A three-dimensional digital atlas of the zebrafish brain

Ullmann, Jeremy F. P., Cowin, Gary, Kurniawan, Nyoman D. and Collin, Shaun P. (2010) A three-dimensional digital atlas of the zebrafish brain. NeuroImage, 51 1: 76-82. doi:10.1016/j.neuroimage.2010.01.086

Author Ullmann, Jeremy F. P.
Cowin, Gary
Kurniawan, Nyoman D.
Collin, Shaun P.
Title A three-dimensional digital atlas of the zebrafish brain
Journal name NeuroImage   Check publisher's open access policy
ISSN 1053-8119
Publication date 2010-05-15
Sub-type Article (original research)
DOI 10.1016/j.neuroimage.2010.01.086
Volume 51
Issue 1
Start page 76
End page 82
Total pages 7
Place of publication San Diego, CA, United States
Publisher Academic Press
Collection year 2011
Language eng
Subject C1
920111 Nervous System and Disorders
060805 Animal Neurobiology
Formatted abstract
In the past three decades, the zebrafish has become a vital animal model in a range of biological sciences. To augment current neurobiological research, we have developed the first three-dimensional digital atlas of the zebrafish brain from T2∗-weighted magnetic resonance histology (MRH) images acquired on a 16.4-T superconducting magnet. We achieved an isotropic resolution of 10 μm, which is the highest resolution achieved in a vertebrate brain and, for the first time, is comparable in slice thickness to conventional histology. By using manual segmentation, 53 anatomical structures, including fiber tracts as small as 40 μm, were delineated. Using Amira software, structures were also individually segmented and reconstructed to create three-dimensional animations. Additional quantitative information including, volume, surface areas, and mean gray scale intensities were also determined. Finally, we established a stereotaxic coordinate system as a framework in which maps created from other modalities can be incorporated into the atlas.
© 2010 Elsevier Inc. All rights reserved.
Keyword Zebrafish
Magnetic resonance histology (MRH)
Three-dimensional (3D)
Q-Index Code C1
Q-Index Status Confirmed Code
Institutional Status UQ

Document type: Journal Article
Sub-type: Article (original research)
Collections: Official 2011 Collection
School of Biomedical Sciences Publications
Centre for Advanced Imaging Publications
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Citation counts: TR Web of Science Citation Count  Cited 31 times in Thomson Reuters Web of Science Article | Citations
Scopus Citation Count Cited 31 times in Scopus Article | Citations
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Created: Sun, 25 Apr 2010, 00:01:49 EST