期刊
NATURE METHODS
卷 9, 期 7, 页码 735-U316出版社
NATURE PUBLISHING GROUP
DOI: 10.1038/NMETH.2076
关键词
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资金
- European Commission [223744, 222999]
- Excellence Initiative of the German Federal Government (Centre for Biological Signalling Studies
- Freiburg Institute for Advanced Studies) [EXC 294]
- Excellence Initiative of the German State Government (Centre for Biological Signalling Studies
- Freiburg Institute for Advanced Studies) [EXC 294]
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.
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