A great challenge in neuroscience is understanding how activity in the brain gives rise to behavior. The zebrafish is an ideal vertebrate model to address this challenge, thanks to the capacity, at the larval stage, for precise behavioral measurements, genetic manipulations, and recording and manipulation of neural activity noninvasively and at single-neuron resolution throughout the whole brain. These techniques are being further developed for application in freely moving animals and juvenile stages to study more complex behaviors including learning, decision making, and social interactions. We review some of the approaches that have been used to study the behavior of zebrafish and point to opportunities and challenges that lie ahead.


Article metrics loading...

Loading full text...

Full text loading...


Literature Cited

  1. Abrahamsson S, Chen J, Hajj B, Stallinga S, Katsov AY. et al. 2012. Fast multicolor 3D imaging using aberration-corrected multifocus microscopy. Nat. Methods 10:60–63 [Google Scholar]
  2. Abril-de Abreu R, Cruz AS, Oliveira RF. 2015. Social dominance modulates eavesdropping in zebrafish. R. Soc. Open Sci. 2:150220 [Google Scholar]
  3. Ahrens MB, Li JM, Orger MB, Robson DN, Schier AF. et al. 2012. Brain-wide neuronal dynamics during motor adaptation in zebrafish. Nature 485:471–77 [Google Scholar]
  4. Ahrens MB, Orger MB, Robson DN, Li JM, Keller PJ. 2013. Whole-brain functional imaging at cellular resolution using light-sheet microscopy. Nat. Methods 10:413–20 [Google Scholar]
  5. Aizenberg M, Schuman EM. 2011. Cerebellar-dependent learning in larval zebrafish. J. Neurosci. 31:8708–12 [Google Scholar]
  6. Al-Imari L, Gerlai R. 2008. Sight of conspecifics as reward in associative learning in zebrafish (Danio rerio). Behav. Brain Res. 189:216–19 [Google Scholar]
  7. Amo R, Fredes F, Kinoshita M, Aoki R, Aizawa H. et al. 2014. The habenulo-raphe serotonergic circuit encodes an aversive expectation value essential for adaptive active avoidance of danger. Neuron 84:1034–48 [Google Scholar]
  8. Arganda S, Pérez-Escudero A, de Polavieja GG. 2012. A common rule for decision making in animal collectives across species. PNAS 109:20508–13 [Google Scholar]
  9. Arrenberg AB, Bene FD, Baier H. 2009. Optical control of zebrafish behavior with halorhodopsin. PNAS 106:17968–73 [Google Scholar]
  10. Arunachalam M, Raja M, Vijayakumar C, Malaiammal P, Mayden RL. 2013. Natural history of zebrafish (Danio rerio) in India. Zebrafish 10:1–14 [Google Scholar]
  11. Auer TO, Duroure K, De Cian A, Concordet JP, Del Bene F. 2014. Highly efficient CRISPR/Cas9-mediated knock-in in zebrafish by homology-independent DNA repair. Genome Res 24:142–53 [Google Scholar]
  12. Bak-Coleman J, Smith D, Coombs S. 2015. Animal behaviour. Anim. Behav. 107:7–17 [Google Scholar]
  13. Barker AJ, Baier H. 2015. Sensorimotor decision making in the zebrafish tectum. Curr. Biol. 25:2804–14 [Google Scholar]
  14. Beck JC, Gilland E, Tank DW, Baker R. 2004. Quantifying the ontogeny of optokinetic and vestibuloocular behaviors in zebrafish, medaka, and goldfish. J. Neurophysiol. 92:3546–61 [Google Scholar]
  15. Bergeron SA, Carrier N, Li GH, Ahn S, Burgess HA. 2014. Gsx1 expression defines neurons required for prepulse inhibition. Mol. Psychiatry 20:974–85 [Google Scholar]
  16. Berman GJ, Choi DM, Bialek W, Shaevitz JW. 2014. Mapping the stereotyped behaviour of freely moving fruit flies. J. R. Soc. Interface 11:20140672 [Google Scholar]
  17. Bernhardt RR, Chitnis AB, Lindamer L, Kuwada JY. 1990. Identification of spinal neurons in the embryonic and larval zebrafish. J. Comp. Neurol. 302:603–16 [Google Scholar]
  18. Bianco IH, Engert F. 2015. Visuomotor transformations underlying hunting behavior in zebrafish. Curr. Biol. 25:831–46 [Google Scholar]
  19. Bianco IH, Kampff AR, Engert F. 2011. Prey capture behavior evoked by simple visual stimuli in larval zebrafish. Front. Syst. Neurosci. 5:101 [Google Scholar]
  20. Bianco IH, Ma LH, Schoppik D, Robson DN, Orger MB. et al. 2012. The tangential nucleus controls a gravito-inertial vestibulo-ocular reflex. Curr. Biol. 22:1285–95 [Google Scholar]
  21. Billeh YN, Schaub MT, Anastassiou CA, Barahona M, Koch C. 2014. Revealing cell assemblies at multiple levels of granularity. J. Neurosci. Methods 236:92–106 [Google Scholar]
  22. Borla MA, Palecek B, Budick S, O'Malley DM. 2002. Prey capture by larval zebrafish: evidence for fine axial motor control. Brain Behav. Evol. 60:207–29 [Google Scholar]
  23. Bouchard MB, Voleti V, Mendes CS, Lacefield C, Grueber WB. et al. 2015. Swept confocally-aligned planar excitation (SCAPE) microscopy for high speed volumetric imaging of behaving organisms. Nat. Photonics 9:113–19 [Google Scholar]
