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An automated system was developed to image the 3-D distribution of fluorescent magnetic nanoparticles in tissue samples. It enables easy measurement of magnetic nanoparticle distributions, for small and large tissue samples (currently up to a maximum size of 25 mm × 25 mm × 25 mm), in 3-D, with about 70 resolution in plane and 1 μm in the vertical direction. There is a linear correlation between particle concentration and fluorescence intensity, hence the system provides a quantitative measure of the nanoparticle distribution, but the tissue sample is destroyed during the imaging process. The system was demonstrated by measuring the particle distribution in rat ear and brain samples.