Photo Analysis

Plate photos are analyzed the same way than settlement tiles. Several options are possible: quantification of the grey areas to get a measure of percent cover – annotation of functional groups – annotation at the lower taxonomic levels. The following guidelines are only provided to help you design your plate photo analysis. Depending on the specific question, protocols can be modified by the user.

Materials:

Procedures:

  1. The first step, if you want to work on higher resolution photos to access higher taxonomic resolution is to stich the plate images together. Whether you have taken 4 or more photos per plate side, you will need to stich them back together and make sure that their final size is compatible with the annotation program you will be using (CPCe or CoralNet).
  2. We use a stratified random point generation method with a minimum of 50 points per plate (ex: 2 rows, 5 columns and 5 points per cell).
  3. Annotation categories used by NOAA CRED program are already available in CoralNet, and you can upload these labels into your own project.
  4. The following annotations are for identifications at the functional level, you can modify the list below to better match your project

 

CORALNET Label Names
CORALNET Labels
CORALNet Functional Group
CORALNET Description

ARMS-CRED-CCA

_CCA

Algae

Commonly grows in patches on hard substrates, forming hard pink patches. Hard substrates range from pavement flats to basalt formation to bare carbonate (i.e. coral skeleton) structures

ARMS-CRED-Blue-green macroalga

_BGMA

Algae

Cyanobacteria (blue-green macroalgae). Often form deep purple to black filamentous tufts or mats that may stretch for multiple centimeters in length, and therefore look different from turf algae.  They may also form mucilaginous masses that are white or pale yellow in color.

ARMS-CRED-Brown encrusting macroalgae

_BREN

Algae

Unidentified brown encrusting macroalgae

ARMS-CRED-Brown upright macroalgae

_BRUP

Algae

Unidentified brown upright macroalgae

ARMS-CRED-Caulerpa

_CAUL

Algae

Caulerpa species

ARMS-CRED-Dictyopteris/Dictyota

_DICO

Algae

Dictyopteris or Dictyota species

ARMS-CRED-Green encrusting macroalgae

_GREN

Algae

Unidentified green encrusting macroalgae

ARMS-CRED-Green upright macroalgae

_GRUP

Algae

Unidentified green upright macroalgae

ARMS-CRED-Halimeda spp

_HALI

Algae

Halimeda species

ARMS-CRED-Lobophora spp

_LOBO

Algae

Lobophora species

ARMS-CRED-Neomeris spp

_NEOM

Algae

Neomeris species

ARMS-CRED-Peyssonnelia spp

_PESP

Algae

Peyssonnelia species

ARMS-CRED-Red encrusting macroalgae

_RDEN

Algae

Unidentified red encrusting macroalgae

ARMS-CRED-Red upright macroalgae

_RDUP

Algae

Unidentified red upright macroalgae

ARMS-CRED-Coral

_CO

Hard coral

Stony corals or hard corals of Order Scleractinia.

ARMS-CRED-No Recruitment

_NR

Other

No recruiment has taken place.

ARMS-CRED-Unavailable

_UNAV

Other

The survey point is located on an area of the plate that is unavailable for recruitment due to position of cross bar or hardware.

ARMS-CRED-Mobile fauna

_MOBF

Other

This category is appropriate when the point falls on fauna that are not permanently affixed to a single location on the sea floor (e.g. sea cucumbers, seastars, sea urchins, fish, marine mammals). Effort should be made to discern what the benthic classification is under the point, if that is not possible, this category should be used.

ARMS-CRED-Calcareous Worm Tube

_CAW

Other invertebrates

Annelids that secrete tubes of calcium carbonate.  Includes the following families: Serpulidae, Sabellidae, etc

ARMS-CRED-Eggs

_EGG

Other invertebrates

Egg masses from mobile fauna that are deposited on hard substrate

ARMS-CRED-Foraminifera

_FORM

Other invertebrates

Single-cell protists with shells or test. Shell or test may have many shapes. Can be white to hot pink in color. Often seen on plates is Homotrema sp. (Bright pink/red spikey branches).

ARMS-CRED-Gastropoda

_GAS

Other invertebrates

The Gastropoda or gastropods, more commonly known as snails and slugs, are a large taxonomic class within the phylum Mollusca. The class Gastropoda includes snails and slugs of all kinds and all sizes from microscopic to large.

