About

Florian Engert is a Professor of Molecular and Cellular Biology at Harvard University. His laboratory focuses on understanding how biological structures produce complex behaviors generated by the nervous system. The research aims to build a comprehensive, multi-level picture of simple neural circuits to advance the understanding of brain function and neuronal activity underlying complex behaviors. A primary approach involves identifying and examining neural circuits controlling behavior in larval zebrafish, a translucent vertebrate that exhibits visually induced behaviors. Using behavioral assays combined with calcium indicators and two-photon microscopy, his lab monitors neuronal activity throughout the fish brain in awake, intact preparations. The research also explores how behavioral variations are reflected in neuronal activity, developing quantitative learning assays and tools for in vivo monitoring and control of neural activity in freely swimming larvae.

Research topics

• Neuroscience
• Biology
• Computer Science
• Bioinformatics
• Physics
• Human–computer interaction
• Fishery
• Psychology

Selected publications

• Dissecting Larval Zebrafish Hunting using Deep Reinforcement Learning Trained RNN Agents

  2026-01-01

  articleOpen access

  Larval zebrafish hunting provides a tractable setting to study how ecological and energetic constraints shape adaptive behavior in both biological brains and artificial agents. Here we develop a minimal agent-based model, training recurrent policies with deep reinforcement learning in a bout-based zebrafish simulator. Despite its simplicity, the model reproduces hallmark hunting behaviors -- including eye vergence-linked pursuit, speed modulation, and stereotyped approach trajectories -- that closely match real larval zebrafish. Quantitative trajectory analyses show that pursuit bouts systematically reduce prey angle by roughly half before strike, consistent with measurements. Virtual experiments and parameter sweeps vary ecological and energetic constraints, bout kinematics (coupled vs. uncoupled turns and forward motion), and environmental factors such as food density, food speed, and vergence limits. These manipulations reveal how constraints and environments shape pursuit dynamics, strike success, and abort rates, yielding falsifiable predictions for neuroscience experiments. These sweeps identify a compact set of constraints -- binocular sensing, the coupling of forward speed and turning in bout kinematics, and modest energetic costs on locomotion and vergence -- that are sufficient for zebrafish-like hunting to emerge. Strikingly, these behaviors arise in minimal agents without detailed biomechanics, fluid dynamics, circuit realism, or imitation learning from real zebrafish data. Taken together, this work provides a normative account of zebrafish hunting as the optimal balance between energetic cost and sensory benefit, highlighting the trade-offs that structure vergence and trajectory dynamics. We establish a virtual lab that narrows the experimental search space and generates falsifiable predictions about behavior and neural coding.

  PublisherOA PDFDOI

• A neuron-glia circuit anticipates hypoxia to regulate organismal oxygen use

  bioRxiv (Cold Spring Harbor Laboratory) · 2026-04-14

  articleOpen access

  Abstract Organisms must regulate metabolic resources such as oxygen (O 2 ) and nutrients despite environmental variability and the energetic costs of their own actions 1–3 . Such regulation can occur reactively, through homeostatic corrections of recent imbalances, or predictively, through allostatic adjustments that anticipate future demand 4,5 . Predictive regulation is particularly important because metabolic resources often continue to be consumed for seconds to minutes after motor actions cease as tissues repay incurred costs, making it advantageous to prevent depletion before it occurs 6 . However, the cellular and circuit mechanisms for allostatic control remain largely unknown 5,7,8 . Using whole-brain neuronal and astroglial imaging and O 2 measurements in behaving zebrafish, we identified a noradrenergic–astroglial circuit that detects, anticipates, and prevents internal O 2 depletion. We found that swimming exacerbated internal hypoxia with a multi-second delay, but behavioral adaptations occurred before such self-generated hypoxia manifested, suggesting predictive control, confirmed using computational modeling. Noradrenergic neurons in the nucleus of the solitary tract directly detected brain hypoxia and received efference copies of swimming actions; these inputs summed at the level of membrane voltage to increase spiking and norepinephrine release when actions and resource scarcity co-occurred. Astroglia integrated noradrenergic input into prolonged Ca 2+ elevation that tracked the O 2 cost of recent actions and thereby predicted O 2 debt relative to O 2 availability, rising ~8 s before O 2 fell. This astroglial prediction reorganized brain-wide activity to suppress locomotion and promote respiration, preempting O 2 depletion. Silencing noradrenergic neurons or astroglial signaling abolished these hypoxia coping behaviors, whereas selective activation evoked them. This neuronal–astroglial mechanism constitutes a predictive control system that integrates physiological state with behavioral intent to avert metabolic crisis, revealing a cellular substrate for proactive energy management.

  PublisherDOI

• Lrrn-mediated retinal ganglion cell targeting drives visual circuit assembly for brightness and contrast detection

  Science Advances · 2026-01-23 · 1 citations

  articleOpen access

  Brightness and contrast are fundamental features of vision, crucial for object detection, environmental navigation, and feeding. Here, we identify a brightness- and contrast-processing circuit in the zebrafish visual system and uncover the role of leucine-rich repeat neuronal (Lrrn) cell adhesion molecules (CAMs) in regulating its assembly. We show that deep-projecting retinal ganglion cells serve as the first synaptic relay to the brain, requiring Lrrn2 and Lrrn3a for precise axonal targeting within the optic tectum. Using a new reporter line, we achieved high-resolution mapping of this previously undercharacterized vertebrate visual circuit. Genetic disruption of Lrrn CAMs leads to disorganization of the circuit and impairments in brightness and contrast sensitivity, resulting in deficits in visually guided behavior. Additionally, ultrastructural circuit reconstruction and functional imaging analysis identified both its synaptic partners and revealed its critical role in luminance processing. These studies define a core visual processing pathway and establish Lrrn CAMs as essential molecular drivers of its assembly.

