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

硅藻是一种微小的藻类，对水生生态系统的功能至关重要，通常用于重建过去和监测湖泊、湿地、河流和海洋盆地的当前环境变化。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，并便于访问德雷克塞尔大学(ANS)自然科学学院的硅藻标本馆。传统上，硅藻研究人员一直在观察和识别硅藻，方法是将永久性硅藻切片放在光学显微镜下，然后观察、测量和拍摄个别标本，以记录它们的外观。在这个项目中，现代的载玻片扫描技术将被用来创建高分辨率的硅藻载玻片图像，这些图像可以通过虚拟显微镜应用程序在线查看和研究。这种方法将使数据收集自动化，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并节省旅行、运输和显微镜成本来实现研究的民主化。它还将为图像分析工具的开发以及教育公众了解微生物多样性和微生物在生物圈中的作用开辟新的视角。将使用定制的自动显微镜载玻片扫描系统，通过油浸和差示对比光学技术以高分辨率数字化6,000张显微镜载玻片。这些幻灯片代表了不同的地理区域、水体类型和研究主题。将开发一个基于网络的虚拟显微镜应用程序，用于查看这些虚拟幻灯片，以适应硅藻研究人员和教育工作者的需求，并模拟真实显微镜的使用。这些幻灯片的数字图像包含数百万个硅藻标本，代表了整个硅藻组合的快照，将在网上免费提供，以支持和催化专注于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的研究计划。虚拟幻灯片将通过ANS收集网站提供，这是促进生物多样性收集数字化的国家资源(http://www.idigbio.com)和其他在线生物多样性门户网站)。一批学生将参与“虚拟显微镜”网络平台的幻灯片扫描和开发，获得在多学科团队中工作的经验，并使用技术来解决环境问题。该奖项反映了NSF的法定使命，并通过使用基金会的智力优势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.