Fig. 2

Microglial morphologies change in human ALS and correlate with CD68 and Iba1 levels. Microglial cell bodies and processes were identified using Iba1 immunoreactivity (A, yellow) and used to quantify morphology measures per cell (A, white): cell body area (B), process number (C), outgrowth (D), and branch number (E). Single-cell measures were averaged across all microglia in each case to give a mean measure per cell which was compared between control, stage 1–3 ALS, and stage 4 ALS cases. Data presented as truncated violin plots with median and quartiles shown; control n = 10, stage 1–3 ALS n = 5, and stage 4 ALS n = 5. All morphology measures were compared between case groups with multiple Mann-Whitney tests and multiple comparisons were controlled for using a False Discovery Rate of 0.01, as determined by the two-stage step-up method of Benjamini, Krieger, and Yekutieli. Significances of difference between case groups: *p ≤ 0.05. Measures of pTDP-43 pathology, microglial marker intensities, and microglial morphology were sequentially correlated in all cases (n = 20) using Spearman correlations (F). The resulting r value from each correlation is presented in the correlation matrix and colour coded relative to strength. When r ≤ -0.7 or r ≥ 0.7 and p ≤ 0.05, correlations were considered statistically significant and strong. When − 0.7 < r ≤ -0.4 or 0.7 > r ≥ 0.4 and p ≤ 0.05, correlations were considered statistically significant and moderate