Fig. 4

Unsupervised spectral clustering of microglial profiles reveals three distinct phenotypes. a Heatmap depicts the unsupervised spectral clustering of 6226 IBA1+ microglial profiles based on their mean gray intensity (MGI) for the other 5 microglial markers. Note that MGI z-scores were scaled from 0 to 100 to facilitate comparison across markers. Three clusters are evident, which we termed “homeostatic,” “intermediate,” and “reactive.” b High-plex images from representative microglial cells of each of these clusters. Scale bar: 5 µm. c Stacked bar graphs show the proportions of microglial states by diagnosis and the proportions of diagnoses by microglial state. d Box and whisker plots illustrate the distribution (box: median and interquartile range [IQR]; whiskers: 1.5 × IQR) of MGI z-scores for each microglial marker across the homeostatic, intermediate, and reactive phenotypes. Statistical comparisons between states are available in Table S3: Additional file 1