  24. Britten KH. 2008. Mechanisms of self-motion perception. Annu. Rev. Neurosci. 31:389–410 [Google Scholar]
  25. Brockerhoff SE, Hurley JB, Janssen-Bienhold U, Neuhauss SC, Driever W, Dowling JE. 1995. A behavioral screen for isolating zebrafish mutants with visual system defects. PNAS 92:10545–49 [Google Scholar]
  26. Brown AEX, Yemini EI, Grundy LJ, Jucikas T, Schafer WR. 2013. A dictionary of behavioral motifs reveals clusters of genes affecting Caenorhabditis elegans locomotion. PNAS 110:791–96 [Google Scholar]
  27. Brown KH, Dobrinski KP, Lee AS, Gokcumen O, Mills RE. et al. 2012. Extensive genetic diversity and substructuring among zebrafish strains revealed through copy number variant analysis. PNAS 109:529–34 [Google Scholar]
  28. Bruni G, Rennekamp AJ, Velenich A, McCarroll M, Gendelev L. et al. 2016. Zebrafish behavioral profiling identifies multitarget antipsychotic-like compounds. Nat. Chem. Biol. 12:559–66 [Google Scholar]
  29. Budick S, O'Malley DM. 2000. Locomotor repertoire of the larval zebrafish: swimming, turning and prey capture. J. Exp. Biol. 203:2565–79 [Google Scholar]
  30. Burgess HA, Granato M. 2007a. Modulation of locomotor activity in larval zebrafish during light adaptation. J. Exp. Biol. 210:2526–39 [Google Scholar]
  31. Burgess HA, Granato M. 2007b. Sensorimotor gating in larval zebrafish. J. Neurosci. 27:4984–94 [Google Scholar]
  32. Burgess HA, Schoch H, Granato M. 2010. Distinct retinal pathways drive spatial orientation behaviors in zebrafish navigation. Curr. Biol. 20:381–86 [Google Scholar]
  33. Buske C, Gerlai R. 2011. Shoaling develops with age in zebrafish (Danio rerio). Prog. Neuro-Psychopharmacol. Biol. Psychiatry 35:1409–15 [Google Scholar]
  34. Buss RR, Drapeau P. 2001. Synaptic drive to motoneurons during fictive swimming in the developing zebrafish. J. Neurophysiol. 86:197–210 [Google Scholar]
  35. Butail S, Polverino G, Phamduy P, Del Sette F, Porfiri M. 2014. Influence of robotic shoal size, configuration, and activity on zebrafish behavior in a free-swimming environment. Behav. Brain Res. 275:269–80 [Google Scholar]
  36. Cachat J, Stewart A, Utterback E, Hart P, Gaikwad S. et al. 2011. Three-dimensional neurophenotyping of adult zebrafish behavior. PLOS ONE 6:e17597 [Google Scholar]
  37. Chen S, Chiu CN, McArthur KL, Fetcho JR, Prober DA. 2015. TRP channel mediated neuronal activation and ablation in freely behaving zebrafish. Nat. Methods 13:147–50 [Google Scholar]
  38. Chen X, Engert F. 2014. Navigational strategies underlying phototaxis in larval zebrafish. Front. Syst. Neurosci. 8:39 [Google Scholar]
  39. Cheng RK, Krishnan S, Jesuthasan S. 2016. Activation and inhibition of tph2 serotonergic neurons operate in tandem to influence larval zebrafish preference for light over darkness. Sci. Rep. 6:20788 [Google Scholar]
  40. Chhetri RK, Amat F, Wan Y, Höckendorf B, Lemon WC, Keller PJ. 2015. Whole-animal functional and developmental imaging with isotropic spatial resolution. Nat. Methods 12:1171–78 [Google Scholar]
  41. Choleris E, Pfaff DW, Kavaliers M. eds; 2013. Oxytocin, Vasopressin and Related Peptides in the Regulation of Behavior Cambridge, UK: Cambridge Univ. Press [Google Scholar]
  42. Clark DT. 1981. Visual responses in developing zebrafish (Brachydanio rerio) PhD Thesis, Univ Oregon, Eugene:
  43. Couzin ID. 2009. Collective cognition in animal groups. Trends Cogn. Sci. 13:36–43 [Google Scholar]
  44. Cunningham JP, Yu BM. 2014. Dimensionality reduction for large-scale neural recordings. Nat. Neurosci. 17:1500–9 [Google Scholar]
  45. Daie K, Goldman MS, Aksay ERF. 2015. Spatial patterns of persistent neural activity vary with the behavioral context of short-term memory. Neuron 85:847–60 [Google Scholar]
  46. Darrow KO, Harris WA. 2004. Characterization and development of courtship in zebrafish. Danio rerio. Zebrafish 1:40–45 [Google Scholar]
  47. Dell AI, Bender JA, Branson K, Couzin ID, de Polavieja GG. et al. 2014. Automated image-based tracking and its application in ecology. Trends Ecol. Evol. 29:417–28 [Google Scholar]
  48. Dreosti E, Lopes G, Kampff A, Wilson S. 2015. Development of social behaviour in young zebrafish. Front. Neural Circuits 9:39 [Google Scholar]
  49. Dunn TW, Gebhardt C, Naumann EA, Riegler C, Ahrens MB. et al. 2016a. Neural circuits underlying visually evoked escapes in larval zebrafish. Neuron 89:613–28 [Google Scholar]
  50. Dunn TW, Mu Y, Narayan S, Randlett O, Naumann EA. et al. 2016b. Brain-wide mapping of neural activity controlling zebrafish exploratory locomotion. eLife 5:e12741 [Google Scholar]
