Sensing Plankton: Acoustics and Optics

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Sensing Plankton: Acoustics and Optical Imaging

Jules. S. Jaffe

Marine Physical Lab, Scripps Institution of Oceanography, La Jolla, CA

1. Introduction

Of the myriad of creatures that live in the sea, it cannot be debated that the fundamental role that plankton play cannot be ignored. In the case of the phytoplankton, as considered in other chapters in the volume, the important role that they play in the planetary budget, the availability of food which fuels both the aquatic and terrestrial (to some extent) kingdoms cannot be disputed. In the case of zooplankton, they are the fundamental link, in many cases, between the phytoplankton and the higher trophic levels. Our abilities to monitor their abundance, dynamics, and the interrelationship between our effects on them and their effects on us are a vital area where improved sensor technologies can play a role.

The goal of this article is to give provide the reader with a contemporary review of the acoustical and optical technologies which have been developed for monitoring zooplankton acoustically. In addition, a survey about underwater optical imaging of both zooplankton and phytoplankton is presented. As a general outline, first, a review of the basic physics of sound scattering from pelagic organisms is presented. This is then followed by an introduction to the propagation of light in the sea and its special relevance to underwater optical imaging. The background information is presented so that the reader will have a good idea of what the underlying physical and environmental principles of operation of the current generation of underwater systems are. A survey of these systems is presented in the section that considers applications. Here, many examples of contemporary underwater acoustical and optical systems are presented. These systems range from commercially available conventional off-the-shelf technology (COTS) to one-of-a-kind instruments that may someday transition into the standard repertoire of oceanographic facilities. Finally, the prospects and opportunities for a new generation of such systems is presented, both in acoustics and optics.

2. Physics:

In this section the basic physics of the process of sound scattering from organisms will be reviewed with special emphasis on applications to zooplankton. This will be followed by a review of the properties of light propagation and scattering and the principles of underwater imaging.

2.1 Foundations of Acoustical Sensing of Zooplankton

As we will find out in the following sections, the opportunities for underwater optical imaging of zooplankton at ranges of even 10’s of meters can be quite limited. As such, the biologist interested in monitoring the density and behavior of zooplankton in-situ is led to consider the use of acoustical techniques. Over the last years, due to the ease of creating, recording and processing sound, there has been a proliferation in the use of acoustical techniques for sensing zooplankton. Several excellent surveys of sound scatter by organisms in the sea and the contemporary instruments, which have evolved to sense zooplankton (Griffiths et al., 2002, Wiebe or Stanton review articles?), have been written. In addition, there are several text books which consider the use of acoustics for fisheries assessment (McClennan and Simmonds, 1992). Certainly, the general principles of fisheries acoustics can be applied to the study of zooplankton (and micronekton) as well. The interested reader is referred to these documents for further information and perhaps, a different view of these topics from those of this author.

A general appreciation for the basic physics that needs to be considered in order to understand the advantages and limitations of acoustic sensing of animals can be obtained by considering relatively few parameters. One set of factors, the absorption and scattering of sound by the medium and the animals is necessary. In addition, the geometry of any given sonar system is important in that the source intensities incident on the animal must be high enough and the receiving equipment must be sensitive enough so that the reflected energy can be heard above both the system and environmental noise. Although a host of signal processing techniques can then be applied to these systems such as phased arrays, pulse compressed signals and other algorithms for tracking animals, we consider here just these fundamental features of the sonar systems. The relatively straightforward part of these topics is understanding the geometry and the system parameters. The complicated part can be the scattering of sound by organisms as a function of frequency and animal orientation.

In general, the scattering function from a target is a function of the orientation of the target to the incident sound and the reflected sound. Figure nn demonstrates that in the most general formulation, this is a four dimensional function. However, generally, both the designer and scientist who desires to interpret the results of a bioacoustics experiment make some types of simplifications to reduce the dimensionality of the interpretation. Common ones are that the source and receiver are collocated and that the animals posses some type of either spherical or cylindrical symmetry (Stanton et al….euphausiids).

