Name: spotting cheetahs: identifying individuals by their footprints
Uploaded: 2016-05-01T14:00:00.000+00:00
Duration: 9 min 47 s
Description: Watch this Scientific Journal Video about Spotting Cheetahs: Identifying Individuals by Their Footprints at JoVE.com

The authors would like to acknowledge the support of the N/a'an ku s&#234; Foundation, Namibia; the JMP division (jmp.com) of SAS (sas.com) USA; Chester Zoo, U.K., Cheetah Conservation Botswana, Botswana; and Foundation SPOTS, Netherlands.

伦理声明:本足迹识别技术是一种非侵入性的技术。任何生物样本进行。与许可文件只有注册俘虏猎豹被使用。猎豹的参与仅限于沿沙走小道留下足迹，以换取食物奖励。 注意:此协议说明了使用一个数据可视化软件的如JMP，以下简称为"数据可视化软件"来分类使用足迹识别技术的脚印。 安全声明:猎豹从来没有离开无人防守的（2人），并放置在单独关押设施在可能的情况。用于处理圈养猎豹直接在沙道上，使脚印引诱。较难搬运其他动物在从机箱外面的诱惑。 术语: 追踪:一个足迹; 开拓者:コnbroken系列由一个单一的动物制成的脚印。 1.收集脚印<ol><li> 贴剂和协议 <ol><li>收集该协议的下列材料:细耙，或粗耙和篡改，手洒水或喷壶，两个标准的统治者（厘米）或者一个木匠"折尺诬陷打印，标准的数码相机（最小分辨率1200点¯x1600 PIX），遮阳如果与数据记录所需的空间和标准足迹标签来记录拍摄，日期，足迹系列，离散打印ID，动物ID，位置和深度，如果&gt; 2的厘米）的名字一把伞。 </li><li>有关打印最大光造影工作，清晨或傍晚。如果这是不可能的，从一把伞人工遮阳可以提高脚跟和脚趾垫定义当太阳开销。 </li><li>无论是莱天然底物或建筑商的沙约1厘米深的路径。请确保它是关于2-3米宽并运行用于沿周边围栏或惯常移动路径3和15微米之间。 </li><li>湿并平滑标准园艺工具基材，以提高打印质量和清晰度。如果存在手动删除树叶和石块。 </li></ol></li><li> 采集脚印的训练数据集 <ol><li>引诱横跨沙路猎豹用食物奖励。足迹已作出后，导致动物从路径了。 </li><li>成像每个脚印线索后（参见1.3）刷线分开，并记录下一个线索准备表面。 </li><li>只有收集训练数据集左后打印。左侧后足具有领先的趾（趾3），趾4和趾5制作一个斜坡到左边。前脚比后脚更广。花时间学习如何成像之前识别它们。 </li></ol></li><li> 使用成像足迹识别技术协议的足迹 <ol&gt; <li>通过手动绘制每个左右后留下的足迹了一圈突出沿着小道个人足迹的位置。用棍子或任何其他合适的地方的工具。 </li><li>图像的第一足迹如下<ol><li>放置一个公制比例低于约1厘米至足迹的左侧。 </li><li>下的比例，并没有触及足迹，放置一个带照片的身份证滑移，​​并在预分配空间摄影师，日期，足迹系列，深度的名称写（如果&gt; 2的厘米）离散打印ID，动物编号和位置。 </li></ol></li><li>多空打印并指出照相机镜头正上方的足迹，避免图像中的任何视差与关系的规模或带照片的身份证滑。使用三脚架或助理，以检查是否有必要。 </li><li>确保足迹，规则和照片的身份证滑完全填充框架。 </li><li>收集大约20个质量好左后打印完成收集动物。如果20 PR整数不可从第一踪迹，重复处理从1.1.6至1.3.5具有相同的动物。 </li></ol></li></ol> 2.图像特征提取此前的足迹识别技术分析<ol><li>在足迹识别技术图标，双击并打开它作为一个附加到数据可视化软件。观察屏幕上的主窗口。选择"图像特征提取"，以显示这个新窗口。足迹识别技术在编码语言JSL数据可视化软件脚本运行。主菜单示于图。 1。 </li><li>使用鼠标，拖动和第一足迹图像拖放到图像特征提取窗口。特征提取模板导向显示在窗口的左侧。 </li><li>单击并选择"调整大小"按钮，以确保足迹图像图形窗口中。点击在外面脚趾（趾最低分25）放置标记，然后选择"旋转"。观察到图像上线加入点水平旋转，标准化方向。观察一组十字的自动显示在步骤2.6中使用。 </li><li>如果基材深1厘米以上，通过点击"衬底深度"按钮，进行深度修正算法。 </li><li>点击所需的规模放置两个刻度分。对于猎豹设置比例为10厘米，上规模的因素中设置的。 </li><li>在图形窗口的左侧使用模板，依次放置25标志点。标志点都在足迹定义解剖点，例如最前，后，每个脚趾和脚跟的外侧和内侧分。使用十字线，以提高对于新手用户的准确性。观察提示出现在图像的左上角显示的点的序列。 </li><li>选择"导出点"，生成另外的十五点FROM具有里程碑意义的点。该方法增强了的可用于算法开发的变量数。 </li><li>完成对图像的足迹所有数据字段;猎豹，轨道，小径，日期，时间和地点点（GPS） 图。 2所示阶段2.2-2.8。 </li><li>按"添加行"按钮发送136脚本变量（距离，角度，面积），以一排在数据库中。 </li><li>重复步骤2.1至2.9为所有的脚印，直到数据库被填充了XY坐标为每一个地标和派生点和所有的每个足迹计算的变量。 </li><li>数据库中的所有行复制并粘贴数据库下方。这种重复设置被称为参考价值重心（RCV），其作用是稳定的足迹小径随后的两两比较的足迹识别技术模型。 </li></ol> 3.足迹识别技术的算法猎豹发展<ol&gt; <li> 成对强大的交叉验证判别分析 <ol><li>从主菜单中，选择并打开强大的交叉验证配对分析窗口（ 图3）。足迹识别技术模型使用分类器来确定一对属于同一个人或小径两个不同的个体（ 图4）的可能性。 </li><li>开展利用已知的个人训练数据库如下步道两两比较: <ol><li>选择猎豹为"输入X，模型分类&#39;，并作为"输入步道"小径。在Y列（足迹测量），为连续变量，会自动填充。 </li><li>选择"运行"。观察显示进度分析进度条。观察数据表出现显示步道的两两比较。 </li><li>观察两个输出，分配的自体/非自表来描述各V之间的距离分类alidation对，并示出所选的用于比较的不同路径分类矩阵窗口，和轮廓概率。观察显示模型按钮示出了用于每个比较的变量，而这使得质心之间的距离的距离阈值框。 </li><li>在指定的自体/非自表的基础上选择"集群"按钮。观察两个表。第一个节目任意两条路径之间的距离。第二个是"集群"树状图 - 对选择的变量分类的最终输出。通过点击树形图彩色编码它的任何分行可视化的分类集群。 </li><li>通过改变的变量（测量）的数目和轮廓概率（围绕质心值置信区间）检验分类的准确性。重新显现在使用18个变量（ 图5a）所产生的聚类图中的数据。这给出了七个正确的预测猎豹。 图5b（24个变量）和C（10个变量）显示通过测试不同的变量和轮廓概率投入获得猎豹号不同的估计。 注:同比例增减的分布曲线给出了由100％预测数的相对概率（几率）。作为滑动刻度被移动为示出了预测值的每个估值任一侧的相对概率。 图5D示出了具有18个变量的结果，与在一个方向上移动的滑尺表明十猎豹的几率小于50 ％。 </li><li>选择一致地给出了最高的准确性的算法。调整阈值，以允许该算法被设置以产生最佳的近似于在训练数据库（ 图5a）已知的动物的数量的结果。 </li></ol></li></ol></li><li> 全回扣试验进行验证 &lt;登记/&gt;验证为个人的预期数目和聚类分类用卡合部的试验和随机分配在数据集中的各个猎豹测试和训练集（ 图6）的准确度的算法。要使用的步骤如下: <ol><li>从参考数据库，决定为数据集的顺序划分成测试和训练集大小合适的时间间隔。对于猎豹数据库，使用间隔为4。 </li><li>随机选择四个人作为测试数据集（训练集中离开34）。隐藏所选择的四个测试个体的身份。 </li><li>点击"成对数据分析"选项，并选择了四个测试个人所有的小径。 </li><li>点击"运行"，启动足迹识别技术分析。该分析将给出预测在测试数据集的个人的数量。重复这个过程9次（共10个），每个时间随机选取四个人。 </li><li>计算该试验大小的平均值的预测值（ 即四个）。然后重复过程顺序地八个随机选择的个体（取决于间隔大小），然后12等与10次重复每个测试大小。计算每个测试的平均规模预测值。 </li><li>使用作图软件图的曲线图，如图所示。 6，红线表示实际的测试规模暗算自己，绿星号显示每个迭代和蓝线的个人的预测数字显示为每个测试规模的平均预测值。红色和蓝色线条的接近程度是所述足迹识别技术分析的精度的指标。 </li></ol></li></ol>

