Length and width measurements of Fragilariopsis kerguelensis valves from sediment core PS1768-8

Light microscopy analysis of diatom frustules is widely used in basic and applied research, notably taxonomy, morphometrics, water quality monitoring and paleo-environmental studies. Although there is a need for automation in these applications, various developments in image processing and analysis methodology supporting these tasks have not become widespread in diatom-based analyses. We have addressed this issue by combining our automated diatom image analysis software SHERPA with a commercial slide-scanning microscope. The resulting workflow enables mass-analyses of a broad range of morphometric features from individual frustules mounted on permanent slides. Extensive automation and internal quality control of the results helps to minimize user intervention, but care was taken to allow the user to stay in control of the most critical steps (exact segmentation of valve outlines and selection of objects of interest) using interactive functions for reviewing and revising results. In this contribution, we describe our workflow and give an overview of factors critical for success, ranging from preparation and mounting through slide scanning and autofocus finding to final morphometric data extraction. To demonstrate the usability of our methods we finally provide an example application by analysing Fragilariopsis kerguelensis valves originating from a sediment core, which substantially extends the size range reported in the literature.硅藻壳（diatom frustules）的光学显微镜分析在基础与应用研究中应用广泛，尤其在分类学、形态测量学、水质监测及古环境研究领域发挥着重要作用。尽管此类应用存在自动化需求，但支持此类任务的图像处理与分析方法学的各类进展，在硅藻相关分析中尚未得到广泛普及。我们通过将自研的自动化硅藻图像分析软件SHERPA与商用玻片扫描显微镜相结合，解决了这一难题。由此形成的工作流可对固定玻片上的单个硅藻壳开展大规模分析，提取涵盖多类形态测量特征。该流程通过高度自动化与内部结果质控，尽可能减少用户干预，同时通过交互式复核与修正功能，允许用户对核心关键步骤——如壳面轮廓的精准分割与目标对象选取——进行自主把控。本文详细阐述了该工作流，并概述了实验成功的关键影响因素，覆盖从样品制备、玻片封片、玻片扫描、自动对焦直至最终形态测量数据提取的全流程。为验证所提方法的实用性，我们以取自沉积物岩芯的凯氏脆杆藻（Fragilariopsis kerguelensis）壳面为分析对象，提供了一则应用实例。该实例大幅拓展了文献中已报道的该物种尺寸范围。