In general, the basic framework that most bioacousticians think of sound scattering of organisms is considered in Figure nn, a graph of acoustical backscatter target strength versus ka. Here, k is the wave number for the system 2 / and a is the equivalent spherical radius. “a” is roughly proportional to size, however the proportionality can be different for different animals. Note that target strength is a defined as TS = 10 log Ir/Ii where Ii and Ir are the intensity of the incident sound wave (watts/cm2). An alternative representation uses the concept of acoustic cross section (interpreted as the……). In this formulation, sigmal = and sigma is the scattering cross section (similar to the radar concept). Additional physical motivation for these definitions can be found in standard texts. However, note that the parameterization of such a graph implies that the important parameter for understanding sound scatter is the ratio of wavelength of the incident sound to the equivalent size of the object. Large objects will scatter low frequency sound with the same efficiency as smaller objects will scatter high frequency sound. Note also, the dependency on cross sectional area is the tangent line to the slope = 20 (this is often ignored as it is implicit in many treatments). Thus higher frequencies will produce more scatter. An important aspect of this graph is the presence of the deep nulls in the function (status of experimental verification of these nulls).

The graph was produced using a model (Stanton, ..) which required assumptions about the two important parameters of material composition: animal density (g ) and sound speed contrast ( h) between the scatterer and the surrounding water. The product of these parameters gh is called the acoustic impedance (similar to the refractive index in optics). Greater amounts of acoustic contrast leads to higher reflectivity (similar to the refractive index of optics).

The graph clearly shows a transition from a steeper region where a small increase in ka will result in a larger increase in scatter (whose slope is lambda^^4) to a more gently increasing region where the slope asymptotes to 20 (due to the dependence on cross sectional area). The former area is called the Rayleigh regime and the larger ka region is called the geometrical or Mie scatter regime. Most system designers try to “tune” their wavelengths so that ka > = 1 as this leads to an efficient use of power. Naturally, it is important to also consider the attenuation due to the absorption of sound because higher frequencies are absorbed more, however this function is usually quadratic (sound absorption reference), making the ka = 1 point a goal in designing the systems. So, for example, considering a 2 mm copepod (of equivalent spherical radius a= mm) the ka = 1 frequency would be f = . Low frequency sonars (< 5 kHz) are therefore of little use in detecting small organisms unless their abundance is extremely high.

Considering the various different types of zooplankton makes it is clear that there are a wide variety of morphological traits that need to be considered. Zooplankton comprise over 30 phyla with diverse body plans. Some of the more important ones are the crustaceous zooplankton (euphausiids, copepods), the gelatinous ones (salps, jellies), animals with hard shells (pterapods), and some zooplankton even have gas inclusions (siphonophores). Certainly, the broad classes of animals can be used to predict backscatter, however, in each case, the prediction of sound backscatter will likely be dependent on the details of animal morphology and composition. Note that the animal composition changes based on animal health, food availability. Flagg and Smith: salps, backscatter by salps (recent paper). Moreover since the exact density and sound speed contrast are a function of animal composition

The excellent review by Griffiths et al (2002) notes that there are several classes of animal sound scattering models which have been considered. Fluid like (euphausiids, copepods), animals with hard shells (pterapods), and animals with gas inclusions (siphonophores). An added complication in the case of the animals with gas inclusions is that there is a resonance frequency for the bubble. However, even far away from this resonance peak, the presence of a gas filled inclusion will produce a large degree of backscatter. Figure nn from Griffiths summarizes a comparison of a number of different scattering models. The graph makes it clear that the simple interpretation that acoustic scatter is proportional to animal abundance or biomass is not possible for diverse assemblages of animals. In one recent example of the difficulties associated with a simplistic approach, it was note that the scattering from a 2 mm pterapod is the same as that from a 30 mm euphausiid (Griffiths, 2002, Wiebe et al., nnnn).

An interesting option, extensively considered by Van Holliday (references), is to use multiple frequency bands of interrogation. Since the reflected energy is approximately a linear superposition of the frequency dependent scatter from the animals, providing the individual scattering functions are linearly independent, in principle, an inversion can be performed to compute the relative contributions of each component. Subsequent work by Van Holliday revealed that the inversion was ill-posed, however by positively constraining the inverse, it was demonstrated that it was possible to compute the relative contributions of the different scatterers.

One further complication that should be considered in any attempt to perform a “routine” survey is the effect introduced by the dependence of backscatter upon animal orientation. Figure nn (McGehee et al. , 2003) shows the result of a computer model of the backsatter from a euphausiid (source/ receiver at the same location) as the animal orientation changes from “head on” to a side view. Clearly, the increase in the effective cross sectional area normal to the beam direction shows that the scattering is greatly reduced for the head on view with respect to broadside. Moreover this effect can be large for small changes in tilt angle, resulting in a large change in the amount of reflected energy. Complications due to this effect in the field are particularly severe for elongated animals that do not have gas inclusions (euphausiids). Increased knowledge of animal orientation, or “behavior” is thus a prerequisite for higher accuracy in echo sounder survey results.

