Quantification of Lung Abnormalities in Cystic Fibrosis using Deep Networks

Filipe Marques; Florian Dubost; Mariette Kemner-van de Corput; Harm A. W. Tiddens; Marleen de Bruijne

doi:10.1117/12.2292188

Quantification of Lung Abnormalities in Cystic Fibrosis using Deep Networks

Filipe Marques, Florian Dubost, Mariette Kemner-van de Corput, Harm A. W. Tiddens, Marleen de Bruijne

3 Citations (Scopus)

Abstract

Cystic fibrosis is a genetic disease which may appear in early life with structural abnormalities in lung tissues. We propose to detect these abnormalities using a texture classification approach. Our method is a cascade of two convolutional neural networks. The first network detects the presence of abnormal tissues. The second network identifies the type of the structural abnormalities: bronchiectasis, atelectasis or mucus plugging.We also propose a network computing pixel-wise heatmaps of abnormality presence learning only from the patch-wise annotations. Our database consists of CT scans of 194 subjects. We use 154 subjects to train our algorithms and the 40 remaining ones as a test set. We compare our method with random forest and a single neural network approach. The first network reaches a sensitivity of 0,62 for disease detection, 0,10 higher than the random forest classifier and 0,17 higher than the single neural network. Our cascade approach yields a final class-averaged F1-score of 0,38, outperforming the baseline method and the single network by 0,15 and 0,10.

Original language	English
Title of host publication	Medical Imaging 2018 : Image Processing
Number of pages	7
Publisher	SPIE - International Society for Optical Engineering
Publication date	2018
Article number	105741G
DOIs	https://doi.org/10.1117/12.2292188
Publication status	Published - 2018
Event	SPIE Medical Imaging 2018 - Houston, United States Duration: 10 Feb 2018 → 15 Feb 2018

Conference

Conference	SPIE Medical Imaging 2018
Country/Territory	United States
City	Houston
Period	10/02/2018 → 15/02/2018

Series	Proceedings of SPIE International Symposium on Medical Imaging
Volume	10574

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10.1117/12.2292188

https://arxiv.org/pdf/1803.07991

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Marques, F., Dubost, F., Corput, M. K. D., Tiddens, H. A. W., & Bruijne, M. D. (2018). Quantification of Lung Abnormalities in Cystic Fibrosis using Deep Networks. In Medical Imaging 2018: Image Processing [105741G] SPIE - International Society for Optical Engineering. Proceedings of SPIE International Symposium on Medical Imaging Vol. 10574 https://doi.org/10.1117/12.2292188

Quantification of Lung Abnormalities in Cystic Fibrosis using Deep Networks. / Marques, Filipe; Dubost, Florian; Corput, Mariette Kemner-van de et al.

Medical Imaging 2018: Image Processing. SPIE - International Society for Optical Engineering, 2018. 105741G (Proceedings of SPIE International Symposium on Medical Imaging, Vol. 10574).

Research output: Chapter in Book/Report/Conference proceeding › Article in proceedings › Research › peer-review

Marques, F, Dubost, F, Corput, MKD, Tiddens, HAW & Bruijne, MD 2018, Quantification of Lung Abnormalities in Cystic Fibrosis using Deep Networks. in Medical Imaging 2018: Image Processing., 105741G, SPIE - International Society for Optical Engineering, Proceedings of SPIE International Symposium on Medical Imaging, vol. 10574, SPIE Medical Imaging 2018, Houston, United States, 10/02/2018. https://doi.org/10.1117/12.2292188

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abstract = "Cystic fibrosis is a genetic disease which may appear in early life with structural abnormalities in lung tissues. We propose to detect these abnormalities using a texture classification approach. Our method is a cascade of two convolutional neural networks. The first network detects the presence of abnormal tissues. The second network identifies the type of the structural abnormalities: bronchiectasis, atelectasis or mucus plugging.We also propose a network computing pixel-wise heatmaps of abnormality presence learning only from the patch-wise annotations. Our database consists of CT scans of 194 subjects. We use 154 subjects to train our algorithms and the 40 remaining ones as a test set. We compare our method with random forest and a single neural network approach. The first network reaches a sensitivity of 0,62 for disease detection, 0,10 higher than the random forest classifier and 0,17 higher than the single neural network. Our cascade approach yields a final class-averaged F1-score of 0,38, outperforming the baseline method and the single network by 0,15 and 0,10.",

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AU - Bruijne, Marleen de

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N2 - Cystic fibrosis is a genetic disease which may appear in early life with structural abnormalities in lung tissues. We propose to detect these abnormalities using a texture classification approach. Our method is a cascade of two convolutional neural networks. The first network detects the presence of abnormal tissues. The second network identifies the type of the structural abnormalities: bronchiectasis, atelectasis or mucus plugging.We also propose a network computing pixel-wise heatmaps of abnormality presence learning only from the patch-wise annotations. Our database consists of CT scans of 194 subjects. We use 154 subjects to train our algorithms and the 40 remaining ones as a test set. We compare our method with random forest and a single neural network approach. The first network reaches a sensitivity of 0,62 for disease detection, 0,10 higher than the random forest classifier and 0,17 higher than the single neural network. Our cascade approach yields a final class-averaged F1-score of 0,38, outperforming the baseline method and the single network by 0,15 and 0,10.

AB - Cystic fibrosis is a genetic disease which may appear in early life with structural abnormalities in lung tissues. We propose to detect these abnormalities using a texture classification approach. Our method is a cascade of two convolutional neural networks. The first network detects the presence of abnormal tissues. The second network identifies the type of the structural abnormalities: bronchiectasis, atelectasis or mucus plugging.We also propose a network computing pixel-wise heatmaps of abnormality presence learning only from the patch-wise annotations. Our database consists of CT scans of 194 subjects. We use 154 subjects to train our algorithms and the 40 remaining ones as a test set. We compare our method with random forest and a single neural network approach. The first network reaches a sensitivity of 0,62 for disease detection, 0,10 higher than the random forest classifier and 0,17 higher than the single neural network. Our cascade approach yields a final class-averaged F1-score of 0,38, outperforming the baseline method and the single network by 0,15 and 0,10.

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Quantification of Lung Abnormalities in Cystic Fibrosis using Deep Networks

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