In this paper, a methodology for the analysis of subcellular morphology with chemical specificity, for images obtained by Stimulated Raman Scattering microscopy, is described. In order to detect microstructures inside the cells, a segmentation method based on a threshold algorithm and on a region growing process is proposed. Validation tests on images of polystyrene beads and of on adipocyte cells are reported, demonstrating the feasibility of our approach.