An imaging system for cell-based therapies is provided. The imagining system includes one or more optical tags configured for insertion into a cell or biological tissue, an excitation light source configured to illuminate the one or more optical tags; a detector configured to measure optical emission of the one or more optical tags; an imaging subsystem configured to determine a three-dimensional location of each of the one or more optical tags in the cell or biological tissue; and a controller in electrical communication with the excitation light source, the detector, and the imaging subsystem. Each of the one or more optical tags has a contrasting feature and includes a fluorescent material. The contrasting feature may be defined by at least one of a refractive index, shape, color, and laser emission of each optical tag of the one or more optical tags.