# Automatically Segmenting the Left Atrium from Cardiac Images Using Successive 3D U-Nets and a Contour Loss

arXiv: https://arxiv.org/abs/1812.02518 · HTML: https://mlsanity.com/paper/1812.02518/

## Key facts

- Cited by 8 papers in the map (data through 14 Oct 2026).
- First posted on arXiv 6 Dec 2018.

## Built on by (most cited first, 8 of 8)

- [Medical Image Analysis on Left Atrial LGE MRI for Atrial Fibrillation Studies: A Review](https://mlsanity.com/paper/2106.09862/) (2021)
- [Explicit Differentiable Slicing and Global Deformation for Cardiac Mesh Reconstruction](https://mlsanity.com/paper/2409.02070/) (2024)
- [Inner-ear Augmented Metal Artifact Reduction with Simulation-based 3D Generative Adversarial Networks](https://mlsanity.com/paper/2104.12510/) (2021)
- [Towards contrast-agnostic soft segmentation of the spinal cord](https://mlsanity.com/paper/2310.15402/) (2023)
- [A Dense Siamese U-Net trained with Edge Enhanced 3D IOU Loss for Image Co-segmentation](https://mlsanity.com/paper/2108.07491/) (2021)
- [Multi-Modality Cardiac Image Analysis with Deep Learning](https://mlsanity.com/paper/2111.04736/) (2021)
- [TMS-Net: A Segmentation Network Coupled With A Run-time Quality Control Method For Robust Cardiac Image Segmentation](https://mlsanity.com/paper/2212.10877/) (2022)
- [Advances in Medical Image Segmentation: A Comprehensive Survey with a Focus on Lumbar Spine Applications](https://mlsanity.com/paper/2510.03318/) (2025)

## Abstract (arXiv)

Radiological imaging offers effective measurement of anatomy, which is useful in disease diagnosis and assessment. Previous study has shown that the left atrial wall remodeling can provide information to predict treatment outcome in atrial fibrillation. Nevertheless, the segmentation of the left atrial structures from medical images is still very time-consuming. Current advances in neural network may help creating automatic segmentation models that reduce the workload for clinicians. In this preliminary study, we propose automated, two-stage, three-dimensional U-Nets with convolutional neural network, for the challenging task of left atrial segmentation. Unlike previous two-dimensional image segmentation methods, we use 3D U-Nets to obtain the heart cavity directly in 3D. The dual 3D U-Net structure consists of, a first U-Net to coarsely segment and locate the left atrium, and a second U-Net to accurately segment the left atrium under higher resolution. In addition, we introduce a Contour loss based on additional distance information to adjust the final segmentation. We randomly split the data into training datasets (80 subjects) and validation datasets (20 subjects) to train multiple models, with different augmentation setting. Experiments show that the average Dice coefficients for validation datasets are around 0.91 - 0.92, the sensitivity around 0.90-0.94 and the specificity 0.99. Compared with traditional Dice loss, models trained with Contour loss in general offer smaller Hausdorff distance with similar Dice coefficient, and have less connected components in predictions. Finally, we integrate several trained models in an ensemble prediction to segment testing datasets.