Reviews in Fish Biology and Fisheries

, Volume 28, Issue 4, pp 839–864 | Cite as

Individual identification and marking techniques for zebrafish

  • Johann DelcourtEmail author
  • Michaël Ovidio
  • Mathieu Denoël
  • Marc Muller
  • Hélène Pendeville
  • Jean-Louis Deneubourg
  • Pascal Poncin


In laboratory fish research, the zebrafish Danio rerio (Cyprinidae) represents the equivalent of the mouse in mammalian research. This species has become a major model for studies in developmental and behavioural genetics, neurophysiology, biomedicine, ecotoxicology, and behavioural and evolutionary ecology. To meet the need for accurate and reproducible data in both fundamental and applied sciences, it is of primary importance to be able to tag and/or recognize individual zebrafish. However, classic methods used in fish ecology and aquaculture are generally difficult to apply to such small fish. Recently, various new tagging methods have been developed. This paper presents a first review of current identification and marking methods applied to zebrafish, from external observation methods (such as skin pattern recognition, fin clipping, scale regeneration, colour and transgenic methods) to the most advanced technological developments in electronic (low- and high- radio-frequencies PIT tags, microchip) and image analysis methods (video tracking). This review aims to help researchers and zebrafish facility managers select the identification method (ID) best adapted to their needs. The main characteristics of each ID method are examined (including detection range, durability, speed and repetitiveness, ID code combination, size dependence and ethical considerations), and their pros and cons are summarized in a decision table to help select the most appropriate option for a research or management program. Finally, contextual applications of these ID methods and future developments are discussed.


Animal ID Danio rerio Passive integrated transponder Tagging Video tracking VIE tag 



This study was funded by the Fonds de la Recherche Scientifique – FNRS PDR Grant No. T.1064.14. JD is an Assistant-researcher funded by the PDR (ULiège-FNRS). MO is a Scientific Expert of the University of Liège. MD, JLD and MM are Senior Research Associates at the F.R.S.–FNRS. PP and JLD are promotors of the PDR project. We thank G. Rimbaud for logistical support. We are grateful also to C. Orban, A. Dierckx, J.-P. Benitez and B. Nzau Matondo for their comments.

Supplementary material

11160_2018_9537_MOESM1_ESM.tif (2.2 mb)
Supplementary material 1 (TIFF 2261 kb)


  1. Ahmad F, Noldus LPJJ, Tegelenbosch RAJ, Richardson MK (2012) Zebrafish embryos and larvae in behavioural assays. Behaviour 149:1241–1281. CrossRefGoogle Scholar
  2. Alcobendas M, Lecomte F, Castanet J, Meunier FJ, Maire P, Holl M (1991) Technique de marquage en masse de civelles (Anguilla anguilla) par balnéation rapide dans le fluorochrome: application au marquage à la tétracycline de 500 kg de civelles. Bull Fr Peche Piscic 321:43–54. CrossRefGoogle Scholar
  3. Ariyomo T, Carter M, Watt PJ (2013) Heritability of boldness and aggressiveness in the zebrafish. Behav Genet 43:161–167. CrossRefPubMedGoogle Scholar
  4. Avdesh A, Chen M, Martin-Iverson MT, Mondal A et al (2012) Regular care and maintenance of a zebrafish (Danio rerio) laboratory: an introduction. JoVE 69:4196. CrossRefGoogle Scholar
  5. Azevedo AS, Grotek B, Jacinto A, Weidinger G, Saúde L (2011) The regenerative capacity of the zebrafish caudal fin is not affected by repeated amputations. PLoS ONE 6:e22820. CrossRefPubMedPubMedCentralGoogle Scholar
  6. Baatrup E (2009) Measuring complex behavior patterns in fish: effects of endocrine disruptors on the guppy reproductive behavior. Hum Ecol Risk Assess 15:53–62. CrossRefGoogle Scholar
  7. Bashey F (2004) A comparison of the suitability of alizarin red S and calcein for inducing a nonlethally detectable mark in juvenile guppies. Trans Am Fish Soc 133:1516–1523. CrossRefGoogle Scholar
  8. Bolger DT, Morrison TA, Vance B, Lee D, Farid H (2012) A computer-assisted system for photographic mark–recapture analysis. Methods Ecol Evol 3:813–822. CrossRefGoogle Scholar
  9. Bolliet V, Labonne J (2008) Individual patterns of rhythmic swimming activity in Anguilla anguilla glass eel. J Exp Mar Biol Ecol 362:125–130. CrossRefGoogle Scholar
  10. Bolliet V, Lambert P, Rives J, Bardonnet A (2007) Rhythmic swimming activity in Anguilla anguilla glass eels: synchronisation to water current reversal under laboratory conditions. J Exp Mar Biol Ecol 344:54–66. CrossRefGoogle Scholar
  11. Brown C, Laland KN (2003) Social learning in fishes: a review. Fish Fish 4:280–288. CrossRefGoogle Scholar
  12. Brown C, Laland K, Krause J (2011) Fish cognition and behavior, 2nd edn. Wiley, Hoboken, p 472. CrossRefGoogle Scholar
  13. Butail S, Paley DA (2010) 3D reconstruction of fish schooling kinematics from underwater video. In: Proceedings of IEEE international conference on robotics and automation, Anchorage, Alaska, pp 2438–2443.
