Three-dimensional imaging of the teleost brain

Jeremy F.P. Ullmann (2010). Three-dimensional imaging of the teleost brain PhD Thesis, School of Biomedical Sciences, The University of Queensland.

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Author Jeremy F.P. Ullmann
Thesis Title Three-dimensional imaging of the teleost brain
School, Centre or Institute School of Biomedical Sciences
Institution The University of Queensland
Publication date 2010
Thesis type PhD Thesis
Supervisor Shaun Collin
Andrew Barnes
Shelby Temple
Total pages 152
Total colour pages 24
Total black and white pages 128
Subjects 11 Medical and Health Sciences
Abstract/Summary Magnetic resonance imaging (MRI) is a vital technique for neuroscience. The ability to non-invasively image the central nervous system (CNS) has drastically improved our understanding of the structure and function of the brain. While in vivo and functional magnetic resonance imaging (fMRI) scans are desirable, as they are true representations of the living brain, they require larger radiofrequency coils, larger acquisition matrixes and shorter scan times. Consequently, in situ or ex vivo scans are often preferable as longer scan times can be used, resulting in increased contrast and signal to noise ratios. MRI was initially developed as a clinical technique; however, over the past thirty years the brains of a wide range of other taxa have also been examined. In particular, mice have been well studied and today MRI is an important tool for anatomical analyses of phenotype. Surprisingly, teleosts, the largest group of vertebrates and an important model for a range of neuroscience fields, have scarcely been studied with MRI. Consequently, the aim of the thesis was to perform the first thorough examination of the teleost central nervous system using MRI. Since the logistics for in vivo imaging of teleosts are challenging, in this original study we sought to image the teleost CNS in situ and ex vivo. Fixation and ‘staining’ of samples is routinely performed for in situ and ex vivo imaging, however, their effects on a whole brain sample were unknown. Therefore, as part of our objective of creating a protocol to obtain high-quality images of the brains of teleosts, we examined the relaxation rates of seven fixatives and two commercially available contrast agents. We determined that immersing a brain in a solution of 4% paraformaldehyde (in a 0.1M phosphate buffered saline) and 0.5% Magnevist® for a period of 12 hours resulted in the best images. Subsequently, we scanned two teleost species, zebrafish (Danio rerio) a common laboratory model and barramundi (Lates calcarifer) a representative perciform, and acquired high-resolution and high-contrast T2*-weighted images of their brains. The resolutions obtained were some of the highest achieved in a vertebrate brain and allowed us to delineate a large number of neuronal structures. In the zebrafish brain, we segmented 53 neuronal structures and created the first three-dimensional anatomical and quantitative zebrafish brain atlas, while in the barramundi nearly 100 brain regions were identified including, cellular layers, fiber tracts and numerous ventricles. The ability to identify neuronal regions and obtain quantitative information also makes MRI an ideal method for comparative brain studies. As few studies have utilized MRI for comparative studies, we sequentially compared brain volumes of three different brain regions (olfactory bulbs, telencephalon and optic tectum) obtained via MRI, the ellipsoid method and histology. We found that histology and the ellipsoid method are poor measures of brain volumes as histological processing results in significant heterogeneous shrinkage in all brain areas and the ellipsoid method significantly overestimates brain volumes. Therefore, when possible, we suggest future studies should utilize MRI. Additional contrast was investigated by performing diffusion weighted imaging (DWI). Images were acquired with a 24 µm isotropic resolution that provided unique information about fiber orientation in the zebrafish brain. Lamination not seen in T2*-weighted images could be distinguished and 27 fiber bundles were tracked. However, in contrast to T2*-weighted imaging, resolution not contrast was the limiting factor. Magnetic resonance imaging (MRI) is a vital technique to acquire detailed neuroanatomical information of an intact brain. Although a greater number of structures can be delineated with conventional histology, MRI presents exciting opportunities for imaging the anatomy and physiology of the CNS. This study is vital to that future research as it establishes teleosts as a model for MRI contrast and resolution studies and provides the crucial framework for a range of future research areas.
Keyword Magnetic Resonance Imaging (mri)
Diffusion weighted imaging (dwi)
Central nervous system
Danio Rerio
Lates calcarifer
Comparative neuroanatomy
Additional Notes color: 1,9,20,26,27,35,55,63,66,68,75,98,105,112,113,115,118,125,130,131,134,136,139,150

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Created: Thu, 01 Apr 2010, 11:23:48 EST by Mr Jeremy Ullmann on behalf of Library - Information Access Service