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 larg...
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 Universi...
Expansion Era, 1875-1922
• 1877 - INHS renamed as State Laboratory of
Natural History with Stephen Forbes as first
directo...
Era of Comprehensive Faunistic Treatments 1923-1950’s
Under Theodore Frison and Herbert Ross
• Systematics of Illinois fau...
Era of Globalization, 1950’s-present
Extensive globalization of collecting efforts, many funded by
NSF
North America
• Her...
Globally-represented groups
•
•
•
•
•
•
•
•
•
•

Collembola (springtails)
Coleoptera (beetles)
Diptera (true flies)
Hemipt...
Contributions of private collections
•
•
•
•
•
•
•
•
•

Charles Robertson: insects visiting flowers near Carlinville
(1884...
The Present: Digital Age
• Specimen-level electronic database, 1990’s
• NSF funded projects
• Digitize label data
• Retros...
NSF Advancing Digitization of Biological
Collections (ADBC) Goals
• digitize 1 billion specimens in 10 years for $100
mill...
Tri-Trophic Thematic Collection Network
• AMNH – lead organization
• 34 participating museums
(including INHS).
• The goal...
Collection curation

FileMaker
SQL Server
Online data entry form
INHS Insect collection digitization workflow

•Nomenclature
•Unit tray label
with taxon code

Storage unit
profiling

•Par...
Parsing verbatim labels
•Matching with existing parsed records (~40% match)
•Finding date (~80% records)
•Finding collecto...
Collection curation
INHS collection profiling
(Colin Favret et al. 2007)

Amy Bader
processing loan return
InvertNet
• Digitize all holdings of 22 arthropod collections (>50 million
specimens)
• Provide access to images and other...
Collection digitization: drawers
• Custom designed
precision robotics
system
– Integrated and
customized for InvertNet
» C...
Collection digitization: drawers

Top-down view

• Delta Robot, digital
camera, telecentric
lens captures grid
of single, ...
Collection digitization: drawers

1. capture image of drawer +
metadata (location, contents)

2. segment unit trays
(image...
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 c...
Fossil insect collaborative.
INHS is processing Milton
Sanderson’s Dominican
amber collection which was
stored in 5 gallon...
Fossil insect collaborative
Amber is being polished, scanned for
inclusions, sorted, photographed, and databased.

Termite
Collection Digitization: Global Coverage
2008

2013
GBiF

Today, ~800,000 records (2 million specimens)

http://data.gbif....
Outreach

C. Dietrich

INHS Image Archive

C. Dietrich

•
•
•
•

Annual Prairie Research Institute Expo
Illinois Wilds Ins...
Acknowledgements
•Collaborators:
C. Dietrich, F. Soto-Adames, E. DeWalt, T. Schuh, C. Bartlet,
S. Heads, M. Yoder, B. Morr...
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  • Photo courtesy of INHS Historic Image Archive
    Harlow B. Mills in “A Century of Biological Research in Illinois” INHS Bulletin (Dec. 1958)
  • Photo courtesy of INHS Historic Image Archive
    Harlow B. Mills in “A Century of Biological Research in Illinois” INHS Bulletin (Dec. 1958)
  • Photo courtesy of INHS Historic Image Archive
    Harlow B. Mills in “A Century of Biological Research in Illinois” INHS Bulletin (Dec. 1958)
  • Photo courtesy of INHS Historic Image Archive
    Harlow B. Mills in “A Century of Biological Research in Illinois” INHS Bulletin (Dec. 1958)
  • Photo courtesy of INHS Historic Image Archive
    Harlow B. Mills in “A Century of Biological Research in Illinois” INHS Bulletin (Dec. 1958)
    Me
  • Our method for capturing images of drawers is different and we think this will be one of the most innovative aspects of our project. Here we’re taking the approach similar to one that has been adopted at a few other institutions (e.g., NCSU, BMNH) in which a high resolution image of the entire drawer is captured by first moving a camera over the drawer in a grid pattern, capturing lots of close-up photos of different parts of the drawer and then stitching these together into a single gigapixel-scale image. Our system captures this basic top-down view of the drawer, but the delta robot we’re using is more flexible in its movements so we are also able to capture images from multiple perspectives. So, for example, if, in addition to the top-down images we also capture images at a 45 degree angle from front, back, left and right sides of the drawer, this will enable us to provide a partial 3D reconstruction of the drawer that will allow virtual tilting. This is important because in a top down view, the specimens often obscure parts of the labels pinned beneath them. If we are able to virtually tilt the image, we can reveal more of the top label, as well as labels pinned farther down, in addition to showing more of the specimen itself.
  • I’ll close by just reminding you that, although it doesn’t yet have a lot of content, InvertNet.org is up and running. Registration is available and open to all, so I urge you to join us.
  • Inhs.illinois.edu (delete slide?)
  • Dmitriev ecn2013

