Difference between revisions of "Digitization Resources"

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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.
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[[Category: Videos]]
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{| class="wikitable" style="float:right; margin-left:"
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! colspan="2" style="background:#D58B28;width:200px;font-size:10pt" | Digitizing the Past and Present for the Future
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| 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 />
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| colspan="2" style="background:#D58B28;text-align:center;font-size:9pt" | Digitization
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| 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]]
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| 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]
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| colspan="2" style="background:#D58B28;text-align:center;font-size:9pt" | Connect with iDigBio
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| style="font-size:9pt" | [https://www.idigbio.org/portal Specimen Portal] || style="font-size:9pt" | [https://www.idigbio.org/outreach-events-sidebar| Upcoming Events]
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| style="font-size:9pt" | [http://www.facebook.com/iDigBio  iDigBio on facebook] || style="font-size:9pt" | [https://twitter.com/iDigBio Follow iDigBio on twitter]
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|}<!--THE INFO BOX ENDS HERE-->
  
==iDigBio==
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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/content/intro-idigbio Introduction to iDigBio Slide Set]
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* [https://www.idigbio.org/wiki/images/e/e2/Intro_to_iDigBio.pdf Intro to iDigBio pdf file]
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==Workshop Logistics==
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==iDigBio Introduction==
* [https://www.idigbio.org/wiki/images/6/68/Pre_Workshop_Instructions.pdf Pre-Workshop Instructions]
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{| cellpadding=5
* [https://www.idigbio.org/wiki/images/e/ef/IDigBio_Plant_Digitization_Workshop_Logistics.pdf Workshop Logistics]
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|style="vertical-align:top;"|[[File:PlayVideo2.jpg|thumb|300px|link=https://vimeo.com/67570758|"Introduction to iDigBio" 02:04]]  
* [https://www.idigbio.org/wiki/images/1/11/VSU_Campus_Map.pdf VSU Campus Map]
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|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.
* [https://www.idigbio.org/wiki/images/7/7e/Participant_List.pdf Participant List]
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|}
  