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本文概述的足迹识别技术的理论应用及其潜在作为一个新的具有成本效益的，社区友好的方式来监测，并且因此帮助保护猎豹。在工具的广泛应用的下一步将是更广泛的现场测试，在地区范围内人口的猎豹。 足迹鉴定技术不同于以前的尝试，以确定在几个关键方面脚印个人;标准化的和严格的足迹集合协议，一个简化的图形用户界面软件，图像分析前的取向和优化，为分类的新的统计模型。 有必要的协议的成功几个关键步骤。首先，沙道必须正确准备和动物领导在沙在一个正常的放松步行速度。当成像的脚印，在photographer必须直接开销打印的中心。往往是有用的观察员进行检查。最后，这是非常重要的，摄影师（或助理，谁可能是一个专家跟踪器）能识别地面上的猎豹足迹，并有技能沿行进路线向前或向后跟踪脚印的痕迹。 跟踪技能是有效的进一步实施该技术的监控未知或自由放养的猎豹是必不可少的。功力不足会导致不同的动物可能会一起旅行的小径之间不够明确的脚印或混乱的集合。这后一点是猎豹，其中年轻男性，有时形成3个或更多的动物，一起移动的联盟尤为重要。然而，这种关注已经解决了另一种社会的物种，白犀牛，其中一起移动多达13个人组成的团体均正确鉴定通过使用向前或向后的小径跟踪足迹识别技术田间（Alibhai 等，2008）17。 虽然现在很少有剩余的专家土著跟踪，协调正在努力与他们接触和他们的技能传授给他们的社区的年轻成员。其中一项举措，古代技能学院，将由N / a&#39;an区SE基金会在纳米比亚举行。同样，跟踪培训认证项目的快速增长，使科学家和业余博物学家学习这些重要领域的技术。 在足迹图像的标志点精确手动定位的核心是技术的准确性。此外，运营商必须熟悉脚并导致足迹的基本解剖。作者目前正在尝试开发自动化，以减少所涉及的体力劳动，并帮助解决有关斯坦任何问题在不同的运营商dardization。在此期间，它被简单地建议里程碑式的定位是一个操作员在每个字段站点的责任。目前正在努力从事数据采集和分析公民科学家，这将极大放大领域的应用。尽管有这些目前的限制，这个软件协议已经成功部署在该领域进行了一系列物种，包括黑与白犀牛，貘低地和东北虎。 与脚印的工作有一个明显的局限性 - 基材必须允许其清晰的印象。部分打印或印刷质量差的不足，提供详细的32。然而，猎豹范围的大面积是理想的足迹采集，并为小，否则不适宜地区，它甚至有可能通过将人工砂的小径收集脚印绕过这个限制。这些足迹印象焊盘可以与CA组合可以有效地使用梅拉陷阱，例如在已知的猎豹标志的职位/棵。跟踪能力和当地知识可以大大有助于寻找和确定合适的衬底区域。 因为足迹识别技术是非侵入性的，它不会造成任何干扰动物的生态或行为。许多研究显示捕获，固定化，处理的潜在和实际风险，和仪器的嵌合，在这种做法产生的成本，并收集不可靠的数据33的风险。足迹鉴定作为一种技术在养护管理的另一个优势。基于传统的跟踪能力和成本效益，它可以从事水土保持监测的过程以前被边缘化的当地社区。机架34和35利本伯格独立处理和证明养护监测技能和包括这些群体的价值。 在监测猎豹的足迹鉴定技术能力，未来的发展是持续的，包括现场试验与自由放养的猎豹验证，楼龄级算法（包括在一段时间内的个人脚形态的变化）和底物的控制。笔者也调查计算机视觉技术，使图像分割，优化的准确性和一致性标记标志点。 由于足迹的最普遍的动物的标志之一，而且往往更容易找到比动物本身，更广泛地采用的足迹鉴定可能是改变游戏规则的养护监测。世界上主要的保护陆地面积获得每年36估计有8个十亿休闲访问。大多数游客现在随身携带的智能手机。使用正在为WildTrack开发的应用程序占用数据的收集将是简单，快速并可能Ëffect前所未有样本大小和空间尺度的一个数据集。凭借高性价比的数据采集协议，足迹识别技术可以随时适应网格到任何保护工具箱。作为图像分类系统，它的强大模式也可能在医疗，法医学应用，和执法领域（ 如反盗猎）。

