Digitization Resources: Difference between revisions

From iDigBio
Jump to navigation Jump to search
 
(436 intermediate revisions by 15 users not shown)
Line 1: Line 1:
This page provides resources and information for the series of digitization training workshops being conducted by iDigBio. Included is a growing list of links to documents, websites, videos, presentations, and other important information related to biological collection digitization.
<!--THIS IS THE INFO BOX, EACH CELL CONTAINS A LINK, TO CHANGE LINK CHANGE CELL CONTENT-->
[[Category: Videos]]
{| class="wikitable" style="float:right; margin-left:"
! colspan="2" style="background:#D58B28;width:200px;font-size:10pt" | Digitizing the Past and Present for the Future
|-
| colspan="2" style="text-align:center;font-size:7pt" |<!--YOU CAN INSERT A NEW LOGO BETWEEN THE COLON AND THE PIPE-->[[Image:IDigBio Logo RGB.png|center|300px|IDigBio Logo RGB.png]]<br />
|-
| colspan="2" style="background:#D58B28;text-align:center;font-size:9pt" | Digitization
|-
| style="font-size:9pt" |[http://zookeys.pensoft.net/articles.php?id=2926| How to digitize? (Five clusters)] || style="font-size:9pt" | [[IDigBio_Workshops|Workshops and Symposia]]
|-
| style="font-size:9pt" | [https://www.idigbio.org/wiki/index.php/Specimen_Image_Capture Digitization Videos]|| style="font-size:9pt" | [https://www.idigbio.org/biblio  Biblio entries]
|-
| colspan="2" style="background:#D58B28;text-align:center;font-size:9pt" | Connect with iDigBio
|-
| style="font-size:9pt" | [https://www.idigbio.org/portal Specimen Portal] || style="font-size:9pt" | [https://www.idigbio.org/outreach-events-sidebar| Upcoming Events]
|-
| style="font-size:9pt" | [http://www.facebook.com/iDigBio  iDigBio on facebook] || style="font-size:9pt" | [https://twitter.com/iDigBio Follow iDigBio on twitter]
|}<!--THE INFO BOX ENDS HERE-->


==iDigBio==
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.
* [https://www.idigbio.org/sites/default/files/sites/default/files/Intro_to_iDigBio.pptx Introduction to iDigBio Slide Set]
* [https://www.idigbio.org/sites/default/files/sites/default/files/Intro_to_iDigBio.pdf Intro to iDigBio pdf file]


==Preparation-specific Workshop Wikis==
==iDigBio Introduction==
* [https://www.idigbio.org/wiki/index.php/Hebarium_Digitization_Workshop Herbarium Workshop Wiki]
{| cellpadding=5
* [https://www.idigbio.org/wiki/index.php/Wet_Collections_Digitization_Workshop Wet Collections Workshop Wiki]
|style="vertical-align:top;"|[[File:PlayVideo2.jpg|thumb|300px|link=https://vimeo.com/67570758|"Introduction to iDigBio" 02:04]]  
* [https://www.idigbio.org/wiki/index.php/Dried_Insect_Digitization_Workshop Dried Insect Digitization Workshop Wiki]
|rowspan="1" colspan="2" style="vertical-align:top"|More than 1,600 natural history collections across the United States house over 1 billion biological specimens ranging from fungi to fish to fossils. This video describes the iDigBio project. It explains why digitized information and ready access to it are important, provides an overview of the digitization process and highlights some of the challenges faced when working with different types of natural history collections.
|}


==Workshop Summaries==
==Digitization Academy==
* [https://www.idigbio.org/wiki/index.php/IDigBio_Workshops#Workshop_Documentation iDigBio Workshop Summary Page]
The Digitization Academy offers a set of complementary courses on topics related to digitizing data about biodiversity. Digitization Academy courses are online, free, and open to everyone from the world’s biodiversity collections and research communities. There are two formats. Short, 2-hour courses on emerging topics simply require registration; multi-day courses provide a deeper dive on foundational topics and involve smaller cohorts and an application process. More information, including the current course catalog, is available at [https://digitizationacademy.org/ digitizationacademy.org].


