Figure 5. Trajectories of excitatory axons in the apical dendrite volume illustrate necessity of 3DEM for unambiguous identification.

(a) Three axonal profiles appeared to be identical on one section. (b) 3D reconstruction revealed the diversity in synaptic contacts along their length. Five synapses were made along ax024 (7.9 μm) in this volume while the other two (ax118, 5.3 μm and ax047, 6.0 μm) made only one synapse each. These axons appear to run in parallel in section 93; however, 3DEM shows instead that their paths crossed. The illustrated dendrite (d020, yellow) had two spines that synapsed (red) on different varicosities of the same axon (ax024). (c) EM illustrating one of the synapses between ax024 and d020 (named d020c04Ax024e). (d) EM with 4 ambiguous objects that look essentially identical on this section. (e) Object 1 was identified as a dendritic spine neck, as its head formed an asymmetric synapse with ax149 on section 111. (f) Object 2 from section 118 was similarly discovered to be part of a spine on dendrite d020 (synapse named d020c05Ax046e). (g) Object 3 from section 118 was found to be part of ax148, which made one synapse in the reconstructed volume with a nonspiny dendritic segment (d005, orange) that had 12 asymmetric, presumably excitatory synapses (red) and one symmetric, presumably inhibitory synapse (blue) along its length. (h) Object 4 was identified as ax018, which formed one synapse (d010c16Ax018e) in the reconstructed volume with dendrite 10 (d010). (i) All of the objects on section 118 were identified through 3D reconstructions and are colorized and labeled in this EM (spiny dendrites, yellow; excitatory axons, green; glia, light blue). All scale bars are 1 micron, and scale cubes are 1 μm³.