Pulmonary nodule segmentation with CT sample synthesis using adversarial networks
Purpose Segmentation of pulmonary nodules is critical for the analysis of nodules and lung cancer diagnosis. We present a novel framework of segmentation for various types of nodules using convolutional neural networks (CNNs). Methods The proposed framework is composed of two major parts. The first...
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Veröffentlicht in: | Medical physics (Lancaster) 2019-03, Vol.46 (3), p.1218-1229 |
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creator | Qin, Yulei Zheng, Hao Huang, Xiaolin Yang, Jie Zhu, Yue‐Min |
description | Purpose
Segmentation of pulmonary nodules is critical for the analysis of nodules and lung cancer diagnosis. We present a novel framework of segmentation for various types of nodules using convolutional neural networks (CNNs).
Methods
The proposed framework is composed of two major parts. The first part is to increase the variety of samples and build a more balanced dataset. A conditional generative adversarial network (cGAN) is employed to produce synthetic CT images. Semantic labels are generated to impart spatial contextual knowledge to the network. Nine attribute scoring labels are combined as well to preserve nodule features. To refine the realism of synthesized samples, reconstruction error loss is introduced into cGAN. The second part is to train a nodule segmentation network on the extended dataset. We build a three‐dimensional (3D) CNN model that exploits heterogeneous maps including edge maps and local binary pattern maps. The incorporation of these maps informs the model of texture patterns and boundary information of nodules, which assists high‐level feature learning for segmentation. Residual unit, which learns to reduce residual error, is adopted to accelerate training and improve accuracy.
Results
Validation on LIDC‐IDRI dataset demonstrates that the generated samples are realistic. The mean squared error and average cosine similarity between real and synthesized samples are 1.55×10−2 and 0.9534, respectively. The Dice coefficient, positive predicted value, sensitivity, and accuracy are, respectively, 0.8483, 0.8895, 0.8511, and 0.9904 for the segmentation results.
Conclusions
The proposed 3D CNN segmentation framework, based on the use of synthesized samples and multiple maps with residual learning, achieves more accurate nodule segmentation compared to existing state‐of‐the‐art methods. The proposed CT image synthesis method can not only output samples close to real images but also allow for stochastic variation in image diversity. |
doi_str_mv | 10.1002/mp.13349 |
format | Article |
fullrecord | <record><control><sourceid>proquest_hal_p</sourceid><recordid>TN_cdi_hal_primary_oai_HAL_hal_02073173v1</recordid><sourceformat>XML</sourceformat><sourcesystem>PC</sourcesystem><sourcerecordid>2159982641</sourcerecordid><originalsourceid>FETCH-LOGICAL-c3899-660ce75499958656f43bf12d15c4dd8316fa45a1e1c5ad85211376379538a2ce3</originalsourceid><addsrcrecordid>eNp1kE1Lw0AQQBdRbK2Cv0By1EPq7Geyx1LUChUr1POyTTbt6ubDbNLSf29qa_HiaWDm8WAeQtcYhhiA3OfVEFPK5AnqExbRkBGQp6gPIFlIGPAeuvD-AwAE5XCOehR4xIGJPnqbtS4vC11vg6JMW2cCb5a5KRrd2LIINrZZBeN54HVe7W7bolkZb33QelssA52uTe11bbULCtNsyvrTX6KzTDtvrg5zgN4fH-bjSTh9fXoej6ZhQmMpQyEgMRFnUkoeCy4yRhcZJinmCUvTmGKRacY1NjjhOo05wZhGgkaS01iTxNAButt7V9qpqrZ594MqtVWT0VTtdkAgojiia9yxt3u2qsuv1vhG5dYnxjldmLL1imAuZUwE-4Mmdel9bbKjG4PaxVZ5pX5id-jNwdoucpMewd-6HRDugY11ZvuvSL3M9sJveUGGlQ</addsrcrecordid><sourcetype>Open Access Repository</sourcetype><iscdi>true</iscdi><recordtype>article</recordtype><pqid>2159982641</pqid></control><display><type>article</type><title>Pulmonary nodule segmentation with CT sample synthesis using adversarial networks</title><source>MEDLINE</source><source>Wiley Online Library Journals Frontfile Complete</source><source>Alma/SFX Local Collection</source><creator>Qin, Yulei ; Zheng, Hao ; Huang, Xiaolin ; Yang, Jie ; Zhu, Yue‐Min</creator><creatorcontrib>Qin, Yulei ; Zheng, Hao ; Huang, Xiaolin ; Yang, Jie ; Zhu, Yue‐Min</creatorcontrib><description>Purpose
Segmentation of pulmonary nodules is critical for the analysis of nodules and lung cancer diagnosis. We present a novel framework of segmentation for various types of nodules using convolutional neural networks (CNNs).
