Combining semi-automated image analysis techniques with machine learning algorithms to accelerate large-scale genetic studies
Genetic analyses of plant root systems require large datasets of extracted architectural traits. To quantify such traits from images of root systems, researchers often have to choose between automated tools (that are prone to error and extract only a limited number of architectural traits) or semi-a...
| Main Authors: | , , , , , |
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| Format: | Article |
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Oxford University Press
2017
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| Online Access: | https://eprints.nottingham.ac.uk/47203/ |
| _version_ | 1848797488872423424 |
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| author | Atkinson, Jonathan A. Lobet, Guillaume Noll, Manuel Meyer, Patrick E. Griffiths, Marcus Wells, Darren M. |
| author_facet | Atkinson, Jonathan A. Lobet, Guillaume Noll, Manuel Meyer, Patrick E. Griffiths, Marcus Wells, Darren M. |
| author_sort | Atkinson, Jonathan A. |
| building | Nottingham Research Data Repository |
| collection | Online Access |
| description | Genetic analyses of plant root systems require large datasets of extracted architectural traits. To quantify such traits from images of root systems, researchers often have to choose between automated tools (that are prone to error and extract only a limited number of architectural traits) or semi-automated ones (that are highly time consuming). We trained a Random Forest algorithm to infer architectural traits from automatically extracted image descriptors. The training was performed on a subset of the dataset, then applied to its entirety. This strategy allowed us to (i) decrease the image analysis time by 73% and (ii) extract meaningful architectural traits based on image descriptors. We also show that these traits are sufficient to identify the quantitative trait loci that had previously been discovered using a semi-automated method. We have shown that combining semi-automated image analysis with machine learning algorithms has the power to increase the throughput of large-scale root studies. We expect that such an approach will enable the quantification of more complex root systems for genetic studies. We also believe that our approach could be extended to other areas of plant phenotyping. |
| first_indexed | 2025-11-14T20:04:41Z |
| format | Article |
| id | nottingham-47203 |
| institution | University of Nottingham Malaysia Campus |
| institution_category | Local University |
| last_indexed | 2025-11-14T20:04:41Z |
| publishDate | 2017 |
| publisher | Oxford University Press |
| recordtype | eprints |
| repository_type | Digital Repository |
| spelling | nottingham-472032020-05-04T19:02:03Z https://eprints.nottingham.ac.uk/47203/ Combining semi-automated image analysis techniques with machine learning algorithms to accelerate large-scale genetic studies Atkinson, Jonathan A. Lobet, Guillaume Noll, Manuel Meyer, Patrick E. Griffiths, Marcus Wells, Darren M. Genetic analyses of plant root systems require large datasets of extracted architectural traits. To quantify such traits from images of root systems, researchers often have to choose between automated tools (that are prone to error and extract only a limited number of architectural traits) or semi-automated ones (that are highly time consuming). We trained a Random Forest algorithm to infer architectural traits from automatically extracted image descriptors. The training was performed on a subset of the dataset, then applied to its entirety. This strategy allowed us to (i) decrease the image analysis time by 73% and (ii) extract meaningful architectural traits based on image descriptors. We also show that these traits are sufficient to identify the quantitative trait loci that had previously been discovered using a semi-automated method. We have shown that combining semi-automated image analysis with machine learning algorithms has the power to increase the throughput of large-scale root studies. We expect that such an approach will enable the quantification of more complex root systems for genetic studies. We also believe that our approach could be extended to other areas of plant phenotyping. Oxford University Press 2017-08-23 Article PeerReviewed Atkinson, Jonathan A., Lobet, Guillaume, Noll, Manuel, Meyer, Patrick E., Griffiths, Marcus and Wells, Darren M. (2017) Combining semi-automated image analysis techniques with machine learning algorithms to accelerate large-scale genetic studies. GigaScience, 6 (10). pp. 1-7. ISSN 2047-217X https://academic.oup.com/gigascience/article/6/10/1/4091593/Combining-semiautomated-image-analysis-techniques doi:10.1093/gigascience/gix084 doi:10.1093/gigascience/gix084 |
| spellingShingle | Atkinson, Jonathan A. Lobet, Guillaume Noll, Manuel Meyer, Patrick E. Griffiths, Marcus Wells, Darren M. Combining semi-automated image analysis techniques with machine learning algorithms to accelerate large-scale genetic studies |
| title | Combining semi-automated image analysis techniques with machine learning algorithms to accelerate large-scale genetic studies |
| title_full | Combining semi-automated image analysis techniques with machine learning algorithms to accelerate large-scale genetic studies |
| title_fullStr | Combining semi-automated image analysis techniques with machine learning algorithms to accelerate large-scale genetic studies |
| title_full_unstemmed | Combining semi-automated image analysis techniques with machine learning algorithms to accelerate large-scale genetic studies |
| title_short | Combining semi-automated image analysis techniques with machine learning algorithms to accelerate large-scale genetic studies |
| title_sort | combining semi-automated image analysis techniques with machine learning algorithms to accelerate large-scale genetic studies |
| url | https://eprints.nottingham.ac.uk/47203/ https://eprints.nottingham.ac.uk/47203/ https://eprints.nottingham.ac.uk/47203/ |