Hypothalamic tanycytes are specialized ependymal cells that line the floor of the third ventricle and emit processes into the surrounding hypothalamic parenchyma. Given their strategic location, these cells are believed to play several key functions, including energy homeostasis, nutrient sensing, and hormonal transport and regulation. Here, we used an adenoviral vector expressing GFP (Rad-GFP) to label the ependymal walls, including tanycytes and their processes, providing fine structural detail throughout these structures. By imaging a series of consecutive brain slices we obtained a collection of fluorescence z-stacks which we later re-combined into a continuous volume spanning the basal hypothalamus. This was accomplished by applying a global elastic registration procedure guided by local inter-stack landmark pairs, using an image analysis pipeline we developed for the software package Fiji and its plugin TrakEM2. Following this procedure, we were able to map the three-dimensional distribution of tanycytes processes throughout the sampled volume, as well as to describe and quantify several parameters, including the type and percentage of processes that extend to the different hypothalamic nuclei, their overall morphology and orientation, and the distribution of contact classes based on morphological criteria. Altogether, our results provide valuable insights for the further understanding of these intriguing cells and their putative roles in the hypothalamic physiology.