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Digitizing Fluid-preserved Vertebrate Specimens: Difference between revisions

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Digitizing Fluid-preserved Vertebrate Specimens (view source)

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→‎AgendaTuesday, March 15, 2016
(Created page with "<br><br> ==iDigBio Workshops== ==Logistics== *[http://www.hawthorn.com/hotels/illinois/champaign/hawthorn-suites-by-wyndham-champaign/hotel-overview/ Ho...")
 
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*[https://www.idigbio.org/content/digitizing-fluid-preserved-vertebrate-specimens/ Original workshop announcement]
*[https://www.idigbio.org/content/digitizing-fluid-preserved-vertebrate-specimens/ Original workshop announcement]


===Agenda<br>Tuesday, March 15, 2016===
===Agenda<br>Tuesday, March 15, 2016==
{| class="wikitable" style="background-color:#FFF8DC;"
!colspan="3" | Day One
|-
! scope="col" | Time
! scope="col" | Topic
! scope="col" | Presenter(s)/Leader(s)
|-
|-
|style="vertical-align:top;"|6:30 - 7:30 a.m.
|rowspan="1" colspan="2" style="vertical-align:top; background-color:#FFF8DC;"|Breakfast at Hotel<br>Complimentary breakfast 6:30 - 9:30 a.m.
|-
|-
|style="vertical-align:top;"|8:00-8:15 a.m.
|rowspan="1" style="vertical-align:top; background-color:#FFF8DC;"|Welcome and Workshop Introduction and Logistics
|Gil Nelson, iDigBio/Florida State University<br>Chris Phillips, Illinois Natural History Survey
|-
|-
|style="vertical-align:top; text-align: left;"|8:15-8:45 a.m.
|rowspan="1" style="vertical-align:top; background-color:#FFF8DC;"|
Introduction to ADBC, iDigBio, and TCN Development
|Larry Page, iDigBio/Florida Museum of Natural History
|-
|-
|style="vertical-align:top;"|8:45-9:15 a.m.
|rowspan="1" style="vertical-align:top; background-color::#eed1a9;"|Why this Workshop?<br>Workshop Goals, Discussion, agenda additions
|Larry Page <br> Gil Nelson
|-
|-
|style="vertical-align:top;"|8:40-9:00
|rowspan="1" style="vertical-align:top; background-color:#FFF8DC;"|Audubon Core & Data Aggregation to iDigBio
|Shelley James, Data Management Coordinator, iDigBio
|-
|style="vertical-align:top;"|9:00-9:20
|rowspan="1" style="vertical-align:top; background-color:#FFF8DC;"|Sampling and Preservation of Genomic Data and Linking Tissue Samples to Vouchers
|Charlotte Seid, Ocean Genome Legacy Center, Northeastern University
|-
|-
|style="vertical-align:top;"|9:20-9:40
|rowspan="1" style="vertical-align:top; background-color:#FFF8DC;"|Data Management Discussion/Q&A
|David Bloom and Shelley James, Moderators
|-
|-
|style="vertical-align:top;"|9:40-10:00
|rowspan="1" style="vertical-align:top; background-color:#FFF8DC;"|Selecting What Should be Transcribed and Databased: Fully Populated vs Skeletal Records
|Carla Cicero, MVZ
|-
|-
|style="vertical-align:top;"|10:00-10:20
|rowspan="1" style="vertical-align:top; background-color:#FFF8DC;"|Digitizing and Linking Source Materials
|Christina Fidler, MVZ
|-
|-
|style="vertical-align:top;"|10:20-10:40
|rowspan="1" colspan="2" style="vertical-align:top; background-color:#FFF8DC;"|Break
|-
|-
|colspan="3" style="text-align:center; vertical-align:top; background-color:#eed1a9;"|<b>Data Issues, Concurrent Breakouts</b>
|-
|-
|style="vertical-align:top;"|10:40-11:10
|rowspan="1" style="vertical-align:top; background-color:#FFF8DC;"|Aggregators and Serving Data to the Web<br>Dave Bloom<br>Carol Spencer, MVZ, University of California, Berkeley
|Digital Asset Management systems and workflows<br>Chris Hoffman, Manager of Informatics Services, IST-Research Information Technologies, UC Berkeley
