Methods in Oceanography: Perspective

Methods in Oceanography 1–2 (2012) 49–77
Contents lists available at SciVerse ScienceDirect
Methods in Oceanography
journal homepage: www.elsevier.com/locate/mio
Full length article
30 years of advances in active bioacoustics: A personal

perspective
Timothy K. Stanton ∗
Woods Hole Oceanographic Institution, Woods Hole, MA 02543-1053, United States
article info abstract

Article history: The area of active bioacoustics involves the use of sound to study
Received 16 March 2012 distributions of fish and zooplankton in aquatic environments.
Received in revised form There have been significant advances in this area over the past
25 May 2012
30 years, covering many categories, spanning technology and
Accepted 14 July 2012
Available online 1 September 2012
modeling. These advances, as witnessed throughout my career, are
reviewed. Issues with past and current approaches are discussed as
well as projections into the future.
© 2012 Published by Elsevier B.V.
1. Introduction
The principles of operation of an acoustic echosounder have remained the same since its invention
in the early 1900s (Fig. 1). A burst of sound is transmitted into the water through a combination of a
power amplifier and electromechanical transducer. The sound travels through the water and scatters
off of various heterogeneities in the water, such as fish and zooplankton. The portion of the sound
scattered back to the transducer, the ‘‘echo’’, is then converted back into voltage and recorded for
analysis.
Use of such a system to study marine organisms in their aquatic environment is generally referred
to as ‘‘active bioacoustics’’ where ‘‘active’’ refers to the fact that the system transmits an acoustic signal
into the water. Analysis includes interpreting the echo in terms of meaningful biological quantities
such as length, numerical density, and species of the organisms. This is in contrast to the area of
‘‘passive bioacoustics’’ which involves a system that does not transmit an acoustic signal into the water
and is used strictly to listen to sounds created by the organisms.
Acoustics is used to study marine organisms because sound can travel such great distances
(depending upon the frequency, tens and hundreds of meters to many kilometers). Thus, synoptic
information concerning marine organisms can be obtained rapidly with acoustics. This is in contrast
∗ Tel.: +1 508 289 2757; fax: +1 508 457 2194.

E-mail address: tstanton@whoi.edu.
2211-1220/$ – see front matter © 2012 Published by Elsevier B.V.

doi:10.1016/j.mio.2012.07.002
50 T.K. Stanton / Methods in Oceanography 1–2 (2012) 49–77
Fig. 1. Cartoon sketch of single beam echosounder, beampattern (exaggerated width), and echo voltage.
Source: From Clay (1983).
Fig. 2. Gray-scale paper chart recording of data collected in 1981 at Trout Lake, Wisconsin, by Lars Rudstam, a former student of
Clarence Clay, using a portable, battery-powered, 70 kHz Simrad EYM echosounder deployed from a small boat. The data were
also stored on an analog tape recorder and processed by Rudstam and Stanton in separate studies using the Powell/Stanton
prototype digital echo processor. Those analyses are reviewed in Stanton and Clay (1986).
to the use of nets which are considered ‘‘point’’ samples. The challenge lies in interpreting the
acoustic data in terms of biologically meaningful parameters. There is a wide range of technologies
and interpretation methods that have been developed to aid in the use of sound to study marine
organisms. Because of the many uncertainties associated with acoustic methods, acoustic sampling
generally needs to be conducted in concert with direct sampling methods such as nets. In essence, the
acoustic data can spatially ‘‘connect’’ samples collected with the nets.
The technologies and interpretation methods associated with echosounders have advanced
significantly since I entered this field in 1980 (Table 1). At that time, all systems contained analog
electronics and were noisy, deployment modes were generally limited to the ship’s hull or a towbody,
narrowband gated sine waves (single frequency) were used in combination with a single beam
transducer, real-time displays were limited to gray-scale paper charts (Fig. 2), data were recorded on
analog tape recorders, and the echo data were interpreted using simplistic models (either a regression
equation or an oversimplified analytical model).
Today (c. 2012), systems are digital all the way down to near the transducer which significantly
reduces noise and increases dynamic range, there are various deployment modes available including
autonomous underwater vehicles (AUVs) and fixed stations for long-term observations, multiple
frequencies and multi-beams (including split-beam) are available, narrowband and broadband linear
frequency modulated signals (chirps) are used, calibrated data are displayed in real time in color on
a computer monitor, data are recorded digitally on various forms of computer-based storage media
T.K. Stanton / Methods in Oceanography 1–2 (2012) 49–77 51
Table 1
Direct path echosounders. Characteristics and qualities, past and present.
1980 2012
Sonar hardware Analog Digital

Single beam Single-, split-, multi-beam
Single frequency Single- and multi-frequency, broadband
Gated sine wave transmit signal Gated sine wave and linear frequency
(narrowband) modulated
Issues: noisy, limited dynamic range,
limitations in interpretation
from single beam at single
frequency
Modality of operation Ship-based (hull-mounted or Ship-based (hull-mounted or towbody)

towbody)
Cable- or battery-powered (fixed
observatory or AUV)
Short-term deployment Short-or long-term deployment
Human controlled Human controlled or autonomous
Issues: only used for short-term
(days/weeks) deployments
Post-processing and software Hard-wired processor Programmable processor

Mostly researcher-derived software Mostly commercial software
Display (real-time) and data storage Paper display (black and white, Computer monitor display (color,
uncalibrated) calibrated)
Analog tape recorder (serial access) Digital, computer-based storage
medium (random access)
Echo counting Single beam output—various Split-beam output—direct approach
statistical approaches
Echo integration Single beam output Single beam output
Scattering models-fish Resonance frequency (physics-based) Resonance frequency (physics-based)