As a final note in this section, we remark that there are two traditional modes for performing sonar studies: Echo integration and echo counting. In the echo integration mode, the volume backscatter is recorded and animal abundance is then estimated using either a single frequency or multiple frequency type inversion. In the echo counting mode, the reflections from individual animals are recorded and the number of animals can be inferred from the multiplicity of traces. In practice, problems with the echo counting approach arise in that animal abundances can “saturate” the echo-counting technique in that individual traces are no longer distinguishable. In this case, the total energy in the recorded sound is estimated and the abundance of animals is estimated.

Future methods for acoustic surveys might incorporate different types of collection geometries or via the utilization of more information. An interesting demonstration of multi-frequency recordings from individuals (Demer, 1999) demonstrated that several animal types resident in the Antarctic ecosystem (euphausiids, siphonophores, myctophids) could be spatially discriminated (in some cases) using this approach. Alternative future methods could incorporate phase coherent processing of wide band echoes from individuals. Other alternatives would be to use Doppler processing techniques in order to glean information about animal behavior. As one final opportunity it possible that other aspects of the scattered field like forward scatter or side scatter might offer more information which could be used to improve species discrimination.
2.2 Principles of Underwater Optical Imaging

The basic principles of underwater optical imaging have been known for some time now and the use of optical imaging systems for underwater sensing, exploration and discovery are commonplace to every diver or snorkeler who has marveled at the underwater landscape. On a basic level, one usually discriminates between “passive” imaging and “active” imaging systems as those which are illuminated by either ambient light or by light that the user has created themselves. In the case of passive systems, underwater cameras have been used to record information for many years now. Unfortunately, except in some of the clearest waters, these systems are not capable of producing images of zooplankton, animals who in fact, place a premium on being transparent. As such, in every case that this author can identify, imaging systems for observing underwater zooplankton all use an “active” source of illumination. This source can be either a CW (continuous wave) light source such as a underwater flashlight, a strobe light, or some kind of laser, either pulsed or CW as well. Many of these systems will be reviewed in the section on applications, however first, some physics.

The propagation light underwater can be described in a straightforward way via the concept of radiance. Simply put, radiance is the three dimensional directional intensity of light propagation at a give location and time. Given that radiance is the state variable for the system under consideration, with polarization, the radiant distribution completely specifies the light field. Since this quantity is spatially, spectrally, and temporally variable, its measurement provides quite a challenge for the underwater instrument designer. As covered in companion chapters to this volume, many sensors which have been devised which permit the measurement of either this quantity or one its moments. Cameras measure radiant energy by integrating radiance over each pixel in the camera.

In considering the basic components of an imaging system, Figure nn, shows that the light provided from an artificial source can suffer several fates: (1) Absorption by the intervening water or the subject. (2) Scatter from the intervening water. (3) Reflection from the subject. The goal of any underwater imaging system is to maximize the contribution of (3) while at the same time, minimizing the effects of (1) and (2).

Insert Figure nn (components of an underwater imaging)
The environmental parameters that describe the propagation of light determine how well one can see. These parameters are the absorption and scattering of the water and the reflectivity of the subject. Although these parameters have been measured in some number of cases, the details of every environmental situation can, in fact, play a predominant role in determining the outcome of an underwater optical imaging experiment. This is because, not surprisingly, the ocean can maintain large gradients in absorbers and scatterers (at for example, density discontinuities, or near the sea floor) that can also vary in time. Absorption can be understood by a scalar: a(x,t) however, the more complicated situation of scatter, which must be described by a vector function which indicates how much scattered light can be expected as a function of incident angle and observation angle. In most cases, in the water column, this function can be considered to be cylindrically symmetric, which reduces the dimensionality of the problem, however still leaves a function beta (phi, theta) to be measured.

An additional complication, which can be exploited in many situations, is the possibility of the absorbed light being re-radiated in some form. This can be via fluorescence (basic reference on fluorescence) or Raman Scatter. Both elastic scatter (at the same wavelength of the incident light) and inelastic scatter (at some other, typically longer wavelength) can play a substantial role in the observations of an underwater optical imaging system.

