Czymmek Kirk J, Benitez-Alfonso Yoselin, Burch-Smith Tessa, Di Costanzo Luigi F, Drakakaki Georgia, Facette Michelle, Kierzkowski Daniel, Klebanovych Anastasiya, Radin Ivan, Roychoudhry Suruchi, McFarlane Heather E
Advanced Bioimaging Laboratory, Donald Danforth Plant Science Center, St. Louis, MO 63132, USA.
Centre for Plant Sciences, School of Biology, University of Leeds, Leeds LS2 9JT, UK.
Plant Cell. 2025 Jul 1;37(7). doi: 10.1093/plcell/koaf143.
Microscopy is a fundamental approach for plant cell and developmental biology as well as an essential tool for mechanistic studies in plant research. However, setting up a new microscopy-based experiment can be challenging, especially for beginner users, when implementing new imaging workflows or when working in an imaging facility where staff may not have extensive experience with plant samples. The basic principles of optics, chemistry, imaging, and data handling are shared among all cell types. However, unique challenges are faced when imaging plant specimens due to their waxy cuticles, strong/broad spectrum autofluorescence, recalcitrant cell walls, and air spaces that impede fixation or live imaging, impacting sample preparation and image quality. As expert plant microscopists, we share our collective experience on best practices to improve the quality of published microscopy results and promote transparency, reproducibility, and data reuse for meta-analyses. We offer plant-specific advice and examples for microscope users at all stages of fluorescence microscopy workflows, from experimental design through sample preparation, image acquisition, processing, and analyses, to image display and methods reporting in manuscripts. We also present standards for methods reporting that will be valuable to all users and offer tools to improve reproducibility and data sharing.
显微镜检查是植物细胞与发育生物学的基本方法，也是植物研究中进行机理研究的重要工具。然而，开展一项基于显微镜检查的新实验可能具有挑战性，尤其是对于新手用户而言，当实施新的成像工作流程时，或者在成像设施中工作时，那里的工作人员可能对植物样本没有丰富的经验。光学、化学、成像和数据处理的基本原理在所有细胞类型中都是共通的。然而，对植物标本进行成像时会面临独特的挑战，这是由于其蜡质角质层、强烈/广谱的自发荧光、顽固的细胞壁以及阻碍固定或活体成像的气腔，这些都会影响样本制备和图像质量。作为专业的植物显微镜专家，我们分享我们的集体经验，介绍最佳实践方法，以提高已发表的显微镜检查结果的质量，并促进元分析的透明度、可重复性和数据重用。我们为荧光显微镜工作流程各个阶段的显微镜用户提供针对植物的建议和示例，从实验设计到样本制备、图像采集、处理和分析，再到图像展示以及稿件中的方法报告。我们还提出了对所有用户都有价值的方法报告标准，并提供提高可重复性和数据共享的工具。
