Development of brain templates for whole brain atlases

AbstractEnvironmental perturbation can drive the evolution of behavior and associated changes in brain structure and function. The generation of computationally-derived whole-brain atlases have provided insight into neural connectivity associated with behavior in many model systems. However, these approaches have not been used to study the evolution of brain structure in vertebrates. The Mexican tetra, A. mexicanus, comprises river-dwelling surface fish and multiple independently evolved populations of blind cavefish, providing a unique opportunity to identify neuroanatomical and functional differences associated with behavioral evolution. We employed intact brain imaging and image registration on 684 larval fish to generate neuroanatomical atlases of surface fish and three different cave populations. Analyses of brain regions and neural circuits associated with behavioral regulation identified convergence on hypothalamic expansion, as well as changes in transmitter systems including elevated numbers of catecholamine and hypocretin neurons in cavefish populations. To define evolutionarily-derived changes in brain function, we performed whole brain activity mapping associated with feeding and sleep. Feeding evoked neural activity in different sensory processing centers in surface and cavefish. We also identified multiple brain regions with sleep-associated activity across all four populations, including the rostral zone of the hypothalamus and tegmentum. Together, these atlases represent the first comparative brain-wide study of intraspecies variation in a vertebrate model, and provide a resource for studying the neural basis underlying behavioral evolution.

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High precision registration between zebrafish brain atlases using symmetric diffeomorphic normalization

10.1101/081000 ◽

2016 ◽

Cited By ~ 3

Author(s):

Gregory D. Marquart ◽

Kathryn M. Tabor ◽

Eric J. Horstick ◽

Mary Brown ◽

Harold A. Burgess

Keyword(s):

Gene Expression ◽

Medulla Oblongata ◽

Cell Morphology ◽

Brain Atlas ◽

Fixed Tissue ◽

Whole Brain ◽

Zebrafish Brain ◽

Larval Zebrafish ◽

Reference Space ◽

Brain Atlases

AbstractAtlases provide a framework for information from diverse sources to be spatially mapped and integrated into a common reference space. In particular, brain atlases allow regional annotation of gene expression, cell morphology, connectivity and activity. In larval zebrafish, advances in genetics, imaging and computational methods have enabled the collection of large datasets providing such information on a whole-brain scale. However, datasets from different sources may not be aligned to the same spatial coordinate system, because technical considerations may necessitate use of different reference templates. Two recent brain atlases for larval zebrafish exemplify this problem. The Z-Brain atlas contains information on gene expression, neural activity and neuroanatomical segmentation acquired using immunohistochemical staining of fixed tissue. In contrast, the Zebrafish Brain Browser (ZBB) atlas was constructed from live scans of fluorescent reporter genes in transgenic larvae. Although different reference brains were used, the two atlases included several transgene patterns in common that provided potential 'bridges' for transforming each into the other’s coordinate space. We therefore tested multiple bridging channels and registration algorithms. The symmetric diffeomorphic normalization (SyN) algorithm in ANTs improved the precision of live brain registration while better preserving cell morphology than the previously used B-spline elastic registration algorithm. SyN could also be calibrated to correct for tissue distortion introduced during fixation and permeabilization. Finally, multi-reference channel optimization provided a transformation matrix that enabled Z-Brain and ZBB to be co-aligned with acceptable precision and minimal perturbation of cell and tissue morphology. This study demonstrates the feasibility of integrating whole brain datasets, despite disparate acquisition protocols and reference templates, when sufficient information is present for bridging.Anatomical abbreviationsacanterior commissureDTThalamusGTGriseum tectaleHaHabenulaHcHypothalamus caudal zoneHiHypothalamus intermediate zoneMOMedulla oblongataNXmVagus motor neuronsOBOlfactory bulbOEOlfactory epitheliumIOInferior oliveLCLocus coeruleusMNMauthner neuronMOMedulla oblongataPalPalliumpcposterior commissurePrPretectumSRSuperior rapheTegTegmentumTeOnOptic tectum neuropilTGTrigeminal ganglionTLTorus longitudinalis

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