Using k-NN to analyse images of diverse germination phenotypes and detect single seed germination in Miscanthus sinensis

• Published in: Plant methods Vol. 14; no. 1; p. 5
• Main Authors: Awty-Carroll, Danny, Clifton-Brown, John, Robson, Paul
• Format: Journal Article
• Language: English
• Published: London BioMed Central 17.01.2018; BioMed Central Ltd; BMC
• Subjects: algorithms; artificial intelligence; Biological Techniques; Biomedical and Life Sciences; Classification; Comparative analysis; energy crops; Genetic aspects; Germination; humans; k-NN; Life Sciences; Machine learning; Methodology; Miscanthus; Miscanthus sinensis; phenotype; Physiological aspects; Plant Sciences; Plants in Computer Vision; rhizomes; Seed; seed germination; United Kingdom; NN; Image analysis; Seed; Germination; Machine learning; Classification; Robust classification; Seed imaging; Bio-energy; k-NN; Miscanthus
• ISSN: 1746-4811; 1746-4811
• DOI: 10.1186/s13007-018-0272-0

Background Miscanthus is a leading second generation bio-energy crop. It is mostly rhizome propagated; however, the increasing use of seed is resulting in a greater need to investigate germination. Miscanthus seed are small, germination is often poor and carried out without sterilisation; therefore, automated methods applied to germination detection must be able to cope with, for example, thresholding of small objects, low germination frequency and the presence or absence of mould. Results Machine learning using k -NN improved the scoring of different phenotypes encountered in Miscanthus seed. The k -NN-based algorithm was effective in scoring the germination of seed images when compared with human scores of the same images. The trueness of the k -NN result was 0.69–0.7, as measured using the area under a ROC curve. When the k -NN classifier was tested on an optimised image subset of seed an area under the ROC curve of 0.89 was achieved. The method compared favourably to an established technique. Conclusions With non-ideal seed images that included mould and broken seed the k -NN classifier was less consistent with human assessments. The most accurate assessment of germination with which to train classifiers is difficult to determine but the k -NN classifier provided an impartial consistent measurement of this important trait. It was more reproducible than the existing human scoring methods and was demonstrated to give a high degree of trueness to the human score.