  14. Castranova D, Lawton A, Lawrence C, Baumann DP et al (2011) The effect of stocking densities on reproductive performance in laboratory zebrafish (Danio rerio). Zebrafish 8:141–146. CrossRefPubMedPubMedCentralGoogle Scholar
  15. Champagne CE, Austin JD, Jelks HL, Jordan F (2008) Effects of fin clipping on survival and position-holding behavior of brown darters, Etheostoma edwini. Copeia 2008:916–919. CrossRefGoogle Scholar
  16. Chapman P, Warburton K (2006) Postflood movements and population connectivity in gambusia (Gambusia holbrooki). Ecol Freshw Fish 15:357–365. CrossRefGoogle Scholar
  17. Chen C, Durand E, Wang J, Zon LI, Poss KD (2013) Zebraflash transgenic lines for in vivo bioluminescence imaging of stem cells and regeneration in adult zebrafish. Development 140:4988–4997. CrossRefPubMedPubMedCentralGoogle Scholar
  18. Chen CH, Puliafito A, Cox BD, Primo L, Fang Y, Di Talia S, Poss KD (2016) Multicolor cell barcoding technology for long-term surveillance of epithelial regeneration in zebrafish. Dev Cell 36:668–680. CrossRefPubMedPubMedCentralGoogle Scholar
  19. Cheung E, Chatterjee D, Gerlai R (2014) Subcutaneous dye injection for marking and identification of individual adult zebrafish (Danio rerio) in behavioral studies. Behav Res Methods 46:619–624. CrossRefPubMedGoogle Scholar
  20. Coe TS, Hamilton PB, Griffiths AM, Hodgson DJ, Wahab MA, Tyler CR (2008) Genetic variation in strains of zebrafish (Danio rerio) and the implications for ecotoxicology studies. Ecotoxicology 18:144–150. CrossRefPubMedGoogle Scholar
  21. Cooke SJ, Woodley CM, Eppard MB, Brown RS, Nielsen JL (2011) Advancing the surgical implantation of electronic tags in fish: a gap analysis and research agenda based on a review of trends in intracoelomic tagging effects studies. Rev Fish Biol Fish 21:127–151. CrossRefGoogle Scholar
  22. Cooke SJ, Hinch SG, Lucas MC, Lutcavage M (2012) Biotelemetry and biologging. In: Zale AV, Parrish DL, Sutton TM (eds) Fisheries techniques, 3rd edn. American Fisheries Society, Bethesda, pp 819–860Google Scholar
  23. Correia M, Palma J, Koldewey H, Andrade JP (2014) The use of a non-invasive tool for capture-recapture studies on a seahorse Hippocampus guttulatus population. J Fish Biol 84:872–884. CrossRefPubMedGoogle Scholar
  24. Cousin X, Daouk T, Péan S, Lyphout L, Schwartz ME, Bégout ML (2012) Electronic individual identification of zebrafish using radio frequency identification (RFID) microtags. J Exp Biol 215:2729–2734. CrossRefPubMedGoogle Scholar
  25. Croft DP, Krause J, James R (2004) Social networks in the guppy (Poecilia reticulata). Proc R Soc Lond B (Suppl) 271:S516–S519. CrossRefGoogle Scholar
  26. Cucherousset J, Roussel JM, Keeler R, Cunjak RA, Stump R (2005) The use of two new portable 12-mm PIT tag detectors to track small fish in shallow streams. N Am J Fish Manag 25:270–274. CrossRefGoogle Scholar
  27. Curtis JMR (2006) Visible implant elastomer color determination, tag visibility, and tag loss: potential sources of error for mark-recapture studies. N Am J Fish Manag 26:327–337. CrossRefGoogle Scholar
  28. Dala-Corte RB, Moschetta JB, Becker FB (2016) Photo-identification as a technique for recognition of individual fish: a test with the freshwater armored catfish Rineloricaria aequalicuspis Reis & Cardoso, 2001 (Siluriformes: Loricariidae). Neotrop Ichthyol 14:e150074. CrossRefGoogle Scholar
  29. Delcourt J, Poncin P (2012) Shoals and schools: back to the heuristic definitions and quantitative references. Rev Fish Biol Fish 22:595–619. CrossRefGoogle Scholar
  30. Delcourt J, Becco C, Ylieff MY, Caps H, Vandewalle N, Poncin P (2006) Comparing the EthoVision 2.3 system and a new computerized multitracking prototype system to measure the swimming behavior in fry fish. Behav Res Methods 38:704–710. CrossRefPubMedGoogle Scholar
  31. Delcourt J, Becco C, Vandewalle N, Poncin P (2009) A video multitracking system for quantification of individual behavior in a large fish shoal: advantages and limits. Behav Res Methods 41:228–235. CrossRefPubMedGoogle Scholar
  32. Delcourt J, Ylieff M, Bolliet V, Poncin P, Bardonnet A (2011) Video tracking in the extreme: a new possibility for tracking nocturnal underwater transparent animals with fluorescent elastomer tags. Behav Res Methods 43:590–600. CrossRefPubMedGoogle Scholar
  33. Delcourt J, Denoël M, Ylieff M, Poncin P (2013) Video multitracking of fish behavior: a synthesis and future perspectives. Fish Fish 14:186–204. CrossRefGoogle Scholar
  34. Delcourt J, Bode N, Denoël M (2016) Collective vortex behaviors: diversity, proximate, and ultimate causes of circular animal group movements. Q Rev Biol 91:1–24. CrossRefPubMedGoogle Scholar
  35. Delcourt J, Miller NY, Couzin ID, Garnier S (2018) Methods for the effective study of collective behavior in a radial arm maze. Behav Res Methods 50:1673–1685. CrossRefPubMedGoogle Scholar
  36. Denoël M, Libon S, Kestemont P, Brasseur C, Focant JF, De Pauw E (2013) Effects of a sublethal pesticide exposure on locomotor behavior: a video-tracking analysis in larval amphibians. Chemosphere 90:945–951. CrossRefPubMedGoogle Scholar
