Accelerating Automated Stomata Analysis Through Simplified Sample Collection and Imaging Techniques.

Abstract

Digital image processing is commonly used in plant health and growth analysis, aiming to improve research efficiency and repeatability. One focus is analysing the morphology of stomata, with the aim to better understand the regulation of gas exchange, its link to photosynthesis and water use and how they are influenced by climatic conditions. Despite the key role played by these cells, their microscopic analysis is largely manual, requiring intricate sample collection, laborious microscope application and the manual operation of a graphical user interface to identify and measure stomata. This research proposes a simple, end-to-end solution which enables automatic analysis of stomata by introducing key changes to imaging techniques, stomata detection as well as stomatal pore area calculation. An optimal procedure was developed for sample collection and imaging by investigating the suitability of using an automatic microscope slide scanner to image nail polish imprints. The use of the slide scanner allows the rapid collection of high-quality images from entire samples with minimal manual effort. A convolutional neural network was used to automatically detect stomata in the input image, achieving average precision, recall and F-score values of 0.79, 0.85, and 0.82 across four plant species. A novel binary segmentation and stomatal cross section analysis method is developed to estimate the pore boundary and calculate the associated area. The pore estimation algorithm correctly identifies stomata pores 73.72% of the time. Ultimately, this research presents a fast and simplified method of stomatal assay generation requiring minimal human intervention, enhancing the speed of acquiring plant health information.

Plant phenotyping relevance

気孔の画像取得、検出、孔面積推定を自動化するエンドツーエンドの植物表現型測定法を開発・評価しており、方法が研究の中心である。

Code and data availability

The article describes paper-specific stomata phenotype data (slide-scanner images of nail polish imprints from four species, AlexNet training data, and pore measurement results), but no public deposit, code release, or authors' URL for these assets appears in the supplied blocks. The data availability statement only承诺s

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