A system for analyzing a plurality of nucleic acid molecules, comprising: a microfluidic device comprising a plurality of partitions, wherein said plurality of partitions are each configured to permit gas flow through at least one barrier to an environment external to said plurality of partitions, wherein said plurality of partitions are each configured to contain a solution comprising said nucleic acid molecules; a support unit configured to hold said device; a detector configured to detect one or more signals from said solution contained in each of said plurality of partitions; and a computer system including, one or more computer processors operatively coupled to said detector, and a memory having instructions stored thereon that, when executed by said one or more computer processors, cause said one or more computer processors individually or collectively to perform functions including, receiving said one or more signals collected by said detector from each of said plurality of partitions, wherein said one or more signals are collected while said nucleic acid molecules are undergoing a nucleic acid amplification reaction, and processing said one or more signals to yield data indicative of a number of said nucleic acid molecules. a microfluidic device comprising a plurality of partitions, wherein said plurality of partitions are each configured to permit gas flow through at least one barrier to an environment external to said plurality of partitions, wherein said plurality of partitions are each configured to contain a solution comprising said nucleic acid molecules; a support unit configured to hold said device; a detector configured to detect one or more signals from said solution contained in each of said plurality of partitions; and a computer system including, one or more computer processors operatively coupled to said detector, and a memory having instructions stored thereon that, when executed by said one or more computer processors, cause said one or more computer processors individually or collectively to perform functions including, receiving said one or more signals collected by said detector from each of said plurality of partitions, wherein said one or more signals are collected while said nucleic acid molecules are undergoing a nucleic acid amplification reaction, and processing said one or more signals to yield data indicative of a number of said nucleic acid molecules. one or more computer processors operatively coupled to said detector, and a memory having instructions stored thereon that, when executed by said one or more computer processors, cause said one or more computer processors individually or collectively to perform functions including, receiving said one or more signals collected by said detector from each of said plurality of partitions, wherein said one or more signals are collected while said nucleic acid molecules are undergoing a nucleic acid amplification reaction, and processing said one or more signals to yield data indicative of a number of said nucleic acid molecules. receiving said one or more signals collected by said detector from each of said plurality of partitions, wherein said one or more signals are collected while said nucleic acid molecules are undergoing a nucleic acid amplification reaction, and processing said one or more signals to yield data indicative of a number of said nucleic acid molecules.