PUBLICATION

ViBE-Z: a framework for 3D virtual colocalization analysis in zebrafish larval brains

Authors
Ronneberger, O., Liu, K., Rath, M., Rueβ, D., Mueller, T., Skibbe, H., Drayer, B., Schmidt, T., Filippi, A., Nitschke, R., Brox, T., Burkhardt, H., Driever, W.
ID
ZDB-PUB-150330-1
Date
2012
Source
Nature Methods   9(7): 735-742 (Journal)
Registered Authors
Driever, Wolfgang, Filippi, Alida, Mueller, Thomas
Keywords
Bioinformatics, Microscopy, Gene expression, Imaging
MeSH Terms
  • Animals
  • Brain*/embryology
  • Brain*/metabolism
  • Brain*/ultrastructure
  • Databases, Genetic*
  • Embryonic Development/genetics
  • Gene Expression*
  • Imaging, Three-Dimensional/methods*
  • Larva
  • Neurons/metabolism
  • Neurons/ultrastructure
  • Software
  • Zebrafish*/embryology
  • Zebrafish*/genetics
PubMed
22706672 Full text @ Nat. Methods
Abstract
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.
Genes / Markers
Figures
Expression
Phenotype
Mutations / Transgenics
Human Disease / Model
Sequence Targeting Reagents
Fish
Antibodies
Orthology
Engineered Foreign Genes
Mapping