Sonar Estimates Research Articles

Development and Validation of a Model to Combine NDVI and Plant Height for High-Throughput Phenotyping of Herbage Yield in a Perennial Ryegrass Breeding Program

Sensor-based phenotyping technologies may offer a non-destructive, high-throughput and efficient assessment of herbage yield (HY) to replace current inefficient phenotyping methods. This paper assesses the feasibility of combining normalised difference vegetative index (NDVI) from multispectral imaging and ultrasonic sonar estimates of plant height to estimate HY of single plants in a large perennial ryegrass breeding program. For sensor calibration, fresh HY (FHY) and dry HY (DHY) were acquired destructively, and plant height was measured at four dates each in 2017 and 2018 from a selected subset of 480 plants. Global multiple linear regression models based on K-fold and random split cross-validation methods were used to evaluate the relationship between observed vs. predicted HY. The coefficient of determination (R2) = 0.67–0.68 and a root mean square error (RMSE) between 5.43–7.60 g was obtained for the validation of predicted vs. observed DHY. The mean absolute error (MAE) and mean percentage error (MPE) ranged between 3.59–5.44 g and 22–28%, respectively. For the FHY, R2 values ranged from 0.63 to 0.70, with an RMSE between 23.50 and 33 g, MAE between 15.11 and 24.34 g and MPE between ~22% and 31%. Combining NDVI and plant height is a robust method to enable high-throughput phenotyping of herbage yield in perennial ryegrass breeding programs.

Using acoustic telemetry to expand sonar escapement indices of Chinook salmon to in-river abundance estimates

Acoustic telemetry was combined with a project that uses sonar and drift gillnetting methods to estimate Chinook salmon Oncorhynchus tshawytscha escapement in the Nushagak River, Alaska. The sonar project uses dual-frequency identification sonars (DIDSONs) to count passing fish and drift gillnetting to apportion sonar estimates to species. These estimates are indices because the river’s width (∼300 m) and uneven bottom topography allow for only a third of the river to be sampled. This range is enough to fully enumerate sockeye salmon O. nerka, the dominate species, but not Chinook salmon, which are known to migrate beyond the sampling range. Acoustic telemetry was used to determine what proportion of Chinook salmon traveled within the sampling range of the sonar project. We inserted acoustic tags into Chinook salmon ∼13 km downriver and deployed an array of acoustic receivers at the sonar site to track tagged fish. From 2011 to 2014, 799 Chinook salmon were tagged. The tagged fish used the entire river width while migrating through the acoustic array exhibiting a wide variety of behaviors that included moving straight through the array, making multiple up and down trips, holding, and crossing over from one side of the river to the other. On average, 57% of tagged fish traveled through regions sampled by the sonar with annual percentages of 65% (2011), 54% (2012), 64% (2013), and of 47% (2014). These proportions were used to expand the sonar-derived indices to in-river abundance estimates.

Reliability of Fish Size Estimates Obtained From Multibeam Imaging Sonar

Abstract Multibeam imaging sonars have considerable potential for use in fisheries surveys because the video-like images are easy to interpret, and they contain information about fish size, shape, and swimming behavior, as well as characteristics of occupied habitats. We examined images obtained using a dual-frequency identification sonar (DIDSON) multibeam sonar for Atlantic sturgeon Acipenser oxyrinchus oxyrinchus, striped bass Morone saxatilis, white perch M. americana, and channel catfish Ictalurus punctatus of known size (20–141 cm) to determine the reliability of length estimates. For ranges up to 11 m, percent measurement error (sonar estimate – total length)/total length × 100 varied by species but was not related to the fish's range or aspect angle (orientation relative to the sonar beam). Least-square mean percent error was significantly different from 0.0 for Atlantic sturgeon (x̄ = −8.34, SE = 2.39) and white perch (x̄ = 14.48, SE = 3.99) but not striped bass (x̄ = 3.71, SE = 2.58) or channel catfish (x̄ = 3.97, SE = 5.16). Underestimating lengths of Atlantic sturgeon may be due to difficulty in detecting the snout or the longer dorsal lobe of the heterocercal tail. White perch was the smallest species tested, and it had the largest percent measurement errors (both positive and negative) and the lowest percentage of images classified as good or acceptable. Automated length estimates for the four species using Echoview software varied with position in the view-field. Estimates tended to be low at more extreme azimuthal angles (fish's angle off-axis within the view-field), but mean and maximum estimates were highly correlated with total length. Software estimates also were biased by fish images partially outside the view-field and when acoustic crosstalk occurred (when a fish perpendicular to the sonar and at relatively close range is detected in the side lobes of adjacent beams). These sources of bias are apparent when files are processed manually and can be filtered out when producing automated software estimates. Multibeam sonar estimates of fish size should be useful for research and management if these potential sources of bias and imprecision are addressed.

