Apparatus and methods for analyzing the output of microfluidic devices

A microfluidic device for analyzing droplets comprising

• a substrate;
• a microfluidic channel formed on the substrate, the microfluidic channel including a plurality of passages, each of the plurality of passages having a mask pattern, the mask pattern configured to modulate a fluorescence signal of a droplet passing through the passage, such that droplets passing through the plurality of passages produce a plurality of fluorescence signals;
• and
• a detector configured to detect the plurality of fluorescence signals,
• wherein the mask pattern of each of the plurality of passages comprises one or more signal emitting portions and one or more signal dampening portions, which correspond to a binary pattern of at least 100 bits.

A method of analyzing a plurality of droplets with a microfluidic device having a microfluidic channel formed on a substrate, the microfluidic channel including a plurality of passages, the method comprising

• passing a plurality of droplets through the plurality of passages,
• wherein each of the plurality of passages has a mask pattern;
• modulating a plurality of signals from the plurality of droplets using the mask pattern;
• and
• detecting the plurality of signals,
• wherein the mask pattern of each of the plurality of passages comprises one or more signal emitting portions and one or more signal dampening portions, which correspond to a binary pattern of at least 100 bits.