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

CSBR：自然历史收藏：通过全幻灯片成像和虚拟显微镜促进德雷塞尔大学自然科学院硅藻幻灯片收藏的获取

• 批准号: 1938128
• 负责人: Marina Potapova
• 金额: $ 50.73万
• 依托单位: Academy of Natural Sciences Philadelphia
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2020
• 资助国家: 美国
• 起止时间: 2020-09-15 至 2024-08-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1938128&HistoricalAwards=false
• 关键词: CSBR; Natural; History; Collections; Advancing

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.

硅藻是水生生态系统功能所必需的微观藻类，通常用于重建湖泊，湿地，河流和海洋盆地的过去和监测当前环境变化。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，并方便查阅德雷克塞尔大学自然科学院硅藻标本馆的藏品。传统上，硅藻研究人员一直通过手动将永久性硅藻载玻片置于光学显微镜下观察和识别硅藻，并观察，测量和拍摄个体标本以记录其外观。在这个项目中，现代的幻灯片扫描技术将被用于创建硅藻幻灯片的高分辨率图像，可以使用“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前景。一个定制的自动显微镜载玻片扫描系统将采用油浸和微分对比光学技术以高分辨率对6,000张显微镜载玻片进行数字化。这些幻灯片代表了不同的地理区域、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，适合硅藻研究人员和教育工作者的需求，并模拟使用一个真实的显微镜将开发用于查看这些虚拟幻灯片。幻灯片的数字图像，包含数百万个个体硅藻标本，并代表整个硅藻组合的快照，将在网上免费提供，以支持和促进研究计划，重点是环境变化及其对水生生物群的影响，以及硅藻系统学，生态学和地理学。将通过ANS收藏网站、促进生物多样性收藏数字化的国家资源（http：//www.example.com）和其他在线生物多样性门户网站提供虚拟幻灯片。www.idigbio.com一批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，并使用技术解决环境问题。该奖项反映了NSF的法定使命，并通过使用基金会的智力价值和更广泛的影响审查标准进行评估，被认为值得支持。