Stomata Detector: High-throughput automation of stomata counting in a population of African rice (Oryza glaberrima) using transfer learning.

Abstract

Stomata are dynamic structures that control the gaseous exchange of CO2 from the external to internal environment and water loss through transpiration. The density and morphology of stomata have important consequences in crop productivity and water use efficiency, both are integral considerations when breeding climate change resilient crops. The phenotyping of stomata is a slow manual process and provides a substantial bottleneck when characterising phenotypic and genetic variation for crop improvement. There are currently no open-source methods to automate stomatal counting. We used 380 human annotated micrographs of O. glaberrima and O. sativa at x20 and x40 objectives for testing and training. Training was completed using the transfer learning for deep neural networks method and R-CNN object detection model. At a x40 objective our method was able to accurately detect stomata (n = 540, r = 0.94, p<0.0001), with an overall similarity of 99% between human and automated counting methods. Our method can batch process large files of images. As proof of concept, characterised the stomatal density in a population of 155 O. glaberrima accessions, using 13,100 micrographs. Here, we present developed Stomata Detector; an open source, sophisticated piece of software for the plant science community that can accurately identify stomata in Oryza spp., and potentially other monocot species.

Plant phenotyping relevance

イネの気孔を画像から自動検出・計数するオープンソース手法を開発し、手動計数との精度比較で検証しているため、植物表現型取得法が研究の中心です。

Code and data availability

The paper describes the Stomata Detector software, 380 annotated micrographs, and 13,100 population micrographs, but no block provides a public deposit URL, repository, or availability statement for the authors' code, trained model, images, or phenotype data. The only GitHub links (labelImg, Faster R-CNN) are generic/c

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