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 Groups

• International Whole-Drawer Digitization Interest Group
• Small Herbarium Interest 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)
• Digitizing from Source Materials (March 2014, Yale Peabody Museum)

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

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 Bevan's Blog on Digital Imaging
• Mike Bevans' So, you want to digitize plant specimens
• Mike Bevan's: 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

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