High frequency (regression-based) High frequency (regression- and
physics-based)
Scattering models-zooplankton Regression-based or physics-based Physics-based models specific to
sphere model boundary conditions and shape
(for later advanced processing, display, and analysis), and interpretation methods involve a range of
sophisticated models grounded in data specific to the species.
In this paper, I review the advances that I have witnessed (and, in some cases, contributed to) in my
career in active bioacoustics. The focus will be on active systems involving the ‘‘direct path’’ scattering
geometry which involves a system looking directly beneath (or nearly so) the ship and has also been
the principal focus of the field. However, there will be some discussion on long-range systems that
look horizontally, but remain principally in development. I also present my perspective on various
qualitative aspects of the field including the current issues, where the field might be in 20 years, and
what some of the ultimate limitations of the field are. Thus, this paper will span roughly 50 years of
the past, present, and projected future. Because of the large span of material, coverage of each topic is
necessarily brief and incomplete. Details can be obtained from references given below, including the
monographs by Medwin (2005), Medwin and Clay (1998), and Simmonds and MacLennan (2005).
Inline Supplementary Video 1 can be found online at http://dx.doi.org/10.1016/j.mio.2012.07.002.
2. A bit about myself
I was trained in both theoretical and experimental physics. My first papers from my research in
graduate school (Physics) at Brown University involved laboratory measurements (Stanton and Beyer,
1978) and instrumentation development (Stanton and Beyer, 1979) in underwater acoustics. From
1978 to 1980, I was at the Submarine Signal Division of Raytheon Company where I designed and
ocean-tested advanced multi-beam sonar systems. I then went to the University of Wisconsin in 1980
where I began a long and productive relationship with Clarence S. Clay in bioacoustics. In addition to
our scientific interactions, we also downhill skied and played music together (he on euphonium and
I on piano or trombone). From 1988 to the present, I have continued my bioacoustics research at the
Woods Hole Oceanographic Institution.
From my start in this field in 1980 to the present, I have always been intrigued by the use
of sound as a remote sensing tool to infer important characteristics of marine organisms. It is an
incredible challenge to begin with a recording of echo voltage versus time and convert that data
into biological parameters. It has also been very rewarding to develop a new approach, whether it
is theoretical or experimental, to extract new information from the signal or to improve on existing
methods.
Overall, my career in bioacoustics has involved a combination of theoretical modeling, labora-
tory experimentation, instrumentation development, and at-sea experiments. My first paper in
bioacoustics involved a numerical study of errors in echo integration due to transducer motion
(Stanton, 1982). I believe that my modeling of scattering by marine organisms, which began in the
paper Stanton (1988) concerning modeling elongated zooplankton as a finite-length cylinder and is
summarized in Stanton and Chu (2000) and Stanton (2009), has made the most impact to date. Key
papers in the development were the deformed finite cylinder model (Stanton, 1989a) which has been
used in modeling scattering by fish and elongated zooplankton, application of the distorted wave
Born approximation (DWBA) to fluid-like zooplankton such as euphausiids (Chu et al., 1993; Stanton
et al., 1993, 1998), and the observations (and associated modeling) of the importance of grouping
zooplankton into gross anatomical groups according to their different material properties (Stanton
et al., 1994; Wiebe et al., 1996; Lavery et al., 2007).
The modeling was inspired and grounded to a large extent by my laboratory experiments
of scattering by marine organisms. These experiments helped to identify dominant scattering
mechanisms of the organisms whose shapes and material property profiles were complex which, in
turn, served as a basis for the modeling. An important element of the laboratory experiments was
the use of broadband sound which led to an important ‘‘by-product’’ of broadband signal processing
methods for use in bioacoustics. These methods are first described in detail in the laboratory
measurement paper by Chu and Stanton (1998). Later key papers in this area involved new calibration
methods of broadband systems (Stanton and Chu, 2008) and a new broadband ocean instrument for
resonance classification of fish (Stanton et al., 2010, 2012).
Another key element of the research involved echo statistics, since the scattering is inherently
stochastic. This led to a series of papers in the 1980s which describes the echo statistics concerning
both the seafloor and marine organisms (see the review in Stanton and Clay, 1986). Key results
in those studies involved estimating numerical density of marine organisms and roughness of the
seafloor from the shape parameters of the echo amplitude probability density function (PDF). Papers
were also written on echo statistics, using similar formulations, concerning the sea surface (Stanton,
1985a) and sea ice (Stanton et al., 1986). Echo statistics were ingrained in many later papers, such as
concerning the randomly rough elastic cylinder (Stanton and Chu, 1992), randomly rough deformed
finite fluid cylinder in application to zooplankton (Stanton et al., 1998), randomly oriented marine
organisms (Stanton et al., 2004) and became a major area of focus very recently in modeling echo
statistics concerning multiple scatterers or patches of scatterers in the sonar beam (Stanton and Chu,
2010; Chu and Stanton, 2010).
Last, but not least, my work could not have been possible without the inspiration and guidance of
Clarence (‘‘Clay’’) Clay and Van Holliday as well as the collaboration with many, as documented by the
many co-authors on my papers, especially Dezhang Chu (Fig. 3).
3. Some definitions
There are two principal quantities that are analyzed in active bioacoustics: target strength, TS, and
volume backscattering strength, Sv . The target strength describes the efficiency with which a single
Fig. 3. Photo of scientific party in the ocean bioacoustic experiment, Echofront85, in the summer of 1985. The cruise, which took
place about 100 miles offshore at the Gulf-Stream boundary, had just been completed and had returned to the Duke University
Marine Laboratory. The cruise involved a combination of the Holliday/Pieper 21-frequency system, the Clay/Stanton/Jech
multiple frequency system (several independent single-frequency systems connected together), and the Powell/Stanton real-
time sonar echo processor. Also, on this cruise Stanton conducted his first laboratory experiment of acoustic scattering by
freshly caught organisms involving various fish and zooplankton species (including euphausiids, siphonophores, pterapods,
mychtophid, and hatchet fish). The laboratory experiment involved a 5-foot-diameter tank filled with water on-board the ship,
with laboratory pulse-echo equipment. Although that work was never published, it inspired the laboratory experiments started
later by Stanton at the Woods Hole Oceanographic Institution. Front row, L-R: Steve Brandt, U, John Magnuson, U, U. Middle
row, L-R: Tim Stanton (striped shirt), Paul Jacobson, Van Holliday (with sunglasses), Bob Eastwood, Clarence Clay, U, U, Gary
Hitchcock. Back row, L-R: Mike Jech (with sunglasses, his head is shown between Jacobson and Holliday), U, Richard Nash
(standing just to the right of the pole), Ben Abernathy (blocking Rick Pieper’s right shoulder), Rick Pieper (no shirt), U, U, U.
U = unidentified. Photo provided by Mike Jech.
object scatters sound and is given on a logarithmic scale. It is defined in terms of the backscattering
amplitude fbs and differential backscattering cross section as
TS = 10 log |fbs |2
= 10 log σbs (1)
where σbs = |fbs | . The units of fbs and TS are m and dB, respectively. The backscattering amplitude is
2
expressed in terms of the backscattered pressure, ps , measured at the echosounder transducer as
eikr
ps = P0 fbs (2)
r
where P0 is the√pressure of the incident field at the scatterer, r is the range from the echosounder to the
scatterer, i = −1, and k is the acoustic wavenumber (=2π /λ where λ is the acoustic wavelength).
Interestingly, although these are definitions of fundamental quantities, there has been confusion
and associated errors in this field. The definition of backscattering cross section sometimes comes with
a factor of 4π (MacLennan et al., 2002). Once defined in the context of TS in Eq. (1), there is no problem.
However, there have been errors in the literature of 11 dB (=10 log 4π ; i.e., a factor of 12.6 error) in
biomass estimates when the 4π is not correctly accounted for. For example, if the backscattering cross
section is defined with a factor of 4π and then the 4π is not subsequently removed in the TS − σbs
definition, then the error of 10 log 4π will occur.
The volume backscattering strength is the target strength per unit volume (one cubic meter) of
scatterers averaged (before the logarithm is taken) over an ensemble of statistically independent
pings. For a collection of scatterers with a numerical density nij and average backscattering cross
(ij)
section σ bs of each ith size class and jth taxon, the volume backscattering strength, in dB, is
(ij)

Sv = 10 log nij σ bs . (3)
i,j
The terms TS and Sv are determined from data through use of the sonar equation (Urick, 1983)
where geometrical spreading and system parameters such as source level and receiver sensitivity
are accounted for. TS is derived from echo envelope data and Sv is determined from echo integration.
Echo integration involves calculating the echo energy in a range bin (typically 1 m or less) by squaring
the echo voltage and accumulating the sum of those squared values throughout the bin. The statistics
of TS and Sv are normally analyzed—principally the mean values (averaged before the logarithms are
taken), but also the statistical distribution of the values (both before and after the logarithms are
taken). Sometimes the volume backscattering strength is integrated over a range of depths (on a linear
scale before the logarithm is taken) to calculate the area backscattering strength.
4. Hardware—electronics
Electronics in this field has experienced a profound change as systems that were originally 100%
analog have evolved, through the revolution in digital electronics, to being mostly digital.
4.1. 1980
Although digital electronics were making their way into various hardware systems in the 1980s,
many systems, including echosounders, were initially all analog. Most settings were ‘‘hardwired’’
(i.e., fixed) with the only options to change settings, such as time varying gain and master gain,
being available through several analog knobs on the front panel. Thus, the systems had relatively little
flexibility in use. Also, the signals in cables connecting the transmitter/receiver electronics with the
transducer were also analog. Because of this, there were significant issues concerning noise in the
cable. The analog cables behaved electrically like an antenna, picking up electromagnetic interference
which contaminated the sonar echoes, hence limiting the detection range. This was particularly an
issue with towed systems that required long cables. Because of these many limitations, there were
many digital systems in the developmental stage in the early 1980s as discussed later (Fig. 4).
4.2. 2012
Now, the systems are fully digital except where analog circuitry is required (such as analog
preamps at the transducer). The electronics contain DSP’s (digital signal processor) which makes them
extremely flexible and compact. In essence, the electronics are programmable and software-based,
which allows users to change settings via computer control. In addition, signals traveling along cables
between the transducer and electronics can be digital, which greatly reduces noise issues, especially
for long cables.
5. Hardware—systems and signals
Echosounder hardware and associated signals have evolved from use of one single beam transducer
emitting a single frequency, gated sine wave signal, to split- or multi-beam systems spanning multiple
frequencies. In some developments, broadband signals are used along with pulse-compression
processing.
Fig. 4. Prototype digital sonar echo processor (Powell and Stanton, 1983). (a) 1981 Apple-II+ personal computer (left)
integrated with processor (right). Two floppy disk drives are shown. With two, data could be recorded continuously—when
one disk filled up, the system automatically began writing to the other disk while the first disk was replaced with a blank
one. (b) Echo processor. The analog board contained a low-noise preamplifier with a gain switchable via manual dual-in-line
(DIP) switches as well as an analog-to-digital converter (ADC). The solid state components on the digital board performed
basic operations such as add, shift, and multiply. The digital board fed into a computer interface board (not shown) which we
designed and built and was, in turn, controlled by assembly language routines which we wrote. We also wrote our own disk
operating system to greatly reduce the time it took to save data files onto the disks (60 ms vs. 3 s). These photos were taken by
a University of Wisconsin photographer and are appearing for the first time in this paper.
5.1. 1980
Echosounders consisted of a transducer which served as both a transmitter and receiver and
produced a single (transmit/receive) beam at a single frequency (Fig. 1). The transducer may have
been composed of multiple active elements, but all elements were electrically connected to form a
single, unsteered beam in a direction normal to the flat face of the transducer. The beamwidth was
typically 5–10°. The frequency was typically 38, 120, or 200 kHz—one frequency per echosounder. This
was actually a ‘‘band-limited’’ or narrowband signal, as it was produced via transmitting a gated sine
wave with a duration of the order of several tenths of a millisecond. The bandwidths were typically
Fig. 5. Sketch of vertical plane multi-beam sonar used to image aggregations of fish. A reconstructed image of a fish school is
shown (Gerlotto et al., 2003).
5%–10% of the center frequency of the system (e.g., a 200 kHz signal spanning 195–205 kHz). The range
resolution is given by the equation:
1r = c τ /2 (range resolution—gated sine wave) (4)
where c is the speed of sound in water (nominally 1500 m/s) and τ is the duration of the sine wave.
For the gate durations used, this range resolution was typically several tens of centimeters.
5.2. 2012
5.2.1. Split- and multi-beam; multi-frequency; and broadband systems