  37. Devlin RH, Sundström LF, Leggatt RA (2015) Assessing ecological and evolutionary consequences of growth-accelerated genetically engineered fishes. Bioscience 65:685–700. CrossRefGoogle Scholar
  38. Dolado R, Gimeno E, Beltran FS, Quera V, Pertusa JF (2015) A method for resolving occlusions when multitracking individuals in a shoal. Behav Res Methods 47:1032–1043. CrossRefPubMedGoogle Scholar
  39. Drechsler A, Helling T, Steinfartz S (2015) Genetic fingerprinting proves cross-correlated automatic photo-identification of individuals as highly efficient in large capture–mark–recapture studies. Ecol Evol 5:141–151. CrossRefPubMedGoogle Scholar
  40. Engeszer RE, Wang G, Ryan MJ, Parichy DM (2008) Sex-specific perceptual spaces for a vertebrate basal social aggregative behavior. Proc Natl Acad Sci USA 105:929–933. CrossRefPubMedGoogle Scholar
  41. Fadeev A, Krauss J, Frohnhofer HG, Irion U, Usslein-Volhard C (2015) Tight junction protein 1a regulates pigment cell organisation during zebrafish colour patterning. eLife 4:e06545. CrossRefPubMedCentralGoogle Scholar
  42. 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 211:1305–1316. CrossRefPubMedGoogle Scholar
  43. Frederick JL (1997) Evaluation of fluorescent elastomer injection as a method for marking small fish. Bull Mar Sci 61:399–408Google Scholar
  44. Freret-Meurer NV, Andreata JV, Alves MAS (2013) Seahorse fingerprints: a new individual identification technique. Environ Biol Fish 96:1399–1405. CrossRefGoogle Scholar
  45. Frohnhöfer HG, Krauss J, Maischein HM, Nüsslein-Volhard C (2013) Iridophores and their interactions with other chromatophores are required for stripe formation in zebrafish. Development 140:2997–3007. CrossRefPubMedPubMedCentralGoogle Scholar
  46. Frohnhöfer HG, Geiger-Rudolph S, Pattky M, Meixner M, Huhn C, Maischein H-M et al (2016) Spermidine, but not spermine, is essential for pigment pattern formation in zebrafish. Biol Open 5:736–744. CrossRefPubMedPubMedCentralGoogle Scholar
  47. Frommen JG, Hanak S, Schmidl CA, Thünken T (2015) Visible implant elastomer tagging influences social preferences of zebrafish (Danio rerio). Behaviour 152:1765–1777. CrossRefGoogle Scholar
  48. Fürtbauer I, King AJ, Heistermann M (2015) Visible implant elastomer (VIE) tagging and simulated predation risk elicit similar physiological stress responses in three-spined stickleback Gasterosteus aculeatus. J Fish Biol 86:1644–1649. CrossRefPubMedGoogle Scholar
  49. Gerhard G, Kauffman E, Wang X, Stewart R, Moore J, Kasales C, Demidenko E, Cheng K (2002) Life spans and senescent phenotypes of zebrafish (Danio rerio). Exp Gerontol 37:1055–1068. CrossRefPubMedGoogle Scholar
  50. Gerlai R (2015) Zebrafish phenomics: behavioral screens and phenotyping of mutagenized fish. Curr Opin Behav Sci 2:21–27. CrossRefGoogle Scholar
  51. Gerlai R, Lahav M, Guo S, Rosenthal A (2000) Drinks like a fish: zebrafish (Danio rerio) as a behavior genetic model to study alcohol effects. Pharmacol Biochem Behav 67:773–782. CrossRefPubMedGoogle Scholar
  52. Gibert Y, Trengove MC, Ward AC (2013) Zebrafish as a genetic model in pre-clinical drug testing and screening. Curr Med Chem 20:2458–2466. CrossRefPubMedGoogle Scholar
  53. Gómez-Laplaza LM, Gil-Carnicero P (2008) Imprinting in fish: a little explored phenomenon with possible implications for fish welfare. Ann Rev Biomed Sci 10:T51–T62. CrossRefGoogle Scholar
  54. Gong Z, Wan H, Tang TL, Wang H, Chen M, Yan T (2003) Development of transgenic fish for ornamental and bioreactor by strong expression of fluorescent proteins in the skeletal muscle. Biochem Biophys Res Commun 308:58–63. CrossRefPubMedGoogle Scholar
  55. Gruda MC, Pinto A, Craelius A, Davidowitz H, Kopacka W, Li J, Qian J, Rodriguez E, Kuspiel E, Mandecki W (2010) A system for implanting laboratory mice with light-activated microtransponders. J Am Assoc Lab Anim 49:826–831Google Scholar
  56. Halperin JRP, Dunham DW (1993) Increased aggressiveness after brief social isolation of adult fish: a connectionist model which organizes this literature. Behav Process 28:123–144. CrossRefGoogle Scholar
  57. Hampel S, Chung P, McKellar C, Hall D, Looger L, Simpson J (2011) Drosophila Brainbow: a recombinase-based fluorescence labelling technique to subdivide neural expression patterns. Nat Methods 8:253–260. CrossRefPubMedPubMedCentralGoogle Scholar
  58. Hansen LP (1988) Effects of Carlin tagging and fin clipping on survival of Atlantic salmon (Salmo salar L.) released as smolts. Aquaculture 70:391–394. CrossRefGoogle Scholar
  59. Hansen LA, Skajaa K, Damsgard B (2008) Measuring aggression and threat-sensitive behavior in cod differing in size and nutritional state. In: Spink AJ, Ballintijn MR, Bogers ND, Grieco F, Loijens LWS, Noldus LPPJ, Smit G, Zimmerman PH (eds) Proceedings in measuring behavior 2008, Maastricht, The Netherlands, 26–29 August 2008, pp 169Google Scholar
  60. Harper C, Lawrence C (2011) The laboratory zebrafish. CRC Press, Boca RatonGoogle Scholar
