Abstract
Zebrafish (Danio rerio) are increasingly used to investigate spine development, growth, and for studying the etiology of spinal deformity, such as scoliosis. Here, we present a micro-computed tomography-based pipeline for visualizing the zebrafish skeleton. We describe steps for sample preparation, imaging, data management, and processing. We then detail analysis of vertebral and spine morphology using open-source software. This protocol will be useful for scientists using zebrafish to understand spine development and disease. For complete details on the use and execution of this protocol, please refer to Bearce et al. (2022).1.