Biology subjects

Scott, E. K.

Publications and source records attributed to Scott, E. K..

11 recordsLinked to original sources

bioRxiv2025

Plug-and-Play automated behavioral tracking of zebrafish larvae with DeepLabCut and SLEAP: pre-trained networks and datasets of annotated poses

Zebrafish are an important model system in behavioral neuroscience due to their rapid development and suite of distinct, innate behaviors. Quantifying many of these larval behaviors requires detailed tracking of eye and tail kinematics, which in turn demands imaging at high spatial and temporal resolution, ideally using semi or fully automated tracking methods for throughput efficiency. However, creating and validating accurate tracking models is time-consuming and labor intensive, with many research groups duplicating efforts on similar images. With the goal of developing a useful community resource, we trained pose estimation models using a diverse array of video parameters and a 15-keypoint pose model. We deliver an annotated dataset of free-swimming and head-embedded behavioral videos of larval zebrafish, along with four pose estimation networks from DeepLabCut and SLEAP (two variants of each). We also evaluated model performance across varying imaging conditions to guide users in optimizing their imaging setups. This resource will allow other researchers to skip the tedious and laborious training steps for setting up behavioral analyses, guide model selection for specific research needs, and provide ground truth data for benchmarking new tracking methods. SIGNIFICANCE STATEMENTLarval zebrafish are an emerging model in systems neuroscience, offering unique advantages for linking brain activity to behavior. However, detailed behavioral tracking, essential for such studies, requires time- and labor-intensive annotation and model training. To eliminate this bottleneck, here we provide a high-quality, annotated dataset of zebrafish behaviors for both free-swimming and head-embedded preparations alongside four pre-trained pose estimation models using DeepLabCut and SLEAP. We benchmark models performance across diverse imaging conditions to guide optimal setup choices. This community resource will allow researchers to bypass the most time-consuming stages of data annotation and training, enabling immediate behavioral analysis. By removing this key hurdle, this work will accelerate project initiation, support reproducibility, and provide a foundation for future tracking method development.

animal behavior and cognition↗

bioRxiv2024

Brain-wide circuitry underlying altered auditory habituation in zebrafish models of autism.

Auditory processing is widely understood to occur differently in autism, though the patterns of brain activity underlying these differences are not well understood. The diversity of autism also means brain-wide networks may change in various ways to produce similar behavioral outputs. We used larval zebrafish to investigate auditory habituation in four genetic lines relevant to autism: fmr1, mecp2, scn1lab and cntnap2. In free-swimming behavioral tests, we found each line had a unique profile of auditory hypersensitivity and/or delayed habituation. Combining the optical transparency of larval zebrafish with genetically encoded calcium indicators and light-sheet microscopy, we then observed brain-wide activity at cellular resolution during auditory habituation. As with behavior, each line showed unique alterations in brain-wide spontaneous activity, auditory processing, and adaptation in response to repetitive acoustic stimuli. We also observed commonalities in activity across our genetic lines that indicate shared circuit changes underlying certain aspects of their behavioral phenotypes. These were predominantly in regions involved in sensory integration and sensorimotor gating rather than primary auditory areas. Overlapping phenotypes include differences in the activity and functional connectivity of the telencephalon, thalamus, dopaminergic regions, and the locus coeruleus, and excitatory/inhibitory imbalance in the cerebellum. Unique phenotypes include loss of activity in the habenula in scn1lab, increased activity in auditory regions in fmr1, and differences in network activity over time in mecp2 and cntnap2. Comparing these distinct but overlapping brain-wide auditory networks furthers our understanding of how diverse genetic factors can produce similar behavioral effects through a range of circuit- and network-scale mechanisms.

neuroscience↗

bioRxiv2024

Probabilistic modeling reveals coordinated social interaction states and their multisensory bases

