# AbdomenAtlas: A Large-Scale, Detailed-Annotated, & Multi-Center Dataset for Efficient Transfer Learning and Open Algorithmic Benchmarking

arXiv: https://arxiv.org/abs/2407.16697 · HTML: https://mlsanity.com/paper/2407.16697/

## Key facts

- Cited by 65 papers in the map (data through 14 Oct 2026).
- Builds on 44 of its 69 references that are in the map.
- First posted on arXiv 23 Jul 2024.

## Builds on (most cited first, 30 of 44)

- [Language Models are Few-Shot Learners](https://mlsanity.com/paper/2005.14165/) (2020)
- [U-Net: Convolutional Networks for Biomedical Image Segmentation](https://mlsanity.com/paper/1505.04597/) (2015)
- [Microsoft COCO: Common Objects in Context](https://mlsanity.com/paper/1405.0312/) (2014)
- [LAION-5B: An open large-scale dataset for training next generation image-text models](https://mlsanity.com/paper/2210.08402/) (2022)
- [On the Opportunities and Risks of Foundation Models](https://mlsanity.com/paper/2108.07258/) (2021)
- [Shortcut Learning in Deep Neural Networks](https://mlsanity.com/paper/2004.07780/) (2020)
- [Swin UNETR: Swin Transformers for Semantic Segmentation of Brain Tumors in MRI Images](https://mlsanity.com/paper/2201.01266/) (2022)
- [The Medical Segmentation Decathlon](https://mlsanity.com/paper/2106.05735/) (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)
- [3D MRI brain tumor segmentation using autoencoder regularization](https://mlsanity.com/paper/1810.11654/) (2018)
- [Med3D: Transfer Learning for 3D Medical Image Analysis](https://mlsanity.com/paper/1904.00625/) (2019)
- [AbdomenCT-1K: Is Abdominal Organ Segmentation A Solved Problem?](https://mlsanity.com/paper/2010.14808/) (2020)
- [CLIP-Driven Universal Model for Organ Segmentation and Tumor Detection](https://mlsanity.com/paper/2301.00785/) (2023)
- [Sequential Modeling Enables Scalable Learning for Large Vision Models](https://mlsanity.com/paper/2312.00785/) (2023)
- [DeepOrgan: Multi-level Deep Convolutional Networks for Automated Pancreas Segmentation](https://mlsanity.com/paper/1506.06448/) (2015)
- [Models Genesis: Generic Autodidactic Models for 3D Medical Image Analysis](https://mlsanity.com/paper/1908.06912/) (2019)
- [Data Determines Distributional Robustness in Contrastive Language Image Pre-training (CLIP)](https://mlsanity.com/paper/2205.01397/) (2022)
- [On the Challenges and Perspectives of Foundation Models for Medical Image Analysis](https://mlsanity.com/paper/2306.05705/) (2023)
- [Recent advances and clinical applications of deep learning in medical image analysis](https://mlsanity.com/paper/2105.13381/) (2021)
- [Merlin: A Computed Tomography Vision-Language Foundation Model and Dataset](https://mlsanity.com/paper/2406.06512/) (2024)
- [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)
- [Towards Generalizable Tumor Synthesis](https://mlsanity.com/paper/2402.19470/) (2024)
- [Label-Free Liver Tumor Segmentation](https://mlsanity.com/paper/2303.14869/) (2023)
- [UniMiSS: Universal Medical Self-Supervised Learning via Breaking Dimensionality Barrier](https://mlsanity.com/paper/2112.09356/) (2021)
- [Unleashing the Strengths of Unlabeled Data in Pan-cancer Abdominal Organ Quantification: the FLARE22 Challenge](https://mlsanity.com/paper/2308.05862/) (2023)
- [Abdominal multi-organ segmentation with organ-attention networks and statistical fusion](https://mlsanity.com/paper/1804.08414/) (2018)
- [Learning Fixed Points in Generative Adversarial Networks: From Image-to-Image Translation to Disease Detection and Localization](https://mlsanity.com/paper/1908.06965/) (2019)
- [SQUID: Deep Feature In-Painting for Unsupervised Anomaly Detection](https://mlsanity.com/paper/2111.13495/) (2021)

