Application of deep learning for the analysis of stomata: a review of current methods and future directions

Plant physiology and metabolism rely on the function of stomata, structures on the surface of above-ground organs that facilitate the exchange of gases with the atmosphere. The morphology of the guard cells and corresponding pore that make up the stomata, as well as the density (number per unit area), are critical in determining overall gas exchange capacity. These characteristics can be quantified visually from images captured using microscopy, traditionally relying on time-consuming manual analysis. However, deep learning (DL) models provide a promising route to increase the throughput and accuracy of plant phenotyping tasks, including stomatal analysis. Here we review the published literature on the application of DL for stomatal analysis. We discuss the variation in pipelines used, from data acquisition, pre-processing, DL architecture, and output evaluation to post-processing. We introduce the most common network structures, the plant species that have been studied, and the measurements that have been performed. Through this review, we hope to promote the use of DL methods for plant phenotyping tasks and highlight future requirements to optimize uptake, predominantly focusing on the sharing of datasets and generalization of models as well as the caveats associated with utilizing image data to infer physiological function. This review discusses the application of deep learning approaches for the assessment of stomata, including variations in the pipeline used, from data collection to parameter extraction.