image cataloging as a tool for marine biodiversity discovery

Claude Nozères

From photos to data:an introduction to image catalogingas a tool for biodiversity

email: claudenozeres@gmail.com

Fisheries and Oceans Canada, Maurice Lamontagne Institute850 route de la mer, Mont-Joli, QC, Canada G5H 3Z4

This is not a software review Default programs on PCs:

MS PhotoEditorWindows Live Photo GalleryApple iPhoto

Other softwareGoogle Picasa (free, basic)IrfanView (free, basic)Adobe Photoshop (expensive, complicated)

This is about work examples recent cases with biodiversity projects: using

catalogs to turn photos into reliable data all examples done with Adobe Lightroom

Case study 1

Conservation zones

Several areas in the St. Lawrence are of special interest for marine life

high biological productivitydiversity of benthic habitats

Q: how to document the biodiversity?

Surveys: grabs & tow camera

shrimp often seenin bottom photos

Benthic sled photo transects

keywords: photo 2007, Leptasterias polaris...

keywords: photo 2006, Pandalus borealis, Ophiura sarsii,

individual photos by transect (yellow thumbnails are endpoints)

• photo of sea bottom every 10 s. • identify and count epifauna in view

IKU Grab photos

keywords: sediment, grab, grab IKU 2008

keywords: tray, grab IKU 2008

keywords: Neoamphitrite groenlandica,Polychaeta, Terebellidae, grab IKU 2008

The problem: many images At first, a solution was sought for

organizing the underwater photosselecting good shots for analysisadding or correcting dates and locations

However, the sampling surveys also had photos (field samples, lab examination)these were very useful to consult for

questions about species and stations

Case Study 2

Trawl bycatch Capture a large diversity of organisms

Taxonomic expertise not available while at sea

Q: how to record the diversity in bycatch?

Non-commercial species in capture

Capture sorted by type

Giving an initial ID based on photos

posters produced usingfiles in an image catalog

Individual images by type

keywords: unknown, Ascidiacea, TE-008

do not need a photo for every specimen, but useful for new or uncertain species

The problem: effort for species ID

no time to identify all taxa while at sea BUT need a name & a weight to record

sort by types, give names, take photossave some specimens for validation later

later in the lab, can give correct namesphotos show original appearance & colourphotos can help to correct data, e.g., counts

Solutions: image management

Digital Asset Management (DAM) for images & their databrowsing (sorting & comparing)organizing (grouping)editing (image properties)

DAM makes use of standardized types of metadata intended for commercial photographycan exploit these data fields for marine projects

Image metadata—info. on photosData fields are useful for sorting and comparing: capture date (EXIF) – original camera clock date keyword (IPTC)– subject tags for species, scenes location (IPTC) – tag for station name GPS (EXIF) latitude and longitude coordinates

example of filtering for metadata in a Lightroom image catalog

Why an image catalog?

browser: metadata in images read as they are being examinede.g., Windows Explorer, Photoshop

(Bridge)

catalog: metadata in images is also stored in a database, or catalog, filecan do more with organization & taggingcan work with files offline (files not present)NB: all work here is with Lightroom catalogs

Image catalogs: added value

It takes work to tag & organize photos in a catalog!

Benefits include: rapid browsing and comparison of photos quick confirmation of correct names or values, such

as date, species, station, or GPS coordinates bulk export of image data into database archives and

for use in data analyses easier to generate graphic products on-demand,

e.g., posters and photo galleries

Benefits: ‘Discovered species’

By comparing image results across surveys, severallesser-known species were discovered or corrected from the established records and literature for the region

Notable examples in St. Lawrence Estuary

• bivalves: Mya pseudoarenaria; Panomya vs. Mya truncata• large deepwater amphipod: Neohela monstrosa• sea cucumber: Pentamera calcigera• brittlestars: Ophiacantha, Stegophiura, Amphiura• sea anemones: Actinostola callosa (not Actinauge)• sea pens: Anthoptilum grandiflorum (not Pennatula)

revealed in 2011

Discovering from catalogs

photo 2006

Gulf 8/2011

DFO surveys in 2011 revealed errors in sea pens–was easy to confirm in the image catalog

Confusion with sea pens dates back to 1919

Anthoptilum(not Pennatula)

photo 2006

trawl 2006

Difficult to ID seaanemones in underwater photos - finally validated with trawl photos

Easy to return tocatalog and update records, species keyword

Actinostola(not Actinauge)

Actinauge

Actinostola

Discovering from public images

Blog: BIO’s Offshore Benthic Ecology Group did a cruise blog in June 2011posted images while at sea—became inspiration to

confirm Anthoptilum from captures in the St. Lawrence

Article (Belley et al. 2010) contained images – revealed errors in IDerrors would have continued if kept to internal reports or

publications without images

Photogallery: export images to a web gallerywhen errors are discovered, update catalog & re-export

Web photogallery: CaRMS

• IML collection in LR catalog• export key images to CaRMS

file export

Exporting data for analyses Lightroom uses a sqlite3 database engine

provides a graphical interface for easy to do queries & edits

built-in data tools are limited, but the user community has produced shareware plugins (donation/small fee) Photographer’s Toolbox jfriedl (Jeffrey’s Lightroom Goodies)

in current projects, exported text (csv) is put to use in Excel, Access, Oracle (w/Spatial Database Engine), and Primer (multivariate analyses)

The Photographer’s toolbox

Summarystandard metadata was used to tag images in

a Lightroom catalogbrowsing catalog images across surveys

resulted in more species being identifiedexporting images for public viewing provided

opportunities for verificationexporting image metadata enabled their use

in external databases for analyses

Key resources The DAM Book by Peter Krogh, also a forum:

http://www.thedambook.com/smf/index.php

Best practices for digital photography (website)http://www.dpbestflow.org/

Adobe Photoshop Lightroom 3: The Missing FAQ by Victoria Bampton (paper & PDF)

CaRMS photogallery user guide, Kennedy et al. 2011. DFO Tech. Rep. 2933. (paper & PDF)

NIDM image data guide (report to be published)