# Application of the nnU-Net for automatic segmentation of lung lesion on CT images, and implication on radiomic models

arXiv: https://arxiv.org/abs/2209.12027 · HTML: https://mlsanity.com/paper/2209.12027/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 4 of its 51 references that are in the map.
- First posted on arXiv 24 Sep 2022.

## Builds on (most cited first, 4 of 4)

- [Deep Residual Learning for Image Recognition](https://mlsanity.com/paper/1512.03385/) (2015)
- [PyTorch: An Imperative Style, High-Performance Deep Learning Library](https://mlsanity.com/paper/1912.01703/) (2019)
- [U-Net and its variants for medical image segmentation: theory and applications](https://mlsanity.com/paper/2011.01118/) (2020)
- [PHiSeg: Capturing Uncertainty in Medical Image Segmentation](https://mlsanity.com/paper/1906.04045/) (2019)

## Abstract (arXiv)

Lesion segmentation is a crucial step of the radiomic workflow. Manual segmentation requires long execution time and is prone to variability, impairing the realisation of radiomic studies and their robustness. In this study, a deep-learning automatic segmentation method was applied on computed tomography images of non-small-cell lung cancer patients. The use of manual vs automatic segmentation in the performance of survival radiomic models was assessed, as well. METHODS A total of 899 NSCLC patients were included (2 proprietary: A and B, 1 public datasets: C). Automatic segmentation of lung lesions was performed by training a previously developed architecture, the nnU-Net, including 2D, 3D and cascade approaches. The quality of automatic segmentation was evaluated with DICE coefficient, considering manual contours as reference. The impact of automatic segmentation on the performance of a radiomic model for patient survival was explored by extracting radiomic hand-crafted and deep-learning features from manual and automatic contours of dataset A, and feeding different machine learning algorithms to classify survival above/below median. Models' accuracies were assessed and compared. RESULTS The best agreement between automatic and manual contours with DICE=0.78 +(0.12) was achieved by averaging predictions from 2D and 3D models, and applying a post-processing technique to extract the maximum connected component. No statistical differences were observed in the performances of survival models when using manual or automatic contours, hand-crafted, or deep features. The best classifier showed an accuracy between 0.65 and 0.78. CONCLUSION The promising role of nnU-Net for automatic segmentation of lung lesions was confirmed, dramatically reducing the time-consuming physicians' workload without impairing the accuracy of survival predictive models based on radiomics.