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The plasma cell membrane is organised in a non-homogenous manner consisting of an assortment of membrane microdomains. These include protein clusters and lipid rafts which occur on a range of short temporal and spatial scales. Super-resolution imaging techniques such as photoactivated localisation microscopy (PALM) have shifted the resolution limit of fluorescent imaging. This improved resolution has allowed the examination of the structure and function of protein clusters at the single molecule level (10-100 nm). PALM employs photoswitchable fluorescent probes to control the density of fluorescent emitters. By imaging photoswitching events repeatedly over thousands of frames we can build up a precise map of fluorophore positions. Using PALM we have studied the plasma membrane organisation of two SNARE proteins: SNAP25 and SNAP23. These proteins play a central role in neuronal and endocrine cell communication, leading to the release of vesicle cargo across the cell membrane. Applying a quantitative cluster analysis method based on Bayesian statistics we have systematically compared the molecular clustering of SNAP25 and SNAP23. A greater understanding of SNARE protein clustering will provide insight into diseases such as Type 2 Diabetes, where modifications to normal clustering behavior could affect endocrine cell function.