# Automatically Segment the Left Atrium and Scars from LGE-MRIs Using a Boundary-focused nnU-Net

arXiv: https://arxiv.org/abs/2304.14071 · HTML: https://mlsanity.com/paper/2304.14071/

## Key facts

- Cited by 2 papers in the map (data through 14 Oct 2026).
- Builds on 14 of its 28 references that are in the map.
- First posted on arXiv 27 Apr 2023.

## Builds on (most cited first, 14 of 14)

- [U-Net: Convolutional Networks for Biomedical Image Segmentation](https://mlsanity.com/paper/1505.04597/) (2015)
- [Attention U-Net: Learning Where to Look for the Pancreas](https://mlsanity.com/paper/1804.03999/) (2018)
- [Boundary loss for highly unbalanced segmentation](https://mlsanity.com/paper/1812.07032/) (2018)
- [Boundary IoU: Improving Object-Centric Image Segmentation Evaluation](https://mlsanity.com/paper/2103.16562/) (2021)
- [The Importance of Skip Connections in Biomedical Image Segmentation](https://mlsanity.com/paper/1608.04117/) (2016)
- [Spatial Uncertainty-Aware Semi-Supervised Crowd Counting](https://mlsanity.com/paper/2107.13271/) (2021)
- [Medical Image Analysis on Left Atrial LGE MRI for Atrial Fibrillation Studies: A Review](https://mlsanity.com/paper/2106.09862/) (2021)
- [AtrialJSQnet: A New Framework for Joint Segmentation and Quantification of Left Atrium and Scars Incorporating Spatial and Shape Information](https://mlsanity.com/paper/2008.04729/) (2020)
- [Bridging Category-level and Instance-level Semantic Image Segmentation](https://mlsanity.com/paper/1605.06885/) (2016)
- [Atrial Scar Quantification via Multi-scale CNN in the Graph-cuts Framework](https://mlsanity.com/paper/1902.07877/) (2019)
- [Simultaneous Left Atrium Anatomy and Scar Segmentations via Deep Learning in Multiview Information with Attention](https://mlsanity.com/paper/2002.00440/) (2020)
- [AtrialGeneral: Domain Generalization for Left Atrial Segmentation of Multi-Center LGE MRIs](https://mlsanity.com/paper/2106.08727/) (2021)
- [BI-GCN: Boundary-Aware Input-Dependent Graph Convolution Network for Biomedical Image Segmentation](https://mlsanity.com/paper/2110.14775/) (2021)
- [Combating Uncertainty with Novel Losses for Automatic Left Atrium Segmentation](https://mlsanity.com/paper/1812.05807/) (2018)

## Built on by (most cited first, 2 of 2)

- [Integrating Deep Learning in Cardiology: A Comprehensive Review of Atrial Fibrillation, Left Atrial Scar Segmentation, and the Frontiers of State-of-the-Art Techniques](https://mlsanity.com/paper/2407.09561/) (2024)
- [How good nnU-Net for Segmenting Cardiac MRI: A Comprehensive Evaluation](https://mlsanity.com/paper/2408.06358/) (2024)

## Abstract (arXiv)

Atrial fibrillation (AF) is the most common cardiac arrhythmia. Accurate segmentation of the left atrial (LA) and LA scars can provide valuable information to predict treatment outcomes in AF. In this paper, we proposed to automatically segment LA cavity and quantify LA scars with late gadolinium enhancement Magnetic Resonance Imagings (LGE-MRIs). We adopted nnU-Net as the baseline model and exploited the importance of LA boundary characteristics with the TopK loss as the loss function. Specifically, a focus on LA boundary pixels is achieved during training, which provides a more accurate boundary prediction. On the other hand, a distance map transformation of the predicted LA boundary is regarded as an additional input for the LA scar prediction, which provides marginal constraint on scar locations. We further designed a novel uncertainty-aware module (UAM) to produce better results for predictions with high uncertainty. Experiments on the LAScarQS 2022 dataset demonstrated our model's superior performance on the LA cavity and LA scar segmentation. Specifically, we achieved 88.98% and 64.08% Dice coefficient for LA cavity and scar segmentation, respectively. We will make our implementation code public available at https://github.com/level6626/Boundary-focused-nnU-Net.