猎豹（ 猎豹jubatus）是非洲最濒危的猫科动物和脆弱，人口趋势，由IUCN红色名录濒危物种1所列下降。全局猎豹人口估计为7-10,000个体1和纳米比亚是公认的自由测距猎豹的最大据点之间，也许超过三分之一的世界人口4,6,7的更多。人口估计为南部非洲在2007年的下一个最近的范围状态博茨瓦纳放在纳米比亚猎豹人口为2000与1800，其次是南非（550），津巴布韦（400），赞比亚（100），莫桑比克（&lt;5）。有几个国家是未经评估7。 纳米比亚当局有明确规定的愿景"安全，可行的猎豹种群在一系列的生态系统，与成功共存的，和纳米比亚人重视。"然而，家畜与游戏的农业是主要的土地在纳米比亚8,9和地主经常使用陷阱，企图以减少牲畜或有价值的野生动物捕食杀死它们的属性猎豹。 1200多只猎豹被拆除1991年至2006年，但并非所有"offtakes"记录10。此外，还有对这个是否是一个有效的解决了农民猎豹冲突的辩论。视为造成冲突，动物杀死或易位的去除可能比通过其他手段，如更好家畜保护11缓和冲突的效果较差。 12个月后易位生存发布率介于18％至11％40 12。 在纳米比亚的人数，身份和猎豹的分布收集可靠数据的关键是解决人类猎豹冲突局势。目前猎豹监测技术的范围从纳米针对性的问卷调查环境和旅游部陈水扁向游客和政府相关部门4伺机观察报告4，利用相机陷阱13，GPS或VHF项圈10,14，农民的采访调查8，甚至斑点图案15。然而，如果没有一个共同的基准或调查努力的量化这些技术的有效性的比较是困难的。每个人都有局限性; GPS卫星和VHF项圈价格昂贵，而且往往不可靠，有针对性的问卷调查范围有限，和相机陷阱范围有限。 通过这些不同的方法产生的估计值变化很大。标记等 10强调了一个更加协调的方式的必要性。各种各样的方法已经被用在农田估计猎豹人口密度，这些已经产生了一系列的估计。举例来说，无线电遥测研究估计2.5（±0.73）猎豹/千公里<suP&gt; 2，而估计的4.1相机陷阱研究（±0.4）猎豹/ 1,000 平方公里 （标记等，2007）。这种变化突出了用不同的方法来估算密度的问题，但至今没有一个单一的，有效的，可重复的技术已被认定可能在整个大范围的猎豹在纳米比亚占据栖息地被使用。这仍然是有效的猎豹监测和保护的问题。 这个挑战引发了一个强大的，高性价比和灵活的工具的开发监测猎豹。足迹识别技术最初是为黑犀牛16开发并随后适用于范围广泛的物种包括白犀牛17，东北虎18日 ，山狮19，和其他人。 各种研究表明，它有可能使用足迹由物种，个体和性别识别大型食肉动物。这个过程已经从脚印20的形状简单描述进化到测量21的比较，以一个或几个测量16,17,22-30统计分析和形状分析31。这些努力取得了不同程度的成功，上的严格性在很大程度上取决于数据收集和分析程序，和用于开发训练数据集试验动物的数目。有使用的脚印几个实用的优点。首先，图像可以与其他的非侵入性的方法来收集（ 例如 ，相机俘获，从头发/粪便等的DNA集合）用很少的额外的努力或成本。其次，足迹，其中基材许可证，动物活动的最普遍的迹象。 足迹鉴定技术是猎豹描述的第一个健壮的足迹识别技术，并在脚印的地方被发现的任何站点都是适用的。足迹必须sufficiently定义的打印的脚趾和脚跟可以清楚地用肉眼看到。现场操作员必须与猎豹足部的基本解剖熟习并能够识别在感兴趣的区域的打印，并从任何其他同域大型食肉动物的打印区分开。该技术可以被用来作为一个普查技术（ 例如，多少猎豹被脚印收集？表示），或作为一个工具来监视特定的个人。脚印还可以用来作为标志重捕分析"标记"，使用该技术来识别个人，然后计算出物种的本地密度。数据收集只需要一个基本的数字相机和规模。

