IDigBio Vertebrate Digitization Workshop Two

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iDigBio Vertebrate Digitization Workshop Two Sponsored by the UCB Integrative Biology Graduate Students Association

iDigBio Workshops



Monday, April 4, 2016

Day One
Time Topic Presenter(s)/Leader(s)
7:00-8:00 Breakfast
8:00-8:10 Welcome, Workshop Introduction, Logistics Michael Nachman, Director, Museum of Vertebrate Zoology
Gil Nelson, iDigBio/Florida State University
David Bloom, VertNet Coordinator, iDigBio/University of California, Berkeley

Brief Introduction to iDigBio

Gil Nelson
Data Issues, Plenaries
8:20-8:40 Data Standards: Darwin Core David Bloom, Laura Russell
8:40-9:00 Audubon Core & Data Aggregation to iDigBio Shelley James, Data Management Coordinator, iDigBio
9:00-9:20 Sampling and Preservation of Genomic Data and Linking Tissue Samples to Vouchers Charlotte Seid, Ocean Genome Legacy Center, Northeastern University
9:20-9:40 Data Management Discussion/Q&A
Discussion Notes
David Bloom and Shelley James, Moderators
9:40-10:00 Selecting What Should be Transcribed and Databased:
Fully Populated vs Skeletal Records
Carla Cicero, MVZ
10:00-10:20 Digitizing and Linking Source Materials Christina Fidler, MVZ
10:20-10:40 Break
Data Issues, Concurrent Discussion Breakouts
Stage End of the Room Non-stage End of the Room
10:40-11:10 Aggregators and Serving Data to the Web
Dave Bloom
Carol Spencer, MVZ, University of California, Berkeley
Digital Asset Management Systems and Workflows
Chris Hoffman, Manager of Informatics Services, IST-Research Information Technologies, UC Berkeley
11:10-11:40 Evaluating and Selecting a Database
Greg Schneider, University of Michigan
Issues in Data Preservation for Biodiversity Collections
Diego Barroso and Cody Thompson, University of Michigan
Laura Abraczinskas, Michigan State University
11:40-12:10 Symbiota as a Tool for Online Data Management for Vertebrate Collections
Lynda Loucks, University of Central Oklahoma
Gil Nelson
Issues in Database Migration

Discussion Notes
Kevin Love, Shelley James, iDigBio, University of Florida
Greg Schneider, University of Michigan

12:10-12:15 Q&A, Discussion, Morning Wrap-up David Bloom
12:15-1:00 Lunch (provided)
Imaging Vertebrate Collections
1:00-1:20 Value of imaging: Herpetology Hinrich Kaiser, Victor Valley College
1:20-1:40 Value of imaging: Ichthyology John Sullivan, Cornell Univesity
1:40-2:00 Value of imaging: Ornithology and Mammalogy Molly Hagemann, Bishop Museum
2:00-2:15 Discussion: What Should be Imaged and Why? Emily Braker (moderator), University of Colorado
Product: Composite Accounting of the Values and Uses of Specimen Images
Notes Document: What to Image?
2:15-2:35 Break
2:35-2:55 Research and Other Uses of Images and Digitized Specimen Data Mary Thompson, Idaho Museum of Natural History
2:55-3:15 Research and Other Uses of Images and Digitized Specimen Data Beth Wommack, University of Wyoming Museum of Vertebrates
3:15-3:35 Safe and Efficient Preservation of Images and Other Media Mike Webster, Cornell University
3:35-4:30 Standard Photographic Views for Herps, Ichs, Birds, and Mammals Group discussion
Notes & conclusions recorded in Google Docs
Laura Abraczinskas, Michigan State University, moderator
5:00-7:00 Reception hosted by the Museum of Vertebrate Zoology (venue: MVZ Gallery)
7:00 Dinner on Your Own

