Fig. 2

Analytical methods to quantify morphological structure. a xy projection of the montage of CLSM tiled image stacks from a wildtype mouse layer 3 frontal cortical pyramidal neuron. Scale bar 40 μm. b Tree structure from the data shown in (a), extracted using NeuronStudio. c Automatic spine detection and visualization in NeuronStudio. Left automatically detected spines overlaid on a maximum projection of a typical dataset; right the same data and spines volume-rendered in 3D. d Left 2D Rayburst sample used for diameter estimation. Rays cast using the sampling core is shown in orange with the one chosen as the diameter shown in blue. The green line indicates the surface detected by the Rayburst samples. Right spine diameter estimation using a 2D Rayburst run at the center of mass (small green squares) of a single layer. The blue line indicates the resulting width of the structure as calculated by Rayburst, and provides an approximate length of 0.7 μm. e Optimized fits of scaling exponents (black fitted lines) and optimal scaling regions (gray shaded bands) for the apical dendrites of a typical layer 3 pyramidal cell projecting from superior temporal cortex to area 46 (see Kabaso et al. (2009) for details). f Contributions of branching and tapering exponents to global mass scaling (measured by total area exponent dA) in spine-corrected apical dendrites of long projection neurons of young rhesus monkeys, in the proximal and medial scaling regions (I, II in e). The total branching and tapering vary across the two scaling regions, yet the total area in each region is conserved [modified from Wearne et al. (2005) and Kabaso et al. (2009)]