The design of “efficient” underwater optical imaging systems can be aided by the development of computer models which can, in large part, mimic the propagation of light underwater and predict the outcome of a given situation. The computer system permits the user to place both cameras and lights at different locations with various orientations with respect to the subject matter. Predictions from the system can then be produced which will indicate the properties of the image field. Of course, this assumes that the environment has been adequately characterized with respect to absorption and volume scatter. Although the absorption measurements can generally be found, the scattering function information is rarely available. Nevertheless, a set of volume scatter functions (Petzold,19nn) have been used for many years and produce quite believable results. (McGlamery reference, Jaffe comparative imaging reference, Sea Technology article reference). The models can range from either Monte Carlo simulations, which keep track of every photon, to those which use a semi-analytic formulation (Zege, 19nn). The conventional formulation for understanding image propagation utilizes concepts from linear systems theory (image processing reference). In this context, the point spread function describes the transformation that occurs from object to image under scattering phenomena. Some measurements of these functions have been made and several parameterizations exist (Voss, Zege). Although there have been relative few situations where the models have been compared with a complete environmental suite of measurements, in most cases, the models have been used in a comparative sense, weighing different geometries. Most image modelers generally feel comfortable operating in this comparative mode, even if the absolute predictions are off.

In the case of zooplankton, perhaps an even greater unknown is the animals’ reflectivity. As is widely appreciated, many of the animals are quite transparent, this conferring reduced visibility from predators. As such, zooplankton imaging system designers use an empirical approach, simply collecting animals and trying ideas out. Some of the more successful systems (VPR, Critter Cam) use a geometry which …….(learn a bit more about these). Naturally, one would also like to negotiate a degree of “non-invasiveness”, especially if behavioral observations are desired. This can be quite difficult for underwater imaging, since the options for propagating light far are limited and for systems that are in close proximity, the animals are sensitive to hydrodynamic disturbances. Moreover, high light levels might affect the animals’ behavior. The underwater lighting system designer whose goal is to image zooplankton needs to trade off all of the factors.

Note…..the above section could be made a bit more technical with equations for attenuation, scatter and some linear systems theory for image blurring….let me know, your call.

3. Applications: With special relevance to real time sensing

3.1 Acoustical Systems for Sensing Zooplankton

Although there are a variety of different acoustic systems that have been designed for recording reflections from fish the utilization of acoustics for zooplankton, on a commercial basis is limited. In turn, this has limited the types of acoustics systems that can be purchased off-the-shelf for measuring responses from zooplankton. As described above, and with reference to Figure nn-n it is clear that the largest gains to be made in recording sound are when the transition from Rayleigh to Mie or Geometric scattering occurs. An additional complication of the diagram is that the equivalent spherical radius a, is not generally theoretically known. Nevertheless, the user of an acoustics system who desires to “sense” zooplankton must make some decision as to which frequency, or range of frequencies will be used.

In looking at the practical realizations of the different sonar systems it is important to note that there are different types of array geometries that have been used. Assuming that the desired characteristics can be characterized by number of beams and the number of frequencies, Table 1 contains a list of systems known to this author.
Table….Beam considerations: Split Beams, Dual Beams, Multbeams

Single Frequency Systems, Multiple frequency systems, Wide Band Systems.

This section needs a lot of work…..
Examples of the use of different acoustic systems for sensing zooplankton:

Single Frequency Systems

Split Beam

Dual Beam


Multibeam systems:

Commercial systems: Simrad, Denmark

Experimental Systems: FishTV (Jaffe lab)

Multi-frequency Systems

Taps System (Van Holliday)

Bio-mapper II (Wiebe et al…IEEE Ocean Engineering Article)

Prospects for real time acoustical monitoring of zooplankton

TAPS system (Van Holliday….system with

ADCP’s on moorings (British?)

3.1 Optical Imaging of Zooplankton

As described, the use of optical systems for measuring the the goal of using optical imaging systems to measure in-situ behavior of zooplankton has remained elusive.


One system that has been used extensively in the field to characterize zooplankton distributions is the Video Plankton Recorder [Davis et al., 1994]. The system uses forward scattered light to image these animals which are nearly transparent. Several cameras image several volume sizes simultaneously in order to provide information on several size scales. The Video Plankton Recorder is an underwater microscope with coupled video system that can be towed through the water column to make observations of small organisms. Mesozooplankton, or zooplankton in the approximate size range 0.2 - 20 mm, can be imaged. These include copepods, which are among the most numerous macroscopic organisms on earth, and other species such as hydroids and medusa. The quality of the images is generally sufficient to distinguish among species, and the same images can be classified automatically, as by a trained neural network, even at a video-image acquisition rate of 60 frames per second (60 Hz). Such automated classification effects a rapid reduction of a vast quantity of data to figures describing patterns of concentration.

The VPR was developed during the U.S. GLOBEC Georges Bank Regional Program, to which it contributed unique and valuable data about mesozooplankton. It is presently being refined at the Woods Hole Oceanographic Institution for more routine surveying operations.

