Comparison of New Software for Rapid, Automated Processing of Hydroacoustic Data for Fisheries Related Applications fisheries related applications

E. Munday, B. Moore, J. Dawson, M. Burger – BioSonics, Inc., Seattle WA, USA

Abstract  A new processing utility added to BioSonics Visual Acquisition (VisAcq) software was evaluated to determine its relative efficiency and accuracy as a means to rapidly process hydroacoustic data.  VisAcq’s Trace Formation (AutoTrack) capability represents a potential paradigm shift in the conventional methods for obtaining fish counts, density and distributional information from hydroacoustic fisheries data sets.  Conventional methods involve two primary tasks; data collection and data processing.  VisAcq AutoTrack processes during data collection by detecting, classifying and accepting or rejecting echo returns based on user-selected parameters.  Fish tracks or traces are automatically formed in near-real time from the accepted echoes and logged or displayed.  The new software calculates sample volume, based on distance traveled, range, and beam angle, thus allowing for automated fish density measurements.  A hydroacoustic data set collected in Lake Washington, Seattle was processed to determine fish density by depth strata, horizontal and vertical distribution, and total count.  Data were processed in real time using VisAcq AutoTrack and post-processed using three other commercially available and widely-used programs. The analysis results across the four different software applications demonstrated that VisAcq Autotrack provides provisional information as accurate as data provided by the other software while eliminating nearly all post processing effort.

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Specialized Tools for Biological Assessment Using Split Beam Hydroacoustics

Eric Munday, Tim Acker, James Dawson




Split beam echosounders are a standard instrument of scientific fisheries acoustics.  To augment the information gained from mobile hydroacoustic surveys, researchers have developed innovative methods, devices, and platforms to deploy split beam echosounders in new environments.   This article describes three recent inventions that facilitate the use of split beam echosounders in non-conventional applications; a hybrid split beam and imaging sonar system for defense related applications, an autonomous, submersible echosounder for long-term seafloor observation, and a towed echosounder engineered for use with a Liquid Robotics Wave Glider.

  2. Project Overview

Split beam echosounders detect, locate, and measure targets at relatively long-ranges (+500m) and are largely unaffected by turbidity or light. Imaging sonars provide high resolution data for visual verification of targets, but are more range-limited and affected by water conditions than split beam.  BioSonics, Inc. and Teledyne BlueView, Inc. developed a prototype system integrating split beam and imaging sonar to combine long-range detection with visual ground truthing capabilities.

Active sonar systems for security applications are designed to detect and classify specific targets. Performance can be diminished due to nuisance alarms caused by non-threatening targets (debris, aquatic vegetation and marine mammals) that reflect acoustic energy in a similar way when compared to an intruder. An experiment was conducted to identify the acoustic signatures that could potentially cause nuisance alarms. Information gained will aid in the development of data filtering and target classification algorithms to minimize the Nuisance Alarm Rate (NAR) for active sonar systems used in security applications.

  1. Experimental Design/Installation

A BlueView P900-130-D multibeam sonar and a BioSonics DT-X split beam echosounder were deployed as an integrated system that operated continuously for 3-weeks. The two systems were aimed at an overlapping 7 sq. m study region that varied in depth from 1-4 m.

Each sonar head was mounted on a dual-axis rotator, precisely installed to insure coverage of the vertical extent of the study region during all tidal cycles. Alignment of the sonar beams was verified using a point-source reflector carried by tethered scuba divers.

Figure 1 shows the study region and installation points and aiming geometry of the two sonars. A bin detection range of 60 to 68 m was programmed into the BioSonics sonar to insure that target detections inside the study region were the only ones to trigger an alert.

  1. Control Unit Description

Both sonar systems were controlled by a BioSonics Automated Monitoring System Control Unit (AMSCU) (Figure 2), a rack-mount electronics package consisting of a heavy-duty computer, uninterruptible power supply (UPS), broadband firewall/router, and a remote power management system (RPMS) all contained in an environmental controlled enclosure (Purcell RAC 48). BioSonics System Watchdog software monitored the system status and sent daily reports via cellular internet that included a record of power outages, sonar aim, operational status, and all alert activities. The cellular communication system also allowed for remote control of each sonar system.

  1. Data Collection and Analysis

All sonar data were time stamped by the system clock and logged to RAID storage in daily directory file folders.


