UVSD: Software for Detection of Color Underwater Features

Underwater Video Spot Detector (UVSD) is a software package designed to analyze underwater video for continuous spatial measurements (path traveled, distance to the bottom, roughness of the surface etc.) Laser beams of known geometry are often used in underwater imagery to estimate the distance to the bottom. This estimation is based on the manual detection of laser spots which is labor intensive and time consuming so usually only a few frames can be processed this way. This allows for spatial measurements on single frames (distance to the bottom, size of objects on the sea-bottom), but not for the whole video transect. We propose algorithms and a software package implementing them for the semi-automatic detection of laser spots throughout a video which can significantly increase the effectiveness of spatial measurements. The algorithm for spot detection is based on the Support Vector Machines approach to Artificial Intelligence. The user is only required to specify on certain frames the points he or she thinks are laser dots (to train an SVM model), and then this model is used by the program to detect the laser dots on the rest of the video. As a result the precise (precision is only limited by quality of the video) spatial scale is set up for every frame. This can be used to improve video mosaics of the sea-bottom. The temporal correlation between spot movements changes and their shape provides the information about sediment roughness. Simultaneous spot movements indicate changing distance to the bottom; while uncorrelated changes indicate small local bumps. UVSD can be applied to quickly identify and quantify seafloor habitat patches, help visualize habitats and benthic organisms within large-scale landscapes, and estimate transect length and area surveyed along video transects

RRS James Cook Cruise 36, 19 Jul-28 Jul 2009. The Geobiology of Whittard Submarine Canyon

The biological and geological research programme for James Cook cruise 36 was built around a series of ROV video transects to determine variations in species and community structure and composition in different geological and topographic settings down the canyon. ROV transects were planned to undertake detailed studies of recognised biological hotspots on both hard and soft substrates, to collect specimens for taxonomic studies, including molecular genetics, and to carry out biological experiments, including the use of in situ incubation chambers and tracer feeding experiments to study the physiology of deep-water fauna. Additional coring, CTD and water column particulate sampling programmes were planned to investigate the recent geological history of the canyon, and, in particular, to investigate whether significant sediment is currently accumulating in any part of the canyon, to sample macro- and meiofauna in areas of soft substrate, and to investigate the fate of organic carbon in the canyon. JC36 was highly successful. The cruise built on the successful mapping of the canyon, using swath bathymetry and 30 kHz sidescan sonar, undertaken during JC35. The main achievements of JC36 included the completion of 26 ROV dives, totalling 340 hr. Seafloor video and photographs along 12 transects from the eastern and western canyon branches between 500 and 3600 m waterdepth were collected. A collection of over 240 biological specimens was collected to verify species identification from the video transects. Pushcores for sedimentology, organic geochemistry, biology and microbiology were also collected. Ultra high-resolution swath bathymetry of the canyon floor using the multibeam system mounted on the ROV was collected on 8 dives. A total of 10 dives were dedicated to placing, initiating and recovering a variety of biological experiments on the seafloor, mainly to examine respiration rates of individual animals or animal communities. The coring programme completed 19 successful piston core stations and 29 successful megacore stations. Most of the latter were processed for macrofauna and meiofauna but some were subsampled for sedimentology and geochemistry. A preliminary assessment suggests that most of the sediment recovered is late glacial in age, and that little Holocene sediment has been deposited in the canyon. 6 CTD profiles and 5 SAPS (stand-alone pump) stations were completed to characterise the suspended particulate matter above the canyon floor. A total of 30 pushcores and megacores also sampled for organic geochemistry

Biogeographic analysis of the Tortugas Ecological Reserve: Examining the refuge effect following reserve establishment

