Name: development of new methods for quantifying fish density using underwater stereo-video tools
Uploaded: 2017-11-20T14:00:00
Description: Watch this Scientific Journal Video about Development of New Methods for Quantifying Fish Density Using Underwater Stereo-video Tools at JoVE.com

This work was funded by The Nature Conservancy and private donors, Resources Legacy Fund Foundation, Gordon and Betty Moore Foundation, Environmental Defense Fund, California Sea Grant Program, the NMFS National Cooperative Research Program, and a NOAA Saltonstall-Kennedy Grant #13-SWR-008. Marine Applied Research and Exploration (Dirk Rosen, Rick Botman, Andy Lauerman, and David Jefferies) developed, constructed and maintained the video Lander tool. We thank Jim Seager and SeaGIS&#8482; software for technical support. Captain and commercial fisherman Tim Maricich and crew onboard the F/V Donna Kathleen provided support in deploying the Lander from 2012-2015. Thank you to all who participated in video data collection or analysis (Anne Tagini, Donna Kline, Lt. Amber Payne, Bryon Downey, Marisa Ponte, Rebecca Miller, Matt Merrifield, Walter Heady, Steve Rienecke, EJ Dick, and John Field).

NOTE: Screenshots of software steps are included as Supplementary Files. Please note that the software steps described below are specific to the chosen software (see the Table of Materials). The overall approach can be extended to any stereo software platform.
1. Prepare Stereo-camera Footage for Analysis
NOTE: Calibration using a calibration cube is recommended. A calibration cube is a three-dimensional aluminum-frame with precisely ...

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The traditional MaxN metric is predicated on the idea of counting a guaranteed minimum number of individuals present during a survey. If a certain number of fish are simultaneously visible in a single video frame, there cannot be any fewer present, but because fish are mobile and heterogeneously distributed, the likelihood of seeing all individuals simultaneously during a single video frame is low. It is therefore likely that traditional MaxN underestimates true fish abundance16,<sup cl...

Along the U.S. Pacific Coast, many of the species important to commercial and recreational groundfish fisheries (e.g., the rockfish complex (Sebastes spp.) and Lingcod (Ophiodon elongatus)) are strongly associated with high-relief, hard-bottom habitats1,2,3,4,5. Stereo-video drop cameras are an attractive non-extractive tool to use in rocky habitats due to the relative ease and simplicity of operation. A variety of stereo-video camera systems have been developed and deployed in southern-hemisphere, shallow-water ecosystems6,7,8,9,10, and recently, video drop-cameras have gained traction as a management tool for deep water rocky-reef environments along the Pacific Coast11,12,13. We sought to modify these existing stereo-camera designs by using a stereo-video camera system (hereafter referred to as &#34;Lander&#34;) to more efficiently characterize fish populations in high-relief seafloors along the central Pacific Coast (see Table of Materials). The Lander used was different than existing video systems because cameras were mounted to a central rotating bar, which allowed for a full 360&#176; of coverage of the seafloor at the drop location14. The Lander completed one full rotation per minute, which allowed us to rapidly characterize the abundance and community composition of an area and achieve the same level of statistical power with fewer Lander deployments. (See Starr (2016)14 for greater detail on the specifics of the Lander configuration). Preliminary tests in the study system suggested that eight rotations of the cameras in our surveys were sufficient to characterize species abundance and richness. This determination was made by an observation of diminishing returns in species abundance and fish density over longer drops. We recommend that a pilot study including longer soak times be conducted in any new system to determine the optimal soak time for a given ecosystem/study species.
By using paired stereo cameras, both total survey area and absolute fish density can be calculated for each video survey; however, the use of rotating cameras necessitated the modification of traditional fish count metrics. Stationary video systems most often use &#34;MaxN&#34; as a conservative count of fishes on a deployment6,10. Traditional MaxN describes the maximum number of fish of a given species observed together in a single video frame, in order to avoid double counting a fish that has left and returned to frame. MaxN has therefore been an estimate of the minimum number of fish known to be present and may underestimate true fish abundance6,10. The MaxN metric was redefined to represent the greatest number of fish seen in each full rotation of the cameras.
The second modification to previous stereo video methods was to account for the fact that species of various sizes, color, and shapes have different maximum distances of reliable identification. For example, large species such as O. elongatus have a distinct elongated shape and can reliably be identified at much greater distances compared with small and cryptic species such as the Squarespot Rockfish (Sebastes hopkinsi). These different maximum ranges of detectability change the effective area sampled by the Lander for each species. Because the stereo cameras allow us to place every fish in three-dimensional space with a high degree of accuracy, one can determine the distance from the cameras that each fish was measured (i.e., the &#34;Z distance&#34;, named for the &#34;z-axis&#34; which is perpendicular to the straight line drawn between the cameras). For each species, the distance within which 95% of all individuals were observed (hereafter &#34;95% Z distance&#34;) was considered to be the radius of the survey area, and was used to calculate the total area surveyed. In addition to species-specific characteristics, identifiability will be impacted by environmental conditions such as water turbidity. Because these factors can vary in time and space, it is important to use the 95% Z statistic only in aggregate. While it will be highly accurate for large samples, any one individual survey may vary in area surveyed.
The protocol detailed below provides guidance on how to create and use these metrics. Though the focus was to characterize deep-water rocky habitat along the Pacific Coast, the methodology described for modified MaxN count is readily applicable to any rotating drop-camera system. The number of camera rotations needed to characterize fish populations will depend on local ecosystem dynamics, but the conceptualization of the modified MaxN will remain the same. Similarly, whereas we used 3D photogrammetric software to analyze stereo video, the techniques described herein are easily applied across software platforms, as long as the precise location of fish in three-dimensional space is possible. Additionally, the approach of applying a 95% Z distance value could be considered in future studies with stereo-cameras to account for species-specific ranges of detectability and to more accurately calculate fish abundance.

