The Cell-CT is an optical projection tomography microscope (OPTM) developed for high resolution 3D imaging of single cells based on absorption stains and brightfield microscopy. In this study we demonstrate the use of the Cell-CT in multi-color mode for simultaneous imaging of cellular 3D morphology and the 3D distribution of nanoparticle clusters in the cytoplasm. The ability to image cellular processes in relation to cellular compartments with a non-fluorescence 3D technology opens new perspectives for molecular research.