Due to advances in electron microscopy and to the development of novel nanoparticle structures with different morphologies and the dependence of physical properties on the nanoparticle morphology, there is a need for a more precise analysis of nanoparticle structure and morphology. That should provide a simple and unambiguous comparison of nanoparticles‘ shapes and of material properties that depend on the shape, which has been lacking thus far. Here we study nanochains consisting of silica-coated iron oxide (maghemite, γ-Fe2O3) nanoparticle clusters covered by an additional layer of silica (core-shell structure). We have developed an algorithm for image segmentation and a quantitative analysis of nanochain shape from real TEM images. To that end we used two distinct measures of circularity and elongation measure (the aspect ratio measure). We show that the relative position and the area of the links, as well as the links‘ shape lead to significant differences in the measured aspect ratio of the entire nanochain (substantially influence the elongation of nanochains). We have also analyzed the core-shell structures in nanochains, and computed the shell's share in the overall area of observed nanochains. A Matlab code was developed and used for the computation of the elongation measure of shapes appearing in electron microscopy images. Here we have investigated magnetic properties of synthetic nanochains, that revealed superparamagnetic behavior at room temperature (SPION) with the possibility of tuning the magnetization values (approx. from 19 to 46 emu/g). We have compared of magnetization M(H) curves of the anisotropic nanochains and of isotropic nanoparticle (nanochain links), with the conclusion that the nanochains have a higher magnetic susceptibility, which fact can be understood as a consequence of their anisotropic shapes. The nanochains may be applied in biomedicine and magnetic separation, due to their morphology and magnetic properties.