Cell-cell interactions are at the core of many of today’s most challenging ailments like cancer, autoimmune, and neurodegenerative diseases. Studying cell-cell interactions requires live-cell imaging and analyses to accurately observe cells through space and time. However, isolating cells of interest based on observed cell-cell interaction events and associated phenotypes remains a challenge. For instance, current techniques for T cell enrichment rely on surface markers for T cell activation or killing, yet these markers do not fully capture a T cell’s exhibited cytotoxicity or specificity for a target cell. While cytotoxicity assays using microscopy have been developed to screen live T cells based on these interactions and phenotypes, no single technique can isolate actively cytotoxic T cells based on their level of interaction with specific target cells. Narwhal Bio Inc. seeks to overcome this challenge by developing an instrument, software, and consumable for on-the-fly cell identification, tagging, and downstream isolation. The live-cell-in, live-cell-out process could allow downstream applications like animal studies, further cell engineering, and multiomics drug and target discovery which are not feasible with today’s spatial techniques. We have applied this system to the enrichment of CAR-T cells involved in cell-killing events. Using our platform, we assayed and tagged T cells based on serial cytotoxicity in real time. We then isolated the live active T cells and confirmed the CAR representation in the more cytotoxic cell population, and performed downstream multiomic analysis on some of the samples. We showed how the process can be performed on the order of millions of cells in a day.