Name: development of new methods for quantifying fish density using underwater stereo-video tools
Uploaded: 2017-11-20T14:00:00.000+00:00
Duration: 9 min 32 s
Description: Watch this Scientific Journal Video about Development of New Methods for Quantifying Fish Density Using Underwater Stereo-video Tools at JoVE.com

这项工作是由自然保护和私人捐助者, 资源遗留基金基金会, 戈登和贝蒂摩尔基金会, 环境防御基金, 加利福尼亚海洋赠款计划, 海洋国家合作研究计划, 和 NOAASaltonstall-肯尼迪格兰特 #13-SWR-008海洋应用研究和探索 (德克罗森, 瑞克 Botman, 安迪 Lauerman 和大卫 Jefferies) 开发, 建造和维护了视频着陆器工具。我们感谢 Jim 西格和 SeaGIS™软件的技术支持。船长和商业渔民 Tim Maricich 和船员船上的 F/V唐娜凯瑟琳提供了支持, 在部署着陆器从2012-2015。感谢所有参与视频数据收集或分析的人 (安妮 Tagini, 唐娜克莱恩, 琥珀佩恩, 布唐尼, 玛丽莎蓬, 丽贝卡米勒, 马特乙烯, 沃尔特兴奋, 史蒂夫 Rienecke, EJ 迪克, 和约翰领域)。