Through a series of developments, transducers and associated electronics are now commercially
available to produce a split- or multi-beam in addition to a single beam (Fig. 5). Furthermore,
commercial echosounders have the option to operate several transducers (typically up to six), each at
a different frequency so that multiple frequencies can be used in the same measurement. In addition,
some transducers have been designed to produce a broadband signal with roughly one octave
bandwidth (e.g., 100–200 kHz). Development of the multiple frequency systems was inspired, in part,
by research prototypes (Holliday et al., 1989; Wiebe et al., 2002). Broadband echosounder systems
have only recently become available (Ross and Lawson, 2009; Stanton et al., 2010, 2012; Lavery
et al., 2010a,b). Calibration of the transducers (while fully integrated into the system) has become
standardized through use of a standard spherical target (narrowband: Foote, 1982; broadband:
Stanton and Chu, 2008).
The split-beam approach was developed so that TS could be measured directly. It can also be used
for target tracking. Another technology, the dual beam approach, could also measure TS directly, but
ultimately the split-beam approach prevailed due to its advantages over the dual beam (Ehrenberg,
1979). The multi-beam is used to produce 3-D images of patches of biological scatterers. These systems
typically have many narrow 1° beams to insonify much of the water beneath the ship in up to a
150° swath in a plane perpendicular to the direction of the ship (Gerlotto et al., 1999; Mayer et al.,
2002; Trenkel et al., 2008). Multi-frequency and broadband systems are used to exploit the frequency
dependence of the scattering by the organisms for various types of classification as discussed below.
5.2.2. Chirp signals and pulse-compression processing

While most narrowband systems still transmit a gated sine wave, at least one commercial
system transmits a narrowband linear frequency modulated signal (‘‘chirp’’) which is post-processed
through pulse-compression processing (Ehrenberg and Torkelson, 2000). Also, the broadband systems
transmit a similar signal, but spanning a much larger range of frequencies. Whether it be a narrowband
or broadband signal, pulse-compression processing can significantly improve the signal-to-noise ratio
(SNR) and range resolution of the system. The pulse-compression processing is normally done in real-
time so that a high-resolution image is displayed in real-time. The processing is done through the
equation:
cpr (t ) = kcp vr (t ) ⊗ vrep (t ) pulse-compression processing (5)
where cpr (t ) is the pulse-compressed received voltage signal, t is time, kcp is a normalization constant,
vr (t ) is the raw, unprocessed received voltage, vrep (t ) is the ‘‘replica’’ signal, and ‘‘⊗’’ is the cross-
correlation operator. Mathematically, the pulse-compression processing is conducted through cross
correlating the received voltage with a replica signal. This is similar to matched filter processing,
where the replica signal is identical to the received signal of interest (Turin, 1960; Chu and Stanton,
1998). In practice, the applied voltage signal may be used as the replica, but with some degradation
of performance.
The improvements in the SNR and the range resolution due to pulse compression processing are:
∆(SNR) = 10 log (2τ BW ) (dB) improved SNR (6)