==General Digitization Resources==
==Recommendations for the Acquisition, Processing, and Archiving of Digital Media==
* [http://pensoft.net/journals/zookeys/issue/209 No specimen left behind: mass digitization of natural history collections (ZooKeys Special Issue)]
iDigBio has created recommendations for capturing, processing, and storing digital media.
* [https://www.idigbio.org/wiki/images/d/d5/3135-G-3-layout.pdf Five task clusters that enable efficient and effective digitization]
* [https://www.idigbio.org/wiki/images/f/f2/Overview.pdf Gil Nelson: Herbarium Digitization Tasks and Components Overview]
* [https://www.idigbio.org/content/idigbio-intellectual-property-policy iDigBio's Intellectual Property Rights statement]
*[https://www.idigbio.org/sites/default/files/workshop-presentations/dpc2012/PrePostDigitizationCurationDP.pptx Deborah Paul: Pre & Post Digitization Curation]
** pdf version [https://www.idigbio.org/wiki/index.php/File:PrePostDigitizationCurationDP.pdf Pre & Post Digitization Curation]
*[http://tools.gbif.org/dwca-assistant/ Just What is a Darwin Core Archive File?]
*[http://code.google.com/p/google-refine/ Cleaning Data in a Spreadsheet - Try Google Refine]


==Leveraging the Library and Other Institutional Resources==
[[Recommendations for the Acquisition, Processing, and Archiving of Digital Media]]
*[https://www.idigbio.org/content/digitization-herbarium-specimens-collaborative-project  Digitization of Herbarium Specimens, a Collaborative Project (Larry Schmidt)]


==Example Digitization Protocols==
==Interest/Working Groups==
* [https://www.idigbio.org/wiki/images/6/63/Imaging_Protocol_v5b.pdf Florida State University Herbarium Imaging Protocol]
The following links take you to Interest/Working Groups focused on Digitization. For other working groups please use the following link [https://www.idigbio.org/wiki/index.php/IDigBio_Working_Groups iDigBio Working Groups]
* [https://www.idigbio.org/wiki/images/9/98/VSUImagingProtocol.pdf Valdosta State University Herbarium (VSC) Vascular Plant Imaging Protocol]
*[[Drawer Imaging Group| International Whole-Drawer Digitization Interest Group]]
* [https://www.idigbio.org/wiki/images/f/fb/VSU_Bryophyte_Imaging_Protocol.pdf Valdosta State Herbarium (VSC) Bryophyte Packet Imaging Protocol]
*[[Small Herbarium Interest Group| NANSH Working Group]] (North American Network of Small Herbaria)
* [https://www.idigbio.org/wiki/images/e/e8/Image_Dust_Off_Protocol_for_Nikon_Cameras.pdf Valdosta Herbarium image processing with Nikon Dust Off process included]
*[[Fluid Preserved Arthropds| Fluid-preserved Arthropod and Microscopic Slide Imaging Interest Group]]
* [http://insects.oeb.harvard.edu/MCZ/PDFs/Guide_to_digitizing.pdf A Guide to Digitizing Insect Collections (MCZ Entomology Type Image Project)]
*[[Paleo Digitization Working Group| Paleontology Digitization Working Group]]
* [http://www.kvmagruder.net/hos/blog/ApertureWorkflow.pdf Digitization Workflow Using Aperture (Scanners, Cameras,Books)]
*[[SCNet| Small Collections Network Working Group]]
*[[vert digi interest group | Vertebrate Digitization Intererst Group]]
*[[Field Station Interest Group| Field Station Interest Group]]


