SeedExtractor: An open-source GUI for seed image analysis
Accurate measurement of seed size parameters is essential for both breeding efforts aimed at enhancing yields and basic research focused on discovering genetic components that regulate seed size. To address this need, we have developed an open-source graphical user interface (GUI) software, SeedExtr...
| Autores principales: | , , , , , , , , , |
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| Formato: | Journal Article |
| Lenguaje: | Inglés |
| Publicado: |
Frontiers Media
2021
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| Materias: | |
| Acceso en línea: | https://hdl.handle.net/10568/164354 |
| _version_ | 1855540010350018560 |
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| author | Zhu, Feiyu Paul, Puneet Hussain, Waseem Wallman, Kyle Dhatt, Balpreet K. Sandhu, Jaspreet Irvin, Larissa Morota, Gota Yu, Hongfeng Walia, Harkamal |
| author_browse | Dhatt, Balpreet K. Hussain, Waseem Irvin, Larissa Morota, Gota Paul, Puneet Sandhu, Jaspreet Walia, Harkamal Wallman, Kyle Yu, Hongfeng Zhu, Feiyu |
| author_facet | Zhu, Feiyu Paul, Puneet Hussain, Waseem Wallman, Kyle Dhatt, Balpreet K. Sandhu, Jaspreet Irvin, Larissa Morota, Gota Yu, Hongfeng Walia, Harkamal |
| author_sort | Zhu, Feiyu |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | Accurate measurement of seed size parameters is essential for both breeding efforts aimed at enhancing yields and basic research focused on discovering genetic components that regulate seed size. To address this need, we have developed an open-source graphical user interface (GUI) software, SeedExtractor that determines seed size and shape (including area, perimeter, length, width, circularity, and centroid), and seed color with capability to process a large number of images in a time-efficient manner. In this context, our application takes ∼2 s for analyzing an image, i.e., significantly less compared to the other tools. As this software is open-source, it can be modified by users to serve more specific needs. The adaptability of SeedExtractor was demonstrated by analyzing scanned seeds from multiple crops. We further validated the utility of this application by analyzing mature-rice seeds from 231 accessions in Rice Diversity Panel 1. The derived seed-size traits, such as seed length, width, were used for genome-wide association analysis. We identified known loci for regulating seed length (GS3) and width (qSW5/GW5) in rice, which demonstrates the accuracy of this application to extract seed phenotypes and accelerate trait discovery. In summary, we present a publicly available application that can be used to determine key yield-related traits in crops. |
| format | Journal Article |
| id | CGSpace164354 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2021 |
| publishDateRange | 2021 |
| publishDateSort | 2021 |
| publisher | Frontiers Media |
| publisherStr | Frontiers Media |
| record_format | dspace |
| spelling | CGSpace1643542024-12-19T14:13:37Z SeedExtractor: An open-source GUI for seed image analysis Zhu, Feiyu Paul, Puneet Hussain, Waseem Wallman, Kyle Dhatt, Balpreet K. Sandhu, Jaspreet Irvin, Larissa Morota, Gota Yu, Hongfeng Walia, Harkamal plant science Accurate measurement of seed size parameters is essential for both breeding efforts aimed at enhancing yields and basic research focused on discovering genetic components that regulate seed size. To address this need, we have developed an open-source graphical user interface (GUI) software, SeedExtractor that determines seed size and shape (including area, perimeter, length, width, circularity, and centroid), and seed color with capability to process a large number of images in a time-efficient manner. In this context, our application takes ∼2 s for analyzing an image, i.e., significantly less compared to the other tools. As this software is open-source, it can be modified by users to serve more specific needs. The adaptability of SeedExtractor was demonstrated by analyzing scanned seeds from multiple crops. We further validated the utility of this application by analyzing mature-rice seeds from 231 accessions in Rice Diversity Panel 1. The derived seed-size traits, such as seed length, width, were used for genome-wide association analysis. We identified known loci for regulating seed length (GS3) and width (qSW5/GW5) in rice, which demonstrates the accuracy of this application to extract seed phenotypes and accelerate trait discovery. In summary, we present a publicly available application that can be used to determine key yield-related traits in crops. 2021-02-01 2024-12-19T12:53:46Z 2024-12-19T12:53:46Z Journal Article https://hdl.handle.net/10568/164354 en Open Access Frontiers Media Zhu, Feiyu; Paul, Puneet; Hussain, Waseem; Wallman, Kyle; Dhatt, Balpreet K.; Sandhu, Jaspreet; Irvin, Larissa; Morota, Gota; Yu, Hongfeng and Walia, Harkamal. 2021. SeedExtractor: An open-source GUI for seed image analysis. Front. Plant Sci., Volume 11 |
| spellingShingle | plant science Zhu, Feiyu Paul, Puneet Hussain, Waseem Wallman, Kyle Dhatt, Balpreet K. Sandhu, Jaspreet Irvin, Larissa Morota, Gota Yu, Hongfeng Walia, Harkamal SeedExtractor: An open-source GUI for seed image analysis |
| title | SeedExtractor: An open-source GUI for seed image analysis |
| title_full | SeedExtractor: An open-source GUI for seed image analysis |
| title_fullStr | SeedExtractor: An open-source GUI for seed image analysis |
| title_full_unstemmed | SeedExtractor: An open-source GUI for seed image analysis |
| title_short | SeedExtractor: An open-source GUI for seed image analysis |
| title_sort | seedextractor an open source gui for seed image analysis |
| topic | plant science |
| url | https://hdl.handle.net/10568/164354 |
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