==Workshop Outlines==
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==Recommendations for the Acquisition, Processing, and Archiving of Digital Media==
* [https://www.idigbio.org/wiki/images/7/77/Herbarium_Digitization_Workshop_Agenda.pdf Herbarium Digitization Workshop Agenda]
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iDigBio has created recommendations for capturing, processing, and storing digital media.
* [https://www.idigbio.org/wiki/images/1/13/Monday_Afternoon_Schedule.pdf Monday Afternoon Schedule]
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* [https://www.idigbio.org/wiki/images/8/86/Schedule_Detail_Day3.pdf Schedule detail, Mid-day Day 3]
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* [http://tinyurl.com/HerbariumWorkshopNotes Collaborative Workshop Notes - Day 2]
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* [http://tinyurl.com/Worshop-Notes-Day2 Collaborative Workshop Notes - Day 3]
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* [https://www.idigbio.org/wiki/index.php/IDigBio_Workshops#Workshop_Documentation iDigBio Workshop Summary Page]
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*[https://www.idigbio.org/biblio?f%5bkeyword%5d=59 Workshop Presentations]
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==General Digitization Resources==
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[[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)]
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* [https://www.idigbio.org/wiki/images/d/d5/3135-G-3-layout.pdf Five task clusters that enable efficient and effective digitization]
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* [https://www.idigbio.org/wiki/images/f/f2/Overview.pdf Gil Nelson: Herbarium Digitization Tasks and Components Overview]
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* [https://www.idigbio.org/content/idigbio-intellectual-property-policy iDigBio's Intellectual Property Rights statement]
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*[https://www.idigbio.org/wiki/index.php/File:PrePostDigitizationCurationDP.pdf Deborah Paul: Pre & Post Digitization Curation]
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*[http://tools.gbif.org/dwca-assistant/ Just What is a Darwin Core Archive File?]
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==Imaging Documents and Resources==
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==Interest/Working Groups==
* [https://www.idigbio.org/wiki/images/5/58/Image_File_Format_Recommendations_and_Standards.pdf iDigBio's Image File Format Policy and Recommendations]
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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]
* [http://www.adobe.com/digitalimag/pdfs/dng_primer.pdf Introducing the Digital Negative Specification]
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*[[Drawer Imaging Group| International Whole-Drawer Digitization Interest Group]]
* [https://www.idigbio.org/sites/default/files/sites/default/files/BeginnersGuideToImagingGlossary.pdf Beginner's Guide to Digital Imaging - Glossary]
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*[[Small Herbarium Interest Group| NANSH Working Group]] (North American Network of Small Herbaria)
* [http://wwwimages.adobe.com/www.adobe.com/content/dam/Adobe/en/products/photoshop/pdfs/DNG_primer_manufacturers.pdf  Digital Negative Specification for Manufacturers]
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*[[Fluid Preserved Arthropds| Fluid-preserved Arthropod and Microscopic Slide Imaging Interest Group]]
* [https://www.idigbio.org/wiki/images/1/15/Herbarium_Image_Editing_Guidelines.pdf Mike Bevans' Herbarium Image Editing Guidelines]
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*[[Paleo Digitization Working Group| Paleontology Digitization Working Group]]
* [https://www.idigbio.org/wiki/images/3/36/Standardized_Digital_Imaging_NYBG.pdf Mike Bevans' Digital Imaging and Archiving]
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*[[SCNet| Small Collections Network Working Group]]
* [https://www.idigbio.org/wiki/images/b/b1/Intro_to_Photoshop.pdf Mike Bevans' Intro to Photoshop]
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*[[vert digi interest group | Vertebrate Digitization Intererst Group]]
*[http://digitalphotorepro.blogspot.com/ Mike Bevan's Blog on Digital Imaging]
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*[[Field Station Interest Group| Field Station Interest Group]]
* [https://www.idigbio.org/wiki/images/8/82/Imaging_Manual.pdf Mike Bevans' So, you want to digitize plant specimens]
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*[https://docs.google.com/open?id=0B5L2FF0VryJnNkp5NG1EY3Ffd2s Mike Bevan's: Digitizing Plant Collections VSU Workshop - link to power point]
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* [http://cbe.ivic.ve/ftp/clasebioest/pdf/Digital_Imaging_Ethics.pdf Douglas Cromey's Digital Imaging Ethics]
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* [http://www.atiz.com/resources/DPI-PPI-Megapixels-and-Resolution.pdf Atiz Innovation, Inc.: Making sense of DPI, PPI, Megapixels and Resolution]
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* [http://www.nikonusa.com/pdf/manuals/software/CapNX2/CAPNX2_UM_EN.pdf Nikon's Capture NX2 Software User's Manual]
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* [http://lbcc.limnology.wisc.edu/node/4 Lichen/Bryophyte TCN Imaging Recommendations]
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* [http://www.pnwherbaria.org/documentation/specimenimaging.php Pacific Northwest Herbaria imaging resources]
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* [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]
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* [https://www.idigbio.org/wiki/images/9/98/VSUImagingProtocol.pdf Valdosta State University Herbarium (VSC) Vascular Plant Imaging Protocol]
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* [https://www.idigbio.org/wiki/images/f/fb/VSU_Bryophyte_Imaging_Protocol.pdf Valdosta State Herbarium (VSC) Bryophyte Packet Imaging Protocol]
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==Camera Manuals & Specifications==
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==Digitization Avenue==
* [http://www.nikonusa.com/pdf/manuals/software/ccp_en.pdf Nikon Camera Control Pro Reference Manual]
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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].
* [http://gdlp01.c-wss.com/gds/7/0300007447/03/dpp311w3-en.pdf Canon Digital Photo Professional 3.11 Instruction Manual]
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*[[ Pre-digitization Curation and Staging | Pre-digitization Curation and Staging]]
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*[[ Specimen Image Capture | Specimen Image Capture]]
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*[[ Specimen Image Processing | Specimen Image Processing]]
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*[[ Electronic Data Capture | Electronic Data Capture]]
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*[[ Georeferencing locality descriptions | Georeferencing Locality Descriptions]]
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*[[ Digitization Workflows and Protocols | Digitization Workflows and Protocols]]
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*[[ More on digitization  |More on digitization  ]]
  
==Workflows and Protocols==
 
* [https://www.idigbio.org/content/digitization-workflow-workshop-report iDigBio Digitization Workflow Workshop (DROID) report]
 
* [https://www.idigbio.org/content/digitization-workflows iDigBio's Collaborative Workflows Page]
 
* [http://lbcc.limnology.wisc.edu/node/3 Bryophyte/Lichen TCN workflow]
 
* [https://www.idigbio.org/wiki/images/6/63/Imaging_Protocol_v5b.pdf Florida State University Herbarium Imaging Protocol]
 
* [http://www.snsb.info/SNSBInfoOpenWiki/attach/Attachments/JSTOR-Plants-Handbook.pdf JSTOR PLANTS Handbook]
 
* [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]
 
* [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]
 
