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.

1. Digitization Software & Equipment

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. 1. Producing a mobile copy station for herbaria
2. Providing a logistical software (SilverImage) to aid in
rapidly imaging vascular collections
3. Developing open source software for housing biodiversity
images online
4. Providing consulting on methods to scan and digitize
index cards and 35mm slides

4. Available in Fall 2012

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. 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. 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. 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. 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. Open Source Server Software to House & Manage Images

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. 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. 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. Biodiversity Image Server Software
• RESTful web services for web developers
• HTML5 Zoom Engine
• SDK’s in PHP, NodeJS
• Example use cases

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 18'S1"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. Biodiversity Image Server Software
Sample JPG label
JSON output

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. 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. 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. Biodiversity Image Server Software
Official Release: September 2012
Biodiversity Image Server Software:
http://code.google.com/p/biodiversity-imageserver/
BIS Desktop Client:
http://code.google.com/p/biodiversity-imageserver-client/
SilverBiology
Website: http://www.silverbiology.com
Email: mikegiddens@silverbiology.com
Twitter: @silverbiology