AbdomenAtlas-8K: Annotating 8,000 CT Volumes for Multi-Organ Segmentation in Three Weeks

Published: 26 Sept 2023, Last Modified: 02 Nov 2023NeurIPS 2023 Datasets and Benchmarks PosterEveryoneRevisionsBibTeX
Keywords: Organ Segmentation, Active Learning, Interactive Segmentation, Medical Image Analysis
TL;DR: We introduce AbdomenAtlas-8K, a substantial multi-organ dataset with the spleen, liver, kidneys, stomach, gallbladder, pancreas, aorta, and IVC annotated in 8,448 CT volumes, totaling 3.2 million CT slices.
Abstract: Annotating medical images, particularly for organ segmentation, is laborious and time-consuming. For example, annotating an abdominal organ requires an estimated rate of 30-60 minutes per CT volume based on the expertise of an annotator and the size, visibility, and complexity of the organ. Therefore, publicly available datasets for multi-organ segmentation are often limited in data size and organ diversity. This paper proposes an active learning procedure to expedite the annotation process for organ segmentation and creates the largest multi-organ dataset (by far) with the spleen, liver, kidneys, stomach, gallbladder, pancreas, aorta, and IVC annotated in 8,448 CT volumes, equating to 3.2 million slices. The conventional annotation methods would take an experienced annotator up to 1,600 weeks (or roughly 30.8 years) to complete this task. In contrast, our annotation procedure has accomplished this task in three weeks (based on an 8-hour workday, five days a week) while maintaining a similar or even better annotation quality. This achievement is attributed to three unique properties of our method: (1) label bias reduction using multiple pre-trained segmentation models, (2) effective error detection in the model predictions, and (3) attention guidance for annotators to make corrections on the most salient errors. Furthermore, we summarize the taxonomy of common errors made by AI algorithms and annotators. This allows for continuous improvement of AI and annotations, significantly reducing the annotation costs required to create large-scale datasets for a wider variety of medical imaging tasks. Code and dataset are available at https://github.com/MrGiovanni/AbdomenAtlas
Supplementary Material: pdf
Submission Number: 288