Digitization Template 1: Difference between revisions
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*[[Data Carpentry|Data Carpentry Workshop at iDigBio, ( | *[[Summit 2014| iDigBio Summit 2014 Workshop Wiki, University of Florida, Gainesville (October 27-28 2014)]] | ||
*[[Data Carpentry|Data Carpentry Workshop at iDigBio, (September 29 - 30 2014)]] | |||
*[[Leveraging_Digitization|Leveraging Digitization Practices across Multiple Domains, University of California, Santa Barbara (October 6-9 2014)]] | *[[Leveraging_Digitization|Leveraging Digitization Practices across Multiple Domains, University of California, Santa Barbara (October 6-9 2014)]] | ||
*[[Small_Herbarium_Workshop_Botany_2014 | Small Herbarium Workshop, Botany 2014, Boise, ID (July 31 2014)]] | *[[Small_Herbarium_Workshop_Botany_2014 | Small Herbarium Workshop, Botany 2014, Boise, ID (July 31 2014)]] | ||
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*[[Small Collections Symposium SPNHC 2014 | Small Collections Symposium, SPNHC 2014, Cardiff, Wales (June 25 2014)]] | *[[Small Collections Symposium SPNHC 2014 | Small Collections Symposium, SPNHC 2014, Cardiff, Wales (June 25 2014)]] | ||
*[[TORCH VIII + iDigBio Workshop|TORCH VIII + iDigBio Workshop, Sul Ross State University, Alpine, TX (May 24 2014)]] | *[[TORCH VIII + iDigBio Workshop|TORCH VIII + iDigBio Workshop, Sul Ross State University, Alpine, TX (May 24 2014)]] | ||
*[[SPNHC 2014 DemoCamp| SPNHC 2014 DemoCamp, Millennium Centre Cardiff Bay, Cardiff, Wales (June 26 2014)]] | *[[SPNHC 2014 DemoCamp| SPNHC 2014 DemoCamp, Millennium Centre Cardiff Bay, Cardiff, Wales (June 26 2014)]] | ||
*[[Specify for Paleo Workshop | Specify for Paleo Collections Workshop, University of Kansas Biodiversity Institute, Lawrence Kansas ( May 20 - 23 2014)]] | *[[Specify for Paleo Workshop | Specify for Paleo Collections Workshop, University of Kansas Biodiversity Institute, Lawrence Kansas ( May 20 - 23 2014)]] | ||
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*[[Education_and_Outreach_Workshop| iDigBio Education and Outreach Workshop Wiki, University of Florida, Gainesville (January 16-17 2014)]] | *[[Education_and_Outreach_Workshop| iDigBio Education and Outreach Workshop Wiki, University of Florida, Gainesville (January 16-17 2014)]] | ||
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*iDigBio Summit 2014 Report | |||
*Data Carpentry Workshop at iDigBio | *Data Carpentry Workshop at iDigBio | ||
*Leveraging Digitization Practices across Multiple Domains | *Leveraging Digitization Practices across Multiple Domains | ||
*[https://www.idigbio.org/content/idigbio-and-nansh-host-small-herbarium-digitization-workshop-botany-2014 Small Herbarium Digitization Workshop at Botany 2014- Report] | *[https://www.idigbio.org/content/idigbio-and-nansh-host-small-herbarium-digitization-workshop-botany-2014 Small Herbarium Digitization Workshop at Botany 2014- Report] | ||
*Digitized natural history collections records in traditional research, collaborative research, and big data research, Report to be added | *Digitized natural history collections records in traditional research, collaborative research, and big data research, (Report to be added) | ||
*Georeferencing Natural History Collections (Report to be added) | |||
*SPNHC Symposium Progress in Digitization to be added | *SPNHC 2014 Special Interest Group (Report to be added) | ||
*SPNHC 2014 | *SPNHC 2014 Symposium Progress in Digitization (Report to be added) | ||
*Small Collections Symposium Report to be added | *SPNHC 2014 DemoCamp Report | ||
*Small Collections Symposium (Report to be added) | |||
*[https://www.idigbio.org/content/idigbio-digitization-workshop-torch-2014 TORCH VIII and iDigBio Workshop Report] | *[https://www.idigbio.org/content/idigbio-digitization-workshop-torch-2014 TORCH VIII and iDigBio Workshop Report] | ||
*[https://www.idigbio.org/content/specify-workshop-paleontologists-and-collaborating-make-it-easier-start-digitizing Specify for Paleo Workshop - Appliance Report] | *[https://www.idigbio.org/content/specify-workshop-paleontologists-and-collaborating-make-it-easier-start-digitizing Specify for Paleo Workshop - Appliance Report] | ||