1
1r = c (BW )−1 range resolution—exploiting bandwidth (7)
2
where τ is the duration of the chirp and BW is the bandwidth of the signal. These improvements can
be realized not only for broadband signals, but also for a narrowband signal provided full use of the
band is made with the signal such as through a chirp signal. Also, an interesting aspect of this type of
processing, as can be seen from Eq. (6), is that the SNR can be improved by increasing the duration
of the transmitted signal. However, in contrast to the use of gated sine waves where an increase in
duration corresponds directly to a degradation (a larger value) of range resolution (Eq. (4)), the range
resolution after pulse-compression processing is independent of transmit signal duration (Eq. (7)). The
resolution is improved (i.e., changes to a smaller value) by an increase in bandwidth. To summarize,
through pulse-compression processing of a signal, the SNR can be increased through an increase in
signal duration and bandwidth and the range resolution can be improved to a smaller value through
an increase in bandwidth.
For example, for the case of a narrowband 200 kHz signal with a 10 kHz bandwidth, a chirp signal
is applied spanning 195–205 kHz and that is 10 ms long. Normally, a 10 ms-long gated sine wave
would have a range resolution of 7.5 m (using Eq. (4)). However, after pulse-compression processing,
the range resolution is 7.5 cm (using Eq. (7)). In addition, the improvement in SNR over a gated sine
wave is 23 dB (using Eq. (6)). For a genuinely broadband signal where bandwidths are comparable to
an octave, the results are even more striking. For example, in an operational broadband transducer
with a usable frequency range of 30–105 kHz, pulse-compression processing of a 2 ms-long signal
is temporally compressed to 11.4 µs long (Fig. 6). This compression corresponds to improving the
range resolution, which was originally 1.5 m to 3 cm, while at the same time improving the SNR.
Note that the value of 11.4 µs was determined numerically and differs slightly from the 13.3 µs
calculated from (BW )−1 . Also, once the non-uniform transducer response is accounted for, as well
as an imperfect (operational) replica signal, this value increases to 35 µs, resulting in the 3 cm range
resolution (Stanton and Chu, 2008). In another example involving an operational broadband system,
for the low frequency channel used for resonance classification where the bandwidth is about 6 kHz
(centered around 3 kHz), the range resolution is about 20 cm (Stanton et al., 2010). This resolution is
finer than that of a traditional gated sine wave system at 200 kHz, even though the wavelengths are
100 times greater. Note that the value of 20 cm accounts for a non-uniform transducer response and
imperfect replica as in the previous example.
Fig. 6. Effects of pulse-compression of a broadband signal. The original 2 ms-long signal in (a) has a frequency range of
30–105 kHz and is compressed via pulse-compression processing (matched filter processing in this case) to being 11.4 µs
long in (c). The spectra of the signals are preserved throughout the process ((b) and (d)).
Source: From Stanton and Chu (2008).
6. Software
Along with the hardware evolution, software evolved just as rapidly over the past 30 years. We
went from ‘‘home-brew’’ software in the 1980s to commercial software that could be downloaded
from the internet in 2012. The internet didn’t exist in 1980!
6.1. 1980
Mainframe computers had dominated the computer market up to this point and personal
computers were just beginning to emerge. On the mainframe computers, software was written in
various versions of Fortran with standard math functions and graphics packages available. In these
days, computers were actually used to compute (vs. e-mail, preparation of documents, surfing the
web, etc., in 2012)! The disadvantage was the accessibility of the computer. After data were provided
to the computer (via reel-to-reel tape), the software that was punched on a stack of cards was fed into
the computer. Writing software was clearly a cumbersome task, especially since it involved punching
one computer card for every line of code (each character was denoted via a hole punched in the card).
One syntax error could cost you a day in time!
The emergence of personal computers helped address the cumbersome aspect of the mainframes.
However, the computers came ‘‘bare’’ in that there was a very basic operating system and not much
more. Users spent much time writing all software from scratch, as the software was not developed yet
as it had been with the mainframes. For example, in my own simulations (such as in Stanton, 1982), I
wrote my own code to calculate Bessel functions. The simulations used the language ‘‘Forth’’, a stack-
oriented program, that was one level above assembly language. It was very time consuming to write.
Since there were no graphics packages, I wrote my own such as to display plots for simulations or the
real-time display in the echo processor I co-developed, as described later (Powell and Stanton, 1983).
My software controlled each pixel on the display to draw axes, numbers, and data values. Another
issue is that this field was so new, being a computer programmer was not established as a career
path, thus there were few ‘‘experts’’ in software to consult.
6.2. 2012
Now, commercially available software is ubiquitous and highly evolved. The software is so
sophisticated, that one can install and run it themselves without the assistance of a computer
expert. Users still write their own software, but have easy access to established graphics and math
routines. Software not only is used to process data, but also to control hardware (see discussions
on ‘‘programmable hardware’’). Software is available both online (via ‘‘downloads’’) or through a
physical medium such as a CD.
7. Deployment modes and associated instrument platforms
Modes of deployment and associated instrument platforms have evolved over the past three
decades, in part, because of the shrinking of electronics and reduction in power requirements, but
also because of engineering developments of new platforms (observatories and AUV’s) (Edson et al.,
2002; Curtin and Bellingham, 2001).
7.1. 1980
Deployment of systems was generally limited to being hull-mounted on the ship or towed from
the ship. In each of these cases, electrical power was supplied by the ship. In this period, electronics
generally consumed relatively much electrical power, hence requiring a significant source of power
such as what could be provided by the ship.
7.2. 2012
There were several major developments that significantly affected the types of modes of
deployment available for echosounders: (1) miniaturization of electronics and reduction of power
requirements, (2) development of batteries with increased ratios of energy to volume, and (3)
development of AUV’s for scientific use (which exploited #1 and #2). As a result, in addition to the
hull-mounted and towbody deployments, echosounders can also be deployed on AUVs (Fernandes
et al., 2003) and long-term observatories (Trevorrow, 2005; Pawlowicz and McClure, 2010). In each
of these latter cases, batteries are generally used, although some observatories close to shore are also
cabled with shore-based power.
8. Display and recording of data
8.1. 1980
In 1980, personal computers were in their infancy and, as discussed above, echosounder hardware
was entirely analog. This had significant implications in the display and recording of data. The real-
time displays were the so-called paper charts which involved a constantly and quickly scrolling device
that marked the paper along the depth dimension while, at the same time, the paper was constantly
slowly scrolling along the other dimension (which represented time at a fixed station, or distance
along a transect for a ship moving at a constant speed). The marks indicated the presence of an echo.
The displays were uncalibrated, in black and white, and had a very small dynamic range (Fig. 2). Thus,
Fig. 7. False-color echogram reconstructed during post-processing and shown in relation to latitude and longitude.
Source: From Wiebe et al. (1997).
it was important to maintain a watch on the display and to adjust the display sensitivity according to
when the overall echo levels changed. In addition to the scientific limitations of the paper recorders,
they frequently gave off an unpleasant odor and needed to be vented!
Memory devices were also generally in analog form, as digital memory was very expensive. Data
were normally recorded on analog tape, either through use of a scientific reel-to-reel recorder or
sometimes on cassette tape. There were a number of significant issues with this approach: (1) tapes
are inherently a serial access medium. In order to access data, the entire portion of the tape preceding
the desired data must first be passed through to access the data of interest. (2) There is no indication
on the tape of the precise time at which the data were recorded. Thus, it was necessary to relate a
measurement of how much tape had passed through the heads to time. There was inherent error in
this process, thus time was not known to the desired precision. (3) Since the data were stored in analog
form, there was a drift in sensitivity of the tape as a function of use. Thus, if a tape were reprocessed
several times, after each time the tape was used, the echo levels were reduced slightly. (4) Analog
data on tapes had a relatively small dynamic range (in amplitude of signal), thus limiting the quality
of data recorded. (5) The analog tapes were also limited to audio frequencies. Thus, recordings were
limited to base-banded signals whose carrier frequency was at an audio frequency. Or, sometimes the
echo envelope was recorded. Thus, there was never an option to record the full original waveform for
the high frequency systems.
8.2. 2012
The great advances in electronics over the past 30 years have addressed the above issues with
correspondingly great improvements. Displays are now presented on a computer monitor, provide
much information, and are very flexible. For example, calibration can be used in a false-color display
to show, in real-time, calibrated TS or Sv over a wide dynamic range. The displays are flexible so that
multiple channels (such as from multiple frequencies) can be displayed in real time. Post-processed
displays of single- and multi-beam data provide great new insight (Figs. 5, 7). In addition, the monitors
are quiet and do not emit an odor like the original paper recorders!
Memory devices are all dense with high speed random access and have completely replaced tape
storage media. They come in the form of, for example, internal and external hard drives which now
exceed 1 TB of memory. The cost of memory is relatively low and not a major consideration in data
acquisition systems.
9. Processing of data
9.1. 1980
9.1.1. Hardware
Processing of data was done almost entirely from recorded data, hence ‘‘post-processing’’, although
real-time processors were being developed in the 1970s and early 1980s. The processing was
performed either with a dedicated processor or via computer using digitized data. The dedicated
processors were hardware systems that were generally not programmable. A key challenge was the
fact that, without real-time processing, all data (which were stored on analog tapes) had to be played
back at the same rate at which it was stored. Imagine collecting 200 h of data and taking at least
another 200 h after the experiment to replay the data for processing! This problem helped to drive
the development of real-time processors.
As the microcomputers and personal computers became widely available in the 1970s and early
1980s, there was the emergence of prototype hardware processors that were programmable and
permitted real-time processing (Thorne, 1977; Kanemori and Ehrenberg, 1978; Powell and Stanton,
1983; the review of the Bergen echo integrator in Foote et al., 1991). However, memory was very
expensive then and posed a significant challenge. For example, in the echo processor that Powell and
I developed, there was a total of about 10,000 bytes (8-bits) of random access memory (RAM) available
on-board the personal computer (Fig. 4). Because of that, and what would be considered in 2012 as a
slow clock speed (1 MHz), a combination of assembly language and another low level macro language
(‘‘Forth’’, as described above) was used so that the personal computer could keep up with the rate
at which the processed data were being acquired (Stanton and Powell, 1982). Furthermore, in order
for data to be stored onto a permanent storage medium (5 1/4′′ floppy disks and, later, Bernoulli
disks) fast enough in between pings so that data would not be lost, the disk operating system (DOS)
of the computer was bypassed and we wrote the data directly to disk with assembly language. This
reduced what had been a 3 s operation for storing a data file into a 60 ms operation. In spite of the
challenges, the performance of the system was maximized and yielded useful results, such as the
analysis of combining echo integration and echo statistics to estimate the numerical density of fish
(Fig. 8).
9.1.2. Determining TS and Sv from single beam data

