As image processing and analysis techniques improve, an increasing number of procedures in bio-medical analyses can be automated. This brings many benefits, e.g improved speed and accuracy, leading to more reliable diagnoses and follow-up, ultimately improving patients outcome. Many automated procedures in bio-medical imaging are well established and typically consist of detecting and counting various types of cells (e.g. blood cells, abnormal cells in Pap smears, and so on). In this article we propose to automate a different and difficult set of measurements, which is conducted on the cilia of people suffering from a variety of respiratory tract diseases. Cilia are slender, microscopic, hair-like structures or organelles that extend from the surface of nearly all mammalian cells. Motile cilia, such as those found in the lungs and respiratory tract, present a periodic beating motion that keep the airways clear of mucus and dirt. In this paper, we propose a fully automated method that computes various measurements regarding the motion of cilia, taken with high-speed video-microscopy. The advantage of our approach is its capacity to automatically compute robust, adaptive and regionalized measurements, i.e. associated with different regions in the image. We validate the robustness of our approach, and illustrate its performance in comparison to the state-of-the-art.