Fig. 3

Identification of homeostatic and activated Alzheimer-associated microglia clusters a Example of mIF image of an Alzheimer patient. b Exemplary images of segmented microglia in a control and an Alzheimer patient. c Number of identified cells in the GM and WM of controls (blue; n = 9) and Alzheimer patients (red; n = 12)(Mean, Student’s t-test). d Heatmap showing the expression of the four different markers (P2RY12, TMEM119, FTL and Iba1), in the 11 identified microglia clusters. e t-SNE plot of all individual cells showing the distinct colour-coded clusters and of control- vs. Alzheimer-patient-derived cells. f t-SNE plots colour-coded for intensity of the four individual markers. g Distribution of clusters in GM and WM. h Prevalence of identified clusters (C1–C11) in individual control (blue; n = 9) and Alzheimer patients (red; n = 12) (Median, Mann–Whitney U test). Scale bar, 100 µm. Scale bar zooms, 20 µm. GM Grey matter, WM White matter