doi:10.3723/ut.37.029 Underwater Technology, Vol. 37, No. 1, pp. 29–33, 2020
A simple in situ labelling approach and adequate tools for photo and video quadrats used in underwater ecological studies Bernabé Moreno Laboratorio de Ecología Marina, Universidad Científica del Sur, Lima 15067, Peru
Technical Briefing
www.sut.org
Received 23 December 2019; Accepted 25 February 2020
Abstract Ecological studies use quadrats to gather qualitative (1/0) and quantitative (density and surface coverage) information in terrestrial and marine sciences. Depending on the spatiotemporal scale of the assessment, this could be a pilot or a monitoring survey. For monitoring surveys, it is necessary to develop a code for the quadrat itself (in situ labelling), for the digital file (ex situ codification), and ideally, for both. The design of the quadrat used for these studies must accomplish ergonomics through certain specifications such as: made of highly resistant material; negative-buoyant but lightweight; anticorrosive (specially for marine environments); able to stay positioned on seafloor habitat; and compatible with the in situ labelling technique. The present paper is a comparison of quadrats of different materials and widths, including the implementation of an in situ and ex situ codification technique. Recommendations are made after several test hours sampling with quadrats. Keywords: scientific diving, NaGISA, underwater imaging, benthic ecology
1. Introduction Quadrats are widely used in terrestrial (Adler et al., 2007) and marine ecological studies (Iken and Konar, 2003) as they enable collection of standardised data at locations; comparison between sites subjected to (dis)similar environmental settings; and construction of extensive time series through monitoring efforts. Quadrat analysis includes assessing quantitative values of species or functional groups, which are key for punctual evaluations and in particular long-term assessments. In marine subtidal ecosystems, when functionality is prioritised over species identification, non-destructive methodologies * Contact author. Email address: 8ernabemoreno@gmail.com
are used to obtain information in a way that avoids collection of the whole macrobenthic community within the area (Peirano et al., 2016; Balazy et al., 2018). Incorporating a less invasive approach into classic photo and video transects has enabled efficient assessments of marine ecosystems (e.g. Beijbom et al., 2015; Bryant et al., 2017). Subtidal sampling protocols particularly designed for long-term evaluations require the ability for replicates and transects to be tracked, for which some sort of codification is necessary. This labelling can be done a) in situ, by using the quadrat itself to show certain codes, and b) during the data download by renaming files (Fig 1); however, ideally both methods are used. It is important to ensure an adequate labelling system for postprocessing image data in software such as VidAna (Hedley, 2003) or CPCe (Kohler and Gill, 2006). There are several standardised quadrat designs (e.g. Cook et al., 2013); some have been developed for specific camera attachments that allow the quadrat to be placed directly onto the camera for more automatic framing (Van Rein et al., 2011; Beijbom et al., 2015; Ashton et al., 2017). The camera-quadrat combination is useful for exhaustive monitoring; however, it is not adequate for environmental conditions such as strong currents, high turbidity and varying seafloor topography. When using a photo or video quadrat it is important to maintain the linearity on the straight lines (Fig 2). Good buoyancy is required from the diver, and the quadrat should not move once positioned over the benthos. The weight effect (opposite to the buoyant force) must be considered in order to manufacture a quadrat that is resistant and heavy enough to remain in place, but light enough to transport without additional help (e.g. other diver
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Moreno. A simple in situ labelling approach and adequate tools for photo and video quadrats used in underwater ecological studies
Fig 1: Two different codification options proposed for photo and video quadrat files labelling. These may vary depending on the timescale of the assessment (punctual or long-term evaluation), the experimental design (e.g. depth variable: stratified random sampling or transects) and the preference of the researcher. (IPA: Project Islas Pachacamac-Asia; AB: Antarctic Benthos Project)
or a lift-bag). Simplicity of the method and sampling gear (i.e. photography equipment) is fundamental as it should not be time consuming, nor require a high degree of expertise.
