A Virtual Look at the Zebrafish Brain
Freiburg Researchers Develop Software for Automatic Comparison of Entire Brains
The picture shows the gene expression (colored) of three different zebrafish larvae in a virtual standard brain.
Scientists have long dreamed of being able to grasp the brain as a whole rather than just understanding the function of individual nerve cells. A research team led by Junior Professor Dr. Olaf Ronneberger from the Department of Computer Science of the University of Freiburg and Prof. Dr. Wolfgang Driever, developmental biologist at the Institute of Biology I, has now taken a big step toward making this dream a reality. The Freiburg researchers developed microscopic imaging techniques and software for observing and comparing all of the genes of the zebrafish brain, and thus also the factors influencing its nerve cells, in a three-dimensional virtual model. The results of the project have been published in the current issue of the renowned journal Nature Methods.
The team’s Virtual Brain Explorer for Zebrafish (ViBE-Z) automatically assigns experientially obtained genetic data to certain points of a brain image created under the same conditions. The zebrafish is particularly popular as a model organism for biologists and doctors due to the fact that many of the developmental and neurobiological findings made on them are transferrable to humans. The very detailed information in the new brain image is compared with the image of a standard brain on a database. This happens automatically and with such precision that differences between individual cells are discernable. In order to achieve this level of precision, Olaf Ronneberger and his team developed a new calculation method that identifies anatomic structures in the brain of the zebrafish and transfers them to a database of the three-dimensional brain.
The scientists can then use the database to determine which genes are active in which areas of the brain and which proteins influence the brain activity under various experimental conditions. This enables them to study the very large number of factors influencing a particular area of the brain at any given time in an integrated fashion. “The new method allows us to understand the complicated network of the brain much better than in the past and to quantitatively compare our data with that from other labs, for instance in Tokyo or Washington, in a three-dimensional space,” explains Wolfgang Driever. The Freiburg researchers will make ViBE-Z available to all interested colleagues on an Internet portal. Researchers from around the world will then be able to enter their own images with genetic data into the system and download a virtual model in the standard brain from the Freiburg server around a half an hour later.
Wolfgang Driever and Olaf Ronneberger are members of the Cluster of Excellence BIOSS. Wolfang Driever is also an Internal Senior Fellow at the Freiburg Institute for Advanced Studies, the research institute of the University of Freiburg. Both institutions receive funding from the Excellence Initiative.
Prof. Dr. Wolfgang Driever
Faculty of Biology, BIOSS, FRIAS
University of Freiburg
Junior-Prof. Dr. Olaf Ronneberger
Department of Computer Science, BIOSS
University of Freiburg