Methods
The proposed framework is composed of two major parts. The first part is to increase the variety of samples and build a more balanced dataset. A conditional generative adversarial network (cGAN) is employed to produce synthetic CT images. Semantic labels are generated to impart spatial contextual knowledge to the network. Nine attribute scoring labels are combined as well to preserve nodule features. To refine the realism of synthesized samples, reconstruction error loss is introduced into cGAN. The second part is to train a nodule segmentation network on the extended dataset. We build a three‐dimensional (3D) CNN model that exploits heterogeneous maps including edge maps and local binary pattern maps. The incorporation of these maps informs the model of texture patterns and boundary information of nodules, which assists high‐level feature learning for segmentation. Residual unit, which learns to reduce residual error, is adopted to accelerate training and improve accuracy.
Results
Validation on LIDC‐IDRI dataset demonstrates that the generated samples are realistic. The mean squared error and average cosine similarity between real and synthesized samples are 1.55×10−2 and 0.9534, respectively. The Dice coefficient, positive predicted value, sensitivity, and accuracy are, respectively, 0.8483, 0.8895, 0.8511, and 0.9904 for the segmentation results.
Conclusions
The proposed 3D CNN segmentation framework, based on the use of synthesized samples and multiple maps with residual learning, achieves more accurate nodule segmentation compared to existing state‐of‐the‐art methods. The proposed CT image synthesis method can not only output samples close to real images but also allow for stochastic variation in image diversity.</description><identifier>ISSN: 0094-2405</identifier><identifier>EISSN: 2473-4209</identifier><identifier>DOI: 10.1002/mp.13349</identifier><identifier>PMID: 30575046</identifier><language>eng</language><publisher>United States: American Association of Physicists in Medicine</publisher><subject>Computer Science ; computer‐aided diagnosis ; convolutional neural networks ; Databases, Factual ; Diagnosis, Computer-Assisted - methods ; generative adversarial networks ; Humans ; Image Processing, Computer-Assisted - methods ; Medical Imaging ; Multiple Pulmonary Nodules - diagnostic imaging ; Multiple Pulmonary Nodules - pathology ; Neural Networks (Computer) ; pulmonary nodule segmentation ; Tomography, X-Ray Computed - methods</subject><ispartof>Medical physics (Lancaster), 2019-03, Vol.46 (3), p.1218-1229</ispartof><rights>2018 American Association of Physicists in Medicine</rights><rights>2018 American Association of Physicists in Medicine.</rights><rights>Distributed under a Creative Commons Attribution 4.0 International License</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c3899-660ce75499958656f43bf12d15c4dd8316fa45a1e1c5ad85211376379538a2ce3</citedby><cites>FETCH-LOGICAL-c3899-660ce75499958656f43bf12d15c4dd8316fa45a1e1c5ad85211376379538a2ce3</cites><orcidid>0000-0002-5217-493X ; 0000-0002-0996-3984 ; 0000-0003-2715-7625 ; 0000-0001-6814-1449</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://onlinelibrary.wiley.com/doi/pdf/10.1002%2Fmp.13349$$EPDF$$P50$$Gwiley$$H</linktopdf><linktohtml>$$Uhttps://onlinelibrary.wiley.com/doi/full/10.1002%2Fmp.13349$$EHTML$$P50$$Gwiley$$H</linktohtml><link.rule.ids>230,314,776,780,881,1411,27901,27902,45550,45551</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/30575046$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink><backlink>$$Uhttps://hal.science/hal-02073173$$DView record in HAL$$Hfree_for_read</backlink></links><search><creatorcontrib>Qin, Yulei</creatorcontrib><creatorcontrib>Zheng, Hao</creatorcontrib><creatorcontrib>Huang, Xiaolin</creatorcontrib><creatorcontrib>Yang, Jie</creatorcontrib><creatorcontrib>Zhu, Yue‐Min</creatorcontrib><title>Pulmonary nodule segmentation with CT sample synthesis using adversarial networks</title><title>Medical physics (Lancaster)</title><addtitle>Med Phys</addtitle><description>Purpose
Segmentation of pulmonary nodules is critical for the analysis of nodules and lung cancer diagnosis. We present a novel framework of segmentation for various types of nodules using convolutional neural networks (CNNs).
