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Transcript of Dmitriev ecn2013
Digitization of the Illinois Natural History Survey insect collection
Dmitry Dmitriev
INHS Image Archive
INHS Insect Collection: Overview
• One of the oldest and most comprehensive insect collections in North America
• 9th largest collection in the USA (~7 million prepared specimens)
• >13,000 primary type specimens
Brief History
• Establishment of the Natural History Society of Illinois (1858)
INHS Image Archive
Brief History of INHS: Early Era (1857-1875)
• 1858 - Establishment of Natural History Society at Illinois Normal University, by small group of active members including Cyrus Thomas, John Powell, Benjamin Walsh, and Stephen Forbes
• 1861 - 60,000 specimens in the collection Cyrus Thomas
John PowellIllinois Normal UniversityOldest specimen in the collection
Expansion Era, 1875-1922
• 1877 - INHS renamed as State Laboratory of Natural History with Stephen Forbes as first director
• 1885 - State Laboratory moved to Urbana • Original paid staff of seven people• 1903 - Charles Hart (true bugs) appointed as first
entomology curator, and assistant curator John Malloch (flies)
University Hall, Urbana, ca. 1870Charles Hart and field party near
Havana, IL, 1894
Natural History Museum, Urbana, 1917
Stephen A. Forbes
Era of Comprehensive Faunistic Treatments 1923-1950’s
Under Theodore Frison and Herbert Ross• Systematics of Illinois fauna • Illinois Natural History Survey
Bulletins• Plecoptera (stoneflies)• Megaloptera (fishflies)• Ephemeroptera (mayflies)• Trichoptera (caddisflies)• Thysanoptera (thrips)
• Other groups covered by visiting entomologists:
• Aphids (F.C. Hottes, T. Frison)• Plant bugs (H.H. Knight)• Leafhoppers (D.M. DeLong)
• 1958 - 2 million specimens by 100th anniversary
Herbert Ross, 1935
Sanderson & Stannard, 1953
Theodore Frison
Era of Globalization, 1950’s-present
Extensive globalization of collecting efforts, many funded by NSF
North America• Herbert Ross
• Caddisflies, leafhoppers, other insects Central America/Caribbean Islands
• Milton Sanderson• Coleoptera• Dominican amber
• Wallace LaBerge, beesWorldwide
• Donald Webb, Diptera• Michael Irwin, Diptera• Christopher Dietrich, Hemiptera
(leafhoppers)• Felipe Soto-Adames, Collembola• Kevin Johnson, Psocodea• Ed DeWalt (aquatic insects)• David Voegtlin (aphids)• Willliam Ruesink (Coleoptera)• George Godfrey (Lepidoptera)
• China, 2010
• Mexico, 2005 • Argentina, 2008
Globally-represented groups
• Collembola (springtails) • Coleoptera (beetles)• Diptera (true flies)• Hemiptera (leafhoppers)• Hymenoptera (bees)• Lepidoptera (moths and butterflies)• Plecoptera (stoneflies)• Psocodea (parasitic lice and barklice)• Thysanoptera (thrips)• Trichoptera (caddisflies)
INHS Image Archive
Contributions of private collections• Charles Robertson: insects visiting flowers near Carlinville
(1884-1914)• Murray Glenn: Microlepidoptera (1927-1976)• Andreas Bolter (all orders)• Emil Bees (Lepidoptera)• C.L. Metcalf (flower flies)• W.P. Hayes (weevils)• A.D. MacGillivray (sawflies)• P.N. Musgrave (water beetles)• K.F. Auden (beetles)
Charles Robertson Murray Glenn
Patrick Conway: Lepidoptera, 2009
William Rose: Coleoptera, 2011
The Present: Digital Age
slide mounted specimens ethanol-preserved specimens
pinned specimens
• Specimen-level electronic database, 1990’s• NSF funded projects
• Digitize label data• Retrospective georeferenced localities• Accessible via GBIF portal
• Ephemeroptera, Plecoptera, Trichoptera• Hymenoptera• Central Asian grassland fauna• Microleafhoppers• Orthoptera
NSF Advancing Digitization of Biological Collections (ADBC) Goals
• digitize 1 billion specimens in 10 years for $100 million ($0.10/specimen)
• build Thematic Collection Networks (TCNs) to address specific research goals
• link TCNs under national HUB
Tri-Trophic Thematic Collection Network
• AMNH – lead organization• 34 participating museums
(including INHS).• The goals to capture label data
for herbivorous Hemiptera (aphids, scales, hoppers, cicadas, and true bugs), their host plants and parasitic wasps.
• ~200,000 INHS specimens entered to the database
Collection curation
FileMaker
SQL Server
Online data entry form
INHS Insect collection digitization workflow
•Nomenclature•Unit tray labelwith taxon code
Storage unit profiling
Slide scanning
•Parsing data (automatic, crowd sourcing, etc.)
•Georeferencing
GBIF
Collection size: ~7,000,000 specimens
Digitized: ~2,000,000 specimens (~800,000 records)
Parsing verbatim labels
•Matching with existing parsed records (~40% match)
•Finding date (~80% records)
•Finding collector (~70% records)
•Finding identifier (~30% records)
•Student parsing
•Crowd-sourcing (have not been tested yet).
Collection curation
Amy Bader
processing loan return
INHS collection profiling
(Colin Favret et al. 2007)
InvertNet• Digitize all holdings of 22 arthropod collections (>50 million
specimens)• Provide access to images and other data via online virtual
museum• Provide platform for research and development of additional
tools and resources
• Custom designed precision robotics system
– Integrated and customized for InvertNet
» Captures images of drawer from multiple positions in X, Y, and Z
» Raw images combined to produce single very high resolution2-D image and 3-D reconstruction
Collection digitization: drawers
Collection digitization: drawers
• Delta Robot, digital camera, telecentric lens captures grid of single, close-up images at 40-60 x/y coordinates and 5 perspectives
• Single images stitched to yield Gigapixel images from multiple viewpoints
Top-down view
Angled view
• Enables virtual tilting
Collection digitization: drawers
2. segment unit trays (image analysis software)
3. segment specimens4. capture label data (crowd-sourcing)
1. capture image of drawer + metadata (location, contents)
Collection digitization: drawers
Collection digitization: slides and vials
InvertNet Website
• InvertNet.org
• Registration is open to all and available now; please join!
Fossil insect collaborative.
• A deep time approach to studying diversification and response to environmental change
• 7 collaborative institutions
Fossil insect collaborative.
INHS is processing Milton Sanderson’s Dominican amber collection which was stored in 5 gallon buckets.
Fossil insect collaborative
Amber is being polished, scanned for inclusions, sorted, photographed, and databased.
Termite
Collection Digitization: Global Coverage
2008
2013
Today, ~800,000 records (2 million specimens)
GBiF
http://data.gbif.org/datasets/provider/75
Outreach
C. Dietrich
C. Dietrich
INHS Image Archive
• Annual Prairie Research Institute Expo• Illinois Wilds Institute for Nature (IWIN) courses• Travelling Science Center• INHS published insect field guides
Acknowledgements
•Collaborators:
C. Dietrich, F. Soto-Adames, E. DeWalt, T. Schuh, C. Bartlet, S. Heads, M. Yoder, B. Morris, A. Bader, J. Zahniser.
•All the students who did the hard work.
•NSF for continuous support of INHS digitization efforts.