Microfluidic system for high-throughput, droplet-based single molecule analysis with low reagent consumption

A method of detecting particles, comprising:

• inputting a sample comprising particles to be detected into an input channel of a microfluidic device of a microfluidic detection system, said sample further comprising a first fluid in which said particles are at least one of suspended or dissolved;
• concentrating said sample in a sample concentration section of said microfluidic device by removing at least a portion of said first fluid through a solvent-permeable membrane of said microfluidic device to provide a concentrated sample;
• mixing said concentrated sample in a mixing section of said microfluidic device with a reagent to label said particles to be detected using said microfluidic device to provide a concentrated, labeled sample;
• generating a droplet from said concentrated, labeled sample in an output channel of said microfluidic device using a droplet generator of said microfluidic device such that said droplet is isolated by a second fluid that is immiscible with said first fluid;
• repeating said inputting, said concentrating, said mixing and said generating a plurality of times to provide a plurality of droplets in said output channel;
• and
• detecting, sequentially, said particles in each of said plurality of droplets after said mixing based on a response of said labels,
• wherein said solvent-permeable membrane is at least partially permeable to a solvent in which said sample will be mixed during operation,
• wherein said sample is greater than about 1 microliter and less than about 1 milliliter, and
• wherein said concentrated sample is reduced in volume by a factor of at least 100.