<table><tbody><tr><td>Garden shovel</td><td></td><td></td><td></td></tr><tr><td>Garden rake</td><td></td><td></td><td></td></tr><tr><td>Substrate tamper</td><td></td><td></td><td></td></tr><tr><td>River or builders sand</td><td></td><td></td><td></td></tr><tr><td>Buckets</td><td></td><td></td><td></td></tr><tr><td>Watering can or sprayer</td><td></td><td></td><td></td></tr><tr><td>Digital camera</td><td></td><td></td><td></td></tr><tr><td>Paper for Photo ID slips</td><td>http://wildtrack.org/citizen-science/photographing-footprints/</td><td></td><td></td></tr><tr><td>Carpenters&#039; cm folding rule</td><td></td><td></td><td></td></tr><tr><td>Laptop or desktop computer</td><td></td><td></td><td></td></tr><tr><td>JMP software</td><td></td><td></td><td></td></tr><tr><td>The footprint identification technique add-in to JMP software</td><td></td><td></td><td></td></tr></tbody></table>

spotting cheetahs: identifying individuals by their footprints

The cheetah (Acinonyx jubatus) is Africa's most endangered large felid and listed as Vulnerable with a declining population trend by the IUCN1. It ranges widely over sub-Saharan Africa and in parts of the Middle East. Cheetah conservationists face two major challenges, conflict with landowners over the killing of domestic livestock, and concern over range contraction. Understanding of the latter remains particularly poor2. Namibia is believed to support the largest number of cheetahs of any range country, around 30%, but estimates range from 2,9053 to 13,5204. The disparity is likely a result of the different techniques used in monitoring.
Current techniques, including invasive tagging with VHF or satellite/GPS collars, can be costly and unreliable. The footprint identification technique5 is a new tool accessible to both field scientists and also citizens with smartphones, who could potentially augment data collection. The footprint identification technique analyzes digital images of footprints captured according to a standardized protocol. Images are optimized and measured in data visualization software. Measurements of distances, angles, and areas of the footprint images are analyzed using a robust cross-validated pairwise discriminant analysis based on a customized model. The final output is in the form of a Ward's cluster dendrogram. A user-friendly graphic user interface (GUI) allows the user immediate access and clear interpretation of classification results.
The footprint identification technique algorithms are species specific because each species has a unique anatomy. The technique runs in a data visualization software, using its own scripting language (jsl) that can be customized for the footprint anatomy of any species. An initial classification algorithm is built from a training database of footprints from that species, collected from individuals of known identity. An algorithm derived from a cheetah of known identity is then able to classify free-ranging cheetahs of unknown identity. The footprint identification technique predicts individual cheetah identity with an accuracy of &gt;90%.

