The present invention provides methods and apparatus for determining an orientation of a cilium relative to a characteristic of the shape of the cell from which the cilium projects. Three-dimensional microscopy data may be used to determine an orientation of a cilium relative to a specified axis, which is determined from a profile for each cell. Such orientation may be used to forecast alter, or otherwise study the growth process of chondrocytes. Results indicate that the shape of chondrocytes, the position of the ciliary basal body, the incidence of cilia, and the orientation of cilium, are not random through the growth plate.