注意: 软件步骤的截图包括在辅助文件中。请注意, 下面介绍的软件步骤特定于所选软件 (请参见材料表)。总体方法可以扩展到任何立体软件平台。
1. 为分析准备立体摄影机素材
注意: 建议使用校准立方体进行校准。校准立方体是一个三维铝框架, 在表面上有精确定位的反射点。与校准软件一起使用时, 校准立方体比棋盘方法9更加精确和准确。
<ol><li>使用立体声校准软件校准着陆器摄像机 (图 1和图 2; 有关软件建议, 请参阅材料表。 注: 校准可在现场使用之前, 通过测量不同距离的已知大小的目标 (请参阅补充视频 1) 进行验证。在3米 (或更低) 距离的50厘米目标的平均测量误差应在已知目标长度的2% 以内。另外请注意, 给定的校准将只有在相机位置不相互改变时才有效。这是至关重要的, 以照顾和避免意外拥挤的摄像头, 直到所有的取样已经执行。</li>
	<li>使用校准的着陆器收集字段数据 (图 1,补充视频 2)。</li>
	<li>完成现场研究后, 创建一个包含视频和校准文件的新项目文件夹。 注意: 在每个项目文件夹中, 至少需要五文件: 左边和右边。Cam "校准文件, 左, 右视频文件 (。MP4 或。AVI 格式), 和物种列表 (.txt 格式)。</li>
	<li>在立体声测量软件中, 启动一个新的测量项目, 并加载适当的视频和校准文件。 注意: 所有软件步骤的截图都在辅助文件中提供。<ol>
<li>导航到 "测量" > "新测量文件"。</li>
		<li>通过导航到 "图片" > "设置图片目录" 来设置图片目录, 然后选择包含所有项目文件的文件夹。</li>
		<li>加载左摄像头 "。Cam "文件通过导航到 ' 立体声 ' > ' 相机 ' > ' 左 ' > ' 加载相机文件 ', 并选择适当的文件。</li>
		<li>重复步骤1.4.3 加载正确的相机 "。Cam "文件 注: 这些文件包含每台摄像机的校准测量 (例如、像素大小、纵横比、径向失真、decentring 失真、等), 并将用于测量鱼和计算距离照相机 (即、Z距离)。</li>
		<li>通过导航到 "图片" > "定义影片序列" 并选择左摄像机视频文件, 定义左侧视频文件的影片序列。</li>
		<li>通过选择 "图片" > "加载图片", 将左侧视频文件加载到测量软件中。 注意: 在加载视频文件之前, 请确保 "锁定" 框未选中。这允许同时加载两个视频。</li>
		<li>使用菜单 "立体声" > "图片" > "定义电影序列" 和 "立体声" > "图片" > "加载图片", 为正确的视频定义影片序列并加载视频文件。</li>
		<li>通过导航到 "测量" > "属性" > "编辑/加载物种文件" 来加载物种列表。</li>
		<li>在 "信息字段" > "编辑字段值" 下输入调查 ID 信息并保存文件以创建。EMObs 项目。</li>
	</ol>
</li>
	<li>使用 flash、喝倒彩、协调通用时间 (UTC) 标记或在两个视频中发生的任何时间特定事件同步视频。<ol>
<li>如果使用 UTC 时间戳, 请在左侧视频中向前跨帧, 直到时间戳开始新的第二个秒。其他帧向前, 直到闪光或喝倒彩发生。</li>
		<li>帧-步骤正确的视频前进, 直到时间戳完全匹配左视频。其他帧向前迈进, 直到准确的时刻, 光闪光或喝倒彩匹配左视频。 注意: 将视频同步到同一帧是很重要的。在分析过程中, 应使用视频时间戳定期检查视频同步, 以避免相机帧漂移。在视频的开始和结束时, 还可以使用拍摄的手拍, 以测试右侧和左侧的视频是否同步到同一帧。</li>
	</ol>
</li>
	<li>单击 "锁定" 按钮以确保视频一起播放并保持同步。</li>
</ol>2. 生成点计数和计算 MaxN
注意: 每条鱼最初都以2D 点标记, 以达到可能的最低分类分辨率。不确定 ID 的鱼应标明以备日后复查。
<ol><li>等待开始计数鱼直到一个完整的相机旋转结束, 以确保一个完整的360度使用。还要等到沉淀物清除 (一般 < 1-2 分钟后接触底部)。<ol>
<li>一旦着陆器开始第一次旋转, 右键单击以定义一个新的采样周期: "周期定义" > "添加新的开始时间"。输入第一个句点名称为 "01", 然后单击 "确定"。</li>
	</ol>
</li>
	<li>当着陆器转动时, 开始标记每条进入框架的鱼, 使用左摄像头的2D 点。<ol>
<li>要添加2D 点, 右键单击, 选择 "添加点", 并选择正确的物种名称。标签到尽可能最低的分类学水平, 选择 "许可证" 的未知物种, 并点击 "OK"。</li>
		<li>根据步骤2.2.1 继续标记每条新的鱼直到旋转的结论。</li>
	</ol>
</li>
	<li>对每个附加的着陆器旋转重复协议步骤 2.1-2.2-确保在每个摄像机旋转开始时定义一个新的周期。 注: 物种积累曲线被用来确定八轮换, 平均而言, 足以描述鱼类丰度在本研究。研究人员应该考虑进行初步测试, 额外的摄像机旋转, 超过更长的浸泡时间, 以确定特定生态系统内的最佳摄像机旋转次数。</li>
	<li>计算每个摄像机旋转观察到的个体的 species-specific 计数。<ol>
<li>在枚举所有旋转后, 通过导航到 "测量" > "测量摘要" > "点测量" 并将2D 点保存为 a.txt 文件, 导出2D 点。</li>
		<li>打开保存的2D.txt 点文件作为电子表格, 并创建一个物种与旋转编号的数据透视表, 通过导航到 "插入" > "数据透视表" 来汇总计数 (表 1)。为 "行标签" 和 "列标签" 的 "周期" 选择 "属和种"。</li>
	</ol>
</li>
	<li>选择具有该种最大数量的个体的摄像机旋转 (表 1), 选取每个物种的 MaxN。</li>
	<li>对于只识别属属的鱼类, 选择一个属级的 MaxN, 它是根据在该特定属中的物种数量最多的人的旋转而定的。 注意: 此步骤有助于避免计算只可识别为较高的分类组的单个鱼 (例如, 只对属或家族)。例如, 在表 1中, "旋转 1" 包含10未识别的许氏和33成员, 其中许氏属物种, 而 "旋转 3" 只包含两个身份不明的许氏许可证. 和43成员标识为物种的许氏属。因此, "旋转 3" 将用于未知的许氏的 MaxN 计数。这样, 保守的假设是, 8 的不确定的许氏在 "旋转 1" 中被识别为 "旋转 8"。</li>
	<li>如果多个旋转对某一给定物种具有相同的 MaxN 计数, 请选择第一个旋转与 MaxN 进行3D 点测量。</li>
	<li>对于每个物种, 在 MaxN 发生的旋转中采取3D 的鱼类测量。<ol>
<li>使用在步骤 2.1-2.3 中收集的保存的2D 点, 导航到与3D 测量完全相同的鱼。</li>
