Fig. 7. Quantitation of Shh::GFP ligand puncta and basal bodies in early ventral neural tubes. Eight-somite-stage mouse neural tubes cut at the level of the heart were analyzed at three distinct volumes (V1, V2, V3) along the D-V axis. (A) The relative positions of V1, V2 and V3 in the xy-plane. Each volume is 9 µm wide (x-axis), 9 µm long (y-axis) and 2.1 µm deep (a stack of six confocal images taken at 0.35 µm steps along the z-axis). Nuclei (blue), Shh::GFP ligand (green), -tubulin (red). (B) Quantification of Shh::GFP ligand puncta and basal bodies within each apical volume. A Shh::GFP punctum is basal-body-associated if it is within 1 µm of a -tubulin punctum. A nucleus is associated with an apical volume if it is laterally positioned to that volume. Ventral midline nuclei are associated with V3. Note that the percentage of Shh::GFP puncta associated with the basal body decreases ventrally.