Boundary-aware glomerulus segmentation: toward one-to-many stain generalization
Autor(a) principal: | |
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Data de Publicação: | 2022 |
Outros Autores: | , , , , , , , , |
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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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 14:32:49.612oai:www.arca.fiocruz.br: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ório 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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 |
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eng |
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eng |
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info:eu-repo/semantics/openAccess |
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openAccess |
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Elsevier |
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Elsevier |
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