (the whole brain in some cases), followed by further anatomical or functional analyses of the neurons involved.

In the visual system, we have characterised the tuning of neurons in the tectum to visual stimuli with different levels of saliency (Thompson et al, 2016).  We have also used calcium imaging, anatomical mapping, ablation experiments, and behavioural analyses to describe a role for the thalamus in detecting changes in luminance, and have described how this information contributes to the likelihood and the direction of escape behaviours in larval zebrafish presented with a threatening visual stimulus (Heap et al, 2018).

The tectum’s responses to predator-like stimuli depend on input from the thalamus, while thalamic input is not involved in the tectum’s responses to other visual stimuli (left).  The animal’s behavioural responses are also dependent on this thalamic activity.  They are less likely to startle, and reverse the direction of their startles, when thalamo-tectal communication is interrupted on the relevant side of the brain (right). Adapted from Heap et al, 2018 

We have recently published the first whole-brain analysis of auditory processing in larval zebrafish, indicating that it is rudimentary in terms of frequency discrimination and tonotopy in larvae.  These auditory responses are, however, useful to characterise, as this now puts us in a position to combine auditory stimuli with stimuli from other modalities in studies of sensory integration.

To study the perception of water flow, we have designed a microfluidics device capable of delivering controlled flow over the trunk of larvae while they remain stationary for calcium imaging.  This permits us to observe the neurons in the brain that respond to water flow, their response properties when the direction or strength of the flow changes, and their locations within the brain.  This will allow us to build models of how flow is perceived in the early stages of this pathway, and how emergent properties, such as representations of accumulated flow over time, arise later in the sensory processing cascade.

A microfluidics device for stimulating the lateral line system during whole-brain calcium imaging (top left). Neural responses to a simple stimulus, alternating reverse flow followed by forward flow, fall into eight categories with distinct response properties (bottom left), and these different types of responsive neurons map back to characteristic locations within the brain (right).  Unpublished data from Gilles Vanwalleghem.

Our work in the vestibular system is aimed at addressing one of the fundamental challenges to studying this modality: vestibular stimuli necessarily move the subject, and this makes most approaches for studying activity (electrophysiology, fMRI, calcium imaging) difficult or impossible.  Using the physics technique of optical trapping, we have applied forces to the otoliths (ear stones) of immobilised zebrafish larvae, tricking them into thinking that they are moving when they are stationary.  This permits us to perform calcium imaging to reveal the cells and circuits involved in vestibular processing.  The optical physics and behaviour for this approach are described in (Favre-Bulle et al, 2017)  and our description of the brain-wide vestibular processing is described in a preprint here

A diagram (left) of our optical setup, where an infrared optical trap is applied to the utricular (vestibular) otolith while we preform whole-brain volumetric calcium imaging.  The centre panels show a larva before and during the application of the optical trap, demonstrating the postural change that the trap elicits.  This tail bend (and eye movements not shown here) scale with the strength of the laser used, and therefore with the perceived magnitude of the fictive vestibular stimulation.  The full story is on Biorxiv.

We observe three distinct functional clusters of neurons responding to vestibular stimulation (mean responses shown on the left), and these are spread across characteristic brain regions (dorsal view shown in the centre, with sagittal views on the right). The full story is on Biorxiv

As we further refine our techniques for stimulating a range of sensory modalities and get baseline data for how each modality is processed in the brain’s circuits, we are shifting our attention to important biological question that are made accessible by these techniques.  These include how information from different modalities influence one another and are integrated, how habituation and attention are manifested in this circuitry, and how there circuits change in models of human sensory disorders.




Functional circuit mapping with optogenetics

The anatomical and imaging approaches described above still don’t concretely demonstrate how information passes through the brain circuits.  To address this, we need to test the functional relationships among the cells that we are studying.  For this, we turn to optogenetics.   By driving activity specifically in one brain region that we are interested in, and performing calcium imaging of the neurons in another region that may be connected, we can see whether and in what way one region’s activity affects cells in the downstream region.  Given the complex and interconnected nature of the nervous system, this does not necessarily mean that the stimulated cells and the responsive cells are synaptic partners (anatomical mapping is needed for that), but it does establish a functional relationship between one region and another.

Optogenetic circuit mapping

Image showing optogenetic circuit mapping.  See text below for explanation.

Optogenetic stimulation using sculpted laser light and Channelrhodopsin2 (blue circle, left) can be used to drive activity in a small patch of the cerebellum.  The resulting activation in tectal neurons is shown in green.  The right panel shows a raster plot of individual tectal cells that respond to this cerebellar stimulation and the average response of this population to three consecutive trials. (Unpublished data from Lucy Heap.)

