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The trend in medical equipment is toward compact and integrated low-cost medical test devices. Fluorescence-based assays are used to identify specific pathogens through the presence of dyes, but typically require specialized microscopes and narrowband optical filters to extract information. We present a novel, high-sensitivity, cost-effective, cross-polarization scheme to filter out excitation light from a fluorescent dye emission spectrum. This concept is demonstrated using an inverted microscope fitted with a halide lamp as the excitation source and an organic photo voltaic (organic photodiode) cell as the intensity detector. The excitation light is linearly polarized and used to illuminate a microfluidic device containing a 1 volume of dye dissolved in ethanol. The detector is shielded by a second polarizer, oriented orthogonally to the excitation light, thus reducing the magnitude of the detector photocurrent by about 25 …