Computer Science Department, Albert-Ludwigs-University Freiburg, Freiburg, Germany.
Nat Methods. 2012 Jun 17;9(7):735-42. doi: 10.1038/nmeth.2076.
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.
精确的三维（3D）映射大量基因表达模式、神经元类型和连接到解剖参考，有助于我们了解脊椎动物大脑及其发育。我们开发了虚拟大脑探索者（ViBE-Z），这是一种软件，可以自动将具有细胞分辨率的基因表达数据映射到 3D 标准幼虫斑马鱼（Danio rerio）大脑。ViBE-Z 通过融合和衰减校正每个标本的多个共聚焦显微镜堆栈来增强数据质量，并使用细胞核荧光染料进行图像配准。它自动检测 14 个预定义的解剖学标志，以便将新数据与参考大脑对齐。ViBE-Z 在表达数据库中执行共定位分析，用于定义任何特定模式的解剖学域或子域；在这里，我们展示了它在映射多巴胺能系统神经元中的效用。ViBE-Z 数据库、图谱和软件通过网络界面提供。
