In the context of (eco)-toxicology or developmental studies 3D imaging shows increased precision in detection and localization of the induced anatomic changes. The recent advances in tissue clearing facilitate performing studies like these on rather big/opaque specimens as zebrafish larvae or organoids. Confocal laser scanning microscopy (CLSM) is a well established technique in the field of biological research. Moreover, resonant CLSM offers the perfect compromise between speed, resolution and depth of light penetration for this range of samples. By combining this technique with automation scripts it is possible to acquire volumetric images of a large number of specimens. As the analysis of the induced phenotypes must be statistically sound a high number of images is needed as input for the bioimage analysis. In this workshop we present a high content screening (HCS) application based on a commercial confocal high content imaging system driven by automation scripts and an automatic data management and analysis pipeline of our own design (file system based database; fsdb). We will also present our tissue clearing protocol and the sample mounting procedure for HCS acquisition.