Fig. 3

a Schematic illustrating the method for measuring microglia morphology with ImageJ Analyze Skeleton (reproduced in part with permission). Confocal z-stacks are converted to maximum intensity projections, and then thresholded to create a binary image. Images were converted into 2D skeletons by the Skeletonize 2D/3D plugin, and pixels were analyzed by the Analyze Skeleton plugin. Pixels with one neighbor (labelled in blue) are branch end points, pixels with two neighbors (labelled in orange) are branches or slabs, and pixels with three or more neighbors (labelled in pink) are junctions. Average number of microglia process end points (an indicator of the number of microglia processes) per cell (b–d), average process length per cell (e–g), and process end points per junction, used here as an indicator of branching complexity (h–j) in the CA1, CA3, and DG. All graphs represent values at 10 days post-intracerebroventricular infusion of amyloid-β 1-40 normalized for non-surgery values, ±SEM. Different letters denote significantly different bars (p < 0.05) as determined by one-way ANOVA with Bonferroni post-test. CA cornu ammonis, DG dentate gyrus, WTSO wild type mice fed safflower oil, fat-1 fat-1 mice fed safflower oil, WTFO wild type mice fed fish oil. SEM standard error of the mean