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Methods. 2018 Nov 1;150:49-62. doi: 10.1016/j.ymeth.2018.06.008. Epub 2018 Jun 21.

Morphometric analysis and neuroanatomical mapping of the zebrafish brain.

Author information

1
Division of Developmental Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, United States.
2
Division of Developmental Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, United States; Neuroscience and Cognitive Science Program, University of Maryland, College Park, MD 20742, United States.
3
Mathematical and Statistical Computing Lab, Office of Intramural Research, Center for Information Technology, National Institutes of Health, Bethesda, MD 20892, United States.
4
Division of Developmental Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, United States. Electronic address: burgessha@mail.nih.gov.

Abstract

Large-scale genomic studies have recently identified genetic variants causative for major neurodevelopmental disorders, such as intellectual disability and autism. However, determining how underlying developmental processes are affected by these mutations remains a significant challenge in the field. Zebrafish is an established model system in developmental neurogenetics that may be useful in uncovering the mechanisms of these mutations. Here we describe the use of voxel-intensity, deformation field, and volume-based morphometric techniques for the systematic and unbiased analysis of gene knock-down and environmental exposure-induced phenotypes in zebrafish. We first present a computational method for brain segmentation based on transgene expression patterns to create a comprehensive neuroanatomical map. This map allowed us to disclose statistically significant changes in brain microstructure and composition in neurodevelopmental models. We demonstrate the effectiveness of morphometric techniques in measuring changes in the relative size of neuroanatomical subdivisions in atoh7 morphant larvae and in identifying phenotypes in larvae treated with valproic acid, a chemical demonstrated to increase the risk of autism in humans. These tools enable rigorous evaluation of the effects of gene mutations and environmental exposures on neural development, providing an entry point for cellular and molecular analysis of basic developmental processes as well as neurodevelopmental and neurodegenerative disorders.

KEYWORDS:

Deformation-field analysis; Neural development; Neuroanatomy; Voxel-based morphometry; Zebrafish

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