STAVOS: A Medaka Larval Cardiac Video Segmentation Method Based on Deep Learning
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Published:2024-02-02
Issue:3
Volume:14
Page:1239
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ISSN:2076-3417
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Container-title:Applied Sciences
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language:en
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Short-container-title:Applied Sciences
Author:
Zeng Kui1, Xu Shutan1, Shu Daode1, Chen Ming1ORCID
Affiliation:
1. Key Laboratory of Fisheries Information, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Hucheng Ring Road 999, Shanghai 201306, China
Abstract
Medaka (Oryzias latipes), as a crucial model organism in biomedical research, holds significant importance in fields such as cardiovascular diseases. Currently, the analysis of the medaka ventricle relies primarily on visual observation under a microscope, involving labor-intensive manual operations and visual assessments that are cumbersome and inefficient for biologists. Despite attempts by some scholars to employ machine learning methods, limited datasets and challenges posed by the blurred edges of the medaka ventricle have constrained research to relatively simple tasks such as ventricle localization and heart rate statistics, lacking precise segmentation of the medaka ventricle edges. To address these issues, we initially constructed a video object segmentation dataset comprising over 7000 microscopic images of medaka ventricles. Subsequently, we proposed a semi-supervised video object segmentation model named STAVOS, incorporating a spatial-temporal attention mechanism. Additionally, we developed an automated system capable of calculating various parameters and visualizing results for a medaka ventricle using the provided video. The experimental results demonstrate that STAVOS has successfully achieved precise segmentation of medaka ventricle contours. In comparison to the conventional U-Net model, where a mean accuracy improvement of 0.392 was achieved, our model demonstrates significant progress. Furthermore, when compared to the state-of-the-art Tackling Background Distraction (TBD) model, there is an additional enhancement of 0.038.
Funder
Research and Development Planning in Key Areas of Guangdong Province Bioinformatics Research and Database Construction of Antifreeze Genes in Fish
Subject
Fluid Flow and Transfer Processes,Computer Science Applications,Process Chemistry and Technology,General Engineering,Instrumentation,General Materials Science
Reference28 articles.
1. Wang, J., and Cao, H. (2021). Zebrafish and Medaka: Important Animal Models for Human Neurodegenerative Diseases. Int. J. Mol. Sci., 22. 2. Cui, M., Su, L., Zhang, P., Zhang, H., Wei, H., Zhang, Z., and Zhang, X. (2020, January 13–16). Zebrafish Larva Heart Localization Using a Video Magnification Algorithm. Proceedings of the 2020 IEEE International Conference on Mechatronics and Automation (ICMA), Beijing, China. 3. An automated assay for the assessment of cardiac arrest in fish embryo;Puybareau;Comput. Biol. Med.,2017 4. Kang, C.-P., Tu, H.-C., Fu, T.-F., Wu, J.-M., Chu, P.-H., and Chang, D.T.-H. (2018). An automatic method to calculate heart rate from zebrafish larval cardiac videos. BMC Bioinform., 19. 5. ZebraBeat: A flexible platform for the analysis of the cardiac rate in zebrafish embryos;Zaccaria;Sci. Rep.,2014
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