Sectioning of the 3D density map obtained by aligning and averaging IFT particles from fla14 mutant cells. The density map was obtained by averaging 15 tomographic volumes from a single train, each one containing three contiguous IFT particles as shown in the inset of Fig. 5 a. The images 1–6 were produced by serial sectioning along the z axis of the cubic volume shown on the left. To illustrate the spatial orientation of sectioning planes in the model, a cross section of it is shown on the frontal face of the cube and a longitudinal section is shown on the top face. The cutting planes, represented by the white lines on the cube, are numbered from 1 to 6, proceeding along the z axis from the top to the bottom of the 3D map. Each section is 0.66 nm thick. The glycocalyx, the flagellar membrane (m), the IFT, and the MT doublet (md) have been manually segmented using the same color coding shown in Fig. 5 (green, glycocalyx; white, membrane; red, IFT particles; yellow, MT doublet). This kind of rendering revealed fine structural details of IFT particles with patterning variations depending on the sectioning level of the 3D density map. Panels are oriented so that the tip of flagellum is oriented downward.