2. Materials and methods In order to determine a standardised method, quadrats were manufactured that followed NaGISA protocol measurements (Iken and Konar, 2003). Specifications such as the material and its width were considered to obtain a quadrat of adequate mass with anticorrosive and resistance properties. Two materials were tested: 1) polyvinyl chloride (PVC) pipes (Æ = 70 mm) that were cut, jointed and pierced to permit water leakage, with negative buoyancy (Fig 2a), and 2) A2 stainless steel (A2-SS) bars (Æ1 = 4.7 mm, Æ2 = 9.5 mm) that were bent into quadrats of different sizes for different measurements. Inner quadrats or joining bars were connected by welding if necessary. Initially a Sony a6000 mirrorless camera with a Sea&Sea YS-01 strobe light was used (for Fig 2a). After several attempts, the photographic rig was changed to a GoPro HERO6 Black edition action camera with two SOLA 2000 video lights connected via flex arms to a dual handle and tray. Prior to any fieldwork activity, time (preferably using 00:00 GMT) and date (yyyymmdd) were synchronised between camera, dive computer, logbooks and any additional electronic gear in order to keep a chronological sequence and facilitate record keeping. Greenwich Mean Time was used, as these tests included dives and surveys within the Warm Temperate Southeastern Pacific (WTSP-MP) and the Scotia Sea (SS-MP) Marine Provinces (sensu Spalding et al., 2007). Diving operations were conducted through either surface-supplied air (‘hookah’) or SCUBA diving, depending on logistics and project 30
planning. Two types of in situ labelling systems were tested in order to choose the most practical and effective method. The first label method was adopted from Kohler and Gill (2006), using a medium-size clipper with an acrylic cell on which the code is written with a pencil and easily erased afterwards (Fig 2b, white arrow). The second method was obtained with cable ties of different colours, whose meaning is attributed by the diver depending on the sampling site and the experimental design. These labelling methods were used in both a) photo quadrats (in Pachacamac and Asia Islands, Peru) and b) video quadrats within transects (in Mackellar Inlet, Antarctica). The upper-left angle of the 0.25 m2 quadrat (white arrows on Fig 2e, f, g) was used as reading indicator. Black cable ties on the horizontal bar indicated a) depth (each one representing +5 m) or b) transect number (Fig 2d), and cable ties on the vertical bar indicated a) replicates (white) or b) transect point (orange). Cable ties were tightened to the A2-SS bar that enabled manual slide but avoided unwanted movements. NaGISA incorporates two levels of target sampling with increasing difficulty: 1) non-destructive (photography or videography of the 1, 0.5 and 0.25 m2 quadrats) and 2) destructive (for identification of collected specimens in the smaller area; Iken and Konar, 2003). If collection was required, labelled (A-E) collection bags (mesh size 500 µm) were placed inside the previous replicate bag (E < D < C < B < A) before entering the water in order to match the macrobenthic replicate samples with the corresponding photo quadrats. At the surface, a preliminary photograph was taken of a plate referring to the sampling station. The survey began with the deepest stratum (i.e. 15 m, three black cable ties towards the indicator angle) and the first replicate (i.e. one white cable tie towards the indicator angle). Quadrats were correctly placed according to NaGISA protocol. Photo and video graphs were taken of all sampling units (considering the visibility), and densities (abundance, estimated cover percentages) were annotated in acrylic slates. Macrobenthic organisms were then collected using the most accessible collection bag (i.e. replicate bag A > E). Cable ties were slid accordingly before changing to the next replicate and/or stratum. These steps were followed at different depths within stations. Once at surface, data was downloaded, renamed, arranged and doublecopied after every daily survey.
