Disconnect to Connect: A Data Augmentation Method for Improving Topology Accuracy in Image Segmentation

arXiv:2503.05541v2 Announce Type: replace Abstract: Accurate segmentation of thin, tubular structures (e.g., blood vessels) is challenging for deep neural networks. These networks classify individual pixels, and even minor misclassifications can break the thin connections within these structures. Existing methods that focus on improving topology accuracy, such as topology loss functions, require very precise training labels with the correct topology, which is difficult to obtain. Low image resolution and contrast can further complicate the annotation by causing these structures to appear disconnected. We present CoLeTra, a data augmentation method that improves topology accuracy, even on datasets with topologically inaccurate training labels. CoLeTra achieves this by artificially breaking the structures in the images while maintaining the original labels, incorporating to the models the prior knowledge that structures can be continuous even if they appear disconnected. Our extensive experiments, involving different architectures, loss functions, and datasets, demonstrate that CoLeTra leads to segmentations topologically more accurate while often improving the Dice coefficient and clDice. We also release a dataset specifically suited for image segmentation methods with a focus on topology accuracy. CoLetra's code can be found at https://jmlipman.github.io/CoLeTra.