		<li>放大至少 4X, 以更好地识别鱼嘴和尾鳍边缘的尖端 (图 3)。 注意: 可能有必要向前或向后帧, 以找到鱼的最佳方向的3D 测量。"最佳" 定位是在两个摄像头都能看到尾鳍的口鼻和边缘。</li>
		<li>手动点击吻口的尖端, 然后在左边的摄像头的尾巴的边缘, 然后在正确的视频重复选择相同的顺序。</li>
		<li>从下拉菜单中选择正确的物种标识, 就像在2.2.1 中那样。</li>
		<li>如果3D 长度测量不是可能的, 例如, 如果鱼的头和尾巴在两个照相机不是可看见的, 然后标记一个3D 点, 而不是左点击鱼的同样位置在左和正确录影。填写之前的信息字段, 并保留注释 "从长度测量中排除"。 注意: 不同种类的摄像机在不同的旋转过程中可能发生 MaxN;但是, 对于任何给定的物种, 测量只应在一次旋转中发生 (表 1)。</li>
	</ol>
</li>
	<li>完成对所有鱼类的3D 测量后, 导出数据 as.txt 文件进行进一步分析。<ol>
<li>导航到 "测量" > "测量摘要" > "3D 点和长度测量", 以及要导出的 save.txt 文件。</li>
	</ol>
</li>
</ol>3. species-specific 测量区域的 95% Z 距离程序
注: 95% Z 距离是一个物种在给定的研究中可以可靠地识别的平均距离的估计, 同时排除了水清澈或光照的特殊情况。这一计算考虑到了一项研究的平均海洋学条件, 每项新的研究都需要重新。
<ol><li>使用简单的引导来确定样本大小是否足够大, 以表征每个物种的可靠检测距离。<ol>
<li>对于每个样本大小类 (例如, 5 条鱼的取样大小箱), 选取1000随机抽取的样本大小, 并从样本填充中进行替换, 并计算这些1000绘制距离的平均95% 位, 并绘制结果渐近曲线。请参见补充文件 1 & 2中提供的代码。</li>
		<li>通过将实际样本大小与 95% Z 距离渐近线的样本大小进行比较, 验证是否获得了足够的样本。</li>
	</ol>
</li>
	<li>计算 95% Z 距离值为95% 位的距离-从相机测量一个物种在所有的调查。</li>
	<li>使用 95% Z 值计算每个物种的有效面积。 注: 在旋转着陆器的情况下, 95% Z 值表示被调查的一幅幅的外半径, 其内部半径由工具的物理设置和摄像机能够观察到的底座的距离决定。当着陆器旋转时, 形成一个 "甜甜圈" 形状的测量区域 (图 4)。<ol>
<li>计算被调查的区域: <img alt="Equation 1" src="/files/ftp_upload/56635/56635eq1.jpg"> 注: 例如, 一个相对较大的物种, 如 Yelloweye 石斑鱼 (许氏 ruberrimus) 的 95% Z 距离3.3 米, 有效的测量面积为 30.9 m2每个着陆器部署: 34.3 m2 (外圆)-3.4 m2 (内部圆圈) = 30.9 m2 (总计调查区域)。</li>
	</ol>
</li>
	<li>使用所调查的计算区域 (步骤 3.3.1), 将单个物种计数 (MaxN) 转换为每个可视化测量的密度估计值 (使用公式: <img alt="Equation 2" src="/files/ftp_upload/56635/56635eq2v3.jpg"> 注: 类似的程序可以用来计算体积密度, 而不是面积密度;但是, 这里没有描述这个过程。</li>
</ol><img alt="Table 1" src="/files/ftp_upload/56635/56635table1.jpg"> 表 1: 示例 MaxN 摘要表.每个物种的 MaxN 的选择是用红色和粗体文本显示的。请注意, 对于身份不明的许氏的保守 MaxN 是由确定为物种的最许氏的旋转确定的 (旋转 3)。此外, 虽然这项研究使用了八相机旋转, 但在表 1中仅显示四轮换, 以简化操作。无论旋转多少, 选择 MaxN 的过程都是相同的。
<img alt="Figure 1" class="xfigimg" src="/files/ftp_upload/56635/56635fig1.jpg"> 图 1: 立体声视频着陆器。密钥硬件是编号为(1) 300 m 脐, (2)两个数字视频录像机 (DVR) 与可拆卸32GB 存储卡在防水瓶, (3)两个 LED 灯输出3000流明在色温为 5000 K, 和(4)两个摄像头, 具有620电视线 (TVL) 分辨率。<a href="//cloudflare-jove-com.bdigitaluss.remotexs.co/files/ftp_upload/56635/56635fig1large.jpg" target="_blank">请单击此处查看此图的较大版本.</a>
<img alt="Figure 2" class="xfigimg" src="/files/ftp_upload/56635/56635fig2.jpg"> 图 2: 校准立方体 (500 mm x 500 mm x 300 mm)。以两种不同方向显示的 "校准立方体" 的校准示例: (a)多维数据集的右侧被推向照相机, 而(B)立方体的表面与摄像机的表面平行。红色点表示此特定校准方法中使用的参考点, 并且必须始终以编号顺序标识。<a href="//cloudflare-jove-com.bdigitaluss.remotexs.co/files/ftp_upload/56635/56635fig2large.jpg" target="_blank">请单击此处查看此图的较大版本.</a>
<img alt="Figure 3" class="xfigimg" src="/files/ftp_upload/56635/56635fig3.jpg"> 图 3: 在许氏 miniatus上放置的3D 测量。在每个摄像头的帧中都发现了尾端的尖吻和尾部, 以便进行立体测量。<a href="//cloudflare-jove-com.bdigitaluss.remotexs.co/files/ftp_upload/56635/56635fig3large.jpg" target="_blank">请单击此处查看此图的较大版本.</a>
<img alt="Figure 4" class="xfigimg" src="/files/ftp_upload/56635/56635fig4.jpg"> 图 4: 着陆器工具调查的区域。着陆器工具探测到的有效面积是由最小 z 距离和每个物种的 95% z 距离限定的。请注意, 该区域在着陆器周围创建了一个 "甜甜圈" 形状的测量量。<a href="//cloudflare-jove-com.bdigitaluss.remotexs.co/files/ftp_upload/56635/56635fig4large.jpg" target="_blank">请单击此处查看此图的较大版本.</a>