  51. Easter SS, Nicola GN. 1997. The development of eye movements in the zebrafish (Danio rerio). Dev. Psychobiol. 31:267–76 [Google Scholar]
  52. Eaton RC, Farley RD. 1973. Development of the Mauthner neurons in embryos and larvae of the zebrafish. Brachydanio rerio. Copeia 4:673–82 [Google Scholar]
  53. Eaton RC, Nissanov J, Wieland CM. 1984. Differential activation of Mauthner and non-Mauthner startle circuits in the zebrafish: implications for functional substitution. J. Comp. Physiol. 155:813–20 [Google Scholar]
  54. Emran F, Rihel J, Dowling JE. 2008. A behavioral assay to measure responsiveness of zebrafish to changes in light intensities. J. Vis. Exp. 20:e923 [Google Scholar]
  55. Enquist M, Ghirlanda S. 2005. Neural Networks and Animal Behavior Princeton, NJ: Princeton Univ. Press
  56. Fajardo O, Zhu P, Friedrich RW. 2013. Control of a specific motor program by a small brain area in zebrafish. Front. Neural Circuits 7:67 [Google Scholar]
  57. Feierstein CE, Portugues R, Orger MB. 2015. Seeing the whole picture: a comprehensive imaging approach to functional mapping of circuits in behaving zebrafish. Neuroscience 296:26–38 [Google Scholar]
  58. Fernandes AM, Fero K, Arrenberg AB, Bergeron SA, Driever W, Burgess HA. 2012. Deep brain photoreceptors control light-seeking behavior in zebrafish larvae. Curr. Biol. 22:2042–47 [Google Scholar]
  59. Fero K, Yokogawa T, Burgess HA. 2011. The behavioral repertoire of larval zebrafish. Neuromethods 52 Zebrafish Models in Neurobehavioral Research AV Kaleuff, JM Cachat 249–91 New York: Humana Press [Google Scholar]
  60. Filosa A, Barker AJ, Maschio MD, Baier H. 2016. Feeding state modulates behavioral choice and processing of prey stimuli in the zebrafish tectum. Neuron 90:596–608 [Google Scholar]
  61. Fontaine E, Lentink D, Kranenbarg S, Müller UK, Van Leeuwen JL. et al. 2008. Automated visual tracking for studying the ontogeny of zebrafish swimming. J. Exp. Biol. 211:1305–16 [Google Scholar]
  62. Fosque BF, Sun Y, Dana H, Yang CT, Ohyama T. et al. 2015. Labeling of active neural circuits in vivo with designed calcium integrators. Science 347:755–60 [Google Scholar]
  63. Friedmann D, Hoagland A, Berlin S, Isacoff EY. 2014. A spinal opsin controls early neural activity and drives a behavioral light response. Curr. Biol. 25:69–74 [Google Scholar]
  64. Gabriel JP, Mahmood R, Walter AM, Kyriakatos A, Hauptmann G. et al. 2007. Locomotor pattern in the adult zebrafish spinal cord in vitro. J. Neurophysiol. 99:37–48 [Google Scholar]
  65. Gahtan E. 2005. Visual prey capture in larval zebrafish is controlled by identified reticulospinal neurons downstream of the tectum. J. Neurosci. 25:9294–303 [Google Scholar]
  66. Gerlai R. 2014. Social behavior of zebrafish: from synthetic images to biological mechanisms of shoaling. J. Neurosci. Methods 234:59–65 [Google Scholar]
  67. Gerlai R, Lahav M, Guo S, Rosenthal A. 2000. Drinks like a fish: zebra fish (Danio rerio) as a behavior genetic model to study alcohol effects. Pharmacol. Biochem. Behav. 67:773–82 [Google Scholar]
  68. Gillis DM, Kramer DL. 1987. Ideal interference distributions: population density and patch use by zebrafish. Anim. Behav. 35:1875–82 [Google Scholar]
  69. Girdhar K, Gruebele M, Chemla YR. 2015. The behavioral space of zebrafish locomotion and its neural network analog. PLOS ONE 10:e0128668 [Google Scholar]
  70. Gomez-Marin A, Paton JJ, Kampff AR, Costa RM, Mainen ZF. 2014. Big behavioral data: psychology, ethology and the foundations of neuroscience. Nat. Neurosci. 17:1455–62 [Google Scholar]
  71. Goodson JL. 2005. The vertebrate social behavior network: evolutionary themes and variations. Horm. Behav. 48:11–22 [Google Scholar]
  72. Gould TD, Gottesman II. 2006. Psychiatric endophenotypes and the development of valid animal models. Genes Brain Behav 5:113–19 [Google Scholar]
  73. Grabowicz PA, Romero-Ferrero F, Lins T, de Polavieja GG, Benevenuto F, Gummadi KP. 2015. An experimental study of opinion influenceability. arXiv1512.00770 [physics.soc-ph]
  74. Grant JW, Kramer DL. 1992. Temporal clumping of food arrival reduces its monopolization and defence by zebrafish. Brachydanio rerio. Anim. Behav. 44:101–10 [Google Scholar]
  75. Green MH, Ho RK, Hale ME. 2011. Movement and function of the pectoral fins of the larval zebrafish (Danio rerio) during slow swimming. J. Exp. Biol. 214:3111–23 [Google Scholar]
  76. Haesemeyer M, Robson DN, Li JM, Schier AF, Engert F. 2015. The structure and timescales of heat perception in larval zebrafish. Cell Syst 1:338–48 [Google Scholar]