Tuesday, April 5, 2016

Day Two
Time Topic Presenter(s)/Leader(s)
7:00-8:00 Breakfast
8:00-8:15 Lingering comments, observations, questions, discussion from day one Gil Nelson
8:15-8:30 Audio/Video/2D Imaging Metadata and Licensing Mike Webster, Cornell University
Dave Bloom
Imaging Plenary Sessions
8:30-8:50 2D Imaging Stations: Components & Setup John Sullivan, Cornell University
8:50-9:10 Lighting and White Balance (this & previous presentation combined) John Sullivan
9:10-9:30 2D Image Processing Software Andy Williston, MCZ, Harvard University
9:30-9:50 Light Box vs. Copy Stand vs. Squeeze Tank Imaging Systems Zach Randall, Florida Museum of Natural History
9:50-10:10 Imaging Eggs and Nests Carla Cicero
10:10-10:30 Break
10:30-10:50 Workflow Modules and Tasks Gil Nelson
10:50-11:10 DIY: Imaging on a Budget Mark O'Brien, University of Michigan
11:10-11:30 Cataloguing and Archiving Images: Australian National Fish Collection's
Cross-polarisation Photography Process
Carlie Devine, Photographer & Image Manager ANFC, CSIRO
11:30-11:50| A Prototype for Rapid 3D Multi-view Imaging for Photogrammetry Nelson Rios, Tulane Unitersity
11:50-12:10 Using Mobile Devices for Collections Management Cody Thompson, University of Michigan
12:10-12:20 Morning wrap-up/Discussion/Q&A Cody Thompson
12:20-1:15 Lunch (provided)
Imaging Breakouts
Stage End of the Room Non-stage End of the Room
1:15-1:45 2D Imaging Techniques and Workflows for Fluid-preserved Specimens (Herps)
Hinrich Kaiser
2D Imaging Workflows for Dry-preserved Specimens (mammals and birds)
Verity Mathis, University of Florida, Florida Museum of Natural History
Gil Nelson, Tall Timbers Research Station
iDigBio Vertebrate Digitization Workflow Video
Tall Timbers Imaging Protocols
1:45-2:15 2D Imaging Workflows for Fluid-preserved specimens (Fish)
Andy Williston, MCZ, Harvard University
Mining Images for Character Traits (Software for analysis links)
Mary Thompson
2:15-2:45 Anticipating Storage Requirements: Management and Archiving
Greg Schneider
Imaging Microscope Slides
Peter Oboyski, Essig Museum, UC Berkeley
2:45-3:15 Cameras and Lenses for 2D Imaging
John Sullivan
2D Image File Types, Conversion, and Management
Jon Woodward, MCZ, Harvard
3:15-3:35 Break
3:35-4:05 Strategies for Imaging Paper Labels
Brandi Coyner, Sam Noble Museum, University of Oklahoma
Issues of Scale: Imaging Micro to Oversized Objects
Laura Vietti, University of Wyoming
4:05-4:30 Daily Wrap-up: Discussions, Observations, Questions Gil Nelson
6:00 Dinner on Your Own

Wednesday, April 6, 2016

Day Three
Topic Facilitator(s)
Breakfast, 7:00-8:00
Demonstrations, 8:30-10:00
(1) Image Stacking Mark O'Brien
Gil Nelson
(2) Pre-processing and Cleaning Data Laura Russell, VertNet/iDigBio
David Bloom
(3) Microscope Slide Scanning Peter Oboyski
(4) Data Migration from Excel (PDF) Dusty McDonald, University of Alaska, Fairbanks
Break, 10:00-10:30
Demonstrations, 10:30-12:00
(5) Using Mobile Devices for Collections Management Cody Thompson
(6) Imaging Paper Labels
PDF of Skin Tag Capture: An Illustrated Guide
Brandi Coyner, SNOMNH Mammal Collection, 05/12/2015
Brandi Coyner
(7) Using a Light Box Verity Mathis, Gil Nelson
(8) Squeeze Tank Imaging Zach Randall
Lunch (provided), 12:00-1:00
Collection tours, 2:00-4:30
Wrap up and group picture, 4:30-5:00
VLSB Atrium
Dinner on your own, 6:00

Workshop Recordings

Monday April 4, 2016

Tuesday April 5,2016

Workshop Planning Team

  • Laura Abraczinskas, Michigan State University
  • David Bloom, iDigBio/VertNet
  • Emily Braker, University of Colorado
  • Carla Cicero, Museum of Vertebrate Zoology
  • Molly Hagemann, Bishop Museum
  • Gil Nelson, iDigBio/Florida State University
  • Cody Thompson, University of Michigan
  • Mike Webster, Cornell Laboratory of Ornithology
  • Andy Williston, Museum of Comparative Zoology