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Ser. 350, 245-254 (2007).</li><li>Watson, J. L., Huntington, B. E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Assessing+the+performance+of+a+cost-effective+video+lander+for+estimating+relative+abundance+and+diversity+of+nearshore+fish+assemblages.">Assessing the performance of a cost-effective video lander for estimating relative abundance and diversity of nearshore fish assemblages.</a> J. Exp. Mar. Bio. Ecol. 483, 104-111 (2016).</li><li>Easton, R. R., Heppell, S. S., Hannah, R. W. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Quantification+of+Habitat+and+Community+Relationships+among+Nearshore+Temperate+Fishes+Through+Analysis+of+Drop+Camera+Video.">Quantification of Habitat and Community Relationships among Nearshore Temperate Fishes Through Analysis of Drop Camera Video.</a> Mar. Coast. Fish. 7 (1), 87-102 (2015).</li><li>Hannah, R. W., Blume, M. T. O. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Tests+of+an+experimental+unbaited+video+lander+as+a+marine+fish+survey+tool+for+high-relief+deepwater+rocky+reefs.">Tests of an experimental unbaited video lander as a marine fish survey tool for high-relief deepwater rocky reefs.</a> J. Exp. Mar. Bio. Ecol. 430, 1-9 (2012).</li><li>Starr, R. M., Gleason, M. G., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Targeting+Abundant+Fish+Stocks+while+Avoiding+Overfished+Species:+Video+and+Fishing+Surveys+to+Inform+Management+after+Long-Term+Fishery+Closures.">Targeting Abundant Fish Stocks while Avoiding Overfished Species: Video and Fishing Surveys to Inform Management after Long-Term Fishery Closures.</a> Plos One. 11 (12), 0168645 (2016).</li><li>Love, M. S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> Certainly more than you want to know about the fishes of the Pacific Coast: a postmodern experience. , (2011).</li><li>Campbell, M. D., Pollack, A. G., Gledhill, C. T., Switzer, T. S., DeVries, D. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Comparison+of+relative+abundance+indices+calculated+from+two+methods+of+generating+video+count+data.">Comparison of relative abundance indices calculated from two methods of generating video count data.</a> Fish. Res. 170, 125-133 (2015).</li><li>Cappo, M., Speare, P., De'ath, G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Comparison+of+baited+remote+underwater+video+stations+(BRUVS)+and+prawn+(shrimp)+trawls+for+assessments+of+fish+biodiversity+in+inter-reefal+areas+of+the+Great+Barrier+Reef+Marine+Park.">Comparison of baited remote underwater video stations (BRUVS) and prawn (shrimp) trawls for assessments of fish biodiversity in inter-reefal areas of the Great Barrier Reef Marine Park.</a> J. Exp. Mar. Bio. Ecol. 302 (2), 123-152 (2004).</li><li>Schobernd, Z. H., Bacheler, N. M., Conn, P. B., Trenkel, V. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Examining+the+utility+of+alternative+video+monitoring+metrics+for+indexing+reef+fish+abundance.">Examining the utility of alternative video monitoring metrics for indexing reef fish abundance.</a> Can. Jour. Fish. Aquat. Sci. 71 (3), 464-471 (2014).</li><li>Hansen, M. J., Schorfhaar, R. G., Selgeby, J. H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Gill-Net+Saturation+by+Lake+Trout+in+Michigan+Waters+of+Lake+Superior.">Gill-Net Saturation by Lake Trout in Michigan Waters of Lake Superior.</a> North Am. J. Fish. Manag. 18 (4), 847-853 (1998).</li><li>Dauk, P. C., Schwarz, C. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Catch+estimation+in+the+presence+of+declining+catch+rate+due+to+gear+saturation.">Catch estimation in the presence of declining catch rate due to gear saturation.</a> Biometrics. 57 (1), 287-293 (2001).</li><li>Hilborn, R., Walters, C. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> Quantitative Fisheries Stock Assessment Choice, Dynamics and uncertainty. , (1992).</li><li>Erisman, B. E., Allen, L. G., Claisse, J. T., Pondella, D. J., Miller, E. F., Murray, J. H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+illusion+of+plenty:+hyperstability+masks+collapses+in+two+recreational+fisheries+that+target+fish+spawning+aggregations.">The illusion of plenty: hyperstability masks collapses in two recreational fisheries that target fish spawning aggregations.</a> Can. Jour. Fish. Aquat. Sci. 68, 1705-1716 (2011).</li><li>Buckland, S. T., Anderson, D. R., Burnham, K. P., Laake, J. L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> Distance Sampling: Estimating abundance of biological populations. , (1993).</li><li>Ronconi, R. A., Burger, A. E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Estimating+seabird+densities+from+vessel+transects:+Distance+sampling+and+implications+for+strip+transects.">Estimating seabird densities from vessel transects: Distance sampling and implications for strip transects.</a> Aquat. Bio. 4 (3), 297-309 (2008).</li><li>Caselle, J. E., Rassweiler, A., Hamilton, S. L., Warner, R. R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Recovery+trajectories+of+kelp+forest+animals+are+rapid+yet+spatially+variable+across+a+network+of+temperate+marine+protected+areas+Recovery+trajectories+of+kelp+forest+animals+are+rapid+yet+spatially+variable+across+a+network+of+temperate+marine+protected.">Recovery trajectories of kelp forest animals are rapid yet spatially variable across a network of temperate marine protected areas Recovery trajectories of kelp forest animals are rapid yet spatially variable across a network of temperate marine protected.</a> Nat. Publ. Gr. , 1-14 (2015).</li><li>Starr, R. M., Wendt, D. E., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Variation+in+Responses+of+Fishes+across+Multiple+Reserves+within+a+Network+of+Marine+Protected+Areas+in+Temperate+Waters.">Variation in Responses of Fishes across Multiple Reserves within a Network of Marine Protected Areas in Temperate Waters.</a> Plos One. 10 (3), 0118502 (2015).</li><li>Lester, S., Halpern, B., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Biological+effects+within+no-take+marine+reserves:+a+global+synthesis.">Biological effects within no-take marine reserves: a global synthesis.</a> Mar. Ecol. Prog. Ser. 384, 33-46 (2009).</li></ol>