Social behavior across animal species ranges from simple pairwise interactions to thousands of individuals coordinating goal-directed movements. Regardless of the scale, these interactions are governed by the interplay between multimodal sensory information and the internal state of each animal. Here, we investigate how animals use multiple sensory modalities to guide social behavior in the highly social zebrafish (Danio rerio) and uncover the complex features of pairwise interactions early in development. To identify distinct behaviors and understand how they vary over time, we developed a new hidden Markov model with constrained linear-model emissions to automatically classify states of coordinated interaction, using the movements of one animal to predict those of another. We discovered that social behaviors alternate between two interaction states within a single experimental session, distinguished by unique movements and timescales. Long-range interactions, akin to shoaling, rely on vision, while mechanosensation underlies rapid synchronized movements and parallel swimming, precursors of schooling. Altogether, we observe spontaneous interactions in pairs of fish, develop novel hidden Markov modeling to reveal two fundamental interaction modes, and identify the sensory systems involved in each. Our modeling approach to pairwise social interactions has broad applicability to a wide variety of naturalistic behaviors and species and solves the challenge of detecting transient couplings between quasi-periodic time series. HIGHLIGHTSO_LIZebrafish exhibit distinct correlated interaction states with unique timescales. C_LIO_LIDelayed interactions are visual while synchronization requires mechanosensation. C_LIO_LIA new class of hidden Markov model segments social interactions into discrete states. C_LIO_LIStates alternate within a session, revealing real-time dynamics of social behavior. C_LI

animal behavior and cognition↗

bioRxiv2024

Evidence for auditory stimulus-specific adaptation but not deviance detection in larval zebrafish brains

Animals receive a constant stream of sensory input, and detecting changes in this sensory landscape is critical to their survival. One signature of change detection in humans is the auditory mismatch negativity (MMN), a neural response to unexpected stimuli that deviate from a predictable sequence. This process requires the auditory system to adapt to specific repeated stimuli while remaining sensitive to novel input (stimulus-specific adaptation). MMN was originally described in humans, and equivalent responses have been found in other mammals and birds, but it is not known to what extent this deviance detection circuitry is evolutionarily conserved. Here we present the first evidence for stimulus-specific adaptation in the brain of a teleost fish, using whole-brain calcium imaging of larval zebrafish at single-neuron resolution with selective plane illumination microscopy. We found frequency-specific responses across the brain with variable response amplitudes for frequencies of the same volume, and created a loudness curve to model this effect. We presented an auditory oddball stimulus in an otherwise predictable train of pure tone stimuli, and did not find a population of neurons with specific responses to deviant tones that were not otherwise explained by stimulus-specific adaptation. Further, we observed no deviance responses to an unexpected omission of a sound in a repetitive sequence of white noise bursts. These findings extend the known scope of auditory adaptation and deviance responses across the evolutionary tree, and lay groundwork for future studies to describe the circuitry underlying auditory adaptation at the level of individual neurons.

neuroscience↗

bioRxiv2024

Brain-wide impacts of sedation on spontaneous activity and auditory processing in larval zebrafish

Despite their widespread use, we have limited knowledge of the mechanisms by which sedatives mediate their effects on brain-wide networks. This is, in part, due to the technical challenge of observing activity across large populations of neurons in normal and sedated brains. In this study, we examined the effects of the sedative dexmedetomidine, and its antagonist atipamezole, on spontaneous brain dynamics and auditory processing in zebrafish larvae. Our brain-wide, cellular-resolution calcium imaging reveals, for the first time, the brain regions involved in these network-scale dynamics and the individual neurons that are affected within those regions. Further analysis reveals a variety of dynamic changes in the brain at baseline, including marked reductions in spontaneous activity, correlation, and variance. The reductions in activity and variance represent a "quieter" brain state during sedation, an effect that causes highly correlated evoked activity in the auditory system to stand out more than it does in un-sedated brains. We also observe a reduction in auditory response latencies across the brain during sedation, suggesting that the removal of spontaneous activity leaves the core auditory pathway free of impingement from other non-auditory information. Finally, we describe a less dynamic brain-wide network during sedation, with a higher energy barrier and a lower probability of brain state transitions during sedation. In total, our brain-wide, cellular-resolution analysis shows that sedation leads to quieter, more stable, and less dynamic brain, and that against this background, responses across the auditory processing pathway become sharper and more prominent. Significance StatementAnimals brain states constantly fluctuate in response to their environment and context, leading to changes in perception and behavioral choices. Alterations in perception, sensorimotor gating, and behavioral selection are hallmarks of numerous neuropsychiatric disorders, but the circuit- and network-level underpinnings of these alterations are poorly understood. Pharmacological sedation alters perception and responsiveness and provides a controlled and repeatable manipulation for studying brain states and their underlying circuitry. Here, we show that sedation of larval zebrafish with dexmedetomidine reduces brain-wide spontaneous activity and locomotion but leaves portions of brain-wide auditory processing and behavior intact. We describe and computationally model changes at the levels of individual neurons, local circuits, and brain-wide networks that lead to altered brain states and sensory processing during sedation.

neuroscience↗

bioRxiv2020

Broad frequency sensitivity and complex neural coding in the larval zebrafish auditory system

