To improve particle radiotherapy, we need a better understanding of the biology of targeted and non-targeted radiation effects. This is particularly important in the field of heavy ion radiation therapy where global effects are observed, yet only a subset of cells receive a high energy deposition from ion tracks. To allow real-time 3D imaging of living biological samples during and after irradiation with a focused ion beam, we have integrated a high-speed light sheet fluorescence imaging system (swept confocally aligned planar excitation, SCAPE microscopy) into the focused ion beam irradiation platform (FIBIP) at the Columbia University Radiological Research Accelerator Facility (RARAF). The RARAF FIBIP is centered on a 7 T superconducting solenoid magnet, which focuses an ion beam, generated by RARAF’s ion accelerators, to a field size of between 5 mm and 2 µm. An integrated SCAPE volumetric imaging system with associated environmental control allows sub-second observation of 3D cell cultures sample over extended periods before, during, and after radiation treatments. The developed system enables exploration of the mechanistic effects of ion radiotherapy at the cellular and tissue levels. Here, we report details of the integrated system, and show an example of intracellular calcium signaling following ionizing radiation in U87 human glioblastoma 3D cultures using the integrated system.