Difference between revisions of "Digitization Template 2"

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(Created page with "== Digitization Workshops Symposia Wikis and Reports == ===2014 Workshops and Symposia Wikis=== *Data Carpentry Workshop at iDigBio, (date to be announced)...")
 
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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.
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==iDigBio Intro==
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* [https://www.idigbio.org/sites/default/files/sites/default/files/Intro_to_iDigBio.pptx Introduction to iDigBio Slide Set]
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* [https://www.idigbio.org/sites/default/files/sites/default/files/Intro_to_iDigBio.pdf Intro to iDigBio pdf file]
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==Interest/Working Groups==
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*[[Drawer Imaging Group| International Whole-Drawer Digitization Interest Group]]
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*[[Small Herbarium Interest Group| NANSH Working Group]] (North American Network of Small Herbaria)
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*[[Fluid Preserved Arthropds| Fluid-preserved Arthropod and Microscopic Slide Imaging Interest Group]]
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*[[Paleo Digitization Working Group| Paleontology Digitization Working Group]]
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*[[SCNet| Small Collections Network Working Group]]
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== Digitization Workshops Symposia Wikis and Reports ==
 
== Digitization Workshops Symposia Wikis and Reports ==
 
===2014 Workshops and Symposia Wikis===  
 
===2014 Workshops and Symposia Wikis===  
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*[https://www.idigbio.org/content/careers-and-graduate-study-biological-sciences Careers and Graduate Study in Biological Sciences]
 
*[https://www.idigbio.org/content/careers-and-graduate-study-biological-sciences Careers and Graduate Study in Biological Sciences]
 
*[https://www.idigbio.org/content/education-outreach-workshop-0 Education & Outreach Workshop Report]
 
*[https://www.idigbio.org/content/education-outreach-workshop-0 Education & Outreach Workshop Report]
 
  
 
===2013 Workshops and Symposia Wikis===  
 
===2013 Workshops and Symposia Wikis===  
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*[https://www.idigbio.org/content/1st-annual-idigbio-augumenting-ocr-hackathon-fort-worth-texas-february-13-14 iDigBio Augmenting OCR Hackathon Workshop Report]
 
*[https://www.idigbio.org/content/1st-annual-idigbio-augumenting-ocr-hackathon-fort-worth-texas-february-13-14 iDigBio Augmenting OCR Hackathon Workshop Report]
 
*[https://www.idigbio.org/content/hackathon-and-iconference-update-part-ii iDigBio Augmenting OCR Hackathon Update Part II Workshop Report]
 
*[https://www.idigbio.org/content/hackathon-and-iconference-update-part-ii iDigBio Augmenting OCR Hackathon Update Part II Workshop Report]
 
  
 
===2012 Workshops and Symposia Wikis===  
 
===2012 Workshops and Symposia Wikis===  
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*[https://www.idigbio.org/content/wet-collections-digitization-workshop-report Wet Collections Workshop Report]
 
*[https://www.idigbio.org/content/wet-collections-digitization-workshop-report Wet Collections Workshop Report]
 
*[https://www.idigbio.org/content/herbarium-digitization-training-workshop Herbarium Digitization Workshop Report]
 
