Field test of a novel, low-cost, scanner-based sediment profile imaging camera

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1 LIMNOLOGY and OCEANOGRAPHY: METHODS Limnol. Oceanogr.: Methods 4, 2006, , by the American Society of Limnology and Oceanography, Inc. Field test of a novel, low-cost, scanner-based sediment profile imaging camera Adrian Patterson, Robert Kennedy, Ronan O Reilly, and Brendan F. Keegan Zoology Department, Environmental Change Institute, National University of Ireland, Galway, Ireland. Abstract Sediment profile imagery (SPI) is a well-established technique for mapping benthic habitat quality in soft marine sediments, but several limitations exist in the apparatus employed, particularly the degree of penetration achieved by the sampling device into more compacted subtidal sands and capped sediments. To address this problem and others, such as the high cost of purchasing and maintaining commercially available instruments and illuminating the area to be photographed, a novel scanning sediment profile camera was designed and constructed. This prototypic system was deployed alongside the existing technology in a survey along an established gradient of organic enrichment and in an area of dredge spoil disposal in Galway Bay on the west coast of Ireland. The results of the survey revealed that the novel system, termed SPIScan, achieved a greater degree of penetration than the digital SPI while losing none of the image quality. Although it addresses most of the limitations of existing SPI technology, the new system has one drawback: it is not suitable for deployments in deeper water because of an air-filled space in the imaging module. This disadvantage is offset by the incorporation of an air reservoir attached to the prism. The volume of the reservoir is the dependent factor limiting the operating depth of the system. It is important to note, however, that the SPIScan is a prototype, and the problem of depth limitation can be solved completely with further development of the instrument. Introduction Sediment profile imagery (SPI) (Rhoads and Cande, 1971) facilitates the in situ visualization and analysis of the upper layers of the soft sea floor, including biogenic features and processes. Several types of layers can be identified by SPI images, including the apparent redox potential discontinuity (arpd) layer, a recognizable division between oxidized sediment and reduced sediment (Rosenberg et al., 2001); the dredge spoil layer, which occurs in areas where dredged uncontaminated marine sediment is disposed of in empty marine sand borrow pits (Valente et al., 1998); and fish waste layers, the sedimentation of organic material, especially fish food, beneath fish farm cages Acknowledgments This work was carried out with funding from the Environmental Change Institute, National University of Ireland, Galway, under the HEA PTRLI Cycle II programme. Thanks to Prof. Mike Guiry of the Martin Ryan Marine Science Institute for extending the facilities of the Institute to the authors for the work to be carried out. Thanks are also due to David Burke, skipper of the r.v. Conamara, and crewmembers John Galvin and Albert Lawless of the Department of Zoology NUI, Galway, and Mr. P.J. Walsh of Seaborg Oceanics Ltd for technical support during the study. We would also like to thank Jules Jaffe and the three anonymous reviewers for their constructive comments. (Karakassis et al., 2002). Information returned from images can be used to estimate the quality of soft sea floor habitats (Rhoads and Germano, 1986; Nilsson and Rosenberg, 1997). Although SPI is in itself a versatile technique for mapping benthic habitat quality, it has several limitations, which were the driving factor behind the construction and development of a new method for acquiring sediment profile images, termed SPIScan. The primary consideration for the survey was whether the prototypic system would achieve greater penetration. Sediment profile cameras work by taking an image of the sediment which is reflected by a mirror at the back of a wedge-shaped prism, much like an inverted periscope. This wedge angle is usually 45 degrees. The load-bearing surface of the prism is equal to penetration (cm) 2 prism width (cm). Typically, the load-bearing surface (cm 2 ) is approximately 30 penetration depth (cm). This makes it difficult for the apparatus to penetrate some of the coarser subtidal sands and capped sediments. Modern SPI systems use digital single lens reflex (SLR) cameras, which acquire images via a standard photographic lens focused on a charged couple device (CCD). These lenses create images with relatively large depths of field (up to 5 cm from the faceplate). In other words, features far away from the camera are in focus as well as features touching the faceplate. 30

