InvertNet: An Integrative Platform for Research on Environmental Change, Species Discovery and Identification
- 1 Digitization TCN: InvertNet: An Integrative Platform for Research on Environmental Change, Species Discovery and Identification
- 2 PENs
Digitization TCN: InvertNet: An Integrative Platform for Research on Environmental Change, Species Discovery and Identification
Arthropods (insects, spiders, crabs) are the most diverse and abundant group of macro-organisms in biological collections, but are underrepresented in databases accessible online or elsewhere. This project will centralize access to and synthesize information from 160 years of North American arthropod collections. It will use innovative technology, including optical 3D imaging and reconstruction, to support scientific inquiry on the effects of land use change on biodiversity, and basic research on species discovery and identification. The award will provide IT infrastructure for collection digitization, digitally-assisted curation, and collection management; availability of specimen-level data for scientific inquiry on human impacts on biodiversity; and greater use of and appreciation for scientific collections by non-scientists through access to specimen images and related data.
Proposed Research ideas:
The main research focus of the InvertNet team over the past year has been on developing robust hardware and efficient workflows for digitizing various kinds of objects deposited in arthropod collections (vials, slides, and pinned specimens). We published a paper in a special volume of the journal ZooKeys (doi:10.3897/zookeys.209.3571) describing our overall approach, the ultimate goal of which is to achieve the $0.10/specimen cost benchmark established by the overall ADBC program while, at the same time, minimizing the possibility of damage to specimens through excessive handling and obtaining the highest quality of data (images as well as occurrence data from labels) possible. To date, we have tested and implemented workflows for digitizing vials of ethanol-preserved specimens and trays of slide-mounted specimens and collaborators at several InvertNet institutions are using these workflows to digitize their holdings of such materials. We have also tested three different prototype robotic systems for capturing images of whole drawers of pinned specimens. The most recent prototype, based on a four-armed linear delta robot, is in the final stages of testing and we anticipate implementing the system at collaborating institutions beginning later this year. Two graduate students in computer science have so far been involved in developing and testing algorithms that will enable us to create 3D models of drawers of pinned insects, allowing for virtual tilting to reveal details of specimens and labels not visible in a top-down view.
Project Websites & Social Media
Citizen Science & Outreach Projects
Project Sponsor: University of Illinois at Urbana-Champaign (NSF Award 1115112)
Principal Investigators (PIs): Christopher Dietrich (PI), Umberto Ravaioli (Co-PI), Nahil Sobh (Co-PI), John Hart (Co-PI), Christopher Taylor (Co-PI)
Collaborating Award PIs:
Gregory Zolnerowich, Kansas State University (NSF Award 1114823)
Anthony Cognato, Michigan State University (NSF Award 1114856)
Paul Tinerella, University of Minnesota, Twin Cities (NSF Award 1114845)
Paul Johnson, South Dakota State University (NSF Award 1114881)
Daniel Young, University of Wisconsin, Madison (NSF Award 1114998)
Johannes Klompen, Ohio State University (NSF Award 1115005)
Jennifer Zaspel, University of Wisconsin, Oshkosh (NSF Award 1115043)
Andrew Short, University of Kansas (NSF Award 1115051)
Jeffrey Holland, Purdue University (NSF Award 1339379)
John Rawlins, Carnegie Institute (NSF Award 1115075)
Robert Sites, University of Missouri, Columbia (NSF Award 1115149)
Gregory Courtney, Iowa State University (NSF Award 1115156)
David Rider, North Dakota State University, Fargo (NSF Award 1115198)
Carnegie Museum of Natural History
Eastern Illinois University
Illinois State University
Iowa State University
Kansas State University
Michigan State University
Milwaukee Public Museum
North Dakota State University
Northern Michigan University
Ohio State University
South Dakota State University
Southern Illinois University
University of Illinois, Natural History Survey
University of Kansas
University of Minnesota
University of Missouri
University of North Dakota
University Wisconsin – Madison
University Wisconsin – Oshkosh
Valley City State University
Western Illinois University
Protocols & Workflows
- Short, Andrew E.Z., Torsten Dikow, and Corrie D. Moreau. "Entomological collections in the age of big data." Annual Review of Entomology (2018) 63: 513-30.
