Microfluidic analysis system

A biological sample analysis system comprising:

• a carrier fluid supply;
• a sample supply;
• a sample preparation stage for providing a flow of sample droplets enveloped in an immiscible primary carrier fluid;
• at least one channel for continuous flow of the carrier fluid which carries the sample droplets;
• at least one analysis stage for performing analysis of the sample in the continuous flow while enveloped within the primary carrier fluid without the sample contacting a solid surface of the channel;
• and
• a controller for controlling the system,
• wherein there are a plurality of analysis stages, and said analysis stages comprise a thermal cycling stage and an optical detection stage for performance of a polymerase chain reaction;
• wherein the sample preparation stage comprises a centrifuge for separation of samples from an input fluid and for introduction of the samples to the primary carrier fluid;
• and wherein the centrifuge comprises a pair of opposed primary carrier fluid channels on either side of a vortex chamber, whereby flow of primary carrier fluid in said channels causes centrifuging of sample in the vortex chamber and flow of sample from the chamber into said channels.