2 Patterson et al. Fig. 1. The modified body of a Canon 1220u scanner with the faceplate removed and the body machined down to the faceplate support pegs. Possibly one of the most widespread problems with SPI is achieving even illumination of the faceplate, owing to the high cost of engineering prism units without illumination defects. An important aspect of analyzing SPI images is the ability to reliably and reproducibly determine the mean depth of the cline in reflectance between pale oxidized and dark reduced sediments (Rhoads and Germano, 1986; Nilsson and Rosenberg, 1997; Diaz et al., 2003). Even and consistent illumination of the faceplate is vital. Ideally, the flash bulb in the prism is angled (usually 45 degrees to the horizontal) so that it illuminates the faceplate and not the mirror. Only reflected light is incident on the mirror; the camera photographs this image. Low tolerance in the placement of the flash bulb in relation to the geometry of the prism has meant that attempts Fig. 3. The prism unit with the modified scanner installed. to change the geometry of the prism to improve penetration have led to illumination defects. The original SPI systems used photographic film, some of which had a relatively small image storage capacity. Modern SPI systems using digital cameras store images on flash-card storage units which can then be downloaded to a PC through waterproof connectors. With these systems, the number of high-quality images that can be stored depends on the size of the card and the capacity of the power supply. The increased need for monitoring under new legislative requirements, such as the European Union Water Framework Directive (EUWFD), has prompted increased interest in SPI as a low-cost means of surveying benthic habitats and processes and has given rise to the need for standardization of image analysis. The developing technique of in situ timelapse sediment profile imagery (tspi; Solan and Kennedy, 2002) for benthic observatories has added to the requirement for automatic or semiautomatic image analysis so that processed data can be relayed remotely to a base station; that is, we hope to deploy SPI cameras at key locations and have selected data measured from the images and transmitted to a base station. Methods and procedures Fig. 2. The prism unit of the SPIScan system prior to the scanner being inserted. The SPIScan system With the limitations of conventional SPI systems in mind, a novel sediment profiling camera incorporating a flatbed A4 scanner (SPIScan) was developed with two goals, namely, achieving greater penetration and reducing the cost of SPI systems. The image capture device in SPIScan is a Canon N1220u flatbed A4 scanner. The glass faceplate of an unmodified scanner is supported on plastic pegs inside a plastic housing. In SPIScan this faceplate has been removed and the scanner body machined down to the level of the support pegs (Fig. 1). The scanner is then housed in an underwater housing (Figs. 2 and 31

3 Fig. 4. The SPIScan prism with the faceplate o-ring sealed to the body and held in place with stainless steel beading. 3), and a 4-mm tempered glass faceplate is o-ring sealed on the housing with stainless steel beading (Fig. 4). This type of scanner has two important characteristics. First, while CCD-based scanners are a superior imaging device, they are much larger than contact image sensors (CIS). Using a CIS-based scanner in the SPIScan system facilitates the construction of a much thinner prism. Second, CIS-based devices have a very low depth of field when imaging, approximately 2 mm beyond the outer surface of the faceplate. The power requirements to operate a CIS are also much lower than those of a CCD. The use of the glass faceplate provides greater rigidity than a Plexiglas faceplate; however, glass is more susceptible to scratching than plexiglas and may need more frequent replacement. Replacement is a simple procedure that affords an opportunity to simultaneously service the o-ring. Fig. 5. Diagram of the imaging module/prism of SPIScan. 1 = waterproof USB connectors, 2 = studs for the attachment of the prism to the lander frame, 3 = prism housing, 4 = o-ring bed, 5 = stainless steel beading to clamp down the faceplate, 6 = area of the faceplate, 7 = guide bar for the CIS, 8 = imaging unit of the CIS, 9 = CIS body, 10 = nylon blade. A = 80 mm, B = 257 mm, C = 40 mm, D = 40 mm, E = 50 mm, F = 300 mm, G = 40 mm. The imaging module for the SPIScan system (Fig. 5) consists of a prism containing the scanner mounted vertically on the inner frame. A small nylon blade cut at a 45-degree angle is attached to the bottom of the prism. The control module containing the computer (Toshiba Corp., Japan), 12 V 300 hamp power supply (Sonnenschein GmBh, Germany), and electronics (Seaborg Oceanics, Ireland) is attached to the cross piece at the top of the inner frame in an underwater housing (Fig. 6). The stainless steel beading along with the nylon blade creates a leading edge of approximately 13 cm in length. The imaging and control module are connected via underwater connectors