Deep machine learning provides state-of-the-art performance in image-based plant phenotyping
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Abstract
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.
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Now published in GigaScience doi: 10.1093/gigascience/gix083
Michael P. Pound 1The School of Computer Science, University of Nottingham,UKFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Michael P. PoundAlexandra J. Burgess 2The School of Biosciences, University of Nottingham, UKFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Alexandra J. BurgessMichael H. Wilson 3Centre for Plant Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, UKFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Michael H. WilsonJonathan A. Atkinson 2The School of Biosciences, University of Nottingham, UKFind this author on Google ScholarFind this author on …
Now published in GigaScience doi: 10.1093/gigascience/gix083
Michael P. Pound 1The School of Computer Science, University of Nottingham,UKFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Michael P. PoundAlexandra J. Burgess 2The School of Biosciences, University of Nottingham, UKFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Alexandra J. BurgessMichael H. Wilson 3Centre for Plant Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, UKFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Michael H. WilsonJonathan A. Atkinson 2The School of Biosciences, University of Nottingham, UKFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Jonathan A. AtkinsonMarcus Griffiths 2The School of Biosciences, University of Nottingham, UKFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteAaron S. Jackson 1The School of Computer Science, University of Nottingham,UKFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteAdrian Bulat 1The School of Computer Science, University of Nottingham,UKFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteyorgos Tzimiropoulos 1The School of Computer Science, University of Nottingham,UKFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for yorgos TzimiropoulosDarren M. Wells 2The School of Biosciences, University of Nottingham, UKFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Darren M. WellsErik H. Murchie 2The School of Biosciences, University of Nottingham, UKFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Erik H. MurchieTony P. Pridmore 1The School of Computer Science, University of Nottingham,UKFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Tony P. PridmoreAndrew P. French 1The School of Computer Science, University of Nottingham,UK2The School of Biosciences, University of Nottingham, UKFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Andrew P. FrenchFor correspondence: andrew.p.french@nottingham.ac.uk
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/gix083 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.100812 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.100813
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