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*[https://www.idigbio.org/content/digitizing-source-materials-workshop-step-toward-best-practices Digitizing from Source Materials Workshop Report] | *[https://www.idigbio.org/content/digitizing-source-materials-workshop-step-toward-best-practices Digitizing from Source Materials Workshop Report] | ||
*[https://www.idigbio.org/content/outsider%E2%80%99s-view-inside-nsf-trends-and-tips An Outsider’s view inside NSF: E&O Trends and Tips Workshop Report] | *[https://www.idigbio.org/content/outsider%E2%80%99s-view-inside-nsf-trends-and-tips An Outsider’s view inside NSF: E&O Trends and Tips Workshop Report] | ||
*Fossil Kickoff Meeting Report to be added | *Fossil Kickoff Meeting (Report to be added) | ||
*NAPC Symposium Report to be added | *NAPC Symposium (Report to be added) | ||
*[https://www.idigbio.org/content/careers-and-graduate-study-biological-sciences Careers and Graduate Study in Biological Sciences] | *[https://www.idigbio.org/content/careers-and-graduate-study-biological-sciences Careers and Graduate Study in Biological Sciences] | ||
*[https://www.idigbio.org/content/education-outreach-workshop-0 Education & Outreach Workshop Report] | *[https://www.idigbio.org/content/education-outreach-workshop-0 Education & Outreach Workshop Report] | ||
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*[[Transcription Hackathon| CITSCribe Hackathon, University of Florida, Gainesville (December 16-20 2013)]] | *[[Transcription Hackathon| CITSCribe Hackathon, University of Florida, Gainesville (December 16-20 2013)]] | ||
*[[Small Herbarium Workshop FSU| Small Herbarium Digitization Workshop Wiki, Florida State University (December 9-12 2013)]] | *[[Small Herbarium Workshop FSU| Small Herbarium Digitization Workshop Wiki, Florida State University (December 9-12 2013)]] | ||
*[[Summit 2013| Summit 2013 Workshop Wiki, Aloft Tallahassee (November 19- 20 2013)]] | |||
*[[Paleo Digitization Workshop| Paleo Collections Digitization Workshop Wiki, Yale Peabody Museum (September 22-25 2013)]] | *[[Paleo Digitization Workshop| Paleo Collections Digitization Workshop Wiki, Yale Peabody Museum (September 22-25 2013)]] | ||
*[[Fluid Preserved Invertebrate Imaging| Fluid-preserved Invertebrate and Microscopic Slide Imaging, University of Michigan (September 16-19 2013)]] | *[[Fluid Preserved Invertebrate Imaging| Fluid-preserved Invertebrate and Microscopic Slide Imaging, University of Michigan (September 16-19 2013)]] | ||
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*[https://www.idigbio.org/content/citscribe-hackathon CITSCribe Hackathon Report] | *[https://www.idigbio.org/content/citscribe-hackathon CITSCribe Hackathon Report] | ||
*[https://www.idigbio.org/content/mobilizing-small-herbaria-workshop-attracts-enthusiastic-participants Mobilizing Small Herbaria Workshop Report] | *[https://www.idigbio.org/content/mobilizing-small-herbaria-workshop-attracts-enthusiastic-participants Mobilizing Small Herbaria Workshop Report] | ||
*[https://www.idigbio.org/content/idigbio-summit-iii Summit 2013 Report] | |||
*[https://www.idigbio.org/content/idigbio%E2%80%99s-paleo-digitization-workshop-draws-more-60-attendees-new-haven Paleontology Digitization Workshop Report] | *[https://www.idigbio.org/content/idigbio%E2%80%99s-paleo-digitization-workshop-draws-more-60-attendees-new-haven Paleontology Digitization Workshop Report] | ||
*[https://www.idigbio.org/content/entomologists-gather-ann-arbor-explore-fluid-preserved-arthropod-imaging Fluid-preserved Arthropod and Microscopic Slide Imaging Workshop Report] | *[https://www.idigbio.org/content/entomologists-gather-ann-arbor-explore-fluid-preserved-arthropod-imaging Fluid-preserved Arthropod and Microscopic Slide Imaging Workshop Report] | ||
Latest revision as of 16:14, 23 September 2014
This page provides resources and information for the series of digitization training workshops being conducted by iDigBio as well as a plethora of digitization information and resources. Included is a growing list of links to documents, websites, videos, presentations, and other important information related to biological collection digitization.
