A Lightweight Framework for Semantic Segmentation of Biomedical Images

We introduce a lightweight framework for semantic segmentation that utilizes structured classifiers as an alternative to deep learning methods. Biomedical data is known for being scarce and difficult to label. However, this framework provides a lightweight, easy-to-apply, and fast-to-train approach that can be adapted to changes in image material though efficient retraining. Moreover, the framework is able to adapt to various input sizes making it robust against changes in resolution and is not tied to specialized hardware, which allows efficient application on standard laptops or desktops without GPUs. We benchmark two distinct models, a single structured classifier and an ensemble of structured classifiers, against a U-Net, evaluating overall performance and training speed. The framework is versatile and can be applied to multi-class semantic segmentation. Our study shows that the proposed framework can effectively compete with established deep learning methods on diverse datasets in terms of performance while reducing training time immensely

Mask R-CNN Outperforms U-Net in Instance Segmentation for Overlapping Cells

U-Net is the go-to approach for biomedical segmentation applications. However, it is not designed to segment overlapping objects, a challenge Mask R-CNN has shown to have great potential in. Yet, Mask R-CNN receives little attention in biomedicine. Hence, we evaluate both approaches on a publicly available biomedical dataset. We find that Mask RCNN outperforms U-Net in segmenting overlapping cells and achieves comparable performance if they do not intersect. Our study provides valuable decision support to practitioners in selecting an appropriate method when solving instance segmentation tasks using deep learning, as well as important insights into enhancing the accuracy of such approaches in biomedical image analysis