was used to outline the lung, and the autofluorescent signal was used to threshold and generate tissue area measurements in each section. The same section profile region was overlaid on the nanotube image and a dark objects thresholded to generate an area measurement of the nanotubes within the lung. In the final images shown in Fig. 3a the lung tissue is shown in red, the tube image was inverted (such that the tubes are now bright) and pseudocolored green. The scale bar is 1 mm. Detection of SWCNT aggregates Unstained paraffin embedded lung tissue sections from MPO k/ o and w/t mice were scanned using the IN Cell Analyser 1000 high content screening and analysis system to distinguish between the organic tissue and the inorganic SWCNT (under bright field imaging settings). Optically detectable SWCNT aggregates were counted and their distribution and sizes were calculated using IN Cell Investigator software. 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