Spatial Imaging and Quantification of Hydrogen Peroxide in Arabidopsis Roots: From Sample Preparation to Image...

Reactive oxygen species (ROS) are central regulators of plant development and stress responses, with hydrogen peroxide (H₂O₂) acting as a key signaling molecule whose spatial distribution determines adaptive versus damaging outcomes. Accurate detection of H₂O₂ at tissue and cellular resolution is therefore essential for understanding redox-dependent regulation of plant growth. A variety of techniques have been used to monitor H₂O₂, including bulk spectrophotometric and fluorometric assays, genetically encoded sensors for real-time measurements, and chemical probes for in situ detection. While these approaches differ in sensitivity, specificity, and temporal resolution, many are limited by a lack of spatial information, technical complexity, or dependence on transgenic material. Here, we present a detailed protocol for 3,3'-diaminobenzidine (DAB)-based histochemical detection of H₂O₂ in seedling roots, covering staining, imaging, and semi-quantitative image analysis using open-source software (FIJI/ImageJ). The method relies on peroxidase-mediated oxidation of DAB, resulting in a stable, light-resistant, and insoluble precipitate that enables visualization of H₂O₂ accumulation with high spatial resolution. This protocol provides a robust, accessible, and genetically independent approach for spatial analysis of H₂O₂ in plant tissues. Its simplicity, compatibility with diverse genotypes and treatments, and suitability for semi-quantitative analysis make it a valuable tool for examining the spatial distribution of H₂O₂, thereby providing spatial insight into redox-related regulatory processes during plant development and stress responses. Key features • Built upon methods developed by Thordal-Christensen et al. [1] and Daudi and O'Brien [2], with a specific focus on root staining. • Includes a downstream image analysis pipeline for semi-quantitative H₂O₂ measurement in DAB-stained roots using the open-source software FIJI/ImageJ. • Provides detailed, step-by-step video tutorials for image analysis in FIJI/ImageJ. • Includes a Fiji/ImageJ script (Macro 1) for automating the application of fixed-intensity scaling using Spectrum LUT.