Related Experiment Video
Updated: Jul 12, 2025
Author Spotlight: In Vivo Whole-Brain Imaging of Zebrafish Larvae Using Three-Dimensional Fluorescence Microscopy
Published on: April 28, 2023
Brain Registration and Evaluation for Zebrafish (BREEZE)-mapping: A pipeline for whole-brain structural and activity
David S Jin1, Uma Neelakantan2, Cheryl M Lacadie3
1Child Study Center, Yale School of Medicine, New Haven, CT 06510, USA; Department of Neuroscience, Yale University, New Haven, CT 06510, USA; Interdepartmental Neuroscience Program, Yale School of Medicine, New Haven, CT 06510, USA; Department of Neurology, Yale School of Medicine, New Haven, CT 06510, USA.
Abstract:
Here, we present Brain Registration and Evaluation for Zebrafish (BREEZE)-mapping, a user-friendly pipeline for the registration and analysis of whole-brain images in larval zebrafish. We describe steps for pre-processing, registration, quantification, and visualization of whole-brain phenotypes in zebrafish mutants of genes associated with neurodevelopmental and neuropsychiatric disorders. By utilizing BioImage Suite Web, an open-source software package originally developed for processing human brain imaging data, we provide a highly accessible whole-brain mapping protocol developed for users with general computational proficiency. For complete details on the use and execution of this protocol, please refer to Weinschutz Mendes et al. (2023).1.
