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

Academy Of Natural Sciences Philadelphia, Philadelphia PA

Investigators

Abstract

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.