CONTEXT Stereoscopic vision is a substantial aspect of three-dimensional visualization approaches. Although most recent animation movies created for cinemas are shown in stereoscopic 3D (S3D), there are still many areas which do not take advantage of this technology. One of these areas is cell visualization. Despite the fact that many protein crystallographers have preferred working with stereoscopic devices for over a decade, it is quite astonishing that cell visualization seems to have ignored S3D completely, even though stereoscopic visualization of the cellular cosmos not accessible to the human eye bears high potential. Furthermore, the scientific community often works with interactive visualization environments. These tools usually provide S3D for different hardware configurations, but the intensity of the stereoscopic effect can only be manually adjusted by using slider buttons. This technique is sufficient to explore a single instance of a molecule, but it is inconvenient when navigating through a large environment on multiple scales. OBJECTIVE In this work approaches will be discussed to apply S3D to 1) rendered cell animations and 2) interactive cell environments by using freely available open source tools. A very important aspect in cell visualization is the bridging of scales. The mesoscopic level starts at a few thousands of nanometers – related to the cell and its components – whereas the molecular level goes down to a few Angstrom, where single atoms are visible. Therefore, both scales may differ by a factor of 100,000. This is especially a problem if the stereoscopic effect should be adjusted during an interactive navigation process. METHOD For the rendered animations it will be shown how to use Blender in combination with Schneider’s Stereoscopic Camera plug-in. An exemplary short movie was created, starting in the blood vessels, proceeding with the inner cell components and finally showing the translation and transcription process based on protein/PDB models. The interactive exploration environments are provided by the CELLmicrocosmos project. On the molecular level, the MembraneEditor is used to show a fixed projection plane S3D method. The mesoscopic level is represented by CellExplorer which is equipped with a dynamic projection plane S3D method. RESULTS The stereoscopic cell animations rendered with Blender were successfully shown on notebook monitors and power walls as well as on large cinema projection screens. The CELLmicrocosmos projects were optimized to provide adequate interactive cell environments which were successfully used during different university projects and presentations. Because the software developer is not able to define the relative position of the user to the point of interest, the fixed projection plane S3D method was used in combination with smaller membrane structures. But the dynamic projection plane is furthermore compatible with cell environments featuring large scale differences. NOVELTY Cell visualization is an emerging area in scientific communication. This work should encourage cytological researchers to take S3D technology into account for future projects. Moreover, the stereoscopic capabilities of the CELLmicrocosmos project are shown which have been developed over several years and which have never been discussed in our previous publications.