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

Gibbs, Jonathon A.; Burgess, Alexandra J.

Abstract

Plant physiology and metabolism relies on the function of stomata, structures on the surface of above ground organs, which facilitate the exchange of gases with the atmosphere. The morphology of the guard cells and corresponding pore which 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 microscopes, 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 optimise uptake; predominantly focusing on the sharing of datasets and generalisation of models as well as the caveats associated with utilising image data to infer physiological function.

Citation

Gibbs, J. A., & Burgess, A. J. (2024). Application of deep learning for the analysis of stomata: a review of current methods and future directions. Journal of Experimental Botany, 75(21), 6704-6718. https://doi.org/10.1093/jxb/erae207

• Journal Article Type: Article
• Acceptance Date: May 3, 2024
• Online Publication Date: May 8, 2024
• Publication Date: Nov 15, 2024
• Deposit Date: May 14, 2024
• Publicly Available Date: May 16, 2024
• Journal: Journal of Experimental Botany
• Print ISSN: 0022-0957
• Electronic ISSN: 1460-2431
• Publisher: Oxford University Press
• Peer Reviewed: Peer Reviewed
• Volume: 75
• Issue: 21
• Pages: 6704-6718
• DOI: https://doi.org/10.1093/jxb/erae207
• Public URL: https://nottingham-repository.worktribe.com/output/34858893
• Publisher URL: https://academic.oup.com/jxb/article/75/21/6704/7666955