A Deep Learning-Based Approach for High-Throughput Hypocotyl Phenotyping.
Orsolya DobosPeter HorvathFerenc NagyTivadar DankaAndrás VicziánPublished in: Plant physiology (2019)
Hypocotyl length determination is a widely used method to phenotype young seedlings. The measurement itself has advanced from using rulers and millimeter papers to assessing digitized images but remains a labor-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.
Keyphrases
- deep learning
- high throughput
- convolutional neural network
- arabidopsis thaliana
- artificial intelligence
- high resolution
- single cell
- machine learning
- endothelial cells
- transcription factor
- big data
- rna seq
- magnetic resonance
- photodynamic therapy
- optical coherence tomography
- electronic health record
- fluorescence imaging
- induced pluripotent stem cells
- high intensity
- resistance training
- liquid chromatography
- data analysis