Zebrafish models of Autism Spectrum Disorder

Psychiatric disorders necessarily have their origins in the dysfunction or loss of neural circuitry.  Our lab has recently begun modelling Autism Spectrum Disorder (ASD) by mutating genes linked to ASD in humans.  The strength of the zebrafish model system is that it permits access to the functioning brain, thus allowing analyses of developmental dynamics, population-level neural coding, and synapse dynamics in vivo. 

We are currently in the process of using CRISPRs to mutate a number of zebrafish homologs to ASD-linked human genes.  These mutants will be used to gauge the anatomical, developmental, and physiological mechanisms underlying ASD etiology, at the cellular level. 

Whole-brain calcium imaging of neural activity

The mechanisms by which signals from the outside world are perceived, processed, and integrated are largely mysterious.  We hope to reveal some of these processes with whole-brain imaging of neural activity while our animals are experiencing sensory stimuli.  This involves expression of GCaMP6 (a genetically encoded calcium indicator developed at HHMI Janelia Research Campus) throughout the brain, combined with selective plane illumination microscopy (SPIM).  You can learn about our home-made SPIM microscopes and bioinformatics approaches on our Methods and Machines page.

To investigate a range of sensory modalities, we have designed microscopes that provide open space around the larva.  This permits us to surround the larva with LCD screens for visual stimuli, auditory speakers, and even microfluidics devices for generating water flow across the animal’s body.  We then look at activity across tens of thousands of neurons while these stimuli are presented alone or in combination.  The result is a map of what types of stimuli elicit what types of neural responses, where the responding neurons are, and what their relationships with each other are.  All of this moves us a little closer to understanding how these senses are encoded and integrated by the brain.

Sensory stimulation imaging



Itia Favre-Bulle, Gilles Vanwallehem, Michael Taylor, Halina Rubinsztein-Dunlop, and Ethan K. Scott (2018). Cellular resolution imaging of vestibular processing across the larval zebrafish brain. Biorxiv.

Michael Taylor, Gilles Vanwalleghem, Itia Favre-Bulle, and Ethan K. Scott (2018). Diffuse light-sheet microscopy for stripe-free imaging of neural populations. Journal of Biophotonics. Published online on 19/06/2018.

Lucy A.L. Heap, Gilles Vanwalleghem, Andrew W. Thompson,Itia A. Favre-Bulle, and Ethan K. Scott (2018).  Luminance changes drive directional startle through a thalamic pathway. Neuron. Published online on 05/07/2018

Lucy Heap, Gilles Claude Vanwalleghem, Andrew Thompson, Itia Favre-Bulle, Halina Rubinsztein-Dunlop, and Ethan K Scott (2018). Hypothalamic projections to the optic tectum in larval zebrafish. Frontiers in Neuroanatomy, 11:135.

Gilles Vanwalleghem, Misha Ahrens, and Ethan K. Scott (2018). Integrative whole-brain neuroscience in larval zebrafish. Current Opinion in Neurobiology.  50: 136-145. 


Gilles Vanwalleghem, Lucy Heap, and Ethan K. Scott (2017). A profile of auditory-responsive neurons in the larval zebrafish brain. Journal of Comparative Neurology, 525 (14): 3031-3043. 

Itia Favre-Bulle, Alexander Stilgoe, Halina Rubinsztein-Dunlop, and Ethan Scott (2017). Optical trapping of otoliths drives vestibular behaviours in larval zebrafish. Nature Communications 8: 630

Lilach Avitan, Zac Pujic, Jan Molter, Matthew Van De Poll, Biao Sun, Haotian Teng, Rumelo Amor, Ethan Scott, and Geoffrey Goodhill (2017). Spontaneous Activity in the Zebrafish Tectum Reorganizes over Development and Is Influenced by Visual Experience. Current Biology, 27 (16): 2407-2419.


Andrew W. Thompson and Ethan K. Scott (2016).
Characterisation of sensitivity and orientation tuning for visually responsive ensembles in the zebrafish tectum.
Scientific Reports, 6 (3487): 1-10 
URL: Thompson et al, 2016.

Lilach Avitan, Zac Pujic, Nicholas Hughes, Ethan K. Scott, and Geoffrey J. Goodhill (2016).
Limitations of neural map topography for decoding spatial information.
The Journal of Neuroscience. 36 (19): 5385-5396. 
URL: Avitan et al, 2016.

