3D Atlas of adult zebrafish brain development
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1
Leiden University, Netherlands
The zebrafish (Danio rerio) is an important model system in developmental genetics and vertebrate developmental biology. Over last two decades, several organizations had investigated zebrafish in many different aspects. Three dimensional atlases of the zebrafish have been constructed. On top of the atlases that we have developed, an atlas of the adult zebrafish brain has designed. We have used different imaging modalities so that it can be matched to different kinds of experimental work. The relative small size compared to other vertebrates (e.g. mouse, rat) is provides a challenge in the composition of the, multimodal zebrafish brain studies.
The two key elements in the construction of the atlas are the high resolution image acquisition approaches and improved 3D reconstruction software tools. There are two main approaches to obtain brain images, stained physical sections and other in vivo methods.
We have built a 3D atlas model of adult zebrafish brain using 3D reconstruction software tools, TRD-3Dbase (http://bio-imaging.liacs.nl/tdr3dbase.html). The models are obtained from three different imaging approaches, stained section images, Magnetic Resonance Microscopy (MRM) images (http://www.ssnmr.leidenuniv.nl) and Synchrotron X-ray Tomographic Microscopy (SRX-ray) images (http://www.biomed.ee.ethz.ch/research/x-ray_microscopy). The modalities are glued together through specific ontology terms; initially, we have restricted to structures that could be visualized in either of the tree modalities. This atlas supports 3D understanding of the structures in adult zebrafish brain more easily. In the future we will further zoom into the specific resolutions of the different modalities and resolve the more complex structures.
Conference:
Neuroinformatics 2009, Pilsen, Czechia, 6 Sep - 8 Sep, 2009.
Presentation Type:
Poster Presentation
Topic:
Digital atlasing
Citation:
Yang
P,
Lamers
G,
Bout
R and
Verbeek
F
(2019). 3D Atlas of adult zebrafish brain development.
Front. Neuroinform.
Conference Abstract:
Neuroinformatics 2009.
doi: 10.3389/conf.neuro.11.2009.08.011
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Received:
21 May 2009;
Published Online:
09 May 2019.
*
Correspondence:
Peng Yang, Leiden University, Leiden, Netherlands, pengyang@liacs.nl