Journal Article

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

Allain, Jean-Marc, Frachisse, Jean-Marie, Bianchi, Michele Wolfe, Guichard, Marjorie

2019

Overview

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.

• Publisher: BioMed Central,BioMed Central Ltd,Springer Nature B.V,BMC
• Subject: Algorithms / Artificial intelligence / Automation / Biological Techniques / Biomechanics / Biomedical and Life Sciences / Botanical research / Cell elongation / computer software / Data analysis / Differentiation / Elongated structure / Fiji / Growth rate / Image analysis / Image analysis equipment / Image detection / Image processing / Image processing equipment / Legumes / Life Sciences / Machine learning / Mathematical models / Measurement / Mechanics / Medicago truncatula / Methodology / Methods / Nutrient uptake / Parameters / phenotype / Phenotyping / Physics / Physiological aspects / Plant Sciences / Position measurement / Root / Root hair / Root hairs / root tips / Roots (Botany) / soil / Soils