Image-Based Quantification of <i>Arabidopsis thaliana</i> Stomatal Aperture from Leaf Images
Image-Based Quantification of <i>Arabidopsis thaliana</i> Stomatal Aperture from Leaf Images
复制标题
基于图像的叶子图像中的拟南芥气孔孔径定量
DOI：
10.1093/pcp/pcad018
复制
发表时间：
2023
影响因子：
4.9
通讯作者：
Toda Yosuke
中科院分区：
文献类型：
--
作者：
Takagi Momoko;Hirata Rikako;Aihara Yusuke;Hayashi Yuki;Mizutani-Aihara Miya;Ando Eigo;Yoshimura-Kono Megumi;Tomiyama Masakazu;Kinoshita Toshinori;Mine Akira;Toda Yosuke
气孔孔径的定量分析一直是了解植物在环境适应中生理反应的基本途径。这种方法的自动化不仅减少了人工劳动和偏见，而且通过大量的分析实现了新的实验研究方法。在这里，我们提出了一个图像分析管道，自动量化气孔孔径ofArabidopsis thalianaleaves从明场显微镜图像含有叶肉组织作为噪声背景。通过结合You Only Look Once基于X的气孔检测子模块和基于U-Net的孔分割子模块，我们实现了平均平均精度，其中联合交叉点（IoU）阈值为50%，值为0.875（气孔检测性能），IoU为0.745（孔分割性能）。此外，我们设计了一种便携式成像设备，可以轻松地从现场分离/未分离的完整叶子中获取气孔图像。我们证明，该设备与我们在这里生成的管道的微调模型相结合，提供了强大的测量，可以替代人工测量气孔对病原体接种的反应。利用我们的硬件和管道自动气孔孔径测量，预计将加快模式双子叶植物气孔生物学的研究。
The quantification of stomatal pore size has long been a fundamental approach to understand the physiological response of plants in the context of environmental adaptation. Automation of such methodologies not only alleviates human labor and bias but also realizes new experimental research methods through massive analysis. Here, we present an image analysis pipeline that automatically quantifies stomatal aperture ofArabidopsis thalianaleaves from bright-field microscopy images containing mesophyll tissue as noisy backgrounds. By combining a You Only Look Once X–based stomatal detection submodule and a U-Net-based pore segmentation submodule, we achieved a mean average precision with an intersection of union (IoU) threshold of 50% value of 0.875 (stomata detection performance) and an IoU of 0.745 (pore segmentation performance) against images of leaf discs taken with a bright-field microscope. Moreover, we designed a portable imaging device that allows easy acquisition of stomatal images from detached/undetached intact leaves on-site. We demonstrated that this device in combination with fine-tuned models of the pipeline we generated here provides robust measurements that can substitute for manual measurement of stomatal responses against pathogen inoculation. Utilization of our hardware and pipeline for automated stomatal aperture measurements is expected to accelerate research on stomatal biology of model dicots.