URL: http://vibez.informatik.uni-freiburg.de/
Proper Citation: ViBE-Z (RRID:SCR_005895)
Description: An imaging and image analysis framework for virtual colocalization studies in larval zebrafish brains, currently available for 72hpf, 48hpf and 96hpf old larvae. ViBE-Z contains a database with precisely aligned gene expression patterns (1����m^3 resolution), an anatomical atlas, and a software. This software creates high-quality data sets by fusing multiple confocal microscopic image stacks, and aligns these data sets to the standard larva. The ViBE-Z database and atlas are stored in HDF5 file format. They are freely available for download. ViBE-Z provides 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. The ViBE-Z database, atlas and software are provided via a web interface.
Abbreviations: ViBE-Z
Synonyms: Virtual Brain Explorer for Zebrafish, Virtual Brain Explorer, ViBE-Z: The Virtual Brain Explorer for Zebrafish
Resource Type: software resource, database, data or information resource, data processing software, software application, atlas, image processing software
Defining Citation: PMID:22706672
Keywords: brain, larval zebrafish, gene expression, confocal microscopy
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