ColourQuant: a high-throughput technique to extract and quantify colour phenotypes from plant images

Abstract: Colour patterning contributes to important plant traits that influence ecological interactions, horticultural breeding, and agricultural performance. High-throughput phenotyping of colour is valuable for understanding plant biology and selecting for traits related to colour during plant breeding. Here we present ColourQuant, an automated high-throughput pipeline that allows users to extract colour phenotypes from images. This pipeline includes methods for colour phenotyping using mean pixel values, Gaussian density estimator of Lab colour, and the analysis of shape-independent colour patterning by circular deformation.