Abstract. Natural products offer excellent sources of health-promoting medicines yet challenges in efficiently and economically sourcing these value-add bio-compounds have prevented their greater availability and promotion to public health. We address this problem by developing a novel image-based screening technology that offers highly sensitive, phenotypic bioassays of metabolite concentrations on live single cells. This allows a greatly improved method for identification of better natural product producers, as well as quantitative information about the production per cell and production distribution across the population. This high-resolution, non- destructive, label-free cell screening and cell sorting system is based on vibrational photothermal microscopy which uses mid-infrared light to probe molecular vibrational absorptions at resolutions comparable to visible light microscopes. To demonstrate the utility of the approach we focus on the production of essential polyunsaturated fatty acids (PUFAs) in lipid droplets sourced from microalgae (thraustochytrids) – a natural producer of PUFAs. These long-chain fatty acids play a vital role in the physiological health of cells and tissues throughout the body are commercialized as a prominent nutraceutical. To develop enriched cell lines, we will engineer and prototype a multichannel microfluidic chip with an active piezoelectric actuator to selectively save cells identified through photothermal as being highly productive. Our goal is to provide an attractive method to non-destructively evaluate metabolite content in engineered microbes including bacteria and yeast, not just algae, and for a variety of high-value metabolites. To accomplish these goals, we have established a team of qualified experts including specialists in advanced microscopy, microfluidics design, and algae cultivation for industrial applications. Ultimately, the methods developed here will showcase a roadmap toward rare-cell discovery and active cell sorting based on chemical mapping allowed through the photothermal imaging contrast.