作者没有透露

传统的 MaxN 度量是基于在调查过程中计算出有保证的最小数量的个人的想法。如果在单个视频帧中同时显示一定数量的鱼, 则不会有任何更少的当前, 但由于鱼是移动和异分布的, 因此在单个视频帧中同时看到所有个人的可能性很低.因此, 传统的 MaxN 可能会低估真正的鱼丰度16,17。此外, 已证明传统的 MaxN 可能显示非线性的负偏置关系与增加鱼丰度<sup class...

在美国太平洋沿岸, 许多对商业和休闲底层渔业很重要的物种 (例如, 石斑鱼复合体 (许氏) 和蛇 (Ophiodon 细长)) 都与浮雕, hard-bottom 栖息地1,2,3,4,5。立体声视频下降相机是一个有吸引力的非工具, 使用在岩石生境由于相对容易和简单的操作。各种立体声摄像系统已经开发并部署在南半球, 浅水生态系统6,7,8,9,10, 以及最近, 视频降摄相机作为一种管理工具, 在太平洋沿岸的深海岩石礁环境中获得了牵引力11,12,13。我们试图通过使用立体声摄像系统 (以下简称 "着陆器") 来修改这些现有的立体相机设计, 以便更有效地描述太平洋沿岸浮雕海底的鱼类种群 (见表材料)。使用的着陆器与现有的视频系统不同, 因为摄像头安装在一个中央旋转杆上, 在下落位置14允许完全360°覆盖海底。着陆器每分钟完成一次完全旋转, 这使我们能够快速地描述一个地区的丰度和群落组成, 并获得相同级别的统计能力, 减少登陆者的部署。(有关着陆器配置的详细信息, 请参见斯塔尔 (2016)14 。研究系统的初步试验表明, 在我们的调查中, 八的摄影机旋转足以描述物种丰度和丰富程度。这一决定是通过观察物种丰度和鱼类密度在较长的下降中的收益递减而作出的。我们建议在任何新的系统中进行一项包括更长浸泡时间在内的试验性研究, 以确定特定生态系统/研究物种的最佳浸泡时间。
通过使用配对立体摄像机, 可以计算每个视频测量的总测量面积和绝对鱼密度;然而, 使用旋转相机需要修改传统的鱼类计数指标。固定视频系统通常使用 "MaxN" 作为部署610上的鱼类的保守计数。传统的 MaxN 描述了一个特定物种的鱼的最大数量在一个单一的视频帧一起观察, 以避免重复计数一条鱼已经离开并返回到帧。因此, MaxN 已经估计出已知存在的鱼的最小数量, 并且可能会低估真正的鱼丰度6,10。MaxN 指标被重新定义, 以代表在每一个摄像机的旋转中看到的最大数量的鱼。
对以前的立体声视频方法进行的第二次修改是考虑到各种大小、颜色和形状的种类具有不同的最大可靠识别距离的事实。例如, 像O. 细长这样的大型物种具有明显的细长形状, 而且与小型和隐蔽的物种 (如 Squarespot 石斑鱼 (许氏 hopkinsi) 相比, 可以可靠地识别出更大的距离。这些不同的最大可探测范围改变了着陆器为每个物种取样的有效面积。因为立体声摄像机允许我们将每条鱼放在三维空间中, 精确度很高, 你可以确定每条鱼的测量距离 (即, "Z 距离", 它的命名为 "z-axis", 这是垂直于相机之间绘制的直线。对于每个物种, 95% 的所有个体被观察到的距离 (以后 "95% Z 距离") 被认为是测量区域的半径, 并被用来计算调查的总面积。除 species-specific 特性外, 可还会受到水浊度等环境条件的影响。由于这些因素在时间和空间上都有变化, 所以仅在聚合中使用 95% Z 统计数据是很重要的。虽然对于大型样品来说是非常准确的, 但在调查的地区, 任何一项单项调查都可能有所不同。
下面详述的协议提供了如何创建和使用这些指标的指导。虽然重点是在太平洋沿岸的深水岩石栖息地的特点, 该方法所描述的修改 MaxN 计数很容易适用于任何旋转落相机系统。对鱼类种群进行定性所需的摄像机旋转数量将取决于当地的生态系统动态, 但修改后的 MaxN 的概念化将保持不变。同样, 虽然我们使用3D 摄影测量软件来分析立体声视频, 但是, 只要在三维空间中的鱼的精确位置是可能的, 这里描述的技术很容易在软件平台上应用。此外, 在未来的研究中, 应用 95% Z 距离值的方法可以考虑 species-specific 范围的可探测性和更准确地计算鱼类丰度。

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

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

在鱼类生态学研究中使用摄像系统继续作为一种可行的、非的测量鱼长和估计鱼类丰度的方法而得到牵引。我们开发和实施了一个旋转的立体声视频相机工具, 涵盖了一个完整的360度采样, 这将最大程度的采样努力相比, 固定相机工具。各种研究都详细说明了静态、立体摄像系统的能力, 以获得高度精确和精确的鱼类测量;这里的重点是开发方法方法, 用旋转摄像系统来量化鱼的密度。第一种方法是发展对公制 MaxN 的修改, 这通常是在给定的相机测量中观察到的最小鱼数的保守计数。我们重新定义 MaxN 是在任何给定的摄像机系统旋转中观察到的最大鱼数。当采取预防措施, 以避免重复计数, 这种方法的 MaxN 可能更准确地反映真正的丰度比从固定相机。其次, 因为立体声视频允许鱼在三维空间中被映射, 所以每条鱼的距离相机的精确估计可以得到。通过使用观察到的距离的95% 位数从照相机建立 species-specific 区域勘测, 我们解释了不同在可探测性之间, 并且避免稀释密度估计用最大距离一个种类是观察.对这一系列可探测性的核算是准确估计鱼类丰度的关键。这种方法将促进旋转立体视频工具在应用科学和管理环境中的集成。

在2013和2014之间, 我们进行了816调查与旋转立体声视频着陆器 (图 1) 沿中央加利福尼亚海岸和收集 MaxN 和 95% Z 距离 (图 4) 数据在超过20种。由于物种的大小、形状和颜色的相互作用 (图 5), 在有效检测到的物种范围内存在明显的模式。例如, 标志石斑鱼 (许氏 rubrivinctus) 在其两侧有明显的条纹, 允许在?...

