title: UKBOB: One Billion MRI Labeled Masks for Generalizable 3D Medical Image
    Segmentation
summary: In medical imaging, the primary challenge is collecting large-scale labeled
  data due to privacy concerns, logistics, and high labeling costs. In this work,
  we present the UK Biobank Organs and Bones (UKBOB), the largest labeled dataset
  of body organs, comprising 51,761 MRI 3D samples (equivalent to 17.9 million 2D
  images) and more than 1.37 billion 2D segmentation masks of 72 organs, all
  based on the UK Biobank MRI dataset. We utilize automatic labeling, introduce
  an automated label cleaning pipeline with organ-specific filters, and manually
  annotate a subset of 300 MRIs with 11 abdominal classes to validate the quality
  (referred to as 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 demonstrating zero-shot generalization of trained
  models on the filtered UKBOB to other small labeled datasets from similar
  domains (e.g., abdominal MRI). To further mitigate the effect of noisy labels,
  we propose a novel method called 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 the Swin-UNetr architecture,
  achieving state-of-the-art results in several benchmarks in 3D medical imaging,
  including the BRATS brain MRI tumor challenge (with a 0.4% improvement) and the
  BTCV abdominal CT scan benchmark (with a 1.3% improvement). The pre-trained
  models and the code are available at https://emmanuelleb985.github.io/ukbob ,
  and the filtered labels will be made available with the UK Biobank.
paper_authors._id: 67fd59c56a3c533dc1b21c91
paper_authors.name: Emmanuelle Bourigault
paper_authors._id: 67fd59c56a3c533dc1b21c92
paper_authors.name: Amir Jamaludin
paper_authors._id: 67fd59c56a3c533dc1b21c93
paper_authors.name: Abdullah Hamdi
paper_title: UKBOB: One Billion MRI Labeled Masks for Generalizable 3D Medical Image
    Segmentation
paper_summary: In medical imaging, the primary challenge is collecting large-scale labeled
  data due to privacy concerns, logistics, and high labeling costs. In this work,
  we present the UK Biobank Organs and Bones (UKBOB), the largest labeled dataset
  of body organs, comprising 51,761 MRI 3D samples (equivalent to 17.9 million 2D
  images) and more than 1.37 billion 2D segmentation masks of 72 organs, all
  based on the UK Biobank MRI dataset. We utilize automatic labeling, introduce
  an automated label cleaning pipeline with organ-specific filters, and manually
  annotate a subset of 300 MRIs with 11 abdominal classes to validate the quality
  (referred to as 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 demonstrating zero-shot generalization of trained
  models on the filtered UKBOB to other small labeled datasets from similar
  domains (e.g., abdominal MRI). To further mitigate the effect of noisy labels,
  we propose a novel method called 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 the Swin-UNetr architecture,
  achieving state-of-the-art results in several benchmarks in 3D medical imaging,
  including the BRATS brain MRI tumor challenge (with a 0.4% improvement) and the
  BTCV abdominal CT scan benchmark (with a 1.3% improvement). The pre-trained
  models and the code are available at https://emmanuelleb985.github.io/ukbob ,
  and the filtered labels will be made available with the UK Biobank.
paper_ai_summary: UKBOB, a large dataset of labeled body organs, enhances 3D medical image segmentation using automatic labeling, a cleaning pipeline, and Entropy Test-time Adaptation, improving performance in benchmarks like BRATS and BTCV.
paper_ai_keywords: UKBOB MRI 3D samples segmentation masks automated label cleaning Entropy Test-time Adaptation (ETTA) Swin-BOB Swin-UNetr 3D medical image segmentation BRATS BTCV