TopoMortar: A dataset to evaluate image segmentation methods focused on topology accuracy

We present TopoMortar, a brick wall dataset that is the first dataset specifically designed to evaluate topology-focused image segmentation methods, such as topology loss functions. Motivated by the known sensitivity of methods to dataset challenges, such as small training sets, noisy labels, and out-of-distribution test-set images, TopoMortar is created to enable in two ways investigating methods' effectiveness at improving topology accuracy. First, by eliminating dataset challenges that, as we show, impact the effectiveness of topology loss functions. Second, by allowing to represent different dataset challenges in the same dataset, isolating methods' performance from dataset challenges. TopoMortar includes three types of labels (accurate, pseudo-labels, and noisy labels), two fixed training sets (large and small), and in-distribution and out-of-distribution test-set images. We compared eight loss functions on TopoMortar, and we found that clDice achieved the most topologically accurate segmentations, and that the relative advantageousness of the other loss functions depends on the experimental setting. Additionally, we show that data augmentation and self-distillation can elevate Cross entropy Dice loss to surpass most topology loss functions, and that those simple methods can enhance topology loss functions as well. TopoMortar and our code can be found at https://jmlipman.github.io/TopoMortar