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

arXiv: https://arxiv.org/abs/2305.09666 · HTML: https://mlsanity.com/paper/2305.09666/

## Key facts

- Cited by 52 papers in the map (data through 14 Oct 2026).
- Builds on 42 of its 109 references that are in the map.
- First posted on arXiv 16 May 2023.

## Builds on (most cited first, 30 of 42)

- [U-Net: Convolutional Networks for Biomedical Image Segmentation](https://mlsanity.com/paper/1505.04597/) (2015)
- [Segment Anything](https://mlsanity.com/paper/2304.02643/) (2023)
- [CheXpert: A Large Chest Radiograph Dataset with Uncertainty Labels and Expert Comparison](https://mlsanity.com/paper/1901.07031/) (2019)
- [UNETR: Transformers for 3D Medical Image Segmentation](https://mlsanity.com/paper/2103.10504/) (2021)
- [Deep Bayesian Active Learning with Image Data](https://mlsanity.com/paper/1703.02910/) (2017)
- [The Medical Segmentation Decathlon](https://mlsanity.com/paper/2106.05735/) (2021)
- [A Survey of Deep Active Learning](https://mlsanity.com/paper/2009.00236/) (2020)
- [The RSNA-ASNR-MICCAI BraTS 2021 Benchmark on Brain Tumor Segmentation and Radiogenomic Classification](https://mlsanity.com/paper/2107.02314/) (2021)
- [The Liver Tumor Segmentation Benchmark (LiTS)](https://mlsanity.com/paper/1901.04056/) (2019)
- [Self-Supervised Pre-Training of Swin Transformers for 3D Medical Image Analysis](https://mlsanity.com/paper/2111.14791/) (2021)
- [A large annotated medical image dataset for the development and evaluation of segmentation algorithms](https://mlsanity.com/paper/1902.09063/) (2019)
- [AMOS: A Large-Scale Abdominal Multi-Organ Benchmark for Versatile Medical Image Segmentation](https://mlsanity.com/paper/2206.08023/) (2022)
- [3D MRI brain tumor segmentation using autoencoder regularization](https://mlsanity.com/paper/1810.11654/) (2018)
- [PadChest: A large chest x-ray image dataset with multi-label annotated reports](https://mlsanity.com/paper/1901.07441/) (2019)
- [Embracing Imperfect Datasets: A Review of Deep Learning Solutions for Medical Image Segmentation](https://mlsanity.com/paper/1908.10454/) (2019)
- [AbdomenCT-1K: Is Abdominal Organ Segmentation A Solved Problem?](https://mlsanity.com/paper/2010.14808/) (2020)
- [The state of the art in kidney and kidney tumor segmentation in contrast-enhanced CT imaging: Results of the KiTS19 Challenge](https://mlsanity.com/paper/1912.01054/) (2019)
- [DeepOrgan: Multi-level Deep Convolutional Networks for Automated Pancreas Segmentation](https://mlsanity.com/paper/1506.06448/) (2015)
- [A Survey on Active Learning and Human-in-the-Loop Deep Learning for Medical Image Analysis](https://mlsanity.com/paper/1910.02923/) (2019)
- [Suggestive Annotation: A Deep Active Learning Framework for Biomedical Image Segmentation](https://mlsanity.com/paper/1706.04737/) (2017)
- [STU-Net: Scalable and Transferable Medical Image Segmentation Models Empowered by Large-Scale Supervised Pre-training](https://mlsanity.com/paper/2304.06716/) (2023)
- [DoDNet: Learning to segment multi-organ and tumors from multiple partially labeled datasets](https://mlsanity.com/paper/2011.10217/) (2020)
- [Efficient Active Learning for Image Classification and Segmentation using a Sample Selection and Conditional Generative Adversarial Network](https://mlsanity.com/paper/1806.05473/) (2018)
- [Active Learning by Feature Mixing](https://mlsanity.com/paper/2203.07034/) (2022)
- [Towards Fewer Annotations: Active Learning via Region Impurity and Prediction Uncertainty for Domain Adaptive Semantic Segmentation](https://mlsanity.com/paper/2111.12940/) (2021)
- [Label-Free Liver Tumor Segmentation](https://mlsanity.com/paper/2303.14869/) (2023)
- [Towards Robust and Reproducible Active Learning Using Neural Networks](https://mlsanity.com/paper/2002.09564/) (2020)
- [CTSpine1K: A Large-Scale Dataset for Spinal Vertebrae Segmentation in Computed Tomography](https://mlsanity.com/paper/2105.14711/) (2021)
- [Learning from Multiple Datasets with Heterogeneous and Partial Labels for Universal Lesion Detection in CT](https://mlsanity.com/paper/2009.02577/) (2020)
- [Making Your First Choice: To Address Cold Start Problem in Vision Active Learning](https://mlsanity.com/paper/2210.02442/) (2022)

