# Improving Cross-Site Whole-Heart Segmentation

arXiv: https://arxiv.org/abs/2608.25109 · HTML: https://mlsanity.com/paper/2608.25109/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 17 of its 25 references that are in the map.
- First posted on arXiv 25 Aug 2026.

## Builds on (most cited first, 17 of 17)

- [TotalSegmentator: robust segmentation of 104 anatomical structures in CT images](https://mlsanity.com/paper/2208.05868/) (2022)
- [SynthSeg: Segmentation of brain MRI scans of any contrast and resolution without retraining](https://mlsanity.com/paper/2107.09559/) (2021)
- [Boundary loss for highly unbalanced segmentation](https://mlsanity.com/paper/1812.07032/) (2018)
- [Causality-inspired Single-source Domain Generalization for Medical Image Segmentation](https://mlsanity.com/paper/2111.12525/) (2021)
- [Anatomically Constrained Neural Networks (ACNN): Application to Cardiac Image Enhancement and Segmentation](https://mlsanity.com/paper/1705.08302/) (2017)
- [SAM-Med3D: Towards General-purpose Segmentation Models for Volumetric Medical Images](https://mlsanity.com/paper/2310.15161/) (2023)
- [Evaluation of Algorithms for Multi-Modality Whole Heart Segmentation: An Open-Access Grand Challenge](https://mlsanity.com/paper/1902.07880/) (2019)
- [STU-Net: Scalable and Transferable Medical Image Segmentation Models Empowered by Large-Scale Supervised Pre-training](https://mlsanity.com/paper/2304.06716/) (2023)
- [MedSAM2: Segment Anything in 3D Medical Images and Videos](https://mlsanity.com/paper/2504.03600/) (2025)
- [SegVol: Universal and Interactive Volumetric Medical Image Segmentation](https://mlsanity.com/paper/2311.13385/) (2023)
- [TotalSegmentator MRI: Robust Sequence-independent Segmentation of Multiple Anatomic Structures in MRI](https://mlsanity.com/paper/2405.19492/) (2024)
- [Rethinking Data Augmentation for Single-source Domain Generalization in Medical Image Segmentation](https://mlsanity.com/paper/2211.14805/) (2022)
- [BayeSeg: Bayesian Modeling for Medical Image Segmentation with Interpretable Generalizability](https://mlsanity.com/paper/2303.01710/) (2023)
- [UU-Mamba: Uncertainty-aware U-Mamba for Cardiac Image Segmentation](https://mlsanity.com/paper/2405.17496/) (2024)
- [Robust COVID-19 Detection in CT Images with CLIP](https://mlsanity.com/paper/2403.08947/) (2024)
- [Robustly Optimized Deep Feature Decoupling Network for Fatty Liver Diseases Detection](https://mlsanity.com/paper/2406.17338/) (2024)
- [Diffusion-empowered AutoPrompt MedSAM](https://mlsanity.com/paper/2502.06817/) (2025)

## Abstract (arXiv)

Whole-heart segmentation from CT and MRI is essential for quantitative cardiac image analysis, but remains challenging under multi-center and multi-modality distribution shift. In the CARE whole-heart segmentation task, models must generalize from limited labeled sites to unseen acquisition distributions, where variation in spacing, intensity, reconstruction texture, and anatomy can degrade out-of-distribution performance. We propose a modality-routed 3D cardiac segmentation pipeline that combines TotalSegmentator-initialized nnU-Netv2 models with site-characterized, label-preserving appearance augmentation. We first characterize the available sites using measurable image properties and use this analysis to motivate candidate data-space generalization routes. The final retained recipe applies Bias Field + Bezier appearance augmentation, combining smooth spatial intensity perturbation with nonlinear intensity remapping, followed by lightweight class-wise largest-connected-component cleanup. On the primary held-out-site validation splits, the final configuration improves CT mean Dice from 0.8350 to 0.9135 and MRI mean Dice from 0.7695 to 0.7830, while also reducing HD95. These results suggest that site-motivated appearance augmentation is a practical strategy for improving cross-site robustness in limited-data whole-heart segmentation. Our code can be found in https://github.com/Purdue-M2/Improving-Cross-Site-Whole-Heart-Segmentation