gil ecn2013 ppt
TRANSCRIPT
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 Network9 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.
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A little bit about iDigBio
Advancing Digitization of Biodiversity Collections
Integrated Digitized Biocollections (iDigBio)University of Florida
Florida State University Florida Museum of Natural History
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The goal is to digitize and make available via the Web at least 1 billionbiological and paleontological records over the 10-year life of the project.
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
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To date: 10 TCNs, 2 PENs, 160+ participating institutions, 50 states
National Resource (iDigBio), Thematic Collection Networks (TCNs)
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Working and Interest Groups
International Whole-drawer Digitization Interest Group
Fluid-preserved Arthropod and Microscopic Slide
Imaging Interest Group
Working and Interest Groups
International Whole-drawer Digitization Interest Group
Fluid-preserved Arthropod and Microscopic Slide
Imaging Interest Group
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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
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https://www.idigbio.org/wiki/index.php/Drawer_Imaging_Group
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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
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GigaPan
North Carolina State Insect Museum(Andy Deans and Brian Wiegmann)
USDA/SI Systematic Entomology Laboratory
(Matt Buffington)
USDA/SI Systematic Entomology Laboratory
(Matt Buffington)
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Sat Scan (Nicole Fisher and Vlad Blagoderov)Sat Scan (Nicole Fisher and Vlad Blagoderov)
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Dscan (Stefan Schmidt)
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InvertNet Robot (Chris Dietrich and David Raila)
Upgraded to 200 MP
Hasselblad (Geoff Thompson, Queensland Museum)
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Courtesy of Geoff ThompsonQueensland Museum
Brisbane, Australia
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Building a Long-Bed Inverted Scanner for Digitizing Biological Collections
(Jeff Holland, Purdue, InvertNet)
A lesson in how to void a warranty!
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Meta-Data CreatorVlad BlagoderovBritish Museum of Natural History
Extracting Specimen-based Data
InvertNetChris DietrichIllinois Natural History Survey
KU Insect MuseumJennifer ThomasUniversity of Kansas
InvertNetChris DietrichIllinois Natural History Survey
KU Insect MuseumJennifer ThomasUniversity of Kansas
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SatScan
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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 cannotbe done with “insect soups” and crowdsourcing andbuild communities that can help us mine this richsource of data.” (Flemons and Mantle)
Soups, Bycatch, Bulk Samples (Paul Flemons)
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Soup ImagingPaul Flemons and Beth Mantle
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http://australianbioinformatics.net/cvab-2013-challenge#.UlfcT1AiWrMhttp://australianbioinformatics.net/cvab-2013-challenge#.UlfcT1AiWrM
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Related domains (virtually any tray-oriented prep type):• Paleontology (Ann Molineux, UT)• Vertebrate zoology• Anything stored in drawers and trays
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Fluid-preserved Arthropod and Microscopic Slide Imaging Interest Group
https://www.idigbio.org/wiki/index.php/Fluid_Preserved_Arthropds
Ann Arbor Workshop16-18 September 2013Emanated from wet collections workshopRecordings on the workshop wiki
Starting points:• Image
sharing/critiquing• Standard views• Microscopic slides
