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

STAR Protocols (Dec 2023)

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

Affiliations

David S. Jin: 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
Uma Neelakantan: Child Study Center, Yale School of Medicine, New Haven, CT 06510, USA
Cheryl M. Lacadie: Department of Radiology and Biomedical Imaging, Yale School of Medicine, New Haven, CT 06510, USA
Tianying Chen: Child Study Center, Yale School of Medicine, New Haven, CT 06510, USA
Brendan Rooney: Child Study Center, Yale School of Medicine, New Haven, CT 06510, USA
Yunqing Liu: Department of Biostatistics, Yale School of Public Health, New Haven, CT 06510, USA
Weimiao Wu: Department of Biostatistics, Yale School of Public Health, New Haven, CT 06510, USA
Zuoheng Wang: Department of Biostatistics, Yale School of Public Health, New Haven, CT 06510, USA
Xenophon Papademetris: 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
Ellen J. Hoffman: Child Study Center, Yale School of Medicine, New Haven, CT 06510, USA; Department of Neuroscience, Yale University, New Haven, CT 06510, USA; Corresponding author

Journal volume & issue: Vol. 4, no. 4
p. 102647

Abstract

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Summary: 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 : Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics.

Published in STAR Protocols

ISSN: 2666-1667 (Online)
Publisher: Elsevier
Country of publisher: United States
LCC subjects: Science: Science (General)
Website: https://star-protocols.cell.com/

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Abstract

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