Skip to main content
Top
Published in: Journal of Digital Imaging 3/2020

01-06-2020 | Pulmonary Nodule

Deep Deconvolutional Residual Network Based Automatic Lung Nodule Segmentation

Authors: Ganesh Singadkar, Abhishek Mahajan, Meenakshi Thakur, Sanjay Talbar

Published in: Journal of Imaging Informatics in Medicine | Issue 3/2020

Login to get access

Abstract

Accurate and automatic lung nodule segmentation is of prime importance for the lung cancer analysis and its fundamental step in computer-aided diagnosis (CAD) systems. However, various types of nodule and visual similarity with its surrounding chest region make it challenging to develop lung nodule segmentation algorithm. In this paper, we proposed the Deep Deconvolutional Residual Network (DDRN) based approach for the lung nodule segmentation from the CT images. Our approach is based on two key insights. Proposed deep deconvolutional residual network trained end to end and captures the diverse variety of the nodules from the 2D set of the CT images. Summation-based long skip connection from convolutional to deconvolutional part of the network preserves the spatial information lost during the pooling operation and captures the full resolution features. The proposed method is evaluated on the publicly available Lung Image Database Consortium and Image Database Resource Initiative (LIDC/IDRI) dataset. Results indicate that our proposed method can successfully segment nodules and achieve the average Dice scores of 94.97%, and Jaccard index of 88.68%.
Literature
2.
go back to reference Messay T, Hardie RC, Rogers SK: A new computationally efficient cad system for pulmonary nodule detection in ct imagery. Med Image Anal 14 (3): 390–406, 2010PubMedCrossRef Messay T, Hardie RC, Rogers SK: A new computationally efficient cad system for pulmonary nodule detection in ct imagery. Med Image Anal 14 (3): 390–406, 2010PubMedCrossRef
3.
go back to reference Kubota T, Jerebko AK, Dewan M, Salganicoff M, Krishnan A: Segmentation of pulmonary nodules of various densities with morphological approaches and convexity models. Med Image Anal 15 (1): 133–154, 2011PubMedCrossRef Kubota T, Jerebko AK, Dewan M, Salganicoff M, Krishnan A: Segmentation of pulmonary nodules of various densities with morphological approaches and convexity models. Med Image Anal 15 (1): 133–154, 2011PubMedCrossRef
4.
go back to reference Lassen BC, Jacobs C, Kuhnigk JM, van Ginneken B, van Rikxoort EM: Robust semi-automatic segmentation of pulmonary subsolid nodules in chest computed tomography scans. Phys Med Biol 60 (3): 1307–1323, 2015PubMedCrossRef Lassen BC, Jacobs C, Kuhnigk JM, van Ginneken B, van Rikxoort EM: Robust semi-automatic segmentation of pulmonary subsolid nodules in chest computed tomography scans. Phys Med Biol 60 (3): 1307–1323, 2015PubMedCrossRef
5.
go back to reference Messay T, Hardie RC, Tuinstra TR: Segmentation of pulmonary nodules in computed tomography using a regression neural network approach and its application to the lung image database consortium and image database resource initiative dataset. Med Image Anal 22 (1): 48–62, 2015PubMedCrossRef Messay T, Hardie RC, Tuinstra TR: Segmentation of pulmonary nodules in computed tomography using a regression neural network approach and its application to the lung image database consortium and image database resource initiative dataset. Med Image Anal 22 (1): 48–62, 2015PubMedCrossRef