|-
|-
|style="vertical-align:top;"|11:10-11:40
|rowspan="1" style="vertical-align:top; background-color:#FFF8DC;"|Evaluating and Selecting a Database<br>Greg Schneider, University of Michigan
|Core Data to Preserve for Biodiversity Collections<br>Diego Barroso and Cody Thompson, University of Michigan<br>Laura Abraczinskas, Michigan State University
|-
|-
|style="vertical-align:top;"|11:40-12:10
|rowspan="1" style="vertical-align:top; background-color:#FFF8DC;"|Symbiota as a Tool for Online Data Management for Vertebrate Collections<br>Lynda Loucks, University of Central Oklahoma<br>Gil Nelson
|Issues in Database Migration<br>Kevin Love, Shelley James, iDigBio, University of Florida<br>Greg Schneider, University of Michigan
|-
|-
|style="vertical-align:top;"|12:10-12:20
|rowspan="1" style="vertical-align:top; background-color:#FFF8DC;"|Q&A, Discussion, Morning Wrap-up
|David Bloom
|-
|-
|style="vertical-align:top;"|12:20-1:15
|rowspan="1" colspan="2" style="vertical-align:top; background-color:#FFF8DC;"|Lunch (provided)
|-
|-
|colspan="3" style="text-align:center; vertical-align:top; background-color:#eed1a9;"|<b>Imaging Vertebrate Collections</b>
|-
|-
|style="vertical-align:top;"|1:15-1:35
|rowspan="1" style="vertical-align:top; background-color:#FFF8DC;"|Value of imaging: Herpetology
|Hinrich Kaiser, Victor Valley College
|-
|-
|style="vertical-align:top;"|1:35-1:55
|rowspan="1" style="vertical-align:top; background-color:#FFF8DC;"|Value of imaging: Ichthyology
|John Sullivan, Cornell Univesity
|-
|-
|style="vertical-align:top;"|1:55-2:15
|rowspan="1" style="vertical-align:top; background-color:#FFF8DC;"|Value of imaging: Ornithology and Mammalogy 
|Molly Hagemann, Bishop Museum
|-
|-
|style="vertical-align:top;"|2:15-2:35
|rowspan="1" style="vertical-align:top; background-color:#FFF8DC;"|Discussion: What Should be Imaged and Why?
|Emily Baker (moderator), University of Colorado<br>Product: Composite Accounting of the Values and Uses of Specimen Images
|-
|-
|style="vertical-align:top;"|2:35-3:00
|rowspan="1" colspan="2" style="vertical-align:top; background-color:#FFF8DC;"|Break
|-
|-
|style="vertical-align:top;"|3:00-3:20
|rowspan="1" style="vertical-align:top; background-color:#FFF8DC;"|Research and Other Uses of Images and Digitized Specimen Data
|Mary Thompson, Idaho Museum of Natural History
|-
|-
|style="vertical-align:top;"|3:20-3:40
|rowspan="1" style="vertical-align:top; background-color:#FFF8DC;"|Research and Other Uses of Images and Digitized Specimen Data
|Beth Wommack, University of Wyoming Museum of Vertebrates
|-
|-
|style="vertical-align:top;"|3:40-4:00
|rowspan="1" style="vertical-align:top; background-color:#FFF8DC;"|Safe and Efficient Preservation of Images and Other Media
|Mike Webster, Cornell University
|-
|-
|style="vertical-align:top;"|4:00-4:30
|rowspan="1" style="vertical-align:top; background-color:#FFF8DC;"|Standard Photographic Views for Herps, Ichs, Birds, and Mammals
|Discussion group breakouts<br>Notes & conclusions recorded in Google Docs
|-
|-
|style="vertical-align:top;"|4:30-5:00
|rowspan="1" style="vertical-align:top; background-color:#FFF8DC;"|Discussion Group Reports
|Laura Abraczinskas, Michigan State University, moderator<br>
|-
|-
|style="vertical-align:top;"|6:00
|rowspan="1" colspan="2" style="vertical-align:top; background-color:#FFF8DC;"|Dinner on Your Own
|-
|}
 
===Tuesday, April 5, 2016===
{| class="wikitable" style="background-color:#FFF8DC;"
!colspan="3" | Day Two
|-
! scope="col" | Time
! scope="col" | Topic
