This work focuses on the visualization and quantification of Super-paramagnetic iron oxide nanoparticles (SPIO-NPs) inside macrophages using transmission electron microscope (TEM) images. Macrophages have been extensively used as probes for cell and subcellular structure labeling, as well as for drug and gene delivery. In order to track the macrophages movement inside the body, SPIO-NPs are introduced to help in the visualization of macrophages by MRI imaging and then to control process of the drug and gene delivery. The mechanism of interaction between macrophages and SPIO-NPs is still not fully understood by scientists. Estimating the quantity of NPs inside microphages will certainly improve the understanding of this mechanism. In this work a 3D reconstruction and visualization, using transmission electron microscopy (TEM), of macrophages filled with SPIO-NPs is being developed. An estimation of the quantities of the NPs inside macrophages has been achieved. The visual interaction between macrophages and SPIO-NPs had been discovered.