3. Results and discussion Features of the manufactured and tested sampling units are presented in Table 1. Despite achieving
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Fig 2: Quadrats of different materials using different labelling systems for benthic assessments in various sites within the Warm Temperate Southeastern Pacific Marine Province (WTSP-MP), except for d) in maritime Antarctica, Scotia Sea Marine Province (SS-MP): a) 0.25 m2 PVC quadrat without in situ label; b) stainless steel (A2-SS) quadrat (0.5 m2 with an embedded 0.25 m2) where the light reflection on the acrylic cell (white arrow) avoids a proper in situ labelling; c) effective placement of the 0.5 m2 quadrat in a vertical wall (white arrows indicating anchorage points) enables a proper photography and density annotation; d) a dense aggregation of the Antarctic phaeophyte Adenocystis utricularis on boulders within a very shallow subtidal video-transect, cable ties were used to indicate transect-point (orange) within transect #1 (black) at Mackellar Inlet, King George Island, South Shetland Archipelago; e) a photo quadrat from the Pachacamac Island sampling station #5 (‘P05’ within the code below) showing 100 random points generated in the CPCe software; f) annotation with strong currents within a boulder environment of the photo quadrat in e); g) deepest stratum (15 m) of the station #2 in Pachacamac Island showing five echinoids Caenocentrotus gibbosus and large coverage of crustose coralline algae; h) sampling of the 0.25 m2 quadrat maintaining a peak performance buoyancy on station #1, Asia Island. Focal length f = 3 mm for all photographs, except in a) f = 16 mm.
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Moreno. A simple in situ labelling approach and adequate tools for photo and video quadrats used in underwater ecological studies
Table 1: Detailed features of the sampling units manufactured with different materials and widths (PVC: polyvinyl chloride; A2-SS: A2 stainless steel) Sampling unit
Material/density Total length Pipe/bar d (g cm-3) required (cm) diameter (Æ) (mm)
Mass in air m (g)
Manufacture cost (GBP/PEN)*
0.5 m2 w/internal 0.25 m2 quadrats 1 m2 quadrat with 1 m middle bar
PVC/ 1.38 A2-SS/ 8 A2-SS/ 8 A2-SS/ 8
800 1700 1100 3200
5/20 35/150 40/170 70/300
250 250 500 500
70 9.5 4.7 9.5
*
Sampling units were manufactured in Lima, Peru. PEN: Peruvian Nuevo Sol and its equivalent in GBP: British Pound Sterling
the main aim of surveying a specified area, PVC quadrats did not always remain still over the benthos as they did not have the required negative buoyancy, especially under strong currents. Additionally, the quadrats were not resistant enough as they seemed to be damaged after minor use. PVC quadrats have been widely used for subtidal studies (e.g. Kohler and Gill, 2006; Balazy et al., 2014) owing to cost (Table 1), accessibility and ability to be easily gridded with a cord (Marine Biodiversity Observation Network, 2019). As the PVC pipe diameter was the thickest of the materials (Æ = 70 mm) used in the present study, shadows were generated which affected the quality of the photo quadrat. The shadows caused issues in the post-processing as several plotted points in the CPCe software fell into shadowed surfaces, skewing the image analysis. However, when experimenting with different material (A2-SS bar) and width (Æ1 = 4.7 mm) with the 1 m2 quadrat, shadows were unnoticeable, the quadrat remained still over the benthos and photo quadrats were effectively achieved. Nonetheless, given the length and the flexibility acquired with the width of the bar, uncomfortable vibrations occurred, and the angles were slightly bent while diving through strong currents. The A2-SS 0.5 m2 quadrat (Æ2 = 9.5 mm) had a mass of 1.7 kg, and the 1m2 quadrat had a mass of 3.2 kg (Table 1). Both were reasonable weights to transport with bare hands, easily attach, or clip to a harness or lift-bag if necessary. Both quadrats were deployed in different substrate types (rugosity and inclination). These highly resistant, anticorrosive and negative-buoyant quadrats enabled a good framing over the transect line. Their stability on vertical walls were also tested, and they remained stationary for the duration of photography and annotation through anchoring to the substrate or attached macrofauna (Fig 2c, white arrows). Stainless steel has been effectively used in photo quadrats with ‘framers’ (0.35 m2; Beijbom et al., 2015) and gridded to generate a high-definition mosaic image by stitching the 25 sub-cells (0.5 m2; Cook et al., 2013). The utilisation of (non)framed 32
