Surgical and intravital microscopy protocol to image Trypanosoma brucei–host interactions in live rodent models

Intravital microscopy (IVM) involves surgical procedures to expose the internal organs of live anesthetized animals to visualize fluorescently labeled components in situ, in vivo at subcellular resolution. Here, we provide an IVM protocol for time-lapse imaging of dynamic Trypanosoma brucei-host interactions in ten mammalian organs and in systemic circulation. We describe intraperitoneal or intradermal injection of mice with T.brucei. We then detail surgical procedures to prepare ten organs for IVM, followed by imaging of host-T. brucei interactions. For complete details on the use and execution of this protocol, please refer to De Niz et al. (2021).