Andrew W. Thompson, Gilles C. Vanwalleghem, Lucy A. Heap, and Ethan K. Scott (2016).
Functional profiles of visual, auditory, and water flow responsive neurons in the zebrafish tectum. 
Current Biology. 26: 1-12. 
URL: Thompson et al, 2016.

Kelsey Chalmers, Elizabeth M. Kita, Ethan K. Scott, and Geoffrey J. Goodhill (2016).
Quantitative analysis of axonal branch dynamics in the developing nervous system.
PLoS Computational Biology.  12 (3). 
URL: Chalmers et al, 2016.


Itia A. Favre-Bulle, Daryl Preece, Timo A. Nieminen, Lucy A. Heap, Ethan K. Scott*, and Halina Rubinsztein-Dunlop* (*co-corresponding).
Scattering of Sculpted Light in Intact Brain Tissue, with Implications for Optogenetics.
Scientific Reports. 5: 11501. 
URL: Favre-Bulle et al, 2015.

Jacob H. Hines, Andrew R. Ravanelli, Rani Schwindt, Ethan K. Scott, and Bruce Appel (2015).
Activity-dependent competition for axon selection during myelination in vivo.
Nature Neuroscience. 18: 683-689. 
URL: Hines et al, 2015.

Geoffrey J. Goodhill, Richard A. Faville, Daniel J. Sutherland, Brendan A. Bicknell, Andrew W. Thompson, Zac Pujic, Biao Sun, Elizabeth M. Kita, and Ethan K. Scott (2015).
The dynamics of growth cone morphology. 
BMC Biology.  13:10. 
URL: Goodhill et al, 2015.

Elizabeth M. Kita , Ethan K. Scott, and Geoffrey J. Goodhill (2015).
The influence of activity on axon pathfinding in the optic tectum.
Developmental Neurobiology. Published online February 2015.
URL: Kita et al, 2015.

Elizabeth M. Kita , Ethan K. Scott, and Geoffrey J. Goodhill (2015).
Topographic wiring of the retinotectal connection in zebrafish.
Developmental Neurobiology. 75(6): 542-556.
URL: Kita et al, 2015.


Lucy A. Heap, Chi-Ching Goh, Karin S. Kassahn, and Ethan K. Scott (2013).
Cerebellar output in zebrafish: an analysis of spatial patterns and topography in eurydendroid cell projections.
Frontiers in Neural Circuits.  7: 53.
URL: Heap et al. 2013

Hugh D. Simpson, Elizabeth M. Kita, Ethan K. Scott, and Geoffrey J. Goodhill (2013).
A quantitative analysis of branching, growth cone turning and directed growth in zebrafish retinotectal axon guidance.
Journal of Comparative Neurology.  521: 1409-1429.
URL: Simpson et al. 2013


Isabel Formella, Ethan K. Scott, Tom H.J. Burne, Lauren R. Harms, Ashley Liu, Karly M. Turner, Xiaoying Cui, and Darryl W. Eyles (2012).
Transient Knockdown of Tyrosine Hydroxylase during Development Has Persistent Effects on Behaviour in Adult Zebrafish (Danio rerio).
PLoS One. 7 (8).
URL: Formella et al, 2012.

Joshua Simmich, Eric Staykov, and Ethan K. Scott (2012).
Zebrafish as an appealing model system for optogenetics.
Progress in Brain Research. 196: 145-162. 
URL: Simmich et al, 2012.

Phil McClenahan, Michael Troup, and Ethan K. Scott (2012).
Fin-tail Coordination During Escape and Predatory Behavior in Larval Zebrafish. 
PLoS One. 7(2). 
URL: McClenahan et al, 2012


Thomas Burne, Ethan K. Scott, Bruno van Swinderen, Massimo Hilliard, Judith
Reinhard, Charles Claudianos, Darryl Eyles, and John McGrath (2011).
Big ideas for small brains: what can psychiatry learn from worms, flies, bees and fish?
Molecular Psychiatry. 16: 7-16. 
URL: Burne et al, 2011.


Filippo Del Bene, Claire Wyart, Estuardo Robles, Amanda Tran, Loren Looger, Ethan K, Scott, Ehud Y. Isacoff, and Herwig Baier (2010).
Filtering of visual information in the tectum by an identified neural circuit.
Science. 330: 669-673.
URL: Del Bene et al, 2010.

Linda Nevin, Estuardo Robles, Herwig Baier, and Ethan K. Scott (2010).
Focusing on optic tectum circuitry through the lens of genetics.
BMC Biology. 8: 126.
URL: Nevin et al, 2010.

