small herbaria michigan - silvercollection

SILVERBIOLOGY BIODIVERSITY INFORMATICS SERVICES

WWW.SILVERBIOLOGY.COM

MICHAEL GIDDENS @SILVERBIOLOGY

MIKEGIDDENS@SILVERBIOLOGY.COM

Formed in 2008

Provides consulting and software to advance digitization and

research in the scientific community

Created SilverImage (rapid digitization workflow)

Finalizing Biodiversity Image Server (management software

for scientific images)

Developing HelpingScience.org (cit izen science data transcription)

Created SilverCollection (web research portal)

Created Mobile Copy Station (designed for col lection digit ization )

Provides Herbarium Barcode Labels

SILVERBIOLOGY HISTORY

Cyberflora Louisiana Herbaria

Mississippi Herbaria Project

Georgia Herbaria Project

Rio de Janeiro Jardim Botânico

Denver Botanic Gardens

California Academy of Sciences

Angelo State Natural History Museum

The Netherlands all collections

Kansas State

University of Queensland Australia

And others…

WHO WE HELP

We will be providing:

A mobile copy station to share among the collections.

Remote technical support on how to image your collection.

60k barcode labels

A server running the Biodiversity Image Server software to house and manage all 60k+ specimen images that will be captured.

SilverCollection web portal through the MiCOB website to access both images and occurrence data as that information becomes available.

Workflows and methods on how to transcribe label data using the digital specimen images that are taken.

Digital maps of georeferenced data.

Consulting on how to make us of your images and occurrence data for research, websites, and public projects.

Helping to submit your occurrence data to Global Biodiversity Information Facility (GBIF) Currently 388 million indexed records.

SMALL HERBARIA OF MICHIGAN

Complete Kit

115lbs but does have wheels

Assembly & Instruction Guides

<1hr to setup & breakdown

Uses SilverImage to manage images

Images automatically

upload to project

Great for sharing

Can fit in most cars

Container can be

shipped as is

MOBILE COPY STATION

We provide 9-6 MST technical support for mobile

copy stations and SilverImage

Skype

LogMeIn

TECHNICAL SUPPORT

Image management tools

Grouping images by collection

Metadata tagging (Darwin Core, Dublin Core, user defined)

Associating images to geographical regions

Events – great for use in expeditions, field trips, bioblitz , etc…

Sets – used for image matrices

Thumbnail generation

OCR Analysis (Tesseract OCR)

Taxonomic resolution services

Barcode Detection

RESTful web service

SDK’s for software developers

BIODIVERSITY IMAGE SERVER

Manage all local images before sending to BIS server

Synchronization of all metadata and tags from BIS server

Advanced tools for tagging images in bulk

Uploads many images at once

Great for:

Microscopy stations

Living plant photography

Field station computer

Home computer

Office computer

Lab computer

BioBlitz event

BIS DESKTOP CLIENT

Web portal for all collection data

Mobile version coming soon to Apple Store & Google Play

DEMO http://data.cyberfloralouisiana.com/lsu/

SILVERCOLLECTION

Developed by

SilverBiology

LABEL PROCESSING METHOD

HELPINGSCIENCE.ORG

From This To This

• StateProvince: Arkansas

• County: Bradley

• Genus: Botrychium

• SpecificEpithet: biternatum

• Authorship: (Sav.) Underwood

• Collector: Sherri Leslie, Kaylon

Cornish

• CollectorNumber: 593

• DateCollected: 1984-09-23

• TRS: Sec. 3, T12S, R9W

GOAL (REPEAT 60+ MILLION TIMES)

Species Lookup: http://ecat-dev.gbif.org/usage/2650191

From This To This

• StateProvince: Arkansas

• County: Bradley

• Genus: Botrychium

• SpecificEpithet: biternatum

• Authorship: (Sav.) Underwood

• Collector: Sherri Leslie, Kaylon

Cornish

• CollectorNumber: 593

• DateCollected: 1984-09-23

• TRS: Sec. 3, T12S, R9W

GOAL (REPEAT 60+ MILLION TIMES)

