Clearing techniques for deeper imaging of plants and plant-microbe interactions.

Abstract

Plant cells are uniquely characterized by exhibiting cell walls, pigments, and phenolic compounds, which can impede microscopic observations by absorbing and scattering light. The concept of clearing was first proposed in the late nineteenth century to address this issue, aiming to render plant specimens transparent using chloral hydrate. Clearing techniques involve chemical procedures that render biological specimens transparent, enabling deep imaging without physical sectioning. Drawing inspiration from clearing techniques for animal specimens, various protocols have been adapted for plant research. These procedures include (i) hydrophobic methods (e.g., Visikol™), (ii) hydrophilic methods (ScaleP and ClearSee), and (iii) hydrogel-based methods (PEA-CLARITY). Initially, clearing techniques for plants were mainly utilized for deep imaging of seeds and leaves of herbaceous plants such as Arabidopsis thaliana and rice. Utilizing cell wall-specific fluorescent dyes for plants and fungi, researchers have documented the post-penetration behavior of plant pathogenic fungi within hosts. State-of-the-art plant clearing techniques, coupled with microbe-specific labeling and high-throughput imaging methods, offer the potential to advance the in planta characterization of plant microbiomes.

Plant phenotyping relevance

植物試料を透明化して深部画像を取得する技術を体系的に扱うレビューであり、植物の形態や植物—微生物相互作用の観察に用いる画像取得法が中心です。

Code and data availability

This is a review article on plant clearing techniques. It contains no paper-specific phenotype datasets, images, analysis code, or trained models; all figures are adapted from cited prior work. The only availability statement is 'Data and materials are available on request', which does not constitute a public asset.

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