# STU-Net: Scalable and Transferable Medical Image Segmentation Models Empowered by Large-Scale Supervised Pre-training

arXiv: https://arxiv.org/abs/2304.06716 · HTML: https://mlsanity.com/paper/2304.06716/

## Key facts

- Cited by 100 papers in the map (data through 14 Oct 2026).
- Builds on 30 of its 46 references that are in the map.
- First posted on arXiv 13 Apr 2023.

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

- [Attention Is All You Need](https://mlsanity.com/paper/1706.03762/) (2017)
- [Deep Residual Learning for Image Recognition](https://mlsanity.com/paper/1512.03385/) (2015)
- [Language Models are Few-Shot Learners](https://mlsanity.com/paper/2005.14165/) (2020)
- [An Image is Worth 16x16 Words: Transformers for Image Recognition at Scale](https://mlsanity.com/paper/2010.11929/) (2020)
- [U-Net: Convolutional Networks for Biomedical Image Segmentation](https://mlsanity.com/paper/1505.04597/) (2015)
- [Swin Transformer: Hierarchical Vision Transformer using Shifted Windows](https://mlsanity.com/paper/2103.14030/) (2021)
- [Segment Anything](https://mlsanity.com/paper/2304.02643/) (2023)
- [Scaling Laws for Neural Language Models](https://mlsanity.com/paper/2001.08361/) (2020)
- [EfficientNet: Rethinking Model Scaling for Convolutional Neural Networks](https://mlsanity.com/paper/1905.11946/) (2019)
- [On the Opportunities and Risks of Foundation Models](https://mlsanity.com/paper/2108.07258/) (2021)
- [Wide Residual Networks](https://mlsanity.com/paper/1605.07146/) (2016)
- [V-Net: Fully Convolutional Neural Networks for Volumetric Medical Image Segmentation](https://mlsanity.com/paper/1606.04797/) (2016)
- [TransUNet: Transformers Make Strong Encoders for Medical Image Segmentation](https://mlsanity.com/paper/2102.04306/) (2021)
- [Attention U-Net: Learning Where to Look for the Pancreas](https://mlsanity.com/paper/1804.03999/) (2018)
- [Scaling Vision Transformers](https://mlsanity.com/paper/2106.04560/) (2021)
- [UNETR: Transformers for 3D Medical Image Segmentation](https://mlsanity.com/paper/2103.10504/) (2021)
- [Revisiting Unreasonable Effectiveness of Data in Deep Learning Era](https://mlsanity.com/paper/1707.02968/) (2017)
- [Swin UNETR: Swin Transformers for Semantic Segmentation of Brain Tumors in MRI Images](https://mlsanity.com/paper/2201.01266/) (2022)
- [Scaling Vision Transformers to 22 Billion Parameters](https://mlsanity.com/paper/2302.05442/) (2023)
- [The Medical Segmentation Decathlon](https://mlsanity.com/paper/2106.05735/) (2021)
- [UNet++: Redesigning Skip Connections to Exploit Multiscale Features in Image Segmentation](https://mlsanity.com/paper/1912.05074/) (2019)
- [The RSNA-ASNR-MICCAI BraTS 2021 Benchmark on Brain Tumor Segmentation and Radiogenomic Classification](https://mlsanity.com/paper/2107.02314/) (2021)
- [AMOS: A Large-Scale Abdominal Multi-Organ Benchmark for Versatile Medical Image Segmentation](https://mlsanity.com/paper/2206.08023/) (2022)
- [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)
- [The Importance of Skip Connections in Biomedical Image Segmentation](https://mlsanity.com/paper/1608.04117/) (2016)
- [DoDNet: Learning to segment multi-organ and tumors from multiple partially labeled datasets](https://mlsanity.com/paper/2011.10217/) (2020)
- [A Computed Tomography Vertebral Segmentation Dataset with Anatomical Variations and Multi-Vendor Scanner Data](https://mlsanity.com/paper/2103.06360/) (2021)
- [Medical Image Analysis on Left Atrial LGE MRI for Atrial Fibrillation Studies: A Review](https://mlsanity.com/paper/2106.09862/) (2021)
- [Exploring Vanilla U-Net for Lesion Segmentation from Whole-body FDG-PET/CT Scans](https://mlsanity.com/paper/2210.07490/) (2022)