个体识别 足迹识别技术的个别猎豹分类的能力是两个因素，利用一种标准化的足迹集合协议和基于与一个病区的聚类分析一个交叉验证成对判别分析一个新的统计模型而定。这些是由一个集成的图形用户界面，用于数据可视化（ 图1）的促进。最少的设备是需要的，使得这种技术成本效益（材料清单）。与足迹收集的数据包括每猎豹和猎豹的年龄范围（ 表1）步道猎豹的数量，收集足迹的影像数量，每猎豹的脚印范围，步道数量范围。 781脚印（M:F 395:386），属于110小径，从38个人，共收集训练数据集表1给出。数据的摘要收集。使用特征提取窗口（ 图2）的一组25标志点能够产生15衍生的每个脚印的图像上的点。从这些标志性建筑和派生点，每个足迹生成136变量，包括距离，角度和面积。数据库中的每行，因此表示由单个足迹产生的136的变量。脚印是由线索处理。不同数量的行表示的每个线索，并分别注明。 这些数据被复制到数据表作为一个实体，然后称该行为的参考价值重心（RCV）以稳定所必需的个人分类步道的两两比较。成对的分析窗口（ 图3）旨在帮助验证从未知人群的数据中的数据和/或测试。 图4显示了相同的IND步道成对比较的结果ividual（A）和基于该足迹识别技术定制模型中的两个不同的个人（B）中。并入模型分类是基于椭圆之间存在或不存在重叠。注意，该分析是在第三实体， 即存在每对比较进行时，参考质心值（RCV）。 使用与沃德的聚类分析一个强大的两两交叉验证判别分析，生成一种算法，以提供个人有效的分类。足迹识别技术算法是基于三个可调实体;用的测量次数，椭圆的大小（用置信区间），以及用于确定集群的截止值的阈值。直到分类精确度最高为训练集已知身份的动物取得这些实体中的每一个中的软件进行调整。同样ALGOR然后ithm可以用来鉴定未知猎豹。例如， 图5a，B和C示出的小径的样品的七个猎豹树形表示正确的预测时，算法进行了优化（a）和当算法是次优（B＆C）。 回扣试验进行了验证，从训练集"已知"个人取得的算法。这些通过改变在测试和训练集猎豹的比例依次进行。而不是随意摊派猎豹以训练和测试台，分析依次进行增加测试集的大小。对于每个测试集，10次迭代，用被随机选择每次迭代猎豹进行。对于每一个测试集，这允许将计算出的平均值; 图6图示出作图本身（红色）变化的测试尺寸，并在y轴的预测值对于每个测试大小迭代（绿）和平均预测的每个测试的大小（蓝）值。积表明，即使当测试集的大小显着增加（28）与训练集的大小（N = 10）相比，平均预测值是类似的期望值。 使用多个回扣试验中，个体识别准确率始终&gt; 90％为个人的预测数量，同样重要的是，创新的分类， 即是否来自同一个人（自道）和来自步道不同的个人（非自小径）正确分类。代表所有38个人猎豹集群树状图所示（ 图7）。共有110道，产生共计5,886成对比较。这些年，有46错误分类给予的99％（ 表2）的精度。 <table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always"><tbody><tr><td></td><td> 猎豹＃ </td><td> 足迹图像＃ </td><td> 每猎豹足迹范围 </td><td> 步道＃ </td><td> 每猎豹步道范围 </td><td> 年龄范围（岁） </td></tr><tr><td> 女性 </td><td> 16 </td><td> 386 </td><td> 12 - 36 </td><td> 55 </td><td> 2 - 5 </td><td> 2.5 - 8.5 </td></tr><tr><td> 男性 </td><td> 22 </td><td> 395 </td><td> 7 - 32 </td><td> 54 </td><td> 1 - 4 </td><td> 1 - 11 </td></tr><tr><td> 总 </td><td> 38 </td><td> 781 </td><td> 7 - 36 </td><td> 109 </td><td> 1 - 5 </td><td> 1 - 11 </td></tr></tbody></table> 表1总结收集到的数据 。猎豹的数量，收集的足迹的图像的数量，footp的范围每猎豹rints，足迹的数量，每猎豹步道的范围和猎豹的年龄范围。 <table fo:keep-together.within-page="1" fo:keep-with-next.within-page="always"><tbody><tr><td></td><td> 自 </td><td> 非自 </td><td> 总 </td><td> 分类错误 </td></tr><tr><td> 自我（N） </td><td> 117 </td><td> 9 </td><td> 126 </td><td> 9 </td></tr><tr><td> 自我（％） </td><td> 93 </td><td> 7 </td><td> 100 </td><td> 7 </td></tr><tr><td> 非自（N） </td><td> 37 </td><td> 5,723 </td><td> 5760 </td><td> 37 </td></tr><tr><td> 非自（％） </td><td> 1 </td><td> 99 </td><td> 100 </td><td> 1 </td></tr><tr><td> 合计（N） </td><td> - </td><td> - </td><td> 5,886 </td><td> 46 </td></tr><tr><td> 合计（％）&lt;/ TD&gt; <td> - </td><td> - </td><td> 100 </td><td> 1 </td></tr></tbody></table> 表2 中的足迹识别技术软件的输出示出了基于成对比较小径的分类。自我"指的是从同一个体和"非自身"，来自不同个体的小径的小径。每一个线索是使用定制的强大的交叉验证判别分析模型对所有其他线索匹配。 110道造成5,886两两比较，总体分类精度为99％。 <img alt="图1" src="/files/ftp_upload/54034/54034fig1.jpg" /> 图1.足迹识别技术开启的主菜单窗口。这是一个图像识别外接的数据可视化软件，旨在通过分类脚印INDI<html>维杜阿尔，性别和年龄级从形态学测量。图形用户界面允许不同的选项之间的无缝导航。 <a href="https://www.jove.com/files/ftp_upload/54034/54034fig1large.jpg" target="_blank">请点击此处查看该图的放大版本。</a> <img alt="图2" src="/files/ftp_upload/54034/54034fig2.jpg" /> 图2.特征提取窗口。功能包括拖放图像，自动调整大小的窗口，标准化，基底深度保理等图像旋转预分配的具有里程碑意义的点手动定位，并产生了一系列的脚本派生点来启用指标中的距离，角度和区域的形式提取。输出是在数据提供在xy坐标和所述指标中的行的形式。ANK"&gt;点击此处查看该图的放大版本。 <img alt="图3" src="/files/ftp_upload/54034/54034fig3.jpg" /> 在足迹识别技术图3.成对数据分析窗口，一旦测量数据库已经建立，成对的分析窗口旨在帮助验证从未知人群的数据的数据和/或测试。该分析是基于合并恒定的，参考价值重心（RCV）定制的模式，这对比较顺序的小径16,17的。最终的输出是一个聚类图，提供了个人的数量和创新之间的关系预测的形式。 <a href="https://www.jove.com/files/ftp_upload/54034/54034fig3large.jpg" target="_blank">请点击此处查看该图的放大版本。</a> <im摹ALT ="图4"SRC ="/文件/ ftp_upload / 54034 / 54034fig4.jpg"/&gt; 图4.配对比较。该图显示了从相同的个体（A）和基于在数据可视化软件定制模型中的两个不同的个人（B）的路径的成对比较的结果。并入模型分类是基于椭圆之间存在或不存在重叠。请注意，分析是在第三实体， 即存在每对比较进行，参考值质心（RCV）。 <a href="https://www.jove.com/files/ftp_upload/54034/54034fig4large.jpg" target="_blank">请点击此处查看该图的放大版本。</a> <img alt="图5" src="/files/ftp_upload/54034/54034fig5.jpg" /> 图5.从七个猎豹显示正确的预计值步道样品的树状图iction当算法被优化（a）和当算法是次优（B＆C）。D显示具有18个变量的结果，与在一个方向上移动的滑尺表明十猎豹的几率小于50％ 。该算法是基于三个可调实体;使用的测量次数，椭圆的大小（用置信区间），最终，这决定了集群截止值的阈值。 <a href="https://www.jove.com/files/ftp_upload/54034/54034fig5large.jpg" target="_blank">请点击此处查看该图的放大版本。</a> <img alt="图6" src="/files/ftp_upload/54034/54034fig6.jpg" /> 图6.回扣试验通过改变在测试和训练集猎豹的比例依次进行。而不是按比例分配猎豹以训练和测试本身TS随意，进行连续增加测试集的大小进行了分析。对于每个测试集，10次重复用被随机选择每次迭代猎豹进行。对于每一个测试集，这允许将计算出的平均值。图中显示绘制了本身（红色）变化的测试尺寸，而在Y轴对每个测试大小迭代（绿色）和平均的预测值预测的每个测试的大小（蓝）值。该图表明，即使在测试集的大小大大增加（N = 28）的训练集尺寸相比（N = 10），平均预测值是类似的预期值。 <a href="https://www.jove.com/files/ftp_upload/54034/54034fig6large.jpg" target="_blank">请点击此处查看大图这个数字。</a> <img alt="图7" src="/files/ftp_upload/54034/54034fig7.jpg" /> 图7.树状表示当所有的预测结果从38猎豹110小径纳入分析，注意形成集群创新的保真度。有趣的是，很多错误分类的是同窝之间， 如猎豹Letotse /杜马和Vincent /盆景。 <a href="https://www.jove.com/files/ftp_upload/54034/54034fig7large.jpg" target="_blank">请点击此处查看该图的放大版本。</a>

