Imaging flow cytometry (IFC) characterize hundreds thousands of cellular images using hundreds of measurements of morphological and fluorescence cellular features. Complex morphology of host-intracellular parasite interaction can be quantified in statistically robust manner using IFC. Feature Finder algorithm is useful in defining statistically significant differences in morphological and fluorescent features of cells. IFC revealed that M. tuberculosis internalized bacilli were co-localized to a greater degree at late endosome/lysosome CD107 and late endosome Rab7 compartment than Rab5 early endosome compartment.