Flux is an easy-to-use microfluidic device that empowers the high-throughput analysis of single cells using Semi-Permeable Capsules (SPCs). At the press of a button, Flux can process up to 8 samples simultaneously, encapsulating as many as 100,000 single cells into biocompatible SPCs in just 30 minutes. Generated SPCs maintain stability under a wide range of biochemical conditions and are suitable for diverse downstream reactions, which can be performed in a bulk-like manner using standard laboratory equipment.