Significance We present a unique acoustic well approach that can precisely control cell-to-cell distance and cell–cell interactions. Our technology can achieve high precision and high throughput simultaneously while preserving the integrity of cells. It is capable of creating cell assemblies with precise spatial control both in suspension and on a substrate. We envision the exploitation of this powerful technology, for example, in the study of cell–cell interactions in fields, such as immunology, developmental biology, neuroscience, and cancer metastasis, and in the studies of cell–cell and cell–matrix adhesion.

Controlling cell–cell interactions using surface acoustic waves