<table border="0" cellpadding="0" cellspacing="0" style="width:877px;" width="876">
	<colgroup>
		<col />
		<col />
		<col />
		<col />
	</colgroup>
	<tbody>
		<tr height="84">
			<td height="84" style="height:84px;width:201px;">calibration cube</td>
			<td style="width:193px;">SeaGIS</td>
			<td style="width:279px;">http://www.seagis.com.au/hardware.html</td>
			<td style="width:204px;">1000x1000x500 mm is the preferred dimensions. Other methods of calibration are available.&#160;</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:201px;">CAL calibration software</td>
			<td style="width:193px;">SeaGIS</td>
			<td style="width:279px;">http://www.seagis.com.au/bundle.html</td>
			<td style="width:204px;"></td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:201px;">EventMeasure stereo measurement software</td>
			<td style="width:193px;">SeaGIS</td>
			<td style="width:279px;">http://www.seagis.com.au/event.html</td>
			<td style="width:204px;"></td>
		</tr>
		<tr height="84">
			<td height="84" style="height:84px;width:201px;">Statistical software</td>
			<td style="width:193px;">R Core Team 2017 (v. 3.4.0)</td>
			<td style="width:279px;"></td>
			<td style="width:204px;">Bootstrapping code can be found: https://github.com/rfields2017/JoVE-Bootstrap-Function</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:201px;">Spreadsheet Software</td>
			<td style="width:193px;">Microsoft Excel</td>
			<td style="width:279px;"></td>
			<td style="width:204px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:201px;">2&#160; waterproof cameras</td>
			<td style="width:193px;">Deep Sea Power and Light</td>
			<td style="width:279px;"></td>
			<td style="width:204px;">HD quality preferred</td>
		</tr>
		<tr height="63">
			<td height="63" style="height:63px;width:201px;">2 depth rated, waterproof lights</td>
			<td style="width:193px;">Deep Sea Power and Light : 3000 lumen LED with 5000k color temperature</td>
			<td style="width:279px;"></td>
			<td style="width:204px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:201px;">DVR recorder</td>
			<td style="width:193px;">Stack LTD DVR</td>
			<td style="width:279px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:201px;">standard PC</td>
			<td style="width:193px;"></td>
			<td style="width:279px;"></td>
			<td>Windows 10 preferred OS</td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:201px;">rotating Lander platform</td>
			<td style="width:193px;">Marine Applied Research and Engineering (MARE)</td>
			<td style="width:279px;"></td>
			<td></td>
		</tr>
	</tbody>
</table>

development of new methods for quantifying fish density using underwater stereo-video tools

The use of video camera systems in ecological studies of fish continues to gain traction as a viable, non-extractive method of measuring fish lengths and estimating fish abundance. We developed and implemented a rotating stereo-video camera tool that covers a full 360 degrees of sampling, which maximizes sampling effort compared to stationary camera tools. A variety of studies have detailed the ability of static, stereo-camera systems to obtain highly accurate and precise measurements of fish; the focus here was on the development of methodological approaches to quantify fish density using rotating camera systems. The first approach was to develop a modification of the metric MaxN, which typically is a conservative count of the minimum number of fish observed on a given camera survey. We redefine MaxN to be the maximum number of fish observed in any given rotation of the camera system. When precautions are taken to avoid double counting, this method for MaxN may more accurately reflect true abundance than that obtained from a fixed camera. Secondly, because stereo-video allows fish to be mapped in three-dimensional space, precise estimates of the distance-from-camera can be obtained for each fish. By using the 95% percentile of the observed distance from camera to establish species-specific areas surveyed, we account for differences in detectability among species while avoiding diluting density estimates by using the maximum distance a species was observed. Accounting for this range of detectability is critical to accurately estimate fish abundances. This methodology will facilitate the integration of rotating stereo-video tools in both applied science and management contexts.

Between 2013 and 2014, we conducted 816 surveys with the rotating stereo-video Lander (Figure 1) along the central California coast and collected MaxN and 95% Z distance (Figure 4) data on more than 20 species. There were clear patterns in the effective detectable range of species observed, likely due to the interaction of species&#39; size, shape, and coloration (Figure 5). For instance, the Flag Ro...

Watch this Scientific Journal Video about Development of New Methods for Quantifying Fish Density Using Underwater Stereo-video Tools at JoVE.com

Development of New Methods for Quantifying Fish Density Using Underwater Stereo-video Tools

We describe a new method for counting fishes, and estimating relative abundance (MaxN) and fish density using rotating stereo-video camera systems. We also demonstrate how to use distance from camera (Z distance) to estimate species-specific detectability.

The use of video camera systems in ecological studies of fish continues to gain traction as a viable, non-extractive method of measuring fish lengths and ...

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