Regardless of which processor was used, data were generally processed to obtain echo envelope
time series and volume scattering strength. From the time series, peaks were picked so that TS could
be estimated through various indirect techniques. Sv was always determined from echo integration
methods. The challenge involved in determining TS was that the fish or zooplankton were randomly
located in the single beam of the echosounder. The value of the echo voltage is proportional to the
product of the backscattering amplitude of the organism and the value of the beampattern. However,
with the organism randomly located in the beam, the beampattern value is, in turn, random. Hence
the component of variability in the echo associated with these (random) beampattern effects needed
to be removed from the data. Once removed, the remaining echo variability is due solely to the
organism.
Various approaches were used to remove beampattern effects, including the Craig and Forbes
(1969) algorithm, the deconvolution approach (Ehrenberg, 1972; Clay, 1983; Stanton and Clay, 1986),
and a method using maximum likelihood (Hedgepeth et al., 1999; Moszynski, 2002). While these non-
parametric (i.e., no assumption of scattering statistics) methods are based on the same principles, the
developments were made for improved efficiency and accuracy (Rudstam et al., 1988; reviewed in
Ehrenberg, 1989).
The end result of the post-processing was calibrated echograms of Sv at one frequency and
distributions of TS. Contours of Sv were frequently hand drawn!
Fig. 8. Echo peak histograms versus depth, as determined from the output of the sonar echo processor developed by Powell
and Stanton (1983). The transition from non-Rayleigh to Rayleigh statistics near 65 m depth was used to estimate the numerical
density of fish at that depth which, in turn, allowed for density estimates for the entire water column using the echo integration
values. The data were collected and recorded on analog tape by University of Wisconsin researchers in Lake Michigan in the
early 1980s.
Source: From Stanton (1985b).
9.2. 2012
Fixed hardware systems and prototype programmable systems have given way to commercial
programmable hardware for real-time processing with high clock speeds (>2 GHz). Echograms of Sv
are obtainable in real-time displays in addition to post-processing. Very importantly, TS is determined
directly through use of split-beam processing rather than through the indirect methods cited above
(Ehrenberg, 1979; Foote et al., 1986). Although determined directly, TS remains a stochastic quantity,
even for a single organism, and a TS distribution is still determined. Based on this distribution, TS is
frequently expressed as a mean quantity.
With many systems being multi-frequency, color contours (computer generated) of Sv vs. depth
and transect distance (or time at a fixed station) are made for each frequency. The multi-frequency and
broadband data are used to create echo spectra (discrete or continuous) (Fig. 9). Synthetic echograms
are also created to illustrate differences in echo levels across frequencies. Interpretation of these
frequency dependencies derived from these different approaches are discussed below.
In addition to the above processing associated with a single (or split) narrow beam, multi-beam
images are constructed during post-processing (Fig. 5). Through advanced post- processing software,
images of entire aggregations of organisms can be visualized, rotated, and analyzed, such as in terms
of school morphometry (Paramo et al., 2007, 2010).
10. Interpretation of data
In the absence of quantitative methods for interpretation, acoustic echoes are used to indicate
the presence and absence of biological sound scatterers. There have been significant advances made
toward translating the echoes into meaningful biological parameters such as numerical density, size,
Fig. 9. Using resonance classification to spectrally resolve two major size classes of collocated swimbladder-bearing fish that
are otherwise not spatially resolvable. The approach relies on a broadband acoustic system, 1–6 kHz, that excites the resonances
of the fish swimbladders (Stanton et al., 2010). The lower and upper frequency resonance peaks correspond to larger and smaller
fish, respectively.
Source: From Stanton et al. (2012).
species, and spatial variability of the fish or zooplankton. Scattering models for TS and fbs in Eqs. (1)
and (2) are central in these interpretation methods.
Development of advanced scattering models has enabled the field to exploit multi-frequency and
broadband data for advanced interpretation of the acoustic data. For example, inversions of multi-
frequency and broadband data, using scattering models, has led to accurate estimates of size and
numerical density of fish and zooplankton (Holliday and Pieper, 1995; Lawson et al., 2008; Stanton
et al., 2010, 2012; Lavery et al., 2010a). These inversions were inspired, to a large extent, by the multi-
frequency inverse theory presented in Holliday (1977a). Synthetic echograms based on the differences
in scattering levels across the different frequencies have also been developed to classify organisms
based on their scattering properties (Warren et al., 2003; Korneliussen et al., 2009a).
In addition to scattering-model-based methods, there have been other methods involving
statistically characterizing the morphometry of aggregations of organisms as derived from echograms,
such as the physical dimensions of the aggregation, distance above the seafloor, texture of the echo
data, etc. These methods classify species according to their behavior as inferred from the morphometry
(Haralabous and Georgakarakos, 1996; Scalabrin et al., 1996; Paramo et al., 2007; Cox et al., 2010).
Initially, the methods involved use of echograms from single-beam echosounders where parameters
associated with a 2-D plane were analyzed. As multi-beam systems became available, the methods
expanded into characterizing the full 3-D information of the distributions of the organisms.
Interpretation of acoustics data can be further improved by combining data from multiple acoustic
technologies. For example, multi-beam and multi-frequency systems provide complementary
information regarding the morphometry and scattering response of an aggregation of organisms,
respectively. When those systems are used simultaneously and the respective acoustic inferences are
combined, there is potential for reducing uncertainties in the interpretation of the data compared
with using either technology alone (Korneliussen et al., 2009b).
Regardless of the interpretation method, concomitant use of nets or other direct sampling methods
is imperative. Acoustical methods are inherently under-determined. Through use of direct sampling
of the organisms, although sampling a far smaller volume than that of the acoustics system, the
acoustical interpretation method can be constrained to fewer unknown parameters.
Since the focus of my research involving interpretation methods has been in the development of
scattering models, the following sections will focus in that area.
10.1. 1980
Scattering models were generally quite primitive, with some exceptions. For fish, there were
models for the two regimes—resonance scattering by the swimbladder and high frequency (well above
resonance). For zooplankton, there were also two types of models, not according to frequency regime,
but rather of different approaches, one based on an analytical model and the other with an empirical
formula.
10.1.1. Fish—resonance scattering model for swimbladder-bearing fish

For frequencies near the resonance frequency of the swimbladder, an analytical model was
derived assuming that the swimbladder dominated the scattering and was a monopole scatterer
(Love, 1978):
2
a2 ρw /ρf

σbs = 2 resonance scattering model (8)
f02 /(fH )2 + f02 /f 2 − 1

where a is the equivalent spherical radius of the swimbladder, ρw and ρf are the mass densities of
water and fish flesh, respectively, f is the frequency, f0 is the resonance frequency, and H is related to
the damping of the swimbladder. At resonance, H is equal to the quality factor of the resonator which
is equal to the ratio of the resonance frequency to the width of the resonance.
This theory had been developed over a number of years, beginning with Minnaert (1933) and
including Andreeva (1964). The term H is quite complex and includes viscous and thermal damping
from the tissue, surface tension, and radiation damping. By the time Love had derived this equation,
there had been much activity in determining the damping parameters of the swimbladder, as well as
the depth-dependence of the resonance frequency and adaptation time of the swimbladder resonance
to rapid changes in depth (reviewed in Diachok, 2005).
For common sized fish, the resonance frequency occurs in the upper 100’s Hz to lower kHz. Thus
the frequencies at which the model applies are generally below 10 kHz.
10.1.2. Fish—high frequency scattering model for swimbladder-bearing fish

For frequencies well above 10 kHz, a regression equation was used for fish:
TS = A log L + C high frequency regression equation (9)
where L is the length of the fish and A and C are empirically-determined parameters. In the early uses
of this equation, the equation was generally fitted to fish from a large range of species and sizes. As a
result, the variance was significant. The term A was generally near the value of 20, representing the
L2 dependence of scattering.
10.1.3. Zooplankton—analytical models

The first attempts toward analytically modeling zooplankton scattering involved use of the exact
modal series solution to the fluid sphere (Anderson, 1950; Pieper and Holliday, 1984). The form was:
∞
i 
fbs = bm (−1)m modal series solution (10)
k m=0
where bm is the modal series coefficient. Holliday and Pieper determined that in order for the theory
to fit multi-frequency backscatter data, the series needed to be truncated to include only the first two
terms.
This model was applicable for all frequencies and sizes of zooplankton. However, it approximated
all zooplankton to resemble a sphere, with no orientation dependence of the scattering. Furthermore,
it treated all zooplankton as having the same material properties (fluid-like), regardless of whether
they are composed principally of tissue, or also have a hard shell or contain gas. For applications to
copepods, which is what inspired this model, the fluid assumption was valid.
Because of the complexity of the model, efforts were made to formulate a simplified version of
the modal series so that the overall levels were maintained at all frequencies, but not necessarily the
structure, such as nulls. Johnson formulated the so-called ‘‘high-pass’’ model, where the terminology
makes the analogy that the scattering function resembles a high pass electrical filter (‘‘passing’’ higher
frequencies and rejecting lower frequencies) (Johnson, 1977). This formulation was generalized in
Stanton (1989b) to describe a range of shapes—sphere, straight finite cylinder, bent finite cylinder,
and prolate spheroid in the general expression:
 −1
σbs(≪)