Influence of Different Factors on Abundance Estimates Obtained from Simultaneous Sonar and Echo Sounder Recordings

Use of horizontal guided sonar in addition to vertical echo sounder may improve biomass estimation of pelagic fish schooling near the surface. But proportions of horizontal guided sonar to vertical echo integration estimates have been shown to be very variable, and it is necessary to provide better knowledge on factors that influence acoustic recordings of fish near surface before a reliable method of combining sonar and echo integration estimates can be established. To explore factors that influence horizontal sonar recordings of fish biomass near surface, we collected and analysed data from two acoustic surveys on Norwegian spring-spawning herring (Clupea harengus L.) in the Norwegian Sea in 1997 and 1998, and two acoustic surveys off the southwest coast of Africa, investigating pilchard (Sardinops sagax), anchovy (Engraulis capensis) and round herring (Etrumeus whiteheadi) off the coast of Namibia in 1994, and sardinella (Sardinella sp.) off the coast of Angola in 1995. The ratios of fish densities obtained by sonar to those obtained by echo sounder varied both with respect to location and between different years within a specific location. For three of the four surveys, the biomass estimated by sonar was significantly higher than the estimates by echo sounder, whereas in the remaining survey there was no significant difference in estimated biomass. Periods of bad weather, shallow, or low- density patchy fish distributions and mixture of the target species with other species contributed to the higher and more variable sonar estimates. Still a goal should be to improve knowledge about the factors that contributes to variations between simultaneously recorded echo sounder and sonar data. An aim should be to combine the recordings from both methods in the biomass estimations, or at least assess which of the estimates that are less biased under the prevailing environmental conditions and actual school distribution.

Comparison of DIDSON sonar based estimates of Chinook salmon escapement with other methods in the Coweeman River, Washington.

The Coweeman River supports a small spawning population of Tule fall Chinook salmon (200–2000 adults), which are listed for protection under the US Endangered Species Act but harvested in mixed stock Pacific Ocean and mainstem Columbia River fisheries. The Coweeman Chinook stock has a low proportion of hatchery spawners and has been used as an index population for other less intensively monitored Tule populations. Over the last decade the Washington Department of Fish and Wildlife (WDFW) and partners have funded numerous studies to determine effective methods to accurately estimate Chinook salmon escapement for this population. From 2007 to 2009, a DIDSON sonar was operated below the major spawning area to estimate escapement. Concurrently, independent escapement estimates were made using more traditional methods such as mark‐recapture, red counts, and area‐under‐the curve surveys. Bayesian approaches to estimate salmon escapement for all methods will be presented, with an emphasis on the use of mixture models for sonar‐based estimates and a comparison of the sonar estimates with more traditional approaches.

A Novel Technique for Mapping Habitat in Navigable Streams Using Low‐cost Side Scan Sonar

An inexpensive and rapid technique for mapping instream habitat of navigable rivers is needed by natural resource professionals. Unlike more expensive side scan sonar devices, the Humminbird® Side Imaging system employs a boat‐mounted transducer enabling the survey of shallow, rocky streams. This device can be used to obtain high resolution, georeferenced images of underwater habitat. We developed a technique employing geographic information systems (GIS) to transform raw sonar images to fit the configuration of a stream channel. The end product is a GIS layer that can be interpreted to map instream habitat. We demonstrated this approach by mapping substrate and large woody debris in a southwest Georgia stream, and evaluated the technique through a comprehensive accuracy assessment. An overall classification accuracy of 77% was observed for substrate mapping and sonar estimates of large woody debris were correlated (r2 = 0.79) with actual wood abundance. Sonar mapping generated estimates of reach and substrate area comparable to a traditional field approach, and reduced the time investment by 90%. Applications for high resolution habitat maps are widespread and numerous; the ability to produce these maps at low cost is now within the grasp of researchers and managers alike.

The Use of Phased-Array Doppler Sonars near Shore

Phased-array Doppler sonars (PADS) have been used to probe an area several hundred meters on a side with 8-m spatial resolution, sampling every second or less with under 2 cm s 21 rms velocity error per sample. Estimates from two systems were combined to produce horizontal velocity vectors. Here, concerns specific to use of PADS in shallow water are addressed. In particular, the shallower the water is, the larger the fraction of bottom backscatter, so the stronger the bias is toward zero Doppler shift in the estimates. First, direct comparisons are made with other current measurements made during the multi-investigator field experiment ‘‘SandyDuck,’’ sponsored by the Office of Naval Research, which took place in the autumn of 1997 off the coast of Duck, North Carolina. The coherences between PADS and in situ current measurements are high, but the amplitude of the sonar response is generally low. To explore this further, a simplified model of wave shoaling is developed, permitting estimates of wave-frequency velocity variances from point measurements to be extrapolated over the whole field of view of PADS for comparison. The resulting time‐space movies of sonar response are consistent with quasi-steady acoustic backscatter intensity from the bottom competing with a variable backscatter level from the water volume. The latter may arise, for example, from intermittent injection of bubbles by breaking waves, producing patches of high or low acoustic response that advect with the mean flow. Once this competition is calibrated via the surface wave variance comparison, instantaneous measured total backscatter intensities can be compared with an estimated bottom backscatter level (which is updated on a longer timescale, appropriate to evolution of the water depth or bottom roughness) to provide corrected sonar estimates over the region.

