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Deep machine learning provides state-of-the-art performance in image-based plant phenotyping

Pound, Michael P.; Atkinson, Jonathan A.; Townsend, Alexandra J.; Wilson, Michael H.; Griffiths, Marcus; Jackson, Aaron S.; Bulat, Adrian; Tzimiropoulos, Georgios; Wells, Darren M.; Murchie, Erik H.; Pridmore, Tony P.; French, Andrew P.


Future Food Beacon:Technologist in Phenomics

Future Food Beacon:Technologist in Bioinformatics/Computational Biology

Marcus Griffiths

Adrian Bulat

Georgios Tzimiropoulos

Principal Research Fellow

Professor of Applied Plant Physiology

Professor of Computer Science


© The Author 2017. In plant phenotyping, it has become important to be able to measure many features on large image sets in order to aid genetic discovery. The size of the datasets, now often captured robotically, often precludes manual inspection, hence the motivation for finding a fully automated approach. Deep learning is an emerging field that promises unparalleled results on many data analysis problems. Building on artificial neural networks, deep approaches have many more hidden layers in the network, and hence have greater discriminative and predictive power. We demonstrate the use of such approaches as part of a plant phenotyping pipeline. We show the success offered by such techniques when applied to the challenging problem of image-based plant phenotyping and demonstrate state-of-the-art results (>97% accuracy) for root and shoot feature identification and localization. We use fully automated trait identification using deep learning to identify quantitative trait loci in root architecture datasets. The majority (12 out of 14) of manually identified quantitative trait loci were also discovered using our automated approach based on deep learning detection to locate plant features. We have shown deep learning-based phenotyping to have very good detection and localization accuracy in validation and testing image sets. We have shown that such features can be used to derive meaningful biological traits, which in turn can be used in quantitative trait loci discovery pipelines. This process can be completely automated. We predict a paradigm shift in image-based phenotyping bought about by such deep learning approaches, given sufficient training sets.


Pound, M. P., Atkinson, J. A., Townsend, A. J., Wilson, M. H., Griffiths, M., Jackson, A. S., …French, A. P. (2017). Deep machine learning provides state-of-the-art performance in image-based plant phenotyping. GigaScience, 6(10),

Journal Article Type Article
Acceptance Date Aug 16, 2017
Online Publication Date Aug 23, 2017
Publication Date Oct 1, 2017
Deposit Date Oct 16, 2017
Publicly Available Date Oct 16, 2017
Journal GigaScience
Electronic ISSN 2047-217X
Publisher Oxford University Press (OUP)
Peer Reviewed Peer Reviewed
Volume 6
Issue 10
Article Number gix083
Keywords Phenotyping; Deep learning; Root; Shoot; QTL; Image analysis
Public URL
Publisher URL
Copyright Statement Copyright information regarding this work can be found at the following address:


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Copyright Statement
Copyright information regarding this work can be found at the following address:

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