Machine learning aided single cell image analysis improves understanding of morphometric heterogeneity of human mesenchymal stem cells

The multipotent stem cells of our body have been largely harnessed in biotherapeutics. However, as they are derived from multiple anatomical sources, from different tissues, human mesenchymal stem cells (hMSCs) are a heterogeneous population showing ambiguity in their in vitro behavior. Intra-clonal population heterogeneity has also been identified and pre-clinical mechanistic studies suggest that these cumulatively depreciate the therapeutic effects of hMSC transplantation. Although various biomarkers identify these specific stem cell populations, recent artificial intelligence-based methods have capitalized on the cellular morphologies of hMSCs, opening a new approach to understand their attributes. A robust and rapid platform is required to accommodate and eliminate the heterogeneity observed in the cell population, to standardize the quality of hMSC therapeutics globally. Here, we report our primary findings of morphological heterogeneity observed within and across two sources of hMSCs namely, stem cells from human exfoliated deciduous teeth (SHEDs) and human Wharton jelly mesenchymal stem cells (hWJ MSCs), using real-time single-cell images generated on immunophenotyping by imaging flow cytometry (IFC). We used the ImageJ software for identification and comparison between the two types of hMSCs using statistically significant morphometric descriptors that are biologically relevant. To expand on these insights, we have further applied deep learning methods and successfully report the development of a Convolutional Neural Network-based image classifier. In our research, we introduced a machine learning methodology to streamline the entire procedure, utilizing convolutional neural networks and transfer learning for binary classification, achieving an accuracy rate of 97.54%. We have also critically discussed the challenges, comparisons between solutions and future directions of machine learning in hMSC classification in biotherapeutics.