Implementation of transfer learning for the segmentation of human mesenchymal stem cells-A validation study

Document Type



Dental-oral, Maxillo-facial Surgery


Introduction: Stem cell therapy has been gaining interest in the regeneration rather than repair of lost human tissues. However, the manual analysis of stem cells prior to implantation is a cumbersome task that can be automated to improve the efficiency and accuracy of this process.
Objective: To develop a Deep Learning (DL) algorithm for segmentation of human mesenchymal stem cells (MSCs) on micrographic images and to validate its performance relative to the ground truth laid down via annotation.
Methodology: Pre-trained DeepLab algorithms were trained on annotated images of human MSCs obtained from the open-source EVICAN dataset. This dataset comprises of partially annotated images; a limitation that is overcome by blurring backgrounds of these images which consequently blurs the unannotated cells. Two algorithms were trained on the two different kinds of images from this dataset; with blurred and normal backgrounds, respectively. Algorithm 1 was trained on 139 images with blurred backgrounds and algorithm 2 was trained on 37 images from the same dataset with normal backgrounds to replicate real-life scenarios.
Results: The performance metrics of algorithm 1 included accuracy of 99.22%, dice co-efficient of 99.66% and Intersection over Union (IoU) score of 0.84. Algorithm 2 was 96.34% accurate with dice co-efficient and IoU scores of 98.39% and 0.48, respectively.
Conclusion: Both algorithms showed adequate performance in the segmentation of human MSCs with performance metrics close to the ground truth. However, algorithm 2 has better clinical applicability, even with smaller dataset and relatively lower performance metrics.


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Publication ( Name of Journal)

Tissue and cell