iDigBio Intro
Interest/Working Groups
- International Whole-Drawer Digitization Interest Group
- NANSH Working Group (North American Network of Small Herbaria)
- Fluid-preserved Arthropod and Microscopic Slide Imaging Interest Group
- Paleontology Digitization Working Group
- Small Collections Network Working Group
Calendar Year 2014
Calendar Year 2013
Calendar Year 2012
| Workshops and Symposia Wikis | Workshop Reports |
|---|---|
General Digitization Resources
- No specimen left behind: mass digitization of natural history collections (ZooKeys Special Issue)
- Five task clusters that enable efficient and effective digitization
- Gil Nelson: Herbarium Digitization Tasks and Components Overview
- iDigBio's Intellectual Property Rights statement
- Deborah Paul: Pre & Post Digitization Curation
- pdf version Pre & Post Digitization Curation
- Just What is a Darwin Core Archive File?
- Cleaning Data in a Spreadsheet - Try OpenRefine formerly known as GoogleRefine
- Raw Data Cleaning, Validation and Enhancement: Using Open Refine, Deborah Paul
- Identifiers and Sharing Data, Deborah Paul
Leveraging the Library and Other Institutional Resources
Example Digitization Protocols
- Florida State University Herbarium Imaging Protocol
- Valdosta State University Herbarium (VSC) Vascular Plant Imaging Protocol
- Valdosta State Herbarium (VSC) Bryophyte Packet Imaging Protocol
- Valdosta Herbarium image processing with Nikon Dust Off process included
- A Guide to Digitizing Insect Collections (MCZ Entomology Type Image Project)
- Digitization Workflow Using Aperture (Scanners, Cameras,Books)
- Workflows, protocols, etc. from Tri-Trophic TCN (NYBG and AMNH docs)
Imaging Documents and Resources
- iDigBio Imaging Equipment Recommendations (Joanna McCaffrey)
- Workflows, protocols, etc. from Tri-Trophic TCN (NYBG and AMNH docs)
- Beginner's Guide to Digital Imaging - Glossary
- Mike Bevans' Herbarium Image Editing Guidelines
- Mike Bevans' Digital Imaging and Archiving
- Mike Bevans' Intro to Photoshop
- Mike Bevans' Blog on Digital Imaging
- Mike Bevans' So, you want to digitize plant specimens
- Mike Bevans' Digitizing Plant Collections VSU Workshop - link to power point
- Douglas Cromey's Digital Imaging Ethics
- Nikon's Capture NX2 Software User's Manual
- Lichen/Bryophyte TCN Imaging Recommendations
- Pacific Northwest Herbaria imaging resources
- The AIC Guide to Digital Photography and Conservation Documentation
- Northern Arizona University's Imaging videos and ppt's
- Imaging References
Image File Types and File Specifications
- iDigBio's Image File Format Policy and Recommendations
- Introducing the Digital Negative Specification
- Digital Negative Specification for Manufacturers
- Atiz Innovation, Inc.: Making sense of DPI, PPI, Megapixels and Resolution
Imaging Station Equipment and Specifications
- Photo EBox Imaging Station
- iDigBio Imaging Equipment Recommendations
- Assembling Custom Components for Specimen Imaging (NW Herbaria Consortium)
- Sam Noble Musuem's optimization of the efficiency of stackshot, including 3D printing plans for SNO's Focus Stacking Stand, contributed by Roger Burkhalter
