Products & Licenses


BrainWarp is a tool that supports the automatic integration of large collections of data on a common reference space – known as a standard brain. It provides functionalities for collaborative quality assurance, and supports the subsequent integration of data in BrainBase.

BrainBase, BrainBaseWeb und BrainGazer support the anatomical, spatial or structural search for very large collections of confocal microscopy images of the brain of the fruit fly, fruit fly larva or zebrafish. Our patented data structures allow an intuitive search for corresponding expression patterns of neurons in tens of thousands of 3D images almost in real-time. BrainGazer and BrainBaseWeb also provide a variety of visual analytics and visualization tools for the data.

At present, there are four instances of software that support public data collections:

  • Standard version of larval fruit fly brain (Drosophila melanogaster) with anatomical annotations and a collection of genetic lines. The data collection was developed and made available within the framework of a project promoted by the DFG (German Research Foundation) and the FWF (Austrian Science Fund) in collaboration with the University of Leipzig (Professor Andreas Thum), UCLA (Professor Hartenstein), RWTH Aachen (Professor Dorit Merhof) and VRVis (Dr Katja Bühler).

  • and A collection of confocal microscopy images with neural structures provided by the TEFOR infrastructure.

  • Older version of BrainBaseWeb with a collection of over 15,000 3D images of VT lines in the adult fruit fly (Drosophila melanogaster), which have been generated by Barry Dickson at IMP in Vienna.

BrainTrawler – integrative analysis system for complex brain networks:

  • Together with neuroscientists at the Haubensak Lab at IMP Vienna and Boehringer-Ingelheim, we are developing BrainTrawler, a web-based framework for studying heterogeneous neurobiological data from mice and humans. Using spatial indexing, we are able to analyse gene expression data and complex brain networks in real time. Classifying the data to hierarchically organised anatomical structures makes it possible to search at different anatomical levels. Together with intuitive network visualization, iterative visual questions and quantitative information, BrainTrawler enables multimodal networks to be genetically dissected at local/global level within the spatial context. Further information can be found here.


License information and information about collaborating on a joint research project can be obtained on request. Please contact DI Dr. Gerd Hesina via products(at)!

Further information

More about the research work of our Biomedical Image Informatics research group.