In confocal microscopy the specimen is scanned with a focused laser beam. Before detection, emitted fluorescent light has to pass a pinhole that is positioned within the light path in such a way that only light from the focal plane reaches the detector, while light below and above the focal plane is blocked. This has the significant advantage that non-focused structures within the specimen do not contribute to image acquisition. In order to generate a three-dimensional model of the imaged sample, a stack of images has to be recorded and processed using dedicated software tools.