System for transporting emulsions from an array to a detector

A system for performing a droplet-based assay, comprising:

• a droplet transporter including an inlet end, a channel junction, a source of carrier fluid including oil, and a detection region formed by a microfluidic channel, wherein the channel junction is connected to the inlet end, the source, and the detection region, wherein the inlet end is configured to be placed into each well of an array of wells, with each well holding an emulsion including a plurality of droplets disposed in a continuous phase, and wherein the droplet transporter is configured to (a) drive travel of droplets and the continuous phase of each emulsion into the inlet end and from the inlet end to the channel junction, (b) add carrier fluid from the source to the continuous phase at the channel junction, to spatially separate droplets from one another, and (c) drive travel of the spatially separated droplets through the detection region from the channel junction;
• a detector configured to collect data related to one or more analytes from individual droplets of each emulsion as such individual droplets travel through the detection region;
• and
• a processor programmed to analyze the data to determine (i) a number of droplets containing at least one copy of an analyte and/or a number of droplets containing no copies of the analyte, and (ii) a concentration of the analyte using at least one of the numbers.