and 8 pin cables (BIRNS Inc., USA). SPIScan has a very low-profile prism, 30 cm wide by 4 cm deep by 46.7 cm high. This design gives it a blade-like characteristic intended to improve penetration in a greater variety of sediment types. A rubber bladder of air is attached to the prism using high-pressure tubing. As the SPIScan system is subjected to external pressure at depth, the bladder collapses to equalize pressure within and outside the prism. SPIScan has a very low depth of field (approximately 2.0 mm beyond the outer surface of the faceplate). Material not in direct contact with the faceplate is out of focus, making the sediment-water interface much easier to define. This is especially true of sediments where the dumping of dredged material has taken place and the sediment-water interface is not clear. This low depth of field may lead to the development of automatic or semiautomatic image analysis where software interprets the sediment-water interface and depth of arpd and dredge spoil layers, allowing operators to more rapidly assess benthic habitat quality. Like all scanners, the imaging module in SPIScan travels along the faceplate to collect the image data. An integrated light source in the scanning module illuminates the sediment touching the faceplate. The distance from the CIS to the inside of the faceplate is 1.5 mm. Reflected light is digitized and used to create the image. This obviates the need for a flash bulb (and the precise engineering necessary for proper flash placement). In essence, SPIScan uses its illumination source as the image capture device dually, so there are no illumination defects and there is a total and even illumination of the image. Because the control module of the SPIScan system is a PC, the possible number of images stored is determined by the size of the hard drive of that computer and the capacity of the power supply of the system. This tends to be much greater than even the biggest flash cards; therefore the system can be deployed for long periods of time (especially in a time-lapse capacity) before images have to be removed. A further advantage of using a PC as the storage device is that images are downloaded through a 100 Mbps LAN connection, which increases the speed of downloading images from the system by several orders of magnitude. The traditional SPI system used for comparison The imaging module for the digital SPI system is housed horizontally above the wedge-shaped prism at the base of the inner frame and 32

4 As the winch wire slackens, the inner support frame continues to descend at a controlled rate (~6-7 cm s 1 ) that is governed by the oil-filled hydraulic piston. At the point where the prism intersects the sediment-water interface, a mechanical trigger initiates a time delay. This delay (20 s) allows the electronics to power the flash (in the digital SPI system) and for the prisms of both systems to penetrate fully into the sea floor before an image is taken. SPIScan requires approximately 90 s after this delay to acquire an image because the CIS must travel the length of the scanner. After image acquisition, both systems are reset, ready for the capture of the next image. As the imaging module ascends through the lander on retrieval, a rubber wiper clears away mud adhering to the faceplate. Fig. 6. Diagram of the SPIScan prism and control module mounted on the lander frame (A) and penetrating the sediment (B). 1 = inner frame of the lander, 2 = outer frame of the lander, 3 = weight carriage, 4 = piston, 5 = control module, 6 = prism, 7 = air reservoir, 8 = air line, 9 = waterproof USB cable connecting the scanner to the control module, 10 = underwater connectors. incorporates a Kodak DCS 315 SLR camera and a custom-built internal flash unit. The back plate of the prism contains a mirror mounted at a 45-degree angle to reflect the profile of the sediment-water interface up to the camera. To ensure high image quality, the transparent prism faceplate is of similar optical density to seawater (Plexiglas), and the prism itself is filled with distilled water to eliminate the effect of pressure on the prism at depth and reduce any refraction and/or distortion of light along the image pathway. The Plexiglas faceplate is held on with stainless steel beading that creates a leading edge of approximately 5 cm at the apex of the prism. The lander system and deployments The lander frame for both the SPI and the SPIScan systems consists of 2 parallel stainless steel support frames. The inner support frame incorporates the imaging module and also supports an adjustable weighting system. The outer support frame holds the hydraulic piston system used to control the descent of the inner support frame, mesh mud doors to prevent the apparatus from sinking in a soft substratum, and the main weight-supporting legs. At each deployment, the apparatus is lowered from the stern of an anchored research vessel. During deployment, the frame, complete