The axoneme, which forms the core of eukaryotic flagella and cilia, is one of the largest macromolecular machines with a structure that is largely conserved from Microtubule doublets isolated from sea urchin sperm were studied by cryo-electron tomography. Groups of up to nine parallel doublets, apparently from a single axoneme, are often found in our frozen-hydrated samples, as shown in Figs. 1 and S2. The protofilaments (PFs) as well as the 4 nm tubulin monomer repeat along the PFs, are already resolved in the unaveraged tomographic reconstructions (Figs. 1 and 2a). As described in the methods section, small 3D volumes along each doublet were extracted from the tomograms and then aligned and averaged. Combining data from nine doublets produced an improved density map, as