Gil ecn2013 ppt

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Gil ecn2013 ppt

  1. 1. International Whole-drawer Digitization Interest Group Gil Nelson (iDigBio, Florida State University), Nicole Fisher (Australian National Insect Collection), Matthew Buffington (Systematic Entomology Laboratory, National Museum of Natural History), Vladimir Blagoderov (Natural History Museum, London), Andy Deans (Frost Entomological Museum at Penn State), Chris Dietrich (InvertNet, Illinois Natural History Survey), David Raila (InvertNet, University of Illinois, Computer Sciences), Paul Flemons (Australian Museum), Jeff Holland (InvertNet, Purdue University), Roy Larimer (Visionary Digital), Joanna McCaffrey (iDigBio), Joost van Leusen (Naturalis Biodiversity Center), Stefan Schmidt (Zoologische Staatssammlung München), Bernhard Schurian (Museum fuer Naturkunde, Berlin), Jennifer Thomas (University of Kansas, Biodiversity Institute, Entomology), Geoff Thompson (Queensland Museum), Gretchen Wilbrandt (University of Minnesota), Jennifer Zaspel (InvertNet, Purdue University), Ann Molineux (The University of Texas at Austin), Vince Smith (Natural History Museum, London) Entomological Collections Network 9 November 2013 Austin, TX This material is based upon work supported by the National Science Foundation under Cooperative Agreement EF-1115210. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation. 1
  2. 2. A little bit about iDigBio 2
  3. 3. Advancing Digitization of Biodiversity Collections Integrated Digitized Biocollections (iDigBio) University of Florida Florida State University Florida Museum of Natural History The goal is to digitize and make available via the Web at least 1 billion biological and paleontological records over the 10-year life of the project. 3
  4. 4. Ten Thematic Collections Networks (TCNs) plus several Partner to Existing Networks (PENs) • InvertNet: An Integrative Platform for Research on Environmental Change, Species Discovery and Identification (Illinois Natural History Survey, University of Illinois) http://invertnet.org • Plants, Herbivores, and Parasitoids: A Model System for the Study of Tri-Trophic Associations (American Museum of Natural History) http://tcn.amnh.org • North American Lichens and Bryophytes: Sensitive Indicators of Environmental Quality and Change (University of Wisconsin – Madison) http://symbiota.org/nalichens/index.php http://symbiota.org/bryophytes/index.php (plus 2 PENs) • Digitizing Fossils to Enable New Syntheses in Biogeography - Creating a PALEONICHES-TCN (University of Kansas) • The Macrofungi Collection Consortium: Unlocking a Biodiversity Resource for Understanding Biotic Interactions, Nutrient Cycling and Human Affairs (New York Botanical Garden) • Mobilizing New England Vascular Plant Specimen Data to Track Environmental Change (Yale University) • Southwest Collections of Anthropods Network (SCAN): A Model for Collections Digitization to Promote Taxonomic and Ecological Research (Northern Arizona University) http://hasbrouck.asu.edu/symbiota/portal/index.php New as of 1 July 2013 • iDigPaleo: Fossil Insect Collaborative: A Deep-Time Approach to Studying Diversification and Response to Environmental Change • Developing a Centralized Digital Archive of Vouchered Animal Communication Signals • The Macroalgal Herbarium Consortium: Accessing 150 Years of Specimen Data to Understand Changes in the Marine/Aquatic Environment 4
  5. 5. National Resource (iDigBio), Thematic Collection Networks (TCNs) 5 To date: 10 TCNs, 2 PENs, 160+ participating institutions, 50 states
  6. 6. Working and Interest Groups International Whole-drawer Digitization Interest Group Fluid-preserved Arthropod and Microscopic Slide Imaging Interest Group 6