*[https://www.idigbio.org/content/herbarium-digitization-training-workshop Herbarium Digitization Workshop Report]
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==General Digitization Resources==
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* [http://pensoft.net/journals/zookeys/issue/209 No specimen left behind: mass digitization of natural history collections (ZooKeys Special Issue)]
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* [[Media:3135-G-3-layout.pdf|Five task clusters that enable efficient and effective digitization]]
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* [[Media: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/sites/default/files/workshop-presentations/dpc2012/PrePostDigitizationCurationDP.pptx Deborah Paul: Pre & Post Digitization Curation]
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** pdf version [[Media:PrePostDigitizationCurationDP.pdf| 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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* [http://openrefine.org/ Cleaning Data in a Spreadsheet - Try OpenRefine] formerly known as GoogleRefine
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* [https://www.idigbio.org/sites/default/files/workshop-presentations/chicago2013/OpenRefineFieldMuseum2013.pptx Raw Data Cleaning, Validation and Enhancement: Using Open Refine, Deborah Paul]
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* [https://www.idigbio.org/sites/default/files/workshop-presentations/chicago2013/IdentifiersAndSharingDataFieldMuseumV2.pptx Identifiers and Sharing Data, Deborah Paul]
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==Leveraging the Library and Other Institutional Resources==
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* [[Media:Schmidt.pdf|Digitization of Herbarium Specimens, a Collaborative Project (Larry Schmidt)]]
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==Example Digitization Protocols==
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* [[Media:Imaging_Protocol_v5b.pdf|Florida State University Herbarium Imaging Protocol]]
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* [[Media:VSUImagingProtocol.pdf|Valdosta State University Herbarium (VSC) Vascular Plant Imaging Protocol]]
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* [[Media:VSU_Bryophyte_Imaging_Protocol.pdf|Valdosta State Herbarium (VSC) Bryophyte Packet Imaging Protocol]]
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* [[Media:Image_Dust_Off_Protocol_for_Nikon_Cameras.pdf|Valdosta Herbarium image processing with Nikon Dust Off process included]]
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* [http://insects.oeb.harvard.edu/MCZ/PDFs/Guide_to_digitizing.pdf A Guide to Digitizing Insect Collections (MCZ Entomology Type Image Project)]
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* [http://www.kvmagruder.net/hos/blog/ApertureWorkflow.pdf Digitization Workflow Using Aperture (Scanners, Cameras,Books)]
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* [http://tcn.amnh.org/documents Workflows, protocols, etc. from Tri-Trophic TCN (NYBG and AMNH docs)]
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==Imaging Documents and Resources==
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* [[Media:IDigBioImagingGeneralEquipmentRecommendations1_0.pdf|iDigBio Imaging Equipment Recommendations (Joanna McCaffrey)]]
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* [http://tcn.amnh.org/documents Workflows, protocols, etc. from Tri-Trophic TCN (NYBG and AMNH docs)]
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* [https://www.idigbio.org/sites/default/files/sites/default/files/BeginnersGuideToImagingGlossary.pdf Beginner's Guide to Digital Imaging - Glossary]
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* [[Media:Herbarium_Image_Editing_Guidelines.pdf|Mike Bevans' Herbarium Image Editing Guidelines]]
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* [[Media:Standardized_Digital_Imaging_NYBG.pdf|Mike Bevans' Digital Imaging and Archiving]]
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* [[Media:Intro_to_Photoshop.pdf|Mike Bevans' Intro to Photoshop]]
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* [http://digitalphotorepro.blogspot.com/ Mike Bevans' Blog on Digital Imaging]
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* [[Media:Imaging_Manual.pdf|Mike Bevans' So, you want to digitize plant specimens]]
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* [https://docs.google.com/open?id=0B5L2FF0VryJnNkp5NG1EY3Ffd2s Mike Bevans' Digitizing Plant Collections VSU Workshop - link to power point]
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* [[Media:Digital_Imaging_Ethics.pdf|Douglas Cromey's Digital Imaging Ethics]]
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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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* [[Databasing_References#The_AIC_Guide_to_Digital_Photography_and_Conservation_Documentation| The AIC Guide to Digital Photography and Conservation Documentation]]
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* [http://cpbc.bio.nau.edu/imaging_facility/howto.html Northern Arizona University's Imaging videos and ppt's]