  PublisherDOI

• Chronic Artificial Light Pollution Disrupts Sleep and Neuronal Genomic Stability in Wild Reef Fish

  SSRN Electronic Journal · 2026-01-01

  preprintOpen access
  PublisherDOI

• Synchronization of behavioral and cardiac dynamics in larval zebrafish

  Cell Reports · 2026-02-01 · 1 citations

  articleOpen access

  Animals reprioritize behavioral goals in response to internal physiological states. Using larval zebrafish, we investigated whether engagement with a visuomotor task, the optomotor response (OMR), is coupled to cardiac dynamics. We discovered that threats lead to tachycardia that is synchronized with behavioral suppression. The change in heart rate is represented in the activity of specific neuronal populations. Severing the input to the sympathetic ganglia or ablating the vagus nerve revealed that the threat-related changes to behavioral state do not require interoceptive pathways. Direct tachycardic optopacing of the heart similarly suppressed the OMR response, but by reducing cardiac filling during diastole, thereby impacting oxygen delivery to the CNS. Optopacing also changed the activity of specific brain regions but in neurons distinct from those associated with threat-induced tachycardia. These cardiac function-associated central changes may have relevance to autonomic imbalances in anxiety, stress, and orthostatic disorders.

  PublisherDOI

• A lineage-based model of scalable positional information in vertebrate brain development

  Neuron · 2026-03-02 · 2 citations

  article
  PublisherDOI

• Social interactions in medaka fish depend on discrete kinematic states of swimming behavior

  Current Biology · 2026-02-17

  articleOpen accessSenior author

  we tested how medaka translate social information from neighbors into actions across these kinematic states. The models revealed distinct computations governing social information processing and movement responses in each state. Moreover, social responsiveness varied significantly between states: it was strongest during constant-speed epochs, intermediate during accelerations, and lowest during decelerations. These findings highlight discrete behavioral modes as key modulators of social interaction computations underlying collective behavior.

  PublisherDOI

• Cardiac interoception impacts behavior and brain-wide neuronal dynamics

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-04-29 · 1 citations

  preprintOpen access

  SUMMARY We sought to explore the question as to whether an animal’s behavior can be modified by internal physiological changes. We focused on the optomotor response, in which an animal moves in response to visual gratings, because it is quantitative, robust, and evolutionarily conserved. Using larval zebrafish, we demonstrate that engagement in the optomotor response is inversely related to heart rate. We modulate heart rate by external threat, activation or blockade of the sympathetic nervous system, pharmacological blockade of the cardiac pacemaker channel, and direct optogenetic pacing of the heart, and find that the correlation persists through all perturbations. We find neurons in the primary sensory ganglia and several regions of the brain whose activity reflects changes in heart rate, some more active during bradycardia and some during tachycardia. Specifically, we show that the area postrema, known to be a center of cardiovascular integration, shows particularly strong encoding of heart rate, both following threat and during optogenetic cardiac pacing. We suggest that there may be neural mechanisms to assess heart rate changes over time, and that this interoceptive measurement is used to regulate other neural circuits and behavioral output.

  PublisherOA PDFDOI

• Fishexplorer: A multimodal cellular atlas platform for neuronal circuit dissection in larval zebrafish

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-07-15 · 1 citations

  preprintOpen access

  Understanding how neural circuits give rise to behavior requires comprehensive knowledge of neuronal morphology, connectivity, and function. Atlas platforms play a critical role in enabling the visualization, exploration, and dissemination of such information. Here, we present FishExplorer, an interactive and expandable community platform designed to integrate and analyze multimodal brain data from larval zebrafish. FishExplorer supports datasets acquired through light microscopy (LM), electron microscopy (EM), and X-ray imaging, all co-registered within a unified spatial coordinate system which enables seamless comparison of neuronal morphologies and synaptic connections. To further assist circuit analysis, FishExplorer includes a suite of tools for querying and visualizing connectivity at the whole-brain scale. By integrating data from recent large-scale EM reconstructions (presented in companion studies), FishExplorer enables researchers to validate circuit models, explore wiring principles, and generate new hypotheses. As a continuously evolving resource, FishExplorer is designed to facilitate collaborative discovery and serve the growing needs of the teleost neuroscience community.

  PublisherOA PDFDOI

• Swimming motions evoke Piezo1-dependent Ca2+ events in vascular endothelial cells of larval zebrafish

  Current Biology · 2025-11-13 · 3 citations

  articleOpen access
  PublisherOA PDFDOI

Recent grants

• NIH Grant DP1OD008240

  NIH · $845k · 2012

• NIH Grant RC2NS069407

  NIH · $3.1M · 2012

• CRCNS US-German Research Proposal: Neural Computations Underlying Mechanical -Flow Sensing in Zebrafish

  NSF · $507k · 2019–2022

• NIH Grant R24NS086601

  NIH · $1.2M · 2019

• The Heart and the Mind: An Integrative Approach to Brain-Body Interactions in the Zebrafish

  NIH · $65.3M · 2017–2027

Frequent coauthors

• Alexander F. Schier

  University of Basel

  96 shared

• Simone Fulda

  University Hospital Ulm

  55 shared

• Owen Randlett

  Université Claude Bernard Lyon 1

  46 shared

• Misha B. Ahrens

  Janelia Research Campus

  32 shared

• Martin Haesemeyer

  The Ohio State University

  30 shared

• Lilly Magdalena Weiβ

  26 shared

• Rubén Portugués

  Max Planck Institute of Neurobiology

  23 shared

• Alex Chen

  Harvard University Press

  22 shared