  77. Hale ME, Katz HR, Peek MY, Fremont RT. 2016. Neural circuits that drive startle behavior, with a focus on the Mauthner cells and spiral fiber neurons of fishes. J. Neurogenet. 30:89–100 [Google Scholar]
  78. Herbert-Read JE, Krause S, Morrell LJ, Schaerf TM, Krause J, Ward AJW. 2013. The role of individuality in collective group movement. Proc. R. Soc. B 280:20122564 [Google Scholar]
  79. Hinz FI, Aizenberg M, Tushev G, Schuman EM. 2013. Protein synthesis-dependent associative long-term memory in larval zebrafish. J. Neurosci. 33:15382–87 [Google Scholar]
  80. Hoffman EJ, Turner KJ, Fernandez JM, Cifuentes D, Ghosh M. et al. 2016. Estrogens suppress a behavioral phenotype in zebrafish mutants of the autism risk gene, CNTNAP2. Neuron 89:725–33 [Google Scholar]
  81. Horstick EJ, Mueller T, Burgess HA. 2016. Motivated state control in larval zebrafish: behavioral paradigms and anatomical substrates. J. Neurogenet. 30:122–32 [Google Scholar]
  82. Huang YY, Tschopp M, Neuhauss SCF. 2009. Illusionary self-motion perception in zebrafish. PLOS ONE 4:e6550 [Google Scholar]
  83. Huber-Reggi SP, Mueller KP, Neuhauss SCF. 2012. Analysis of optokinetic response in zebrafish by computer-based eye tracking. Methods in Molecular Biology 935 Retinal Degeneration: Methods and Protocols BHF Weber, T Langmann 139–60 Totowa, NJ: Humana Press [Google Scholar]
  84. Hwang WY, Fu Y, Reyon D, Maeder ML, Tsai SQ. et al. 2013. Efficient genome editing in zebrafish using a CRISPR-Cas system. Nat. Biotechnol. 31:227–29 [Google Scholar]
  85. Ioannou CC, Guttal V, Couzin ID. 2012. Predatory fish select for coordinated collective motion in virtual prey. Science 337:1212–15 [Google Scholar]
  86. Jetti SK, Vendrell-Llopis N, Yaksi E. 2014. Spontaneous activity governs olfactory representations in spatially organized habenular microcircuits. Curr. Biol. 24:434–39 [Google Scholar]
  87. Kabra M, Robie AA, Rivera-Alba M, Branson S, Branson K. 2012. JAABA: interactive machine learning for automatic annotation of animal behavior. Nat. Methods 10:64–67 [Google Scholar]
  88. Kalueff AV, Cachat J. 2011. Neuromethods 52 Zebrafish Models in Neurobehavioral Research New York: Humana Press, 1st ed..
  89. Kalueff AV, Gebhardt M, Stewart AM, Cachat JM, Brimmer M. et al. 2013. Towards a comprehensive catalog of zebrafish behavior 1.0 and beyond. Zebrafish 10:70–86 [Google Scholar]
  90. Kimmel CB, Patterson J, Kimmel RO. 1974. The development and behavioral characteristics of the startle response in the zebra fish. Dev. Psychobiol. 7:47–60 [Google Scholar]
  91. Kimura Y, Satou C, Fujioka S, Shoji W, Umeda K. et al. 2013. Hindbrain V2a neuronsin the excitation of spinal locomotor circuits during zebrafish swimming. Curr. Biol. 23:843–49 [Google Scholar]
  92. Kinkhabwala A, Riley M, Koyama M, Monen J, Satou C. et al. 2011. A structural and functional ground plan for neurons in the hindbrain of zebrafish. PNAS 108:1164–69 [Google Scholar]
  93. Kobak D, Brendel W, Constantinidis C, Feierstein CE, Kepecs A. et al. 2016. Demixed principal component analysis of neural population data. eLife 5:e10989 [Google Scholar]
  94. Kohashi T, Nakata N, Oda Y. 2012. Effective sensory modality activating an escape triggering neuron switches during early development in zebrafish. J. Neurosci. 32:5810–20 [Google Scholar]
  95. Kokel D, Bryan J, Laggner C, White R, Cheung CYJ. et al. 2010. Rapid behavior-based identification of neuroactive small molecules in the zebrafish. Nat. Methods 6:231–37 [Google Scholar]
  96. Kokel D, Dunn TW, Ahrens MB, Alshut R, Cheung CYJ. et al. 2013. Identification of nonvisual photomotor response cells in the vertebrate hindbrain. J. Neurosci. 33:3834–43 [Google Scholar]
  97. Kokko H. 2007. Modelling for Field Biologists and Other Interesting People Cambridge, UK: Cambridge Univ. Press
  98. Koyama M, Kinkhabwala A, Satou C, Higashijima SI, Fetcho J. 2011. Mapping a sensory-motor network onto a structural and functional ground plan in the hindbrain. PNAS 108:1170–75 [Google Scholar]
  99. Koyama M, Minale F, Shum J, Nishimura N, Schaffer CB, Fetcho JR. 2016. A circuit motif in the zebrafish hindbrain for a two alternative behavioral choice to turn left or right. eLife 5:e16808 [Google Scholar]
  100. Krause J, Ruxton GD. 2002. Living in Groups Oxford, UK: Oxford Univ. Press
  101. Kubo F, Hablitzel B, Maschio MD, Driever W, Baier H, Arrenberg AB. 2014. Functional architecture of an optic flow-responsive area that drives horizontal eye movements in zebrafish. Neuron 81:1344–59 [Google Scholar]