  61. Hemelrijk CK, Hildenbrandt H, Reinders J, Stamhuis EJ (2010) Emergence of oblong school shape: models and empirical data of fish. Ethology 116:1099–1112. CrossRefGoogle Scholar
  62. Hesse S, Anaya-Rojas JM, Frommen JG, Thünken T (2015) Social deprivation affects cooperative predator inspection in a cichlid fish. R Soc Open Sci 2:140451. CrossRefPubMedPubMedCentralGoogle Scholar
  63. Higashijima S (2008) Transgenic zebrafish expressing fluorescent proteins in central nervous system neurons. Dev Growth Differ 50:407–413. CrossRefPubMedGoogle Scholar
  64. Hill AJ, Teraoka H, Heideman W, Peterson RE (2005) Zebrafish as a model vertebrate for investigating chemical toxicity. Toxicol Sci 86:6–19. CrossRefPubMedGoogle Scholar
  65. Hill JE, Kapuscinski AR, Pavlowich T (2011) Fluorescent transgenic zebra Danio more vulnerable to predators than wild-type fish. Trans Am Fish Soc 140:1001–1005. CrossRefGoogle Scholar
  66. Ho DH, Burggren WW (2012) Parental hypoxic exposure confers offspring hypoxia resistance in zebrafish (Danio rerio). J Exp Biol 215:4208–4216. CrossRefPubMedGoogle Scholar
  67. Hohn C, Petrie-Hanson L (2013) Evaluation of visible implant elastomer tags in zebrafish (Danio rerio). Biol Open 2:1397–1401. CrossRefPubMedPubMedCentralGoogle Scholar
  68. Huang Y, Zhang J, Han X, Huang T (2014) The use of zebrafish (Danio rerio) behavioral responses in identifying sublethal exposures to deltamethrin. Int J Environ Res Public Health 11:3650–3660. CrossRefPubMedPubMedCentralGoogle Scholar
  69. Hutter S, Penn DJ, Magee S, Zala SM (2010) Reproductive behaviour of wild zebrafish (Danio rerio) in large tanks. Behaviour 147:641–660. CrossRefGoogle Scholar
  70. Hutter S, Zala SM, Penn DJ (2011) Sex recognition in zebrafish (Danio rerio). J Ethol 29:55–61. CrossRefGoogle Scholar
  71. Hutter S, Hettyey A, Penn DJ, Zala SM (2012) Ephemeral sexual dichromatism in zebrafish (Danio rerio). Ethology 118:1208–1218. CrossRefGoogle Scholar
  72. Im JH, Gil HW, Park I-S, Choi ChY, Lee TH, Yoo KY, Kim ChH, Kim BS (2017) Evaluation of visible fluorescent elastomer tags implanted in marine medaka, Oryzias dancena. Fish Aquat Sci 20:21. CrossRefGoogle Scholar
  73. Ioannou CC, Tosch CR, Neville L, Krause J (2008) The confusion effect: from neural networks to reduced predation risk. Behav Ecol 19:126–130. CrossRefGoogle Scholar
  74. Irion U, Frohnhöfer HG, Krauss J, Champollion TC, Maischein H-M et al (2014) Gap junctions composed of connexins 41.8 and 39.4 are essential for colour pattern formation in zebrafish. eLife 3:e05125. CrossRefPubMedPubMedCentralGoogle Scholar
  75. Iwashita M, Watanabe M, Ishii M, Chen T, Johnson SL, Kurachi Y et al (2006) Pigment pattern in jaguar/obelix zebrafish is caused by a Kir7.1 mutation: implications for the regulation of melanosome movement. PLoS Genet 2:e197. CrossRefPubMedPubMedCentralGoogle Scholar
  76. Jepsen N, Schreck C, Clements S, Thorstad E (2005) A brief discussion on the 2% tag/bodymass rule of thumb. In: Spedicato MT, Lembo G, Marmulla G (eds) Aquatic telemetry: advances and applications—proceedings of the fifth conference on fish telemetry, Ustica, Italy, 9–13 June 2005. FAO, Rome, pp 255–259Google Scholar
  77. Jepsen N, Thorstad EB, Havn T, Lucas MC (2015) The use of external electronic tags on fish: an evaluation of tag retention and tagging effects. Anim Biotelem 3:49. CrossRefGoogle Scholar
  78. Jiang P, Bai JJ, Ye X, Jian Q, Chen M, Chen XQ (2011) Shoaling and mate choice of wild-type Tanichthys albonubes in the presence of red fluorescent transgenic conspecifics. J Fish Biol 78:127–137. CrossRefPubMedGoogle Scholar
  79. Jolley-Rogers G, Yeates DK, Croft J, Cawsey EM, Suter P, Webb J, Morris RG, Qian Z, Rodriguez E, Mandecki W (2012) Ultra-small RFID p-Chips on the heads of entomological pins provide an automatic and durable means to track and label insect specimens. Zootaxa 3359:31–42Google Scholar
  80. Kalueff AV (2017) The right and the wrongs of zebrafish: behavioural phenotyping of zebrafish. Springer, Berlin, p 327. CrossRefGoogle Scholar
  81. 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. CrossRefPubMedPubMedCentralGoogle Scholar
  82. Kalueff AV, Stewart AM, Gerlai R (2014) Zebrafish as an emerging model for studying complex brain disorders. Trends Pharmacol Sci 35:63–75. CrossRefPubMedPubMedCentralGoogle Scholar
  83. Kato S, Nakagawa T, Ohkawa M, Muramoto K et al (2004) A computer image processing system for quantification of zebrafish behavior. J Neurosci Methods 134:1–7. CrossRefPubMedGoogle Scholar
  84. Kelsh RN, Brand M, Jiang YJ, Heisenberg CP, Lin S, Haffter P, Odenthal J et al (1996) Zebrafish pigmentation mutations and the processes of neural crest development. Development 123:369–389PubMedGoogle Scholar
  85. Khee SW (2006) Possible ecological impacts caused by GFP transgenic Zebrafish, Danio rerio. Doctoral dissertation, National University of Singapore, SingaporeGoogle Scholar
  86. Krause J, James R, Franks DW, Croft DP (2015) Animal social networks. Oxford University Press, Oxford, p 260Google Scholar
  87. Laale HW (1977) The biology and use of zebrafish, Brachydanio rerio in fisheries research: a literature review. J Fish Biol 10:121–173. CrossRefGoogle Scholar
