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The platform is used here for the selective encapsulation of differentially labeled cells within a discrete droplet array. Copyright © 2020 Author(s).In this work, we developed a microfluidic system for immunoassays where we combined the use of magnetic nanoparticles as immunosupport, a microfluidic magnetic trap, and a fluorogenic substrate in continuous flow for detection which, together with the optimization of the functionalization of surfaces to minimize nonspecific interactions, resulted in a detection limit in the order of femtomo