In the present work, a methodology for the analysis of subcellular morphology with chemical specificity for images from Stimulated Raman Scattering is suggested. In particular, a segmentation method based on a threshold algorithm and on a region growing process, to detect microstructures inside the cells, is proposed. Moreover, quantitative features for the segmented objects are extracted, in order to provide information about the possible morphological variations of microstructures in images acquired by means SRS technique.