  88. Lahiri M, Tantipathananandh C, Warungu R, Rubenstein DI, Berger-Wolf TY (2011) Biometric animal databases from field photographs: identification of individual zebra in the wild. In: Proceedings of the 1st ACM international conference on multimedia retrieval, Trento, ItalyGoogle Scholar
  89. Larson ET, O’Malley DM, Melloni RH Jr (2006) Aggression and vasotocin are associated with dominant-subordinate relationships in zebrafish. Behav Brain Res 167:94–102. CrossRefPubMedGoogle Scholar
  90. Laurel BJ, Laurel CJ, Brown JA, Gregory RS (2005) A new technique to gather 3-D spatial information using a single camera. J Fish Biol 66:429–441. CrossRefGoogle Scholar
  91. Lawrence Ch (2007) The husbandry of zebrafish (Danio rerio): a review. Aquaculture 269:1–20. CrossRefGoogle Scholar
  92. Leips J, Baril CT, Rodd FH, Reznick DN, Bashey F, Visser GJ, Travis J (2001) The suitability of calcein to mark poeciliid fish and a new method of detection. Trans Am Fish Soc 130:501–507.;2 CrossRefGoogle Scholar
  93. Liew WC, Orbán L (2014) Zebrafish sex: a complicated affair. Brief Funct Genomics 13:172–187. CrossRefPubMedGoogle Scholar
  94. Livet J, Weissman TA, Kang H, Draft RW, Lu J, Bennis RA, Sanes JR, Lichtman JW (2007) Transgenic strategies for combinatorial expression of fluorescent proteins in the nervous system. Nature 450:56–62. CrossRefPubMedGoogle Scholar
  95. Lucas MC, Baras E (2001) Migration of freshwater fishes. Blackwell, Oxford, p 352pCrossRefGoogle Scholar
  96. Maaswinkel H, Zhu L, Weng W (2013) Using an automated 3D-tracking system to record individual and shoals of adult zebrafish. JoVE 82:50681. CrossRefGoogle Scholar
  97. Maclean N, Laight RJ (2000) Transgenic fish: an evaluation of benefits and risks. Fish Fish 1:146–172. CrossRefGoogle Scholar
  98. Maderspacher F, Nüsslein-Volhard Ch (2003) Formation of the adult pigment pattern in zebrafish requires leopard and obelix dependent cell interactions. Development 130:3447–3457CrossRefGoogle Scholar
  99. Magalhães DP, Armando da Cunha R, Albuquerque dos Santos JA, Buss DF, Baptista DF (2007) Behavioral response of zebrafish Danio rerio Hamilton 1822 to sublethal stress by sodium hypochlorite: ecotoxicological assay using an image analysis biomonitoring system. Ecotoxicology 16:417–422. CrossRefGoogle Scholar
  100. Maggio E, Cavallaro A (2011) Video tracking: theory and practice. Wiley, New York. CrossRefGoogle Scholar
  101. Mahalwar P, Walderich B, Singh AP, Nüsslein-Volhard Ch (2014) Local reorganization of xanthophores fine-tunes and colors the striped pattern of zebrafish. Science 345:1362–1364. CrossRefPubMedGoogle Scholar
  102. Mahalwar P, Singh AP, Fadeev A, Nüsslein-Volhard C, Irion U (2016) Heterotypic interactions regulate cell shape and density during color pattern formation in zebrafish. Biol Open 5:1680–1690. CrossRefPubMedPubMedCentralGoogle Scholar
  103. Martin P, Bateson P (2007) Measuring behavior, 3rd edn. Cambridge University Press, CambridgeCrossRefGoogle Scholar
  104. McGrath P, Seng WL (2013) Use of zebrafish apoptosis assays for preclinical drug discovery. Expert Opin Drug Dis 8:1191–1202. CrossRefGoogle Scholar
  105. McKenzie JR, Parsons B, Seitz AC, Kopf RK, Mesa M, Phelps Q (2012) Advances in fish tagging and marking technology. American Fisheries Society, Bethesda, p 560Google Scholar
  106. Meunier F (1972) Marquages simples et multiples du tissu osseux de quelques téléostéens par des substances fluorescentes. C R Acad Sci 275:1685–1688Google Scholar
  107. Meunier F (1974) La technique du marquage vital des tissus squelettiques des poissons. Bull Fr Pêche Piscic 255:51–57CrossRefGoogle Scholar
  108. Meunier F, Boivin G (1974) Divers aspects de la fixation du chlorhydrate de tétracycline sur les tissus squelettiques de quelques téléostéens. Bull Soc Zool Fr 99:495–504Google Scholar
  109. Miller N, Gerlai R (2007) Quantification of shoaling behavior in zebrafish (Danio rerio). Behav Brain Res 184:157–166. CrossRefPubMedGoogle Scholar
  110. Miller N, Gerlai R (2011) Shoaling in zebrafish: what we don’t know. Rev Neurosci 22:17–25. CrossRefPubMedGoogle Scholar
  111. Miller N, Gerlai R (2012) From schooling to shoaling: patterns of collective motion in zebrafish (Danio rerio). PLoS ONE 7:e48865. CrossRefPubMedPubMedCentralGoogle Scholar
  112. Miller N, Garnier S, Couzin ID (2013) Both information and social cohesion determine collective decisions in animal groups. Proc Natl Acad Sci USA 110:5263–5268. CrossRefPubMedGoogle Scholar
  113. Mirat O, Sternberg JR, Severi KE, Wyart C (2013) ZebraZoom: an automated program for high-throughput behavioral analysis and categorization. Front Neural Circuit 7:107. CrossRefGoogle Scholar
  114. Mohler JW (2003) Producing fluorescent marks on Atlantic salmon fin rays and scales with calcein via osmotic induction. N Am J Fish Manag 23:1108–1113. CrossRefGoogle Scholar
  115. Moretz JA, Martins EP, Robison BD (2007) The effects of early and adult social environment on zebrafish (Danio rerio) behavior. Environ Biol Fish 80:91–101. CrossRefGoogle Scholar
