Microscopes that record volumetric images (like CT or MRI scans in medicine) are nowadays in daily use in every bigger live science lab. They allow to observe biological structures in the full 3D context. Furthermore they can be used to record volumetric movies of developing model organisms. A manual anaylsis of the vaste amount of resulting data is nearly impossible. In the talk I will show several examples, how we apply image analysis algorithms to extract quantitative data from these images and movies. A special focus will be on a project, where we combine the information of hundreds of volumetric images of the delevoping zebra fish brain into a single atlas [1]. This atlas allows to answer the question, which genes are read out simultaneously at the same location. The image analyis pipeline includes a multi-view recording of the sample, several image fusion steps with variational attenuation correction, a trainable rotation-invariant landmark detection and finally a fast elastic registraion.