An optimized pipeline for live imaging whole Arabidopsis leaves at cellular resolution.

Abstract

Background Live imaging is the gold standard for determining how cells give rise to organs. However, tracking many cells across whole organs over large developmental time windows is extremely challenging. In this work, we provide a comparably simple method for confocal live imaging entire Arabidopsis thaliana first leaves across early development. Our imaging method works for both wild-type leaves and the complex curved leaves of the jaw-1D mutant. Results We find that dissecting the cotyledons, affixing a coverslip above the samples and mounting samples with perfluorodecalin yields optimal imaging series for robust cellular and organ level analysis. We provide details of our complementary image processing steps in MorphoGraphX software for segmenting, tracking lineages, and measuring a suite of cellular properties. We also provide MorphoGraphX image processing scripts we developed to automate analysis of segmented images and data presentation. Conclusions Our imaging techniques and processing steps combine into a robust imaging pipeline. With this pipeline we are able to examine important nuances in the cellular growth and differentiation of jaw-D versus WT leaves that have not been demonstrated before. Our pipeline is approachable and easy to use for leaf development live imaging.

Plant phenotyping relevance

Arabidopsis葉の生細胞イメージング、画像処理、細胞追跡・形質測定を統合した再利用可能な表現型解析パイプラインの開発が中心である。

Code and data availability

The paper publicly deposits its live-imaging datasets (confocal imaging data for the figures) on OSF under CC-BY 4.0, and its MorphoGraphX/R analysis scripts on the authors' GitHub repositories, all explicitly linked in the Availability of data and materials section.