Fig. 3: Methods for identifying podosomes and site locations.

a TIRF-SIM imaging of actin in a cell with multiple frustrated phagocytosis sites. Color scale shows pixel intensity (arb. units). b, c Smoothed images of the entire cell based on the features of interest (podosomes i.e., pod. or phagocytosis sites i.e., phago.). An insignificant amount of noise is added for uniqueness. Color scales show pixel intensity (arb. units). d, e Persistence diagram based on images from b and c. In d, dots (homology-0) represent connected components, and in e dots (homology-1) represent holes. Significantly persistent features are colored. Due to pixel uniqueness, the birth intensity of significantly persistent features corresponds to maxima of clustered components and minima of holes. f, g Locations of significantly persistent clustered components (f) and holes (g). h Final locations of podosomes and phagocytosis site centers after post-processing to exclude podosomes far away from phagocytosis sites and center phagocytosis sites.