Digitization Resources

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

• Introduction to iDigBio Slide Set
• Intro to iDigBio pdf file

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

Digitization Workshops and Symposia Wikis

2014 Workshops and Symposia Wikis

• Data Carpentry Workshop at iDigBio, (date to be announced)
• Leveraging Digitization Practices across Multiple Domains, University of California, Santa Barbara (October 6-9 2014)
• Small Herbarium Workshop, Botany 2014, Boise, ID (July 31 2014)
• Digitized natural history collections records in traditional research, collaborative research, and big data research, Botany 2014, Boise, ID (July 29 2014)
• Georeferencing Natural History Collections Botany 2014, Boise, ID (July 27 2014)
• SPNHC 2014 Special Interest Group (SIG) Session: Collections Digitization and Opportunities for International Collaboration, Amgueddfa Cymru – National Museum Wales, Cardiff, Wales (June 27 2014)
• SPNHC 2014 Symposium: Progress in Digitization of Natural History Collections, Millennium Centre, Cardiff, Wales (June 26 2014)
• SPNHC 2014 DemoCamp, Millennium Centre Cardiff Bay, Cardiff, Wales (June 26 2014)
• Small Collections Symposium, SPNHC 2014, Cardiff, Wales (June 25 2014)
• TORCH VIII + iDigBio Workshop, Sul Ross State University, Alpine, TX (May 24 2014)
• Specify for Paleo Collections Workshop, University of Kansas Biodiversity Institute, Lawrence Kansas ( May 20 - 23 2014)
• Collections for the 21st Century Symposium, University of Florida (May 5-6 2014)
• Paleo Imaging Workshop, University of Texas (April 29- May 01 2014)
• Recruiting, Supporting, and Retaining Small Collections in Biodiversity Digitization, Central Michigan University (April 7-10 2014)
• Biological Collections Digitization in the Pacific, Honolulu (March 25-27 2014)
• Data Modeling Workshop, Honolulu (March 24-25 2014)
• Digitizing from Source Materials Workshop Wiki,Yale Peabody Museum (March 9-13 2014)
• An Outsider’s view inside NSF: E&O Trends and Tips” iDigBio NSF E&O Webina (February 27 2014)
• FOSSIL Kickoff Meeting (February 19 2014)
• NAPC Symposium: Celebrating Public Participation in Paleontology, University of Florida, Gainesville (February 17 2014)
• Broadening Diversity:Careers and Graduate Study in the Biological Sciences Workshop Wiki, University of Central Florida, Orlando (February 01 2014)
• iDigBio Education and Outreach Workshop Wiki, University of Florida, Gainesville (January 16-17 2014)

2013 Workshops and Symposia Wikis

• CITSCribe Hackathon, University of Florida, Gainesville (December 16-20 2013)
• Small Herbarium Digitization Workshop Wiki, Florida State University (December 9-12 2013)
• Paleo Collections Digitization Workshop Wiki, Yale Peabody Museum (September 22-25 2013)
• Fluid-preserved Invertebrate and Microscopic Slide Imaging, University of Michigan (September 16-19 2013)
• Specify Workshop Wiki, University of Kansas (August 12-16 2013)
• GWG Second Train the Trainers Workshop, Gainesville (August 12-16 2013)
• CSIRO Digitization Workshop, Canberra, Australia (July 2013)
• Dried Insect Digitization Workshop Wiki, Chicago (April 23-26 2013)
• ASB Digitization Workshop and Symposium (April 13 2013)
• Wet Collections Workshop Wiki, University of Kansas, (March 4-6 2013)
• 2013 AOCR Hackathon Wiki (February 13-14 2013)

2012 Workshops and Symposia Wikis

• Summit 2012 Workshop Wiki, Gainesville, Florida (Oct 23-24 2012)
• Herbarium Workshop Wiki, VSU, Valdosta, Georgia (Sept 2012)
• Object To Image To Data Workshop Wiki, Gainesville (May 2012)

Workshop Summaries

• iDigBio Workshop Summary Page

2014 Workshop Reports

• Data Carpentry Workshop at iDigBio
• Leveraging Digitization Practices across Multiple Domains
• Small Herbarium Digitization Workshop at Botany 2014- Report
• TORCH VIII and iDigBio Workshop Report
• Specify for Paleo Workshop - Appliance Report
• Specify for Paleo Workshop Report
• Collections for the 21st Century Report
• Paleoimaging Workshop Report
• Recruiting, Retaining, and Supporting Small Collections Workshop Report
• Biological Collections in the Pacific Workshop Report
• Data Modeling Workshop Report
• An Outsider’s view inside NSF: E&O Trends and Tips Workshop Report
• Digitizing from Source Materials Workshop Report
• Careers and Graduate Study in Biological Sciences
• Education & Outreach Workshop Report

2013 Workshop Reports

• CITSCribe Hackathon Report
• Mobilizing Small Herbaria Workshop Report
• Paleontology Digitization Workshop Report
• Fluid-preserved Arthropod and Microscopic Slide Imaging Workshop Report
• "Progressive Specify" Workshop Report
• iDigBio's 2nd Train the Trainers Georeferencing Workshop from the GWG Report
• CSIRO Digitization Workshop Report
• ASB 2013 Workshop Report
• Dried Insect Digitization Workshop Report
• iDigBio Augmenting OCR Hackathon Workshop Report
• iDigBio Augmenting OCR Hackathon Update Part II Workshop Report

2012 Workshop Reports

• Summit II Workshop Report
• Wet Collections Workshop Report
• Herbarium Digitization Workshop Report

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

• Digitization of Herbarium Specimens, a Collaborative Project (Larry Schmidt)

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

• Nikon Camera Control Pro Reference Manual
• Canon Digital Photo Professional 3.11 Instruction Manual

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

• iDigBio's GUID Guide for Data Providers
• Globally Unique Identifiers (GUID)

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