Watch this Scientific Journal Video about Spotting Cheetahs: Identifying Individuals by Their Footprints at JoVE.com

Spotting Cheetahs: Identifying Individuals by Their Footprints

通过他们的足迹识别个体:合模猎豹

The cheetah (Acinonyx jubatus) is an iconic, endangered species, but conservation efforts are challenged by habitat shrinkage and conflict with commercial farmers. The footprint identification technique, a robust, accurate and cost-effective image classification system, is a new approach to monitoring cheetahs.

The cheetah (Acinonyx jubatus) is Africa's most endangered large felid and listed as Vulnerable with a declining population trend by the IUCN1. It ranges ...

spotting-cheetahs-identifying-individuals-by-their-footprints

Research

JoVE Journal

Environment

14.7K 次观看.  Duke University. The cheetah (Acinonyx jubatus) is an iconic, endangered species, but conservation efforts are challenged by habitat shrinkage and conflict with commercial farmers. The footprint identification technique, a robust, accurate and cost-effective image classification system, is a new approach to monitoring cheetahs.

视频: Spotting Cheetahs: Identifying Individuals by Their Footprints

Low-cost Protocol of Footprint Analysis and Hanging Box Test for Mice Applied the Chronic Restraint Stress

Gait disturbance is frequently observed in patients with movement disorders. In mouse models used for movement disorders, gait analysis is important behavioral test to determine whether the mice mimic the symptoms of patients. Motor deficits are often induced by stress when no spontaneous motor phenotype is observed in the mouse models. Therefore, gait analysis followed by stress loading would be a sensitive method for evaluating the motor phenotype in mouse models. However, researchers face the requirement of an expensive apparatus to obtain quantitative results automatically from gait analysis. For stress, stress loading by simple methods without expensive apparatuses required for electric shock and forced running is desirable. Therefore, we introduce a simple and low-cost protocol consisting of footprint analysis with paper and ink, hanging box test to evaluate motor function, and stress loading defined by restraint with a conical tube. The motor deficits of mice were successfully detected by this protocol.

The low-cost protocol consisting of footprint analysis and hanging box test after restraint stress is useful for evaluating the movement disorders of mouse model.

小鼠应用慢性约束应激的低成本足迹分析和吊箱试验协议

Gait disturbance is frequently observed in patients with movement disorders. In mouse models used for movement disorders, gait analysis is important ...

科研

行为学

Paw-Print Analysis of Contrast-Enhanced Recordings (PrAnCER): A Low-Cost, Open-Access Automated Gait Analysis System for Assessing Motor Deficits

Gait analysis is used to quantify changes in motor function in many rodent models of disease. Despite the importance of assessing gait and motor function in many areas of research, the available commercial options have several limitations such as high cost and lack of accessible, open code. To address these issues, we developed PrAnCER, Paw-Print Analysis of Contrast-Enhanced Recordings, for automated quantification of gait. The contrast-enhanced recordings are produced by using a translucent floor that obscures objects not in contact with the surface, effectively isolating the rat&#8217;s paw prints as it walks. Using these videos, our simple software program reliably measures a variety of spatiotemporal gait parameters. To demonstrate that PrAnCER can accurately detect changes in motor function, we employed a haloperidol model of Parkinson&#8217;s disease (PD). We tested rats at two doses of haloperidol: high dose (0.30 mg/kg) and low dose (0.15 mg/kg). Haloperidol significantly increased stance duration and hind paw contact area in the low dose condition, as might be expected in a PD model. In the high dose condition, we found a similar increase in contact area but also an unexpected increase in stride length. With further research, we found that this increased stride length is consistent with the bracing-escape phenomenon commonly observed at higher doses of haloperidol. Thus, PrAnCER was able to detect both expected and unexpected changes in rodent gait patterns. Additionally, we confirmed that PrAnCER is consistent and accurate when compared with manual scoring of gait parameters.

Paw-Print Analysis of Contrast-Enhanced Recordings PrAnCER: A Low-Cost, Open-Access Automated Gait Analysis System for Assessing Motor Deficits

We describe a novel gait analysis system, Paw-Print Analysis of Contrast-Enhanced Recordings (PrAnCER), an open-access automated system for the quantification of gait characteristics in rats that utilizes a novel semitransparent floor to automatically quantify gait. This system was validated using the haloperidol model of Parkinson&#8217;s Disease.

对比度增强记录 (PrAnCER) 的爪打印分析:用于评估电机缺陷的低成本、开放访问自动步态分析系统

Gait analysis is used to quantify changes in motor function in many rodent models of disease. Despite the importance of assessing gait and motor function ...

3D Kinematic Gait Analysis for Preclinical Studies in Rodents

The utility of three-dimensional (3D) kinematic motion analysis systems is limited in rodents. Part of the reason for this inadequacy is the use of complex algorithms and mathematical modeling that accompany 3D data collection and analysis procedures. This work provides a simple, user-friendly, step-by-step detailed methodology for 3D kinematic gait analysis during treadmill locomotion in healthy and neurotraumatic rats using a six-camera motion capture system. Also provided are details on 1) calibration of the system in an experimental set-up customized for quadrupedal locomotion, 2) data collection for treadmill locomotion in adult rats using markers positioned on all four limbs, 3) options available for video tracking and processing, and 4) basic 3D kinematic data generation and visualization and quantification of data using the built-in data collection software. Finally, it is suggested that the utility of this motion capture system be expanded to studying a variety of motor behaviors before and after neurotrauma.

