At each study site, transect surveys are conducted in which digital still images are taken for further analysis using PointCount99, a computer program developed by Dr Phil Dustan at the College of Charleston. PointCount99 generates random data points on the transect images which are then analyzed to yield bottom composition percentages, eg. live coral, dead coral, rubble, sand etc.

Transect sites are chosen as representative of an ecological zone within the reef. A minimum of two transects must be completed within each zone to provide enough data points for analysis by PointCount99 (minimum 2000 points).

A team of four is required to lay a transect. Equipment required are two weighted buoys labeled A and B, a measuring tape, a digital still camera, underwater writing slates and pencils.

Transects are conducted at a depth between 5 and 10 meters. A 20-meter line is laid, using the measuring tape as a guide, and the weighted buoys are placed at either end of the 20 meter line. A bearing is taken underwater from buoy A to buoy B and the boat tender takes GPS coordinates of each buoy at the surface.

Digital still images are taken in two lines, each line covering the 2-meter span either side of the central guideline. These images are taken every 30 cm at a height of 40-60 cm above the reef. Between 50 and 60 images should be gathered for each transect line.

The transect ‘zone’ created is an 80 m² area (central 20 meter line with 2 meter spans either side). Coral identification and invertebrate identification are conducted within this zone.

Fish identification and population counts are conducted in the area around the transect.

Each transect line should yield at least 50 images, hence a transect survey yields 100 images in total. Each image is analyzed using PointCount99 which generates 10 random data points per image. Hence each transect survey yields 1000 data points. Dr Dustan has advised that 2000 points are required to give an accurate representation of an ecological zone within a reef system.