Complex multi-component systems are dominated in organs. Different functional structures could be partly represented as highly dynamic alterations of light scattering. In our institute we apply micro-lightguides and optical systems for monitoring subcellular structures. By creating 3D images after staining an isolated perfused rat liver with the potential sensitive fluorescence dye Merocyanine-540 we found an astonishing relation between morphological and functional aspects changeable by oxygenation or desoxygenation. Moreover, the simultaneous practice of 2D-spectroscopy could clarify cellular processes like e. g. potential changes. Merocyanine-540 spectra of stained rat liver have shown their maximum in light intensity at 596 +/- 2 nm in dependence on depolarisation, hyper- or repolarisation. In addition, we found lower peaks in difference spectra, which could be associated with the cytochromes aa(3), b and c. There has been an interesting correlation to the redox state of cytochromes during anoxic or oxic liver perfusion. Every peak has shown consistent oscillations with frequencies over 7/sec (420/min), which might be caused by membrane processes. In five experiments we compared functional and morphological aspects in 2D- and 3D-images of stained liver tissue.