Abstract
Registration of larval zebrafish brain scans to a common reference brain enables comparison of transgene and gene expression patterns, neuroanatomy, and morphometry. Here we describe methods for staining and mounting larval zebrafish to facilitate whole-brain fluorescence imaging. Following image acquisition, we provide a template for aligning brain images to a reference atlas using nonlinear registration with the ANTs software package.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Similar content being viewed by others
References
Marquart GD, Tabor KM, Horstick EJ et al (2017) High precision registration between zebrafish brain atlases using symmetric diffeomorphic normalization. Gigascience 6. https://doi.org/10.1093/gigascience/gix056
Rohlfing T, Maurer CR Jr (2003) Nonrigid image registration in shared-memory multiprocessor environments with application to brains, breasts, and bees. IEEE Trans Inf Technol Biomed 7:16–25
Portugues R, Feierstein CE, Engert F, Orger MB (2014) Whole-brain activity maps reveal stereotyped, distributed networks for visuomotor behavior. Neuron 81:1328–1343. https://doi.org/10.1016/j.neuron.2014.01.019
Kenney JW, Steadman PE, Young O et al (2021) A 3D adult zebrafish brain atlas (AZBA) for the digital age. elife 10:e69988. https://doi.org/10.7554/eLife.69988
Avants BB, Epstein CL, Grossman M, Gee JC (2008) Symmetric diffeomorphic image registration with cross-correlation: evaluating automated labeling of elderly and neurodegenerative brain. Med Image Anal 12:26–41. https://doi.org/10.1016/j.media.2007.06.004
Heffer A, Marquart GD, Aquilina-Beck A et al (2017) Generation and characterization of Kctd15 mutations in zebrafish. PLoS One 12:e0189162. https://doi.org/10.1371/journal.pone.0189162
Randlett O, Wee CL, Naumann EA et al (2015) Whole-brain activity mapping onto a zebrafish brain atlas. Nat Methods 12:1039–1046
Choi HMT, Schwarzkopf M, Fornace ME et al (2018) Third-generation in situ hybridization chain reaction: multiplexed, quantitative, sensitive, versatile, robust. Development 145:dev165753. https://doi.org/10.1242/dev.165753
Trivellin G, Tirosh A, Hernández-Ramírez LC et al (2021) The X-linked acrogigantism-associated gene gpr101 is a regulator of early embryonic development and growth in zebrafish. Mol Cell Endocrinol 520:111091. https://doi.org/10.1016/j.mce.2020.111091
Satou C, Kimura Y, Higashijima S (2012) Generation of multiple classes of V0 neurons in zebrafish spinal cord: progenitor heterogeneity and temporal control of neuronal diversity. J Neurosci 32:1771–1783. https://doi.org/10.1523/JNEUROSCI.5500-11.2012
Gupta T, Marquart GD, Horstick EJ et al (2018) Morphometric analysis and neuroanatomical mapping of the zebrafish brain. Methods 150:49–62. https://doi.org/10.1016/j.ymeth.2018.06.008
Geng Y, Peterson RT (2021) Rapid mounting of zebrafish larvae for brain imaging. Zebrafish 18:376–379. https://doi.org/10.1089/zeb.2021.0062
Ma L-H, Gilland E, Bass AH, Baker R (2010) Ancestry of motor innervation to pectoral fin and forelimb. Nat Commun 1:49. https://doi.org/10.1038/ncomms1045
Marquart GD, Tabor KM, Brown M et al (2015) A 3D searchable database of transgenic zebrafish Gal4 and Cre Lines for functional neuroanatomy studies. Front Neural Circ 9:78. https://doi.org/10.3389/fncir.2015.00078
Acknowledgments
This work was supported by the Intramural Research Program of the Eunice Kennedy Shriver National Institute for Child Health and Human Development (NICHD) and utilized the high-performance computational capabilities of the Biowulf Linux cluster at the National Institutes of Health, Bethesda, MD.
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2024 The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature
About this protocol
Cite this protocol
Bhandiwad, A.A., Gupta, T., Subedi, A., Heigh, V., Holmes, G.A., Burgess, H.A. (2024). Brain Imaging and Registration in Larval Zebrafish. In: Amatruda, J.F., Houart, C., Kawakami, K., Poss, K.D. (eds) Zebrafish. Methods in Molecular Biology, vol 2707. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-3401-1_9
Download citation
DOI: https://doi.org/10.1007/978-1-0716-3401-1_9
Published:
Publisher Name: Humana, New York, NY
Print ISBN: 978-1-0716-3400-4
Online ISBN: 978-1-0716-3401-1
eBook Packages: Springer Protocols