Neural circuits for evidence accumulation and decision making in larval zebrafish
Open accessAbstract
To make appropriate decisions, animals need to accumulate sensory evidence. Simple integrator models can explain many aspects of such behavior, but how the underlying computations are mechanistically implemented in the brain remains poorly understood. Here we approach this problem by adapting the random-dot motion discrimination paradigm, classically used in primate studies, to larval zebrafish. Using their innate optomotor response as a measure of decision making, we find that larval zebrafish accumulate and remember motion evidence over many seconds and that the behavior is in close agreement with a bounded leaky integrator model. Through the use of brain-wide functional imaging, we identify three neuronal clusters in the anterior hindbrain that are well suited to execute the underlying computations. By relating the dynamics within these structures to individual behavioral choices, we propose a biophysically plausible circuit arrangement in which an evidence integrator competes against a dynamic decision threshold to activate a downstream motor command.
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The open-source simZFish faithfully reproduces the zebrafish OMR using experimentally observed neural activity.
“Benefitting from detailed experimental data (25, 29–34) and recent advances in physics simulation technologies (35), our open-source simZFish faithfully reproduces the zebrafish OMR, utilizing experimentally observed neural activity (25).”
From Artificial embodied circuits uncover neural architectures of vertebrate visuomotor behaviors (2025) · cites this paper as [29]
The Results sections on motion integration report experimentally observed neural activity in larval zebrafish, and the Introduction identifies their motion-following behavior as the optomotor response (page numbers unavailable). The paper also compares a network model with measured neural dynamics, but it does not assess simZFish or establish that simZFish faithfully reproduces the OMR. (LLM, conf=0.85)
Experimental — accuracy not yet measuredCurrent models of zebrafish visuomotor transformations rely on correlation-based neural activity, lack realistic retina or motor representations, omit neural connectivity manipulation, and exclude closed-loop observations of neural activation during behavior.
“Current models of zebrafish visuomotor transformations rely on correlation-based neural activity, lack realistic representations of the retina or motor systems (25, 29), omit the ability to manipulate neural connectivity, and exclude closed-loop observations of neural activation during behavior, which limits the integrative investigation of the system within its sensory and physical environment.”
From Artificial embodied circuits uncover neural architectures of vertebrate visuomotor behaviors (2025) · cites this paper as [29]
The Online methods (Algorithmic modeling; Anterior hindbrain network modeling, pages unavailable) describe simplified sensory inputs and swim-bout outputs, consistent with the claim that the model lacks realistic retina and motor-system representations. But the same methods say the authors varied connectivity weights and modeled visual feedback. The Two-photon calcium imaging methods also describe simultaneous neural imaging and behavioral readout with stimulus changes triggered by detected bouts, so the broader claims of omitted connectivity manipulation and excluded closed-loop observations are not supported. (LLM, conf=0.85)
Experimental — accuracy not yet measuredNeural circuits involved in egocentric orientation in teleost fish include mainly several stages of the sensory and perceptual systems, some sensorimotor forebrain circuits, the optic tectum, the cerebellum, and various premotor centers and descending pathways in the brainstem and medulla.
“These neural circuits include mainly several stages of the sensory and perceptual systems, some sensorimotor forebrain circuits, the optic tectum, the cerebellum, and various premotor centers and descending pathways in the brainstem and medulla”
From Spatial Cognition in Teleost Fish: Strategies and Mechanisms (2021) · cites this paper as [107]
The Results sections on motion integration and anterior hindbrain imaging identify sensory processing in the pretectum, anterior hindbrain circuits, and projections toward premotor areas (page numbers unavailable). They do not establish the claimed circuit inventory for egocentric orientation in teleost fish, including sensorimotor forebrain circuits, the optic tectum, the cerebellum, or descending pathways in the medulla. (LLM, conf=0.86)
Experimental — accuracy not yet measuredOutput neurons in the intermediate and deep layers of the teleost optic tectum are able to initiate orientation or avoidance responses through their projections to the reticular formation and other pre-motor cell groups in the brainstem, which activate motoneurons in oculomotor nuclei and spinal cord that control orienting eye and body movements.
“the output neurons in the intermediate and deep layers of the teleost optic tectum are able to initiate orientation or avoidance responses through their projections to the reticular formation and other pre-motor cell groups in the brainstem, which in turn activate the motoneurons in the oculomotor nuclei and spinal cord that control orienting eye and body movements”
From Spatial Cognition in Teleost Fish: Strategies and Mechanisms (2021) · cites this paper as [107]
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Self-citation
- Authors
- Bahl, A., & Engert, F.
- Affiliations
- Harvard University (US)
- Corresponding author
- Bahl, Armin
- Venue
- Nature Neuroscience
- Published
- 2019-12-02
- Volume
- 23
- Issue
- 1
- Pages
- 94-102
- ISSN
- 1097-6256 (ISSN-L)
- 1546-1726
- PMC
- PMC7295007
- OpenAlex
- W2991987583
- Cited by
- 166
- References
- 61
- Citations by year
- 2026: 28 · 2025: 31 · 2024: 28 · 2023: 22 · 2022: 15 · 2021: 30 · 2020: 11 · 2018: 1
- FWCI
- 8.29
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Nature Neuroscience (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- KOPS (University of Konstanz) (submittedVersion)
- Funders
- Human Frontier Science Program (LT000626/2016)
- Topics
- Life Sciences › Neuroscience › Cognitive Neuroscience › Neural dynamics and brain function
- Life Sciences › Neuroscience › Cognitive Neuroscience › Visual perception and processing mechanisms
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Cell Biology › Zebrafish Biomedical Research Applications
- Keywords
- evidence accumulation, decision-making, zebrafish larvae, optomotor response, decision threshold, motor command, neural circuits
- MeSH terms
- Animals, Brain, Decision Making, Larva, Models, Neurological, Neural Pathways, Neurons, Zebrafish
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