Digitizing Fluid-preserved Vertebrate Specimens: Difference between revisions

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==<b>Overcoming Challenges for Imaging Fluid-preserved Vertebrates</b>==
==[[IDigBio_Workshops|iDigBio Workshops]]==
==[[IDigBio_Workshops|iDigBio Workshops]]==


==Logistics==
==Logistics==
* Event hashtag: #vertdigi
*[[Media:LOGISTICS_ILNHS_2016.pdf | Workshop Logistics Document]]
*[http://www.hawthorn.com/hotels/illinois/champaign/hawthorn-suites-by-wyndham-champaign/hotel-overview/ Hotel information]
*[http://www.hawthorn.com/hotels/illinois/champaign/hawthorn-suites-by-wyndham-champaign/hotel-overview/ Hotel information]
*[https://www.cumtd.com/ Train information]
*[https://www.cumtd.com/ Mass Transit information]
*[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==
==Shared Documents==
*[https://drive.google.com/folderview?id=0B9zqKK80tdzhWkNSZ1c1dWJoYXc&usp=sharing Google docs folder]
*[https://docs.google.com/document/d/1nkLlcIofDtWdz58mW096uOt6yo4x30FR123eCE0nR7U/edit?usp=sharing Additional agenda items document]
*[https://docs.google.com/document/d/16KZvAfY8ywCn2BE6C4RyGzXhFu7XM00_4BBzaGAg7Wg/edit?usp=sharing Status of imaging]]
*[https://docs.google.com/document/d/1hUKrI8ueCXj_6LxwAutjEPIq59WxJ2XsF3bCwooABD4/edit Imaging Technologies Notes]
 
