We present a quantitative single-particle imaging platform that enables simultaneous measurements of the size, mRNA-payload, and dynamic properties of vaccines in cell-like conditions. By directly imaging the trajectories of many single molecules simultaneously and in a dynamic manner, our Convex Lens-induced Confinement (CLiC) microscopy allows us to investigate and discover the design rules and mechanisms which govern how oligos (or proteins or drug molecules) interact with target sites on nucleic acids (Scott et. al, Nucl. Acid Research. 2018, 2019); and how molecular cargo is released inside cells from lipid nanoparticles (Kamanzi et al. ACS Nano 2021). We investigate the dependence of mRNA-lipid-nanoparticle structure and fusion dynamics on formulation, using commercially available formulations as a starting point. These measurements are made on confined, freely diffusing particles, and during reagent-exchange such as in response to solution pH, in order to emulate intracellular dynamics in a controlled setting. Over the long term and in collaboration with health scientists, we propose to correlate multi-scale data sets including single-particle measurements made in vitro as well as in cells and tissues, with clinical results, to create a throughline of understanding of vaccine effectiveness from the microscopic to clinical scale, to enable and optimize their rational design and engineering.