6.
go back to reference Wang S, Zhou M, Liu Z, Liu . Z, Gu D, Zang Y, Dong D, Gevaert O, Tian J: Central focused convolutional neural networks: developing a data-driven model for lung nodule segmentation. Med Image Anal 40: 172–183, 2017PubMedPubMedCentralCrossRef Wang S, Zhou M, Liu Z, Liu . Z, Gu D, Zang Y, Dong D, Gevaert O, Tian J: Central focused convolutional neural networks: developing a data-driven model for lung nodule segmentation. Med Image Anal 40: 172–183, 2017PubMedPubMedCentralCrossRef
7.
go back to reference Roy R, Chakraborti T, Chowdhurya AS: A deep learning-shape driven level set synergism for pulmonary nodule segmentation. Pattern Recogn Lett 123: 31–38, 2019CrossRef Roy R, Chakraborti T, Chowdhurya AS: A deep learning-shape driven level set synergism for pulmonary nodule segmentation. Pattern Recogn Lett 123: 31–38, 2019CrossRef
8.
go back to reference Shakibapour E, Cunha A, Aresta G, Mendonça AM, Campilho A: An unsupervised metaheuristic search approach for segmentation and volume measurement of pulmonary nodules in lung ct scans. Expert Syst Appl 119: 415–428, 2019CrossRef Shakibapour E, Cunha A, Aresta G, Mendonça AM, Campilho A: An unsupervised metaheuristic search approach for segmentation and volume measurement of pulmonary nodules in lung ct scans. Expert Syst Appl 119: 415–428, 2019CrossRef
9.
go back to reference Boykov Y, Kolmogorov V: An experimental comparison of min-cut/max- flow algorithms for energy minimization in vision. IEEE Trans Pattern Anal Mach Intell 26 (9): 1124–1137, 2004PubMedCrossRef Boykov Y, Kolmogorov V: An experimental comparison of min-cut/max- flow algorithms for energy minimization in vision. IEEE Trans Pattern Anal Mach Intell 26 (9): 1124–1137, 2004PubMedCrossRef
10.
11.
go back to reference Ciresan D, Giusti A, Gambardella LM, Schmidhuber J, Bottou L: Deep neural networks segment neuronal membranes in electron microscopy images. In: (Pereira F, Burges CJC, Weinberger KQ, Eds.) Advances in neural information processing systems, vol 25. Curran Associates, Inc., 2012, pp 2843–2851 Ciresan D, Giusti A, Gambardella LM, Schmidhuber J, Bottou L: Deep neural networks segment neuronal membranes in electron microscopy images. In: (Pereira F, Burges CJC, Weinberger KQ, Eds.) Advances in neural information processing systems, vol 25. Curran Associates, Inc., 2012, pp 2843–2851
12.
go back to reference Dehmeshki J, Amin H, Valdivieso M, Ye X: Segmentation of pulmonary nodules in thoracic ct scans: a region growing approach. IEEE Trans Med Imaging 27 (4): 467–480, 2008PubMedCrossRef Dehmeshki J, Amin H, Valdivieso M, Ye X: Segmentation of pulmonary nodules in thoracic ct scans: a region growing approach. IEEE Trans Med Imaging 27 (4): 467–480, 2008PubMedCrossRef
13.
go back to reference Diciotti S, Picozzi G, Falchini M, Mascalchi M, Villari N, Valli G: 3dd segmentation algorithm of small lung nodules in spiral ct images. Trans Info Tech Biomed 12: 1, 2008CrossRef Diciotti S, Picozzi G, Falchini M, Mascalchi M, Villari N, Valli G: 3dd segmentation algorithm of small lung nodules in spiral ct images. Trans Info Tech Biomed 12: 1, 2008CrossRef
14.
go back to reference Diederich S, Wormanns D, Semik M, Thomas M, Lenzen H, Roos N, Heindel W: Screening for early lung cancer with low-dose spiral ct: prevalence in 817 asymptomatic smokers 1. Radiology 222 (3): 773–781, 2002PubMedCrossRef Diederich S, Wormanns D, Semik M, Thomas M, Lenzen H, Roos N, Heindel W: Screening for early lung cancer with low-dose spiral ct: prevalence in 817 asymptomatic smokers 1. Radiology 222 (3): 773–781, 2002PubMedCrossRef
