Boundary-aware glomerulus segmentation: toward one-to-many stain generalization

Detalhes bibliográficos
Autor(a) principal: Silva, Jefferson
Data de Publicação: 2022
Outros Autores: Souza, Luiz, Chagas, Paulo, Calumby, Rodrigo, Souza, Bianca, Pontes, Izabelle, Duarte, Angelo, Pinheiro, Nathanael, Santos, Washington, Oliveira, Luciano
Tipo de documento: Artigo
Idioma: eng
Título da fonte: Repositório Institucional da FIOCRUZ (ARCA)
Texto Completo: https://www.arca.fiocruz.br/handle/icict/56167
Resumo: Fundação de Amparo à Pesquisa do Estado da Bahia (FAPESB). Inova FIOCRUZ. Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq).
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spelling Silva, JeffersonSouza, LuizChagas, PauloCalumby, RodrigoSouza, BiancaPontes, IzabelleDuarte, AngeloPinheiro, NathanaelSantos, WashingtonOliveira, Luciano2022-12-22T15:59:03Z2022-12-22T15:59:03Z2022SILVA, Jefferson et al. Boundary-aware glomerulus segmentation: toward one-to-many stain generalization. Computerized Medical Imaging and Graphics, v. 100, p. 1-13, 2022.1879-0771https://www.arca.fiocruz.br/handle/icict/5616710.1016/j.compmedimag.2022.102104Fundação de Amparo à Pesquisa do Estado da Bahia (FAPESB). Inova FIOCRUZ. Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq).Universidade Federal do Maranhão, São Luís, MA, Brasil / Universidade Federal da Bahia. Salvador, BA, Brasil.Universidade Federal da Bahia. Salvador, BA, Brasil.Universidade Federal da Bahia. Salvador, BA, Brasil.Universidade Estadual de Feira de Santana. Feira de Santana, BA, Brasil.Universidade Federal da Bahia. Salvador, BA, Brasil /Fundação Oswaldo Cruz, Instituto Gonçalo Muniz. Salvador, BA, Brasil.Universidade Federal da Bahia. Salvador, BA, Brasil.Universidade Estadual de Feira de Santana. Feira de Santana, BA, Brasil.Laboratório Imagepat, Salvador, BA, Brasil.Universidade Federal da Bahia. Salvador, BA, Brasil / Fundação Oswaldo Cruz, Instituto Gonçalo Muniz. Salvador, BA, Brasil.Universidade Federal da Bahia. Salvador, BA, Brasil.The growing availability of scanned whole-slide images (WSIs) has allowed nephropathology to open new possibilities for medical decision-making over high-resolution images. Diagnosis of renal WSIs includes locating and identifying specific structures in the tissue. Considering the glomerulus as one of the first structures analyzed by pathologists, we propose here a novel convolutional neural network for glomerulus segmentation. Our end-to-end network, named DS-FNet, combines the strengths of semantic segmentation and semantic boundary detection networks via an attention-aware mechanism. Although we trained the proposed network on periodic acid-Schiff (PAS)-stained WSIs, we found that our network was capable to segment glomeruli on WSIs stained with different techniques, such as periodic acid-methenamine silver (PAMS), hematoxylin-eosin (HE), and Masson trichrome (TRI). To assess the performance of the proposed method, we used three public data sets: HuBMAP (available in a Kaggle competition), a subset of the NEPTUNE data set, and a novel challenging data set, called WSI_Fiocruz. We compared the DS-FNet with six other deep learning networks: original UNet, our attention version of U-Net called AU-Net, U-Net++, U-Net3Plus, ResU-Net, and DeepLabV3+. Results showed that DS-FNet achieved equivalent or superior results on all data sets: On the HuBMAP data set, it reached a dice score (DSC) of 95.05%, very close to the first place (95.15%); on the NEPTUNE and WSI_Fiocruz data sets, DS-FNet obtained the highest average DSC, whether on PAS-stained images or images stained with other techniques. To the best we know, this is the first work to show consistently high performance in a one-to-many-stain glomerulus segmentation following a thorough protocol on data sets from different medical labs.engElsevierRimSegmentaçãoMolecularImagem celularAprendizagem de ponta a ponta em imagens médicasKidneySegmentationMolecularCellular imagingEnd-to-end learning in medical imagingRimBoundary-aware glomerulus segmentation: toward one-to-many stain generalizationinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleinfo:eu-repo/semantics/openAccessreponame:Repositório Institucional da FIOCRUZ (ARCA)instname:Fundação Oswaldo Cruz (FIOCRUZ)instacron:FIOCRUZLICENSElicense.txtlicense.txttext/plain; charset=utf-82991https://www.arca.fiocruz.br/bitstream/icict/56167/1/license.txt5a560609d32a3863062d77ff32785d58MD51ORIGINALSilva, Jefferson - Boundary-aware glomerulus segmentation.pdfSilva, Jefferson - Boundary-aware glomerulus segmentation.pdfapplication/pdf4589540https://www.arca.fiocruz.br/bitstream/icict/56167/2/Silva%2c%20Jefferson%20-%20Boundary-aware%20glomerulus%20segmentation.pdfe0c4548e6b2ccd2c00b34b6926741569MD52icict/561672023-03-15 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dc.title.en_US.fl_str_mv Boundary-aware glomerulus segmentation: toward one-to-many stain generalization
title Boundary-aware glomerulus segmentation: toward one-to-many stain generalization
spellingShingle Boundary-aware glomerulus segmentation: toward one-to-many stain generalization
Silva, Jefferson
Rim
Segmentação
Molecular
Imagem celular
Aprendizagem de ponta a ponta em imagens médicas
Kidney
Segmentation
Molecular
Cellular imaging
End-to-end learning in medical imaging
Rim
title_short Boundary-aware glomerulus segmentation: toward one-to-many stain generalization
title_full Boundary-aware glomerulus segmentation: toward one-to-many stain generalization
title_fullStr Boundary-aware glomerulus segmentation: toward one-to-many stain generalization
title_full_unstemmed Boundary-aware glomerulus segmentation: toward one-to-many stain generalization
title_sort Boundary-aware glomerulus segmentation: toward one-to-many stain generalization
author Silva, Jefferson
author_facet Silva, Jefferson
Souza, Luiz
Chagas, Paulo
Calumby, Rodrigo
Souza, Bianca
Pontes, Izabelle
Duarte, Angelo
Pinheiro, Nathanael
Santos, Washington
Oliveira, Luciano
author_role author
author2 Souza, Luiz
Chagas, Paulo
Calumby, Rodrigo
Souza, Bianca
Pontes, Izabelle
Duarte, Angelo
Pinheiro, Nathanael
Santos, Washington
Oliveira, Luciano
author2_role author
author
author
author
author
author
author
author
author
dc.contributor.author.fl_str_mv Silva, Jefferson
Souza, Luiz
Chagas, Paulo
Calumby, Rodrigo
Souza, Bianca
Pontes, Izabelle
Duarte, Angelo
Pinheiro, Nathanael
Santos, Washington
Oliveira, Luciano
dc.subject.other.en_US.fl_str_mv Rim
Segmentação
Molecular
Imagem celular
Aprendizagem de ponta a ponta em imagens médicas
topic Rim
Segmentação
Molecular
Imagem celular
Aprendizagem de ponta a ponta em imagens médicas
Kidney
Segmentation
Molecular
Cellular imaging
End-to-end learning in medical imaging
Rim
dc.subject.en.en_US.fl_str_mv Kidney
Segmentation
Molecular
Cellular imaging
End-to-end learning in medical imaging
dc.subject.decs.en_US.fl_str_mv Rim
description Fundação de Amparo à Pesquisa do Estado da Bahia (FAPESB). Inova FIOCRUZ. Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq).
publishDate 2022
dc.date.accessioned.fl_str_mv 2022-12-22T15:59:03Z
dc.date.available.fl_str_mv 2022-12-22T15:59:03Z
dc.date.issued.fl_str_mv 2022
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.citation.fl_str_mv SILVA, Jefferson et al. Boundary-aware glomerulus segmentation: toward one-to-many stain generalization. Computerized Medical Imaging and Graphics, v. 100, p. 1-13, 2022.
dc.identifier.uri.fl_str_mv https://www.arca.fiocruz.br/handle/icict/56167
dc.identifier.issn.en_US.fl_str_mv 1879-0771
dc.identifier.doi.none.fl_str_mv 10.1016/j.compmedimag.2022.102104
identifier_str_mv SILVA, Jefferson et al. Boundary-aware glomerulus segmentation: toward one-to-many stain generalization. Computerized Medical Imaging and Graphics, v. 100, p. 1-13, 2022.
1879-0771
10.1016/j.compmedimag.2022.102104
url https://www.arca.fiocruz.br/handle/icict/56167
dc.language.iso.fl_str_mv eng
language eng
dc.rights.driver.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.publisher.none.fl_str_mv Elsevier
publisher.none.fl_str_mv Elsevier
dc.source.none.fl_str_mv reponame:Repositório Institucional da FIOCRUZ (ARCA)
instname:Fundação Oswaldo Cruz (FIOCRUZ)
instacron:FIOCRUZ
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collection Repositório Institucional da FIOCRUZ (ARCA)
bitstream.url.fl_str_mv https://www.arca.fiocruz.br/bitstream/icict/56167/1/license.txt
https://www.arca.fiocruz.br/bitstream/icict/56167/2/Silva%2c%20Jefferson%20-%20Boundary-aware%20glomerulus%20segmentation.pdf
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