Title: KymoTip: High-throughput Characterization of Tip-growth Dynamics in Plant Cells

Abstract

Summary Live imaging data analysis often requires an objective, local, and accurate way of quantification of cell dynamics. In the research field of polarized tip-growth, the cell fluctuations and/or fluctuations in tip position and growth direction hampers automated analyses of huge amounts of imaging sequences. The fluctuated nature in data makes it unclear how cell shape and growth are linked to intracellular events that could be the actual driving force of cell growth. To overcome these difficulties, we developed a powerful and user-friendly tool called KymoTip with an available format. In this software, novel functions such as coordinate normalization, tip-bottom detection, and signal kymograph were implemented. We confirmed that not only plasma membrane-labeled fluorescent images, but also images such as bright-field and cortical microtubule markers —so long as the cell contours can be identified— are amenable to KymoTip. Furthermore, by combining markers for cell contours with those that visualize intracellular structures, it becomes possible to quantitatively analyze various intracellular events, such as nuclear migration and calcium wave, in conjunction with cellular growth dynamics. Since KymoTip can be handled by non-specialist, it is expected to promote understanding of what happens at the sub- and cellular level with high throughput outcomes. Significance statement Faced with fluctuations in cell coordinates and cell tip positions, position correction of live imaging data and accurate detection of tip position are key challenges in plant developmental biology. We solved them with a powerful and user-friendly tool, KymoTip, that can realize cell position correction, cell tip detection with cell centerline, and quantification of intracellular events.

Plant phenotyping relevance

植物細胞のライブイメージから細胞形状・先端位置・成長動態を定量化する解析ソフトウェアを開発しており、植物フェノタイピング手法が中心です。

Code and data availability

The paper's authors explicitly state that the KymoTip analysis code is publicly available on GitHub at https://github.com/blues0910/KymoTip, which is an allowed URL. This is the authors' own computational tool implementing the paper's tip-growth phenotyping analysis (segmentation, coordinate normalization, tip-bottom,