15.
go back to reference Fakhry A, Zeng T, Ji S: Residual deconvolutional networks for brain electron microscopy image segmentation. IEEE Trans Med Imaging 36 (2): 447–456, 2017PubMedCrossRef Fakhry A, Zeng T, Ji S: Residual deconvolutional networks for brain electron microscopy image segmentation. IEEE Trans Med Imaging 36 (2): 447–456, 2017PubMedCrossRef
16.
go back to reference Farag AA, Munim HEAE, Graham JH, Farag AA: A novel approach for lung nodules segmentation in chest ct using level sets. IEEE Trans Image Process 22 (12): 5202–5213, 2013PubMedCrossRef Farag AA, Munim HEAE, Graham JH, Farag AA: A novel approach for lung nodules segmentation in chest ct using level sets. IEEE Trans Image Process 22 (12): 5202–5213, 2013PubMedCrossRef
17.
18.
go back to reference He K, Zhang X, Ren S, Sun J (2016) Deep residual learning for image recognition. In: The IEEE Conference on computer vision and pattern recognition (CVPR) He K, Zhang X, Ren S, Sun J (2016) Deep residual learning for image recognition. In: The IEEE Conference on computer vision and pattern recognition (CVPR)
19.
go back to reference Jia Y, Shelhamer E, Donahue J, Karayev S, Long J, Girshick R, Guadarrama S, Darrell T: Caffe: convolutional architecture for fast feature embedding.. In: Proceedings of the 22Nd ACM international conference on multimedia, MM ’14. ACM, New York, 2014, pp 675–678 Jia Y, Shelhamer E, Donahue J, Karayev S, Long J, Girshick R, Guadarrama S, Darrell T: Caffe: convolutional architecture for fast feature embedding.. In: Proceedings of the 22Nd ACM international conference on multimedia, MM ’14. ACM, New York, 2014, pp 675–678
20.
go back to reference Kalpathy-Cramer J, Zhao Bg, Goldgof D, Gu Y, Wang X, Yang H, Tan Y, Gillies R, Napel S: A comparison of lung nodule segmentation algorithms: methods and results from a multi-institutional study. J Digit Imaging 29 (4): 476–487, 2016PubMedPubMedCentralCrossRef Kalpathy-Cramer J, Zhao Bg, Goldgof D, Gu Y, Wang X, Yang H, Tan Y, Gillies R, Napel S: A comparison of lung nodule segmentation algorithms: methods and results from a multi-institutional study. J Digit Imaging 29 (4): 476–487, 2016PubMedPubMedCentralCrossRef
21.
go back to reference Kostis WJ, Reeves AP, Yankelevitz DF, Henschke CI: Three-dimensional segmentation and growth-rate estimation of small pulmonary nodules in helical ct images. IEEE Trans Med Imaging 22 (10): 1259–1274, 2003PubMedCrossRef Kostis WJ, Reeves AP, Yankelevitz DF, Henschke CI: Three-dimensional segmentation and growth-rate estimation of small pulmonary nodules in helical ct images. IEEE Trans Med Imaging 22 (10): 1259–1274, 2003PubMedCrossRef
22.
go back to reference Kuhnigk J, Dicken V, Bornemann L, Bakai A, Wormanns D, Krass S, Peitgen H: Morphological segmentation and partial volume analysis for volumetry of solid pulmonary lesions in thoracic ct scans. IEEE Trans Med Imaging 25 (4): 417–434, 2006PubMedCrossRef Kuhnigk J, Dicken V, Bornemann L, Bakai A, Wormanns D, Krass S, Peitgen H: Morphological segmentation and partial volume analysis for volumetry of solid pulmonary lesions in thoracic ct scans. IEEE Trans Med Imaging 25 (4): 417–434, 2006PubMedCrossRef
23.