  116. Muir WM (2004) The threats and benefits of GM fish. EMBO Rep 5:654–659. CrossRefPubMedPubMedCentralGoogle Scholar
  117. Nagare P, Aglave BA, Lokhande MO (2009) Genetically engineered Zebrafish: fluorescent beauties with practical applications. Asian J Anim Sci 4:126–129Google Scholar
  118. Nagiec M, Dabrowski K, Nagiec C, Murawska E (1988) Mass-marking of coregonid larvae and fry by tetracycline tagging of otoliths. Aquac Res 19:171–178. CrossRefGoogle Scholar
  119. Nava SS, An S, Hamil T (2011) Visual detection of UV cues by adult zebrafish (Danio rerio). J Vis 11:2. CrossRefPubMedGoogle Scholar
  120. Noldus LPJJ, Spink AJ, Tegelenbosch RAJ (2001) EthoVision: a versatile video tracking system for automation of behavioural experiments. Behav Res Methods Instrum C 33:398–414. CrossRefGoogle Scholar
  121. Oliva Teles L, Fernandes M, Amorim J, Vasconcelos V (2015) Video-tracking of zebrafish (Danio rerio) as a biological early warning system using two distinct artificial neural networks: probabilistic neural network (PNN) and self-organizing map (SOM). Aquat Toxicol 165:241–248. CrossRefPubMedGoogle Scholar
  122. Oliveira RF (2013) Mind the fish: zebrafish as a model in cognitive social neuroscience. Front Neural Circuit 7:131. CrossRefGoogle Scholar
  123. Ousterhout BH, Semlitsch RD (2014) Measuring terrestrial movement behavior using passive integrated transponder (PIT) tags: effects of tag size on detection, movement, survival, and growth. Behav Ecol Sociobiol 68:343–350. CrossRefGoogle Scholar
  124. Ovidio M, Dierckx A, Bunel S, Grandry L, Spronck C, Benitez JP (2017) poor performance of a retrofitted downstream bypass revealed by the analysis of approaching behaviour in combination with a trapping system. River Res Appl 33:27–36. CrossRefGoogle Scholar
  125. Owen MA, Rohrer K, Howard RD (2012) Mate choice for a novel male phenotype in zebrafish, Danio rerio. Anim Behav 83:811–820. CrossRefGoogle Scholar
  126. Papoulis A, Pillai SU (2002) Probability, random variables and stochastic processes, 4th edn. McGraw-Hill Higher Education, New York, p 852Google Scholar
  127. Parichy DM (2006) Evolution of danio pigment pattern development. Heredity 97:200–210. CrossRefPubMedGoogle Scholar
  128. Patterson LB, Parichy DM (2013) Interactions with iridophores and the tissue environment required for patterning melanophores and xanthophores during zebrafish adult pigment stripe formation. PLoS Genet 9:e1003561. CrossRefPubMedPubMedCentralGoogle Scholar
  129. 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 11:743–748. CrossRefPubMedGoogle Scholar
  130. Petrovska-Delacretaz D, Edwards A, Chiassoli J, Chollet G, Pilliod DS (2014) A reference system for animal biometrics: application to the northern leopard frog. In 1st International conference on advanced technologies for signal and image processing, ATSIPGoogle Scholar
  131. Pfefferli C, Jaźwińska A (2015) The art of fin regeneration in zebrafish. Regeneration 2:72–83. CrossRefPubMedPubMedCentralGoogle Scholar
  132. Pissios P, Bradley RL, Maratos-Flier E (2006) Expanding the scales: the multiple roles of MCH in regulating energy balance and other biological functions. Endocr Rev 27:606–620. CrossRefPubMedGoogle Scholar
  133. Piyapong Ch, Krause J, Chapman BB, Ramnarine IW, Darren VL, Croft P (2010) Sex matters: a social context to boldness in guppies (Poecilia reticulata). Behav Ecol 21:3–8. CrossRefGoogle Scholar
  134. Prenctice EF, Flagg TA, McCutcheon CS (1990) Feasibility of using implantable passive integrated transponder (PIT) tags in salmonids. Am Fish Soc Symp 7:317–322Google Scholar
  135. Qian Z-M, Cheng XE, Chen YQ (2014) Automatically detect and track multiple fish swimming in shallow water with frequent occlusion. PLoS ONE 9:e106506. CrossRefPubMedPubMedCentralGoogle Scholar
  136. Qian Z-M, Wang SH, Cheng XE, Chen YQ (2016) An effective and robust method for tracking multiple fish in video image based on fish head detection. BMC Bioinform 17:251. CrossRefGoogle Scholar
  137. Raldúa D, Piña B (2014) In vivo zebrafish assays for analyzing drug toxicity. Expert Opin Drug Metab 10:685–697. CrossRefGoogle Scholar
  138. Rawls JF, Mellgren EM, Johnson SL (2001) How the zebrafish gets its stripes. Dev Biol 240:301–314. CrossRefPubMedGoogle Scholar
  139. Reed B, Jennings M (2011) Guidance on the housing and care of zebrafish. Research Animals Department, Science Group, Royal Society for the Prevention of Cruelty to Animals (RSPCA), Horsam, p 62. Accessed 23 Mar 2016, last update May 2011
  140. Reznick D, Bryant M (2007) Comparative long-term mark-recapture studies of guppies (Poecilia reticulata): differences among high and low predation localities in growth and survival. Ann Zool Fenn 44:152–160Google Scholar
  141. Ribas L, Piferrer F (2014) The zebrafish (Danio rerio) as a model organism, with emphasis on applications for finfish aquaculture research. Rev Aquac 6:1753–5131. CrossRefGoogle Scholar