## Built on by (most cited first, 30 of 52)

- [Towards Generalizable Tumor Synthesis](https://mlsanity.com/paper/2402.19470/) (2024)
- [Large-Vocabulary Segmentation for Medical Images with Text Prompts](https://mlsanity.com/paper/2312.17183/) (2023)
- [nnInteractive: Redefining 3D Promptable Segmentation](https://mlsanity.com/paper/2503.08373/) (2025)
- [CLIP in Medical Imaging: A Survey](https://mlsanity.com/paper/2312.07353/) (2023)
- [Large-Scale 3D Medical Image Pre-training with Geometric Context Priors](https://mlsanity.com/paper/2410.09890/) (2024)
- [CT-GLIP: 3D Grounded Language-Image Pretraining with CT Scans and Radiology Reports for Full-Body Scenarios](https://mlsanity.com/paper/2404.15272/) (2024)
- [Interactive Medical Image Segmentation: A Benchmark Dataset and Baseline](https://mlsanity.com/paper/2411.12814/) (2024)
- [Learning General-Purpose Biomedical Volume Representations using Randomized Synthesis](https://mlsanity.com/paper/2411.02372/) (2024)
- [Deep Interactive Segmentation of Medical Images: A Systematic Review and Taxonomy](https://mlsanity.com/paper/2311.13964/) (2023)
- [An OpenMind for 3D medical vision self-supervised learning](https://mlsanity.com/paper/2412.17041/) (2024)
- [Primus: Enforcing Attention Usage for 3D Medical Image Segmentation](https://mlsanity.com/paper/2503.01835/) (2025)
- [Medical Multimodal Foundation Models in Clinical Diagnosis and Treatment: Applications, Challenges, and Future Directions](https://mlsanity.com/paper/2412.02621/) (2024)
- [FreeTumor: Advance Tumor Segmentation via Large-Scale Tumor Synthesis](https://mlsanity.com/paper/2406.01264/) (2024)
- [mathrmSAMMed: A medical image annotation framework based on large vision model](https://mlsanity.com/paper/2307.05617/) (2023)
- [ASIGN: An Anatomy-aware Spatial Imputation Graphic Network for 3D Spatial Transcriptomics](https://mlsanity.com/paper/2412.03026/) (2024)
- [LesionLocator: Zero-Shot Universal Tumor Segmentation and Tracking in 3D Whole-Body Imaging](https://mlsanity.com/paper/2502.20985/) (2025)
- [VIBESegmentator: Full Body MRI Segmentation for the NAKO and UK Biobank](https://mlsanity.com/paper/2406.00125/) (2024)
- [Analyzing Tumors by Synthesis](https://mlsanity.com/paper/2409.06035/) (2024)
- [Large Scale MRI Collection and Segmentation of Cirrhotic Liver](https://mlsanity.com/paper/2410.16296/) (2024)
- [UniBiomed: A Universal Foundation Model for Grounded Biomedical Image Interpretation](https://mlsanity.com/paper/2504.21336/) (2025)
- [Medical Image Retrieval Using Pretrained Embeddings](https://mlsanity.com/paper/2311.13547/) (2023)
- [Conformal Risk Control for Semantic Uncertainty Quantification in Computed Tomography](https://mlsanity.com/paper/2503.00136/) (2025)
- [Active Label Correction for Semantic Segmentation with Foundation Models](https://mlsanity.com/paper/2403.10820/) (2024)
- [Calibration and Uncertainty for multiRater Volume Assessment in multiorgan Segmentation (CURVAS) challenge results](https://mlsanity.com/paper/2505.08685/) (2025)
- [DeepSparse: A Foundation Model for Sparse-View CBCT Reconstruction](https://mlsanity.com/paper/2505.02628/) (2025)
- [MedNeXt-v2: Scaling 3D ConvNeXts for Large-Scale Supervised Representation Learning in Medical Image Segmentation](https://mlsanity.com/paper/2512.17774/) (2025)
- [UKBOB: One Billion MRI Labeled Masks for Generalizable 3D Medical Image Segmentation](https://mlsanity.com/paper/2504.06908/) (2025)
- [Less is More Tokens: Efficient Math Reasoning via Difficulty-Aware Chain-of-Thought Distillation](https://mlsanity.com/paper/2509.05226/) (2025)
- [FlexiD-Fuse: Flexible number of inputs multi-modal medical image fusion based on diffusion model](https://mlsanity.com/paper/2509.09456/) (2025)
- [Enhancing Cost Efficiency in Active Learning with Candidate Set Query](https://mlsanity.com/paper/2502.06209/) (2025)

## Abstract (arXiv)

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 method 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 method 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 revision of both AI and annotations and significantly reduces the annotation costs required to create large-scale datasets for a wider variety of medical imaging tasks.