A Field Primer for Monitoring Benthic Ecosystems Using Structure-From-Motion Photogrammetry

This protocol provides a simple overview of how to collect images in the field to produce three dimensional models of underwater ecosystems.This technique allows for the collection of data to produce large scale, high resolution 3D models which helps us answer questions about community composition, geometrical properties, and system complexity.This method is useful for studying benthic ecosystems to gather valuable information on patterns of biodiversity, habitat complexity, community structure and other ecological metrics.As with most field methods, make sure to choose a site that is safe and accessible, and pick a day when weather conditions are favorable.For your first time trying the method Set up a DSLR camera in an underwater housing with the settings described in the text manuscript.If using a waterproof action camera, set it to video or continuous shooting mode at the highest resolution and frame rate possible.Set the video resolution to 4K and the frame rate to 30 frames per second.Select a spool rig with a flanged edge and attachment points for a handle and pole.Ensure that the spool rig is inherently negatively buoyant or made so with the addition of weights.For frequent use or challenging field conditions, select a spool made of a more rugged material such as aluminum.Ensure the spool does not rotate on the pole or spin when in use.Fix the line to the spool at one end and to a detachable clip at the other for connecting to the camera.Although specialized calibration tiles are not necessary, ensure that negatively buoyant, recognizable objects of known size are included in the model for scale.Consider surge and current conditions to ensure suitable materials are used so that tiles remain stationary.during photo collection.Provide divers with a means to measure the depth of the tile such as an electronic depth gauge.Select a site with enough room to swim the entirety of the spiral pattern.In addition to the area being surveyed, incorporate a small buffer area to ensure that the entire survey area is sufficiently photographed to yield high quality data.If possible, assemble a two person team, one to survey shallow sites on snorkel and another to survey deeper sites by scuba.If planning to survey the site regularly, mark the center point where the spool rig will be placed with a tag or a permanent structure.At the very least, take a global positioning system coordinate so that the site can be relocated with assistance from a printout of the orthomosaic.Set the spool in the middle of the site then set out the calibration tiles and record their deaths.Place the calibration tiles face up, approximately two meters away from the center.Ensure that the swimmer attaches the side of the camera closest to the spool to the line and holds the camera facing straight down, approximately one meter from the benthos.Then the swimmer swims with the camera while the assistant tends the spool.The assistant sets the pole and the attached spool upright in the center of the selected site and holds the spool rig upright and stationary.Once the camera is properly positioned, the swimmer begins taking continuous images of the benthos while swimming forward and maintaining tension on the line, ensuring that the swimmer continues to swim in a spiral at a consistent speed while taking photographs until the line is completely unwound from the spool.In highly rugose environments such as coral reefs, include a third worker who can prevent line entanglement by hovering above the center of the line and gently lifting it over obstacles.When the line is completely unspooled, the swimmer reverses directions, reattaching the camera if necessary, and swims the camera in the opposite direction to begin rewinding the line back onto the spool while taking pictures.If a single spiral method is desirable to save time, the swimmer should detach the line from the camera and skip to imaging the center of the site while the assistant winds the line and removes the spool rig from the site.As soon as the swimmer begins to swim in the opposite direction, the assistant rotates the spool to wind the line in half of a turn against the new swimming direction.This ensures that the swimmer's return path is offset from the original path to yield greater photo coverage of the site.Ensure that the swimmer continues to take pictures and swims the reverse spiral until the line is almost completely rewound around the spool.When the swimmers and assistants spacing prevents further progress, the swimmer can stop taking pictures, so that the camera can be detached from the line, and the assistant can remove the spool rig from the center of the site.Once the spool is removed from the site, the swimmer images the center of the site by holding the camera facing straight down and moving the camera in a small spiral pattern over the center of the site.When finished, clean up the site.Never leave trash or equipment at a site and always leave a site cleaner than you found it.This protocol was used to image reef site 2_7 located on Patch Reef 13 in K