==Agenda, Day 1<br>Tuesday, March 15, 2016==
{| class="wikitable" style="background-color:#FFF8DC;"
{| class="wikitable" style="background-color:#FFF8DC;"
!colspan="3" | Day One
!colspan="3" | Day One
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|-
|-
|style="vertical-align:top;"|8:00-8:15 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
|rowspan="1" style="vertical-align:top; background-color:#FFF8DC;"|Welcome, Logistics, and Introductions
|Gil Nelson, iDigBio/Florida State University<br>Chris Phillips, Illinois Natural History Survey
|Gil Nelson, iDigBio/Florida State University<br>Chris Phillips, Illinois Natural History Survey
|-
|-
Line 27: Line 37:
|style="vertical-align:top; text-align: left;"|8:15-8:45 a.m.
|style="vertical-align:top; text-align: left;"|8:15-8:45 a.m.
|rowspan="1" style="vertical-align:top; background-color:#FFF8DC;"|
|rowspan="1" style="vertical-align:top; background-color:#FFF8DC;"|
Introduction to ADBC, iDigBio, and TCN Development
[[Media:Page.Cong.Brief.INHS_2016.pdf|Introduction to ADBC, iDigBio, and TCN Development]]
|Larry Page, iDigBio/Florida Museum of Natural History
|Larry Page, iDigBio/Florida Museum of Natural History
|-
|-
|-
|-
|style="vertical-align:top;"|8:45-9:15 a.m.
|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
|rowspan="1" style="vertical-align:top; background-color::#eed1a9;"|[[Media:Why_this_workshop.pdf|Why this Workshop?]]<br>Workshop Goals, Discussion, agenda additions
|Larry Page <br> Gil Nelson
|Larry Page <br> Gil Nelson
|-
|-
|-
|-
|style="vertical-align:top;"|8:40-9:00
|style="vertical-align:top;"|9:15-9:45 a.m.
|rowspan="1" style="vertical-align:top; background-color:#FFF8DC;"|Audubon Core & Data Aggregation to iDigBio
|rowspan="1" style="vertical-align:top; background-color:#FFF8DC;"|The case for imaging fish
|Shelley James, Data Management Coordinator, iDigBio
|Mark Sabaj-Perez, Drexel
|-
|-
|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;"|9:45-10:15 a.m.
|rowspan="1" style="vertical-align:top; background-color:#FFF8DC;"|[[Media:Kaiser_Illinois.pdf|The case for imaging herps]]
|Hinrich Kaiser, Victor Valley College
|-
|-
|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;"|10:15-10:45 a.m.
|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
|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;"|10:45-11:15 a.m.
|rowspan="1" style="vertical-align:top; background-color:#FFF8DC;"|[[Media:Mark_SabajPerez.pdf|The case for 2D imaging]]
|Mark Sabaj-Perez
|-
|-
|-
|-
|style="vertical-align:top;"|10:40-11:10
|style="vertical-align:top;"|11:15-12:00 p.m.
|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
|rowspan="1" style="vertical-align:top; background-color:#FFF8DC;"|[[Media:Bart_Case_for_3D_Imagineg_Vertebrate_Speciments.pdf|The case for 3D imaging]]<br>[[Media:Rios_photogrammetry_march2016.pdf|Photogrammetry]]
|Digital Asset Management systems and workflows<br>Chris Hoffman, Manager of Informatics Services, IST-Research Information Technologies, UC Berkeley
|Hank Bart, Tulane<br>Nelson Rios, Tulane
|-
|-
|-
|-
|style="vertical-align:top;"|11:10-11:40
|style="vertical-align:top;"|12:00-12:30 p.m.
|rowspan="1" style="vertical-align:top; background-color:#FFF8DC;"|Evaluating and Selecting a Database<br>Greg Schneider, University of Michigan
|rowspan="1" style="vertical-align:top; background-color:#FFF8DC;"|[[Media:CaseForCT_Blackburn_14March2016.pdf|The case for CT imaging]]
|Core Data to Preserve for Biodiversity Collections<br>Diego Barroso and Cody Thompson, University of Michigan<br>Laura Abraczinskas, Michigan State University
|David Blackburn, Florida Museum of Natural History
|-
|-
|-
|-
|style="vertical-align:top;"|11:40-12:10
|style="vertical-align:top;"|12:30-1:30 p.m.
|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
|rowspan="1" colspan="2" style="vertical-align:top; background-color:#FFF8DC;"|Lunch
|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
|style="vertical-align:top;"|1:30-1:45 p.m.
|rowspan="1" style="vertical-align:top; background-color:#FFF8DC;"|Q&A, Discussion, Morning Wrap-up
|rowspan="1" style="vertical-align:top; background-color:#FFF8DC;"|[[Media:SurveySummary.pdf|Review and discussion of pre-workshop survey results]]
|David Bloom
(including discussion of the status of databasing in fish and herp collections)
|-
|Gil Nelson
|-
|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
|style="vertical-align:top;"|1:45-3:00 p.m.
|rowspan="1" style="vertical-align:top; background-color:#FFF8DC;"|Value of imaging: Ichthyology
|rowspan="1" style="vertical-align:top; background-color:#FFF8DC;"|Status of imaging at participating collections:<br>[https://docs.google.com/document/d/16KZvAfY8ywCn2BE6C4RyGzXhFu7XM00_4BBzaGAg7Wg/edit?usp=sharing Document for notetaking]<br>
|John Sullivan, Cornell Univesity
