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 Citationer (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.

Originalsprog	Engelsk
Titel	Medical Imaging 2018 : Image Processing
Antal sider	7
Forlag	SPIE - International Society for Optical Engineering
Publikationsdato	2018
Artikelnummer	105741G
DOI	https://doi.org/10.1117/12.2292188
Status	Udgivet - 2018
Begivenhed	SPIE Medical Imaging 2018 - Houston, USA Varighed: 10 feb. 2018 → 15 feb. 2018

Konference

Konference	SPIE Medical Imaging 2018
Land/Område	USA
By	Houston
Periode	10/02/2018 → 15/02/2018

Navn	Proceedings of SPIE International Symposium on Medical Imaging
Vol/bind	10574

Emneord

cs.CV

Adgang til dokumentet

10.1117/12.2292188

https://arxiv.org/pdf/1803.07991

Citationsformater

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. I Medical Imaging 2018: Image Processing [105741G] SPIE - International Society for Optical Engineering. Proceedings of SPIE International Symposium on Medical Imaging Bind 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, Bind 10574).

Publikation: Bidrag til bog/antologi/rapport › Konferencebidrag i proceedings › Forskning › peer review

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

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title = "Quantification of Lung Abnormalities in Cystic Fibrosis using Deep Networks",

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 - Marques, Filipe

AU - Dubost, Florian

AU - Corput, Mariette Kemner-van de

AU - Tiddens, Harm A. W.

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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