! scope="col" | Presenter(s)/Leader(s)
|-
|-
|style="vertical-align:top;"|7:00-8:00
|rowspan="1" colspan="2" style="vertical-align:top; background-color:#FFF8DC;"|Breakfast
|-
|-
|style="vertical-align:top;"|8:00-8:15
|rowspan="1" style="vertical-align:top; background-color:#FFF8DC;"|Lingering comments, observations, questions, discussion from day one
|Gil Nelson
|-
|-
|style="vertical-align:top; text-align: left;"|8:15-8:30
|rowspan="1" style="vertical-align:top; background-color:#FFF8DC;"|Audio/Video/2D Imaging Metadata
|Mike Webster, Cornell University
|-
|-
|colspan="3" style="text-align:center; vertical-align:top; background-color:#eed1a9;"|<b>Imaging Plenary Sessions</b>
|-
|-
|style="vertical-align:top;"|8:30-8:50
|rowspan="1" style="vertical-align:top; background-color::#eed1a9;"|2D Imaging Stations: Components & Setup
|John Sullivan, Cornell University
|-
|-
|style="vertical-align:top;"|8:50-9:10
|rowspan="1" style="vertical-align:top; background-color:#FFF8DC;"|Lighting and White Balance
|John Sullivan
|-
|-
|style="vertical-align:top;"|9:10-9:30
|rowspan="1" style="vertical-align:top; background-color:#FFF8DC;"|2D Image Processing Software
|Andy Williston, MCZ, Harvard University
|-
|-
|style="vertical-align:top;"|9:30-9:50
|rowspan="1" style="vertical-align:top; background-color:#FFF8DC;"|Light Box vs. Copy Stand vs. Squeeze Tank Imaging Systems
|Zach Randall, Florida Museum of Natural History
|-
|-
|style="vertical-align:top;"|9:50-10:10
|rowspan="1" style="vertical-align:top; background-color:#FFF8DC;"|
|
|-
|-
|style="vertical-align:top;"|10:10-10:30
|rowspan="1" colspan="2" style="vertical-align:top; background-color:#FFF8DC;"|Break
|-
|style="vertical-align:top;"|10:30-10:50
|rowspan="1" style="vertical-align:top; background-color:#FFF8DC;"|Workflow Modules and Tasks
|Gil Nelson
|-
|-
|style="vertical-align:top;"|10:50-11:10
|rowspan="1" style="vertical-align:top; background-color:#FFF8DC;"|DIY: Imaging on a Budget
|Mark O'Brien, University of Michigan
|-
|-
|style="vertical-align:top;"|11:10-11:30
|rowspan="1" style="vertical-align:top; background-color:#FFF8DC;"|Imaging Eggs and Nests
|???Anand Varma, MVZ
|-
|-
|style="vertical-align:top;"|11:30-11:50
|rowspan="1" style="vertical-align:top; background-color:#FFF8DC;"|A Prototype for Rapid 3D Multi-view Imaging for Photogrammetry
|Nelson Rios, Tulane Unitersity
|-
|-
|style="vertical-align:top;"|11:50-12:10
|rowspan="1" style="vertical-align:top; background-color:#FFF8DC;"|Using Mobile Devices for Collections Management
|Cody Thompson, University of Michigan
|-
|-
|style="vertical-align:top;"|12:10-12:20
|rowspan="1" style="vertical-align:top; background-color:#FFF8DC;"|Morning wrap-up/Discussion/Q&A
|Cody Thompson
|-
|-
|style="vertical-align:top;"|12:20-1:15
|rowspan="1" colspan="2" style="vertical-align:top; background-color:#FFF8DC;"|Lunch (provided)
|-
|-
|colspan="3" style="text-align:center; vertical-align:top; background-color:#eed1a9;"|<b>Imaging Breakouts</b>
|-
|-
|style="vertical-align:top;"|1:15-1:45
|rowspan="1" style="vertical-align:top; background-color:#FFF8DC;"|2D Imaging Techniques and Workflows for Fluid-preserved Specimens (Herps)<br>Hinrich Kaiser
|2D Imaging Workflows for Dry-preserved Specimens (mammals and birds)<br>Verity Mathis, University of Florida, Florida Museum of Natural History<br>Gil Nelson, Tall Timbers Research Station
|-
|-
|style="vertical-align:top;"|1:45-2:15
|rowspan="1" style="vertical-align:top; background-color:#FFF8DC;"|2D Imaging Workflows for Fluid-preserved specimens (Fish)<br>Andy Williston, MCZ, Harvard University
