For many experiments in medicine, it is necessary to microscope thousands of model organisms, such as zebrafish eggs, over and over again and search for specific characteristics or deviations. Other applications for automated microscopy include biodiversity research, for example to automatically determine the abundance of zoo plankton in seawater. For this purpose, we have developed different (fluorescence) microscope systems that microscope organisms in-vivo in a high-throughput screening and automatically recognize morphological features. With the help of AI algorithms, features can then be classified, or species can be recognized.