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The most prominent vector-transmitted diseases in the first and third world are Lyme disease and malaria, respectively. In both cases the transmitted agents are introduced into the skin from where they eventually disseminate into the blood using active motility. We are interested in deciphering the molecular mechanisms underlying the motility of these pathogens and how they relate to the ultrastructure of the pathogens. Here we provide an overview of the microscopy techniques that we use to achieve these goals.