Microscopic PhotoSelection (MiPS) of single cells in mother machine microfluidic devices

Techniques for selecting or sorting single cells within large populations of genetic variants are central to synthetic biology and biotechnology. Widely-used methods such as Fluorescence Activated Cell Sorting (FACS) enable rapid processing of large libraries, but are restricted to low-dimensional measurements taken at a single time point. As a result, sorting based on dynamic or multi-trait phenotypes—such as transient properties and properties that occur on fast timescales or in response to dynamic actuating signals—remains fundamentally challenging. Here we introduce Microscopic PhotoSelection (MiPS) which employs an automated robotic platform for single-cell selection based on multiple dynamic criteria, directly on microfluidic mother machine devices. The system couples long-term single-cell imaging with real-time analysis and selective optical targeting, allowing fully automated enrichment using high-intensity UV light or alternative wavelengths with the addition of photosensitisers. By targeting many cells in parallel, our platform overcomes throughput limitations of existing microfluidic-based selection technologies such as optical tweezers or droplet-based methods and provides a direct approach to select cells based on time-resolved, multi-trait phenotypes. We demonstrate the ability to perform in vivo selection and outline how iterative, feedback-based selection strategies can refine enrichment across multiple rounds. Taken together, our work establishes a high-throughput selection framework integrated into microfluidic devices, enabling applications in directed evolution, biosensor optimisation, circuit engineering, and diagnostics, where selection based on dynamic, multi-trait phenotypes is essential.