In this comprehensive research, we have pursued a dual investigation within the scope of tissue engineering: firstly, to investigate the retention of nanoprobe siloxane emulsions in bio-compatible hydrogel matrices in order to be able to measure oxygen saturation within the hydrogel; secondly, to refine the design of 3D printed hydrogel molds to enhance structural integrity of hydrogels for cell encapsulation. We evaluated the retention capabilities of these nanoemulsions, tagged with fluorescent dyes, across varying concentrations, and further advanced the mold design to prevent hydrogel unraveling and ensure complete filling. The findings suggest pivotal implications for the application of these hydrogels in cell transplantation and set a methodological precedent for future empirical studies.