## Built on by (most cited first, 30 of 65)

- [Med-R1: Reinforcement Learning for Generalizable Medical Reasoning in Vision-Language Models](https://mlsanity.com/paper/2503.13939/) (2025)
- [RadGPT: Constructing 3D Image-Text Tumor Datasets](https://mlsanity.com/paper/2501.04678/) (2025)
- [Touchstone Benchmark: Are We on the Right Way for Evaluating AI Algorithms for Medical Segmentation?](https://mlsanity.com/paper/2411.03670/) (2024)
- [Learning General-Purpose Biomedical Volume Representations using Randomized Synthesis](https://mlsanity.com/paper/2411.02372/) (2024)
- [Primus: Enforcing Attention Usage for 3D Medical Image Segmentation](https://mlsanity.com/paper/2503.01835/) (2025)
- [Automatic Organ and Pan-cancer Segmentation in Abdomen CT: the FLARE 2023 Challenge](https://mlsanity.com/paper/2408.12534/) (2024)
- [PanTS: The Pancreatic Tumor Segmentation Dataset](https://mlsanity.com/paper/2507.01291/) (2025)
- [ASIGN: An Anatomy-aware Spatial Imputation Graphic Network for 3D Spatial Transcriptomics](https://mlsanity.com/paper/2412.03026/) (2024)
- [MedSegFactory: Text-Guided Generation of Medical Image-Mask Pairs](https://mlsanity.com/paper/2504.06897/) (2025)
- [Raptor: Scalable Train-Free Embeddings for 3D Medical Volumes Leveraging Pretrained 2D Foundation Models](https://mlsanity.com/paper/2507.08254/) (2025)
- [Scaling Tumor Segmentation: Best Lessons from Real and Synthetic Data](https://mlsanity.com/paper/2510.14831/) (2025)
- [Analyzing Tumors by Synthesis](https://mlsanity.com/paper/2409.06035/) (2024)
- [Learning Segmentation from Radiology Reports](https://mlsanity.com/paper/2507.05582/) (2025)
- [Scaling Artificial Intelligence for Multi-Tumor Early Detection with More Reports, Fewer Masks](https://mlsanity.com/paper/2510.14803/) (2025)
- [Calibration and Uncertainty for multiRater Volume Assessment in multiorgan Segmentation (CURVAS) challenge results](https://mlsanity.com/paper/2505.08685/) (2025)
- [Scaling Self-Supervised and Cross-Modal Pretraining for Volumetric CT Transformers](https://mlsanity.com/paper/2511.17209/) (2025)
- [X-LRM: X-ray Large Reconstruction Model for Extremely Sparse-View Computed Tomography Recovery in One Second](https://mlsanity.com/paper/2503.06382/) (2025)
- [MSWAL: 3D Multi-class Segmentation of Whole Abdominal Lesions Dataset](https://mlsanity.com/paper/2503.13560/) (2025)
- [X-GRM: Large Gaussian Reconstruction Model for Sparse-view X-rays to Computed Tomography](https://mlsanity.com/paper/2505.15235/) (2025)
- [Are Pixel-Wise Metrics Reliable for Sparse-View Computed Tomography Reconstruction?](https://mlsanity.com/paper/2506.02093/) (2025)
- [RadImageNet-VQA: A Large-Scale CT and MRI Dataset for Radiologic Visual Question Answering](https://mlsanity.com/paper/2512.17396/) (2025)
- [Photon: Speedup Volume Understanding with Efficient Multimodal Large Language Models](https://mlsanity.com/paper/2603.25155/) (2026)
- [Expectation-Maximization as the Engine of Scalable Medical Intelligence](https://mlsanity.com/paper/2501.03410/) (2025)
- [MedNeXt-v2: Scaling 3D ConvNeXts for Large-Scale Supervised Representation Learning in Medical Image Segmentation](https://mlsanity.com/paper/2512.17774/) (2025)
- [Label Critic: Design Data Before Models](https://mlsanity.com/paper/2411.02753/) (2024)
- [Efficient MedSAMs: Segment Anything in Medical Images on Laptop](https://mlsanity.com/paper/2412.16085/) (2024)
- [RadThinking: A Dataset for Longitudinal Clinical Reasoning in Radiology](https://mlsanity.com/paper/2605.10761/) (2026)
- [Mamba Goes HoME: Hierarchical Soft Mixture-of-Experts for 3D Medical Image Segmentation](https://mlsanity.com/paper/2507.06363/) (2025)
- [See More, Change Less: Anatomy-Aware Diffusion for Contrast Enhancement](https://mlsanity.com/paper/2512.07251/) (2025)
- [Beyond Adapter Retrieval: Latent Geometry-Preserving Composition via Sparse Task Projection](https://mlsanity.com/paper/2410.09908/) (2024)

## Abstract (arXiv)

We introduce the largest abdominal CT dataset (termed AbdomenAtlas) of 20,460 three-dimensional CT volumes sourced from 112 hospitals across diverse populations, geographies, and facilities. AbdomenAtlas provides 673K high-quality masks of anatomical structures in the abdominal region annotated by a team of 10 radiologists with the help of AI algorithms. We start by having expert radiologists manually annotate 22 anatomical structures in 5,246 CT volumes. Following this, a semi-automatic annotation procedure is performed for the remaining CT volumes, where radiologists revise the annotations predicted by AI, and in turn, AI improves its predictions by learning from revised annotations. Such a large-scale, detailed-annotated, and multi-center dataset is needed for two reasons. Firstly, AbdomenAtlas provides important resources for AI development at scale, branded as large pre-trained models, which can alleviate the annotation workload of expert radiologists to transfer to broader clinical applications. Secondly, AbdomenAtlas establishes a large-scale benchmark for evaluating AI algorithms -- the more data we use to test the algorithms, the better we can guarantee reliable performance in complex clinical scenarios. An ISBI & MICCAI challenge named BodyMaps: Towards 3D Atlas of Human Body was launched using a subset of our AbdomenAtlas, aiming to stimulate AI innovation and to benchmark segmentation accuracy, inference efficiency, and domain generalizability. We hope our AbdomenAtlas can set the stage for larger-scale clinical trials and offer exceptional opportunities to practitioners in the medical imaging community. Codes, models, and datasets are available at https://www.zongweiz.com/dataset