Cell Detection with Star-convex Polygons

Cell Detection with Star-convex Polygons

8 Nov 2018 | Uwe Schmidt, Martin Weigert, Coleman Broaddus, Gene Myers
The paper "Cell Detection with Star-convex Polygons" by Uwe Schmidt, Martin Weigert, Coleman Broaddus, and Gene Myers introduces a novel method for cell and nucleus detection in microscopy images. The authors address the limitations of existing methods, such as per-pixel cell segmentation and bounding box localization, which can lead to segmentation errors in crowded cell images. They propose using *star-convex polygons* as a more accurate shape representation compared to bounding boxes, which do not require shape refinement. The method, called STARDIST, is based on a convolutional neural network (CNN) that predicts a polygon for each pixel, representing the cell instance at that position. The network densely predicts the radial distances to the object boundary and the object probability for each pixel. Non-maximum suppression (NMS) is then applied to select the final set of polygons. The authors evaluate STARDIST on three datasets: synthetic images with touching half-ellipses (ToY), synthetic images of evolving cell populations (TRAGEN), and real fluorescence microscopy images (DSB2018). STARDIST outperforms state-of-the-art methods like Mask R-CNN, especially in challenging conditions with crowded cells. The method is also simpler to train and use, with fewer hyperparameters. The paper highlights the advantages of star-convex polygons in accurately localizing cell nuclei, particularly in images with overlapping cells. STARDIST can handle partially visible cells and provides multiple segmentation hypotheses, making it useful for cell tracking applications.The paper "Cell Detection with Star-convex Polygons" by Uwe Schmidt, Martin Weigert, Coleman Broaddus, and Gene Myers introduces a novel method for cell and nucleus detection in microscopy images. The authors address the limitations of existing methods, such as per-pixel cell segmentation and bounding box localization, which can lead to segmentation errors in crowded cell images. They propose using *star-convex polygons* as a more accurate shape representation compared to bounding boxes, which do not require shape refinement. The method, called STARDIST, is based on a convolutional neural network (CNN) that predicts a polygon for each pixel, representing the cell instance at that position. The network densely predicts the radial distances to the object boundary and the object probability for each pixel. Non-maximum suppression (NMS) is then applied to select the final set of polygons. The authors evaluate STARDIST on three datasets: synthetic images with touching half-ellipses (ToY), synthetic images of evolving cell populations (TRAGEN), and real fluorescence microscopy images (DSB2018). STARDIST outperforms state-of-the-art methods like Mask R-CNN, especially in challenging conditions with crowded cells. The method is also simpler to train and use, with fewer hyperparameters. The paper highlights the advantages of star-convex polygons in accurately localizing cell nuclei, particularly in images with overlapping cells. STARDIST can handle partially visible cells and provides multiple segmentation hypotheses, making it useful for cell tracking applications.
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