(≪)
σbs = σbs G 1 + high-pass model (11)
σbs(≫) R2 F
(≪) (≫)
where σbs is the ka ≪ 1 limit for the case of a fluid object, σbs is the ka ≫ 1 limit for the case of a
rigid/fixed object, G is a heuristic function to produce nulls and/or peaks in the curve, F is a heuristic
function to account for deviations in σbs when the object is irregular and/or lossy, R is the plane-
wave/plane-interface reflection coefficient, and a is the radius of the sphere, cylindrical radius of the
cylinder, or length of the semi-minor axis of the prolate spheroid.
10.1.4. Zooplankton—empirical model

There were also attempts to fit a regression curve between biomass and volume backscattering.
This was based solely on comparisons between echo data and net tows. These curves generally include
contributions from all species and sizes of zooplankton and had a significant variance. In a study
by Wiebe et al. (1996), this high variance for a single regression equation description of a mixed
population of zooplankton is demonstrated, as well as significant improvements once species-specific
models are incorporated as discussed later.
10.1.5. Comparison with nets

Nets generally had a single cod end, although multiple net systems were under development and
in use by some. With only a single cod end, the organisms could only be sampled at a constant depth
or through a range of depths via an oblique tow. As a result, there was a limited amount of net data
that could be used in a given study for adequate direct comparison with acoustics data.
10.2. 2012
There was significant development since 1980 on the models, especially in the high-frequency
regime with fish and all major types of zooplankton.
10.2.1. Fish—resonance scattering model for swimbladder-bearing fish

There were relatively modest developments in this area during this period. I attribute this to the
fact that there was a great expansion of work concentrating in the frequency range of 10’s–100’s kHz,
which was well above resonance and required a different kind of model. The use of seismic sources
such as in the 1960s–1970s which excited the resonance of the fish swimbladder and led to the
development of the resonance model was greatly reduced. Some of the resonance modeling research
involved including elastic aspects of the swimbladder (Feuillade and Nero, 1998). Others involved
alternative types of formulations to model the scattering, including the deformed cylinder formulation
in the Kirchhoff-Ray-Mode (KRM) model (Clay, 1991, 1992; Clay and Horne, 1994), a conformal
mapping method (FMM) (Reeder and Stanton, 2004), and a T -matrix method (Feuillade, 2012). These
latter approaches explicitly account for the elongation of the swimbladder, rather than use of an
eccentricity correction factor as in Love’s sphere-based model.
Fig. 10. Images of the outer boundary of a fish and its swimbladder using a medical computerized tomography (CT) machine.
These data are used for advanced modeling of scattering by fish.
Source: From Reeder et al. (2004).
10.2.2. Fish—high frequency scattering model for swimbladder-bearing fish

The importance of species-specific scattering was accounted for through various means. For
example, the regression equation in Eq. (9) was applied to fish of the same species. As a result, the
variance of the regression was greatly reduced and species-specific values of the regression equation
coefficients were determined (Foote, 1979; McClatchie et al., 1996).
Analytical methods to describe the scattering by the swimbladder were also developed and applied
for selected species. For example, the swimbladder shape was digitized and incorporated into various
models, most involving the Kirchhoff surface integral:

i ⃗ ′
fbs = R k̂inc · n̂ ei2kinc ·⃗r dA (12)
λ A
where ⃗ r ′ is the position vector of the surface, dA

kinc is the wavenumber vector of the incident field, ⃗
is the differential element of the surface A, n̂ is the unit vector of the outward normal of the surface,
and ‘‘ ˆ ’’ denotes a unit vector. This has been applied in many cases, including the KRM model. Besides
the Kirchhoff model, there has been the FMM, deformed cylinder model, T -matrix, and others cited
above that have attempted to account for the shape of the swimbladder at various scales (Fig. 10).
Fig. 11. Laboratory tank used to make measurements of acoustic backscattering by various marine organisms, ranging from
mm-sized pterapods to 20 cm fish. The frequencies ranged from 24 kHz to 1.2 MHz, using a combination of narrowband and
broadband (octave) transducers. The organisms were rotated 0–360°. This setup varied over the 20 years we used it. It was
normally used on land, although twice it was taken to sea on the deck of a ship in which the scattering by freshly caught
zooplankton was measured.
Source: From Stanton et al. (2000).
10.2.3. Fish—high frequency scattering model for fish without swimbladder

Although the vast majority of fish scattering research has focused on swimbladder-bearing fish, the
important problem of investigating the scattering by fish without swimbladders has been addressed.
For example, Gorska and colleagues have developed a deformed cylinder model that accounts for both
the flesh and bone of the fish and have compared the results with data (Gorska et al., 2005). Although
the levels are lower than for fish with swimbladders, the echoes are detectable.
10.2.4. Zooplankton
The diversity of material properties as well as elongation have been accounted for through various
developments. This is an area where I focused much of my work, beginning with the paper, Stanton
(1988), in which elongated organisms were modeled as a finite-length cylinder. This, and several
other modeling papers, were followed by a series of laboratory measurements by myself and various
colleagues of acoustic scattering by a wide range of organisms, and made over a wide range of
frequencies and orientation (Fig. 11). Although most measurements were conducted on land, some
were performed at sea on the deck of a ship using the same apparatus and with freshly caught
organisms. These measurements inspired the development of new models, as well as provided a basis
for validation of the models. See, for example, the review of the experiments and model developments
in Stanton (2009).
Three anatomical groups
Depending upon the species or gross anatomical group, the material properties of zooplankton
can (1) be weakly scattering in which the organism is principally composed of tissue whose material
properties are close to that of the surrounding water, (2) contain a hard elastic shell, or (3) contain a
gas inclusion. Because of the wide range of material properties, the ratio of biomass to echo energy
has been demonstrated in laboratory measurements to vary by up to 19,000:1 over the range of
organisms given above. This observation refutes use of a regression equation that assumes a constant
Fig. 12. Progression of models of the shape of euphausiids for advanced modeling of scattering, as derived by Stanton and
colleagues. The progression begins with the finite-length straight cylinder, which replaced the previous sphere model (Stanton,
1988). The progression ends with two classes of models, one in which the full 3-D shape information based on a CT scan (such
as in Fig. 10) is incorporated into a full 3-D deterministic acoustic scattering model (Lavery et al., 2002) and the other involving
use of a randomly rough boundary superimposed on an otherwise smoothly varying boundary (Stanton et al., 1998).
ratio (Stanton et al., 1994). The resultant models from Stanton et al. (1994) were validated in later
field studies such as Wiebe et al. (1996) and Lavery et al. (2007). Details of scattering models of the
three groups are summarized in Lavery et al. (2007).
Elongation and deformation effects (deformed cylinder formulation)
A key development involved accounting for the elongation of organisms as well as their lengthwise
deformations (Fig. 12). In essence, the shape is being realistically modeled. This was made possible
through development of the deformed cylinder formulation (Stanton, 1989a). The original formulation
was based on the exact modal-series solution of an infinitely long cylinder. This assumption
limited the deformed cylinder predictions to angles near broadside incidence. In Stanton (1992), the
formulation was generalized to being based on any infinite cylinder solution and in Chu et al. (1993)
and Stanton et al. (1993), the distorted wave Born approximation (DWBA) was incorporated into it
for weakly scattering zooplankton. The deformed cylinder formulation from those developments was
shown explicitly in Stanton et al. (1998):
J1 (2k2 a cos βtilt ) 


k1
γκ − γρ e2i (ki )2 ·⃗rpos a
  ⃗ d⃗rpos  ,

fbs = (13)
4 rpos cos βtilt
where k1 and k2 are the wavenumbers of the surrounding water and body of scatterer, respectively,
γκ and γρ are related to the density and sound speed contrasts of the scatterer, βtilt is the tilt angle
rpos , ⃗
(relative to the incident wave) of the local cross section of the cylinder at point ⃗ rpos is the position
vector of the axis of the cylinder, and J1 is the Bessel function of the first kind of order 1.
This formulation is valid for all frequencies, sizes, and orientations of weakly scattering
zooplankton. In Stanton et al. (1998), a randomly rough cylinder was modeled and compared
successfully with backscattering data from a euphausiid over all angles of orientation. A key element
of that development was the randomly rough exterior that was required to predict backscattering at
orientation angles near end-on incidence. The formulation was later applied to scattering by copepods
in Stanton and Chu (2000).
As shown in Chu et al. (1993) and Stanton et al. (1993), the original DWBA formulation is fully
3-D (in contrast to the 1-D line integral of the deformed cylinder formulation). This integral was
exploited by Lavery et al. (2002) in modeling elongated zooplankton as a 3-D volume, rather than
the approximation of a deformed cylinder. This development involved incorporating 3-D data from
medical computerized tomography (CT) scans of the organism into the 3-D DWBA integral.
In summary, significant developments have been made in modeling zooplankton. The models of
euphausiids are most reliable at this point, due to the amount of validation with experimental data.
Development of models of other organisms in that (weakly scattering) class, such as copepods, as well
as gas-bearing and hard elastic shelled organisms has remained limited due, in part, to the lack of data.
10.2.5. Measurements and inferences of model parameters