## Built on by (most cited first, 30 of 100)

- [U-Mamba: Enhancing Long-range Dependency for Biomedical Image Segmentation](https://mlsanity.com/paper/2401.04722/) (2024)
- [Customized Segment Anything Model for Medical Image Segmentation](https://mlsanity.com/paper/2304.13785/) (2023)
- [nnU-Net Revisited: A Call for Rigorous Validation in 3D Medical Image Segmentation](https://mlsanity.com/paper/2404.09556/) (2024)
- [On the Challenges and Perspectives of Foundation Models for Medical Image Analysis](https://mlsanity.com/paper/2306.05705/) (2023)
- [SAM-Med3D: Towards General-purpose Segmentation Models for Volumetric Medical Images](https://mlsanity.com/paper/2310.15161/) (2023)
- [AbdomenAtlas: A Large-Scale, Detailed-Annotated, & Multi-Center Dataset for Efficient Transfer Learning and Open Algorithmic Benchmarking](https://mlsanity.com/paper/2407.16697/) (2024)
- [SA-Med2D-20M Dataset: Segment Anything in 2D Medical Imaging with 20 Million masks](https://mlsanity.com/paper/2311.11969/) (2023)
- [AbdomenAtlas-8K: Annotating 8,000 CT Volumes for Multi-Organ Segmentation in Three Weeks](https://mlsanity.com/paper/2305.09666/) (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)
- [Revisiting MAE pre-training for 3D medical image segmentation](https://mlsanity.com/paper/2410.23132/) (2024)
- [Touchstone Benchmark: Are We on the Right Way for Evaluating AI Algorithms for Medical Segmentation?](https://mlsanity.com/paper/2411.03670/) (2024)
- [Interactive Medical Image Segmentation: A Benchmark Dataset and Baseline](https://mlsanity.com/paper/2411.12814/) (2024)
- [SegRap2023: A Benchmark of Organs-at-Risk and Gross Tumor Volume Segmentation for Radiotherapy Planning of Nasopharyngeal Carcinoma](https://mlsanity.com/paper/2312.09576/) (2023)
- [MIS-FM: 3D Medical Image Segmentation using Foundation Models Pretrained on a Large-Scale Unannotated Dataset](https://mlsanity.com/paper/2306.16925/) (2023)
- [M4oE: A Foundation Model for Medical Multimodal Image Segmentation with Mixture of Experts](https://mlsanity.com/paper/2405.09446/) (2024)
- [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)
- [Automatic Organ and Pan-cancer Segmentation in Abdomen CT: the FLARE 2023 Challenge](https://mlsanity.com/paper/2408.12534/) (2024)
- [How Well Do Supervised 3D Models Transfer to Medical Imaging Tasks?](https://mlsanity.com/paper/2501.11253/) (2025)
- [Medical Multimodal Foundation Models in Clinical Diagnosis and Treatment: Applications, Challenges, and Future Directions](https://mlsanity.com/paper/2412.02621/) (2024)
- [Analysis of the BraTS 2023 Intracranial Meningioma Segmentation Challenge](https://mlsanity.com/paper/2405.09787/) (2024)
- [Deep Rib Fracture Instance Segmentation and Classification from CT on the RibFrac Challenge](https://mlsanity.com/paper/2402.09372/) (2024)
- [Exploring the Effectiveness of Object-Centric Representations in Visual Question Answering: Comparative Insights with Foundation Models](https://mlsanity.com/paper/2407.15589/) (2024)
- [Scaling Tumor Segmentation: Best Lessons from Real and Synthetic Data](https://mlsanity.com/paper/2510.14831/) (2025)
- [SAM-Med3D-MoE: Towards a Non-Forgetting Segment Anything Model via Mixture of Experts for 3D Medical Image Segmentation](https://mlsanity.com/paper/2407.04938/) (2024)
- [SegAnyPET: Universal Promptable Segmentation from Positron Emission Tomography Images](https://mlsanity.com/paper/2502.14351/) (2025)
- [AnatoMask: Enhancing Medical Image Segmentation with Reconstruction-guided Self-masking](https://mlsanity.com/paper/2407.06468/) (2024)
- [BraTS orchestrator : Democratizing and Disseminating state-of-the-art brain tumor image analysis](https://mlsanity.com/paper/2506.13807/) (2025)

## Abstract (arXiv)

Large-scale models pre-trained on large-scale datasets have profoundly advanced the development of deep learning. However, the state-of-the-art models for medical image segmentation are still small-scale, with their parameters only in the tens of millions. Further scaling them up to higher orders of magnitude is rarely explored. An overarching goal of exploring large-scale models is to train them on large-scale medical segmentation datasets for better transfer capacities. In this work, we design a series of Scalable and Transferable U-Net (STU-Net) models, with parameter sizes ranging from 14 million to 1.4 billion. Notably, the 1.4B STU-Net is the largest medical image segmentation model to date. Our STU-Net is based on nnU-Net framework due to its popularity and impressive performance. We first refine the default convolutional blocks in nnU-Net to make them scalable. Then, we empirically evaluate different scaling combinations of network depth and width, discovering that it is optimal to scale model depth and width together. We train our scalable STU-Net models on a large-scale TotalSegmentator dataset and find that increasing model size brings a stronger performance gain. This observation reveals that a large model is promising in medical image segmentation. Furthermore, we evaluate the transferability of our model on 14 downstream datasets for direct inference and 3 datasets for further fine-tuning, covering various modalities and segmentation targets. We observe good performance of our pre-trained model in both direct inference and fine-tuning. The code and pre-trained models are available at https://github.com/Ziyan-Huang/STU-Net.