  142. Robinson EJH, Mandecki W (2011) Distributed decisions: new insights from radio-tagged ants. In: Sun EC (ed) Ant colonies: behavior in insects and computer applications. Nova Science Publishers, Hauppauge, pp 109–128Google Scholar
  143. Robinson EJH, Richardson TO, Sendova-Franks AB, Feinerman O, Franks NR (2009) Radio-tagging reveals the roles of corpulence, experience and social information in ant decision making. Behav Ecol Sociobiol 63:627–636. CrossRefGoogle Scholar
  144. Robinson EJH, Feinerman O, Franks NR (2014) How collective comparisons emerge without individual comparisons of the options. Proc R Soc B Biol Sci 281:20140737. CrossRefGoogle Scholar
  145. Roques JAC, Abbink W, Geurds F, van de Vis H, Flik G (2010) Tailfin clipping, a painful procedure: studies on Nile tilapia and common carp. Physiol Behav 101:533–540. CrossRefPubMedGoogle Scholar
  146. Sacchi R, Scali S, Mangiacotti M, Sannolo M, Zuffi MAL (2016) Digital identification and analysis. In: Dodd Kenneth (ed) Reptile ecology and conservation: a handbook of techniques, chapter: 5, 1st edn. Oxford University Press, Oxford, pp 59–72CrossRefGoogle Scholar
  147. Saunders RL, Allen KR (1967) Effects of tagging and of fin-clipping on the survival and growth of Atlantic salmon between smolt and adult stages. J Fish Res Board Can 24:2595–2611. CrossRefGoogle Scholar
  148. Saverino C, Gerlai R (2008) The social zebrafish: behavioral responses to conspecific, heterospecific, and computer animated fish. Behav Brain Res 191:77–87. CrossRefPubMedPubMedCentralGoogle Scholar
  149. Schartl M (2014) Beyond the zebrafish: diverse fish species for modeling human disease. Dis Models Mech 7:181–192. CrossRefGoogle Scholar
  150. Schilling T (2002) The morphology of larval and adult zebrafish. In: Nüsslein-Volhard C, Dahm R (eds) Zebrafish. Oxford University Press, Oxford, pp 59–94Google Scholar
  151. Schreck CB, Contreras-Sanchez W, Fitzpatrick MS (2001) Effects of stress on fish reproduction, gamete quality, and progeny. Aquaculture 197:3–24. CrossRefGoogle Scholar
  152. Séguret A, Collignon B, Halloy J (2016) Strain differences in the collective behaviour of zebrafish (Danio rerio) in heterogeneous environment. R Soc Open Sci 3:160451. CrossRefPubMedPubMedCentralGoogle Scholar
  153. Singh AP, Nüsslein-Volhard C (2015) Zebrafish stripes as a model for vertebrate color pattern formation. Curr Biol 25:R81–R92. CrossRefPubMedGoogle Scholar
  154. Singh AP, Schach U, Nüsslein-Volhard C (2014) Proliferation, dispersal and patterned aggregation of iridophores in the skin prefigure striped colouration of zebrafish. Nat Cell Biol 16:607–614. CrossRefPubMedGoogle Scholar
  155. Sire JY, Girondot M, Babiar O (2000) Marking zebrafish, Danio rerio (Cyprinidae), using scale regeneration. J Exp Biol 286:297–304.;2-X CrossRefGoogle Scholar
  156. Skalski JR, Buchanan RA, Griswold J (2009) Review of marking methods and release-recapture designs for estimating the survival of very small fish: examples from the assessment of salmonid fry survival. Rev Fish Sci 17:391–401. CrossRefGoogle Scholar
  157. Smircich MG, Kelly JT (2014) Extending the 2% rule: the effects of heavy internal tags on stress physiology, swimming performance, and growth in brook trout. Anim Biotelem 2:16. CrossRefGoogle Scholar
  158. Sneddon LU, Wolfenden DCC, Thomson JS (2016) Stress management and welfare. In: Schreck CB, Tort L, Farrel AP, Brauner CJ (eds) Biology of stress in fish: fish physiology, chapter 12, vol 35. Academic Press, Cambridge, pp 464–521Google Scholar
  159. Snekser JL, McRobert SP, Murphy CE, Clotfelter ED (2006) Aggregation behavior in wild type and transgenic zebrafish. Ethology 112:181–187. CrossRefGoogle Scholar
  160. Sparks JS, Schelly RC, Smith WL, Davis MP, Tchernov D, Pieribone VA, Gruber DF (2014) The covert world of fish biofluorescence: a phylogenetically widespread and phenotypically variable phenomenon. PLoS ONE 9:e83259. CrossRefPubMedPubMedCentralGoogle Scholar
  161. Speed CW, Meekan MG, Bradshaw CJA (2007) Spot the match: wildlife photo-identification using information theory. Front Zool 4:2. CrossRefPubMedPubMedCentralGoogle Scholar
  162. Stewart AM, Braubach O, Spitsbergen J, Gerlai R, Kalueff AV (2014a) Zebrafish models for translational neuroscience research: from tank to bedside. Trends Neurosci 37:264–278. CrossRefPubMedPubMedCentralGoogle Scholar
  163. Stewart AM, Nguyen M, Wong K, Poudel MK, Kalueff AV (2014b) Developing zebrafish models of autism spectrum disorder (ASD). Prog Neuro Psychopharmacol 50:27–36. CrossRefGoogle Scholar
  164. Sumpter JT (2010) Collective animal behavior. Princeton University Press, Princeton, p 302. CrossRefGoogle Scholar
  165. Tenczar P, Lutz CC, Rao VD, Goldenfeld N, Robinson GE (2014) Automated monitoring reveals extreme interindividual variation and plasticity in honeybee foraging activity levels. Anim Behav 95:41–48. CrossRefGoogle Scholar
  166. Thorstad EB, Rikardsen AH, Alp A, Økland F (2013) The use of electronic tags in fish research: an overview of fish telemetry methods. Turk J Fish Aquat Sci 13:881–896. CrossRefGoogle Scholar
