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Peroxisomes are central metabolic organelles whose maturation and function depend on efficient and accurate targeting of peroxisomal membrane proteins (PMPs). Ultrastructural imaging of the PMPs is a quite difficult task as it requires high spatial and temporal resolution. Further, the spatial resolution of conventional light microscopy is limited due to the diffraction of light. However, recent methodological developments in super resolution microscopy showed us to access the nanoscale regimes spatially allowing to elucidate the membrane structures of cell organelles.