|Mining Images for Character Traits<br>Mary Thompson
|-
|-
|style="vertical-align:top;"|2:15-2:45
|rowspan="1" style="vertical-align:top; background-color:#FFF8DC;"|Anticipating Storage Requirements: Management and Archiving<br>???Greg Schneider
|Imaging Microscope Slides<br>Peter Oboyski, Essig Museum, UC Berkeley
|-
|-
|style="vertical-align:top;"|2:45-3:15
|rowspan="1" style="vertical-align:top; background-color:#FFF8DC;"|Cameras and Lenses for 2D Imaging<br>John Sullivan
|2D Image File Types, Conversion, and Management<br>Jon Woodward, MCZ, Harvard
|-
|-
|style="vertical-align:top;"|3:15-3:35
|rowspan="1" colspan="2" style="vertical-align:top; background-color:#FFF8DC;"|Break
|-
|-
|style="vertical-align:top;"|3:35-4:05
|rowspan="1" style="vertical-align:top; background-color:#FFF8DC;"|Strategies for Imaging Paper Labels<br>Brandi Coyner, Sam Noble Museum, University of Oklahoma
|Issues of Scale: Imaging Micro to Oversized Objects<br>Laura Vietti, University of Wyoming
|-
|-
|style="vertical-align:top;"|4:05-4:30
|rowspan="1" style="vertical-align:top; background-color:#FFF8DC;"|Daily Wrap-up: Discussions, Observations, Questions
|Gil Nelson
|-
|-
|style="vertical-align:top;"|6:00
|rowspan="1" colspan="2" style="vertical-align:top; background-color:#FFF8DC;"|Dinner on Your Own
|-
|}
 
===Wednesday, April 6, 2016===
{| class="wikitable" style="background-color:#FFF8DC;"
!colspan="2" | Day Three
|-
! scope="col" | Topic
! scope="col" | Facilitator(s)
|-
|-
|colspan="2" style="text-align:center; vertical-align:top; background-color:#eed1a9;"|<b>Breakfast, 7:00-8:00</b>
|-
|-
|colspan="2" style="text-align:center; vertical-align:top; background-color:#eed1a9;"|<b>Demonstrations, 8:30-10:00</b>
|-
|-
|rowspan="1" style="vertical-align:top; background-color:#FFF8DC;"|(1) Using Mobile Devices for Collections Management
|Cody Thompson
|-
|-
|rowspan="1" style="vertical-align:top; background-color:#FFF8DC;"|(2) Image Stacking
|
|-
|-
|rowspan="1" style="vertical-align:top; background-color:#FFF8DC;"|*(3) Pre-processing and Cleaning Data
|Laura Russell, VertNet/iDigBio<br>Carla Cicero
|-
|-
|rowspan="1" style="vertical-align:top; background-color::#eed1a9;"|(4) Microscope Slide Scanning
|Peter Oboyski
|-
|-
|rowspan="1" style="vertical-align:top; background-color:#FFF8DC;"|(5) Data Migration from Excel
|Dusty McDonald, University of Alaska, Fairbanks
|-
|-
|colspan="3" style="text-align:center; vertical-align:top; background-color:#eed1a9;"|<b>Break, 10:00-10:30</b>
|-
|-
|colspan="2" style="text-align:center; vertical-align:top; background-color:#eed1a9;"|<b>Demonstrations, 10:30-12:00</b>
|-
|-
|rowspan="1" style="vertical-align:top; background-color:#FFF8DC;"|(6) Imaging Paper Labels
|Brandi Coyner
|-
|-
|rowspan="1" style="vertical-align:top; background-color:#FFF8DC;"|(7) Using a Light Box
|Verity Mathis, Gil Nelson
|-
|-
|rowspan="1" style="vertical-align:top; background-color:#FFF8DC;"|(8) Squeeze Tank Imaging
|Zack Randall
|-
|-
|rowspan="1" style="vertical-align:top; background-color:#FFF8DC;"|(9) Imaging Eggs and Nests
|???Anand Varma, MVZ, UC Berkeley
|-
|-
|colspan="3" style="text-align:center; vertical-align:top; background-color:#eed1a9;"|<b>Lunch (provided), 12:00-1:00</b>
|-
|-
|colspan="3" style="text-align:center; vertical-align:top; background-color:#eed1a9;"|<b>Collection tours, 1:00-5:00</b>
|-
|-
|colspan="3" style="text-align:center; vertical-align:top; background-color:#eed1a9;"|<b>Dinner on your own, 6:00</b>
|-
|}
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