Techniques for estimating sediment properties from chirp sonar data

The chirp sonar is a towed wideband FM reflection profiler developed to collect normal incidence reflection data suitable for sediment property inversions; the sonar also generates detailed reflection profiles of the seabed. The chirp sonar system transmits FM pulses with high time-bandwidth products to attain high pulse energy; consequently, the acoustic data have a high signal-to-ambient-noise ratio after correlation processing. The vertical resolution of the images is about 1 cm when transducer bandwidth is approximately 40 kHz. Data processing methods have been developed to automatically map the locations of sediment layer interfaces, and to estimate compressional wave attenuation, acoustic impedance, and compressional wave velocity of sediment layers using normal incidence FM reflection data. The height of sand ripples and the phase dispersion of compressional waves can also be measured from the acoustic imagery. Field data collected by other investigators during the High Frequency Acoustics DRI experiments off Fort Walton Beach were used to verify the acoustic property estimates. Comparisons show that chirp sonar estimates of acoustic properties agree with direct measurements of the properties based on in situ acoustic probe data and sediment core data collected by investigators from Naval Research Laboratory, Stennis Space Center, and APL, Washington State.

Status of Pacific Salmon and Steelhead Escapements in Southeastern Alaska

We evaluated the status of Pacific salmon and steelhead (Oncorhynchus mykiss) in southeastern Alaska. Of 9,296 spawning aggregates identified in this region, some data were available for 4,009 (43%), and 928 (10%) had sufficient information to analyze for escapement trend. Of those analyzed, 333 (36%) were increasing, 556 (60%) were stable, 37 (4%) were declining, and 2 (< 1%) showed precipitous declines. We evaluated risk of extinction of spawning aggregates using criteria similar to surveys outside Alaska. We rated 918 (99%) at no or low risk, 8 (∼ 1%) at moderate risk, and 2 (< 1%) at high risk. No spawning aggregates were identified as extinct based on our evaluation of escapement data dating back to 1960. Prior to 1960, two spawning aggregates, one sockeye salmon (0. nerka) and one chum salmon (0. keta), were identified as extinct based on responses to a postal questionnaire. The Alaska Department of Fish and Game grouped spawning aggregates into management units for each species. Management units vary in number and size for each species. Of 141 management units defined, 129 (92%) had enough information to evaluate; all had stable or increasing escapement trends. However, escapement data for this study had limitations for two reasons. First, monitoring spawning aggregates for escapement in all spawning locations in southeastern Alaska is impractical; interpretations are based instead on estimates of key indicator streams (usually commercially important runs) in the region. Second, most escapement estimates are based on aerial surveys rather than more accurate methods such as weirs or sonar estimates. Our results, based on the limited data, indicated that Pacific salmon in the region were generally in good health at two levels of salmon population structure: spawning aggregates and management units. The small amount of escapement data for steelhead precludes a generalization about their status and overall health.

Side-scan sonar estimates of the utilization of gray whale feeding grounds along Vancouver Island, Canada

Infaunal prey communities and gray whale feeding excavations were found at three sites along the west coast of Vancouver Island: Ahous Bay, Pachena Bay and Port San Juan. Side-scan sonar records indicated that whales disturbed up to 36% of the sea floor. The mean percentage of the bottom covered with feeding excavations was > 17% in each of the three feeding grounds. There was a positive relationship between the biomass of ampeliscid amphipod prey and the total quantity of prey consumed by gray whales from the three feeding grounds. There also was considerable annual variation in the size of feeding excavations, the total area covered by excavations, and the dispersion of excavations over the entire prey community during 3 years of observations at Pachena Bay. In general, two types of gray whale feeding records occurred in the Ampelisca tube mats. One record was composed of large complex excavations (mean > 20.5 m 2): the other contained only small features(mean < 4 m 2). Gray whales expanded the small feeding excavations into large, complex features by feeding along the edges of existing depressions. Edge feeding may increase the energy yield per dive as whales avoid low biomass areas inside existing excavations. It may also require less energy to lift the bottom by suction along the edge of an exposed tube mat. Gray whale feeding suspended over 1000 m 3 of sediment per day. Since sediment grain size was coarser inside feeding excavations (mean = 0.160 mm) compared to outside (mean = 0.124 mm), gray whales may help to maintain the mud poor fine sand habitat of its primary benthic prey, Ampelisca, by winnowing away finer sediments. Certain infaunal prey types (e.g. onuphid polychaetes) are less resilient to gray whale predation than others (e.g. Ampelisca) as a result of their local distribution patterns and life history.

