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Zebrafish vs. Mouse Models: A New Standard in Behavioral Assays

The Rise of Zebrafish Research

In the realm of neuroscience, behavioral studies using animal models are essential for understanding brain functions and developing treatments for neurodegenerative diseases. Traditionally, rodents such as mice have dominated this space, being central to numerous behavioral studies and genetic research due to their well-characterized neurological pathways and the extensive mouse model databases available. However, the zebrafish (Danio rerio) has emerged as a formidable alternative, offering unique advantages that complement and, in some cases, surpass those offered by mouse models.

The genetic similarity of zebrafish share with humans, as well as their transparent embryos, makes them an excellent choice for in vivo imaging and genetic manipulation studies, particularly in the field of developmental biology and neurobehavioral genetics. The rapid development and transparent zebrafish embryos offer unique advantages for embryonic development studies, making zebrafish a compelling model for in vivo development embryonic phenotype analysis. The affordability of housing zebrafish, along with their short generation time, large brood size, lower cost, and fewer regulatory constraints under institutional animal care, makes them an economical and expedient model for studying both behavioral and neural processes.

This shift in preference highlights the ongoing debate in the scientific community about zebrafish vs. mouse models, examining the efficacy and applicability of each in neuroscience research, particularly in the study of clinical phenotypes and behavioral responses. Zebrafish, although a relatively new player in the fields of genetics and neuroscience have seen an exponential increase in their use for behavioral assays over recent decades. The translation of animal behavior from terrestrial to aquatic environments is complex, yet ongoing research is steadily mapping out congruent brain processes and methods to study them.

For some applications, the zebrafish has even emerged as the preferred model. This progress positions zebrafish as an increasingly valuable asset in both basic and translational neuroscience research, especially when considering genetic background and immune response in the context of patients with mutations. This guide aims to assist researchers in selecting zebrafish behavioral assays that closely correspond to established rodent models, thereby enhancing the integration of zebrafish into advanced neuroscientific investigations.

Comparing Mouse to Zebrafish Models for Behavioral Discovery

Motor Activity and Coordination

  • Larval Locomotion Assay1 – Compatible with automated platforms and high throughput compound screening with multiple parameters of locomotion indexed, showcasing a behavioral phenotype that aligns with function mutation studies.

  • Adult Locomotion Assay1 – With automated tracking, provides rich phenotypic data at higher throughput and shorter timelines than rodents, aiding in the exploration of neurological phenotypes and pathogen exposure effects.

Anxiety and Depression

  • Tank Diving Assay 2,3– Zebrafish, like many other fish species, dive defensively in response to a threat. When zebrafish are introduced to an unfamiliar tank, they tend to dive to the bottom and gradually rise to upper levels over several minutes. This behavior is well characterized in zebrafish and automated approaches have been developed for quantification, serving as experimental evidence for the study of autoimmune response.
  • Thigmotaxis 4– This term commonly refers to the tendency of rodents to cling to the outer walls of an enclosure in an open field test. Fish likewise will spend more time swimming near the walls of an unfamiliar tank or well in a microplate, particularly when under stress. 3,5 This is one of multiple behaviors that lend themselves to high throughput measurement in a microplate format.1

Spatial Learning and Memory

  • Conditioned Place Preference

    3,6– Analogous to the rodent assay of the same name, fish are placed in a tank with two or more rooms containing different rewards or punishments, highlighting the functional role of neuronal activity in associative memory.
  • T-Maze or Plus Maze

    7– Also directly analogous to the rodent version. A fish is presented with a choice of two or more differing paths to address questions of learning and cognition as well as navigation.
  • Exploratory Biting

    8– Fish instinctively bite a new object placed in their habitat to learn about what it is. The biting ceases as they gain familiarity with the object. Similar to Novel Object Recognition in which rodents spend more time with new objects than familiar ones in their habitats.

Associative memory

  • Place preference and T-maze assays (described above)

  • Tap-Elicited Startle Reflex

    9– Uses larval escape reflex as a high-throughput readout for neuronal function.
  • Rotating Drum Assay

    10,11– A fish will hide behind a central cylinder in response to a threat-a vertical band on a rotating drum-rotating around its habitat. Also assays the effects of any treatments on vision.
  • Three-chamber Maze

    12– Variation on T-maze to assess non-spatial learning.
  • Shuttle Box

    13– Rapid associative learning assay used to study cognitive impairment.

Social Behavior

  • Shoaling behavior

    14,15– Tests the behavior of a group of fish or a single fish within a conspecific (same species/strain) group.6), illustrating natural fish behaviors and providing insights into the social interaction test dynamics.
  • Social Group Preference

    3,16,17– Scores activity of a fish separated from two distinct groups.
  • Social Interaction Test

    3,16– fish presented with a conspecific partner separated by a barrier
  • Mirror biting test

    16– Tests aggression through presentation of a conspecific challenger.


Navigating the complexities of neuroscience demands a nuanced approach, where the selection of assays should always be guided by their validity in addressing specific questions. Think of our guide not as a definitive map but as a reliable compass, offering a strategic starting point for choosing the most appropriate experimental strategy. Recognizing the inherent differences in accessibility to neuronal processes between zebrafish and mice, our guide emphasizes the importance of selecting assays tailored to the unique demands of your research inquiries, including considerations for animal facilities and the use of 24-well plates in behavioral experiments.

