Many GC cilia are submerged from the cell surface and concealed intracellularly. (A–D) Representative pocket (A), surface (B), and concealed (C and D) cilia from P7 large serial scanning EM volume are displayed. Select z slices of each cilium are presented to the right of the 3D reconstructed image of each cilium. Scale bar: 200 nm. (E) Annotated cilia and centrioles are represented in the 3D space of the serial scanning EM volume. Annotated centrioles are represented as gray spheres and cilia as lines. Cilia color represents the classification of cilia as Pocket (blue), Concealed (yellow), or Surface (red). The positions of the cilia displayed in A–D are indicated. Insets show regions marked (i) and (ii). (F) The depth of mother centrioles is plotted for each type of cilium. In F and H, the y-axis is inverted such that higher depth values fall farther below the Y-axis. (G) Cilium length is plotted for each type of cilium. (H) The length of each annotated cilium is plotted as a function of mother centriole depth. The cilia are color coded as classified. (I) The fractional distribution of cilia in each layer is plotted and colored according to cilia type.