Fig. 1: MorphOMICs dissects microglial morphology in adult healthy brains.

a, Sagittal view of the mouse brain (image from Allen Institute) with annotated brain regions. Confocal images of immunostained microglia (Iba1, green) and cell nuclei (Hoechst, blue) from adult C57BL/6J mice with zoom-in view. Scale bars, 50 μm. b, Schematic of MorphOMICs pipeline covering the TMD with a mock microglia skeleton and plots. Red, longest process with start (#) and end (*). Each traced microglia wass converted into a rooted tree (i), followed by a persistence barcode (ii), a persistence diagram (iii) and a persistence image (iv) with grayscale process density in 2D space. Blue spot, soma location. Arrow 1 indicates the distance from the soma. Arrow 2 indicates the length of processes, which increases with distance from the diagonal. Each persistence image (n) is summarized to an average persistence image of a condition. c, Average persistence images of the seven analyzed brain regions organized by hierarchical clustering (Extended Data Fig. 1b). Top-right corner: representative traced microglia. The darker the green, the higher the frequency distribution of the processes. d, Schematic of MorphOMICs pipeline covering bootstrapping. Left: microglial population (n) contains individual persistence images. Center: average persistence image; x unique persistence images were drawn from each of n microglial pools to generate a bootstrapped persistence image. Right: repeating this process m times forms the bootstrapped pool. e, Schematic of MorphOMICs pipeline covering dimension reduction and data visualization with UMAP. Left: each persistence image is pixelated; each pixel represents a dimension. Middle: reducing dimensions with principal component (PC) analysis. Right: further dimensionality reduction based on the first ten PCs. f, UMAP plot of MorphOMICs-analyzed adult microglia, color-coded for each brain region. Each dot represents a bootstrapped persistence image. n_samples= 500 per condition (‘Average and bootstrapped persistence images’). In d, see Supplementary Table 5 for the number of animals. Points situated close in the UMAP space indicate similar bootstrapped persistence image; however, the point’s actual position is irrelevant.