Massively parallel self-assembly of suspendable microcompartments for functional cell screening

Modern biology increasingly demands platforms that can compartmentalize and analyze single cells and cell-cell interactions at massive scale, yet existing compartmentalization strategies based on microfluidics suffer from critical limitations. Emerging lab-on-a-particle technologies such as nanovials enable anchored single cells or small groups of cells to be isolated and assayed in a fully suspendable and parallelized manner using standard instrumentation, although their open architectures can result in loss of growing or un-attached cells. Here, we introduce capped nanovials: self-assembling hydrogel compartments formed by docking spherical capping particles into bowl-shaped nanovials. We routinely achieve capping of >80% of all nanovials in a sample and >90% sorting yield by flow cytometry, making the capped nanovial system well-suited for preparing and running large-scale assays. Furthermore, we demonstrate stable clonal expansion of single mammalian, yeast, and bacterial cells; growth-based selections of >10,000 colonies; enhanced signal-to-noise in secretion assays; and high-purity selection of antibody-secreting cells based on activation of co-encapsulated T cell reporters (>30-fold signal, up to 100% selection purity). By combining the simplicity of a well plate with the functional precision of droplet microfluidics without requiring oil or custom instrumentation, capped nanovials realize accessible, high-throughput, and high-resolution experimentation.