  
==Georeferencing Resources==
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==[[IDigBio Workshops|iDigBio Workshops, Reports, and Wikis]]==
* [http://www.gbif.org/orc/?doc_id=1288 Biogeomancer, Guide to Best Practices in Georeferencing]
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iDigBio's Workshop and Report page contains links to materials from completed iDigBio workshops, conferences, and symposia.
* [http://www.museum.tulane.edu/geolocate/ Geolocate: Online and Desktop Georeferencing Tools]
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*[[ IDigBio_Workshops#Calendar_Year_2020| Calendar Year 2020]]
* [https://www.idigbio.org/wiki/images/9/9d/Georeferencing.pdf Gil Nelson: Georeferencing with Geolocate]
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*[[ IDigBio_Workshops#Calendar_Year_2019| Calendar Year 2019]]
* [http://manisnet.org/GeorefGuide.html MaNIS/HerpNet/ORNIS Georeferencing Guidelines]
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*[[ IDigBio_Workshops#Calendar_Year_2018| Calendar Year 2018]]
* [http://www.herpnet.org/Gazetteer/GeorefResources.htm Herpnet's georeferencing resources page]
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*[[ IDigBio_Workshops#Calendar_Year_2017| Calendar Year 2017]]
* [https://www.idigbio.org/wiki/index.php/Georeferencing iDigBio Georeferencing Wiki]
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*[[ IDigBio_Workshops#Calendar_Year_2016| Calendar Year 2016]]
* [https://www.idigbio.org/forums/georeferencing-working-group-gwg iDigBio's Georeferencing Working Group Forum]
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*[[ IDigBio_Workshops#Calendar_Year_2015| Calendar Year 2015]]
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*[[ IDigBio_Workshops#Calendar_Year_2014| Calendar Year 2014]]
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*[[ IDigBio_Workshops#Calendar_Year_2013| Calendar Year 2013]]
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*[[ IDigBio_Workshops#Calendar_Year_2012| Calendar Year 2012]]
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*[[ IDigBio_Workshops#Calendar_Year_2011| Calendar Year 2011]]
  
==Database Resources and Tools==
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==Videos- Digitization Resources and Workflows==
* [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]
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{| class="mw-collapsible mw-collapsed wikitable" width="800px"
* [https://www.idigbio.org/content/biological-collections-databases iDigBio's Database, Portals, Aggregators, and Tools Review Page]
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|-
* [http://daryllafferty.com/salix/ Download Salix software here]
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|valign="left"|'''Click for Collapsible List of Videos'''
* [http://nhc.asu.edu/vpherbarium/canotia/SALIX3.pdf Salix software documentation]
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* [https://www.idigbio.org/wiki/images/1/1b/DataTools.pdf Gil Nelson: Database Tools and Techniques]
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|-
* [https://www.idigbio.org/wiki/images/b/bd/Accessing_Specify_on_Amazon.pdf Accessing Specify on the Amazon Cloud]
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|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]]
* [http://specifysoftware.org/sites/specifysoftware.org/files/Publishing%20Specify%20Data%20with%20IPT.pdf Publishing Specify Data with IPT]
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|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.
* [https://www.idigbio.org/wiki/images/b/b6/WorkshopSymbiotaLogin.pdf Symbiota Login Information]
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|-
*[http://code.google.com/p/google-refine/ Try Google Refine to Clean CSV Data]
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|style="vertical-align:top;"|  [[File:Digitization Workflows.jpg|thumb|200px|link=https://vimeo.com/120369455|"Digitization Workflows Overview" 07:21]]
*[http://daks.ucdavis.edu/?page_id=205 Kepler Kurator to Clean Spreadsheet Data]
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|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.
*[http://www.youtube.com/watch?v=DEkPbvLsud0 See Kepler Kurator at work cleaning data in a Filtered PUSH Network]
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|-
 
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|style="vertical-align:top;"|[[File:PlayVideo3.jpg|thumb|200px|link=https://vimeo.com/120369690|"Digitizing Wet Collections" 04:34]]
==Identifiers==
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|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/iDigBio-GUID-Statement20MAR2012.pdf iDigBio's Guidelines for Managing Persistent Identifiers]
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|-
 
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|style="vertical-align:top;"|[[File:Herbarium.jpg|thumb|200px|link=https://vimeo.com/120369768|"Digitizing Herbarium Collections" 07:34]]
==Videos==
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|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.
* [https://vimeo.com/46296902 iDigBio's Introduction to Nikon's Camera Control Pro 2 software]
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|}
* [https://vimeo.com/46312484 iDigBio's Introduction to Nikon's Live View Feature]
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* [https://vimeo.com/42586243 Arizona State University's Orientation to Settings on a Canon Camera]
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* [https://vimeo.com/46950737 iDigBio's Batch Processing with Nikon Capture NX2]
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* [https://vimeo.com/46990833 iDigBio's Nikon D3X Camera Setup for Scientific Specimen Imaging]
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Latest revision as of 15:10, 25 January 2020

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.

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.