Golgi apparatus (GA) is a center for lipid metabolism and the final target of ceramide pathway, which may result in apoptosis. In this work localization of highly hydrophobic hypericin is followed by time-resolved imaging of NBDC6 (fluorescent ceramide) in U87 MG glioma cells. Decrease of NBDC6 fluorescence lifetimes in cells indicates that hypericin can also follow this pathway. It is known that both, ceramide and hypericin can significantly influence protein kinase C (PKC) activity. Western blotting analysis shows increase of PKC delta autophosphorylation at Ser645 (p(S645) PKC delta) in glioma cells incubated with 500 nM hypericin and confocal-fluorescence microscopy distinguishes p(S645) PKC delta localization between GA related compartments and nucleus. Experimental and numerical methods are combined to study p(S645) PKC delta in U87 MG cell line. Image processing based on conceptual qualitative description is combined with numerical treatment via simple exponential saturation model which describes redistribution of p(S645) PKC delta between nucleus and GA related compartments after hypericin administration. These results suggest, that numerical methods can significantly improve quantification of biomacromolecules (p(S645) PKC delta) directly from the fluorescence images and such obtained outputs are complementary if not equal to typical used methods in biology.