%0 Journal Article %1 Ronneberger:2012:Nat-Methods:22706672 %A Ronneberger, O %A Liu, K %A Rath, M %A Rueβ, D %A Mueller, T %A Skibbe, H %A Drayer, B %A Schmidt, T %A Filippi, A %A Nitschke, R %A Brox, T %A Burkhardt, H %A Driever, W %D 2012 %J Nat Methods %K biology registration segmentation software visualization %N 7 %P 735-742 %R 10.1038/nmeth.2076 %T ViBE-Z: a framework for 3D virtual colocalization analysis in zebrafish larval brains %U http://www.ncbi.nlm.nih.gov/pubmed/22706672 %V 9 %X 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.

@article{Ronneberger:2012:Nat-Methods:22706672, 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.}, added-at = {2013-03-25T14:06:56.000+0100}, author = {Ronneberger, O and Liu, K and Rath, M and Rueβ, D and Mueller, T and Skibbe, H and Drayer, B and Schmidt, T and Filippi, A and Nitschke, R and Brox, T and Burkhardt, H and Driever, W}, biburl = {https://www.bibsonomy.org/bibtex/2763effd6aaf0e66f53f962837867a049/alex_ruff}, description = {ViBE-Z: a framework for 3D virtual colocalizatio... [Nat Methods. 2012] - PubMed - NCBI}, doi = {10.1038/nmeth.2076}, interhash = {922643248c7a4db55a4438e169e6c8ad}, intrahash = {763effd6aaf0e66f53f962837867a049}, journal = {Nat Methods}, keywords = {biology registration segmentation software visualization}, month = jul, number = 7, pages = {735-742}, pmid = {22706672}, timestamp = {2013-03-25T14:06:57.000+0100}, title = {ViBE-Z: a framework for 3D virtual colocalization analysis in zebrafish larval brains}, url = {http://www.ncbi.nlm.nih.gov/pubmed/22706672}, volume = 9, year = 2012 }