Automated image analysis of lung branching morphogenesis from microscopic images of fetal rat explants
Autor(a) principal: | |
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Data de Publicação: | 2014 |
Outros Autores: | , , , , |
Tipo de documento: | Artigo |
Idioma: | eng |
Título da fonte: | Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
Texto Completo: | http://hdl.handle.net/11110/685 |
Resumo: | Background: Regulating mechanisms of branching morphogenesis of fetal lung rat explants have been an essential tool for molecular research. This work presents a new methodology to accurately quantify the epithelial, outer contour and peripheral airway buds of lung explants during cellular development from microscopic images. Methods: The outer contour was defined using an adaptive and multi-scale threshold algorithm whose level was automatically calculated based on an entropy maximization criterion. The inner lung epithelial was defined by a clustering procedure that groups small image regions according to the minimum description length principle and local statistical properties. Finally, the number of peripheral buds were counted as the skeleton branched ends from a skeletonized image of the lung inner epithelial. Results: The time for lung branching morphometric analysis was reduced in 98% in contrast to the manual method. Best results were obtained in the first two days of cellular development, with lesser standard deviations. Non-significant differences were found between the automatic and manual results in all culture days. Conclusions: The proposed method introduces a series of advantages related to its intuitive use and accuracy, making the technique suitable to images with different lightning characteristics and allowing a reliable comparison between different researchers. |
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Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
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7160 |
spelling |
Automated image analysis of lung branching morphogenesis from microscopic images of fetal rat explantsimage segmentationregion growingminimum description lengthlung explantsbranching morphogenesisBackground: Regulating mechanisms of branching morphogenesis of fetal lung rat explants have been an essential tool for molecular research. This work presents a new methodology to accurately quantify the epithelial, outer contour and peripheral airway buds of lung explants during cellular development from microscopic images. Methods: The outer contour was defined using an adaptive and multi-scale threshold algorithm whose level was automatically calculated based on an entropy maximization criterion. The inner lung epithelial was defined by a clustering procedure that groups small image regions according to the minimum description length principle and local statistical properties. Finally, the number of peripheral buds were counted as the skeleton branched ends from a skeletonized image of the lung inner epithelial. Results: The time for lung branching morphometric analysis was reduced in 98% in contrast to the manual method. Best results were obtained in the first two days of cellular development, with lesser standard deviations. Non-significant differences were found between the automatic and manual results in all culture days. Conclusions: The proposed method introduces a series of advantages related to its intuitive use and accuracy, making the technique suitable to images with different lightning characteristics and allowing a reliable comparison between different researchers.Computational and mathematical methods in medicine2014-09-11T12:13:25Z2014-09-11T12:13:25Z2014-08-06T00:00:00Zinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articlehttp://hdl.handle.net/11110/685oai:ciencipca.ipca.pt:11110/685eng1748-670Xhttp://hdl.handle.net/11110/685Rodrigues, Pedro L.Rodrigues, Nuno F.Duque, DuarteGranja, SaraCorreia-Pinto, JorgeVilaça, João L.info:eu-repo/semantics/openAccessreponame:Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)instname:Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãoinstacron:RCAAP2022-09-05T12:52:15Zoai:ciencipca.ipca.pt:11110/685Portal AgregadorONGhttps://www.rcaap.pt/oai/openaireopendoar:71602024-03-19T15:01:08.331793Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãofalse |
dc.title.none.fl_str_mv |
Automated image analysis of lung branching morphogenesis from microscopic images of fetal rat explants |
title |
Automated image analysis of lung branching morphogenesis from microscopic images of fetal rat explants |
spellingShingle |
Automated image analysis of lung branching morphogenesis from microscopic images of fetal rat explants Rodrigues, Pedro L. image segmentation region growing minimum description length lung explants branching morphogenesis |
title_short |
Automated image analysis of lung branching morphogenesis from microscopic images of fetal rat explants |
title_full |
Automated image analysis of lung branching morphogenesis from microscopic images of fetal rat explants |
title_fullStr |
Automated image analysis of lung branching morphogenesis from microscopic images of fetal rat explants |
title_full_unstemmed |
Automated image analysis of lung branching morphogenesis from microscopic images of fetal rat explants |
title_sort |
Automated image analysis of lung branching morphogenesis from microscopic images of fetal rat explants |
author |
Rodrigues, Pedro L. |
author_facet |
Rodrigues, Pedro L. Rodrigues, Nuno F. Duque, Duarte Granja, Sara Correia-Pinto, Jorge Vilaça, João L. |
author_role |
author |
author2 |
Rodrigues, Nuno F. Duque, Duarte Granja, Sara Correia-Pinto, Jorge Vilaça, João L. |
author2_role |
author author author author author |
dc.contributor.author.fl_str_mv |
Rodrigues, Pedro L. Rodrigues, Nuno F. Duque, Duarte Granja, Sara Correia-Pinto, Jorge Vilaça, João L. |
dc.subject.por.fl_str_mv |
image segmentation region growing minimum description length lung explants branching morphogenesis |
topic |
image segmentation region growing minimum description length lung explants branching morphogenesis |
description |
Background: Regulating mechanisms of branching morphogenesis of fetal lung rat explants have been an essential tool for molecular research. This work presents a new methodology to accurately quantify the epithelial, outer contour and peripheral airway buds of lung explants during cellular development from microscopic images. Methods: The outer contour was defined using an adaptive and multi-scale threshold algorithm whose level was automatically calculated based on an entropy maximization criterion. The inner lung epithelial was defined by a clustering procedure that groups small image regions according to the minimum description length principle and local statistical properties. Finally, the number of peripheral buds were counted as the skeleton branched ends from a skeletonized image of the lung inner epithelial. Results: The time for lung branching morphometric analysis was reduced in 98% in contrast to the manual method. Best results were obtained in the first two days of cellular development, with lesser standard deviations. Non-significant differences were found between the automatic and manual results in all culture days. Conclusions: The proposed method introduces a series of advantages related to its intuitive use and accuracy, making the technique suitable to images with different lightning characteristics and allowing a reliable comparison between different researchers. |
publishDate |
2014 |
dc.date.none.fl_str_mv |
2014-09-11T12:13:25Z 2014-09-11T12:13:25Z 2014-08-06T00:00:00Z |
dc.type.status.fl_str_mv |
info:eu-repo/semantics/publishedVersion |
dc.type.driver.fl_str_mv |
info:eu-repo/semantics/article |
format |
article |
status_str |
publishedVersion |
dc.identifier.uri.fl_str_mv |
http://hdl.handle.net/11110/685 oai:ciencipca.ipca.pt:11110/685 |
url |
http://hdl.handle.net/11110/685 |
identifier_str_mv |
oai:ciencipca.ipca.pt:11110/685 |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.relation.none.fl_str_mv |
1748-670X http://hdl.handle.net/11110/685 |
dc.rights.driver.fl_str_mv |
info:eu-repo/semantics/openAccess |
eu_rights_str_mv |
openAccess |
dc.publisher.none.fl_str_mv |
Computational and mathematical methods in medicine |
publisher.none.fl_str_mv |
Computational and mathematical methods in medicine |
dc.source.none.fl_str_mv |
reponame:Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) instname:Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação instacron:RCAAP |
instname_str |
Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação |
instacron_str |
RCAAP |
institution |
RCAAP |
reponame_str |
Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
collection |
Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
repository.name.fl_str_mv |
Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação |
repository.mail.fl_str_mv |
|
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1799129880906956800 |