A scattering model, no matter how mathematically complex and rigorous, cannot be effectively
used in interpreting data without accurate model parameters. Key parameters include sound speed
and density contrasts of tissue, damping coefficients of tissue (associated with gas-bearing fish and
zooplankton near resonance), and tilt angle distribution. All of these parameters directly affect the
echo level. The echo from tissue-only organisms (e.g., euphausiids) is particularly sensitive to sound
speed and density contrasts since those values are close to unity. And, because those values are close to
unity, they are correspondingly difficult to measure. The echo is also very sensitive to tilt angle when
the acoustic wavelength is much smaller than the length of the organism. The tilt angle is difficult
to measure because measurements made in the proximity of the organism will tend to disturb it.
Significant progress has been made concerning most of these parameters, with the exception of the
damping coefficients due to a general lack of activity in the field in the resonance region of gas-bearing
organisms.
Measurements of sound speed and density have been made for various zooplankton and fish larvae
(Foote et al., 1990; Chu et al., 2000; Chu and Wiebe, 2005; Wiebe et al., 2010; Smith et al., 2010). The
measurements, or perhaps better stated as inferences based on measurements, included measuring
the speed of sound in a mixture of zooplankton to determine sound speed contrast. The quantities
buoyancy, weight, and resistivity of the zooplankton were measured to determine density contrast.
Measurements of the tilt angle of organisms have also involved several different methods. For
example, the tilt angles of zooplankton have been measured through use of a camera (Lawson et al.,
2006). The tilt angles of fish have also been measured with cameras (Huse and Ona, 1996), equating
the angle at which the fish is swimming (as determined via acoustic tracking) to the tilt angle (Ona,
2001), and relating the angle directly to the duration of a broadband echo (Stanton et al., 2003).
In addition to the above more direct approaches, indirect approaches have involved inferring these
parameters through backscatter data and an assumed scattering model (Foote and Traynor, 1988; Chu
et al., 1993; Martin Traykovski et al., 1998).
10.2.6. Discriminating between echoes from zooplankton and physical microstructure

Zooplankton commonly reside at or near sharp changes in physical properties (density or
temperature) of the water. Since the physical microstructure can be a source of scattering, there
was much controversy in the 1980s regarding whether the echo was due to the zooplankton or
microstructure. It was generally assumed in the early 1980s that the echoes were dominated by
zooplankton and, hence, whatever was seen in the echogram was assumed as being due to the
presence of zooplankton only. Through a series of model developments grounded with experimental
data, it was determined that, although the zooplankton would generally dominate the echoes, there
were important conditions under which the microstructure could dominate (Goodman, 1990; Haury
et al., 1979; Seim, 1999; Seim et al., 1995; Trevorrow, 1998; Lavery et al., 2003, 2010a,b; Geyer et al.,
2010). These conditions involve regions where the microstructure was very energetic, such as in an
internal wave in the open ocean or at the mouth of a freshwater river as it emptied into a saltwater
(ocean) environment.
10.2.7. Comparison with nets

