We developed a multiscale image analysis pipeline to investigate the changes in internal morphology of spheroids upon drug treatment. It combines image segmentation with graph theory and computational topology to obtain quantitative features of the individual cells, the local cell neighbourhood and the global topology of the spheroid. As an output we obtain over 30 features that are relevant in multicellular systems. Our pipeline works very well for spheroids of different sizes (5,000 - 40,000 cells). We now extend it and apply it to data from other specimen including organoids and mouse embryos.