Root Hair Sizer: an algorithm for high throughput recovery of different root hair and root developmental parameters.

Abstract

Background The root is an important organ for water and nutrient uptake, and soil anchorage. It is equipped with root hairs (RHs) which are elongated structures increasing the exchange surface with the soil. RHs are also studied as a model for plant cellular development, as they represent a single cell with specific and highly regulated polarized elongation. For these reasons, it is useful to be able to accurately quantify RH length employing standardized procedures. Methods commonly employed rely on manual steps and are therefore time consuming and prone to errors, restricting analysis to a short segment of the root tip. Few partially automated methods have been reported to increase measurement efficiency. However, none of the reported methods allow an accurate and standardized definition of the position along the root for RH length measurement, making data comparison difficult. Results We developed an image analysis algorithm that semi-automatically detects RHs and measures their length along the whole differentiation zone of roots. This method, implemented as a simple automated script in ImageJ/ Fiji software that we termed Root Hair Sizer, slides a rectangular window along a binarized and straightened image of root tips to estimate the maximal RH length in a given measuring interval. This measure is not affected by heavily bent RHs and any bald spots. RH length data along the root are then modelled with a sigmoidal curve, generating several biologically significant parameters such as RH length, positioning of the root differentiation zone and, under certain conditions, RH growth rate. Conclusions Image analysis with Root Hair Sizer and subsequent sigmoidal modelling of RH length data provide a simple and efficient way to characterize RH growth in different conditions, equally suitable to small and large scale phenotyping experiments.

Plant phenotyping relevance

根毛長などの植物形質を画像から半自動抽出・モデル化するアルゴリズムを開発し、大規模フェノタイピングへの適用を明示しているため。

Code and data availability

The paper's Root Hair Sizer analysis scripts (ImageJ/Fiji macros for Medicago, Brachypodium, and Arabidopsis) are published as open-access supplementary files (Additional files 1, 3, 4, 6) of this article, along with a demonstration movie and example root images. No standalone repository URL is given in the supplied; 1