The BioSonics system is automated to alert when a target of sufficient signal strength enters the detection area and persists for a specified amount of time The BioSonics AMSCU is programmed to trigger an alert when echoes exceed an intensity threshold for a consecutive number of pings at a particular range. Upon alert, the system changes its indicator status from “Green” to “Red” and the information (time, 3D location, speed, and direction of travel) about the echoes that generated the alert are recorded in a track list. The software automatically copies a section of data extending from 10 seconds before the alert to 10 seconds after. The time stamp from this section of raw data is used to make a video clip from the corresponding imaging sonar data. These video clips provide a means to verify the cause of the alerts.

  2. Project Overview

Variability in fish and other biological organism distribution and abundance has been documented as a function of short-term behavioral variation. This variation may be due to predation avoidance, migration between resting and feeding areas, feeding, territorial or spawning activities, or response to environmental changes. These highly-variable biological activities are important to understand for siting and operation of tidal energy generation facilities.

A better understanding of biological distribution and behavior can be obtained through measurements from fixed locations over a period of weeks or months. This type of fixed-station hydroacoustic monitoring typically involves the collection and analysis of water column backscatter data utilizing an upward or side-looking echosounder recording data to a shore-based control station.

Data transmission and configuration of conventional split beam echosounders is accomplished via a continuous communication link (typically Ethernet) with a computer running specialized data acquisition software. Installation of a communication tether cable to the surface can be impractical or impossible in deep water, remote, and offshore projects. Therefore, fixed-station deployments of split beam echosounders in these conditions have been quite rare or previously not possible. Recent invention of a programmable, autonomous, split beam system (BioSonics DT-X SUB) allows for untethered deployments and long-term data collection in remote or deep-water environments. This submersible echosounder system is capable of collecting and recording split beam data over an extended period of time with no surface tether required.

University of Washington and the Northwest National Marine Renewable Energy Center (NNMERC) working with BioSonics, successfully deployed a DT-X SUB echosounder in Admiralty Inlet, Puget Sound for 5-weeks. The study location is a proposed Snohomish Public Utility District tidal energy demonstration project site. Information gained is useful to project developers in assessing the relative suitability of locations for long-term hydrokinetic facility deployments.

  1. Deployment Methods

The DT-X SUB was deployed as part of an array of battery-powered monitoring sensors affixed to a seafloor observatory platform. The system was autonomous and required no surface tether. Echosounder configuration and duty cycle were programmed at the surface. The echosounder operated at a 10% duty cycle, alternating between active pinging and sleep modes, to maximize temporal coverage and battery life. An integrated orientation sensor recorded the aiming angle of the transducer for accurate water column volume and fish target angle calculations.  The system was retrieved using acoustic releases and the data files were processed for fish abundance, distribution, and behavior information. The DT-X SUB system components were as follows:

  • PREVCO A811SS TB pressure housing containing a DT-X split beam echosounder
  • A 200 kHz split beam transducer with internal orientation sensor
  • Electronics and specialized software for automated operation, data handling/storage, and shutdown/restart capabilities
  • Four 80 AH, 24v deep-cycle batteries. manufactured by Deep Sea Power and Light
  • A Sea Spider tripod mount
  1. Results from DT-X SUB Deployement

Processed data verified the expected density distributions across time and space.  Overall, NNMREC concluded that is possible to adapt existing acoustic instrumentation for autonomous deployments in high-flow environments.  However, it was also noted that while data storage capacity is not an issue, limited power availability restricts sampling density and therefore it is important to ensure that power supplies meet sample design requirements.  Researchers also concluded that more pre-deployment testing to optimize echosounder data collection parameter settings would have improved data quality.

  2. Concept Origin and Overview

Rising costs of ship time have reduced ship-borne fisheries survey efforts and compromised their value to fisheries managers.  Autonomous vehicles now carry split beam sonar systems to collect data at a reduced cost and in environments not before possible. A hybrid machine, conceived by Dr. Charles Greene of Cornell University, was co-developed by Liquid Robotics Inc. (LRI) and BioSonics, Inc. The device combines an LRI Wave Glider with a BioSonics DT-X SUB  echosounder housed in missile-shaped towed vehicle attached to the submerged glider unit with a compliant tow cable. This “Fisheries Glider” requires fewer man hours than typical shipboard acoustic surveys, uses no fuel, and thereby operates at a reduced cost.

