Automated droplet manipulation in microfluidic systems

Disclosed herein is a method of operating a microfluidic system, a microfluidic system for manipulating sample objects, and a control system for operating a microfluidic system. The method according to the invention is for operating a microfluidic system that comprises a manipulation zone for manipulating sample objects flowing through the manipulation zone, a first detection zone arranged upstream of or in the manipulation zone and a second detection zone arranged upstream of, in or downstream of the manipulation zone. A first count is determined that characterizes a number of sample objects flowing through the first detection zone. Sample objects are manipulated in the manipulation zone. A second count is determined that characterizes a number of sample objects flowing through the second detection zone. One or more manipulation parameters for manipulating the sample objects in the manipulation zone are adjusted based on the first count and the second count.