  102. LaCoste AMB, Schoppik D, Robson DN, Haesemeyer M, Portugues R. et al. 2015. A convergent and essential interneuron pathway for Mauthner-cell-mediated escapes. Curr. Biol. 25:1526–34 [Google Scholar]
  103. Lange M, Neuzeret F, Fabreges B, Froc C, Bedu S. et al. 2013. Inter-individual and inter-strain variations in zebrafish locomotor ontogeny. PLOS ONE 8:e70172 [Google Scholar]
  104. Lee A, Mathuru AS, Teh C, Kibat C, Korzh V. et al. 2010. The habenula prevents helpless behavior in larval zebrafish. Curr. Biol. 20:2211–16 [Google Scholar]
  105. Leshner A, Pfaff DW. 2011. Quantification of behavior. PNAS 108:Suppl. 315537–41 [Google Scholar]
  106. Levoy M, Ng R, Adams A, Footer M. 2006. Light field microscopy. ACM Trans. Graph. 25:31–11 [Google Scholar]
  107. Li G, Müller UK, Van Leeuwen JL, Liu H. 2012. Body dynamics and hydrodynamics of swimming fish larvae: a computational study. J. Exp. Biol. 215:4015–33 [Google Scholar]
  108. Li G, Müller UK, Van Leeuwen JL, Liu H. 2014. Escape trajectories are deflected when fish larvae intercept their own C-start wake. J. R. Soc. Interface 11:20140848 [Google Scholar]
  109. Li Y, Lee JM, Chon TS, Liu Y, Kim H, Bae MJ. 2013. Analysis of movement behavior of zebrafish (Danio rerio) under chemical stress using hidden Markov model. Mod. Phys. Lett. B 27:1350014 [Google Scholar]
  110. Lindeyer CM, Reader SM. 2010. Social learning of escape routes in zebrafish and the stability of behavioural traditions. Anim. Behav. 79:827–34 [Google Scholar]
  111. Liu KS, Fetcho JR. 1999. Laser ablations reveal functional relationships of segmental hindbrain neurons in zebrafish. Neuron 23:325–35 [Google Scholar]
  112. Liu Y, Lee SH, Chon TS. 2011. Analysis of behavioral changes of zebrafish (Danio rerio) in response to formaldehyde using Self-organizing map and a hidden Markov model. Ecol. Model. 222:2191–201 [Google Scholar]
  113. Liu YC, Hale ME. 2014. Alternative forms of axial startle behaviors in fishes. Zoology 117:36–47 [Google Scholar]
  114. Lorent K, Liu KS, Fetcho JR, Granato M. 2001. The zebrafish space cadet gene controls axonal pathfinding of neurons that modulate fast turning movements. Development 128:2131–42 [Google Scholar]
  115. Lum PY, Singh G, Lehman A, Ishkanov T, Vejdemo-Johansson M. et al. 2013. Extracting insights from the shape of complex data using topology. Sci. Rep. 3:1236 [Google Scholar]
  116. Ma LH, Grove CL, Baker R. 2014. Development of oculomotor circuitry independent of hox3 genes. Nat. Commun. 5:4221 [Google Scholar]
  117. Madirolas G, de Polavieja GG. 2015. Improving collective estimations using resistance to social influence. PLOS Comput. Biol. 11:e1004594 [Google Scholar]
  118. Martineau PR, Mourrain P. 2013. Tracking zebrafish larvae in group – status and perspectives. Methods 62:292–303 [Google Scholar]
  119. Masino MA, Fetcho JR. 2005. Fictive swimming motor patterns in wild type and mutant larval zebrafish. J. Neurophysiol. 93:3177–88 [Google Scholar]
  120. Masseck OA, Hoffmann KP. 2009. Comparative neurobiology of the optokinetic reflex. Ann. N. Y. Acad. Sci. 1164:430–39 [Google Scholar]
  121. McClenahan P, Troup M, Scott EK. 2012. Fin-tail coordination during escape and predatory behavior in larval zebrafish. PLOS ONE 7:e32295 [Google Scholar]
  122. McElligott MB, O'Malley DM. 2005. Prey tracking by larval zebrafish: axial kinematics and visual control. Brain Behav. Evol. 66:177–96 [Google Scholar]
  123. McHenry MJ, Feitl KE, Strother JA, Van Trump WJ. 2009. Larval zebrafish rapidly sense the water flow of a predator's strike. Biol. Lett. 5:477–79 [Google Scholar]
  124. McLean DL, Fan J, Higashijima SI, Hale ME, Fetcho JR. 2007. A topographic map of recruitment in spinal cord. Nature 446:71–75 [Google Scholar]
  125. McLean DL, Fetcho JR. 2008. Using imaging and genetics in zebrafish to study developing spinal circuits in vivo. Dev. Neurobiol. 68:817–34 [Google Scholar]
  126. Miller N, Gerlai R. 2007. Quantification of shoaling behaviour in zebrafish (Danio rerio). Behav. Brain Res. 184:157–66 [Google Scholar]
  127. Mirat O, Sternberg JR, Severi KE, Wyart C. 2013. ZebraZoom: an automated program for high-throughput behavioral analysis and categorization. Front. Neural Circ. 7:107 [Google Scholar]
  128. Miri A, Daie K, Arrenberg AB, Baier H, Aksay E, Tank DW. 2011a. Spatial gradients and multidimensional dynamics in a neural integrator circuit. Nat. Neurosci. 14:1150–59 [Google Scholar]
  129. Miri A, Daie K, Burdine RD, Aksay E, Tank DW. 2011b. Regression-based identification of behavior-encoding neurons during large-scale optical imaging of neural activity at cellular resolution. J. Neurophysiol. 105:964–80 [Google Scholar]