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* [[Imaging References|Imaging References]]
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==Image File Types and File Specifications==
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* [[Media:Image_File_Format_Recommendations_and_Standards.pdf|iDigBio's Image File Format Policy and Recommendations]]
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* [http://www.adobe.com/digitalimag/pdfs/dng_primer.pdf Introducing the Digital Negative Specification]
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* [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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* [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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==Imaging Station Equipment and Specifications==
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* [http://www.eboxbio.com/ Photo EBox Imaging Station]
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*[https://www.idigbio.org/sites/default/files/workshop-presentations/small-herbarium2013/iDigBioImagingEquipmentRecommendations1_0.pdf iDigBio Imaging Equipment Recommendations]
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* [http://www.pnwherbaria.org/documentation/custom-components-v1.pdf Assembling Custom Components for Specimen Imaging (NW Herbaria Consortium)]
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* [[Media:SamNobleStackShotOptimization.pdf|Sam Noble Musuem's optimization of the efficiency of stackshot, including 3D printing plans for SNO's Focus Stacking Stand, contributed by Roger Burkhalter]]
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* [http://sketchup.google.com/3dwarehouse/details?mid=63bb091473549abe520693977acea63e&prevstart=0 Plans for Sam Noble Museum's '''Focus Stacking Stand''' plans and downloads, Roger Burkhalter]
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* [http://sketchup.google.com/3dwarehouse/details?mid=6778558dd7d43111520693977acea63e&prevstart=0 Plans for Sam Noble Museum's '''Focus Stacking Platform''' plans and downloads, Roger Burkhalter]
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* [http://www.macroscopicsolutions.com/aboutus.html Macroscopic Solutions portable, photo stacking device, overcomes lighting hurdles with copy stands: Macropod]
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==3D Imaging and 3D Printing Resources==
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*[https://deals.macupdate.com/deal/14840 Strata Design 3D CX & Foto 3D CX 7.0.7]
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*[https://www.macupdate.com/app/mac/26173/strata-foto-3d-cx Strata Foto 3D CX]
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*[http://www.agisoft.ru/ Image-based 3D modeling: Agisoft PhotoScan]
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*[http://www.pensoft.net/journals/zookeys/article/5768/abstract/rotational-scanning-electron-micrographs-rsem-a-novel-and-accessible-tool-to-visualize-and-communicate-complex-morpholog 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]
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*[http://www.pensoft.net/journals/zookeys/article/5763/abstract/revolving-sem-images-visualising-3d-taxonomic-characters-application-to-six-species-of-the-millipede-genus-ommatoiulus-l 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]
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==Camera Manuals & Specifications==
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* [http://www.nikonusa.com/pdf/manuals/software/ccp_en.pdf Nikon Camera Control Pro Reference Manual]
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* [http://gdlp01.c-wss.com/gds/7/0300007447/03/dpp311w3-en.pdf Canon Digital Photo Professional 3.11 Instruction Manual]
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==[[Collections Digitization Workflows| Links to Workflows--iDigBio and Elsewhere]]==
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==Workflows and Protocols==
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* [[Media:Digitization_Workflows_wet_collections.pdf|Digitization Workflows]]
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* [https://www.idigbio.org/content/digitization-workflow-workshop-report iDigBio Digitization Workflow Workshop (DROID) report]
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* [https://www.idigbio.org/content/digitization-workflows iDigBio's Collaborative Workflows Page (DROID Working Groups)]
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* [http://lbcc.limnology.wisc.edu/node/3 Bryophyte/Lichen TCN workflow]
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* [http://www.snsb.info/SNSBInfoOpenWiki/attach/Attachments/JSTOR-Plants-Handbook.pdf JSTOR PLANTS Handbook]
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* [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]
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* [https://www.idigbio.org/content/workflow-modules-and-task-lists Workflow Modules and Task Lists]
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* [[Media:Workflows.pdf|Gil Nelson: Herbarium Workflows]]
