PUBLICATION
A three-dimensional digital atlas of the zebrafish brain
- Authors
- Ullmann, J.F., Cowin, G., Kurniawan, N.D., and Collin, S.P.
- ID
- ZDB-PUB-100211-22
- Date
- 2010
- Source
- NeuroImage 51(1): 76-82 (Journal)
- Registered Authors
- Ullmann, Jeremy
- Keywords
- zebrafish, brain, magnetic resonance histology (MRH), three-dimensional (3D), atlas, map
- MeSH Terms
-
- Animals
- Atlases as Topic*
- Brain/anatomy & histology*
- Imaging, Three-Dimensional*
- Magnetic Resonance Imaging/methods*
- Organ Size
- Software
- Zebrafish/anatomy & histology*
- PubMed
- 20139016 Full text @ Neuroimage
Citation
Ullmann, J.F., Cowin, G., Kurniawan, N.D., and Collin, S.P. (2010) A three-dimensional digital atlas of the zebrafish brain. NeuroImage. 51(1):76-82.
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 T(2)-weighted magnetic resonance histology (MRH) images acquired on a 16.4 Tesla superconducting magnet. We achieved an isotropic resolution of 10 microm, 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 microm, 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.
Genes / Markers
Expression
Phenotype
Mutations / Transgenics
Human Disease / Model
Sequence Targeting Reagents
Fish
Orthology
Engineered Foreign Genes
Mapping