  1. System Description

The Wave Glider is a vehicle comprised of a submerged glider tethered to a surface float. The vehicle is propelled by the conversion of wave energy into forward thrust. The Wave Glider maintains an average forward speed of about 1m/s (1.5 knots) in seas with 0.5m – 1m wave height. The system uses solar panels and 650 Watt hours of battery capacity to power on board sensors and payloads. The Wave Glider can withstand open-ocean waves and strong winds and is proven capable of trans-oceanic missions.

The DT-X SUB is a programmable split beam echosounder in a submersible housing engineered for deployments where a cable to the surface is not practical. The DT-X SUB can be configured with a range of transducer frequencies for detection of objects ranging in size from zooplankton to marine mammals. The echosounder can provide information including: bathymetry, substrate classification, fish sizing and abundance, and the distribution and location of aquatic plants and or ocean mixing layers.  Data are logged internally and downloaded upon recovery of the vehicle. Real-time data summaries are transmitted via satellite connection during  deployment. The echosounder can be operated continuously for approximately 10 hours between battery recharging from the Wave Glider solar panels.

Researchers use LRIs Wave Glider Management System (WGMS) to monitor and control the vehicle via the Iridium satellite network from any Internet connection. WGMS provides the ability to turn payloads on and off, navigate to desired locations, and monitor vehicle status.

  1. Test Description

Liquid Robotics conducted a series of tests in Kealakekua Bay, Hawaii to evaluate the ability of the system to detect and observe the migration of the mesopelagic boundary community.  The system tested included a Wave Glider and towed echosounder with 70kHz and 200kHz transducers. The Wave Glider was equipped with a custom umbilical cable and payload box to provide power and communications capabilities to the echosounder towed body. The Wave Glider was programmed to collect data in an operational test area of 1 nautical mile x 100 m.  The speed through water of the Wave Glider pulling the tow body during this test was approximately 1.2 knots in a moderate sea state. The operations lasted two nights to test and validate the system’s ability to collect stable, high-quality acoustic data.

  1. Results

The system proved to be an effective platform for collecting acoustic data and studying patterns in the distribution and migration of marine organisms. Biological backscatter was clearly detected by the echo sounder at ranges in excess of 100m and observed to vertically ascend over time.  Significant biological backscatter was visible along the ocean bottom at a depth of 70 to 90 m, as well as a likely aggregation of fish at approximately 30 to 50 m.

The compliant cable provided mechanical isolation from the surging motion of the Wave Glider propulsion system and allowed the towed body to maintain a stable horizontal orientation suitable for the collection of high-quality hydroacoustic data. The towed body contained an orientation sensor logging positional data approximately 9 times per second.  The pitch of the tow body typically stayed within a range of +/- 7 degrees and roll within +/- 2 degrees.

The Wave Glider effectively propelled the echosounder towed body while maintaining an averaged 90% of the velocity of a nearby, un-encumbered Wave Glider.

The testing demonstrated that acoustic data collected from the “Fisheries Glider” are suitable for quantitative analysis. Overall, the system proved suitable and highly efficient for observing aquatic organisms in the water column over extended periods of time.

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Evaluation of a New Hydroacoustic Substrate Classification System for Oyster Reef Mapping in Galveston Bay, Texas

W. Rodney, Texas Parks and Wildlife Department, Galveston, TX, USAE. Munday, BioSonics, Inc., Seattle WA, USA


Abstract  A new hydroacoustic processing software (BioSonics Visual Habitat) for the rapid assessment and mapping of various substrate types (sand, cobble, mud, etc.) was recently evaluated  using data collected by researchers at Texas Parks and Wildlife Department (TPWD) as a means to quantify and map oyster reefs.  Understanding the distribution of oyster reef habitats is vital in guiding restoration and management efforts.  Obtaining quantifiable data on oyster reef resources is important in establishing a baseline for future surveys and developing an index for monitoring temporal changes.  The study area is a 5.7 sq km rectangular grid of 10 transects spaced 200 m apart.  Hydroacoustic data collected from the study area were processed and the results were plotted over side scan sonar imagery.  Visual Habitat was compared with two previously existing processing tools; QTC Impact, BioSonics VBT, and a TPWD proprietary SAS method.   The results from Visual Habitat showed a high agreement with prior results and resulted in a significant reduction in effort as compared to processing with other software.  In addition to the significant reduction in effort, Visual Habitat provided data visualization tools in the form of a transect map view displaying user-defined color gradients for each data layer. Visual Habitat also provides the ability to export results in KML file format for rapid interpretation via Google Earth.