with either imaging system, is lowered on a steel cable attached to the top of the inner support frame. As the assembly is lowered, tension on the winch wire keeps the inner support frame in an elevated position relative to the outer support frame. The outer support frame is first to set down on the seafloor, leaving the area directly under the imaging unit relatively undisturbed. Assessment A survey to compare the performance of the SPIScan prototype against that of an existing SPI system was executed over a 2-day period on Galway Bay, west coast of Ireland. The target stations consisted of 5 stations along an established gradient of organic enrichment (Kennedy et al., 2002) and an additional 7 stations in and around a dump site for spoil dredged from the channel approaching the docks in Galway City (Fig. 7). Four images were taken at each of the 12 stations with each camera, using the same lander frame, research vessel, and personnel. Images taken with the SPI system were 24-bit uncompressed tagged image file format (tiff) with pixels; images taken with the SPIScan system were also 24-bit RGB tiffs but at pixels. The images acquired by both systems were converted to 8-bit grayscale tiffs for arpd and dredge spoil analysis. Images taken with the digital SPI system were converted to pixels; those from the SPIScan system were converted to pixels. The aspect ratios of the images remained the same. (The apparent difference is due to the cropping of housing parts from the images.) The areas of the arpd and dredge spoil were determined by 8-connectivity analysis (connected components labeling) (Moga and Gabbouj, 1997) with a user-defined threshold using Image Analyst (RVSI Europe, UK). In defining the threshold, a color version of the image was displayed on a separate monitor. The image was histogram stretched in Adobe Photoshop to aid in definition of the color arpd. The threshold of the greyscale image was adjusted to select an area matching the arpd or dredge spoil of the color image. The sediment-water interface was manually drawn by the operator in all images. All other analyses were performed in Adobe Photoshop At station 6, the digital SPI system failed to penetrate through the shell cover of the sediment, averaging 1.9 cm; the SPIScan system achieved penetration depths of 20.2 cm. At station 10, the rocky nature of the sediment prevented either system from penetrating successfully. Neither station was included in the comparison of the two imaging systems. The mean results for all of the measured parameters returned by the digital SPI and SPIscan are shown in Tables 1 and 2. A Pearson correlation test of the mean penetration of each system demonstrated that the two camera systems were 33

5 Fig. 7. Inner Galway Bay. Stations 1-5 represent an established gradient of organic enrichment. Stations 6-12 are located in and around an area of a recent dredge spoil dumping event. positively correlated (r = 0.70, P < 0.05). Regression analysis of the penetration results revealed that SPIScan penetration was 1.71 times that of the digital SPI system (r 2 = 0.973, P < 0.001) (Fig. 8), even though the SPIScan system is lighter (430 kg compared to 510 kg for the digital SPI system) and the digital SPI has an 8-cm head start on SPIScan due to the difference in length of the leading edge of the prism. The increased ability of the SPIScan system to penetrate is due to a lesser area of the prism on which the downward force of the weight of the system acts. The digital SPI system has a greater digging force initially, but the load-bearing surface increases due to the angle of the prism; this area increases with penetration and so the digging force decreases. Conversely, the load-bearing surface area of SPIScan reaches a maximum at 5 cm, giving SPIScan a better chance of penetrating a greater variety of sediments (Fig. 9). At a penetration depth of 8 cm, the digging force of SPIScan begins to exceed that of the digital SPI system. Because the initial 5 cm of the digital SPI system s penetration is not viewable, most of the zone where the narrow and heavy SPI system performs well is not acquired. (For comparison, the initial 13 cm of the SPIScan system is not viewable.) Definition of the sediment-water interface was more amenable with the scanning system, especially at the stations that contained dredge spoil. Very little detail (besides what was in direct contact with the faceplate) was discernable or confused with features or sediment further away. By contrast, in several instances with the digital SPI system, the sedimentwater interface was much more difficult to define, especially at the dredge spoil dump stations (Fig. 10). At a resolution of pixels, SPIScan is the equivalent of an 8.95-megapixel camera. When imaging an area of cm, this gives SPIScan a pixel resolution of 85 µm, allowing the differentiation of grain sizes down to very fine sand. It is the equivalent of a 4.70-megapixel camera photographing