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Background  One of the main challenges associated with image-based field phenotyping is the variability of illumination. During a single day’s imaging session, or between different sessions on different days, the sun moves in and out of cloud cover and has varying intensity. How is one to know from consecutive images alone if a plant has become darker over time, or if the weather conditions have simply changed from clear to overcast? This is a significant problem to address as colour is an important phenotypic trait that can be measured automatically from images.    Results  In this work we use an industry standard colour checker to balance the colour in images within and across every day of a field trial conducted over four months in 2016. By ensuring that the colour checker is present in every image we are afforded a ‘ground truth’ to correct for varying illumination conditions across images. We employ a least squares approach to fit a quadratic model for correcting RGB values of an image in such a way that the observed values of the colour checker tiles align with their true values after the transformation.    Conclusions  The proposed method is successful in reducing the error between observed and reference colour chart values in all images. Furthermore, the standard deviation of mean canopy colour across multiple days is reduced significantly after colour correction is applied. Finally, we use a number of examples to demonstrate the usefulness of accurate colour measurements in recording phenotypic traits and analysing variation among varieties and treatments.    Electronic supplementary material  The online version of this article (10.1186/s13007-018-0308-5) contains supplementary material, which is available to authorized users.

Land-based crop phenotyping by image analysis: consistent canopy characterization from inconsistent field illumination