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* [https://www.idigbio.org/sites/default/files/sites/default/files/Workflow_MellonTypePDC_v4.jpeg U. Vermont GPI Pre-digitization Curation Workflow (Audrey Clark)]
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* [https://www.idigbio.org/sites/default/files/workshop-presentations/dpc2012/SharingDataDP.pptx Deborah Paul: Sharing Data]
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==Georeferencing Resources==
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* [http://www.gbif.org/orc/?doc_id=1288 Biogeomancer, Guide to Best Practices in Georeferencing]
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* [http://www.museum.tulane.edu/geolocate/ Geolocate: Online and Desktop Georeferencing Tools]
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* [[Media:Georeferencing.pdf|Gil Nelson: Georeferencing with Geolocate]]
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* [http://manisnet.org/GeorefGuide.html MaNIS/HerpNet/ORNIS Georeferencing Guidelines]
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* [http://www.herpnet.org/Gazetteer/GeorefResources.htm Herpnet's georeferencing resources page]
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* [[Georeferencing|iDigBio Georeferencing Wiki]]
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* [https://www.idigbio.org/forums/georeferencing-working-group-gwg iDigBio's Georeferencing Working Group Forum]
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* [http://www.museum.tulane.edu/coge/ GeoLocate Web Management Portal login]
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* [http://www.museum.tulane.edu/geolocate/web/webcomgeoref.aspx GeoLocate Collaborative Georeferencing Web Client login]
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* [[Media:FSU_Collaborative_Georeferencing_Protocol.pdf|Collaborative Georeferencing with Geolocate Protocol, Florida State University]]
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* [[Media:Mast_Protocol_Geolocate_FSU.pdf|FSU Geolocate Protocol Using a Custom Spreadsheet for Georeferencing]]
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* [http://idigbio.adobeconnect.com/p1wtfeto4kg/ Georeferencing Herbarium Specimens using GeoLocate]
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==Database Resources and Tools==
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* [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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* [https://www.idigbio.org/sites/default/files/workshop-presentations/chicago2013/Chicago_DAMS.pdf Digital Asset Management (DAMS)]
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* [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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* [http://nhc.asu.edu/vpherbarium/canotia/SALIX3.pdf Salix software documentation]
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* [[Media:DataTools.pdf|Gil Nelson: Database Tools and Techniques]]
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* [http://specifysoftware.org/sites/specifysoftware.org/files/Publishing%20Specify%20Data%20with%20IPT.pdf Publishing Specify Data with IPT]
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* [[Media:WorkshopSymbiotaLogin.pdf|Symbiota Login Information]]
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* [http://openrefine.org/ Try Open Refine to Clean CSV Data] formerly known as Google Refine
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* [http://daks.ucdavis.edu/?page_id=205 Kepler Kurator to Clean Spreadsheet Data]
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* [http://www.youtube.com/watch?v=DEkPbvLsud0 See Kepler Kurator at work cleaning data in a Filtered PUSH Network]
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* [[Voice_recognition|Voice Recognition]]
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==Identifiers==
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* [https://www.idigbio.org/sites/default/files/iDigBioGuidGuide-2013-06-26_0.pdf iDigBio's GUID Guide for Data Providers]
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*[https://www.idigbio.org/wiki/index.php/Globally_Unique_IDs_(GUID) Globally Unique Identifiers (GUID)]
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==Videos==
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* [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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* [http://www.youtube.com/watch?v=faCP15wjc4g&feature=plcp Introduction to SilverCollection]

Revision as of 10:32, 21 August 2014

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

Interest/Working Groups

Digitization Workshops Symposia Wikis and Reports

2014 Workshops and Symposia Wikis

2014 Workshop Reports

2013 Workshops and Symposia Wikis

2013 Workshop Reports

2012 Workshops and Symposia Wikis

2012 Workshop Reports

General Digitization Resources

Leveraging the Library and Other Institutional Resources

Example Digitization Protocols

Imaging Documents and Resources

Image File Types and File Specifications

Imaging Station Equipment and Specifications

3D Imaging and 3D Printing Resources

Camera Manuals & Specifications

Links to Workflows--iDigBio and Elsewhere

Workflows and Protocols

Georeferencing Resources

Database Resources and Tools

Identifiers

Videos