a standard cm SPI faceplate. Scanning resolution can be increased to provide greater resolution if necessary, but this setting was considered a good tradeoff between resolution and bottom time from an operational point of view. While the physical properties of the prototypic scanning system (weight, depth of penetration, area imaged) appeared to surpass the older 45 angle SPI prism design, it must be acknowledged that the latter system is a tried and tested technique with an extensive record of successful application (Rhoads and Germano, 1986; Nilsson and Rosenberg, 1997; Karakassis et al., 2002; Solan et al., 2002). For the novel system Table 1. Mean result returned from 4 replicates at each station for the digital SPI system. Presence or absence Depth Depth Depth Surface of of of fecal penetration, dredge arpd, No. Mud pellet Mounds/ Oxic Methane Station cm spoil, cm cm tubes clasts Epifauna layer pits Infauna Burrows voids bubbles

6 Table 2. Mean results returned from 4 replicates at each station for the SPIScan system. Presence or absence Depth Depth of Depth Surface of dredge of fecal penetration, spoil, arpd, No. Mud pellet Mounds/ Oxic Methane Station cm cm cm tubes clasts Epifauna layer pits Infauna Burrows voids bubbles to stand up to this record of achievement, it would be necessary for the system to return comparable results for all measurable parameters in the survey. To test this, the difference of means between the two camera results for each station was calculated, and these differences were compared to zero with a t test. The results returned from this analysis illustrate that greater penetration is achieved with the SPIScan system, and all other apparent parameters return similar results for both systems when the data are standardized for the width of the faceplates (Table 3). Discussion The low construction cost approximately US$5,000 plus labor and ease of use of the prototype system are its most attractive properties. Built almost entirely from readily available off-the-shelf components and incorporating standard PC software, the system is practically universally available to anyone with an interest in mapping benthic habitat quality. Fig. 8. Results of the regression analysis of SPIScan (y-axis) versus a digital SPI (x-axis). Each point represents the average penetration value from 4 replicates. Fig. 9. The digging force of the digital SPI system (SPI2) versus the digging force of the SPIScan system. 35

7 Fig. 10. Comparatively sized images from digital SPI (a) and SPIScan (b) illustrating the larger size of the sample image. Images were taken at Margaretta Station (station 1). (c,d) The difference in the ability to penetrate coarse sediments (shell debris in this case) illustrates the improved penetration of the SPIScan system. The low depth of field in the larger SPIScan image illustrates the ease by which the sediment-water interface is determined compared to an image at the same station using digital SPI. Images were taken at station 6. The artifact visible at the top of panel d is the wiper that cleans the faceplate when the system is being retrieved. From the results of the survey, it is obvious that the prototypic scanning apparatus is comparable to the more established digital SPI systems, returning similar results for all measured parameters except for superior penetration, despite the fact that the digital SPI system has an 8-cm head start on the SPIScan system due to the difference in the length of the leading edge of the prism. An encouraging result of this survey was the greater degree of penetration achieved with the new system without the addition of extra weight, and especially the achievement of penetration at station 6, where the sediment was capped with a layer of bivalve shell. The larger field of view gives a larger sample size, in which features missed by the smaller digital SPI system may be recorded in some instances, influencing decisions of what operators consider the successional stage of a study site. SPIScan deployments in the intertidal zone or in shallow Table 3. Results of t test analysis to compare the results obtained from the SPIScan system with those obtained from the digital SPI system, n = 10. Test Value = 0 95% confidence interval Significance Mean of the difference t df (2-tailed) difference Lower Upper Depth of penetration Depth of dredge spoil Depth of arpd Mud clasts Epifauna Surface fecal pellet layer Tubes Mounds/pits Infauna Burrows Oxic voids Methane bubbles Data are differences between mean measurements for a particular parameter. 36