Most animals have complex auditory systems that identify salient features of the acoustic landscape to direct appropriate responses. In fish, these features include the volume, frequency, complexity, and temporal structure of auditory stimuli transmitted through water. Larval fish have simple brains compared to adults, but swim freely and depend on sophisticated sensory processing for survival. Zebrafish larvae, an important model for studying brain-wide neural networks, have thus far been found to possess a rudimentary auditory system, sensitive to a narrow range of frequencies and without evident sensitivity to auditory features that are salient and ethologically important to adult fish. Here, we have combined a novel method for delivering water-borne sounds, a diverse assembly of acoustic stimuli, and whole-brain calcium imaging to describe the responses of individual auditory neurons across the brains of zebrafish larvae. Our results reveal responses to frequencies ranging from 100Hz to 4kHz, with evidence of frequency discrimination from 100Hz to 2.5kHz. Frequency-selective neurons are located in numerous regions of the brain, and neurons responsive to the same frequency are spatially grouped in some regions. Using functional clustering, we identified categories of neurons that are selective for pure tones of a single frequency, white noise, the sharp onset of auditory stimuli, and stimuli involving a gradual crescendo. These results suggest a more nuanced auditory system than has previously been described in larval fish and provide insights into how a young animals auditory system can both function acutely and serve as the scaffold of a more complex adult system.

neuroscience↗

bioRxiv2020

Functional melanoma cell heterogeneity is regulated by MITF-dependent cell-matrix interactions

Phenotypic heterogeneity of cancer cells plays a critical role in shaping treatment response. This type of heterogeneity is organized spatially with specific phenotypes, such as sharply demarcated clusters of proliferating and cell cycle-arrested cells, predominating within discrete domains within a tumor. What determines the occurrence of specific tumor cell phenotypes in distinct microdomains of solid cancers is poorly understood. Here, we show that in melanoma spatial organization of phenotypic heterogeneity is dictated by the expression and activity of MITF. We reveal that this lineage survival oncogene controls ECM composition and organization, and ROCK-driven mechanotransduction through focal adhesion maturation and actin cytoskeleton functionality. In turn, altered tumor microarchitecture and structural integrity impact tumor solid stress which then mediates phenotypic heterogeneity through p27Kip1. Rho-ROCK-myosin signaling is necessary to transmit the effect of the reciprocal cell-ECM regulation into phenotypic heterogeneity. Our findings place cell-ECM crosstalk as a central driver of phenotypic tumor heterogeneity. SignificancePhenotypic heterogeneity is a major culprit of cancer therapy failure. We demonstrate that phenotypic heterogeneity is controlled through tumor cell-ECM crosstalk resulting in altered tumor microarchitecture, mechanotransduction and Rho-ROCK-myosin signaling. Melanoma shares these physical properties with any solid cancer underscoring the importance of our findings for therapeutically targeting this phenomenon.

cancer biology↗

bioRxiv2020

Brain-wide mapping of water flow perception in zebrafish

Information about water flow, detected by lateral line organs, is critical to the behavior and survival of fish and amphibians. While certain specific aspects of water flow processing have been revealed through electrophysiology, we lack a comprehensive description of the neurons that respond to water flow and the network that they form. Here, we use brain-wide calcium imaging in combination with microfluidic stimulation to map out, at cellular resolution, all neurons involved in perceiving and processing water flow information in larval zebrafish. We find a diverse array of neurons responding to forward flow, reverse flow, or both. Early in this pathway, in the lateral line ganglia, these are almost exclusively neurons responding to the simple presence of forward or reverse flow, but later processing includes neurons responding specifically to flow onset, representing the accumulated volume of flow during a stimulus, or encoding the speed of the flow. The neurons reporting on these more nuanced details are located across numerous brain regions, including some not previously implicated in water flow processing. A graph theory-based analysis of the brain-wide water flow network shows that a majority of this processing is dedicated to forward flow detection, and this is reinforced by our finding that details like flow velocity and the total volume of accumulated flow are only encoded for the simulated forward direction. The results represent the first brain-wide description of processing for this important modality, and provide a departure point for more detailed studies of the flow of information through this network. Significance statementIn aquatic animals, the lateral line is important for detecting water flow stimuli, but the brain networks that interpret this information remain mysterious. Here, we have imaged the activity of individual neurons across the entire brains of larval zebrafish, revealing all response types and their brain locations as water flow processing occurs. We find some neurons that respond to the simple presence of water flow, and others that are attuned to the flows direction, speed, duration, or the accumulated volume of water that has passed during the stimulus. With this information, we modeled the underlying network, describing a system that is nuanced in its processing of water flow simulating forward motion but rudimentary in processing flow in the reverse direction.