Each participant to have 3 minutes to outline the status of imaging at their institution.<br>* Current imaging practices<br>* how are images being used<br>* Issues to resolve<br>* Future plans<br>* Challenges<br>* Institutional choices about what to image<br>* Preferences: 2D, 3D, CT, no imaging<br>* Institutional predispositions regarding the value and use of images
|Greg Watkins-Colwell, Yale Peabody Museum, moderator
|-
|-
|-
|-
|style="vertical-align:top;"|1:55-2:15
|style="vertical-align:top;"|3:00-3:30 p.m.
|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
|rowspan="1" colspan="2" style="vertical-align:top; background-color:#FFF8DC;"|Break
|-
|-
|-
|-
|style="vertical-align:top;"|3:00-3:20
|style="vertical-align:top;"|3:30-4:30 p.m.
|rowspan="1" style="vertical-align:top; background-color:#FFF8DC;"|Research and Other Uses of Images and Digitized Specimen Data
|rowspan="1" style="vertical-align:top; background-color:#FFF8DC;"|[[Media:A_researcher’s_perspective.pdf|Imaging for data collection: An overview]]
|Mary Thompson, Idaho Museum of Natural History
|Miriam Zelditch, U. Michigan<br>Donald Swigerski, U. Michigan
|-
|-
|-
|-
|style="vertical-align:top;"|3:20-3:40
|style="vertical-align:top;"|4:30-4:45 p.m.
|rowspan="1" style="vertical-align:top; background-color:#FFF8DC;"|Research and Other Uses of Images and Digitized Specimen Data
|rowspan="1" style="vertical-align:top; background-color:#FFF8DC;"|Discussion/Q&A: Imaging for data collection
|Beth Wommack, University of Wyoming Museum of Vertebrates
|Miriam & Donald<br>moderators
|-
|-
|-
|-
|style="vertical-align:top;"|3:40-4:00
|style="vertical-align:top;"|4:45-5:00 p.m.
|rowspan="1" style="vertical-align:top; background-color:#FFF8DC;"|Safe and Efficient Preservation of Images and Other Media
|rowspan="1" style="vertical-align:top; background-color:#FFF8DC;"|Daily wrap-up, observations, comments, challenges, criticisms, further discussion
|Mike Webster, Cornell University
|Greg Watkins-Colwell<br>moderator
|-
|-
|-
|-
|style="vertical-align:top;"|4:00-4:30
|rowspan="1" colspan="3" style="text-align:center; background-color:#FFF8DC;"|Dinner on Your Own<br>
|rowspan="1" style="vertical-align:top; background-color:#FFF8DC;"|Standard Photographic Views for Herps, Ichs, Birds, and Mammals
Recommended gathering place: [http://www.houlihans.com/my-houlihans/champaign Houlihans]<br> Reservation at 6:15 pm, Meet in hotel lobby at 6:00 pm
|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===
==Agenda, Day 2<br>Wednesday, March 16, 2016==
{| class="wikitable" style="background-color:#FFF8DC;"
{| class="wikitable" style="background-color:#FFF8DC;"
!colspan="3" | Day Two
!colspan="3" | Day One
|-
|-
! scope="col" | Time
! scope="col" | Time  
! scope="col" | Topic
! scope="col" | Topic
! scope="col" | Presenter(s)/Leader(s)  
! scope="col" | Presenter(s)/Leader(s)  
|-
|-
|-
|-
|style="vertical-align:top;"|7:00-8:00
|style="vertical-align:top;"|6:30 - 7:30 a.m.
|rowspan="1" colspan="2" style="vertical-align:top; background-color:#FFF8DC;"|Breakfast
|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
|style="vertical-align:top;"|8:00-8:15 a.m.
|rowspan="1" style="vertical-align:top; background-color:#FFF8DC;"|Lingering comments, observations, questions, discussion from day one
|rowspan="1" style="vertical-align:top; background-color:#FFF8DC;"|Lingering questions and observations from Day 1
|Gil Nelson
|Larry Page, Moderator
|-
|-
|-
|-
|style="vertical-align:top; text-align: left;"|8:15-8:30
|style="vertical-align:top; text-align: left;"|8:15-9:00 a.m.
|rowspan="1" style="vertical-align:top; background-color:#FFF8DC;"|Audio/Video/2D Imaging Metadata
|rowspan="1" style="vertical-align:top; background-color:#FFF8DC;"|
|Mike Webster, Cornell University
Breakout discussions focused on uses and value of images:
*[https://docs.google.com/document/d/1rry-pVW2rX1nyazW1saURvhaJd--55WAdLrPSl3mBow/edit Fish]
*[https://docs.google.com/document/d/1jJD1xVRhYXOyzj_J6cNF8JsR9sB4d3iQJjo1vx9c2p4/edit Herps]<br>
|Chris Phillips, Moderator
|-
|-
|-
|-
|colspan="3" style="text-align:center; vertical-align:top; background-color:#eed1a9;"|<b>Imaging Plenary Sessions</b>
|style="vertical-align:top;"|9:00-10:00 a.m.
|rowspan="1" style="vertical-align:top; background-color::#eed1a9;"|Breakout discussions:
Important research questions to be answered by a large dataset of fish and herp images?<br>
*[https://docs.google.com/document/d/15QISIVWc0wvQz4x-O9LJICBYW_TIZR1dajbTqj93i84/edit Research questions 1]
*[https://docs.google.com/document/d/1PK1qO9w_j8EHgSOF7PJ80a7QOCvk0GCTLbC3DbiIs-E/edit?usp=sharing Research questions 2]
*[https://docs.google.com/document/d/1UD54G4tHBdk9RtM8gTLhWV-lUbb_YoztTo6cHUQ5pME/edit Research questions 3]
|Chris Phillips, Moderator
|-
|-
|-
|-
|style="vertical-align:top;"|8:30-8:50
|style="vertical-align:top;"|10:00-10:30 a.m.
|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
|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;"|10:30-11:30 a.m.
|rowspan="1" style="vertical-align:top; background-color:#FFF8DC;"|Breakout session reports on potential research questions
|Mark Sabaj-Perez, moderator
|-
|-