Multiple opening and closing nets have been further developed and are more routinely in use
(Wiebe and Benfield, 2003). With these devices, the organisms can be sampled at multiple depths
with one cod end of organisms per depth or multiple sections of the transect at a constant depth.
By sampling with these nets, there was much more data which could be compared with the acoustic
data, such as patchiness of the organisms at constant depth or depth-dependence of organisms. This
provides a better grounding of the acoustic data. For example, consider the case when there is a patch
of organisms within a larger layer of organisms and with a species and numerical density different
from that of the surrounding layer. The acoustic system can ordinarily detect the patch. Furthermore,
a multiple opening and closing net can be directed so that one of its nets is open only when passing
through the patch allowing for one-for-one comparison between the species in the patch and their
corresponding acoustic signature.
11. Other (long-range sonars; broadband impulsive devices)
Although this paper has focused on the devices principally used (i.e., direct path systems using
reciprocal transducers), there have been other systems either used in the past, or are currently in
development, that have merit and are summarized below.
11.1. Broadband impulsive devices
In the 1960s and 1970s, there were experiments performed in which an impulsive device was
used to generate broadband sound in the 100’s Hz to low kHz frequency range. Most approaches
involved use of an explosive device in which the echo was received with an array of hydrophones
(Hersey et al., 1962; Chapman and Marshall, 1966; Holliday, 1972, 1977b; Chapman et al., 1974;
Hall, 1981; Hall and Quill, 1983; Thompson and Love, 1996). In some cases, a seismic arcer was used
(Holliday, 1977b). An advantage of these systems was the strong signal transmitted into the water
and the broad frequency content that could be used for resonance classification of swimbladder-
bearing fish. There were a number of disadvantages, however, which included safety associated with
the explosive devices, repeatability of the transmitted signal, limited repetition rate, and inability to
apply broadband signal processing algorithms (such as matched filter processing, since the outgoing
signal was not well known). As interest in these frequencies reduced in the 1980s and 1990s, so did
use of these approaches. However, interest increased in more recent years, and the impulsive devices
were replaced by transducer-based systems in which the transmitted signal was repeatable, signal
processing algorithms could be applied, and the repetition rate was high (Nero et al., 2004; Stanton
et al., 2010, 2012).
11.2. Long-range sonars
There has been work on this subject nearly continuously since Weston published his work from the
1960s (Weston and Revie, 1971). In his work, he detected fish at (horizontal) distances of up to 65 km
at 1 kHz. There have been many other studies since, with frequencies ranging from low 100’s Hz to
10’s kHz (Rusby et al., 1973; Revie et al., 1990; Farmer et al., 1999; Trevorrow and Pedersen, 2000;
Makris et al., 2006; Jones and Jackson, 2009; Gauss et al., 2009). There is at least one commercial
system available in the 20–30 kHz range. A major advantage of this approach is the fact that fish can
be viewed synoptically across a large area. This is in sharp contrast to downward looking systems
(including high frequency multi-beams) with minimal areal coverage for a given ping and in which
substantial areal coverage can only be obtained by moving the ship, whose speed is typically, at most,
10 knots.
A major disadvantage of the so-called waveguide sonars is the fact that the waveguide (effects of
sea surface, seafloor, and water column properties) is strongly variable along the path of propagation
of the acoustic signal (i.e., a ‘‘range-dependent waveguide’’). It is not only spatially variable, but also
temporally variable, making it very difficult, if not impossible, to adequately model the propagation
loss of the signal over great distances.
Another disadvantage is that the systems cannot resolve depth. For frequencies required for the
acoustic signal to travel long distances, they are near the resonance frequency of swimbladders. As
fish migrate diurnally, the resonance frequency of the swimbladder will change significantly. If the
frequency of the acoustic signal is near the resonance, then the level of the backscattered signal (TS
and Sv ) can change dramatically during migration (quite plausibly, an order of magnitude). Since
a long-range system cannot resolve depth, the strong migration-induced changes in signal will be
ambiguous—is the change in signal due to vertical migration, horizontal migration (and changes in
patch density), or a combination?
Because of these challenges, these systems remain principally at the research level until error bars
for estimates of Sv are determined. Quantitative applications may include studying fish that remain
at fixed depth in a simple waveguide whose acoustical properties are well known.
12. Future
Personally, I am just as excited and optimistic about the future of this field as I was in 1980. By
1980, there had already been significant advances in the area, but it was clear that there was room for
many more important advances. I believe that the same is true for 2012.
Continued advances both in technology and interpretation methods can greatly improve
characterization of distributions of marine organisms. Areas that should see growth are listed below:
Technology. (1) Multi-beam systems. Making these imaging systems standardly used so that
distributions of organisms can be routinely imaged in 3-D. (2) Broadband systems. Development of
standardized commercial broadband systems that continuously span a wide range of frequencies
(100’s Hz to beyond 1 MHz) so that fish and zooplankton can be directly sized through spectral
classification. (3) Signal processing. Incorporation of advanced signal processing methods, such as
matched filter processing into all systems, narrow- and broadband. (4) Hardware. Further decrease in
power consumption of electronics as well as miniaturization for use in long-term observatories and
autonomous vehicles. (5) Long-range sonars. Development of more standardized long-range sonars for
large area synoptic surveys.
Interpretation methods. (1) Scattering models: (a) Fish. Resonance properties of swimbladder-bearing
fish (damping mechanisms, swimbladder size/shape vs. depth, scattering vs frequency and depth)
need to be characterized better for improved resonance classification. Scattering properties of non-
swimbladder-bearing fish need to be better grounded in data. (b) Zooplankton. Scattering properties
of elastic shelled and gas-bearing zooplankton require more modeling and experimental data. (c)
For use in multi-beam systems. All high frequency models need to account for oblique angles
encountered with multi-beam systems. (2) Multi-frequency inverse methods. Further development of
robust methods that will consistently provide reliable results. Key factors include number and range
of frequencies, diversity of size and anatomical groups of organisms, and variable signal-to-noise ratio
in each of the frequency channels. (3) Patch/school morphometry. With multi-beam systems becoming
more commonly used, analysis of new, large sets of morphometry data based on 3-D information will
improve the understanding of species- and environment-dependent morphometry.
13. Challenges
One challenge involves the fact that the new technology is so complex. In spite of the many
problems with the previous analog systems, there were some distinct advantages that have been
lost. For example, those systems were generally easier to use—simply turn them on and go. When
they began to fail, it was a so-called ‘‘graceful degradation’’ in which data could still be collected,
but just with more noise in it. Also, they were easier to troubleshoot: to do so, one would open
up the system while it was in operation and use an oscilloscope probe connected with an analog
oscilloscope to find the source of the problem. Now, there are many steps toward using the advanced
digital systems, with programming skills required. Systems don’t necessarily degrade gracefully, but
sometimes catastrophically such as when the communication protocol has failed between two digital
sub-systems. They are very difficult, if not impossible, to troubleshoot because of the all-digital
components. Because of all of these differences, the new systems seem to be more of a ‘‘black box’’
with the potential for the user to have less intuition involving its use. For example, it is even difficult
to determine if the echo is saturated (such as due to the seafloor) since intermediate tapping points
may not be accessible and filters smooth out the clipping effects of the saturation (hence allowing
it to go undetected). Nonetheless, when working properly, these advanced systems are incredibly
powerful and versatile compared with the previous systems, yielding up to orders of magnitude more
information.
Another challenge involves the fact that the new interpretation methods are so complex. Along
with the complexity is the challenge in understanding the assumptions of the method as well as how
to program complicated mathematical formulas or algorithms. As a result, new advanced methods can
be misused, resulting in erroneous, misleading results, which is completely contrary to the original
intent of the methods. These challenges are common among models of scattering and morphometry,
as well as inversion methods. Much like the above discussion of advanced technology, advanced
interpretation methods may be treated more like a black box than previous simpler approaches (such
as a simple regression equation). And, like with advanced technology, proper informed use of these
methods can yield impressive results, yielding much more information and with greater accuracy (and
less ambiguity) than with previous methods.
There are also challenges with the new software packages. Although there is now a vast and diverse
array of software packages available that can get a user quick results, these packages may not be fully
tested. The user needs to put new packages through a series of tests to fully trust the use of them, as
they would with something they developed themselves.
Even with vastly improved technology and interpretation methods, acoustics used alone and
without a priori information will remain a tool that produces underdetermined information. For
example, there are many thousands of species of marine organisms in the ocean, each with their own
scattering parameters. There are not that many channels of information possible with an acoustic
system, even with frequencies ranging from 100 Hz to 1 MHz at all multi-beam angles (here a
‘‘channel’’ can be a frequency or beam angle). Thus, acoustics must be used in concert with direct
sampling methods so that the number of inferred parameters is reduced to a number comparable to
the number of channels of information. Also, there are acoustic approaches that should be emphasized
to further reduce the number of inferred parameters. For example, the scattering at high frequencies
by elongated organisms depends strongly upon the tilt angle distribution of the organism. By reducing
the frequency, such as to the resonance frequency of a swimbladder, the tilt angle distribution is not
a factor (Stanton et al., 2010).
14. Key to success in the field of bioacoustics
The above focuses principally on technology and associated methods. However, it takes much more
than that to be successful in this field. There is no user manual or publication that can replace having
the right people and training to conduct the research properly. This is a very complex subject and
inherently multi-disciplinary. A big mistake made is to take on the subject alone. For example, for a
person trained in acoustics (from a physics or engineering perspective), fundamental mistakes can
be made without appropriate knowledge from someone trained in biology. Conversely, a biologist
working in this field alone can make fundamental mistakes in the interpretation of the acoustics data.
A good ‘‘model’’ of a team involved that of Drs. Holiday and Pieper, as in the above cited papers, where
they combined expertise from these different areas to make great strides in bioacoustics. Whether
it be for development or operational use, it is important to have a team with diverse training. There
is no such thing as a ‘‘turnkey’’ system that provides ‘‘the answer’’. In addition to appropriate team
building, it is essential that there be formal education at the undergraduate and graduate level to train
future researchers. For example, training fisheries biologists in the areas of technology, physics, and
engineering is important.
15. Summary/conclusion
I have witnessed and participated in significant advances in the field of active bioacoustics over
the past three decades. This field remains an exciting one, as the fruits of previous developments are
being realized and exploited, and there is much room for advancements well into the future. While
there continue to be many changes in the state-of-the-art, one constant is the need for the bioacoustics
team that is composed of experts in biology and acoustics.
Acknowledgments
I thank Dr. Jules Jaffe of the Scripps Institute of Oceanography, La Jolla, CA for inviting me to write
this paper. I am also grateful to Dr. J. Mike Jech of the National Marine Fisheries Service, Northeast,
Woods Hole, MA for his thoughtful comments on an early draft of the manuscript and Shirley Barkley
of the Woods Hole Oceanographic Institution for her assistance in preparing this manuscript. The
writing of this manuscript was supported by the US Office of Naval Research grant N00014-1-10-0127.
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Methods in Oceanography 1–2 (2012) 49–77

Contents lists available at SciVerse ScienceDirect

Full length article

30 years of advances in active bioacoustics: A personal

article info abstract

∗ Tel.: +1 508 289 2757; fax: +1 508 457 2194.

2211-1220/$ – see front matter © 2012 Published by Elsevier B.V.

Sonar hardware Analog Digital

Modality of operation Ship-based (hull-mounted or Ship-based (hull-mounted or towbody)

Post-processing and software Hard-wired processor Programmable processor

Scattering models-fish Resonance frequency (physics-based) Resonance frequency (physics-based)

2. A bit about myself

expressed in terms of the backscattered pressure, ps , measured at the echosounder transducer as

5. Hardware—systems and signals

1r = c τ /2 (range resolution—gated sine wave) (4)

5.2.1. Split- and multi-beam; multi-frequency; and broadband systems

5.2.2. Chirp signals and pulse-compression processing

cpr (t ) = kcp vr (t ) ⊗ vrep (t ) pulse-compression processing (5)

∆(SNR) = 10 log (2τ BW ) (dB) improved SNR (6)

7. Deployment modes and associated instrument platforms

8. Display and recording of data

9.1.2. Determining TS and Sv from single beam data

10. Interpretation of data

10.1.1. Fish—resonance scattering model for swimbladder-bearing fish

10.1.2. Fish—high frequency scattering model for swimbladder-bearing fish

10.1.3. Zooplankton—analytical models

10.1.4. Zooplankton—empirical model

10.1.5. Comparison with nets

10.2.1. Fish—resonance scattering model for swimbladder-bearing fish

10.2.2. Fish—high frequency scattering model for swimbladder-bearing fish

where ⃗ r ′ is the position vector of the surface, dA

10.2.3. Fish—high frequency scattering model for fish without swimbladder

J1 (2k2 a cos βtilt ) 

10.2.5. Measurements and inferences of model parameters

10.2.6. Discriminating between echoes from zooplankton and physical microstructure

10.2.7. Comparison with nets

11. Other (long-range sonars; broadband impulsive devices)

11.1. Broadband impulsive devices

11.2. Long-range sonars

14. Key to success in the field of bioacoustics

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