Sortex: efficient timing-driven synthesis of reconfigurable flow-based biochips for scalable single-cell screening

Abstract

Single-cell screening is used to sort a stream of cells into clusters (or types) based on pre-specified biomarkers, thus supporting type-driven biochemical analysis. Reconfigurable flow-based microfluidic biochips (RFBs) can be utilized to screen hundreds of heterogeneous cells within a few minutes, but they are overburdened with the control of a large number of valves. To address this problem, we present a pin-constrained RFB design methodology for single-cell screening. The proposed design is analyzed using computational fluid dynamics simulations, mapped to an RC-lumped model, and combined with a high-level synthesis framework, referred to as Sortex. Simulation results show that Sortex significantly reduces the number of control pins and fulfills the timing requirements of single-cell screening.