  167. Thorsteinsson MV (2002) Tagging methods for stock assessment and research in fisheries. Report of concerted action FAIR CT.96.1394 (CATAG), Reykjavik, Iceland. Marine Research Institute Technical Report (79)Google Scholar
  168. Tosh CR, Ruxton GD (2006) Artificial neural network properties associated with wiring patterns in the visual projections of vertebrates and arthropods. Am Nat 168:E38–E52. CrossRefPubMedGoogle Scholar
  169. Tucci V, Gerlai R (2017) Behavioral phenotyping in zebrafish: The first models of alcohol induced abnormalities. In: Tucci V (ed) Handbook of neurobehavioral genetics and phenotyping, chapter 3. Wiley, Hoboken, pp 37–52. CrossRefGoogle Scholar
  170. Tunstrøm K, Katz Y, Ioannou CC, Huepe C, Lutz MJ, Couzin ID (2013) Collective states, multistability and transitional behavior in schooling fish. PLoS Comput Biol 9:e1002915. CrossRefPubMedPubMedCentralGoogle Scholar
  171. Turing AM (1952) The chemical basis of morphogenesis. Philos Trans R Soc B 237:37–72. CrossRefGoogle Scholar
  172. Van Tienhoven AM, Den Hartog JE, Reijns RA, Peddemors VM (2007) A computer-aided program for pattern-matching of natural marks on the spotted raggedtooth shark Carcharias taurus. J Appl Ecol 44:273–280. CrossRefGoogle Scholar
  173. Veinotte CJ, Dellaire G, Berman JN (2014) Hooking the big one: the potential of zebrafish xenotransplantation to reform cancer drug screening in the genomic era. Dis Models Mech 7:745–754. CrossRefGoogle Scholar
  174. Viscido SV, Parrish JK, Grünbaum D (2004) Individual behavior and emergent properties of fish schools: a comparison of observation and theory. Mar Ecol Prog Ser 273:239–249. CrossRefGoogle Scholar
  175. Volkening A, Sandstede B (2015) Modelling stripe formation in zebrafish: an agent-based approach. J R Soc Interface 12:20150812. CrossRefPubMedPubMedCentralGoogle Scholar
  176. Wagner CP, Einfalt LM, Scimone AB, Wahl DH (2009) Effects of fin-clipping on the foraging behavior and growth of age-0 muskellunge. N Am J Fish Manag 29:1644–1652. CrossRefGoogle Scholar
  177. Wan H, He J, Ju B, Yan T, Lam TJ, Gong Z (2002) Generation of two-color transgenic zebrafish using the green and red fluorescent protein reporter genes gfp and rfp. Mar Biotechnol 4:146–154. CrossRefPubMedGoogle Scholar
  178. Wang SH, Cheng XE, Qian Z-M, Liu Y, Chen YQ (2016) Automated planar tracking the waving bodies of multiple zebrafish swimming in shallow water. PLoS ONE 11:e0154714. CrossRefPubMedPubMedCentralGoogle Scholar
  179. Watanabe M, Kondo S (2015) Comment on “Local reorganization of xanthophores fine-tunes and colors the striped pattern of zebrafish”. Science 348:297. CrossRefPubMedGoogle Scholar
  180. White RM, Sessa A, Burke Ch, Bowman T, LeBlanc J, Ceol C et al (2008) Transparent adult zebrafish as a tool for in vivo transplantation analysis. Cell Stem Cell 2:183–189. CrossRefPubMedPubMedCentralGoogle Scholar
  181. Winandy L, Denoël M (2011) The use of visual and automatized behavioral markers to assess methodologies: a study case on PIT-tagging in the Alpine newt. Behav Res Methods 43:568–576. CrossRefPubMedGoogle Scholar
  182. Winandy L, Legrand P, Denoël M (2017) Habitat selection and reproduction of newts in networks of fish and fishless aquatic patches. Anim Behav 123:107–115. CrossRefGoogle Scholar
  183. Winter J (1996) Advances in underwater biotelemetry. In: Murphy BR, Willis DW (eds) Fisheries techniques, 2nd edn. American Fisheries Society, Bethesda, pp 555–590Google Scholar
  184. Wright PJ, Panfili J, Folkvord A, Mosegaard H, Meunier FJ (2002) Validation and verification methods. In: Panfili J, de Pontual H, Troadec H, Wright PJ (eds) Manual of fish sclerochronology. Ifremer-IRD coedition, Brest, pp 114–142Google Scholar
  185. Ylieff MY, Poncin P (2003) Quantifying spontaneous swimming activity in fish with a computerized color video tracking system, a laboratory device using last imaging techniques. Fish Physiol Biochem 28:281–282. CrossRefGoogle Scholar
  186. Zhang F, Qin W, Zhang J-P, Hu C-Q (2015a) Antibiotic toxicity and absorption in zebrafish using liquid chromatography-tandem mass spectrometry. PLoS ONE 10:e0124805. CrossRefPubMedPubMedCentralGoogle Scholar
  187. Zhang Q, Cheng J, Xin Q (2015b) Effects of tetracycline on developmental toxicity and molecular responses in zebrafish (Danio rerio) embryos. Ecotoxicology 24:707–719. CrossRefPubMedGoogle Scholar

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© Springer Nature Switzerland AG 2018

Authors and Affiliations

  1. 1.Laboratory of Fish and Amphibian Ethology, Freshwater and OCeanic science Unit of reSearch (U.R. FOCUS), Behavioural Biology GroupUniversity of LiegeLiegeBelgium
  2. 2.Laboratory of Fish Demography and Hydroecology, Freshwater and OCeanic science Unit of reSearch (U.R. FOCUS), Behavioural Biology GroupUniversity of LiegeLiegeBelgium
  3. 3.GIGA-Research, Laboratory for Organogenesis and RegenerationUniversity of LiegeLiegeBelgium
  4. 4.Zebrafish Facility & Transgenics, GIGA-PlatformUniversity of LiegeLiegeBelgium
  5. 5.Unit of Social Ecology (USE)University of BrusselsBrusselsBelgium

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