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

我们描述了一种新的计数鱼类, 并估计相对丰度 (MaxN) 和鱼类密度使用旋转立体摄像系统。我们还演示了如何使用距离相机 (Z 距离), 以估计 species-specific 可探测性。

利用水下立体视频工具量化鱼类密度的新方法研究进展

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 ...

development-new-methods-for-quantifying-fish-density-using-underwater

Universidad San Sebastian

Research

JoVE Journal

Environment

9.2K 次观看.  Moss Landing Marine Laboratories. 我们描述了一种新的计数鱼类, 并估计相对丰度 (MaxN) 和鱼类密度使用旋转立体摄像系统。我们还演示了如何使用距离相机 (Z 距离), 以估计 species-specific 可探测性。

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

Methods for Image-based Surveys of Benthic Macroinvertebrates and Their Habitat Exemplified by the Drop Camera Survey for the Atlantic Sea Scallop

Underwater imaging has long been used in the field of marine ecology but decreasing costs of high-resolution cameras and data storage have made the approach more practical than in the past. Image-based surveys allow for initial samples to be revisited and are non-invasive compared to traditional survey methods that typically involve nets or dredges. Protocols for image-based surveys can vary greatly but should be driven by target species behavior and survey objectives. To demonstrate this, we describe our most recent methods for an Atlantic sea scallop (Placopecten magellanicus) drop camera survey to provide a procedural example and representative results. The procedure is divided into three critical steps that include survey design, data collection, and data products. The influence of scallop behavior and the survey goal of providing an independent assessment of the U.S. sea scallop resource on the survey procedure are then discussed in the context of generalizing the method. Overall, the broad applicability and flexibility of the University of Massachusetts Dartmouth School for Marine Science and Technology (SMAST) drop camera survey demonstrates the method could be generalized and applied to a variety of sessile invertebrates or habitat focused research.

Image based surveying is an increasingly practical, non-invasive method to sample the marine environment. We present the protocol of a drop camera survey that estimates the abundance and distribution of the Atlantic sea scallop (Placopecten magellanicus). We discuss how this protocol can be generalized for application to other benthic macroinvertebrates.

基于图像的海底无脊椎动物及其栖息地调查方法大西洋扇贝落相机调查

Underwater imaging has long been used in the field of marine ecology but decreasing costs of high-resolution cameras and data storage have made the ...

科研

环境科学

Long-term Video Tracking of Cohoused Aquatic Animals: A Case Study of the Daily Locomotor Activity of the Norway Lobster (Nephrops norvegicus)

We present a protocol related to a video-tracking technique based on the background subtraction and image thresholding that makes it possible to individually track cohoused animals. We tested the tracking routine with four cohoused Norway lobsters (Nephrops norvegicus) under light-darkness conditions for 5 days. The lobsters had been individually tagged. The experimental setup and the tracking techniques used are entirely based on the open source software. The comparison of the tracking output with a manual detection indicates that the lobsters were correctly detected 69% of the times. Among the correctly detected lobsters, their individual tags were correctly identified 89.5% of the times. Considering the frame rate used in the protocol and the movement rate of lobsters, the performance of the video tracking has a good quality, and the representative results support the validity of the protocol in producing valuable data for research needs (individual space occupancy or locomotor activity patterns). The protocol presented here can be easily customized and is, hence, transferable to other species where the individual tracking of specimens in a group can be valuable for answering research questions.

Long-term Video Tracking of Cohoused Aquatic Animals: A Case Study of the Daily Locomotor Activity of the Norway Lobster Nephrops norvegicus

Here we present a protocol to individually track animals over a long period of time. It uses computer vision methods to identify a set of manually constructed tags by using a group of lobsters as case study, simultaneously providing information on how to house, manipulate, and mark the lobsters.

生态动物的长期视频跟踪: 挪威龙虾 (诺菲氏肾病) 日生物活动的案例研究

We present a protocol related to a video-tracking technique based on the background subtraction and image thresholding that makes it possible to ...

A Field Primer for Monitoring Benthic Ecosystems Using Structure-From-Motion Photogrammetry

Structure-from-motion (SfM) photogrammetry is a technique used to generate three-dimensional (3D) reconstructions from a sequence of two-dimensional (2D) images. SfM methods are becoming increasingly popular as a noninvasive way to monitor many systems, including anthropogenic and natural landscapes, geologic structures, and both terrestrial and aquatic ecosystems. Here, a detailed protocol is provided for collecting SfM imagery to generate 3D models of benthic habitats. Additionally, the cost, time efficiency, and output quality of employing a Digital Single Lens Reflex (DSLR) camera versus a less expensive action camera have been compared. A tradeoff between computational time and resolution was observed, with the DSLR camera producing models with more than twice the resolution, but taking approximately 1.4-times longer to produce than the action camera. This primer aims to provide a thorough description of the steps necessary to collect SfM data in benthic habitats for those who are unfamiliar with the technique as well as for those already using similar methods.

We provide a detailed protocol for conducting underwater structure-from-motion photogrammetry surveys to generate 3D models and orthomosaics.

利用运动结构摄影测量法监测底栖生态系统的野外入门书

Structure-from-motion (SfM) photogrammetry is a technique used to generate three-dimensional (3D) reconstructions from a sequence of two-dimensional (2D) ...

