Unsupervised semantic segmentation in synchrotron computed tomography with self-correcting pseudo labels

Abstract X-ray computed tomography (CT) is a widely used imaging technique that provides detailed examinations into the internal structure of an object with synchrotron CT (SR-CT) enabling improved data quality by using higher energy, monochromatic x-rays. While SR-CT allows for improved resolution, time-resolved experimentation, and reduced imaging artifacts, it also produces significantly larger datasets than conventional CT. Accurate and efficient evaluation of these datasets is a critical component of these workflows; yet is often done manually representing a major bottleneck in the analysis phase. While deep learning has emerged as a powerful tool capable of providing a wide range of purely data-driven solutions, it requires a substantial amount of labeled data for training and manual annotation of SR-CT datasets is impractical in practice. In this paper, we introduce a novel framework that enables automatic segmentation of large, high-resolution SR-CT datasets by eliminating the need to hand label images for deep learning training. First, we generate pseudo labels by clustering on the voxel values identifying regions in the volume with similar attenuation coefficients producing an initial semantic map. Afterwards, we train a segmentation model on the pseudo labels before utilizing the Unbiased Teacher approach to self-correct them ensuring accurate final segmentations. We find our approach improves pixel-wise accuracy and Mean Intersection over Union by 13.31% and 15.94%, respectively, over the baseline pseudo labels when using a sodium manganate SR-CT sample. Additionally, we extensively evaluate the different components of our workflow including segmentation model, loss function, pseudo labeling strategy, and input type. Finally, we evaluate our approach on two additional samples highlighting our framework’s ability to produce segmentations that are considerably better than the original pseudo labels.