==Imaging Documents and Resources==
==Digitization Avenue==
* [https://www.idigbio.org/sites/default/files/sites/default/files/BeginnersGuideToImagingGlossary.pdf Beginner's Guide to Digital Imaging - Glossary]
The following links provide information on the task clusters that enable efficient and effective digitization of Biological and Paleontological Collections. If you are unfamiliar with the task clusters please read the following  [http://zookeys.pensoft.net/articles.php?id=2926 Five task clusters that enable efficient and effective digitization of biological collections].
* [https://www.idigbio.org/wiki/images/1/15/Herbarium_Image_Editing_Guidelines.pdf Mike Bevans' Herbarium Image Editing Guidelines]
*[[ Pre-digitization Curation and Staging | Pre-digitization Curation and Staging]]
* [https://www.idigbio.org/wiki/images/3/36/Standardized_Digital_Imaging_NYBG.pdf Mike Bevans' Digital Imaging and Archiving]
*[[ Specimen Image Capture | Specimen Image Capture]]
* [https://www.idigbio.org/wiki/images/b/b1/Intro_to_Photoshop.pdf Mike Bevans' Intro to Photoshop]
*[[ Specimen Image Processing | Specimen Image Processing]]
*[http://digitalphotorepro.blogspot.com/ Mike Bevan's Blog on Digital Imaging]
*[[ Electronic Data Capture | Electronic Data Capture]]
* [https://www.idigbio.org/wiki/images/8/82/Imaging_Manual.pdf Mike Bevans' So, you want to digitize plant specimens]
*[[ Georeferencing locality descriptions | Georeferencing Locality Descriptions]]
*[https://docs.google.com/open?id=0B5L2FF0VryJnNkp5NG1EY3Ffd2s Mike Bevan's: Digitizing Plant Collections VSU Workshop - link to power point]
*[[ Digitization Workflows and Protocols | Digitization Workflows and Protocols]]
* [http://cbe.ivic.ve/ftp/clasebioest/pdf/Digital_Imaging_Ethics.pdf Douglas Cromey's Digital Imaging Ethics]
*[[ More on digitization  |More on digitization  ]]
* [http://www.nikonusa.com/pdf/manuals/software/CapNX2/CAPNX2_UM_EN.pdf Nikon's Capture NX2 Software User's Manual]
* [http://lbcc.limnology.wisc.edu/node/4 Lichen/Bryophyte TCN Imaging Recommendations]
* [http://www.pnwherbaria.org/documentation/specimenimaging.php Pacific Northwest Herbaria imaging resources]
* [https://www.idigbio.org/wiki/index.php/Databasing_References#The_AIC_Guide_to_Digital_Photography_and_Conservation_Documentation The AIC Guide to Digital Photography and Conservation Documentation]


==Image File Types and File Specifications==
* [https://www.idigbio.org/wiki/images/5/58/Image_File_Format_Recommendations_and_Standards.pdf iDigBio's Image File Format Policy and Recommendations]
* [http://www.adobe.com/digitalimag/pdfs/dng_primer.pdf Introducing the Digital Negative Specification]
* [http://wwwimages.adobe.com/www.adobe.com/content/dam/Adobe/en/products/photoshop/pdfs/DNG_primer_manufacturers.pdf  Digital Negative Specification for Manufacturers]
* [http://www.atiz.com/resources/DPI-PPI-Megapixels-and-Resolution.pdf Atiz Innovation, Inc.: Making sense of DPI, PPI, Megapixels and Resolution]


