# VesselBridge3D: A Foundation Model Adaptation Framework for Label-Efficient 3D Vessel Segmentation

arXiv: https://arxiv.org/abs/2602.23782 · HTML: https://mlsanity.com/paper/2602.23782/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 16 of its 27 references that are in the map.
- First posted on arXiv 27 Feb 2026.

## Builds on (most cited first, 16 of 16)

- [RoFormer: Enhanced Transformer with Rotary Position Embedding](https://mlsanity.com/paper/2104.09864/) (2021)
- [A ConvNet for the 2020s](https://mlsanity.com/paper/2201.03545/) (2022)
- [VGGT: Visual Geometry Grounded Transformer](https://mlsanity.com/paper/2503.11651/) (2025)
- [3D U-Net: Learning Dense Volumetric Segmentation from Sparse Annotation](https://mlsanity.com/paper/1606.06650/) (2016)
- [DINOv3](https://mlsanity.com/paper/2508.10104/) (2025)
- [UNETR: Transformers for 3D Medical Image Segmentation](https://mlsanity.com/paper/2103.10504/) (2021)
- [Swin UNETR: Swin Transformers for Semantic Segmentation of Brain Tumors in MRI Images](https://mlsanity.com/paper/2201.01266/) (2022)
- [MedGemma Technical Report](https://mlsanity.com/paper/2507.05201/) (2025)
- [Domain Adaptation for Medical Image Analysis: A Survey](https://mlsanity.com/paper/2102.09508/) (2021)
- [clDice -- A Novel Topology-Preserving Loss Function for Tubular Structure Segmentation](https://mlsanity.com/paper/2003.07311/) (2020)
- [Embracing Imperfect Datasets: A Review of Deep Learning Solutions for Medical Image Segmentation](https://mlsanity.com/paper/1908.10454/) (2019)
- [Self-Supervision with Superpixels: Training Few-shot Medical Image Segmentation without Annotation](https://mlsanity.com/paper/2007.09886/) (2020)
- [Unsupervised domain adaptation in brain lesion segmentation with adversarial networks](https://mlsanity.com/paper/1612.08894/) (2016)
- [DeepVesselNet: Vessel Segmentation, Centerline Prediction, and Bifurcation Detection in 3-D Angiographic Volumes](https://mlsanity.com/paper/1803.09340/) (2018)
- [Domain Generalization for Medical Image Analysis: A Review](https://mlsanity.com/paper/2310.08598/) (2023)
- [Towards automated brain aneurysm detection in TOF-MRA: open data, weak labels, and anatomical knowledge](https://mlsanity.com/paper/2103.06168/) (2021)

## Abstract (arXiv)

State-of-the-art vessel segmentation methods typically require large-scale annotated datasets and suffer from severe performance degradation under domain shifts. In clinical practice, however, acquiring extensive annotations for every new scanner or protocol is unfeasible. To address this, we propose VesselBridge3D, a foundation model adaptation framework that bridges frozen vision foundation models and volumetric vessel segmentation through lightweight 3D adaptation modules. The framework combines a lightweight 3D Adapter, a multi-scale 3D Aggregator, and Z-channel embedding for efficient adaptation to volumetric medical images. We instantiate VesselBridge3D with three frozen foundation encoders (DINOv3, MedSAM, and MedGemma) and evaluate it on the TopCoW (ID) and Lausanne (OOD) datasets. In the extreme low-data regime with 5 training samples, our method achieved a Dice score of 43.42%, marking a 30% relative improvement over the state-of-the-art nnU-Net (33.41%) and outperforming other Transformer-based baselines by up to 45%. The proposed framework was effective across all evaluated frozen foundation encoders, with DINOv3 yielding the best performance in the most label-efficient settings. Furthermore, in the out-of-distribution setting, our model demonstrated superior robustness, achieving a 50% relative improvement over nnU-Net (21.37% vs. 14.22%), which suffered from severe domain overfitting. Ablation studies confirmed the effectiveness of the proposed 3D adaptation modules. Our results demonstrate that VesselBridge3D is an effective framework for label-efficient 3D vessel segmentation under data scarcity and domain shifts.