Avppo remote observatory.

UVP gorsky system: Globec reference, (Stemmann L. et al….Deep Sea Res I, II:

A new system by Benfield [2001] which uses a sheet of strobed white light for illumination promises to yield images of zooplankton over an image field of view of 12 centimeters with a resolution of 50 microns. The zooplankton imaging and visualization system is a profiling instrument designed to collect quantitative images of mesozooplankton to depths of 250 m. The camera is aimed downward into a strobed light sheet that is 12 cm wide and 3 cm deep. By setting the depth of field to match or slightly exceed the depth of the light sheet, only targets that are in focus are illuminated.


An interesting system recently designed and built by Strickler and Hwang [2000] for obtaining information about 3-dimensional trajectories of zooplankton (3D Zooplankton Observatory) uses Schlieren imaging in conjunction with multiple cameras in order to obtain orthogonal projections of the animals in a 1 liter volume. The system permits viewing aquatic organisms ranging from phytoplankton to fish and promises to provide interesting information about zooplankton behavior in the lab.

3.2 Optical Imaging of Phytoplankton


A system which uses a sheet of light to illuminate its subject has substantial advantages for viewing a “slice” of a three-dimensional object. The slice can be illuminated by either laser light or incoherent white light, such as a strobe. Palowitch and Jaffe [1993, 1995] demonstrated a lab based system for imaging the spatial distribution of phytoplankton which was subsequently used by Jaffe et al. [1998] and Franks [2001] in the ocean in both a monochromatic and multispectral mode.

Holographic Imaging (and phytoplankton)



Underwater optical holography has been an area which has seen development in the last decade. In the usual configuration, either “in-line” or “off-axis holography” geometric configurations have been used to record interference patterns on very high resolution film. Next, the interferograms are mounted on an optical bench where a facsimile of the configuration used to collect the images is assembled. A slice through the 3-dimensional volume is then viewed with a video camera or some similar device in order to obtain a set of slices through the 3-dimensional field of view. One of the first contributions to in-situ holography was due to Carder [1979]. One group in the United States which had been working on these problems for some time was under the supervision of A. J. Acosta of the California Institute of Technology. Several Ph. D. theses were authored in this area. Most recently, Katz has developed a holography system which uses an in line configuration in order to record coherent interference patterns that can be assembled into 3-dimensional volumes [Katz et al., 1999]. System resolution is on the order of 10’s of microns dependent upon orientation. Just this year, a group in Aberdeen, Scotland has succeeded in deploying an underwater holographic imaging system which uses both in-line and off axis geometry in order to form a set of images [Watson et al., 2001]. The advantage of the off axis configuration is that it can work at higher densities of particles. Images from both of these systems have been very impressive. Understandably, holographic systems produce prodigious amounts of data, so that the automated analysis of such data is imperative
Flow Cam (extension to underwater)
4. Combining Acoustics and Optics

As considered in detail, the acoustical techniques for sensing zooplankton have the advantage that they can be use at moderate distances (10’s – 100’s of meters) depending on size and frequency. On the other hand, the optical methods can be used for definitive animal identification (providing the magnification is large enough and the water clear). In consideration of this, several investigators have either deployed or synthesized in-situ devices which contained both optical and acoustical devices.

In survely of the George’s bank area Wiebe et al used a VPR system on the biomapper device. The optical information was used to ……. The results indicate that…..

Another example, which permitted exact correspondance between animal taxa, orientation, and backscatter intensity was the author’s labs invention of the OASIS (Jaffe et al…..) The OASIS system combines the FishTV multibeam sonar system with a high resolutiojn sensitive CCD camera. A special location….magic voxel…when the animal was positioned in the exact 3-dimensional location (as sensed by the acoustics system) an optical image was taken of the animal. Deployments of the system over 2 summer seasons resulted in approximately a 100 images of animals. Several taxa were evidenced at the site and can be seen in the pictures. The system was deployed from the ship which was on a mooring. A current vane was placed on the armature so that, in adequate current flow, the system could be pointed “upstream” and thus have no hydrodynamic signature. Behavioral observations of the animal in 3-dimensions, in real time, were consisted with conjecture that the animals were unaware of the device. Figure nn shows the …..of the animals. In addition, a plot of measured target strength vs animal length is shown.

Conclusions(?)…not really the thing in a review article

J. S. Jaffe and would like to thank the Seaver Foundation, the National Science Foundation, and the Office of Naval Research for supporting his research.

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