The Brainstem Navigator toolkit is a collection of in-vivo brainstem nuclei atlas labels, MRI templates and documentation. The atlas is in stereotactic space and includes gray matter brainstem regions involved in arousal/sleep, autonomic, motor, sensory and limbic function. The atlas labels of brainstem nuclei were created by semi-automatic and manual segmentations of multi-contrast MRI of living humans at 7 Tesla. This package has been made available to enable researchers to identify the location of brainstem nuclei in both conventional and advanced MRI (e.g. 3 Tesla, 7 Tesla).