Droplet digital PCR (ddPCR) is an emerging technology for quantifying DNA. By partitioning the target DNA into xe2x88xbc20xe2x80x89000 droplets, each serving as its own PCR reaction compartment, a very high sensitivity of DNA quantification can be achieved. However, manual analysis of the data is time consuming and algorithms for automated analysis of non-orthogonal, multiplexed ddPCR data are unavailable, presenting a major bottleneck for the advancement of ddPCR transitioning from low-throughput to high-throughput.