  130. Mnih V, Kavukcuoglu K, Silver D, Rusu AA, Veness J. et al. 2015. Human-level control through deep reinforcement learning. Nature 518:529–33 [Google Scholar]
  131. Muto A, Ohkura M, Abe G, Nakai J, Kawakami K. 2013. Real-time visualization of neuronal activity during perception. Curr. Biol. 23:307–11 [Google Scholar]
  132. Mwaffo V, Anderson RP, Butail S, Porfiri M. 2015. A jump persistent turning walker to model zebrafish locomotion. J. R. Soc. Interface 12:20140884 [Google Scholar]
  133. Nair A, Azatian G, McHenry MJ. 2015. The kinematics of directional control in the fast start of zebrafish larvae. J. Exp. Biol. 218:3996–4004 [Google Scholar]
  134. Neri P. 2012. Feature binding in zebrafish. Anim. Behav. 84:485–93 [Google Scholar]
  135. Neuhauss SC, Biehlmaier O, Seeliger MW, Das T, Kohler K. et al. 1999. Genetic disorders of vision revealed by a behavioral screen of 400 essential loci in zebrafish. J. Neurosci. 19:8603–15 [Google Scholar]
  136. Nguyen JP, Shipley FB, Linder AN, Plummer GS, Liu M. et al. 2016. Whole-brain calcium imaging with cellular resolution in freely behaving Caenorhabditis elegans. PNAS 113:E1074–81 [Google Scholar]
  137. Norton W, Bally-Cuif L. 2010. Adult zebrafish as a model organism for behavioural genetics. BMC Neurosci 11:90 [Google Scholar]
  138. O'Connell LA, Hofmann HA. 2011. The vertebrate mesolimbic reward system and social behavior network: a comparative synthesis. J. Comp. Neurol 519:3599–639 [Google Scholar]
  139. Olive R, Wolf S, Dubreuil A, Bormuth V, Debrégeas G, Candelier R. 2016. Rheotaxis of larval zebrafish: behavioral study of a multi-sensory process. Front. Syst. Neurosci. 10:413 [Google Scholar]
  140. Oliveira RF. 2013. Mind the fish: zebrafish as a model in cognitive social neuroscience. Front. Neural Circ. 7:131 [Google Scholar]
  141. Oliveira RF, Silva JF, Simões JM. 2011. Fighting zebrafish: characterization of aggressive behavior and winner–loser effects. Zebrafish 8:73–81 [Google Scholar]
  142. Olszewski J, Haehnel M, Taguchi M, Liao JC. 2012. Zebrafish larvae exhibit rheotaxis and can escape a continuous suction source using their lateral line. PLOS ONE 7:e36661 [Google Scholar]
  143. O'Malley DM, Kao YH, Fetcho JR. 1996. Imaging the functional organization of zebrafish hindbrain segments during escape behaviors. Neuron 17:1145–55 [Google Scholar]
  144. Ono F, Higashijima S, Shcherbatko A, Fetcho JR, Brehm P. 2001. Paralytic zebrafish lacking acetylcholine receptors fail to localize rapsyn clusters to the synapse. J. Neurosci. 21:5439–48 [Google Scholar]
  145. Orger MB, Baier H. 2005. Channeling of red and green cone inputs to the zebrafish optomotor response. Visual Neurosci 22:275–81 [Google Scholar]
  146. Orger MB, Kampff AR, Severi KE, Bollmann JH, Engert F. 2008. Control of visually guided behavior by distinct populations of spinal projection neurons. Nat. Neurosci. 11:327–33 [Google Scholar]
  147. Panier T, Romano SA, Olive R, Pietri T, Sumbre G. et al. 2013. Fast functional imaging of multiple brain regions in intact zebrafish larvae using Selective Plane Illumination Microscopy. Front. Neural Circ. 7:65 [Google Scholar]
  148. Parichy DM. 2015. Advancing biology through a deeper understanding of zebrafish ecology and evolution. eLife 4:e05635 [Google Scholar]
  149. Pelkowski SD, Kapoor M, Richendrfer HA, Wang X, Colwill RM, Creton R. 2011. A novel high-throughput imaging system for automated analyses of avoidance behavior in zebrafish larvae. Behav. Brain Res. 223:135–44 [Google Scholar]
  150. Pérez-Escudero A, Vicente-Page J, Hinz RC, Arganda S, de Polavieja GG. 2014. idTracker: tracking individuals in a group by automatic identification of unmarked animals. Nat. Methods 11:743–48 [Google Scholar]
  151. Petreanu L, Gutnisky DA, Huber D, Xu N, O'Connor DH. et al. 2012. Activity in motor–sensory projections reveals distributed coding in somatosensation. Nature 489:299–303 [Google Scholar]
  152. Portugues R, Engert F. 2011. Adaptive locomotor behavior in larval zebrafish. Front. Syst. Neurosci. 5:72 [Google Scholar]
  153. Portugues R, Feierstein CE, Engert F, Orger MB. 2014. Whole-brain activity maps reveal stereotyped, distributed networks for visuomotor behavior. Neuron 81:1328–43 [Google Scholar]
  154. Portugues R, Haesemeyer M, Blum ML, Engert F. 2015. Whole-field visual motion drives swimming in larval zebrafish via a stochastic process. J. Exp. Biol. 218:1433–43 [Google Scholar]
  155. Portugues R, Severi KE, Wyart C, Ahrens MB. 2013. Optogenetics in a transparent animal: circuit function in the larval zebrafish. Curr. Opin. Neurobiol. 23:119–26 [Google Scholar]
