Zubairova Ulyana S, Verman Pavel Yu, Oshchepkova Polina A, Elsukova Alina S, Doroshkov Alexey V
Institute of Cytology and Genetics SB RAS, Prospekt Lavrentyeva 10, Novosibirsk, 630090, Russia.
A.P. Ershov Institute of Informatics Systems SB RAS, Prospekt Lavrentyeva 6, Novosibirsk, 630090, Russia.
BMC Syst Biol. 2019 Mar 5;13(Suppl 1):22. doi: 10.1186/s12918-019-0689-8.
Microscopic images are widely used in plant biology as an essential source of information on morphometric characteristics of the cells and the topological characteristics of cellular tissue pattern due to modern computer vision algorithms. High-resolution 3D confocal images allow extracting quantitative characteristics describing the cell structure of leaf epidermis. For some issues in the study of cereal leaves development, it is required to apply the staining techniques with fluorescent dyes and to scan rather large fragments consisting of several frames. We aimed to develop a tool for processing multi-frame multi-channel 3D images obtained from confocal laser scanning microscopy and taking into account the peculiarities of the cereal leaves staining.
We elaborated an ImageJ-plugin LSM-W that allows extracting data on Leaf Surface Morphology from Laser Scanning Microscopy images. The plugin is a crucial link in a workflow for obtaining data on structural properties of leaf epidermis and morphological properties of epidermal cells. It allows converting large lsm-files (laser scanning microscopy) into segmented 2D/3D images or tables with data on cells and/or nuclei sizes. In the article, we also represent some case studies showing the plugin application for solving biological tasks. Namely the plugin is applied in the following cases: defining parameters of jigsaw-puzzle pattern for maize leaf epidermal cells, analysis of the pavement cells morphological parameters for the mature wheat leaf grown under control and water deficit conditions, initiation of cell longitudinal rows, and detection of guard mother cells emergence at the initial stages of the stomatal morphogenesis in the growth zone of a wheat leaf.
The proposed plugin is efficient for high-throughput analysis of cellular architecture for cereal leaf epidermis. The workflow implies using inexpensive and rapid sample preparation and does not require the applying of transgenesis and reporter genetic structures expanding the range of species and varieties to study. Obtained characteristics of the cell structure and patterns further could act as a basis for the development and verification for spatial models of plant tissues formation mechanisms accounting for structural features of cereal leaves.
The implementation of this workflow is available as an ImageJ plugin distributed as a part of the Fiji project (FijiisjustImageJ: https://fiji.sc/ ). The plugin is freely available at https://imagej.net/LSM_Worker , https://github.com/JmanJ/LSM_Worker and http://pixie.bionet.nsc.ru/LSM_WORKER/ .
由于现代计算机视觉算法，显微图像在植物生物学中被广泛用作细胞形态计量特征和细胞组织结构拓扑特征的重要信息来源。高分辨率三维共聚焦图像能够提取描述叶片表皮细胞结构的定量特征。对于谷物叶片发育研究中的一些问题，需要应用荧光染料染色技术并扫描由多个帧组成的相当大的片段。我们旨在开发一种工具，用于处理从共聚焦激光扫描显微镜获得的多帧多通道三维图像，并考虑谷物叶片染色的特点。
我们精心制作了一个ImageJ插件LSM-W，它可以从激光扫描显微镜图像中提取叶片表面形态学数据。该插件是获取叶片表皮结构特性和表皮细胞形态特性数据工作流程中的关键环节。它可以将大型lsm文件（激光扫描显微镜文件）转换为分割后的二维/三维图像或包含细胞和/或细胞核大小数据的表格。在本文中，我们还展示了一些案例研究，展示了该插件在解决生物学任务中的应用。具体来说，该插件应用于以下情况：确定玉米叶片表皮细胞拼图图案的参数、分析在对照和水分亏缺条件下生长的成熟小麦叶片的铺路细胞形态参数、细胞纵向排的起始以及在小麦叶片生长区气孔形态发生初始阶段保卫母细胞出现的检测。
所提出的插件对于谷物叶片表皮细胞结构的高通量分析是有效的。该工作流程意味着使用廉价且快速的样品制备方法，并且不需要应用转基因和报告基因结构，从而扩大了可研究的物种和品种范围。获得的细胞结构和图案特征进一步可以作为开发和验证考虑谷物叶片结构特征的植物组织形成机制空间模型的基础。
此工作流程的实现作为一个ImageJ插件提供，作为Fiji项目的一部分进行分发（FijiisjustImageJ: https://fiji.sc/ ）。该插件可在https://imagej.net/LSM_Worker 、https://github.com/JmanJ/LSM_Worker 和http://pixie.bionet.nsc.ru/LSM_WORKER/ 免费获取。