- Plans for Sam Noble Museum's Focus Stacking Stand plans and downloads, Roger Burkhalter
- Plans for Sam Noble Museum's Focus Stacking Platform plans and downloads, Roger Burkhalter
- Macroscopic Solutions portable, photo stacking device, overcomes lighting hurdles with copy stands: Macropod
3D Imaging and 3D Printing Resources
- Strata Design 3D CX & Foto 3D CX 7.0.7
- Strata Foto 3D CX
- Image-based 3D modeling: Agisoft PhotoScan
- ZooKeys 328 (2013) : 47-57 Rotational Scanning Electron Micrographs (rSEM): A novel and accessible tool to visualize and communicate complex morphology David Koon-Bong Cheung, Adam Brunke, Nesrine Akkari, Carina Mara Souza, Thomas Pape
- ZooKeys 328 (2013) : 5-45 Revolving SEM images visualising 3D taxonomic characters: application to six species of the millipede genus Ommatoiulus Latzel, 1884, with description of seven new species and an interactive key to the Tunisian members of the genus (Diplopoda, Julida, Julidae) Nesrine Akkari, David Koon-Bong Cheung, Henrik Enghoff, Pavel Stoev
Camera Manuals & Specifications
Links to Workflows--iDigBio and Elsewhere
Workflows and Protocols
- Digitization Workflows
- iDigBio Digitization Workflow Workshop (DROID) report
- iDigBio's Collaborative Workflows Page (DROID Working Groups)
- Bryophyte/Lichen TCN workflow
- JSTOR PLANTS Handbook
- Developing integrated workflows for the digitisation of herbarium specimens using a modular and scalable approach
- Workflow Modules and Task Lists
- Gil Nelson: Herbarium Workflows
- U. Vermont GPI Pre-digitization Curation Workflow (Audrey Clark)
- Deborah Paul: Sharing Data
Georeferencing Resources
- Biogeomancer, Guide to Best Practices in Georeferencing
- Geolocate: Online and Desktop Georeferencing Tools
- Gil Nelson: Georeferencing with Geolocate
- MaNIS/HerpNet/ORNIS Georeferencing Guidelines
- Herpnet's georeferencing resources page
- iDigBio Georeferencing Wiki
- iDigBio's Georeferencing Working Group Forum
- GeoLocate Web Management Portal login
- GeoLocate Collaborative Georeferencing Web Client login
- Collaborative Georeferencing with Geolocate Protocol, Florida State University
- FSU Geolocate Protocol Using a Custom Spreadsheet for Georeferencing
- Georeferencing Herbarium Specimens using GeoLocate
Database Resources and Tools
- Joanna McCaffrey: Considerations When Choosing Collections Management Software
- Digital Asset Management (DAMS)
- iDigBio's Database, Portals, Aggregators, and Tools Review Page
- Download Salix software here
- Salix software documentation
- Gil Nelson: Database Tools and Techniques
- Publishing Specify Data with IPT
- Symbiota Login Information
- Try Open Refine to Clean CSV Data formerly known as Google Refine
- Kepler Kurator to Clean Spreadsheet Data
- See Kepler Kurator at work cleaning data in a Filtered PUSH Network
- Voice Recognition
Identifiers
Videos
- iDigBio's Introduction to Nikon's Camera Control Pro 2 software
- iDigBio's Introduction to Nikon's Live View Feature
- Arizona State University's Orientation to Settings on a Canon Camera
- iDigBio's Batch Processing with Nikon Capture NX2
- iDigBio's Nikon D3X Camera Setup for Scientific Specimen Imaging
- Introduction to SilverCollection