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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.

Authors

JONATHAN ATKINSON JONATHAN.ATKINSON@NOTTINGHAM.AC.UK
Future Food Beacon:Technologist in Phenomics

Guillaume Lobet

Manuel Noll

Patrick E. Meyer

Marcus Griffiths

DARREN WELLS DARREN.WELLS@NOTTINGHAM.AC.UK
Principal Research Fellow



Abstract

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.

Journal Article Type Article
Publication Date Oct 1, 2017
Journal GigaScience
Electronic ISSN 2047-217X
Publisher Oxford University Press
Peer Reviewed Peer Reviewed
Volume 6
Issue 10
APA6 Citation Atkinson, J. A., Lobet, G., Noll, M., Meyer, P. E., Griffiths, M., & Wells, D. M. (2017). Combining semi-automated image analysis techniques with machine learning algorithms to accelerate large-scale genetic studies. GigaScience, 6(10), https://doi.org/10.1093/gigascience/gix084
DOI https://doi.org/10.1093/gigascience/gix084
Publisher URL https://academic.oup.com/gigascience/article/6/10/1/4091593/Combining-semiautomated-image-analysis-techniques
Copyright Statement Copyright information regarding this work can be found at the following address: http://creativecommons.org/licenses/by/4.0

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Copyright Statement
Copyright information regarding this work can be found at the following address: http://creativecommons.org/licenses/by/4.0





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