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

• 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

Digitization Workshop Wikis

• Herbarium Workshop Wiki (Sept 2012)
• Wet Collections Workshop Wiki (March 2013)
• Dried Insect Digitization Workshop Wiki April 2013
• ASB Digitization Workshop and Symposium (April 2013
• CSIRO Digitization Workshop, Canberra, Australia (July 2013)
• Specify Workshop Wiki (August 2013)
• Fluid-preserved Invertebrate and Microscopic Slide Imaging (Sept 2013)
• Paleo Collections Digitization Workshop Wiki (Sept 2013, Yale Peabody Museum)
• Small Herbarium Digitization Workshop Wiki (December 2013, Florida State University)
• CITSCribe Hackathon (16-20 December 2013, University of Florida, Gainesville)
• Digitizing from Source Materials Workshop Wiki (March 2014, Yale Peabody Museum)
• Paleo Imaging Workshop (April-May 2014, University of Texas)

Workshop Summaries

• iDigBio Workshop Summary Page
• Herbarium Digitization Workshop Report
• Wet Collections Workshop Report
• Dried Insect Digitization Workshop Report
• ASB 2013 Workshop Report
• "Progressive Specify" Workshop Report
• Fluid-preserved Arthropod and Microscopic Slide Imaging Workshop Report
• Paleontology Digitization Workshop Report
• Mobilizing Small Herbaria 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

• 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

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
• 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

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

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

Identifiers

• iDigBio's GUID Guide for Data Providers

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