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
Citation
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. (2012) ViBE-Z: a framework for 3D virtual colocalization analysis in zebrafish larval brains. Nature Methods. 9(7):735-742.
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
Expression
Phenotype
Mutations / Transgenics
Human Disease / Model
Sequence Targeting Reagents
Fish
Orthology
Engineered Foreign Genes
Mapping