    1. 1. Digitization of the Illinois Natural History Survey insect collection Dmitry Dmitriev INHS Image Archive
    2. 2. 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
    3. 3. Brief History • Establishment of the Natural History Society of Illinois (1858) INHS Image Archive
    4. 4. 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 Oldest specimen in the collection Cyrus Thomas Illinois Normal University John Powell
    5. 5. 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) Stephen A. Forbes Natural History Museum, Urbana, 1917 Charles Hart and field party near University Hall, Urbana, ca. 1870 Havana, IL, 1894
    6. 6. 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 Theodore Frison Herbert Ross, 1935 Sanderson & Stannard, 1953
    7. 7. 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, bees Worldwide • 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) • Mexico, 2005 • China, 2010 • Argentina, 2008
    8. 8. 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
    9. 9. 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
    10. 10. The Present: Digital Age • 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 slide mounted specimens ethanol-preserved specimens pinned specimens
    11. 11. 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
    12. 12. 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
    13. 13. Collection curation FileMaker SQL Server
    14. 14. Online data entry form
    15. 15. INHS Insect collection digitization workflow •Nomenclature •Unit tray label with taxon code Storage unit profiling •Parsing data (automatic, crowd sourcing, etc.) •Georeferencing Collection size: ~7,000,000 specimens Slide scanning Digitized: ~2,000,000 specimens (~800,000 records) GBIF
    16. 16. 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).
    17. 17. Collection curation INHS collection profiling (Colin Favret et al. 2007) Amy Bader processing loan return
    18. 18. 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
    19. 19. Collection digitization: drawers • 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 resolution 2-D image and 3-D reconstruction
    20. 20. Collection digitization: drawers Top-down view • 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 Angled view • Enables virtual tilting
    21. 21. Collection digitization: drawers 1. capture image of drawer + metadata (location, contents) 2. segment unit trays (image analysis software) 3. segment specimens 4. capture label data (crowd-sourcing)
    22. 22. Collection digitization: drawers
    23. 23. Collection digitization: slides and vials
    24. 24. InvertNet Website • InvertNet.org • Registration is open to all and available now; please join!
    25. 25. Fossil insect collaborative. • A deep time approach to studying diversification and response to environmental change • 7 collaborative institutions
    26. 26. Fossil insect collaborative. INHS is processing Milton Sanderson’s Dominican amber collection which was stored in 5 gallon buckets.
    27. 27. Fossil insect collaborative Amber is being polished, scanned for inclusions, sorted, photographed, and databased. Termite
    28. 28. Collection Digitization: Global Coverage 2008 2013 GBiF Today, ~800,000 records (2 million specimens) http://data.gbif.org/datasets/provider/75
    29. 29. Outreach C. Dietrich INHS Image Archive C. Dietrich • • • • Annual Prairie Research Institute Expo Illinois Wilds Institute for Nature (IWIN) courses Travelling Science Center INHS published insect field guides
    30. 30. 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.

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