neuroscience↗

bioRxiv2019

Multiscale activity imaging in the mammary gland reveals how oxytocin enables lactation

The mammary epithelium is indispensable for the continued survival of more than 5000 mammalian species. For some, the volume of milk ejected in a single day exceeds their entire blood volume. Here, we unveil the spatiotemporal properties of physiological signals that orchestrate milk ejection. Using quantitative, multidimensional imaging of mammary cell ensembles, we reveal how stimulus evoked Ca2+ oscillations couple to contractions in basal epithelial cells. Moreover, we show that Ca2+-dependent contractions generate the requisite force to physically deform the innermost layer of luminal cells, compelling them to discharge the fluid that they produced and housed. Through the collective action of thousands of these biological positive displacement pumps, each linked to a contractile ductal network, milk is delivered into the mouth of the dependent neonate, seconds after the command. Significance StatementThe mammary gland is functional for only a brief period of a females lifetime--if at all. During this time, it operates not for the survival of the individual, but for the survival of her species. Here, we visualize the nature of alveolar contractions in the functionally-mature mammary gland, revealing how specialized epithelial cells, which possess the ability to behave like smooth muscle cells, undergo Ca2+-dependent contractions. We demonstrate that individual oscillators can be electrically coupled to achieve global synchrony, a phenomenon that has not yet been observed in the mammary gland. By imaging activity across scales, we provide a window into the organization, dynamics and role of epithelial Ca2+ oscillations in the organ principally responsible for sustaining neonatal life in mammals.

cell biology↗

bioRxiv2019

Early migration of precursor neurons initiates cellular and functional regeneration after spinal cord injury in zebrafish.

Zebrafish have a remarkable capacity to regenerate following spinal cord (SC) injury but the responsible cellular events are not well understood. We used in vivo imaging and genetics to pin-point specific cellular processes controlling SC regeneration in zebrafish. We identified two temporally and mechanistically distinct phases of cellular regeneration in the SC. The initial phase relies on migration of precursor neurons to the injury, enabling rapid functional recovery, and activation of quiescent neural progenitor cells (NPCs). A second phase of regenerative neurogenesis compensates for both the lost tissue and cells depleted due to precursor neuron migration. We propose a critical role of precursor neurons recruitment in initiating neuronal circuit recovery and buying sufficient time for regenerative neurogenesis to take place. Taken together, our data suggests an unanticipated role of precursor cell recruitment in driving neural repair and functional recovery during the regenerative response. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=110 SRC="FIGDIR/small/539940v1_ufig1.gif" ALT="Figure 1"> View larger version (45K): org.highwire.dtl.DTLVardef@12c5be9org.highwire.dtl.DTLVardef@1461e99org.highwire.dtl.DTLVardef@82d28aorg.highwire.dtl.DTLVardef@cc6870_HPS_FORMAT_FIGEXP M_FIG C_FIG

neuroscience↗

bioRxiv2018

Cellular resolution imaging of vestibular processing across the larval zebrafish brain

The vestibular system, which reports on motion and gravity, is essential to postural control, balance, and egocentric representations of movement and space. The motion needed to stimulate the vestibular system complicates studying its circuitry, so we previously developed a method for fictive vestibular stimulation in zebrafish, using optical trapping to apply physical forces to the otoliths. Here, we combine this fictive stimulation with whole-brain calcium imaging at cellular resolution, delivering a comprehensive map of the brain regions and cellular responses involved in basic vestibular processing. We find these responses to be broadly distributed across the brain, with unique profiles of cellular responses and topography in each brain region. The most widespread and abundant responses involve excitation that is rate coded to the stimulus strength. Other responses, localized to the telencephalon and habenulae, show excitation that is only weakly rate coded and that is sensitive to weak stimuli. Finally, numerous brain regions contain neurons that are inhibited by vestibular stimuli, and these inhibited neurons are often tightly localised spatially within their regions. By exerting separate control over the left and right otoliths, we explore the laterality of brain-wide vestibular processing, distinguishing between neurons with unilateral and bilateral vestibular sensitivity, and revealing patterns by which conflicting vestibular signals from the two ears can be mutually cancelling. Our results show a broader and more extensive network of vestibular responsive neurons than has previously been described in larval zebrafish, and provides a framework for more targeted studies of the underlying functional circuits.

neuroscience↗