Brain Registration and Evaluation for Zebrafish (BREEZE)-mapping: A pipeline for whole-brain structural and activity analyses

David S Jin; Uma Neelakantan; Cheryl M Lacadie; Tianying Chen; Brendan Rooney; Yunqing Liu; Weimiao Wu; Zuoheng Wang; Xenophon Papademetris; Ellen J Hoffman

doi:10.1016/j.xpro.2023.102647

Brain Registration and Evaluation for Zebrafish (BREEZE)-mapping: A pipeline for whole-brain structural and activity analyses

STAR Protoc. 2023 Dec 15;4(4):102647. doi: 10.1016/j.xpro.2023.102647. Epub 2023 Oct 26.

Authors

Affiliations

¹ Child 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.
² Child Study Center, Yale School of Medicine, New Haven, CT 06510, USA.
³ Department of Radiology and Biomedical Imaging, Yale School of Medicine, New Haven, CT 06510, USA.
⁴ Department of Biostatistics, Yale School of Public Health, New Haven, CT 06510, USA.
⁵ Department of Radiology and Biomedical Imaging, Yale School of Medicine, New Haven, CT 06510, USA; Section of Biomedical Informatics and Data Science, Yale School of Medicine, New Haven, CT 06510, USA; Department of Biomedical Engineering, Yale University, New Haven, CT 06510, USA.
⁶ Child Study Center, Yale School of Medicine, New Haven, CT 06510, USA; Department of Neuroscience, Yale University, New Haven, CT 06510, USA. Electronic address: ellen.hoffman@yale.edu.

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.

Keywords: Computer Sciences; Genetics; Microscopy; Model Organisms; Neuroscience.

MeSH terms

Animals
Brain Mapping
Brain* / diagnostic imaging
Humans
Larva
Phenotype
Zebrafish*

Abstract

MeSH terms

Grants and funding