Methods
The proposed framework is composed of two major parts. The first part is to increase the variety of samples and build a more balanced dataset. A conditional generative adversarial network (cGAN) is employed to produce synthetic CT images. Semantic labels are generated to impart spatial contextual knowledge to the network. Nine attribute scoring labels are combined as well to preserve nodule features. To refine the realism of synthesized samples, reconstruction error loss is introduced into cGAN. The second part is to train a nodule segmentation network on the extended dataset. We build a three‐dimensional (3D) CNN model that exploits heterogeneous maps including edge maps and local binary pattern maps. The incorporation of these maps informs the model of texture patterns and boundary information of nodules, which assists high‐level feature learning for segmentation. Residual unit, which learns to reduce residual error, is adopted to accelerate training and improve accuracy.
Results
Validation on LIDC‐IDRI dataset demonstrates that the generated samples are realistic. The mean squared error and average cosine similarity between real and synthesized samples are 1.55×10−2 and 0.9534, respectively. The Dice coefficient, positive predicted value, sensitivity, and accuracy are, respectively, 0.8483, 0.8895, 0.8511, and 0.9904 for the segmentation results.
Conclusions
The proposed 3D CNN segmentation framework, based on the use of synthesized samples and multiple maps with residual learning, achieves more accurate nodule segmentation compared to existing state‐of‐the‐art methods. The proposed CT image synthesis method can not only output samples close to real images but also allow for stochastic variation in image diversity.</description><subject>Computer Science</subject><subject>computer‐aided diagnosis</subject><subject>convolutional neural networks</subject><subject>Databases, Factual</subject><subject>Diagnosis, Computer-Assisted - methods</subject><subject>generative adversarial networks</subject><subject>Humans</subject><subject>Image Processing, Computer-Assisted - methods</subject><subject>Medical Imaging</subject><subject>Multiple Pulmonary Nodules - diagnostic imaging</subject><subject>Multiple Pulmonary Nodules - pathology</subject><subject>Neural Networks (Computer)</subject><subject>pulmonary nodule segmentation</subject><subject>Tomography, X-Ray Computed - methods</subject><issn>0094-2405</issn><issn>2473-4209</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2019</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNp1kE1Lw0AQQBdRbK2Cv0By1EPq7Geyx1LUChUr1POyTTbt6ubDbNLSf29qa_HiaWDm8WAeQtcYhhiA3OfVEFPK5AnqExbRkBGQp6gPIFlIGPAeuvD-AwAE5XCOehR4xIGJPnqbtS4vC11vg6JMW2cCb5a5KRrd2LIINrZZBeN54HVe7W7bolkZb33QelssA52uTe11bbULCtNsyvrTX6KzTDtvrg5zgN4fH-bjSTh9fXoej6ZhQmMpQyEgMRFnUkoeCy4yRhcZJinmCUvTmGKRacY1NjjhOo05wZhGgkaS01iTxNAButt7V9qpqrZ594MqtVWT0VTtdkAgojiia9yxt3u2qsuv1vhG5dYnxjldmLL1imAuZUwE-4Mmdel9bbKjG4PaxVZ5pX5id-jNwdoucpMewd-6HRDugY11ZvuvSL3M9sJveUGGlQ</recordid><startdate>201903</startdate><enddate>201903</enddate><creator>Qin, Yulei</creator><creator>Zheng, Hao</creator><creator>Huang, Xiaolin</creator><creator>Yang, Jie</creator><creator>Zhu, Yue‐Min</creator><general>American Association of Physicists in Medicine</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7X8</scope><scope>1XC</scope><scope>VOOES</scope><orcidid>https://orcid.org/0000-0002-5217-493X</orcidid><orcidid>https://orcid.org/0000-0002-0996-3984</orcidid><orcidid>https://orcid.org/0000-0003-2715-7625</orcidid><orcidid>https://orcid.org/0000-0001-6814-1449</orcidid></search><sort><creationdate>201903</creationdate><title>Pulmonary nodule segmentation with CT sample synthesis using adversarial networks</title><author>Qin, Yulei ; Zheng, Hao ; Huang, Xiaolin ; Yang, Jie ; Zhu, Yue‐Min</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c3899-660ce75499958656f43bf12d15c4dd8316fa45a1e1c5ad85211376379538a2ce3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2019</creationdate><topic>Computer Science</topic><topic>computer‐aided diagnosis</topic><topic>convolutional neural networks</topic><topic>Databases, Factual</topic><topic>Diagnosis, Computer-Assisted - methods</topic><topic>generative adversarial networks</topic><topic>Humans</topic><topic>Image Processing, Computer-Assisted - methods</topic><topic>Medical Imaging</topic><topic>Multiple Pulmonary Nodules - diagnostic imaging</topic><topic>Multiple Pulmonary Nodules - pathology</topic><topic>Neural Networks (Computer)</topic><topic>pulmonary nodule segmentation</topic><topic>Tomography, X-Ray Computed - methods</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Qin, Yulei</creatorcontrib><creatorcontrib>Zheng, Hao</creatorcontrib><creatorcontrib>Huang, Xiaolin</creatorcontrib><creatorcontrib>Yang, Jie</creatorcontrib><creatorcontrib>Zhu, Yue‐Min</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>MEDLINE - Academic</collection><collection>Hyper Article en Ligne (HAL)</collection><collection>Hyper Article en Ligne (HAL) (Open Access)</collection><jtitle>Medical physics (Lancaster)</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Qin, Yulei</au><au>Zheng, Hao</au><au>Huang, Xiaolin</au><au>Yang, Jie</au><au>Zhu, Yue‐Min</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Pulmonary nodule segmentation with CT sample synthesis using adversarial networks</atitle><jtitle>Medical physics (Lancaster)</jtitle><addtitle>Med Phys</addtitle><date>2019-03</date><risdate>2019</risdate><volume>46</volume><issue>3</issue><spage>1218</spage><epage>1229</epage><pages>1218-1229</pages><issn>0094-2405</issn><eissn>2473-4209</eissn><abstract>Purpose
Segmentation of pulmonary nodules is critical for the analysis of nodules and lung cancer diagnosis. We present a novel framework of segmentation for various types of nodules using convolutional neural networks (CNNs).
Methods
The proposed framework is composed of two major parts. The first part is to increase the variety of samples and build a more balanced dataset. A conditional generative adversarial network (cGAN) is employed to produce synthetic CT images. Semantic labels are generated to impart spatial contextual knowledge to the network. Nine attribute scoring labels are combined as well to preserve nodule features. To refine the realism of synthesized samples, reconstruction error loss is introduced into cGAN. The second part is to train a nodule segmentation network on the extended dataset. We build a three‐dimensional (3D) CNN model that exploits heterogeneous maps including edge maps and local binary pattern maps. The incorporation of these maps informs the model of texture patterns and boundary information of nodules, which assists high‐level feature learning for segmentation. Residual unit, which learns to reduce residual error, is adopted to accelerate training and improve accuracy.
Results
Validation on LIDC‐IDRI dataset demonstrates that the generated samples are realistic. The mean squared error and average cosine similarity between real and synthesized samples are 1.55×10−2 and 0.9534, respectively. The Dice coefficient, positive predicted value, sensitivity, and accuracy are, respectively, 0.8483, 0.8895, 0.8511, and 0.9904 for the segmentation results.
Conclusions
The proposed 3D CNN segmentation framework, based on the use of synthesized samples and multiple maps with residual learning, achieves more accurate nodule segmentation compared to existing state‐of‐the‐art methods. The proposed CT image synthesis method can not only output samples close to real images but also allow for stochastic variation in image diversity.</abstract><cop>United States</cop><pub>American Association of Physicists in Medicine</pub><pmid>30575046</pmid><doi>10.1002/mp.13349</doi><tpages>12</tpages><orcidid>https://orcid.org/0000-0002-5217-493X</orcidid><orcidid>https://orcid.org/0000-0002-0996-3984</orcidid><orcidid>https://orcid.org/0000-0003-2715-7625</orcidid><orcidid>https://orcid.org/0000-0001-6814-1449</orcidid><oa>free_for_read</oa></addata></record> |
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subjects | Computer Science computer‐aided diagnosis convolutional neural networks Databases, Factual Diagnosis, Computer-Assisted - methods generative adversarial networks Humans Image Processing, Computer-Assisted - methods Medical Imaging Multiple Pulmonary Nodules - diagnostic imaging Multiple Pulmonary Nodules - pathology Neural Networks (Computer) pulmonary nodule segmentation Tomography, X-Ray Computed - methods |
title | Pulmonary nodule segmentation with CT sample synthesis using adversarial networks |
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