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We examined ten typical natural pigments extracted from food to find that <jats:italic>Monascus<\/jats:italic> pigment (MP) or anthocyanin pigment (AP: purple sweet potato and purple cabbage) with Tris (Trimethylolaminomethane) works as a good indicator of viability assay for dye exclusion test (DET) of <jats:italic>Paramecium<\/jats:italic>. This was confirmed spectrally by scan-free, non-invasive absorbance spectral imaging <jats:italic>A<\/jats:italic> (<jats:italic>x<\/jats:italic>,<jats:italic> y<\/jats:italic>, <jats:italic>\u03bb<\/jats:italic>) microscopy. We developed a new method of cell capture using a metal mesh to confine live <jats:italic>Paramecium<\/jats:italic> in a restricted space. This has the advantage that a low-cost and robust capture can be fabricated without using special equipment, compared to a conventional lab-on-a-chip. As a result, MP and AP stained dead cells as quick as methylene blue (MB), a synthetic dye conventionally used in DET within 1\u00a0min when treated with microwave and benzalkonium chloride. The natural pigments with Tris had little effect on inhibiting the growth of <jats:italic>Paramecium<\/jats:italic>, but MB killed all the cells within 1\u00a0h. MP is most useful because it allows non-invasive DET without Tris. 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