==Imaging Station Equipment and Specifications==
==[[IDigBio Workshops|iDigBio Workshops, Reports, and Wikis]]==
* [http://www.eboxbio.com/ Photo EBox Imaging Station]
iDigBio's Workshop and Report  page contains links to materials from completed iDigBio workshops, conferences, and symposia.
* [http://www.pnwherbaria.org/documentation/custom-components-v1.pdf Assembling Custom Components for Specimen Imaging (NW Herbaria Consortium)]
*[[ IDigBio_Workshops#Calendar_Year_2020| Calendar Year 2020]]
*[[ IDigBio_Workshops#Calendar_Year_2019| Calendar Year 2019]]
*[[ IDigBio_Workshops#Calendar_Year_2018| Calendar Year 2018]]
*[[ IDigBio_Workshops#Calendar_Year_2017| Calendar Year 2017]]
*[[ IDigBio_Workshops#Calendar_Year_2016| Calendar Year 2016]]
*[[ IDigBio_Workshops#Calendar_Year_2015| Calendar Year 2015]]
*[[ IDigBio_Workshops#Calendar_Year_2014| Calendar Year 2014]]
*[[ IDigBio_Workshops#Calendar_Year_2013| Calendar Year 2013]]
*[[ IDigBio_Workshops#Calendar_Year_2012| Calendar Year 2012]]
*[[ IDigBio_Workshops#Calendar_Year_2011| Calendar Year 2011]]


==Camera Manuals & Specifications==
==Videos- Digitization Resources and Workflows==
* [http://www.nikonusa.com/pdf/manuals/software/ccp_en.pdf Nikon Camera Control Pro Reference Manual]
{| class="mw-collapsible mw-collapsed wikitable" width="800px"
* [http://gdlp01.c-wss.com/gds/7/0300007447/03/dpp311w3-en.pdf Canon Digital Photo Professional 3.11 Instruction Manual]
|-
 
|valign="left"|'''Click for Collapsible List of Videos'''
==Workflows and Protocols==
|
* [https://www.idigbio.org/wiki/images/8/83/Digitization_Workflows_wet_collections.pdf Digitization Workflows]
|-
* [https://www.idigbio.org/content/digitization-workflow-workshop-report iDigBio Digitization Workflow Workshop (DROID) report]
|style="vertical-align:top;"|[[File:PlayVideo1.jpeg|thumb|200px|link=https://vimeo.com/160615629|"Imaging Workflows for the Digitization of Dry-preserved Vertebrate Specimens" 07:25]]  
* [https://www.idigbio.org/content/digitization-workflows iDigBio's Collaborative Workflows Page]
|rowspan="1" colspan="2" style="vertical-align:top"| This video details the four primary task clusters associated with digitization and imaging including selecting specimens, pre-digitization specimen curation and staging, image capture, and image processing. The video also gives specific tips for imaging dry collections including deciding which specimens and views to capture, imaging tools and equipment, and image stacking.
* [http://lbcc.limnology.wisc.edu/node/3 Bryophyte/Lichen TCN workflow]
|-
* [http://www.snsb.info/SNSBInfoOpenWiki/attach/Attachments/JSTOR-Plants-Handbook.pdf JSTOR PLANTS Handbook]
|style="vertical-align:top;"|  [[File:Digitization Workflows.jpg|thumb|200px|link=https://vimeo.com/120369455|"Digitization Workflows Overview" 07:21]]
* [http://www.pensoft.net/J_FILES/1/articles/3121/3121-G-3-layout.pdf Developing integrated workflows for the digitisation of herbarium specimens using a modular and scalable approach]
|rowspan="1" colspan="2" style="vertical-align:top"|This workflow video offers an introduction into the digitization process, the rationale behind why museums are digitizing their collections, how iDigBio is facilitating the digitization movement, and what the current challenges are for museum digitization.
* [https://www.idigbio.org/content/workflow-modules-and-task-lists Workflow Modules and Task Lists]
|-
* [https://www.idigbio.org/wiki/images/6/60/Workflows.pdf Gil Nelson: Herbarium Workflows]
|style="vertical-align:top;"|[[File:PlayVideo3.jpg|thumb|200px|link=https://vimeo.com/120369690|"Digitizing Wet Collections" 04:34]]
* [https://www.idigbio.org/sites/default/files/sites/default/files/Workflow_MellonTypePDC_v4.jpeg U. Vermont GPI Pre-digitization Curation Workflow (Audrey Clark)]
|rowspan="1" colspan="2" style="vertical-align:top"| This instructional video details the five step process the Ichthyology Collection at the Florida Museum of Natural History uses to digitize their collection including: selecting specimens, image capturing, image processing, electronic data capture and georefrencing, and curating specimens. The video also gives specific tips for imaging wet collections including squeeze box use, what imaging equipment to use, and what views to capture for use in taxonomic identification.
*[https://www.idigbio.org/sites/default/files/workshop-presentations/dpc2012/SharingDataDP.pptx Deborah Paul: Sharing Data]
|-
 
