Background Plant root research can provide a way to attain stress-tolerant crops that produce greater yield in a diverse array of conditions. Phenotyping roots in soil is often challenging due to the roots being difficult to access and the use of time consuming manual methods. Rhizotrons allow visual inspection of root growth through transparent surfaces. Agronomists currently manually label photographs of roots obtained from rhizotrons using a line-intersect method to obtain root length density and rooting depth measurements which are essential for their experiments. We investigate the effectiveness of an automated image segmentation method based on the U-Net Convolutional Neural Network (CNN) architecture to enable such measurements. We design a data-set of 50 annotated chicory (Cichorium intybus L.) root images which we use to train, validate and test the system and compare against a baseline built using the Frangi vesselness filter. We obtain metrics using manual annotations and line-intersect counts. Results Our results on the held out data show our proposed automated segmentation system to be a viable solution for detecting and quantifying roots. We evaluate our system using 867 images for which we have obtained line-intersect counts, attaining a Spearman rank correlation of 0.9748 and an $$r^2$$r2 of 0.9217. We also achieve an $$F_1$$F1 of 0.7 when comparing the automated segmentation to the manual annotations, with our automated segmentation system producing segmentations with higher quality than the manual annotations for large portions of the image. Conclusion We have demonstrated the feasibility of a U-Net based CNN system for segmenting images of roots in soil and for replacing the manual line-intersect method. The success of our approach is also a demonstration of the feasibility of deep learning in practice for small research groups needing to create their own custom labelled dataset from scratch.

Aims Deep-rooted agricultural crops can potentially utilize deep soil moisture to reduce periods where growth is water limited. Chicory (Cichorium intybus L.) is a deep-rooted species, but the benefits of deep roots to water uptake has not been studied. The aim of this study was to investigate the value of deep roots (>2 m) under topsoil water limitation. Methods Chicory grown in 4 m deep soil-filled rhizotrons was exposed to either topsoil drought or resource competition from the shallow-rooted species ryegrass (Lolium perenne L.) and black medic (Medicago lupulina L.). The effect on deep water uptake was assessed using non-destructive measurements of roots, soil water and tracers. Results Water uptake occurred below 1.7 m depth in 2016, and below 2.3 m depth in 2017 and contributed significantly to chicory water use. However, neither surface soil drying nor intercropping increased deep water uptake to relieve water deficit in the shoots. Conclusion Chicory benefits from deep-roots during drought events, as it acceses deep soil moisture unavailable to more shallow rooted species, yet deep water uptake was unable to compensate for the reduced topsoil water uptake due to soil drying or crop competition.

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AimsDeep-rooted agricultural crops can potentially utilize deep water pools and thus reduce periods where growth is water limited. Chicory (Cichorium intybus L.) is known to be deep-rooted, but the contribution of deep roots to water uptake under well-watered and drought conditions by the deep root system has not been studied. The aim of this study was to investigate whether chicory could reach 3 m depth within a growing season and demonstrate significant water uptake from the deeper part of the root zone.MethodsWe tested if chicory exposed to either topsoil drought or resource competition from the shallow-rooted species ryegrass (Lolium perenne L.) and black medic (Medicago lupulina L.) would increase deep water uptake in compensation for reduced topsoil water uptake. We grew chicory in 4 m deep soil filled rhizotrons and found that the roots reached 3 m depth within a growing season.ResultsWater uptake from below 1.7 m depth in 2016 and 2.3 m depth in 2017 contributed significantly to chicory water use. However, neither drought nor intercropping increased the deep water uptake.ConclusionChicory benefits from being deep-rooted during drought events, yet deep water uptake cannot compensate for the reduced topsoil water uptake during drought.

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