Modeling a Variable Thickness Sea Ice Cover

A numerical framework suitable for simulating a variable thickness sea ice cover over a seasonal cycle is presented. This framework is largely based on the ice thickness distribution model developed by Thorndike et al. (1975). However, the numerical scheme is more general and certain additional developments are included. Namely, a fixed depth mixed-layer formulation including open water heat absorption and lateral melting terms is added, and a mechanical redistribution function consistent with hypothesized and observed physics of the ridging process is proposed. The numerical scheme is formulated in a fixed Eulerian grid and allows an arbitrary number of irregularly spaced thickness levels to be considered. Using this numerical framework in conjunction with a previously developed dynamical model (Hibler, 1979) and a thermodynamic model similar to that of Semtner (1975), a seasonal equilibrium simulation of the Arctic Basin ice cover is carried out. This simulation is performed by doing a 5-year numerical integration at 1-day time steps. Shorter sensitivity simulations are also carried out using the fourth year equilibrium simulation results as initial conditions. Input fields include mean monthly air temperatures and dew points for the heat budget computations together with time-varying observed winds over a 1-year period. The equilibrium simulation produces realistic geographical ice thickness variations with April ice thicknesses in excess of 7 m along the Canadian Archipelago and thicknesses of ∼2 m along the Alaskan North Slope. These spatial variations are in good agreement with submarine sonar estimates. In summer a substantial ice-free region forms off the Alaskan and Siberian coasts. While the geographical shape of this edge is in agreement with observations, the amounts of open water (750 km off the Alaskan North Slope in mid August) were excessive. However, only a small (10%) change in the ice albedo under melting conditions yields a much more realistic ice edge in a sensitivity simulation. Geographical changes in the ice thickness characteristics took about 3 years to fully develop. This evolution included the formation of a “shear zone” of higher annual ridge production ∼400 km off the Canadian Archipelago in agreement with ice roughness observations. Simulated mass balance characteristics are significantly affected by ice deformation and ridging. Over 40% of the basin-averaged ice production for January is due to growth over thin ice (<1 m) largely produced by deformation. Over an annual cycle an equivalent thickness of more than 0.5 m of ice is transferred by ridging to categories thicker than 5.17 m. Spatial variations in ridging and open water creation cause a net annual ice ablation of over 1 m of ice off the Canadian Archipelago concomitant with a net annual growth of over 1.8 m off the Alaskan coast. Ice velocity fields were realistic in shape but ∼25% too large in magnitude when compared to net ice station drift over a year. This velocity discrepancy is probably due to rather small central basin ice strengths (∼1.5×104 N m−1 in January). However, increasing the frictional losses assumed in the ridging process by an order of magnitude yields unrealistically small ice velocities in a sensitivity study and results in an almost total stoppage of ice flow in April and May. The sensitivity simulation also has a reduced average annual ice export rate of ∼0.04 Sv as compared to ∼0.09 Sv for the equilibrium simulation.

"Gestation sac" volumes as determined by sonar in the first trimester of pregnancy.

Sonar estimates of "gestation sac" volumes in the first trimester of pregnancy were made from a series of 319 measurements; the volumes estimated included the amniotic fluid, the extraembryonic coelom and the fetus. The technique employed involved the use of parallel section scans taken in series from one end of the gestation sac to the other, followed by planimetric measurements of the sac areas so produced. The potential errors which may be incurred in these measurements are discussed, and it is considered that the technique carries an overall possible error in the order of plus or minus 10 per cent. Growth curves produced from the measurements in this series show that the sac increases in volume from a mean of 1 ml. at 6 weeks to a mean of 100 ml. at 13 weeks, initially in an exponential fashion but latterly in a more linear manner. The mean values of the sonar gestation sac fluid volumes (after subtraction of the estimated fetal volume) in the 10 to 13 week range, show good correlation with those amniotic fluid values reported in the literature where direct measurements were made at the time of hysterotomy. As a method of assessing the maturity of a pregnancy this technique is of lesser value than the sonar measurement of fetal crown-rump length because of the relatively wider scatter of results. It has, however, found a useful place in clinical practice in the early sonar diagnosis of blighted ova or anembryonic pregnancies.