InVivo Biosystems: Your Research Parter

InVivo Biosystems, a company that originated from the University of Oregon – the birthplace of zebrafish research under George Streisinger18 – is situated at a hub of zebrafish expertise. This includes collaboration with multiple institutes at the University of Oregon and the Zebrafish International Resource Center (ZIRC). Leveraging this unique pool of knowledge, InVivo Biosystems has compiled this guide. Whatever your scientific questions may be, our collective zebrafish expertise is ready to be deployed to help you navigate the complexities of model organism selection. Trust InVivo Biosystems to assist you in selecting an approach that not only meets but exceeds your research goals.

More About Zebrafish as a Model Organism


1. Noldus, L. P. J. J., Spink, A. J. & Tegelenbosch, R. A. J. EthoVision: A versatile video tracking system for automation of behavioral experiments. Behav. Res. Methods Instrum. Comput. 33, 398–414 (2001).

2. Collier, A. D., Kalueff, A. V. & Echevarria, D. J. Zebrafish Models of Anxiety-Like Behaviors. in (ed. Kalueff, A. V.) 45–72 (Springer International Publishing, 2017). doi:10.1007/978-3-319-33774-6_3.

3. Vaz, R., Hofmeister, W. & Lindstrand, A. Zebrafish Models of Neurodevelopmental Disorders: Limitations and Benefits of Current Tools and Techniques. Int. J. Mol. Sci. 20, 1296 (2019).

4. Schnörr, S. J., Steenbergen, P. J., Richardson, M. K. & Champagne, D. L. Measuring thigmotaxis in larval zebrafish. Behav. Brain Res. 228, 367–374 (2012).

5. Baiamonte, M., Parker, M. O., Vinson, G. P. & Brennan, C. H. Sustained Effects of Developmental Exposure to Ethanol on Zebrafish Anxiety-Like Behaviour. PLOS ONE 11, e0148425 (2016).

6. Karnik, I. & Gerlai, R. Can zebrafish learn spatial tasks? An empirical analysis of place and single CS-US associative learning. Behav. Brain Res. 233, 415–421 (2012).

7. Sison, M. & Gerlai, R. Associative learning in zebrafish (Danio rerio) in the plus maze. Behav. Brain Res. 207, 99–104 (2010).

8. Miklósi, Á. & Andrew, R. J. Right eye use associated with decision to bite in zebrafish. Behav. Brain Res. 105, 199–205 (1999).

9. Roberts, A. C. et al. Habituation of the C-Start Response in Larval Zebrafish Exhibits Several Distinct Phases and Sensitivity to NMDA Receptor Blockade. PLOS ONE 6, e29132 (2011).

10. Darland, T. & Dowling, J. E. Behavioral screening for cocaine sensitivity in mutagenized zebrafish. Proc. Natl. Acad. Sci. U. S. A. 98, 11691–11696 (2001).

11. Li, L. & Dowling, J. E. A dominant form of inherited retinal degeneration caused by a non-photoreceptor cell-specific mutation. Proc. Natl. Acad. Sci. U. S. A. 94, 11645–11650 (1997).

12. Levin, E. D. & Cerutti, D. T. Behavioral Neuroscience of Zebrafish. in Methods of Behavior Analysis in Neuroscience (ed. Buccafusco, J. J.) (CRC Press/Taylor & Francis, 2009).

13. Hentig, J., Cloghessy, K. & Hyde, D. R. Shuttle Box Assay as an Associative Learning Tool for Cognitive Assessment in Learning and Memory Studies using Adult Zebrafish. J. Vis. Exp. JoVE (2021) doi:10.3791/62745.

14. Facciol, A. & Gerlai, R. Zebrafish Shoaling, Its Behavioral and Neurobiological Mechanisms, and Its Alteration by Embryonic Alcohol Exposure: A Review. Front. Behav. Neurosci. 14, (2020).

15. Miller, N. & Gerlai, R. From Schooling to Shoaling: Patterns of Collective Motion in Zebrafish (Danio rerio). PLoS ONE 7, e48865 (2012).

16. Ogi, A. et al. Social Preference Tests in Zebrafish: A Systematic Review. Front. Vet. Sci. 7, 590057 (2021).

17. Giongo, F. K. et al. Effects of Taurine in Mice and Zebrafish Behavioral Assays With Translational Relevance to Schizophrenia. Int. J. Neuropsychopharmacol. 26, 125–136 (2023).

18. Streisinger, G., Walker, C., Dower, N., Knauber, D. & Singer, F. Production of clones of homozygous diploid zebra fish (Brachydanio rerio). Nature 291, 293–296 (1981).

19. Atrooz, F., Alkadhi, K. A. & Salim, S. Understanding stress: Insights from rodent models. Curr. Res. Neurobiol. 2, 100013 (2021).

About The Author

Adam Saunders

After studying music at Indiana University, Adam pivoted into biology where he was introduced to C. elegans while working with Dr. Susan Strome and Dr. Bill Saxton. From there, Adam earned a Ph.D. from the Stanford University School of Medicine with Dr. Phil Beachy. In his thesis work, Adam investigated how signaling proteins essential for animal development are packaged and transported through the body. As a postdoctoral researcher with Dr. Victoria DeRose at the University of Oregon, Adam studied how beneficial and disease-causing bacteria use structured RNAs to detect nutrients with a human host. While at Oregon, Adam also taught advanced biology courses and served as a STEM outreach coordinator. Adam joined NemaMetrix (now InVivo Biosystems) as a Research and Development Scientist in April 2019. One of his roles is to oversee experimental design and execution of custom research projects. Adam still plays music–joining groups or jam sessions in the Eugene area–and also enjoys exploring the Oregon mountains by ski or by foot.

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