# Developing Foundation Models for Universal Segmentation from 3D Whole-Body Positron Emission Tomography

arXiv: https://arxiv.org/abs/2603.11627 · HTML: https://mlsanity.com/paper/2603.11627/

## Key facts

- Cited by 1 papers in the map (data through 14 Oct 2026).
- Builds on 20 of its 50 references that are in the map.
- First posted on arXiv 12 Mar 2026.

## Builds on (most cited first, 20 of 20)

- [Segment Anything](https://mlsanity.com/paper/2304.02643/) (2023)
- [Swin UNETR: Swin Transformers for Semantic Segmentation of Brain Tumors in MRI Images](https://mlsanity.com/paper/2201.01266/) (2022)
- [TotalSegmentator: robust segmentation of 104 anatomical structures in CT images](https://mlsanity.com/paper/2208.05868/) (2022)
- [3D MRI brain tumor segmentation using autoencoder regularization](https://mlsanity.com/paper/1810.11654/) (2018)
- [nnU-Net Revisited: A Call for Rigorous Validation in 3D Medical Image Segmentation](https://mlsanity.com/paper/2404.09556/) (2024)
- [AbdomenCT-1K: Is Abdominal Organ Segmentation A Solved Problem?](https://mlsanity.com/paper/2010.14808/) (2020)
- [Metrics reloaded: Recommendations for image analysis validation](https://mlsanity.com/paper/2206.01653/) (2022)
- [Medical Image Segmentation Review: The success of U-Net](https://mlsanity.com/paper/2211.14830/) (2022)
- [BiomedParse: a biomedical foundation model for image parsing of everything everywhere all at once](https://mlsanity.com/paper/2405.12971/) (2024)
- [SAM-Med3D: Towards General-purpose Segmentation Models for Volumetric Medical Images](https://mlsanity.com/paper/2310.15161/) (2023)
- [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)
- [Segment Anything Model for Medical Image Segmentation: Current Applications and Future Directions](https://mlsanity.com/paper/2401.03495/) (2024)
- [SegVol: Universal and Interactive Volumetric Medical Image Segmentation](https://mlsanity.com/paper/2311.13385/) (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)
- [VISTA3D: A Unified Segmentation Foundation Model For 3D Medical Imaging](https://mlsanity.com/paper/2406.05285/) (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)
- [Bridging 2D and 3D Segmentation Networks for Computation Efficient Volumetric Medical Image Segmentation: An Empirical Study of 2.5D Solutions](https://mlsanity.com/paper/2010.06163/) (2020)
- [Universality Reconsidered: Rethinking the Validation of Foundation Models for General-Purpose 3D Medical Segmentation](https://mlsanity.com/paper/2602.07643/) (2026)

## Built on by (most cited first, 1 of 1)

- [MetaStructAtlas: A Grounded 3D Vision-Language Dataset and Benchmark for Functional and Structural Reasoning in Whole-Body PET/CT](https://mlsanity.com/paper/2609.03690/) (2026)

## Abstract (arXiv)

Positron emission tomography (PET) is a key nuclear medicine imaging modality that visualizes radiotracer distributions to quantify in vivo physiological and metabolic processes, playing an irreplaceable role in disease management. Despite its clinical importance, the development of deep learning models for quantitative PET image analysis remains severely limited, driven by both the inherent segmentation challenge from PET's paucity of anatomical contrast and the high costs of data acquisition and annotation. To bridge this gap, we develop generalist foundational models for universal segmentation from 3D whole-body PET imaging. We first build the largest and most comprehensive PET dataset to date, comprising 11041 3D whole-body PET scans with 59831 segmentation masks for model development. Based on this dataset, we present SegAnyPET, an innovative foundational model with general-purpose applicability to diverse segmentation tasks. Built on a 3D architecture with a prompt engineering strategy for mask generation, SegAnyPET enables universal and scalable organ and lesion segmentation, supports efficient human correction with minimal effort, and enables a clinical human-in-the-loop workflow. Extensive evaluations on multi-center, multi-tracer, multi-disease datasets demonstrate that SegAnyPET achieves strong zero-shot performance across a wide range of segmentation tasks, highlighting its potential to advance the clinical applications of molecular imaging.