  7. 7. 7
  8. 8. International Whole-drawer Digitization Interest Group Members •Nicole Fisher (co-coordinator), Australian National Insect Collection •Gil Nelson (co-coordinator), iDigBio •Vladimir Blagoderov, Natural History Museum •Matthew Buffington, Systematic Entomology Laboratory, National Museum of Natural History •Andy Deans, Frost Entomological Museum at Penn State •Chris Dietrich, Illinois Natural History Survey •Paul Flemons, Australian Museum •Jeff Holland, Purdue •Roy Larimer, Visionary Digital •Joanna McCaffrey, iDigBio •Ann Molineux, The University of Texas at Austin •David Raila, University of Illinois, Computer Sciences •Stefan Schmidt, Zoologische Staatssammlung München •Bernhard Schurian, Museum fuer Naturkunde Berlin •Vince Smith (Natural History Museum, London) •Jennifer Thomas, University of Kansas, Biodiversity Institute, Entomology •Geoff Thompson, Queensland Museum •Joost van Leusen, Naturalis Biodiversity Center •Luc Willemse Naturalis Biodiversity Center •Gretchen Wilbrandt, University of Minnesota •Jennifer Zaspel, Purdue 8
  9. 9. https://www.idigbio.org/wiki/index.php/Drawer_Imaging_Group 9
  10. 10. Issues of interest with whole-drawer digitization Getting to specimen level Seeing, extracting, and recording label data Handling continually changing drawer configurations Inventory management Cost Identifiers and barcodes Parallax Spacing within drawers and trays Image size and management Soups Remote annotation Equipment configurations and imaging techniques 10
  11. 11. GigaPan North Carolina State Insect Museum (Andy Deans and Brian Wiegmann) USDA/SI Systematic Entomology Laboratory (Matt Buffington) 11
  12. 12. Sat Scan (Nicole Fisher and Vlad Blagoderov) 12
  13. 13. Dscan (Stefan Schmidt) 13
  14. 14. InvertNet Robot (Chris Dietrich and David Raila) 14
  15. 15. Hasselblad (Geoff Thompson, Queensland Museum) Upgraded to 200 MP 15
  16. 16. Courtesy of Geoff Thompson Queensland Museum Brisbane, Australia 16
  17. 17. Building a Long-Bed Inverted Scanner for Digitizing Biological Collections (Jeff Holland, Purdue, InvertNet) A lesson in how to void a warranty! 26
  18. 18. Extracting Specimen-based Data Meta-Data Creator Vlad Blagoderov British Museum of Natural History 27 InvertNet Chris Dietrich Illinois Natural History Survey KU Insect Museum Jennifer Thomas University of Kansas
  19. 19. SatScan 28
  20. 20. 29
  21. 21. 30
  22. 22. Soups, Bycatch, Bulk Samples (Paul Flemons) Insect richness, diversity, and abundance • Provides for metrics • Comparison across time and space • Opportunities for crowd-sourcing through pattern matching Creating virtual collections Metadata tagging Collections management • Loans • Removal of insects from soups “Set aside our prejudices about what can and cannot be done with “insect soups” and crowdsourcing and build communities that can help us mine this rich source of data.” (Flemons and Mantle) 31
  23. 23. Soup Imaging Paul Flemons and Beth Mantle 32
  24. 24. 33
  25. 25. http://australianbioinformatics.net/cvab-2013-challenge#.UlfcT1AiWrM 34
  26. 26. Related domains (virtually any tray-oriented prep type): • Paleontology (Ann Molineux, UT) • Vertebrate zoology • Anything stored in drawers and trays 35
  27. 27. Fluid-preserved Arthropod and Microscopic Slide Imaging Interest Group https://www.idigbio.org/wiki/index.php/Fluid_Preserved_Arthropds Ann Arbor Workshop 16-18 September 2013 Emanated from wet collections workshop Recordings on the workshop wiki Starting points: • Image sharing/critiquing • Standard views • Microscopic slides 36
  28. 28. Join us! gnelson@bio.fsu.edu 37

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