A deep learning-based approach for high-throughput hypocotyl phenotyping

Dobos, Orsolya and Horváth, Péter and Nagy, Ferenc István and Danka, Tivadar and Viczián, András (2019) A deep learning-based approach for high-throughput hypocotyl phenotyping. PLANT PHYSIOLOGY, AiP. ISSN 0032-0889

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Abstract

Hypocotyl length determination is a widely used method to phenotype young seedlings. The measurement itself has advanced from using rulers and millimetre papers to assessing digitized images but remains a labour-intensive, monotonous and time-consuming procedure. To make high-throughput plant phenotyping possible, we developed a deep learning-based approach to simplify and accelerate this method. Our pipeline does not require a specialized imaging system but works well with low-quality images produced with a simple flatbed scanner or a smartphone camera. Moreover, it is easily adaptable for a diverse range of datasets not restricted to Arabidopsis (Arabidopsis thaliana). Furthermore, we show that the accuracy of the method reaches human performance. We not only provide the full code at https://github.com/biomag-lab/hypocotyl-UNet, but also give detailed instructions on how the algorithm can be trained with custom data, tailoring it for the requirements and imaging setup of the user.

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