Species Lookup: http://ecat-dev.gbif.org/usage/2650191

Identify Labels

OCR Labels

Identify

Primary DwC

Fields

Lexical Grouping & Verification

Enter Values

for Fields

Accept Value

for Each Field

Assemble Label Data

WORKFLOW

Step 1 To This

IDENTIFYING LABELS

Sign In

Request Image

Click & Drag

Click & Drag

<Enter>

Repeat

Average Time: 300/hr

per person

Identify Labels

OCR Labels

Identify

Primary DwC

Fields

Lexical Grouping & Verification

Enter Values

for Fields

Accept Value

for Each Field

Assemble Label Data

WORKFLOW

Sample JPG label

JSON output $5/1GB per month

~ label cost: $0.001

EVERNOTE OCR PROCESSING

AFTER EVERNOTE

Identify Labels

OCR Labels

Identify

Primary DwC

Fields

Lexical Grouping & Verification

Enter Values

for Fields

Accept Value

for Each Field

Assemble Label Data

WORKFLOW

What we capture.

• Scientific Information (Fami ly, Genus , Spec ies , Subspec ies , Author )

• Collection Information (Name, Number, Date )

• Geographical Information (Count r y, S tate , County, Loca l i ty,

Lat/Lon , TRS)

• Determination Information (Determiner, Sc ient i f i c Name, Date

Determined)

• Extra Information (Access ion Number, Type S tatus )

What we leave on the label.

• Habitat Information

• Locality Description

• Collector Notes

• Other

STEP 2) IDENTIFYING LABELS

Identify Labels

OCR Labels

Identify

Primary DwC

Fields

Lexical Grouping & Verification

Enter Values

for Fields

Accept Value

for Each Field

Assemble Label Data

WORKFLOW

Internal Step

Compare words to

OCR value and if

it is distinct assign

to lexical set.

Send image to

data entry.

LEXICAL GROUPING

Internal Step

Look at the value

that will be assigned

to the list of images

if any are not the

correct value move to

manual data entry

blacklist.

Repeat

Based on Lexical Groups

BULK VALIDATION

Identify Labels

OCR Labels

Identify

Primary DwC

Fields

Lexical Grouping & Verification

Enter Values

for Fields

Accept Value

for Each Field

Assemble Label Data

WORKFLOW

Public Step

Multiple Interfaces

Dates

Lat/Lng

Names

Scientific Names

User receive vir tual

tokens to use in the

store for every correct

word

DATA ENTRY

DATA ENTRY VARIATIONS

Identify Labels

OCR Labels

Identify

Primary DwC

Fields

Lexical Grouping & Verification

Enter Values

for Fields

Accept Value

for Each Field

Assemble Label Data

WORKFLOW

Computer: Asplenium Frequency

Volunteer 2: Asplenium Asplenium: 2

Volunteer 3: Asplenlum Asplenlum: 1

Volunteer 4: Asplenium Asplenium: 3

Asplenium: 1

Points Earned: Volunteer 2 & 4

FIELD VERIFICATION

Identify Labels

OCR Labels

Identify

Primary DwC

Fields

Lexical Grouping & Verification

Enter Values

for Fields

Accept Value

for Each Field

Assemble Label Data

WORKFLOW

Export Formats

CSV

Darwin Core Archive

Others on request

Filters

By any combination of Darwin Core Fields

Restful web services

OCCURRENCE DATA

HelpingScience depends on a symbiotic relationship between collections providing specimen sheets and volunteers to perform data entry.

Volunteers are given HS Tokens to be used in the HS Store in exchange for their t ime.

The store is a percentage of the cost per label that is given back to the community.

The Store

Fundraisers

Small micro loans given to botany undergraduate students for research

Sponsorships for students to attend scientific conferences

K12 equipment funding for science departments

Charitable Organizations

Fund Small Herbaria Digitization

SUSTAINABILITY

SILVERBIOLOGY BIODIVERSITY INFORMATICS SERVICES

WWW.SILVERBIOLOGY.COM

MICHAEL GIDDENS @SILVERBIOLOGY

MIKEGIDDENS@SILVERBIOLOGY.COM