CSBR: Natural History Collections: Advancing access to diatom slide collection at the Academy of Natural Sciences of Drexel University by whole-slide imaging and virtual microscopy

硅藻是水生生态系统功能所必需的微观藻类，通常用于重建过去和监测当前湖泊、湿地、河流和海洋盆地的环境变化。该项目的目标是为研究硅藻的科学家开发一种新的研究工具，并方便访问德雷塞尔大学自然科学院硅藻标本馆的馆藏。传统上，硅藻研究人员一直在观察和识别硅藻，方法是手动将永久硅藻载玻片放在光学显微镜下，观察、测量和拍摄单个标本，以记录它们的外观。在这个项目中，现代幻灯片扫描技术将用于创建硅藻幻灯片的高分辨率图像，这些图像可以通过“虚拟显微镜”应用程序在线查看和研究。这种方法将自动化数据收集，为数据共享和协作创造独特的机会，并通过提供对收集的开放访问和节省旅行，运输和显微镜的成本，使研究民主化。它还将为开发图像分析工具以及教育公众有关微生物多样性和微生物在生物圈中的作用开辟新的前景。一个定制的自动显微镜载玻片扫描系统将用于数字化6000显微镜载玻片在高分辨率与油浸和差对比光学。这些幻灯片展示了不同的地理区域、水体类型和研究主题。一个基于网络的虚拟显微镜应用程序适应硅藻研究人员和教育工作者的需要，并模拟真实显微镜的使用，将开发用于观看这些虚拟幻灯片。幻灯片的数字图像包含数百万个硅藻个体标本和整个硅藻组合的快照，将在网上免费提供，以支持和催化研究项目，重点关注环境变化及其对水生生物群的影响，以及硅藻系统学、生态学和生物地理学。虚拟幻灯片将通过美国国家生物多样性馆藏推进数字化网站（http://www.idigbio.com）和其他在线生物多样性门户网站提供。一群学生将参与幻灯片扫描和“虚拟显微镜”网络平台的开发，获得在多学科团队中工作的经验，并利用技术解决环境问题。该奖项反映了美国国家科学基金会的法定使命，并通过使用基金会的知识价值和更广泛的影响审查标准进行评估，被认为值得支持。

Diatoms are microscopic algae essential for the functioning of aquatic ecosystems and commonly used to reconstruct past and monitor current environmental changes in lakes, wetlands, rivers and marine basins. The goal of this project is to develop a novel research tool for scientists studying diatoms and to facilitate access to the holdings of the Diatom Herbarium at the Academy of Natural Sciences of Drexel University (ANS). Traditionally, diatom researchers have been observing and identifying diatoms by manually placing permanent diatom slides under a light microscope and viewing, measuring and photographing individual specimens to document their appearance. In this project the modern slide-scanning technology will be used to create high-resolution images of diatom slides that could be viewed and studied online using a ‘virtual microscopy’ application. This approach will automate data collection, create unique opportunities for data sharing and collaboration and democratize research by providing an open access to the collection and saving the costs of travel, shipping, and microscopy. It will also open new perspectives for the development of image analysis tools as well as for educating the public about microbial diversity and the role of microorganisms in the biosphere.A customized automated microscope slide-scanning system will be employed for digitizing 6,000 microscope slides at high resolution with oil immersion and differential contrast optics. These slides represent various geographic areas, waterbody types and research themes. A web-based virtual microscopy application adapted for the needs of diatom researchers and educators and simulating the use of a real microscope will be developed for viewing these virtual slides. Digital images of the slides, containing millions of individual diatom specimens and representing snapshots of entire diatom assemblages, will be made freely available online to support and catalyze research programs focused on environmental change and its effects on aquatic biota, as well as on diatom systematics, ecology, and biogeography. Access to the virtual slides will be provided via the ANS collection website, the national resource for Advancing Digitization of Biodiversity Collections (http://www.idigbio.com) and other online biodiversity portals. A cohort of students will be involved in slide scanning and developing of the ‘virtual microscope’ web platform, getting experience in working in a multidisciplinary team and using technology to address environmental problems.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.