- Anderson, Timothy J., David L. Wagner, Bruce R. Cooper, Megan E. McCarty, and Jennifer M. Zaspel. "HPLC-MS Analysis of Lichen-Derived Metabolites in the Life Stages of Crambidia cephalica (Grote & Robinson)." Journal of Chemical Ecology 43, no. 1 (2017): 66-74.
- Dietrich, Christopher H., and Dmitry A. Dmitriev. "Insect phylogenetics in the digital age." Current opinion in insect science 18 (2016): 48-52.
- Morris, B. O., and C. H. Dietrich. "Hidden in Plain Sight: A Remarkable New Genus of Nearctic Treehoppers (Hemiptera: Membracidae)." Annals of the Entomological Society of America 109.3 (2016): 488-494.
- Dai, Wu, and Christopher H. Dietrich. “A New Genus of Iassinae (Hemiptera: Cicadellidae) from Peru and a New Species of Daveyoungana Blocker & Webb.” Zootaxa 3946, no. 2 (2015): 285–95. http://www.ncbi.nlm.nih.gov/pubmed/25947692.
- Fasbender, Andrew, and Gregory W. Courtney. “Case 3664: Tipula Contaminata Linnaeus, 1758 (currently Ptychoptera Contaminata; Insecta, Diptera): Proposed Conservation of Prevailing Usage through Designation of a Neotype.” Bulletin of Zoological Nomenclature 71, no. 4 (2014): 237–43. http://iczn.org/node/40474.
- Balke, M., S. Schmidt, A. Hausmann, E.F.A. Toussaint, J. Bergsten, M. Buffington, C.L.Hauser, A. Kroupa, G. Hagedorn, A. Riedel, A. Polaszek, R. Ubaidilla, L. Krogmann, A. Zwick, M. Fikacek, J. Hajek, M.C. Michat, C. Dietrich, J. LaSalle, B. Mantle, P.K.L. "Biodiversity into your hands - a call for a virtual global natural history 'metacollection'," Frontiers in Zoology, v.10, 2013, p. 55.
- Dietrich, Christopher H., John Hart, David Raila, Umberto Ravaioli, Nahil Sobh, Omar Sobh, and Chris Taylor. “InvertNet: A New Paradigm for Digital Access to Invertebrate Collections.” Edited by John Hart, David Raila, Umberto Ravaioli, Nahil Sobh, Omar Sobh, and Chris Taylor. ZooKeys 209, no. 209 (January 2012): 165–81. doi:10.3897/zookeys.209.3571.
- Bhasin, R., Jang, W.J., Hart, J.C.. "A parallel stereo reconstruction algorithm with applications in entomology," Proc. SPIE 8290, 82901G, http://dx.doi.org/10.1117/12.905545, 2012. doi:http://dx.doi.org/10.1117/12.905545
Other project documentation
Digitization PEN: Digitizing the University of Iowa Museum of Natural History's Historic Invertebrate Collections through the InvertNet TCN
An award is made to the University of Iowa Museum of Natural History to connect it to the existing InvertNet Thematic Collections Network by digitizing approximately 28,000 insect and crayfish specimens from the museum's zoological research collections. Capturing 2D and 3D images and digitizing irreplaceable data will ensure long-term data preservation and make collection information accessible online to scientists, educators, students, and the public. Museum collections are crucial to modern biological research, and historic specimens are especially necessary in studying the effects of environmental and land use change. However, the fragility of these specimens and the scattered location of collections can make using them in research difficult and inefficient. Digitizing images and data makes specimen information more visible and accessible, increasing the potential for new research and public understanding.
In concert with digitization, the museum will integrate public education with InvertNet research by creating a "traveling trunk" for educators on the theme of invertebrates in the Midwest, updating an existing exhibit on arthropods to include content from the InvertNet project, and developing a traveling exhibit that can be borrowed by schools, nature centers, museums, and other groups in the region. This award is made as part of the National Resource for Digitization of Biological Collections through the Advancing Digitization of Biological Collections program and all data resulting from this award will be available through the national resource (https://www.idigbio.org).
Project Sponsor: University of Iowa (NSF Award 1303840)
Principal Investigators (PIs): Trina Roberts (PI), Cindy Opitz (Co-PI)