Behavioral Tracking and Neuromast Imaging of Mexican Cavefish

Cave-dwelling animals have evolved a series of morphological and behavioral traits to adapt to their perpetually dark and food-sparse environments. Among these traits, foraging behavior is one of the useful windows into functional advantages of behavioral trait evolution. Presented herein are updated methods for analyzing vibration attraction behavior (VAB: an adaptive foraging behavior) and imaging of associated mechanosensors of cave-adapted tetra, Astyanax mexicanus. In addition, methods are presented for high-throughput tracking of a series of additional cavefish behaviors including hyperactivity and sleep-loss. Cavefish also show asociality, repetitive behavior and higher anxiety. Therefore, cavefish serve as an animal model for evolved behaviors. These methods use free-software and custom-made scripts that can be applied to other types of behavior. These methods provide practical and cost-effective alternatives to commercially available tracking software.

Here, we present methods for high-throughput study of a series of the Mexican cavefish behaviors and vital staining of a mechanosensory system. These methods use free-software and custom-made scripts, providing a practical and cost-effective method for the studies of behaviors.

墨西哥辣鱼的行为跟踪与神经吻合

Cave-dwelling animals have evolved a series of morphological and behavioral traits to adapt to their perpetually dark and food-sparse environments. Among ...

行为学

Automatic Image Processing to Determine the Community Size Structure of Riverine Macroinvertebrates

Body size is an important functional trait that can be used as a bioindicator to assess the impacts of perturbations in natural communities. Community size structure responds to biotic and abiotic gradients, including anthropogenic perturbations across taxa and ecosystems. However, the manual measurement of small-bodied organisms such as benthic macroinvertebrates (e.g., &gt;500 &#181;m to a few centimeters long) is time-consuming. To expedite the estimation of community size structure, here, we developed a protocol to semi-automatically measure the individual body size of preserved river macroinvertebrates, which are one of the most commonly used bioindicators for assessing the ecological status of freshwater ecosystems. This protocol is adapted from an existing methodology developed to scan marine mesozooplankton with a scanning system designed for water samples. The protocol consists of three main steps: (1) scanning subsamples (fine and coarse sample size fractions) of river macroinvertebrates and processing the digitized images to individualize each detected object in each image; (2) creating, evaluating, and validating a learning set through artificial intelligence to semi-automatically separate the individual images of macroinvertebrates from detritus and artifacts in the scanned samples; and (3) depicting the size structure of the macroinvertebrate communities. In addition to the protocol, this work includes the calibration results and enumerates several challenges and recommendations to adapt the procedure to macroinvertebrate samples and to consider for further improvements. Overall, the results support the use of the presented scanning system for the automatic body size measurement of river macroinvertebrates and suggest that the depiction of their size spectrum is a valuable tool for the rapid bioassessment of freshwater ecosystems.

The article is based on the creation of an adapted protocol to scan, detect, sort, and identify digitized objects corresponding to benthic river macroinvertebrates using a semi-automatic imaging procedure. This procedure allows the acquisition of the individual size distributions and size metrics of a macroinvertebrate community in about 1 h.

自动图像处理确定河流大型无脊椎动物群落大小结构

Body size is an important functional trait that can be used as a bioindicator to assess the impacts of perturbations in natural communities. Community ...

Long-term Behavioral Tracking of Freely Swimming Weakly Electric Fish

Long-term behavioral tracking can capture and quantify natural animal behaviors, including those occurring infrequently. Behaviors such as exploration and social interactions can be best studied by observing unrestrained, freely behaving animals. Weakly electric fish (WEF) display readily observable exploratory and social behaviors by emitting electric organ discharge (EOD). Here, we describe three effective techniques to synchronously measure the EOD, body position, and posture of a free-swimming WEF for an extended period of time. First, we describe the construction of an experimental tank inside of an isolation chamber designed to block external sources of sensory stimuli such as light, sound, and vibration. The aquarium was partitioned to accommodate four test specimens, and automated gates remotely control the animals&#39; access to the central arena. Second, we describe a precise and reliable real-time EOD timing measurement method from freely swimming WEF. Signal distortions caused by the animal&#39;s body movements are corrected by spatial averaging and temporal processing stages. Third, we describe an underwater near-infrared imaging setup to observe unperturbed nocturnal animal behaviors. Infrared light pulses were used to synchronize the timing between the video and the physiological signal over a long recording duration. Our automated tracking software measures the animal&#39;s body position and posture reliably in an aquatic scene. In combination, these techniques enable long term observation of spontaneous behavior of freely swimming weakly electric fish in a reliable and precise manner. We believe our method can be similarly applied to the study of other aquatic animals by relating their physiological signals with exploratory or social behaviors.

We describe a set of techniques for studying spontaneous behavior of freely swimming weakly electric fish over an extended period of time, by synchronously measuring the animal&#39;s electric organ discharge timing, body position and posture both accurately and reliably in a specially designed aquarium tank inside a sensory isolation chamber.

自由游泳弱电鱼的长期行为跟踪

Long-term behavioral tracking can capture and quantify natural animal behaviors, including those occurring infrequently. Behaviors such as exploration and ...