Presented here is a protocol to collect and analyze three-dimensional kinematics of quadrupedal locomotion in rodents for preclinical studies.

3D运动性步态分析,用于啮齿动物的临床前研究

The utility of three-dimensional (3D) kinematic motion analysis systems is limited in rodents. Part of the reason for this inadequacy is the use of ...

Gait Analysis of Age-dependent Motor Impairments in Mice with Neurodegeneration

Motor behavior tests are commonly used to determine the functional relevance of a rodent model and to test newly developed treatments in these animals. Specifically, gait analysis allows recapturing disease relevant phenotypes that are observed in human patients, especially in neurodegenerative diseases that affect motor abilities such as Parkinson&#39;s disease (PD), Alzheimer&#39;s disease (AD), amyotrophic lateral sclerosis (ALS), and others. In early studies along this line, the measurement of gait parameters was laborious and depended on factors that were hard to control (e.g., running speed, continuous running). The development of ventral plane imaging (VPI) systems made it feasible to perform gait analysis at a large scale, making this method a useful tool for the assessment of motor behavior in rodents. Here, we present an in-depth protocol of how to use kinematic gait analysis to examine the age-dependent progression of motor deficits in mouse models of neurodegeneration; mouse lines with decreased levels of endophilin, in which neurodegenerative damage progressively increases with age, are used as an example.

In this study, we demonstrate the use of kinematic gait analysis based on ventral plane imaging to monitor the subtle changes in motor coordination as well as the progression of neurodegeneration with advancing age in mouse models (e.g., endophilin mutant mouse lines).

变性小鼠年龄依赖性运动障碍的步态分析

Motor behavior tests are commonly used to determine the functional relevance of a rodent model and to test newly developed treatments in these animals. ...

发育生物学

Low-Cost Gait Analysis for Behavioral Phenotyping of Mouse Models of Neuromuscular Disease

Measurement of animal locomotion is a common behavioral tool used to describe the phenotype of a given disease, injury, or drug model. The low-cost method of gait analysis demonstrated here is a simple but effective measure of gait abnormalities in murine models. Footprints are analyzed by painting a mouse&#8217;s feet with non-toxic washable paint and allowing the subject to walk through a tunnel on a sheet of paper. The design of the testing tunnel takes advantage of natural mouse behavior and their affinity for small dark places. The stride length, stride width, and toe spread of each mouse is easily measured using a ruler and a pencil. This is a well-established and reliable method, and it generates several metrics that are analogous to digital systems. This approach is sensitive enough to detect changes in stride early in phenotype presentation, and due to its non-invasive approach, it allows for testing of groups across life-span or phenotypic presentation.

Footprint analysis is a low-cost alternative to digitized gait analysis programs for researchers quantifying movement abnormalities in mice. Because of its speed, simplicity, and longitudinal potential, it is ideal for behavioral phenotyping of mouse models.

神经肌肉疾病小鼠模型行为花型的低成本盖特分析

Measurement of animal locomotion is a common behavioral tool used to describe the phenotype of a given disease, injury, or drug model. The low-cost method ...

A Noninvasive Hair Sampling Technique to Obtain High Quality DNA from Elusive Small Mammals

Noninvasive genetic sampling approaches are becoming increasingly important to study wildlife populations. A number of studies have reported using noninvasive sampling techniques to investigate population genetics and demography of wild populations1. This approach has proven to be especially useful when dealing with rare or elusive species2. While a number of these methods have been developed to sample hair, feces and other biological material from carnivores and medium-sized mammals, they have largely remained untested in elusive small mammals. In this video, we present a novel, inexpensive and noninvasive hair snare targeted at an elusive small mammal, the American pika (Ochotona princeps). We describe the general set-up of the hair snare, which consists of strips of packing tape arranged in a web-like fashion and placed along travelling routes in the pikas&#x2019; habitat. We illustrate the efficiency of the snare at collecting a large quantity of hair that can then be collected and brought back to the lab. We then demonstrate the use of the DNA IQ system (Promega) to isolate DNA and showcase the utility of this method to amplify commonly used molecular markers including nuclear microsatellites, amplified fragment length polymorphisms (AFLPs), mitochondrial sequences (800bp) as well as a molecular sexing marker. Overall, we demonstrate the utility of this novel noninvasive hair snare as a sampling technique for wildlife population biologists. We anticipate that this approach will be applicable to a variety of small mammals, opening up areas of investigation within natural populations, while minimizing impact to study organisms.

We present a noninvasive sampling approach to efficiently collect hair samples from elusive small mammals, as shown for the American pika. We demonstrate the utility of this method by extracting DNA from sampled hair and amplifying several types of molecular markers commonly used in studies of wildlife ecology and conservation.

一种无创性的发采样技术，以获得难以捉摸的小型兽类高质量的DNA

Noninvasive genetic sampling approaches are becoming increasingly important to study wildlife populations. A number of studies have reported using ...

生物学

Who is Who? Non-invasive Methods to Individually Sex and Mark Altricial Chicks

Many experiments require early determination of offspring's sex as well as early marking of newborns for individual recognition. According to animal welfare guidelines, non-invasive techniques should be preferred whenever applicable. In our group, we work on different species of song birds in the lab and in the field, and we successfully apply non-invasive methods to sex and individually mark chicks. This paper presents a comprehensive non-invasive tool-box. Sexing birds prior to the expression of secondary sexual traits requires the collection of DNA-bearing material for PCR. We established a quick and easy method to sex birds of any age (post hatching) by extracting DNA from buccal swabs. Results can be obtained within 3 hours. For individual marking chick's down feathers are trimmed in specific patterns allowing fast identification within the hatching order. This set of methods is easily applicable in a standard equipped lab and especially suitable for working in the field as no special equipment is required for sampling and storage. Handling of chicks is minimized and marking and sexing techniques are non-invasive thereby supporting the RRR-principle of animal welfare guidelines.