go back to reference Lin T-Y, Maire M, Belongie S, Hays J, Perona P, Ramanan D, Dollár P, Zitnick CL: Microsoft coco: common objects in context. In: (Fleet D, Pajdla T, Schiele B, Tuytelaars T, Eds.) Computer vision – ECCV 2014. Springer International Publishing, Cham, 2014, pp 740–755CrossRef Lin T-Y, Maire M, Belongie S, Hays J, Perona P, Ramanan D, Dollár P, Zitnick CL: Microsoft coco: common objects in context. In: (Fleet D, Pajdla T, Schiele B, Tuytelaars T, Eds.) Computer vision – ECCV 2014. Springer International Publishing, Cham, 2014, pp 740–755CrossRef
24.
go back to reference Mukherjee S, Huang X, Bhagalia RR: Lung nodule segmentation using deep learned prior based graph cut.. In: 2017 IEEE 14th international symposium on biomedical imaging (ISBI 2017), 2017, pp 1205–1208 Mukherjee S, Huang X, Bhagalia RR: Lung nodule segmentation using deep learned prior based graph cut.. In: 2017 IEEE 14th international symposium on biomedical imaging (ISBI 2017), 2017, pp 1205–1208
25.
26.
go back to reference Noh H, Hong S, Han B (2015) Learning deconvolution network for semantic segmentation. In: The IEEE International conference on computer vision (ICCV) Noh H, Hong S, Han B (2015) Learning deconvolution network for semantic segmentation. In: The IEEE International conference on computer vision (ICCV)
27.
go back to reference Ronneberger O, Fischer P, Brox T: U-net: convolutional networks for biomedical image segmentation. In: (Navab N, Hornegger J, Wells WM, Frangi AF, Eds.) Medical image computing and computer-assisted intervention – MICCAI 2015. Springer International Publishing, Cham, 2015, pp 234–241 Ronneberger O, Fischer P, Brox T: U-net: convolutional networks for biomedical image segmentation. In: (Navab N, Hornegger J, Wells WM, Frangi AF, Eds.) Medical image computing and computer-assisted intervention – MICCAI 2015. Springer International Publishing, Cham, 2015, pp 234–241
28.
go back to reference Russakovsky O, Deng J, Su H, Krause J, Satheesh S, Ma S, Huang Z, Karpathy A, Khosla A, Bernstein M, Berg AC, Li F-F: ImageNet large scale visual recognition challenge. Int J Comput Vis (IJCV) 115 (3): 211–252, 2015CrossRef Russakovsky O, Deng J, Su H, Krause J, Satheesh S, Ma S, Huang Z, Karpathy A, Khosla A, Bernstein M, Berg AC, Li F-F: ImageNet large scale visual recognition challenge. Int J Comput Vis (IJCV) 115 (3): 211–252, 2015CrossRef
29.
go back to reference Siegel RL, Miller KD, Jemal A: Cancer statistics, 2016. CA: A Cancer J Clinicians 66 (1): 7–30, 2016 Siegel RL, Miller KD, Jemal A: Cancer statistics, 2016. CA: A Cancer J Clinicians 66 (1): 7–30, 2016
30.
go back to reference Tan Y, Schwartz LH, Zhao B: Segmentation of lung lesions on ct scans using watershed, active contours, and Markov random field. Med Phys 40 (4): 043502, 2013PubMedPubMedCentralCrossRef Tan Y, Schwartz LH, Zhao B: Segmentation of lung lesions on ct scans using watershed, active contours, and Markov random field. Med Phys 40 (4): 043502, 2013PubMedPubMedCentralCrossRef
Metadata
Title
Deep Deconvolutional Residual Network Based Automatic Lung Nodule Segmentation
Authors
Ganesh Singadkar
Abhishek Mahajan
Meenakshi Thakur
Sanjay Talbar
Publication date
01-06-2020
Publisher
Springer International Publishing
Published in
Journal of Imaging Informatics in Medicine / Issue 3/2020
Print ISSN: 2948-2925
Electronic ISSN: 2948-2933
DOI
https://doi.org/10.1007/s10278-019-00301-4

Other articles of this Issue 3/2020

Journal of Digital Imaging 3/2020 Go to the issue