3D Reconstruction via Stereoscopy for the Study of Mosquito Swarms

<strong>Introduction</strong> Male mosquitoes swarm to find mates, but the characteristics of these swarms have not often been quantitatively analyzed in the field. This site includes information on a simple method used to localize individual <em>Anopheles gambiae</em> in a swarm via stereoscopic image analysis of video footage swarms recorded in Doneguebougou, Mali. The methods described represent a streamlining of possibly the most basic method for localizing objects in space in the hope that other researchers will be able to apply the method for studying fundamental questions about flying insects or other taxa. To understand the method and its limitations you should read the "Description of a Method for Localizing Swarming Mosquitoes in 3D Space" and the original Manoukis et al paper ("Structure and Dynamics of Male Swarms of <em>Anopheles gambiae</em>") linked in the References section below. <br> <strong>Software</strong> Manoukis et al used various third-party programs to analyze our data. These are cited in the reference "Description of a Method for Localizing Swarming Mosquitoes in 3D Space" including URLs for download. The researchers also developed two programs to facilitate insect localization, which they make available here: 1) An R function to calculate positions from stereo measurements, called calcxyz.R and 2) a convenience plugin for ImageJ which may be used to easily gather these data (called StereoPointPicker, a small modification of PointPicker by Philippe Thevenaz). The code.zip file contains both programs and a short explanation of how to use them. <br> <strong>Visualization of mosquitoes within swarms</strong> This entry contains visualizations of the estimated locations of <em>Anopheles gambiae</em> mosquitoes filmed in Doneguebougou, Mali, between August and October 2007. You will find two types of visualizations here, described below. The objective is to give the viewer an intuitive understanding of the structure and dynamic of these swarms. Each swarm filmed and analyzed is shown separately. All the positions shown are relative to the swarm centroid. More details are given in the paper. <br> <strong>Time lapse movies (FLV)</strong> Two types of flash (FLV) movies are presented here. On the left are the estimated positions of mosquitoes in each stereo image analyzed (each image is separated by an interval of about 15 seconds in real-time). On the right the same data are presented, but the positions of mosquitoes seen are not removed as time progresses. This allows easier comparison of positions between images and over the entire swarming period. <br> <strong>Cumulative object visualizations (VRML)</strong> VRML (Virtual Reality Modeling Language) plots of cumulative mosquito positions for each swarm are included. These models provide complete freedom for the viewer to explore where mosquitoes were seen throughout the swarm. These models are manipulable by the viewer, but you will most likely have to install specialized software for your browser to be able to view them. The NIST VRML Plugin and Browser Detector page (HERE) will detect your browser and platform and list visualization options with download links. Two options that we have tested and can recommend are FreeWRL (for Mac OS X and Linux) and Flux Player (for MS Windows). <em>NIAID Laboratory of Malaria and Vector Research</em><br> <em>May 2008</em> <br>

<strong>引言</strong>
雄性蚊虫通过群聚行为寻找配偶，但目前针对野外群聚的特征，鲜有定量分析相关研究。本数据集收录了一套简易定位方法的相关信息，该方法通过对马里多内古布古（Doneguebougou）录制的蚊虫群聚视频进行立体图像分析，实现对群聚内单只<em>冈比亚按蚊（Anopheles gambiae）</em>的定位。本次所述方法是对空间物体定位最基础手段的简化优化，旨在为其他研究者提供可用于探究飞行昆虫或其他类群基础科学问题的研究工具。若需了解该方法及其局限性，请阅读下文参考文献部分中链接的《3维空间内群聚蚊虫定位方法描述》（Description of a Method for Localizing Swarming Mosquitoes in 3D Space）以及Manoukis等人的原始论文《冈比亚按蚊雄性群聚的结构与动态》（Structure and Dynamics of Male Swarms of Anopheles gambiae）。
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<strong>软件工具</strong>
Manoukis团队使用多款第三方程序完成数据解析，相关程序的下载链接已在《3维空间内群聚蚊虫定位方法描述》的参考文献中列明。此外，研究团队还开发了两款用于辅助昆虫定位的工具，现于本页面公开：其一为基于立体测量结果计算空间位置的R语言函数，命名为calcxyz.R；其二为适配ImageJ的便捷插件（命名为StereoPointPicker，是对Philippe Thevenaz开发的PointPicker的小幅修改版本），可用于快速采集相关数据。code.zip压缩包中包含上述两款工具及简要使用说明。
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<strong>群聚蚊虫可视化结果</strong>
本条目包含2007年8月至10月于马里多内古布古拍摄的<em>冈比亚按蚊（Anopheles gambiae）</em>群聚场景的估计位置可视化结果。此处提供两类可视化结果，详情如下，旨在帮助使用者直观理解此类群聚行为的结构与动态特征。每一个经拍摄与分析的群聚场景均会单独展示，所有显示的位置均以群聚质心为参照基准，相关详细信息可参阅论文内容。
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<strong>延时影片（FLV格式）</strong>
本页面提供两类FLV格式的延时影片：左侧影片展示了经分析的每帧立体图像中蚊虫的估计位置（每帧图像的实时时间间隔约为15秒）；右侧影片则展示相同数据集，但随时间推移并不会清除已显示的蚊虫位置，便于使用者对比不同图像间以及整个群聚周期内的蚊虫位置分布。
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<strong>累积对象可视化结果（VRML格式）</strong>
本数据集还包含各群聚场景蚊虫累积位置的VRML（虚拟现实建模语言，Virtual Reality Modeling Language）可视化图。此类模型允许使用者自由探索整个群聚周期内蚊虫的出现位置。使用者可对这些模型进行交互操作，但通常需要为浏览器安装专用插件方可查看。美国国家标准与技术研究院（NIST）的VRML插件与浏览器检测页面（链接见HERE）可检测用户的浏览器与操作系统，并提供适配的可视化工具及下载链接。经我们测试并推荐的两款工具分别为适配Mac OS X与Linux系统的FreeWRL，以及适配微软Windows系统的Flux Player。
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<em>美国国家过敏和传染病研究所（NIAID）疟疾与媒介研究实验室</em>
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<em>2008年5月</em>