The plant leaf movement analyzer (PALMA): a simple tool for the analysis of periodic cotyledon and leaf movement in Arabidopsis thaliana .

Abstract

Background The analysis of circadian leaf movement rhythms is a simple yet effective method to study effects of treatments or gene mutations on the circadian clock of plants. Currently, leaf movements are analysed using time lapse photography and subsequent bioinformatics analyses of leaf movements. Programs that are used for this purpose either are able to perform one function (i.e. leaf tip detection or rhythm analysis) or their function is limited to specific computational environments. We developed a leaf movement analysis tool-PALMA-that works in command line and combines image extraction with rhythm analysis using Fast Fourier transformation and non-linear least squares fitting. Results We validated PALMA in both simulated time series and in experiments using the known short period mutant sensitivity to red light reduced 1 ( srr1 - 1 ). We compared PALMA with two established leaf movement analysis tools and found it to perform equally well. Finally, we tested the effect of reduced iron conditions on the leaf movement rhythms of wild type plants. Here, we found that PALMA successfully detected period lengthening under reduced iron conditions. Conclusions PALMA correctly estimated the period of both simulated and real-life leaf movement experiments. As a platform-independent console-program that unites both functions needed for the analysis of circadian leaf movements it is a valid alternative to existing leaf movement analysis tools.

Plant phenotyping relevance

PALMAは、植物の葉運動という表現型を画像から抽出し、周期を解析するソフトウェアとして開発・検証されており、方法論が研究の中心です。

Code and data availability

The paper's authors publicly deposited the PALMA leaf movement analysis code (Additional file 2) on SourceForge; the URL matches an allowed entry. No phenotype datasets or images were separately deposited.