Md Jahid Hasan , Wan Siti Halimatul Munirah Wan Ahmad , Mohammad Faizal Ahmad Fauzi , Jenny Tung Hiong Lee , See Yee Khor , Lai Meng Looi , Fazly Salleh Abas , Afzan Adam , Elaine Wan Ling Chan
{"title":"用于肿瘤生物标记物评分的全切片图像实时分割和分类","authors":"Md Jahid Hasan , Wan Siti Halimatul Munirah Wan Ahmad , Mohammad Faizal Ahmad Fauzi , Jenny Tung Hiong Lee , See Yee Khor , Lai Meng Looi , Fazly Salleh Abas , Afzan Adam , Elaine Wan Ling Chan","doi":"10.1016/j.jksuci.2024.102204","DOIUrl":null,"url":null,"abstract":"<div><div>Histopathology image segmentation and classification are essential for diagnosing and treating breast cancer. This study introduced a highly accurate segmentation and classification for histopathology images using a single architecture. We utilized the famous segmentation architectures, SegNet and U-Net, and modified the decoder to attach ResNet, VGG and DenseNet to perform classification tasks. These hybrid models are integrated with Stardist as the backbone, and implemented in a real-time pathologist workflow with a graphical user interface. These models were trained and tested offline using the ER-IHC-stained private and H&E-stained public datasets (MoNuSeg). For real-time evaluation, the proposed model was evaluated using PR-IHC-stained glass slides. It achieved the highest segmentation pixel-based F1-score of 0.902 and 0.903 for private and public datasets respectively, and a classification-based F1-score of 0.833 for private dataset. The experiment shows the robustness of our method where a model trained on ER-IHC dataset able to perform well on real-time microscopy of PR-IHC slides on both 20x and 40x magnification. This will help the pathologists with a quick decision-making process.</div></div>","PeriodicalId":48547,"journal":{"name":"Journal of King Saud University-Computer and Information Sciences","volume":null,"pages":null},"PeriodicalIF":5.2000,"publicationDate":"2024-10-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":"{\"title\":\"Real-time segmentation and classification of whole-slide images for tumor biomarker scoring\",\"authors\":\"Md Jahid Hasan , Wan Siti Halimatul Munirah Wan Ahmad , Mohammad Faizal Ahmad Fauzi , Jenny Tung Hiong Lee , See Yee Khor , Lai Meng Looi , Fazly Salleh Abas , Afzan Adam , Elaine Wan Ling Chan\",\"doi\":\"10.1016/j.jksuci.2024.102204\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<div><div>Histopathology image segmentation and classification are essential for diagnosing and treating breast cancer. This study introduced a highly accurate segmentation and classification for histopathology images using a single architecture. We utilized the famous segmentation architectures, SegNet and U-Net, and modified the decoder to attach ResNet, VGG and DenseNet to perform classification tasks. These hybrid models are integrated with Stardist as the backbone, and implemented in a real-time pathologist workflow with a graphical user interface. These models were trained and tested offline using the ER-IHC-stained private and H&E-stained public datasets (MoNuSeg). For real-time evaluation, the proposed model was evaluated using PR-IHC-stained glass slides. It achieved the highest segmentation pixel-based F1-score of 0.902 and 0.903 for private and public datasets respectively, and a classification-based F1-score of 0.833 for private dataset. The experiment shows the robustness of our method where a model trained on ER-IHC dataset able to perform well on real-time microscopy of PR-IHC slides on both 20x and 40x magnification. This will help the pathologists with a quick decision-making process.</div></div>\",\"PeriodicalId\":48547,\"journal\":{\"name\":\"Journal of King Saud University-Computer and Information Sciences\",\"volume\":null,\"pages\":null},\"PeriodicalIF\":5.2000,\"publicationDate\":\"2024-10-05\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Journal of King Saud University-Computer and Information Sciences\",\"FirstCategoryId\":\"94\",\"ListUrlMain\":\"https://www.sciencedirect.com/science/article/pii/S1319157824002933\",\"RegionNum\":2,\"RegionCategory\":\"计算机科学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q1\",\"JCRName\":\"COMPUTER SCIENCE, INFORMATION SYSTEMS\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Journal of King Saud University-Computer and Information Sciences","FirstCategoryId":"94","ListUrlMain":"https://www.sciencedirect.com/science/article/pii/S1319157824002933","RegionNum":2,"RegionCategory":"计算机科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q1","JCRName":"COMPUTER SCIENCE, INFORMATION SYSTEMS","Score":null,"Total":0}
Real-time segmentation and classification of whole-slide images for tumor biomarker scoring
Histopathology image segmentation and classification are essential for diagnosing and treating breast cancer. This study introduced a highly accurate segmentation and classification for histopathology images using a single architecture. We utilized the famous segmentation architectures, SegNet and U-Net, and modified the decoder to attach ResNet, VGG and DenseNet to perform classification tasks. These hybrid models are integrated with Stardist as the backbone, and implemented in a real-time pathologist workflow with a graphical user interface. These models were trained and tested offline using the ER-IHC-stained private and H&E-stained public datasets (MoNuSeg). For real-time evaluation, the proposed model was evaluated using PR-IHC-stained glass slides. It achieved the highest segmentation pixel-based F1-score of 0.902 and 0.903 for private and public datasets respectively, and a classification-based F1-score of 0.833 for private dataset. The experiment shows the robustness of our method where a model trained on ER-IHC dataset able to perform well on real-time microscopy of PR-IHC slides on both 20x and 40x magnification. This will help the pathologists with a quick decision-making process.
期刊介绍:
In 2022 the Journal of King Saud University - Computer and Information Sciences will become an author paid open access journal. Authors who submit their manuscript after October 31st 2021 will be asked to pay an Article Processing Charge (APC) after acceptance of their paper to make their work immediately, permanently, and freely accessible to all. The Journal of King Saud University Computer and Information Sciences is a refereed, international journal that covers all aspects of both foundations of computer and its practical applications.