ARMS-CRED-Hydrozoa

_HYD

Other invertebrates

Animals of the class Hydrozoa. The majority of hydroids are colonial

ARMS-CRED-Soft Worm Tube

_SOW

Other invertebrates

Annelids that secrete soft non-calcified tubes.  Includes the following genera: Chaetopterus sp.  Etc

ARMS-CRED-Tunicate Colonial

_TUNC

Other invertebrates

Colonial tunicate

ARMS-CRED-Tunicate Solitary

_TUNS

Other invertebrates

Solitary tunicate

ARMS-CRED-Vermetidae

_VER

Other invertebrates

Family Vermetidae is small to medium sized gastropod that secretes irregularly shaped shells that often cemented on hard substrate. Often known by common names worm snails and worm shells. Many indiviulas can be cemented together forming colonies.

ARMS-CRED-Bivalve

_BI

Other invertebrates

Clams, oysters, and mussels are common examples of bivalves (Class Bivalvia).  For all other non-empty bivalves, use this category.

ARMS-CRED-Bivalve-empty

_BIEM

Other invertebrates

Clams, oysters, and mussels are common examples of bivalves (Class Bivalvia). If the shells are present but empty, use this category.

ARMS-CRED-Bryozoan

_BRY

Other invertebrates

These colonial animals are early colonizers of bare surfaces in coral reefs.  Most attach to solid surfaces but some live in sand.  Each "member" lives in a zooid, or house, and has lophophores, which are "tentacles" that extend out of the house to filter feed.  The lophophores are ciliated and very "regular" in appearance.  However, unless the image is really clear, it will be hard to detect the lophophores and use them to distinguish between a tunicate or sponge.  The individual zoids join to neighboring ones forming bushy, branching, fanlike, or encrusting colonies that may be rigid or flexible.  Most bryozoans have a lace-like appearance and can be confused with algae or sponges.  However, unlike sponges and tunicates, you will not see incurrent and excurrent openings.  This is because the lophophores in bryozoans are used for feeding.  In general, bryozoans will not appear smooth like a tunicate and their upright structure will appear to be "flower" and "plant"- like.

ARMS-CRED-Corallimorph

_CMOR

Other invertebrates

Corallimorphs (Order Corallimorpharia) are anemone-like animals that are found either solitary or in colonies.  Their tentacles are generally much shorter than those of true anemones. They can be invasive and at this stage resemble a fuzzy carpet.

ARMS-CRED-Hydrocoral

_HYCO

Other invertebrates

Refers to non-scleractinian corals with hard skeletons, specifically, the following hydrocorals: Distichopora spp. and Stylaster spp.

ARMS-CRED-Octocoral

_OCTO

Other invertebrates

Refers to gorgonian corals, sea fans, sea whips, sea pens, and other members of Subclass Alcyonaria (octocorals), except blue coral (Order Helioporacea), which should be classified as Non-scleractinian hard coral.  All members of this classification category produce skeletal elements made of protein and calcium carbonate that and give the colony sufficient soft support and the flexibility to sway with the ocean waves and currents.

ARMS-CRED-Sponge

_SP

Other invertebrates

Sponges (Phylum Porifera) have numerous species and growth morphologies, many of which can be confused with other benthic organisms.  Sponges have porous tissue for filter feeding and many have large openings through which expelled water flows (excurrent openings).  To help identify sponges, zoom-in with the photograph and examine the surrounding tissue. In general, sponges are more colorful than tunicates. In general, sponges are not as smooth as a tunicate, rather they are "rougher" around the edges due to a lack of a "tunic" and being composed of spicules.  In general, most sponges, unlike tunicates, are not able to close their excurrent openings. In general sponges can protrude/extend upwards off the benthos from their encrusting state whereas tunicates tend to grow along the contours of the substrate underneath them.

ARMS-CRED-Zoanthid

_ZO

Other invertebrates

Zoanthids (Order Zoanthidea) are colonial anemone-like animals having smooth, flat, broad oral disks with tentacles that radiate outward from their margins. Tentacles are found in two nearby rows, and always are in a number that is a multiple of six.  The polyp's mouth has a ciliated groove at one or both ends of the mouth.  Zoanthids are connected by runners (called stolons) and they lack the hard skeletons of scleractinian corals. Includes the following genera: Palythoa spp, Protopalythoa spp,  Zoanthus spp

ARMS-CRED-Sediment

_SED

Soft subtrate

Sediment on the plate that obscures organism or empty plate.

ARMS-CRED-Unclassified/Unknown

_UNK

Other

This category is appropriate when the point falls on an area that is obscured or blurry and cannot be identified with confidence

 

   5. The program will place the set number of random points on each plate image and the user will be able to identify each organism attributed to each point.

   6. Visualize annotation statistics.

Illustrations:

Example of annotation using CoralNet and 200 stratified random points

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