High-throughput marker-free screening of cytoplasmic vacuoles in adherent cells via Fourier ptychographic microscopy

The formation of intracellular vacuoles in mammalian cells is associated with different dysfunctions, e.g., autophagy, lysosomal storage diseases, and cellular stress. We introduce a pipeline for high-throughput, label-free analysis of adherent cells and vacuoles using Fourier ptychographic microscopy (FPM). In fact, by tailoring the Cellpose model to the case of FPM phase-contrast imaging, we segment and characterize more than 3 × 10⁴ cells and more than 10⁵ vacuoles. We tune the platform using cells engineered to express various types of vacuoles. In pathological cells, our platform can identify distinct subpopulations within the same patient-derived line. By analyzing their content, the platform could yield clues about their origin and machinery, as well as screen conditions highlighted by vacuole formations.