Please use this identifier to cite or link to this item:
https://www.arca.fiocruz.br/handle/icict/56167
Type
ArticleCopyright
Open access
Sustainable Development Goals
04 Educação de qualidadeCollections
Metadata
Show full item record
BOUNDARY-AWARE GLOMERULUS SEGMENTATION: TOWARD ONE-TO-MANY STAIN GENERALIZATION
Segmentação
Molecular
Imagem celular
Aprendizagem de ponta a ponta em imagens médicas
Author
Affilliation
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.
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.
Abstract
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.
Keywords in Portuguese
RimSegmentação
Molecular
Imagem celular
Aprendizagem de ponta a ponta em imagens médicas
Share