8 waters, which allow the operator to establish a live feed to the control module of the scanner software, also permit modification of the size of the area imaged. For example, the software allows for the selection of a particular area of the image, such as the sediment water interface or a particular burrow, to be imaged at the same resolution as an entire image of the sediment. The low depth of field ensures that only features immediately in front of the faceplate are measured, and the even illumination of the scanning system ensures that nothing will be missed. Some operators have modified digital SPI systems for applications involving divers. However, these devices are often cumbersome and difficult to use underwater, as a diver SPI system is essentially the SPI unit without the lander. SPIScan s lightweight construction, the low profile of the prism, and the independence of the prism from the control module make the system more adaptable to diver operations. Comments and recommendations Although SPIScan may be a low-cost alternative to digital SPI, there is one important disadvantage, namely its maximum operational depth, which is dependent on the volume of the air reservoir. The older digital and film-based SPI systems have been deployed and returned images from sediments in waters up to 5000 m deep. In contrast, the maximum operating depth of the SPIScan system depends on the volume of the compressed air reservoir employed to equalize pressure in the airfilled prism. While the system may not survive the pressures at depth, it may provide an alternative for surveying shallower coastal waters where its lightweight construction facilitates the operation of the system from smaller research craft. Considering this disadvantage, it should be remembered that this is a prototypic system in the early stages of development. If the maximum depth issue is to be overcome, 2 problems will have to be addressed. First, pressure-rated electronics must become commercially available. Pressure-rated electronics are not manufactured commercially, and the cost of developing such electronics would be expensive and as such completely negate the ability to build a low-cost SPIScan system. In-house testing of the SPIScan electronics revealed that they will operate at pressures up to 10 bar (~ m depth). Second, the prism is an air-filled space and as such is susceptible to external pressure. The introduction of an electrically inert fluid, such as Fluinert (3M Corp., USA), with a refractive index close to that of water may be a solution to be researched further. Due to the large costs of purchasing an SPI system (up to US$90,000), the number of operators is quite small. However, the new SPIScan system is essentially a scanner attached to a computer and housed in a watertight container. This makes the system more affordable (approximately US$5,000 plus labor), and because it is composed of general office equipment, it is also much easier to use. This affordability and ease of use make the technique of sediment profile imagery more readily available to researchers. References Diaz, R. J., G. R. Cutter, and D. M. Dauer A comparison of two methods for estimating the status of benthic habitat quality in the Virginia Chesapeake Bay. J Exp. Mar. Biol. Ecol : Karakassis, I., M. Tsapakis, C. J. Smith, and H. Rumhor Fish farming impacts in the Mediterranean studied through sediment profile imagery. Mar. Ecol. Prog. Ser. 227: Kennedy, R., M. Solan, and B. F. Keegan Alternatives to quantifying macrobenthic diversity at the species level: the utility of estimating diversity from higher taxonomic levels and sediment profile imagery (SPI). In: Marine Biodiversity in Ireland and Adjacent Waters. J. D. Nunn, Ed. Proceedings of a local meeting of the Estuarine and Coastal Sciences Association (ECSA), Ulster Museum, Belfast, Apr , Museums and Galleries of Northern Ireland, pub. no. 8, Belfast. pp Moga, A. N., and M. Gabbouj Parallel image component labeling with watershed transformation. IEEE Transact. Pattern Anal. Machine Intell. 19: Nilsson, H. C., and R. Rosenberg Benthic habitat quality assessment of an oxygen stressed fjord by surface and sediment profile images. J Mar. Syst. 11: Rhoads, D. C., and S. Cande Sediment profile camera for in situ study of organism sediment relations. Limnol. Oceanogr. 16: , and J. D. Germano Interpreting long-term changes in benthic community structure: a new protocol. Hydrobiologia 142: Rosenberg, R., H. C. Nilsson, and R. J. Diaz Response of benthic fauna and changing sediment redox profiles over a hypoxic gradient. Estuar. Coast. Shelf Sci. 53: Solan, M., and R. Kennedy Observation and quantification of in situ animal-sediment relations using time-lapse sediment profile imagery (tspi). Mar. Ecol. Prog. Ser. 228: , and others Towards a greater understanding of pattern, scale and process in marine benthic systems: a picture is worth a thousand worms. J Exp. Mar. Biol. Ecol : Valente, R. M., H. Y. Hung, S. McChesney, and G. Hodgson An investigation of benthic recolonization at a backfilled marine borrow pit in Hong Kong, In: Proceedings of the Third International Conference on the Marine Biology of the South China Sea. Hong Kong, Oct. 28-Nov. 1, B. Morton, Ed. Hong Kong University Press, pp Submitted 24 November 2004 Revised 21 October 2005 Accepted 10 January