This protocol provides a convenient set of methods, which enables extremely fast, easy, non-invasive, reliable and low-cost, molecular sex determination of birds and their non-invasive, quick, safe and easily recognizable marking shortly after hatching. Only limited handling of chicks is required. This convenient toolbox of methods complies entirely with the RRR-guidelines.

谁是谁？非侵入性的方法，以个别性和马克晚成小鸡

Many experiments require early determination of offspring's sex as well as early marking of newborns for individual recognition. According to animal ...

Multifactorial Assessment of Motor Behavior in Rats after Unilateral Sciatic Nerve Crush Injury

The induction of a peripheral nerve injury is a widely used method in neuroscience for the assessment of repair and pain mechanisms among others. In addition, in the research field of movement disorders, sciatic crush injury has been employed to trigger a dystonia-like phenotype in genetically predisposed DYT-TOR1A rodent models of dystonia. To achieve consistent, reproducible and comparable results after a sciatic nerve crush injury, a standardized method for inducing the nerve crush is essential, in addition to a standardized phenotypical characterization. Attention must be paid not only to the specific assortment of behavioral tests, but also to the technical requirements, the correct execution and consecutive data analysis. This protocol describes in detail how to perform a sciatic nerve crush injury and provides a behavioral test battery for the assessment of motor deficits in rats that includes the open field test, the CatWalk XT gait analysis, the beam walking task, and the ladder rung walking task.

We provide a protocol for the assessment of motor behavior via a behavioral test battery in rats after sciatic nerve crush injury.

单边坐骨神经粉碎损伤后大鼠运动行为的多因素评估

The induction of a peripheral nerve injury is a widely used method in neuroscience for the assessment of repair and pain mechanisms among others. In ...

神经科学

Visually Sexing Loggerhead Shrike (Lanius Ludovicianus) Using Plumage Coloration and Pattern

The loggerhead shrike is a small sexually monomorphic passerine bird using grassland habitats across North America. Based on Breeding Bird Survey data, the species has undergone a drastic decline since the mid-1960s. The cause of decline is unknown, and research is actively underway to address this knowledge gap. These efforts are hindered by an inability to sex the species in hand, which to date was only possible using molecular markers. Here, we present a protocol to sex loggerhead shrikes by visually analyzing the coloration and pattern in the sixth primary feather. The application of the method will facilitate our ability to identify threats on a finer scale than has been possible to date and to address various ecological and evolutionary hypotheses. The methodology is simple and results reliable&#8211;we encourage including this method for research of both in situ and ex situ populations.

Visually Sexing Loggerhead Shrike Lanius Ludovicianus Using Plumage Coloration and Pattern

We present a protocol to characterize the sex of loggerhead shrike visually based on the coloration and pattern of the sixth primary wing feather.

视觉上性感的记录者史莱克 （拉尼乌斯·卢多维丘努斯） 使用羽毛着色和模式

The loggerhead shrike is a small sexually monomorphic passerine bird using grassland habitats across North America. Based on Breeding Bird Survey data, ...

Rodent Identification II

Source: Kay Stewart, RVT, RLATG, CMAR; Valerie A. Schroeder, RVT, RLATG. University of Notre Dame, IN
Animal records must be accurately maintained to ensure that data collection is correct. Records range from maintaining information on cage cards to having a detailed database with all of the relevant information on each animal. The primary component of recordkeeping is the individual identification of research animals. There are a variety of methods suitable for identifying mice and rats. This video describes the procedural techniques for tattooing, microchip placement, and temporary identification methods, and also explores the benefits of each.

Rodent Identification: Tail or Toe Tattoo, Microchip Implant, Temporary Mark

啮齿动物鉴定 (2)

Source: Kay Stewart, RVT, RLATG, CMAR; Valerie A. Schroeder, RVT, RLATG. University of Notre Dame, IN
Animal records must be accurately maintained to ...

通过他们的足迹识别个体:合模猎豹

摘要

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此视频中的章节

小鼠应用慢性约束应激的低成本足迹分析和吊箱试验协议

对比度增强记录 (PrAnCER) 的爪打印分析:用于评估电机缺陷的低成本、开放访问自动步态分析系统

3D运动性步态分析,用于啮齿动物的临床前研究

变性小鼠年龄依赖性运动障碍的步态分析

神经肌肉疾病小鼠模型行为花型的低成本盖特分析

一种无创性的发采样技术，以获得难以捉摸的小型兽类高质量的DNA

谁是谁？非侵入性的方法，以个别性和马克晚成小鸡

单边坐骨神经粉碎损伤后大鼠运动行为的多因素评估

视觉上性感的记录者史莱克（拉尼乌斯·卢多维丘努斯）使用羽毛着色和模式

啮齿动物鉴定 (2)

通过他们的足迹识别个体:合模猎豹

摘要

探索更多视频

此视频中的章节

小鼠应用慢性约束应激的低成本足迹分析和吊箱试验协议

对比度增强记录 (PrAnCER) 的爪打印分析:用于评估电机缺陷的低成本、开放访问自动步态分析系统

3D运动性步态分析,用于啮齿动物的临床前研究

变性小鼠年龄依赖性运动障碍的步态分析

神经肌肉疾病小鼠模型行为花型的低成本盖特分析

一种无创性的发采样技术，以获得难以捉摸的小型兽类高质量的DNA

谁是谁？非侵入性的方法，以个别性和马克晚成小鸡

单边坐骨神经粉碎损伤后大鼠运动行为的多因素评估

视觉上性感的记录者史莱克 （拉尼乌斯·卢多维丘努斯） 使用羽毛着色和模式

啮齿动物鉴定 (2)

视觉上性感的记录者史莱克（拉尼乌斯·卢多维丘努斯）使用羽毛着色和模式