ViBE-Z: A Framework for 3D Virtual Colocalization Analysis in Zebrafish Larval Brains

Abstract: Precise three-dimensional mapping of a large number of gene expression patterns, neuronal types and connections to an anatomical reference greatly helps 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 three-dimensional standard larval zebrafish (Danio rerio) brain. ViBE-Z enhances the data quality by 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 fourteen 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. We demonstrate its utility to map neurons of the dopaminergic system. The ViBE-Z database, atlas and software are provided via a web interface.