Shuichi Kani, Young-Ki Bae, Takashi Shimizu, Koji Tanabe, Chie Satoh, Mike Parsons,Ethan K. Scott, Shin-ichi Higashijima and Masahiko Hibi (2010).
Proneural gene-linked neurogenesis in zebrafish cerebellum.
Developmental Biology. 343 (1-2): 1-17.
URL: Kani et al, 2010.


Claire Wyart, Filippo Del Bene, Erica Warp, Ethan K. Scott, Dirk Trauner, Herwig Baier and Ehud Isacoff (2009).
Optogenetic dissection of a behavioural module in the vertebrate spinal cord.
Nature. 461: 407-410. 
URL: Wyart et al, 2009.

Herwig Baier and Ethan K. Scott (2009).
Optics and genetics cross paths in the zebrafish nervous system.
Current Opinions in Neurobiology. 19(5): 553-560. 
URL: Baier and Scott, 2009.

Ethan K. Scott and Herwig Baier (2009).
The cellular architecture of the larval zebrafish tectum, as revealed by Gal4 enhancer trap lines.
Frontiers in Neural Circuits. 3(13).
URL: Scott and Baier, 2009.

Ethan K. Scott (2009).
The Gal4/UAS toolbox in zebrafish: New approaches for defining behavioral circuits.
Journal of Neurochemistry. 110(2): 441-456.
URL: Scott, 2009. 

Lisette A. Maddison, Jainjun Lu, Tristan Victoroff, Ethan K. Scott, Herwig Baier, and Wenbiao Chen. (2009).
A gain-of-function screen in zebrafish identifies a guanylate cyclase with a role in neuronal degeneration.
Molecular Genetics and Genomics. 281(5): 551-563.
URL: Maddison et al, 2009.


Stephanie Szobota, Pau Gorostiza, Filippo Del Bene, Claire Wyart, Doris L. Fortin, Kate Kolstad, Orapim Tulyathan, Matthew Volgraf, Rika Numano, Holly Aaron, Ethan K. Scott, Richard Kramer, John Flannery, Herwig Baier, Dirk Trauner and Ehud Isacoff (2007).
Remote control of neuronal activity with a light-gated glutamate receptor.
Neuron. 54(4): 535-545.
URL: Szobota et al, 2007.

Ethan K. Scott, Lindsay Mason, Aristides B. Arrenberg, Limor Ziv, Nathan J. Gosse, Tong Xiao, Neil C. Chi, Kazuhide Asakawa, Koichi Kawakami, and Herwig Baier (2007).
Targeting neural circuitry in zebrafish using GAL4 enhancer trapping.
Nature Methods. 4(4): 323-326.
URL: Scott et al, 2007.

Opportunities for new researchers

Our lab spans numerous experimental approaches and techniques, and as a result, we need all kinds of expertise.  The core of our lab comprises neuroscientists with interests including developmental neuroscience, circuit function, and behaviour, and we are always looking to add motivated researchers of this type.  Increasingly, experience with coding (Matlab and Python) is desirable, but for the right candidate, this can be learned after arriving in the lab.

The intricate sensory stimuli that we present during our whole-brain imaging are incompatible with off-the-shelf SPIM microscopes, and our optical physics approaches require flexible access to the light paths.  This means that we build our microscopes from the ground up, customised to our needs and to the particular experiments that we are doing at the time.  This vastly increases our experimental capacities, but it also means that we need capable optical physicists on the team.  Our optical physicists build and maintain our SPIM scopes and use them for physics-based techniques including holographic illumination for optogenetics (Favre-Bulle et al, 2015) and optical trapping for vestibular stimulation (Favre-Bulle et al, 2017 and 2018).  We are always looking for ways to expand and improve our optical physics approaches, and are eager to recruit skilled physicists to our team.

With our SPIM microscopes, we produce vast datasets containing activity from hundreds of thousands or millions of neurons. This leaves us with a great need for people who can code solutions for image analysis, data mining, and the detection of salient patterns among these vast data.  Our mathematical and neuroinformatic approaches have grown more sophisticated over the years (see the progression from Thompson et al, 2015 to Vanwalleghem et al, 2017, and Favre-Bulle et al, 2018), but we are constantly seeking new and better ways to make sense of brain-wide neural function from a computational standpoint.  We welcome applications from researchers interested in explaining neural activity mathematically or in developing testable mathematical models for sensory processing.

Positions are available across our research program for undergraduates, honours students, PhD students, and postdocs, and we are happy to entertain new ideas.  If you are interested in joining the lab, please contact Ethan, providing a CV and ideas for the types of project that you would like to carry out.

Find out more about our research environment and how to apply to do a short or long-term research project with us.