: Nowadays, biologists investigate different causes for deafness. One reason is a damage in a particular region of the auditory brain stem. These differences were discovered by investigating brain slices of different laboratory mice. However, these slices are only a two dimensional representation of the whole brain part. The arising question was how these differences of structure affect the three dimensional representation of this region. Therefore, an interdisciplinary framework was developed, which allows even unknown users to investigate and compare these regions.