Abstract: The disclosure relates to a method and a system for the isolation of picoliter droplets from a continuous stream of carrier fluid in a microfluidic system. In particular the disclosure relates to a system that comprises a sorter, a detector and a collector. The sorter serves for a selection of picoliter droplets with a desired content based upon an optical signal obtained from the picoliter droplets. The selected picoliter droplets are guided towards the detector that comprises a detection channel that is arranged perpendicular to a light beam. By means of a photodetector that is aligned with the optical axis of the light beam the passage of the picoliter droplets can be detected. The collector comprises multiple wells and the detection of the passage of the picoliter droplets results in a relative movement of the detector and a collector such that the picoliter droplet is isolated by depositing it into one of said wells.