SilverBiology

SilverBiologyDigitization Software & Equipment

Company History

• 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???

What is SilverBiology doing to help digitization efforts?

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

Available in Fall 2012

Mobile Copy Station for Herbaria

Everything included to start imaging within 1hr

• Pelican 1780T watertight case• Copymate II + Lights• Canon 5d MkII + 50mm Macro

Lens• Dell Windows 7 laptop• 20" external monitor• SilverImage software ready to

use• Remote switch

• Barcode scanner & assembly tools

• Assembly guide & videos• 9-5 Tech support and remote

training• 5,000 herbarium barcodes

included• Free US ground shipping

Mobile Copy Station

Image Quality

• 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.

Mobile Copy Station

Efficiency of the 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

Mobile Copy Station

Imaging Speeds

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

Mobile Copy Station

Options

Rental Option• Small or dormant herbarium

collection.• Imaging deadlines and

needing an extra copy station to complete your project sooner.

Purchase Option• Group of collections wanting

to share equipment and split the cost.

• Bigger collection that wants to loan out their copy station for regional imaging efforts

• ADBC joint projects to rapidly digitize many herbaria.

• Traveling imagers. If you plan to travel from location to location imaging collections.

Mobile Copy Station

Open Source Server Software to House & Manage ImagesBiodiversity Image Server

Who is it for?

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

Biodiversity Image Server Software

Benefits

• 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

Biodiversity Image Server Software

Some Management Features• 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

Biodiversity Image Server Software

Some Web Features• RESTful web services for web developers• HTML5 Zoom Engine• SDK’s in PHP, NodeJS• Example use cases

Biodiversity Image Server Software

Tesseract OCR Features• 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: ITISTaxon Status: synonymSynonym Of: Poaceae Barnhart

Biodiversity Image Server Software

EverNote OCR Engine

Sample JPG label

JSON output

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

Biodiversity Image Server Software

Use Case for Preliminary Inquiries

• 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

Biodiversity Image Server Software

Desktop 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

Biodiversity Image Server Software

Future release datesOfficial 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/

SilverBiologyWebsite: www.silverbiology.comEmail: [email protected]: @silverbiologySkype: mikegiddens

Biodiversity Image Server Software

Who will be using it?

• CyberFlora Louisiana (1 million+ specimen sheets)• Georgia Virtual Herbarium• Mississippi Virtual Herbarium• California Academy of Sciences• Rio de Janeiro Botanical Garden

Biodiversity Image Server Software