神经科学

Measuring the Structure, Composition, and Change of Underwater Environments with Large-area Imaging

Digital imaging and processing technology have evolved to facilitate the expansion of large-area imaging surveys, which increase our capacity to study the status, trends, and dynamics of organisms living in subtidal habitats. By creating photo-realistic digital twins for ex situ analyses, these approaches allow small field teams to collect substantially more data than was previously possible. Here we present a four-step, large-area imaging survey pipeline and analysis methodology, including image collection, model construction, ecological analysis, and data curation, that has been developed and refined through experimentation over the past decade. Each step described has a consistent focus on the unique value of the original source imagery. While types of data extracted from large-area image surveys are vast, we include here workflows to extract ecological data for structural complexity, community composition, and demographic analyses valuable for monitoring and hypothesis-driven efforts. We additionally include recommendations for metadata standards, which complement the collection of large-area imaging data and support archival efforts facilitating transparency and collaboration between research groups.

This protocol covers a four-step large-area imaging survey methodology used to extract metrics of structural complexity, community composition, and population demographics for coral reef communities. The quality of imagery collected and integrated access to the source imagery are prioritized within each step of the protocol.

Digital imaging and processing technology have evolved to facilitate the expansion of large-area imaging surveys, which increase our capacity to study the ...

Quantifying Fish Swimming Behavior in Response to Acute Exposure of Aqueous Copper Using Computer Assisted Video and Digital Image Analysis

Behavioral responses of aquatic organisms to environmental contaminants can be precursors of other effects such as survival, growth, or reproduction. However, these responses may be subtle, and measurement can be challenging. Using juvenile white sturgeon (Acipenser transmontanus) with copper exposures, this paper illustrates techniques used for quantifying behavioral responses using computer assisted video and digital image analysis. In previous studies severe impairments in swimming behavior were observed among early life stage white sturgeon during acute and chronic exposures to copper. Sturgeon behavior was rapidly impaired and to the extent that survival in the field would be jeopardized, as fish would be swept downstream, or readily captured by predators. The objectives of this investigation were to illustrate protocols to quantify swimming activity during a series of acute copper exposures to determine time to effect during early lifestage development, and to understand the significance of these responses relative to survival of these vulnerable early lifestage fish. With mortality being on a time continuum, determining when copper first affects swimming ability helps us to understand the implications for population level effects. The techniques used are readily adaptable to experimental designs with other organisms and stressors.

Measuring the impacts of environmental contaminants on fish behavior is often subjective and challenging particularly when dealing with sublethal endpoints. We describe methods including video technology to quantify swimming behavior of early life stage white sturgeon (Acipenser transmontanus) during and after 96 hr acute exposures to various concentrations of copper.

使用计算机辅助视频和数字图像分析量化鱼游泳行为应对水铜的急性接触

Behavioral responses of aquatic organisms to environmental contaminants can be precursors of other effects such as survival, growth, or reproduction.  ...

Using an Automated 3D-tracking System to Record Individual and Shoals of Adult Zebrafish

Like many aquatic animals, zebrafish (Danio rerio) moves in a 3D space. It is thus preferable to use a 3D recording system to study its behavior. The presented automatic video tracking system accomplishes this by using a mirror system and a calibration procedure that corrects for the considerable error introduced by the transition of light from water to air. With this system it is possible to record both single and groups of adult zebrafish. Before use, the system has to be calibrated. The system consists of three modules: Recording, Path Reconstruction, and Data Processing. The step-by-step protocols for calibration and using the three modules are presented. Depending on the experimental setup, the system can be used for testing neophobia, white aversion, social cohesion, motor impairments, novel object exploration etc. It is especially promising as a first-step tool to study the effects of drugs or mutations on basic behavioral patterns. The system provides information about vertical and horizontal distribution of the zebrafish, about the xyz-components of kinematic parameters (such as locomotion, velocity, acceleration, and turning angle) and it provides the data necessary to calculate parameters for social cohesions when testing shoals.

The use of a 3D automatic video system that can track individual and groups of zebrafish is described. As application example we explore the effects of the NMDA-receptor antagonist MK-801 on shoals of zebrafish.

Like many aquatic animals, zebrafish (Danio rerio) moves in a 3D space. It is thus preferable to use a 3D recording system to study its behavior. The ...

生物学

Anesthesia-free Heartbeat Measurements in Freely Moving Zebrafish

Zebrafish (Danio rerio) is a widely used model organism in physiological, pharmacological, and toxicological research due to its genetic similarity to humans and transparent embryonic stage, which facilitates non-invasive cardiovascular studies. However, current methods for heart rate assessment in zebrafish often rely on anesthesia to immobilize the subject, introducing physiological alterations that compromise data accuracy and reproducibility. This study presents a novel, anesthesia-free technique for measuring heartbeat in freely moving zebrafish larvae, addressing a critical limitation in cardiovascular research. The proposed approach integrates shortwave-infrared imaging with machine-learning-based heart tracking, allowing for precise and continuous cardiac activity monitoring in non-immobilized specimens. A convolutional neural network was trained to detect the heart region, and a photoplethysmographic signal was extracted from image sequences to determine heart rate. Experimental validation demonstrated the method's reliability and consistency across multiple test conditions. A key benefit of the methodology is its ability to preserve the natural physiological state of zebrafish, minimizing stress-induced artifacts. This non-invasive, label-free technique offers significant advantages for studying cardiovascular physiology, drug cardiotoxicity, and environmental toxicology, expanding the potential applications of zebrafish as a model for biomedical research.

The study aims to develop technology for anesthesia-free heartbeat measurements in moving zebrafish. Our approach combines shortwave-infrared imaging and machine-learning-based tracking of the heart. It is a non-invasive, label-free, and user-friendly technique that suits a wide range of studies on the zebrafish model.

Zebrafish (Danio rerio) is a widely used model organism in physiological, pharmacological, and toxicological research due to its genetic similarity to ...