Provided herein are systems, methods, and articles of manufacture for collecting and merging two different size droplets using a substrate comprising a plurality of trapping sites. In certain embodiments, provided herein are systems composed of a plurality of larger droplets and smaller droplets and a substrate comprising a plurality of trapping sites where each trapping site is configured to trap only one of the larger droplets and only one of the smaller droplets when the larger droplet is already present at the trapping site. In particular embodiments, the larger and/or smaller droplets are sorted prior to being contacted with the substrate to ensure they contain the desired component (e.g., cell or barcoded bead). In other embodiments, each trapping site is composed of one or multiple fluidically linked capture wells. In some embodiments, collected larger and smaller droplets are merged (e.g., via a demulsifier or electricity).