UKBOB: One Billion MRI Labeled Masks for Generalizable 3D Medical Image Segmentation

In the medical imaging domain, it is a fundamental challenge to collect large-scale labeled data due to privacy, involved logistics, and the high cost of labeling medical images. In this work, we present the UK Biobank Organs and Bones (UKBOB), the largest labeled dataset of body organs of 51,761 MRI 3D samples (17.9 M 2D images) and a total of more than 1.37 billion 2D segmentation masks of 72 organs based on the UK Biobank MRI dataset. We utilize automatic labeling, filter the labels with organ-specific filters, and manually annotate a subset of 300 MRIs with 11 abdominal classes to validate the quality (UKBOB-manual). This approach allows for scaling up the dataset collection while maintaining confidence in the labels. We further confirm the validity of the labels by the zero-shot generalization of trained models on the filtered UKBOB to other small labeled datasets from a similar domain ( E.g. abdominal MRI). To further elevate the effect of the noisy labels, we propose a novel Entropy Test-time Adaptation (ETTA) to refine the segmentation output. We use UKBOB to train a foundation model (Swin-BOB) for 3D medical image segmentation based on Swin-UNetr, achieving state-of-the-art results in several benchmarks in 3D medical imaging, including BRATS brain MRI tumour challenge (+0.4% improvement), and BTCV abdominal CT scan benchmark (+1.3% improvement). Pre-trained model and our filtered labels will be made available with the UK Biobank.