ViBE-Z: a framework for 3D virtual colocalization analysis in zebrafish larval brains
ViBE-Z: a framework for 3D virtual colocalization analysis in zebrafish larval brains
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DOI：
10.1038/nmeth.2076
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发表时间：
2012-07-01
期刊：
影响因子：
48
通讯作者：
Driever, Wolfgang
中科院分区：
文献类型：
--
作者：
Ronneberger, Olaf;Liu, Kun;Driever, Wolfgang
大量基因表达模式、神经元类型和与解剖学参考的连接的精确三维（3D）映射有助于我们了解脊椎动物的大脑及其发育。我们开发了虚拟脑资源管理器（ViBE-Z），这是一种软件，可以自动将基因表达数据与细胞分辨率映射到3D标准斑马鱼幼虫（Danio rerio）大脑。ViBE-Z通过融合和衰减校正每个标本的多个共焦显微镜堆栈来提高数据质量，并使用细胞核的荧光染色进行图像配准。它自动检测14个预定义的解剖标志，用于将新数据与参考大脑对齐。ViBE-Z在表达数据库中对任何特定模式定义的解剖结构域或子域进行共定位分析;在这里，我们展示了其用于映射多巴胺能系统神经元的实用性。ViBE-Z数据库、地图集和软件通过网络界面提供。
Precise three-dimensional (3D) mapping of a large number of gene expression patterns, neuronal types and connections to an anatomical reference helps us to understand the vertebrate brain and its development. We developed the Virtual Brain Explorer (ViBE-Z), a software that automatically maps gene expression data with cellular resolution to a 3D standard larval zebrafish (Danio rerio) brain. ViBE-Z enhances the data quality through fusion and attenuation correction of multiple confocal microscope stacks per specimen and uses a fluorescent stain of cell nuclei for image registration. It automatically detects 14 predefined anatomical landmarks for aligning new data with the reference brain. ViBE-Z performs colocalization analysis in expression databases for anatomical domains or subdomains defined by any specific pattern; here we demonstrate its utility for mapping neurons of the dopaminergic system. The ViBE-Z database, atlas and software are provided via a web interface.