Supporting data for "Deep Machine Learning provides state-of-the-art performance in image-based plant phenotyping"

Dataset type: Software, Imaging
Data released on August 24, 2017

Pound MP; Atkinson JA; Burgess AJ; Wilson MH; Griffiths M; Jackson AS; Bulat A; Tzimiropoulos G; Wells DM; Murchie EH; Pridmore TP; French AP (2017): Supporting data for "Deep Machine Learning provides state-of-the-art performance in image-based plant phenotyping" GigaScience Database.


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 localisation. 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 QTL were also discovered using our automated approach based on the deep learning detection to locate plant features.
We have shown deep-learning-based phenotyping to have very good detection and localisation 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 QTL 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.


Additional details

Read the peer-reviewed publication(s):

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), 1–10. doi:10.1093/gigascience/gix083

Related datasets:

doi:10.5524/100343 Cites doi:10.5524/100346

Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
Root Images4565Canadian hard winter wheatbread wheatTriticum aestivum Age:11
Shoot Images4565Canadian hard winter wheatbread wheatTriticum aestivum Life stage:anthesis
Displaying 1-2 of 2 Sample(s).

File NameSample IDData TypeFile FormatSizeRelease Date 
OtherUNKNOWN20.68 KB2017-08-16
Mixed archiveTAR32.07 MB2017-08-16
Mixed archiveTAR128.11 MB2017-08-16
ScriptUNKNOWN0.11 KB2017-08-16
ScriptUNKNOWN0.18 KB2017-08-16
ScriptUNKNOWN0.11 KB2017-08-16
ScriptUNKNOWN0.11 KB2017-08-16
ScriptPython2.17 KB2017-08-16
ScriptPython2.09 KB2017-08-16
ScriptPython3.02 KB2017-08-16
Displaying 1-10 of 39 File(s).
Funding body Awardee Award ID Comments
European Research Council MJ Bennett 294729 FP7 Ideas

Date Action
August 25, 2017 Dataset publish
October 17, 2017 Manuscript Link added : 10.1093/gigascience/gix083