A particle processing system comprising: a plurality of microfluidic sort modules (650, 1200, 1200a, 1200b), each microfluidic sort module including a branched flow-channel defined in a substrate and configured to receive a stream of particles, the branched flow-channel including a flow-path that branches at a branch point into a first output branch channel and a second output branch channel (655, 1214), and each microfluidic sort module includes a particle sorter operable to selectively sort particles between the first output branch channel and the second output branch channel (655, 1214) of the branched flow-channel; a plurality of first sensor systems, each of the first sensor systems optically associated with a respective one of the plurality of microfluidic sort modules upstream of the branch point to sense a particle characteristic of a particle in the stream of particles flowing through the branched flow-channel, each of the first sensor systems having focusing optics and a first optical sensor to control a sorting operation for a respective one of the microfluidic sort modules; a capillary tube fluidically coupled to one of the first output branch channel or the second output branch channel of at least one of the plurality of microfluidic sort modules; and a sort monitoring system having a second sensor system optically coupled to the capillary tube to monitor a performance of the sorting operation by detecting and collecting particle data that characterizes individual particles downstream of the particle sorter using focusing optics to direct light through the capillary tube and onto a second optical sensor, to determine a statistically-based characteristic of a composition of a sorted sample from the data collected from the individual particles detected downstream of the particle sorter, and wherein the sort monitoring system is configured to real-time evaluate the statistically-based characteristic of the composition of the sorted sample. a plurality of microfluidic sort modules (650, 1200, 1200a, 1200b), each microfluidic sort module including a branched flow-channel defined in a substrate and configured to receive a stream of particles, the branched flow-channel including a flow-path that branches at a branch point into a first output branch channel and a second output branch channel (655, 1214), and each microfluidic sort module includes a particle sorter operable to selectively sort particles between the first output branch channel and the second output branch channel (655, 1214) of the branched flow-channel; a plurality of first sensor systems, each of the first sensor systems optically associated with a respective one of the plurality of microfluidic sort modules upstream of the branch point to sense a particle characteristic of a particle in the stream of particles flowing through the branched flow-channel, each of the first sensor systems having focusing optics and a first optical sensor to control a sorting operation for a respective one of the microfluidic sort modules; a capillary tube fluidically coupled to one of the first output branch channel or the second output branch channel of at least one of the plurality of microfluidic sort modules; and a sort monitoring system having a second sensor system optically coupled to the capillary tube to monitor a performance of the sorting operation by detecting and collecting particle data that characterizes individual particles downstream of the particle sorter using focusing optics to direct light through the capillary tube and onto a second optical sensor, to determine a statistically-based characteristic of a composition of a sorted sample from the data collected from the individual particles detected downstream of the particle sorter, and wherein the sort monitoring system is configured to real-time evaluate the statistically-based characteristic of the composition of the sorted sample.