|style="vertical-align:top;"|[[File:Herbarium.jpg|thumb|200px|link=https://vimeo.com/120369768|"Digitizing Herbarium Collections" 07:34]]
==Georeferencing Resources==
|rowspan="1" colspan="2" style="vertical-align:top"|This video details the five step process the University of Florida Herbarium uses for digitizing specimens: specimen staging, image capturing, specimen image processing, electronic data capture and georeferencing, and specimen curating. The video also features the Valdosta State Herbarium's image processing and data capture and georeferencing workflow.
*  [http://www.gbif.org/orc/?doc_id=1288 Biogeomancer, Guide to Best Practices in Georeferencing]
|}
* [http://www.museum.tulane.edu/geolocate/ Geolocate: Online and Desktop Georeferencing Tools]
* [https://www.idigbio.org/wiki/images/9/9d/Georeferencing.pdf Gil Nelson: Georeferencing with Geolocate]
* [http://manisnet.org/GeorefGuide.html MaNIS/HerpNet/ORNIS Georeferencing Guidelines]
* [http://www.herpnet.org/Gazetteer/GeorefResources.htm Herpnet's georeferencing resources page]
* [https://www.idigbio.org/wiki/index.php/Georeferencing iDigBio Georeferencing Wiki]
* [https://www.idigbio.org/forums/georeferencing-working-group-gwg iDigBio's Georeferencing Working Group Forum]
* [http://www.museum.tulane.edu/coge/ GeoLocate Web Management Portal login]
* [http://www.museum.tulane.edu/geolocate/web/webcomgeoref.aspx GeoLocate Collaborative Georeferencing Web Client login]
 
==Database Resources and Tools==
* [https://www.idigbio.org/sites/default/files/sites/default/files/considerations-when-choosing-collection-mgt-software.pdf Joanna McCaffrey: Considerations When Choosing Collections Management Software]
* [https://www.idigbio.org/content/biological-collections-databases iDigBio's Database, Portals, Aggregators, and Tools Review Page]
* [http://daryllafferty.com/salix/ Download Salix software here]
* [http://nhc.asu.edu/vpherbarium/canotia/SALIX3.pdf Salix software documentation]
* [https://www.idigbio.org/wiki/images/1/1b/DataTools.pdf Gil Nelson: Database Tools and Techniques]
* [http://specifysoftware.org/sites/specifysoftware.org/files/Publishing%20Specify%20Data%20with%20IPT.pdf Publishing Specify Data with IPT]
* [https://www.idigbio.org/wiki/images/b/b6/WorkshopSymbiotaLogin.pdf Symbiota Login Information]
*[http://code.google.com/p/google-refine/ Try Google Refine to Clean CSV Data]
*[http://daks.ucdavis.edu/?page_id=205 Kepler Kurator to Clean Spreadsheet Data]
*[http://www.youtube.com/watch?v=DEkPbvLsud0 See Kepler Kurator at work cleaning data in a Filtered PUSH Network]
 
==Identifiers==
* [https://www.idigbio.org/sites/default/files/iDigBio-GUID-Statement20MAR2012.pdf iDigBio's Guidelines for Managing Persistent Identifiers]
 
