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
  • Larva
  • Gene Expression*
  • Databases, Genetic*
  • Imaging, Three-Dimensional/methods*
  • Animals
  • Brain*/embryology
  • Brain*/metabolism
  • Brain*/ultrastructure
  • Software
  • Embryonic Development/genetics
  • Zebrafish*/embryology
  • Zebrafish*/genetics
  • Neurons/metabolism
  • Neurons/ultrastructure
(all 14)
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
No images available
Expression
No data available
Phenotype
No data available
Mutations / Transgenics
Allele Construct Type Affected Genomic Region
b1200TgTransgenic Insertion
    ia2TgTransgenic Insertion
    ia50TgTransgenic Insertion
      m1151TgTransgenic Insertion
        ml2TgTransgenic Insertion
          ot1TgTransgenic Insertion
            pku2EtTransgenic Insertion
              rw0TgTransgenic Insertion
                sb1TgTransgenic Insertion
                  vu12TgTransgenic Insertion
                    1 - 10 of 12
                    Show
                    Human Disease / Model
                    No data available
                    Sequence Targeting Reagents
                    No data available
                    Fish
                    Fish
                    b1200Tg
                    ml2Tg
                    ot1Tg
                    pku2Et
                    rw0Tg
                    zf11Tg
                    zf15Tg
                    1 - 7 of 7
                    Show
                    Antibodies
                    Orthology
                    Engineered Foreign Genes
                    Mapping
                    Your Input Welcome
                    We welcome your input and comments. Please use this form to recommend updates to the information in ZFIN. We appreciate as much detail as possible and references as appropriate. We will review your comments promptly.
                    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.