  156. Pritchard V, Lawrence J, Butlin RK, Krause J. 2001. Shoal choice in zebrafish, Danio rerio: the influence of shoal size and activity. Anim. Behav. 62:1085–88 [Google Scholar]
  157. Prober DA, Rihel J, Onah AA, Sung RJ, Schier AF. 2006. Hypocretin/orexin overexpression induces an insomnia-like phenotype in zebrafish. J. Neurosci. 26:13400–10 [Google Scholar]
  158. Quirin S, Vladimirov N, Yang CT, Peterka DS, Yuste R, Ahrens MB. 2016. Calcium imaging of neural circuits with extended depth-of-field light-sheet microscopy. Opt. Lett. 41:855–58 [Google Scholar]
  159. Renninger SL, Orger MB. 2013. Two-photon imaging of neural population activity in zebrafish. Methods 62:255–67 [Google Scholar]
  160. Rihel J, Prober DA, Arvanites A, Lam K, Zimmerman S. et al. 2010. Zebrafish behavioral profiling links drugs to biological targets and rest/wake regulation. Science 327:348–51 [Google Scholar]
  161. Roberts AC, Bill BR, Glanzman DL. 2013. Learning and memory in zebrafish larvae. Front. Neural Circ. 7:126 [Google Scholar]
  162. Romano SA, Pietri T, Pérez-Schuster V, Jouary A, Haudrechy M, Sumbre G. 2015. Spontaneous neuronal network dynamics reveal circuit's functional adaptations for behavior. Neuron 85:1070–85 [Google Scholar]
  163. Ruhl N, McRobert SP. 2005. The effect of sex and shoal size on shoaling behaviour in Danio rerio. J. Fish Biol. 67:1318–26 [Google Scholar]
  164. Saint-Amant L, Drapeau P. 1998. Time course of the development of motor behaviors in the zebrafish embryo. J. Neurobiol. 37:622–32 [Google Scholar]
  165. Saint-Amant L, Drapeau P. 2000. Motoneuron activity patterns related to the earliest behavior of the zebrafish embryo. J. Neurosci. 20:3964–72 [Google Scholar]
  166. Satou C, Kimura Y, Kohashi T, Takeda H, Oda Y, Higashijima SI. 2009. Functional role of a specialized class of spinal commissural inhibitory neurons during fast escapes in zebrafish. J. Neurosci. 29:6780–93 [Google Scholar]
  167. Saverino C, Gerlai R. 2008. The social zebrafish: behavioral responses to conspecific, heterospecific, and computer animated fish. Behav. Brain Res. 191:77–87 [Google Scholar]
  168. Schlegel T, Schuster S. 2008. Small circuits for large tasks: high-speed decision-making in archerfish. Science 319:104–6 [Google Scholar]
  169. Scott EK, Mason L, Arrenberg AB, Ziv L, Gosse NJ. et al. 2007. Targeting neural circuitry in zebrafish using GAL4 enhancer trapping. Nat. Methods 4:323–26 [Google Scholar]
  170. Sela G, Lauri A, Deán-Ben XL, Kneipp M. 2015. Functional optoacoustic neuro-tomography (FONT) for whole-brain monitoring of calcium indicators. arXiv1501.02450 [q-bio.NC]
  171. Semmelhack JL, Donovan JC, Thiele TR, Kuehn E, Laurell E, Baier H. 2014. A dedicated visual pathway for prey detection in larval zebrafish. eLife 3:e04878 [Google Scholar]
  172. Serra EL, Medalha CC, Mattioli R. 1999. Natural preference of zebrafish (Danio rerio) for a dark environment. Braz. J. Med. Biol. Res 321551–53 [Google Scholar]
  173. Severi KE, Portugues R, Marques JC, O'Malley DM, Orger MB, Engert F. 2014. Neural control and modulation of swimming speed in the larval zebrafish. Neuron 83:692–707 [Google Scholar]
  174. Shoham Y, Leyton-Brown K. 2009. Multiagent Systems: Algorithmic, Game-Theoretic, and Logical Foundations Cambridge, UK: Cambridge Univ. Press
  175. Singh G, Memoli F, Ishkhanov T, Sapiro G, Carlsson G, Ringach DL. 2008. Topological analysis of population activity in visual cortex. J. Vis. 8:11 [Google Scholar]
  176. Snekser JL, Ruhl N, Bauer K, McRobert SP. 2010. The influence of sex and phenotype on shoaling decisions in zebrafish. Int. J. Comp. Psychol. 23:70–81 [Google Scholar]
  177. Spence R, Gerlach G, Lawrence C, Smith C. 2008. The behaviour and ecology of the zebrafish. Danio rerio. Biol. Rev. Camb. Philos. Soc. 83:13–34 [Google Scholar]
  178. Sternberg JR, Severi KE, Fidelin K, Gomez J, Ihara H. et al. 2016. Optimization of a neurotoxin to investigate the contribution of excitatory interneurons to speed modulation in vivo. Curr. Biol. 26:2319–28 [Google Scholar]
  179. Stewart AM, Grieco F, Tegelenbosch RA, Kyzar EJ, Nguyen M. et al. 2015. A novel 3D method of locomotor analysis in adult zebrafish: implications for automated detection of CNS drug-evoked phenotypes. J. Neurosci. Methods 255:66–74 [Google Scholar]
  180. Suli A, Watson GM, Rubel EW, Raible DW. 2012. Rheotaxis in larval zebrafish is mediated by lateral line mechanosensory hair cells. PLOS ONE 7:e29727 [Google Scholar]
  181. Sumpter DJT. 2011. Collective Animal Behavior Princeton, NJ: Princeton Univ. Press
