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Abstract The use of oxygen by cells is an essential aspect of cell metabolism and a reliable indicator of viable and functional cells. Here, we report partial pressure oxygen (pO₂) mapping of live cells as a reliable indicator of viable and metabolically active cells. For pO₂imaging, we utilized trityl OX071-based pulse electron paramagnetic resonance oxygen imaging (EPROI), in combination with a 25 mT EPROI instrument, JIVA-25™, that provides 3D oxygen maps with high spatial, temporal, and pO₂resolution. To perform oxygen imaging in an environment-controlled apparatus, we developed a novel multi-well-plate incubator-resonator (MWIR) system that could accommodate 3 strips from a 96-well strip-well plate and image the middle 12 wells noninvasively and simultaneously. The MWIR system was able to keep a controlled environment (temperature at 37 °C, relative humidity between 70%–100%, and a controlled gas flow) during oxygen imaging and could keep cells alive for up to 24 h of measurement, providing a rare previously unseen longitudinal perspective of 3D cell metabolic activities. The robustness of MWIR was tested using an adherent cell line (HEK-293 cells), a nonadherent cell line (Jurkat cells), a cell-biomaterial construct (Jurkat cells seeded in a hydrogel), and a negative control (dead HEK-293 cells). For the first time, we demonstrated that oxygen concentration in a multi-well plate seeded with live cells reduces exponentially with the increase in cell seeding density, even if the cells are exposed to incubator-like gas conditions. For the first time, we demonstrate that 3D, longitudinal oxygen imaging can be used to assess cells seeded in a hydrogel. These results demonstrate that MWIR-based EPROI is a versatile and robust method that can be utilized to observe the cell metabolic activity nondestructively, longitudinally, and in 3D. This approach may be useful for characterizing cell therapies, tissue-engineered medical products, and other advanced therapeutics.