A simple hand-sectioning approach for cellular-resolution imaging of anatomy and gene expression in small developing organs and boundary regions in Arabidopsis.

Abstract

Background Precise characterization of gene expression patterns across temporal, cellular, and tissue-specific contexts is fundamental to understanding plant development and function. Recent advances in ClearSee-based tissue clearing have enabled high-resolution visualization of internal structures and fluorescent reporter signals in plant tissues. Although hand sectioning can provide optical access to tissues that are not amenable to whole-mount clearing, its application to submillimeter-scale and fragile Arabidopsis organs and tissues, including developing inflorescence apices, flowers, fruits, and organ boundaries, has remained limited. Consequently, analysis of these tissues has largely depended on specialized microdissection techniques and labor-intensive histological workflows, such as wax- or resin-embedded microtomy, which restrict throughput, accessibility, and routine use. Results We developed and optimized a simple hand-sectioning and imaging method that enables routine visualization of anatomical organization and gene expression patterns at cellular resolution in small, fragile Arabidopsis tissues. This method relies only on gentle manual tissue processing under a stereomicroscope and readily available reagents, allowing reproducible preparation of delicate tissues without the need for embedding or specialized equipment. Combined with ClearSee-based clearing and fluorescent reporters, the approach enables high-resolution imaging of internal tissue architecture and gene expression, while preserving tissue integrity and fluorescence signals that are often compromised during conventional embedding and microtomy procedures. Conclusions Our method substantially reduces technical complexity, costs, preparation time, and labor associated with cellular-resolution imaging of small, fragile plant tissues. By providing a simple, scalable, and accessible alternative to conventional histological workflows, this approach facilitates routine analysis of internal developmental processes across diverse plant species.

Plant phenotyping relevance

小型・脆弱な植物組織の解剖学的構造と遺伝子発現を細胞解像度で取得する手法を開発・最適化しており、表現型取得法が研究の中心である。

Code and data availability

The supplied blocks describe a hand-sectioning/ClearSee/CLSM imaging protocol for Arabidopsis tissues, but contain no public phenotype dataset, image collection, analysis code, or trained model deposit. No data or code availability statement with an authors' public URL appears; only accession numbers for TAIR genes (c-

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