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OrgaNet: A Deep Learning Approach for Automated Evaluation of Organoids Viability in Drug Screening
Xuesheng Bian1,2; Gang Li3; Cheng Wang1,2; Siqi Shen1; Weiquan Liu1; Xiuhong Lin1; Zexin Chen4; Mancheung Cheung5; XiongBiao Luo1
2021
Conference Name17th International Symposium on Bioinformatics Research and Applications (ISBRA)
Source PublicationLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume13064
Pages411-423
Conference DateNOV 26-28, 2021
Conference PlaceShenzhen, PEOPLES R CHINA
CountryCHINA
Publication PlaceGERMANY
PublisherSPRINGER-VERLAG BERLIN
Abstract

Organoid, a 3D in vitro cell culture, has high similarities with derived tissues or organs in vivo, which makes it widely used in personalized drug screening. Although organoids play an essential role in drug screening, the existing methods are difficult to accurately evaluate the viability of organoids, making the existing methods still have many limitations in robustness and accuracy. Determination of Adenosine triphosphate (ATP) is a mature way to analyze cell viability, which is commonly used in drug screening. However, ATP bioluminescence technique has an inherent flaw. All living cells will be lysed during ATP determination. Therefore, ATP bioluminescence technique is an end-point method, which only assess cell viability in the current state and unable to evaluate the change trend of cell viability before or after medication. In this paper, we propose a deep learning based framework, OrgaNet, for organoids viability evaluation based on organoid images. It is a straightforward and repeatable solution to evaluate organoid viability, promoting the reliability of drug screening. The OrgaNet consists of three parts: a feature extractor, extracts the representation of organoids; a multi-head classifier, improves feature robustness through supervised learning; a scoring function, measures organoids viability through contrastive learning. Specifically, to optimize our proposed OrgaNet, we constructed the first dedicated dataset, which is annotated by seven experienced experts. Experiments demonstrate that the OrgaNet shows great potential in organoid viability evaluation. The OrgaNet provides another solution to evaluate organoids viability and shows a high correlation compared with ATP bioluminescence technique. Availability: https://github.com/541435721/OrgaNet

KeywordAtp Drug Screening Microscopy Image Organoid
DOI10.1007/978-3-030-91415-8_35
URLView the original
Indexed ByCPCI-S
Language英語English
WOS Research AreaComputer Science ; Mathematical & Computational Biology
WOS SubjectComputer Science, Information Systems ; Computer Science, Interdisciplinary Applications ; Mathematical & Computational Biology
WOS IDWOS:000922632800035
Scopus ID2-s2.0-85120618647
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Citation statistics
Document TypeConference paper
CollectionUniversity of Macau
Corresponding AuthorCheng Wang
Affiliation1.Fujian Key Laboratory of Sensing and Computing for Smart Cities, School of Informatics, Xiamen University, Xiamen, 361005, China
2.National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, 361005, China
3.Otolaryngology-Head and Neck Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, 510000, China
4.Zhuhai UM Science and Technology Research Institute, The University of Macau, Zhuhai, 519000, China
5.Accurate International Biotechnology (GZ) Company, Guangzhou, 510000, China
Recommended Citation
GB/T 7714
Xuesheng Bian,Gang Li,Cheng Wang,et al. OrgaNet: A Deep Learning Approach for Automated Evaluation of Organoids Viability in Drug Screening[C], GERMANY:SPRINGER-VERLAG BERLIN, 2021, 411-423.
APA Xuesheng Bian., Gang Li., Cheng Wang., Siqi Shen., Weiquan Liu., Xiuhong Lin., Zexin Chen., Mancheung Cheung., & XiongBiao Luo (2021). OrgaNet: A Deep Learning Approach for Automated Evaluation of Organoids Viability in Drug Screening. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 13064, 411-423.
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