After deconvolution, confocal stacks were analyzed with NeuronStudio (Rodriguez et al., 2008; Rodriguez et al., 2006; Wearne et al., 2005) (http://www.mssm.edu/cnic) to examine global and local morphometric characteristics of dendrites and spines such as dendritic spine densities, dendritic spine shape (stubby, mushroom, and thin), and dendritic spine volume. This software allows for automated digitization and reconstructions of 3D neuronal morphology from multiple confocal stacks on a spatial scale and averts the subjective errors encountered during manual tracing using a Rayburst-based spine analysis (Rodriguez et al., 2008; Rodriguez et al., 2006). At least three dendritic segments per apical dendrite were analyzed per cell with each segment manually inspected and appropriate corrections made using the NeuronStudio interface. Five neurons were analyzed from each animal and 5 mice were examined from each genotype in both age groups.