==Videos==
* [https://vimeo.com/46296902 iDigBio's Introduction to Nikon's Camera Control Pro 2 software]
* [https://vimeo.com/46312484 iDigBio's Introduction to Nikon's Live View Feature]
* [https://vimeo.com/42586243 Arizona State University's Orientation to Settings on a Canon Camera]
* [https://vimeo.com/46950737 iDigBio's Batch Processing with Nikon Capture NX2]
* [https://vimeo.com/46990833 iDigBio's Nikon D3X Camera Setup for Scientific Specimen Imaging]
* [http://www.youtube.com/watch?v=faCP15wjc4g&feature=plcp Introduction to SilverCollection]

Latest revision as of 23:16, 13 October 2024

Digitizing the Past and Present for the Future
IDigBio Logo RGB.png

Digitization
How to digitize? (Five clusters) Workshops and Symposia
Digitization Videos Biblio entries
Connect with iDigBio
Specimen Portal Upcoming Events
iDigBio on facebook Follow iDigBio on twitter

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

"Introduction to iDigBio" 02:04
 More than 1,600 natural history collections across the United States house over 1 billion biological specimens ranging from fungi to fish to fossils. This video describes the iDigBio project. It explains why digitized information and ready access to it are important, provides an overview of the digitization process and highlights some of the challenges faced when working with different types of natural history collections.

Digitization Academy

The Digitization Academy offers a set of complementary courses on topics related to digitizing data about biodiversity. Digitization Academy courses are online, free, and open to everyone from the world’s biodiversity collections and research communities. There are two formats. Short, 2-hour courses on emerging topics simply require registration; multi-day courses provide a deeper dive on foundational topics and involve smaller cohorts and an application process. More information, including the current course catalog, is available at digitizationacademy.org.

Recommendations for the Acquisition, Processing, and Archiving of Digital Media

iDigBio has created recommendations for capturing, processing, and storing digital media.

Recommendations for the Acquisition, Processing, and Archiving of Digital Media

Interest/Working Groups

The following links take you to Interest/Working Groups focused on Digitization. For other working groups please use the following link iDigBio Working Groups

Digitization Avenue

The following links provide information on the task clusters that enable efficient and effective digitization of Biological and Paleontological Collections. If you are unfamiliar with the task clusters please read the following Five task clusters that enable efficient and effective digitization of biological collections.


iDigBio Workshops, Reports, and Wikis

iDigBio's Workshop and Report page contains links to materials from completed iDigBio workshops, conferences, and symposia.

Videos- Digitization Resources and Workflows

Click for Collapsible List of Videos
"Imaging Workflows for the Digitization of Dry-preserved Vertebrate Specimens" 07:25
 This video details the four primary task clusters associated with digitization and imaging including selecting specimens, pre-digitization specimen curation and staging, image capture, and image processing. The video also gives specific tips for imaging dry collections including deciding which specimens and views to capture, imaging tools and equipment, and image stacking.
"Digitization Workflows Overview" 07:21
 This workflow video offers an introduction into the digitization process, the rationale behind why museums are digitizing their collections, how iDigBio is facilitating the digitization movement, and what the current challenges are for museum digitization.
"Digitizing Wet Collections" 04:34
 This instructional video details the five step process the Ichthyology Collection at the Florida Museum of Natural History uses to digitize their collection including: selecting specimens, image capturing, image processing, electronic data capture and georefrencing, and curating specimens. The video also gives specific tips for imaging wet collections including squeeze box use, what imaging equipment to use, and what views to capture for use in taxonomic identification.
"Digitizing Herbarium Collections" 07:34
 This video details the five step process the University of Florida Herbarium uses for digitizing specimens: specimen staging, image capturing, specimen image processing, electronic data capture and georeferencing, and specimen curating. The video also features the Valdosta State Herbarium's image processing and data capture and georeferencing workflow.
Retrieved from "http://www.idigbio.org/wiki/index.php?title=Digitization_Resources&oldid=35208"