  182. Suriyampola PS, Shelton DS, Shukla R, Roy T, Bhat A, Martins EP. 2016. Zebrafish social behavior in the wild. Zebrafish 13:1–8 [Google Scholar]
  183. Tabor KM, Bergeron SA, Horstick EJ, Jordan DC, Aho V. et al. 2014. Direct activation of the Mauthner cell by electric field pulses drives ultra-rapid escape responses. J. Neurophysiol. 112:834–44 [Google Scholar]
  184. Temizer I, Donovan JC, Baier H, Semmelhack JL. 2015. A visual pathway for looming-evoked escape in larval zebrafish. Curr. Biol. 25:1823–34 [Google Scholar]
  185. Thompson AW, Vanwalleghem GC, Heap LA, Scott EK. 2016. Functional profiles of visual-, auditory-, and water flow-responsive neurons in the zebrafish tectum. Curr. Biol. 26:743–54 [Google Scholar]
  186. Tinbergen N. 1951. The Study of Instinct Oxford, UK: Clarendon Press
  187. Trivedi CA, Bollmann JH. 2013. Visually driven chaining of elementary swim patterns into a goal-directed motor sequence: a virtual reality study of zebrafish prey capture. Front. Neural Circ. 7:86 [Google Scholar]
  188. Valente A, Huang KH, Portugues R, Engert F. 2012. Ontogeny of classical and operant learning behaviors in zebrafish. Learn. Memory 19:170–77 [Google Scholar]
  189. Vendrell-Llopis N, Yaksi E. 2015. Evolutionary conserved brainstem circuits encode category, concentration and mixtures of taste. Sci. Rep. 5:17825 [Google Scholar]
  190. Venkatachalam V, Ji N, Wang X, Clark C, Mitchell JK. et al. 2016. Pan-neuronal imaging in roaming Caenorhabditis elegans. PNAS 113:E1082–88 [Google Scholar]
  191. Vladimirov N, Mu Y, Kawashima T, Bennett DV, Yang CT. et al. 2014. Light-sheet functional imaging in fictively behaving zebrafish. Nat. Methods 11:883–84 [Google Scholar]
  192. Voesenek CJ, Pieters RPM, van Leeuwen JL. 2016. Automated reconstruction of three-dimensional fish motion, forces, and torques. PLOS ONE 11:e0146682 [Google Scholar]
  193. Wang YN, Hou YY, Sun MZ, Zhang CY, Bai G. et al. 2014. Behavioural screening of zebrafish using neuroactive traditional Chinese medicine prescriptions and biological targets. Sci. Rep. 4:5311 [Google Scholar]
  194. Ward AJW, Sumpter DJT, Couzin ID, Hart PJB, Krause J. 2008. Quorum decision-making facilitates information transfer in fish shoals. PNAS 105:6948–53 [Google Scholar]
  195. Warp E, Agarwal G, Wyart C, Friedmann D, Oldfield CS. et al. 2012. Emergence of patterned activity in the developing zebrafish spinal cord. Curr. Biol. 22:93–102 [Google Scholar]
  196. Randlett O, Wee CL, Naumann EA, Nnaemeka O, Schoppik D. et al. 2015. Whole-brain activity mapping onto a zebrafish brain atlas. Nat. Methods 12:1039–46 [Google Scholar]
  197. Wiltschko AB, Johnson MJ, Iurilli G, Peterson RE, Katon JM. et al. 2015. Mapping sub-second structure in mouse behavior. Neuron 88:1121–35 [Google Scholar]
  198. Wolf S, Supatto W, Debrégeas G, Mahou P, Kruglik SG. et al. 2015. Whole-brain functional imaging with two-photon light-sheet microscopy. Nat. Methods 12:379–80 [Google Scholar]
  199. Wolman MA, Jain RA, Liss L, Granato M. 2011. Chemical modulation of memory formation in larval zebrafish. PNAS 108:15468–73 [Google Scholar]
  200. Woods IG, Schoppik D, Shi VJ, Zimmerman S, Coleman HA. et al. 2014. Neuropeptidergic signaling partitions arousal behaviors in zebrafish. J. Neurosci. 34:3142–60 [Google Scholar]
  201. Wright D, Nakamichi R, Krause J, Butlin RK. 2006. QTL analysis of behavioral and morphological differentiation between wild and laboratory zebrafish (Danio rerio). Behav. Genet. 36:271–84 [Google Scholar]
  202. Yao Y, Li X, Zhang B, Yin C, Liu Y. et al. 2016. Visual cue-discriminative dopaminergic control of visuomotor transformation and behavior selection. Neuron 89:598–612 [Google Scholar]
  203. Zhou Y, Cattley RT, Cario CL, Bai Q, Burton EA. 2014. Quantification of larval zebrafish motor function in multiwell plates using open-source MATLAB applications. Nat. Protoc. 9:1533–48 [Google Scholar]
  204. Zhu L, Weng W. 2007. Catadioptric stereo-vision system for the real-time monitoring of 3D behavior in aquatic animals. Physiol. Behav. 91:106–19 [Google Scholar]
  205. Zhu P, Fajardo O, Shum J, Schärer YPZ, Friedrich RW. 2012. High-resolution optical control of spatiotemporal neuronal activity patterns in zebrafish using a digital micromirror device. Nat. Protoc. 7:1410–25 [Google Scholar]
  206. Zhu P, Narita Y, Bundschuh ST, Fajardo O, Schärer YPZ. et al. 2009. Optogenetic dissection of neuronal circuits in zebrafish using viral gene transfer and the Tet system. Front. Neural Circ. 3:21 [Google Scholar]

Data & Media loading...

  • Article Type: Review Article
This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error