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
- Event hashtag: #vertdigi
- Logistics document
- Walking map: hotel to Anna Head Alumnae Hall
- Hotel information
- Train information
- Original workshop announcement
- Adobe Connect Room to join us
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 | 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
|
| 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
- Data Issues, Plenaries
- Imaging Vertebrate Collections (1pm-2:15pm)
- Imaging Vertebrate Collections (2:35pm-3:35pm)
Tuesday April 5,2016
- Imaging Plenary Sessions (8am-10:10am)
- Imaging Plenary Sessions (10:30-12:20pm)
- Issues of Scale: Imaging Micro to Oversized Objects
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