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

Logistics

Agenda

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
8:10-8:20

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
http://csvcoll.org
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