IBA1 positive, chronically activated microglia increase with EAE progression however both early and late tolerisation have no effect on this increase. Representative maximum projected confocal images of IBA1 (white) positive microglial cells and bis-benzamide (blue) in the dorsal funiculus in normal (a, N = 4), day 29 (b, N = 5), day 58 (c, N = 5), day 105-crEAE (d, N = 7) and following early (e, N = 5) and late (f, N = 7) tolerisation. Quantification (g) shows a progressive increase in IBA1 positive cells in the dorsal funiculus that is significantly elevated at day 58 and 105-crEAE (black asterisk, P < 0.01, one-way ANOVA). Neither early (red bar) nor late tolerisation (green bar) had any significant effect on this increase in IBA1 positive microglia. Scale bar = 50 μm for all images.