Almost 120 days at sea aboard three NOAA research vessels and one fishing vessel over the past three years have supported biogeographic characterization of Tortugas Ecological Reserve (TER). This work initiated measurement of post-implementation effects of TER as a refuge for exploited species. In Tortugas South, seafloor transect surveys were conducted using divers, towed operated vehicles (TOV), remotely operated vehicles (ROV), various sonar platforms, and the Deepworker manned submersible. ARGOS drifter releases, satellite imagery, ichthyoplankton surveys, sea surface temperature, and diver census were combined to elucidate potential dispersal of fish spawning in this environment. Surveys are being compiled into a GIS to allow resource managers to gauge benthic resource status and distribution. Drifter studies have determined that within the ~ 30 days of larval life stage for fishes spawning at Tortugas South, larvae could reach as far downstream as Tampa Bay on the west Florida coast and Cape Canaveral on the east coast. Together with actual fish surveys and water mass delineation, this work demonstrates that the refuge status of this area endows it with tremendous downstream spillover and larval export potential for Florida reef habitats and promotes the maintenance of their fish communities. In Tortugas North, 30 randomly selected, permanent stations were established. Five stations were assigned to each of the following six areas: within Dry Tortugas National Park, falling north of the prevailing currents (Park North); within Dry Tortugas National Park, falling south of the prevailing currents (Park South); within the Ecological Reserve falling north of the prevailing currents (Reserve North); within the Ecological Reserve falling south of the prevailing currents (Reserve South); within areas immediately adjacent to these two strata, falling north of the prevailing currents (Out North); and within areas immediately adjacent to these two strata, falling south of the prevailing currents (Out South). Intensive characterization of these sites was conducted using multiple sonar techniques, TOV, ROV, diver-based digital video collection, diver-based fish census, towed fish capture, sediment particle-size, benthic chlorophyll analyses, and stable isotope analyses of primary producers, fish, and, shellfish. In order to complement and extend information from studies focused on the coral reef, we have targeted the ecotone between the reef and adjacent, non-reef habitats as these areas are well-known in ecology for indicating changes in trophic relationships at the ecosystem scale. Such trophic changes are hypothesized to occur as top-down control of the system grows with protection of piscivorous fishes. Preliminary isotope data, in conjunction with our prior results from the west Florida shelf, suggest that the shallow water benthic habitats surrounding the coral reefs of TER will prove to be the source of a significant amount of the primary production ultimately fueling fish production throughout TER and downstream throughout the range of larval fish dispersal. Therefore, the status and influence of the previously neglected, non-reef habitat within the refuge (comprising ~70% of TER) appears to be intimately tied to the health of the coral reef community proper. These data, collected in a biogeographic context, employing an integrated Before-After Control Impact design at multiple spatial scales, leave us poised to document and quantify the postimplementation effects of TER. Combined with the work at Tortugas South, this project represents a multi-disciplinary effort of sometimes disparate disciplines (fishery oceanography, benthic ecology, food web analysis, remote sensing/geography/landscape ecology, and resource management) and approaches (physical, biological, ecological). We expect the continuation of this effort to yield critical information for the management of TER and the evaluation of protected areas as a refuge for exploited species. (PDF contains 32 pages.

Echolocation detections and digital video surveys provide reliable estimates of the relative density of harbour porpoises

Acknowledgements We would like to thank Erik Rexstad and Rob Williams for useful reviews of this manuscript. The collection of visual and acoustic data was funded by the UK Department of Energy & Climate Change, the Scottish Government, Collaborative Offshore Wind Research into the Environment (COWRIE) and Oil & Gas UK. Digital aerial surveys were funded by Moray Offshore Renewables Ltd and additional funding for analysis of the combined datasets was provided by Marine Scotland. Collaboration between the University of Aberdeen and Marine Scotland was supported by MarCRF. We thank colleagues at the University of Aberdeen, Moray First Marine, NERI, Hi-Def Aerial Surveying Ltd and Ravenair for essential support in the field, particularly Tim Barton, Bill Ruck, Rasmus Nielson and Dave Rutter. Thanks also to Andy Webb, David Borchers, Len Thomas, Kelly McLeod, David L. Miller, Dinara Sadykova and Thomas Cornulier for advice on survey design and statistical approache. Data Accessibility Data are available from the Dryad Digital Repository: http://dx.doi.org/10.5061/dryad.cf04gPeer reviewedPublisher PD

A new 3-D modelling method to extract subtransect dimensions from underwater videos

Underwater video transects have become a common tool for quantitative analysis of the seafloor. However a major difficulty remains in the accurate determination of the area surveyed as underwater navigation can be unreliable and image scaling does not always compensate for distortions due to perspective and topography. Depending on the camera set-up and available instruments, different methods of surface measurement are applied, which make it difficult to compare data obtained by different vehicles. 3-D modelling of the seafloor based on 2-D video data and a reference scale can be used to compute subtransect dimensions. Focussing on the length of the subtransect, the data obtained from 3-D models created with the software PhotoModeler Scanner are compared with those determined from underwater acoustic positioning (ultra short baseline, USBL) and bottom tracking (Doppler velocity log, DVL). 3-D model building and scaling was successfully conducted on all three tested set-ups and the distortion of the reference scales due to substrate roughness was identified as the main source of imprecision. Acoustic positioning was generally inaccurate and bottom tracking unreliable on rough terrain. Subtransect lengths assessed with PhotoModeler were on average 20 % longer than those derived from acoustic positioning due to the higher spatial resolution and the inclusion of slope. On a high relief wall bottom tracking and 3-D modelling yielded similar results. At present, 3-D modelling is the most powerful, albeit the most time-consuming, method for accurate determination of video subtransect dimensions