用图像配准增强医学影像数据,提升小样本下的分割精度
++nnU-Net: Scaling nnU-Net with Prefix-Based Data Augmentation

- 在预处理前通过双阶段配准生成新图像和标签
- 2D数据集上平均提升约22%的Dice分数
- 适合数据稀缺但需高精度分割的医疗场景
nnU-Net在医学图像分割任务中表现持续优异,但其性能高度依赖标注数据的数量与多样性。由于隐私限制和标注成本,医学影像数据集构建困难。为此,本文提出++nnU-Net,一种基于图像配准的新型数据增强模块,部署于预处理和训练前。该框架在五个2D数据集上验证:先进行两阶段图像配准生成形变图像,再将变换应用于对应分割图;同时计算磁盘空间、生成合成二值掩码并创建检查点。结果表明,++nnU-Net优于原始nnU-Net,在最显著案例中Dice相似系数提升约22%。研究证明基于配准的数据增强对2D医学影像分割有效,且++nnU-Net为数据受限场景提供了实用可扩展的性能提升方案。源代码见:https://github.com/sofia-adelie/plusplusnnunet.git
原文摘要 · Abstract (English)
The nnU-Net has demonstrated continuous success in medical segmentation tasks, which heavily rely on the availability and diversity of annotated biomedical data. However, assembling medical imaging cohorts remains challenging due to numerous factors such as privacy regulations and annotation costs. As a result, data augmentation plays a crucial role in increasing data availability while maintaining anatomical feasibility. Hence, we propose the ++nnU-Net, a novel data augmentation module based on image registration that operates prior to preprocessing and training take place. Our framework was evaluated across five different 2D datasets. In this workflow, image data go through a two-stage registration process, generating new warped images. The transformations are then applied to the respective segmentation. In addition, the pipeline computes available disk space, generates supplementary binary synthetic masks and generates checkpoints. We demonstrate that the ++nnU-Net outperforms the nnU-Net baseline, yielding improvements in Dice Similarity Coefficient scores. In the most prominent cases, we observe performance gains of approximately 22\%. These findings highlight the effectiveness of registration-based data augmentation, particularly for 2D medical imaging datasets and suggest that the ++nnU-Net provides a practical and scalable approach for enhancing segmentation performance in data-limited settings. The source code for the ++nnU-Net is available at: https://github.com/sofia-adelie/plusplusnnunet.git
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