or (non)gridded photo quadrats will depend on the interest of the present study and the protocol that is being followed. For example, the arising application of artificial neural network (i.e. machine- and deep-learning tools) for automated classification of benthic groups (Beijbom et al., 2015; Ashton et al., 2017) would require an uninterrupted photo quadrat prior to analysis. Regarding the in situ labelling, clipped acrylic cells (Kohler and Gill, 2006) were ineffective as codes had to be erased and changed accordingly, which took an unnecessary amount of time. Additionally, the reflection off the white acrylic prevented the code visualisation, and owing to the cell size, a significant area of the 0.25m2 quadrat was obscured (Fig 2b, white arrow). This in situ labelling method was therefore discarded at the first stages of the research. In contrast, the cable tie method proved to be a very simple but highly effective approach for including relevant information within the photo and video quadrat. During the surveys, multiple dives were carried out together with divers who did not have scientific backgrounds. These non-scientific divers gave positive feedback on the technique, as they managed to set the quadrats correctly and slide the cable ties without problems. The training of parties in sampling techniques was also accomplished, thereby meeting the guidelines and goals of the project. The second photographic rig (1.1 kg on air) was easy to manoeuvre, with the flex arms facilitating the positioning and angulation of the video lights. Three intensities (2000 lumens maximum) were easily changed with the magnetic switch, depending on light requirement of the site. Data download, logbook digitalisation and electronic charge took place once at surface after finishing the daily sampling as programmed. Photo and video quadrats files were renamed and ordered in folders and subfolders following the proposed codification in Fig 1. At any depth, constant graphic register was highly recommended, especially if seasonal or infrequent records, or rare or unregistered animal behaviours were observed. This is achievable when ‘QuikCapture’
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mode is activated on the camera, enabling instant recording when pressing the ‘on’ button. Ideally, wide FOV (field of view), and 1920 × 1080 pixels resolution for photographs, and 1080p–60fps (frames per second) for videos, is recommended. Labelling images with clear, self-interpretative, repetitive codification is achievable with the proposed approach. For successful labelling prior criteria needs to be defined before the sampling takes place. This may vary depending on research aims, researchers and individual preferences, but this must be specified in the metadata of each project. Recommendations from the present work are delivered through material, width and procedures with quadrats; in situ and ex situ labelling and codification techniques; and specifications of the photography rig and its operating modes. Maintaining a simple approach at each stage will enable the development and standardisation of an engaging extended network for benthic ecological assessments.
Acknowledgments The present work was carried out during fieldwork of two projects by the Universidad Científica del Sur. The first included the subtidal component GICS (Grupo de Investigación de Comunidades Submareales) from the project IPA (Pachacamac & Asia Islands), part of the GEF project (ID 4505) Strengthening Sustainable Management of the Guano Islands, Islets and Capes National Reserve System (RNSIIPG), in collaboration with the Peruvian Trust Fund for National Parks and Protected Areas (PROFONANPE) and the National Service of Protected Areas (SERNANP). The second included the hard-bottom component of the project Antarctic Benthos (Factores ambientales que rigen sobre la distribución del macrobentos en Bahía Almirantazgo y Ensenada Mackellar) with the Dirección de Asuntos Antárticos (Ministerio de Relaciones Exteriores del Perú). The author thanks the IPA, the Antarctic Benthos scientific teams and the staff from Naylamp Diving Dive Center for the surface and underwater assistance during the surveys and tests. Geanpierre Guzmán Urteaga is acknowledged as photographer of the image in Fig 2f. The author is grateful to Terri Souster and Báslavi Cóndor-Luján for revising and improving the manuscript with constructive comments, and Aldo Indacochea for feedback and support through the years.
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