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BioSonics Introduces Automated Monitoring Systems for 316(b) Compliance

Is Your Company Ready for 316b?

BioSonics provides cost-effective monitoring solutions for 316(b) entrainment and impingement monitoring at cooling-water intake structures.

Thousands of industrial facilities use large volumes of cooling water from lakes, rivers, or oceans to cool their plants.  Cooling water intake structures pull large numbers of fish and shellfish into a cooling system where the organisms may be killed or injured by heat, stress, or chemicals. Larger organisms may be killed or injured when they are trapped against screens at the front of an intake structure.

Section 316(b) of the Clean Water Act requires EPA to issue regulations on the design and operation of intake structures, in order to minimize adverse environmental impacts.  After many years of litigation and delays, the final 316b rule is expected to be released this summer or early fall.  The Final 316b rule will include regulations for operation of facilities such as:

  • Electric generating plants

  • Pulp and paper mills

  • Chemical manufacturing plants

  • Iron and steel manufacturing plants

  • Petroleum refineries

Download BioSonics 316b Compliance Info Sheet

BioSonics offers state-of-the-art hydroacoustic monitoring systems for 316b and related applications.  Read more here and contact us for more information.

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YOU’RE INVITED  – BioSonics Webinar – Automated Monitoring Systems and Software

You are cordially invited to attend an informative two-part webinar series.  The first session will focus on real-world applications of split beam sonar as used in fixed-station monitoring systems.  The second webinar will focus on the latest in automated processing software for fixed position hydroacoustic deployments.  You are encouraged to register for both sessions, or choose either one.

PART I.  BioSonics Automated Fish Detection/Counting Systems

When: Tuesday, June 10, at 0800h PST (1600h GMT)

Description:  An overview of split beam sonar technology and unique watchdog software specifically applied for use in fixed-station applications.  Learn about the state-of –the-art in unmanned, automated hydroacoustic technology.  Case studies will include:

  • Riverine salmon counting stations
  • Smart hydropower dam
  • Debris monitoring system for cooling water intake

PART II.  Real-Time Automated Target Counting w/VisAcq AutoTrack

When: Thursday June 12, at 0800h PDT (1600h GMT)

Description: Tutorial on how to configure VisAcq AutoTrack software, a real-time processing tool that automatically builds and records fish/target track lists.   Receive step-by-step instructions for using VisAcq AutoTrack to generate CSV files containing information on each fish/target detected including:

  • 3D location (depth, range and bearing)
  • Speed and direction of travel
  • Sizing distribution
  • Total counts

Register by email and receive your meeting invitation and access code. – indicate whether you’d like to join PART I or PART II

Please note that attendance is limited and will be available on first come basis.   We look forward to hearing from you and sharing information about the latest in Hydroacoustic Automated Monitoring Systems and Software.

We hope you can join us on June 10 and or June 12.

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Visual Habitat – NEW Version Now Available!


A new version of Visual Habitat v1.0.6 is now available for download on our website!

If you are not yet a Visual Habitat user Request a Demo Today!

Download the new version for free today! Click on the button:

visHab Button

For more information please contact us!



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VisAcq AutoTrack is Here!


Try VisAcq AutoTrack on your next survey.


BioSonics VisAcq Autotrack Brochure_Page_1

With VisAcq AutoTrack you can automatically:

  • Build fish track lists
  • Calculate fish density by depth strata
  • Measure fish distribution over distance/time
  • Determine fish sizing (TS) distribution

Watch the BioSonics VisAcq AutoTrack Tutorial!

Software Features:

VisAcq AutoTrackAnalysis software for fisheries hydroacoustic data

  • Results are immediately available as CSV files
  • Automatically create echo lists, track lists, and summary reports
  • Reprocessing utility for archived data – Analyzes multiple files in just minutes
  • Compatible with any DT4 files

BioSonics VisAcq Autotrack Brochure_Page_2

Please contact us directly with any questions. We look forward to hearing from you.




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