Learning the meaningful use of the microscope is an essential requirement in school curricula. Modern science and medicine is hardly conceivable without the inclusion of microscopy. The number of didactic studies in this area, however, is negligible. Real microscopy is rarely used to gain knowledge in higher school years. Could the understanding of cell concept and the skills to interpret histological structures be complemented and supported by digital microscopy? The current study investigates this problem in two methodological ways. First, learning effects of modules with interactive whiteboards (IWB) are compared with original microscopy (2012: n = 70; 2013: 25+14; 2013/14: n = 21+27; 2014: n=40) using the example of human biology with pre-service student teachers. The instruments were questionnaires (short scale of intrinsic motivation, flow, and knowledge test) and interviews. Second, eye movements of 12th grade students were measured during histological image processing of retina and nervous tissue in the student laboratory of neuroscience in Tubingen (High Quality Tower mounted eye tracking) (2013: n = 11+26; 2014: n = 28). We measured that fixation in the area of interest (AoI) corresponded with the level of prior knowledge. The estimation of instructional aids (e.g. schematic representation) while viewing demanding histological images also depends on prior knowledge. The same applies to the IWB. The use of the whiteboard is valued because of the possibility to make visible connections and put these in contexts. The use of the whiteboard does not, however, surpass the motivation and flow of real microscopy in problem-oriented learning processes. The IWB is a good supplement but is not a substitute for the microscope.