Abstract: A particle-based assay system is disclosed that uses hydrogel microparticles that capture analytes of interest from a sample which are subsequently bound with catalytic reporter complexes. Catalytic reporter complexes bound to the hydrogel microparticles generate signals that are accumulated in the vicinity of the hydrogel microparticle at high concentration (or on or within the hydrogel microparticles). In some circumstances, the reporter complex-bound hydrogel microparticles are encapsulated in an emulsion. Preferably, the emulsion is substantially uniform and contains one hydrogel microparticle per droplet. The accumulated signal generated by the catalytic reporter complexes is contained inside the emulsion, and/or optionally immobilized onto or inside the hydrogel microparticle. Signals are read and analyzed using optical instruments such as flow cytometers. Breaking the emulsion prior to signal analysis is optional.