The aim of this study is to conduct a comparative assessment of the effectiveness of neural network models-U-Net, DeepLabV3+, SegNet and Mask R-CNN-for the semantic segmentation of micrographs of human mesenchymal stem cells (MSCs). A dataset of 320 cell micrographs annotated by cell biology experts was created. The models were trained using a transfer learning method based on ImageNet pre-trained weights. As a result, the U-Net model demonstrated the best segmentation accuracy according to the metrics of the Dice coefficient (0.876) and the Jaccard index (0.781). The DeepLabV3+ and Mask R-CNN models also showed high performance, although slightly lower than U-Net, while SegNet exhibited the least accurate results. The obtained data indicate that the U-Net model is the most suitable for automating the segmentation of MSC micrographs and can be recommended for use in biomedical laboratories to streamline the routine analysis of cell cultures.