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iDigBio Presentation - Botany 2012


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Presentation given on Friday July 13th, 2012 in Columbus, OH at iDigBio. The presentation discusses a mobile copy station for herbaria and biodiversity image server software to manage scientific images.

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iDigBio Presentation - Botany 2012

  1. 1. Digitization Software & Equipment
  2. 2. • Established in 2008• In 2009, we started digitizing the Louisiana Herbaria• In 2010, we started R&D for processing herbarium labels• In 2011, we started to offer barcode printing services• Summer 2012: release of SilverCollection v1.2 with zoomable image support and mapping using CartoDB• Future???
  3. 3. 1. Producing a mobile copy station for herbaria2. Providing a logistical software (SilverImage) to aid in rapidly imaging vascular collections3. Developing open source software for housing biodiversity images online4. Providing consulting on methods to scan and digitize index cards and 35mm slides
  4. 4. Available in Fall 2012
  5. 5. Mobile Copy Station • Pelican 1780T watertight case • Remote switch • Copymate II + Lights • Barcode scanner & assembly tools • Canon 5d MkII + 50mm Macro Lens • Assembly guide & videos • Dell Windows 7 laptop • 9-5 Tech support and remote training • 20" external monitor • 5,000 herbarium barcodes included • SilverImage software ready to use • Free US ground shipping
  6. 6. Mobile Copy Station • Canon 5d mk II can produce some of the best images from SLR cameras that are on the market. • RAW Resolution 5,616 x 3,744 pixels and average 20-25MB per image.
  7. 7. Mobile Copy Station • You can transport the case via Car, Ground & Air Shipping • Can be assembled and ready to use in less than 1 hour • Can be disassembled in less than 1 hour • Normally does not require interacting with the computer • The barcode-scanner renames files with the proper barcode • Images can be uploaded/transferred to a required server within 24 to 48 hours automatically • Ability to selectively upload images based on barcode numbers
  8. 8. Mobile Copy Station Rates are based on motivated workers imaging vascular specimens. • Specimen images with existing barcodes applied: • 6,000+ images per 40 work week • Average of 150/hr • Specimen images not barcoded: • 3,500+ images per week • Average of 90/hr Workers do get bored, tired, distracted and burned out. • Multiple workers with 4hr shifts
  9. 9. Mobile Copy Station Purchase Option Rental Option • Group of collections wanting to • Small or dormant herbarium share equipment and split the collection. cost. • Imaging deadlines and needing • Bigger collection that wants to an extra copy station to complete loan out their copy station for your project sooner. regional imaging efforts • ADBC joint projects to rapidly digitize many herbaria. • Traveling imagers. If you plan to travel from location to location imaging collections.
  10. 10. Open Source Server Software to House & Manage Images
  11. 11. Biodiversity Image Server Software Biodiversity Image Server is a type of web server software that specializes in managing and delivering scientific images. • All disciplines • Individual or Regional Collections • Natural History Museums • Small to Extremely Large Image Collections
  12. 12. Biodiversity Image Server Software • Provides a place to store specimen, microscopy, radiographs, field notes, field and living images • Works with 100’s to millions of images • Similar to other image hosting companies, except: • The images are stored on your server • There is an emphasis in biodiversity metadata • User controlled access • Web services for future integration
  13. 13. Biodiversity Image Server Software • Grouping images by collection • Associating images to geographical regions or Exif Lat/Lng metadata. • Metadata Tags support (Key/Value Pairs, Triples, Features) • Events • Sets - Used for image matrices • Multiple Store Device Support (NFS & Amazon S3) • Barcode Detection Analysis • Pixel Ratio Detection • Tesseract OCR Label Analysis • EverNote Search Engine
  14. 14. Biodiversity Image Server Software • RESTful web services for web developers • HTML5 Zoom Engine • SDK’s in PHP, NodeJS • Example use cases
  15. 15. Biodiversity Image Server Software • Image -> Text -> GNA Name Finder -> Names -> GBIF CLB -> Results University of Southern Mississippi Herbarium (USMS) iiiiiiii |i|iiiiii FLORA OF THE UNITED STATES OF AMERICA Gramineae MISSISSIPPI: LAMAR County: west of Hattiesburg, Coie Road, just 20- 100 m south of intersection with US Highway 98. T4-N R14W Sec I8 NW/4. 31 18S1"N, 89026/40//W. Eievation 100 m, Roadside and adjacent upiand Iongieaf pine forest, grazed by horses, with limited understory of Persimmon, Hex glabra, sassafras, and taIIowtree. Roadside ditch. Mac H. Alford #3705 I0 August 2006 Gramineae Gramineae Juss. According To: ITIS Taxon Status: synonym Synonym Of: Poaceae Barnhart
  16. 16. Biodiversity Image Server Software Sample JPG label JSON output
  17. 17. Biodiversity Image Server Software • Choose images or collections to send to EverNote Engine within the software • When the image is added it will return the evernote_id associated to your image_id • Use the built in EverNote search service features on your website • User can search and get back corresponding images based on the EverNote fuzzy search engine WARNING!!! • You can get False Positives because it is fuzzy searching • It is a black box so you have no control over how it searches
  18. 18. Biodiversity Image Server Software • Use your image server to send a Collection of images to EverNote with the built in features • Wait an hour to let EverNote index those images • Create your lookup lists, Taxonomy, Geography, etc. • Loop through all values in your list and use the build in EverNote search service to get the image_id’s associate with each name in your list • Store those associations and use those findings to make decisions
  19. 19. Biodiversity Image Server Software • PC & Mac Versions • Used for uploading images to a Biodiversity Image Server • Can upload many images at once • Can monitor changes in images and keep them synchronized online • Ability to tag images with character/value data • Great for Microscopes, Field Images, Living Plant Images
  20. 20. Biodiversity Image Server Software Official Release: September 2012 Biodiversity Image Server Software: BIS Desktop Client: SilverBiology Website: Email: Twitter: @silverbiology