The MyoSITE project explored how to design a digital site-specific life-sciences educational tool that encompasses both the physical and digital sphere and how to present in this space a digital whole-cell model that accurately reflects the dense and differentiated environment of cellular mesoscales. A large animated digital cell model was created to fit the University of Glasgow Advanced Research Centre ARC-XR exhibition space. The mixed reality approach was used to explore the digital content of the model (heartbeat and its regulation within the cell), employing a hand tracking-enabled head-mounted display (HMD). Various types of immersion and interactions were explored for co-opting the digital material whilst retaining access to the outside of the digital environment. The application featured several magnification layers, allowing the user to examine and interact with differently sized molecular structures. The user experience in terms of usability and the educational potential of the application were probed as a part of the project. The multi-user aspect, site-specificity and scalar handling of the material was well received by the specialist panel. The MyoSITE application showed great potential as a proof-of-concept, and the project effectively illustrated the benefits of using extended reality (XR) technologies in life sciences education, emphasizing the importance of further research into mixed reality for this field.