|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;"|11:30-12:00 a.m.
|rowspan="1" style="vertical-align:top; background-color:#FFF8DC;"|Organize for afternoon deliberations:<br>What Should be the Focus of a Fluid-preserved Vertebrate Imaging TCN: goals, outcomes, components, and research basis?
*Determine discussion group themes<br>
**[https://docs.google.com/document/d/1ENCG8CaMtjVcxbIV3TwfNd_bxBYj51PJHnWlVvzvgqo/edit Broader Impacts]
**[https://docs.google.com/document/d/1zgahGenuw3VnpZCVWh7iAnQz97o8TKWD47M25xYy0qk/edit Imaging Focus]
''-Ecological component: looking beyond fishes and herps <br>
''-Digitization of field notes to support digitized images for holistic picture of organisms''<br>
''-Imaging beyond the specimen: utilizing photographs from the field''<br>
''-Broader impacts''<br>
''-Quality of data: Developing standards(Future workshop?)''<br>
*Select discussion group participation
*Outline expected group discussion and afternoon outcomes
*Grand challenge research questions
<br>[https://docs.google.com/document/d/1xhHyOqj-8rZSyQEha7La7lb9WAYvIpB_Vn-0D4yo1bo/edit?usp=sharing Discussion documentation]
|Gil Nelson, moderator
|-
|-
|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;"|12:00-1:00 p.m.
|rowspan="1" colspan="2" style="vertical-align:top; background-color:#FFF8DC;"|Lunch
|-
|-
|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;"|
|rowspan="1" style="vertical-align:top; background-color:#FFF8DC;"|<b>Afternoon theme:
What Should be the Focus of a Fluid-preserved Vertebrate Imaging TCN?</b><br>[https://docs.google.com/document/d/1flC4rgSVuqut7USz4K6XyBCSNXIsGYhk82dkWZ5jXog/edit?usp=sharing Notes document]
*[https://docs.google.com/document/d/158Mf3WqypJPiLHfQHi0N3XVDuTtWVq8owa0H_8Ld1FQ/edit Mechanics]
|Larry Page, moderator
|-
|-
|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)
|-
|-
|style="vertical-align:top;"|1:00-3:00 p.m.
|rowspan="1" style="vertical-align:top; background-color:#FFF8DC;"|Discussion breakouts
|
|-
|-
|colspan="3" style="text-align:center; vertical-align:top; background-color:#eed1a9;"|<b>Imaging Breakouts</b>
|-
|-
|-
|style="vertical-align:top;"|3:00-3:30 p.m.
|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
|rowspan="1" colspan="2" style="vertical-align:top; background-color:#FFF8DC;"|Break
|-
|-
|-
|-
|style="vertical-align:top;"|3:35-4:05
|style="vertical-align:top;"|3:30-5:00 p.m.
|rowspan="1" style="vertical-align:top; background-color:#FFF8DC;"|Strategies for Imaging Paper Labels<br>Brandi Coyner, Sam Noble Museum, University of Oklahoma
|rowspan="1" style="vertical-align:top; background-color:#FFF8DC;"|Discussion group reports and additional plenary discussion
|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
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|-
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|rowspan="1" style="vertical-align:top; background-color:#FFF8DC;"|*(3) Pre-processing and Cleaning Data
|rowspan="1" colspan="3" style="text-align:center; background-color:#FFF8DC;"|Dinner on Your Own
|Laura Russell, VertNet/iDigBio<br>Carla Cicero
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|rowspan="1" style="vertical-align:top; background-color::#eed1a9;"|(4) Microscope Slide Scanning
|Peter Oboyski
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|rowspan="1" style="vertical-align:top; background-color:#FFF8DC;"|(5) Data Migration from Excel
|Dusty McDonald, University of Alaska, Fairbanks
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|colspan="3" style="text-align:center; vertical-align:top; background-color:#eed1a9;"|<b>Break, 10:00-10:30</b>
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|colspan="2" style="text-align:center; vertical-align:top; background-color:#eed1a9;"|<b>Demonstrations, 10:30-12:00</b>
|-
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|rowspan="1" style="vertical-align:top; background-color:#FFF8DC;"|(6) Imaging Paper Labels
|Brandi Coyner
|-
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|rowspan="1" style="vertical-align:top; background-color:#FFF8DC;"|(7) Using a Light Box
|Verity Mathis, Gil Nelson
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|rowspan="1" style="vertical-align:top; background-color:#FFF8DC;"|(8) Squeeze Tank Imaging
|Zack Randall
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|rowspan="1" style="vertical-align:top; background-color:#FFF8DC;"|(9) Imaging Eggs and Nests
|???Anand Varma, MVZ, UC Berkeley
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|colspan="3" style="text-align:center; vertical-align:top; background-color:#eed1a9;"|<b>Lunch (provided), 12:00-1:00</b>
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|colspan="3" style="text-align:center; vertical-align:top; background-color:#eed1a9;"|<b>Collection tours, 1:00-5:00</b>
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|colspan="3" style="text-align:center; vertical-align:top; background-color:#eed1a9;"|<b>Dinner on your own, 6:00</b>
|-
|}

