Cilia are slender, microscopic, hair-like structures or or-ganelles that extend from the surface of nearly all mam-malian cells. Motile cilia, such as those found in the lungs and respiratory tract, present a beating motion that keep the airways clear of mucus and dirt. They are thus of primary importance in many respiratory diseases. The performance of mucous transportation in the nasal cavity can be represented by a ciliary beating frequency. In this paper, we propose a fully automated method that computes the beating frequency from a sequence of images taken with high-speed videomi-croscopy. The advantage of our approach is its capacity in computing regionalized frequencies, i.e., various frequencies each associated with one region in the image. Moreover we propose a preprocessing pipeline to alleviate acquistion artefacts due to the camera or to the cell proper motions. We demonstrate the robustness of our approach, and illustrate its performance in comparison to the state-of-the-art.