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Hyperspectral imaging with enhanced darkfield microscopy (HSI-M) possesses unique advantages in its simplicity and non-invasiveness. In consideration of the urgent need for profound knowledge on the behavior and effects of engineered nanoparticles (NPs), here, we determined the capability of HSI-M for examining cellular uptake of different metal-based NPs, including nanosized metals (silver and gold, both citrate stabilized), metal oxides (copper oxide and titanium dioxide), and CdSe/ZnS core/shell quantum dots at subtoxic concentrations. Specifically, we demonstrated that HSI-M can be used to detect and semi-quantify these NPs in the ciliated protozoan Tetrahymena thermophila as a model aquatic organism. Detection and semi-quantification were achieved on the basis of spectral libraries for the NPs suspended in extracellular substances secreted by this single-celled organism, accounting for matrix …