Latest revision as of 10:56, 28 March 2016



Overcoming Challenges for Imaging Fluid-preserved Vertebrates

iDigBio Workshops

Logistics

Shared Documents

Agenda, Day 1
Tuesday, March 15, 2016

Day One
Time Topic Presenter(s)/Leader(s)
6:30 - 7:30 a.m. Breakfast at Hotel
Complimentary breakfast 6:30 - 9:30 a.m.
8:00-8:15 a.m. Welcome, Logistics, and Introductions Gil Nelson, iDigBio/Florida State University
Chris Phillips, Illinois Natural History Survey
8:15-8:45 a.m.

Introduction to ADBC, iDigBio, and TCN Development

Larry Page, iDigBio/Florida Museum of Natural History
8:45-9:15 a.m. Why this Workshop?
Workshop Goals, Discussion, agenda additions 		Larry Page
Gil Nelson
9:15-9:45 a.m. The case for imaging fish Mark Sabaj-Perez, Drexel
9:45-10:15 a.m. The case for imaging herps Hinrich Kaiser, Victor Valley College
10:15-10:45 a.m. Break
10:45-11:15 a.m. The case for 2D imaging Mark Sabaj-Perez
11:15-12:00 p.m. The case for 3D imaging
Photogrammetry 		Hank Bart, Tulane
Nelson Rios, Tulane
12:00-12:30 p.m. The case for CT imaging David Blackburn, Florida Museum of Natural History
12:30-1:30 p.m. Lunch
1:30-1:45 p.m. Review and discussion of pre-workshop survey results

(including discussion of the status of databasing in fish and herp collections)

Gil Nelson
1:45-3:00 p.m. Status of imaging at participating collections:
Document for notetaking

Each participant to have 3 minutes to outline the status of imaging at their institution.
* Current imaging practices
* how are images being used
* Issues to resolve
* Future plans
* Challenges
* Institutional choices about what to image
* Preferences: 2D, 3D, CT, no imaging
* Institutional predispositions regarding the value and use of images

Greg Watkins-Colwell, Yale Peabody Museum, moderator
3:00-3:30 p.m. Break
3:30-4:30 p.m. Imaging for data collection: An overview Miriam Zelditch, U. Michigan
Donald Swigerski, U. Michigan
4:30-4:45 p.m. Discussion/Q&A: Imaging for data collection Miriam & Donald
moderators
4:45-5:00 p.m. Daily wrap-up, observations, comments, challenges, criticisms, further discussion Greg Watkins-Colwell
moderator
Dinner on Your Own

Recommended gathering place: Houlihans
Reservation at 6:15 pm, Meet in hotel lobby at 6:00 pm

Agenda, Day 2
Wednesday, March 16, 2016

Day One
Time Topic Presenter(s)/Leader(s)
6:30 - 7:30 a.m. Breakfast at Hotel
Complimentary breakfast 6:30 - 9:30 a.m.
8:00-8:15 a.m. Lingering questions and observations from Day 1 Larry Page, Moderator
8:15-9:00 a.m.

Breakout discussions focused on uses and value of images:

Chris Phillips, Moderator
9:00-10:00 a.m. Breakout discussions:

Important research questions to be answered by a large dataset of fish and herp images?

 Chris Phillips, Moderator
10:00-10:30 a.m. Break
10:30-11:30 a.m. Breakout session reports on potential research questions Mark Sabaj-Perez, moderator
11:30-12:00 a.m. Organize for afternoon deliberations:
What Should be the Focus of a Fluid-preserved Vertebrate Imaging TCN: goals, outcomes, components, and research basis?

-Ecological component: looking beyond fishes and herps
-Digitization of field notes to support digitized images for holistic picture of organisms
-Imaging beyond the specimen: utilizing photographs from the field
-Broader impacts
-Quality of data: Developing standards(Future workshop?)

  • Select discussion group participation
  • Outline expected group discussion and afternoon outcomes
  • Grand challenge research questions


Discussion documentation

Gil Nelson, moderator
12:00-1:00 p.m. Lunch
Afternoon theme:

What Should be the Focus of a Fluid-preserved Vertebrate Imaging TCN?
Notes document

Larry Page, moderator
1:00-3:00 p.m. Discussion breakouts
3:00-3:30 p.m. Break
3:30-5:00 p.m. Discussion group reports and additional plenary discussion
Dinner on Your Own
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