MyROOT: a method and software for the semiautomatic measurement of primary root length in Arabidopsis seedlings.

Abstract

Root analysis is essential for both academic and agricultural research. Despite the great advances in root phenotyping and imaging, calculating root length is still performed manually and involves considerable amounts of labor and time. To overcome these limitations, we developed MyROOT, a software for the semiautomatic quantification of root growth of seedlings growing directly on agar plates. Our method automatically determines the scale from the image of the plate, and subsequently measures the root length of the individual plants. To this aim, MyROOT combines a bottom-up root tracking approach with a hypocotyl detection algorithm. At the same time as providing accurate root measurements, MyROOT also significantly minimizes the user intervention required during the process. Using Arabidopsis, we tested MyROOT with seedlings from different growth stages and experimental conditions. When comparing the data obtained from this software with that of manual root measurements, we found a high correlation between both methods (R 2 = 0.997). When compared with previous developed software with similar features (BRAT and EZ-Rhizo), MyROOT offered an improved accuracy for root length measurements. Therefore, MyROOT will be of great use to the plant science community by permitting high-throughput root length measurements while saving both labor and time.

Plant phenotyping relevance

根長を画像から半自動抽出するソフトウェアを開発し、手動測定および既存ソフトウェアと比較検証しており、植物フェノタイピング手法が研究の中心である。

Code and data availability

The authors deposited the MyROOT standalone executable application together with the root-length datasets generated in the study (Figures 3, 5 and S4) in a Zenodo repository with an explicit public DOI, making it a paper-specific, publicly actionable asset.