Cell visualization is an important area of scientific and educational visualization. There is already a number of astonishing animations illustrating the structural and functional properties of biological cells available in the Internet. However, these visualizations usually do not take advantage of three-dimensional (3-D) stereoscopic techniques. The stereoscopic visualization of the microcosmos cell—invisible to the human eye—bears high potential for educational as well as scientific approaches. Using open source tools it will be shown that it is possible to generate statically rendered as well as interactive stereoscopic cell visualizations. First, the 3-D modeling software Blender in conjunction with Schneider’s stereoscopic camera plug-in will be used to generate a stereoscopic cell animation. While static renderings have an advantage in that the stereoscopic effect can be optimized for spectators, interactive stereoscopic visualizations always have to adjust and optimize the stereoscopic effect for users who can freely navigate through space. Cell visualization is paradigmatic for this problem because the scale differences from the mesoscopic to the molecular level account for a factor of 100,000. Therefore, two stereoscopic approaches of the CELLmicrocosmos project will be introduced, which address the stereoscopic scaling problem. The stereoscopic quality was positively evaluated by 20 students.